US20110152115A1 - Methods for identifying, diagnosing, and predicting survival of lymphomas - Google Patents

Methods for identifying, diagnosing, and predicting survival of lymphomas Download PDF

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US20110152115A1
US20110152115A1 US13/008,403 US201113008403A US2011152115A1 US 20110152115 A1 US20110152115 A1 US 20110152115A1 US 201113008403 A US201113008403 A US 201113008403A US 2011152115 A1 US2011152115 A1 US 2011152115A1
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gene expression
lymphoma
genes
expression signature
survival
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Louis M. Staudt
George W. Wright
Sandeep Dave
Bruce K. Tan
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
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    • C12Q2600/00—Oligonucleotides characterized by their use
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
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    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/60—Complex ways of combining multiple protein biomarkers for diagnosis

Definitions

  • Tables 2-1723 and 1725-2358 are contained on 21 CD-ROMs submitted with U.S. patent application Ser. No. 10/934,930, now issued as U.S. Pat. No. 7,711,492, and U.S. patent application Ser. No. 12/592,778, filed Dec. 2, 2009. These CD-ROMs are numbered 1-21 of 22. The name, size, and date of creation for each file is presented in the file entitled “Tableofcontents.txt,” located on CD number 21 of 22. The name of each file incorporates the number of the corresponding table. Any reference to a table or file should be considered an incorporation by reference of the contents of the table and/or file at that particular place in the specification.
  • a computer program listing appendix is contained on one CD-ROM numbered 22 of 22 submitted with U.S. patent application Ser. No. 10/934,930, now issued U.S. as U.S. Pat. No. 7,711,492, and U.S. patent application Ser. No. 12/592,778, filed Dec. 2, 2009.
  • the computer program listing appendix contains files related to the implementation of an algorithm for determining lymphoma type.
  • the name, size, and date of creation for each file in the computer program listing appendix is presented in the file entitled “Table_of_contents.txt,” located on CD-ROM 22. Any reference to a file contained in the computer program listing appendix should be considered an incorporation by reference of the contents of that file at that particular place in the specification.
  • lymphoma type or subtype in a subject suffering from a lymphoproliferative disorder is important for developing an appropriate therapeutic strategy.
  • Previous attempts have been made to identify lymphomas using gene expression data obtained using a microarray.
  • gene expression data obtained using a microarray.
  • there is a need in the art for more accurate and predictive methods of analyzing this gene expression data.
  • the present invention discloses a novel microarray for obtaining gene expression data to be used in identifying lymphoma types and predicting survival in a subject.
  • the present invention further discloses a variety of methods for analyzing gene expression data obtained from a lymphoma sample, and specific algorithms for predicting survival and clinical outcome in a subject suffering from a lymphoma.
  • compositions comprising the set of probes listed in Table 2, which is set forth below and contained in the file entitled “Tableb.-0002_LymphDx_Probe_List.txt.”
  • this composition comprises a microarray.
  • the present invention provides a method of generating a survival predictor for a particular lymphoma type.
  • a method of generating a survival predictor for a particular lymphoma type In this method, one or more biopsy samples that have been diagnosed as belonging to a particular lymphoma type are obtained. Gene expression data is obtained for these samples, and genes with expression patterns associated with longer or shorter survival are identified. Hierarchical clustering is performed to group these genes into gene expression signatures, and the expression of all genes within each signature are averaged to obtain a gene expression signature value for each signature. These gene expression signature values are then used to generate a multivariate survival predictor.
  • the present invention provides a method for predicting survival in a follicular lymphoma (FL) subject.
  • a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample.
  • the expression level of those genes belonging to an immune response-1 or immune response-2 gene expression signature are averaged to generate gene expression signature values for each signature.
  • a survival predictor score is then calculated using an equation: [2.71*(immune response-2 gene expression signature value)] ⁇ [2.36*(immune response-1 gene expression signature value)].
  • a higher survival predictor score is associated with a less favorable outcome.
  • the gene expression data used in this method is obtained using a microarray.
  • the present invention provides another method for predicting survival in a follicular lymphoma (FL) subject.
  • a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample.
  • the expression level of those genes belonging to a B cell differentiation, T-cell, or macrophage gene expression signature are averaged to generate gene expression signature values for each signature.
  • a survival predictor score is then calculated using an equation: [2.053*(macrophage gene expression signature value)] ⁇ [2.344*(T-cell gene expression signature value)] ⁇ [0.729*(B-cell gene expression signature value)].
  • a higher survival predictor score is associated with a less favorable outcome.
  • the gene expression data used in this method is obtained using a microarray.
  • the present invention provides yet another method for predicting survival in a follicular lymphoma (FL) subject.
  • a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample.
  • the expression level of those genes belonging to a macrophage, T-cell, or B-cell differentiation gene expression signature are averaged to generate gene expression signature values for each signature.
  • a survival predictor score is then calculated using an equation: [1.51*(macrophage gene expression signature value)] ⁇ [2.11*(T-cell gene expression signature value)] ⁇ [0.505*(B-cell differentiation gene expression signature value)].
  • a higher survival predictor score is associated with a less favorable outcome.
  • the gene expression data used in this method is obtained using a microarray.
  • the present invention provides a method for predicting survival in a diffuse large B cell lymphoma (DLBCL) subject.
  • a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample.
  • the expression level of those genes belonging to an ABC DLBCL high, lymph node, or MHC class II gene expression signature are averaged to generate gene expression signature values for each signature.
  • a survival predictor score is then calculated using an equation: [0.586*(ABC DLBCL high gene expression signature value)] ⁇ [0.468*(lymph node gene expression signature value)] ⁇ [0.336*(MHC class II gene expression signature value)].
  • a higher survival predictor score is associated with a less favorable outcome.
  • the gene expression data used in this method is obtained using a microarray.
  • the present invention provides another method for predicting survival in a diffuse large B cell lymphoma (DLBCL) subject.
  • a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample.
  • the expression level of those genes belonging to a lymph node, germinal B cell, proliferation, or MHC class II gene expression signature are averaged to generate gene expression signature values for each signature.
  • a survival predictor score is then calculated using an equation: [ ⁇ 0.4337*(lymph node gene expression signature)]+[0.09*(proliferation gene expression signature)] ⁇ [0.4144*(germinal center B-cell gene expression signature)] ⁇ [0.2006*(MHC class II gene expression signature)].
  • a higher survival predictor score is associated with a less favorable outcome.
  • the gene expression data used in this method is obtained using a microarray.
  • the present invention provides yet another method for predicting survival in a diffuse large B cell lymphoma (DLBCL) subject.
  • a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample.
  • the expression level of those genes belonging to a lymph node, germinal B cell, or MHC class II gene expression signature are averaged to generate gene expression signature values for each signature.
  • a survival predictor score is then calculated using an equation: [ ⁇ 0.32*(lymph node gene expression signature)] ⁇ [0.176*(germinal B cell gene expression signature)] ⁇ [0.206*(MHC class II gene expression signature)].
  • a higher survival predictor score is associated with a less favorable outcome.
  • the gene expression data used in this method is obtained using a microarray.
  • the gene expression data is obtained using RT-PCR.
  • the present invention provides a method for predicting survival in a mantle cell lymphoma (MCL) subject.
  • MCL mantle cell lymphoma
  • a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample.
  • the expression level of those genes belonging to a proliferation gene expression signature are averaged to generate a gene expression signature value.
  • a survival predictor score is then calculated using an equation: [1.66*(proliferation gene expression signature value)].
  • a higher survival predictor score is associated with a less favorable outcome.
  • the gene expression data used in this method is obtained using a microarray.
  • the present invention provides a method for determining the probability that a sample X belongs to a first lymphoma type or a second lymphoma type.
  • a set of genes is identified that is differentially expressed between the two lymphoma types in question, and a set of scale factors representing the difference in expression between the lymphoma types for each of these genes are calculated.
  • a series of linear predictor scores are generated for samples belonging to either of the two lymphoma types based on expression of these genes.
  • Gene expression data is then obtained for sample X, and a linear predictor score is calculated for this sample.
  • the probability that sample X belongs to the first lymphoma type is calculated using an equation that incorporates the linear predictor score of sample X and the mean and variance of the linear predictor scores for the known samples of either lymphoma type.
  • the present invention provides a method for determining the lymphoma type of a sample X
  • a set of genes is identified that is differentially expressed between a first lymphoma type and a second lymphoma type, and a set of scale factors representing the difference in expression of each of these genes between the two lymphoma types are calculated.
  • a series of linear predictor scores are generated for samples belonging to either of the two lymphoma types based on expression of these genes.
  • Gene expression data is then obtained for sample X, and a linear predictor score is calculated for this sample.
  • the probability that sample X belongs to the first lymphoma type is calculated using an equation that incorporates the linear predictor score of sample X and the mean and variance of the linear predictor scores for the known samples of either lymphoma type. This entire process is then repeated with various lymphoma types being substituted for the first lymphoma type, the second lymphoma type, or both.
  • the present invention provides another method for determining the lymphoma type of a sample X.
  • a series of lymphoma type pairs are created, with each pair consisting of a first lymphoma type and a second lymphoma type.
  • gene expression data is obtained for a set of genes, and a series of scale factors representing the difference in expression of each of these genes between the two lymphoma types are calculated.
  • a subset of z genes with the largest scale factors are identified, and a series of linear predictor scores are generated for samples belonging to either of the two lymphoma types. Linear predictor scores are calculated for anywhere from 1 to z of these genes.
  • the number of genes from 1 to z that results in the largest difference in linear predictor scores between the two lymphoma types is selected, and gene expression data for these genes is obtained for sample X.
  • a linear predictor score is generated for sample X, and the probability that the sample belongs to the first lymphoma type is calculated using an equation that incorporates the linear predictor score for sample X and the mean and variance of the linear predictor scores for the known samples of either lymphoma type.
  • the present invention provides another method for determining the lymphoma type of a sample X.
  • a series of lymphoma type pairs are created, with each pair consisting of a first lymphoma type and a second lymphoma type.
  • gene expression data is obtained for a set of genes, and a series of scale factors representing the difference in expression of each of these genes between the two lymphoma types are calculated.
  • the set of genes is divided into gene-list categories indicating correlation with a gene expression signature. Within each gene-list category, a subset of z genes with the largest scale factors are identified, and a series of linear predictor scores are generated for samples belonging to either of the two lymphoma types.
  • Linear predictor scores are calculated for anywhere from 1 to z of these genes. The number of genes from 1 to z that results in the largest difference in linear predictor scores between the two lymphoma types is selected, and gene expression data for these genes is obtained for sample X. A linear predictor score is generated for sample X, and the probability q that the sample belongs to the first lymphoma type is calculated using an equation that incorporates the linear predictor score for sample X and the mean and variance of the linear predictor scores for the known samples of either lymphoma type.
  • a high probability q indicates that sample X belongs to the first lymphoma type
  • a low probability q indicates that sample X belongs to the second lymphoma type
  • a middle probability q indicates that sample X belongs to neither lymphoma type.
  • the cut-off point between high, middle, and low probability values is determined by ranking samples of known lymphoma type according to their probability values, then analyzing every possible cut-off point between adjacent samples using the equation: 3.99*[(% of first lymphoma type misidentified as second lymphoma type)+(% of second lymphoma type misidentified as a first lymphoma type)]+[(% of first lymphoma type identified as belonging to neither lymphoma type)+(% of second lymphoma type identified as belonging to neither lymphoma type)].
  • the final cut-off points are those that minimize the value of this equation.
  • FIG. 1 Method for identifying lymphoma type.
  • Flow chart depicts a general method for identifying lymphoma type using gene expression data.
  • FIG. 2 Survival signature analysis. Flow chart depicts method for developing a lymphoma survival predictor based on gene expression patterns.
  • FIG. 3 FL survival data. Survival data for 191 subjects diagnosed with FL. Median age at diagnosis was 51 years (ranging from 23 to 81 years), and the subjects had a median follow-up of 6.6 years (8.1 years for survivors, with a range of ⁇ 1 to 28.2 years).
  • FIG. 4 Hierarchical clustering of survival associated genes in FL samples. Each column represents a single FL sample, while each row represents a single gene. Relative gene expression is depicted according to the scale at the bottom of the figure. The dendrogram to the left indicates the degree to which the expression pattern of each gene is correlated with that of the other genes. The colored bars indicate sets of coordinately regulated genes defined as gene expression signatures. Genes comprising the immune response-1 and immune response-2 gene expression signature are listed on the right.
  • FIG. 5 Kaplan-Meier plot of survival in FL samples based on survival predictor scores. 191 FL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [(2.71*immune response-2 gene expression signature value)] ⁇ [(2.36 ⁇ immune response-1 gene expression signature value)].
  • FIG. 6 Kaplan-Meier plot of survival in FL samples based on IPI score. 96 FL samples were divided into three groups based on their IPI scores.
  • FIG. 7 Kaplan-Meier plot of survival in FL samples with low or high risk IPI scores based on survival predictor scores.
  • 96 FL samples with low risk (left panel) or intermediate risk (right panel) IPI scores were divided into quartiles based on their survival predictor scores.
  • the survival predictor scores were calculated by: [(2.71*immune response-2 gene expression signature value)] ⁇ [(2.36 x immune response-1 gene expression signature value)].
  • FIG. 8 Kaplan-Meier plot of survival in FL samples based on survival predictor scores. 191 FL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [2.053*(macrophage gene expression signature value)] ⁇ [2.344*(T-cell gene expression signature value)] ⁇ [0.729*(B-cell differentiation gene expression signature value)].
  • FIG. 9 Kaplan-Meier plot of survival in FL samples based on survival predictor scores. 191 FL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [1.51*(macrophage gene expression signature value)] ⁇ [2.11*(T-cell gene expression signature value)] ⁇ [0.505*(B-cell differentiation gene expression signature value)].
  • FIG. 10 Kaplan-Meier plot of survival in DLBCL samples based on survival predictor scores. 231 DLBCL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [0.586*(ABC DLBCL high gene expression signature value)] ⁇ [0.468*(lymph node gene expression signature value)] ⁇ [(0.336*MHC Class II gene expression signature value)].
  • FIG. 11 Kaplan-Meier plot of survival in DLBCL samples based on survival predictor scores. 200 DLBCL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [ ⁇ 0.4337*(lymph node gene expression signature value)]+[0.09*(proliferation gene expression signature value)] ⁇ [0.4144*(germinal center B-cell gene expression signature value)] ⁇ [0.2006*(MHC class II gene expression signature value)].
  • FIG. 12 Kaplan-Meier plot of survival in DLBCL samples based on survival predictor scores. 200 DLBCL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [ ⁇ 0.32*(lymph node gene expression signature value)] ⁇ [0.176*(germinal center B-cell gene expression signature value)] ⁇ [0.206*(MHC class II gene expression signature value)].
  • FIG. 13 Kaplan-Meier plot of survival in MCL samples based on survival predictor scores. 21 MCL samples were divided into two equivalent groups based on their survival predictor scores. The survival predictor scores were calculated by: 1.66*(proliferation gene expression signature value).
  • FIG. 14 Kaplan-Meier plot of survival in MCL samples based on survival predictor scores. 21 MCL samples were divided into two equivalent groups based on their survival predictor scores. The survival predictor scores were calculated by: 1.66*(proliferation gene expression signature value).
  • FIG. 15 Predicting lymphoma type using Bayesian analysis. Bayes' rule can be used to determine the probability that an unknown sample belongs to a first lymphoma type rather than a second lymphoma type. A linear predictor score is generated for the sample, and the probability that the sample belongs to the first lymphoma type is determined based on the distribution of linear predictor scores within the first and second lymphoma type.
  • FIG. 16 Performance of MCL predictor model. Results of the gene-expression based predictor model for MCL are shown for three models (MCL vs. ABC, MCL vs. GCB, MCL vs. SLL). Performance is shown for both the training set and the validation set.
  • FIG. 17 Gene expression-based identification of DLBCL. Expression levels for 27 genes in a subgroup predictor are shown for 274 DLBCL samples. Expression levels are depicted according to the scale shown at the left. The 14 genes used to predict the DLBCL subgroups in the Affymetrix data set are indicated with asterisks. The probabilities that the DLBCL samples belong to the ABC or GCB subtypes are graphed at the top, and the DLBCL cases are arranged accordingly. Cases belonging to either ABC or GCB with 90% or greater probability are indicated.
  • FIG. 18 Performance of DLBCL subtype predictor model. Assignments of DLBCL samples to the ABC or GCB subtypes based on hierarchical clustering vs. the predictor model disclosed herein are compared within the training, validation, and total set of samples.
  • FIG. 19 Relationship of gene expression in normal B cell subpopulations to DLBCL subtypes. Relative gene expression in the indicated purified B cell populations is depicted according to the scale in FIG. 17 . The P value of the difference in expression of these genes between the GCB and ABC DLBCL subtypes is shown, and the subtype with the higher expression is indicated.
  • B DLBCL subtype distinction genes that are more highly expressed in plasma cells than at other B cell differentiation stages.
  • FIG. 20 Identification of a PMBL gene expression signature.
  • A Hierarchical clustering identified a set of 23 PMBL signature genes that were more highly expressed in most lymphomas with a clinical diagnosis of PMBL than in lymphomas assigned to the GCB or ABC subtypes. Each row presents gene expression measurements from a single Lymphochip microarray feature representing the genes indicated. Each column represents a single lymphoma biopsy sample. Relative gene expression is depicted according to the scale shown.
  • B Hierarchical clustering of the lymphoma biopsy samples based on expression of the PMBL signature genes identified in (A). A “core” cluster of lymphoma cases was identified that highly expressed the PMBL signature genes.
  • FIG. 21 Development of a gene expression-based molecular diagnosis of PMBL.
  • a PMBL predictor was created based on expression of the 46 genes shown. Relative gene expression for each lymphoma biopsy sample is presented according to the color scale shown in FIG. 20 . The probability that each sample is PMBL or DLBCL based on gene expression is shown at the top.
  • B. The PMBL predictor was used to classify 274 lymphoma samples as PMBL or DLBCL. Prediction results are summarized on the right, and the relative gene expression for each case that was classified by the predictor as PMBL is shown on the left. Average expression of each gene in samples classified as DLBCL is also shown. The 20 genes listed are those represented on the Lymphochip that were more highly expressed in PMBL than in DLBCL. Not shown are eight genes from the PMBL predictor that were more highly expressed in DLBCL than in PMBL.
  • FIG. 22 Clinical characteristics of PMBL patients. Kaplan-Meier plot of overall survival in PMBL, GCB, and ABC patients after chemotherapy.
  • FIG. 23 Optimization of gene number in lymphoma predictor.
  • the optimal number of genes for inclusion in the lymphoma type predictor model is that number which generates a maximum t-statistic when comparing the LPS of two samples from different lymphoma types.
  • FIG. 24 LPS distribution among FL and DLBCL/BL samples. Standard and proliferation LPSs for FL (x) and DLBCL/BL (+) samples. Dotted lines indicate standard deviations from the fitted multivariate normal distributions.
  • FIG. 25 Determination of cut-off points for lymphoma classification.
  • the cut-off points between samples classified as DLBCL/BL, FL, or unclassified were optimized to minimize the number of samples classified as the wrong lymphoma type.
  • FIG. 26 Division of LPSs among FL and DLBCL/FL samples. Illustration of how the cut-off points described in FIG. 25 divided the space between the LPSs of FL (x) and DLBCL/BL (+) samples.
  • FIG. 27 Lymphoma classification results. Results of lymphoma classification based on gene expression. 100% of SLL, MCL, and FH samples were classified correctly, and only 3% of DLBCL/BL and FL samples were classified incorrectly.
  • FIG. 28 DLBCL subtype classification based on gene expression. None of the ABC samples were classified as the wrong subtype, while only one of the BL samples was classified incorrectly. Of the GCB and PMBL samples, only 5% and 6%, respectively, were classified incorrectly.
  • Gene expression profiling of a cancer cell or biopsy reflects the molecular phenotype of a cancer at the time of diagnosis.
  • the detailed picture provided by the genomic expression pattern provides the basis for a new systematic classification of cancers and more accurate predictors of survival and response to treatment.
  • the present invention discloses methods for identifying, diagnosing, and/or classifying a lymphoma, lymphoid malignancy, or lymphoproliferative disorder based on its gene expression patterns.
  • the present invention also discloses methods for predicting survival in a subject diagnosed with a particular lymphoma type or subtype using gene expression data. The information obtained using these methods will be useful in evaluating the optimal therapeutic approach to be employed with regards to a particular subject.
  • lymphoproliferative disorder refers to any tumor of lymphocytes, and may refer to both malignant and benign tumors.
  • lymphocytes and may refer to both malignant and benign tumors.
  • lymphoid malignancy refer specifically to malignant tumors derived from lymphocytes and lymphoblasts.
  • lymphomas include, but are not limited to, follicular lymphoma (FL), Burkitt lymphoma (BL), mantle cell lymphoma (MCL), follicular hyperplasia (FH), small cell lymphocytic lymphoma (SLL), mucosa-associated lymphoid tissue lymphoma (MALT), splenic lymphoma, multiple myeloma, lymphoplasmacytic lymphoma, post-transplant lymphoproliferative disorder (PTLD), lymphoblastic lymphoma, nodal marginal zone lymphoma (NMZ), germinal center B cell-like diffuse large B cell lymphoma (GCB), activated B cell-like diffuse large B cell lymphoma (ABC) and primary mediastinal B cell lymphoma (PMBL).
  • FL follicular lymphoma
  • BL Burkitt lymphoma
  • MCL mantle cell lymphoma
  • FH small cell lymphocytic lympho
  • lymphoma type refers to a diagnostic classification of a lymphoma.
  • the phrase may refer to a broad lymphoma class (e.g., DLBCL, FL, MCL, etc.) or to a subtype or subgroup falling within a broad lymphoma class (e.g., GCB DLBCL, ABC DLBCL).
  • gene expression data refers to information regarding the relative or absolute level of expression of a gene or set of genes in a cell or group of cells.
  • the level of expression of a gene may be determined based on the level of RNA, such as mRNA, encoded by the gene. Alternatively, the level of expression may be determined based on the level of a polypeptide or fragment thereof encoded by the gene.
  • Gene expression data may be acquired for an individual cell, or for a group of cells such as a tumor or biopsy sample.
  • microarray refers to a plurality of nucleic acid probes coupled to the surface of a substrate in different known locations.
  • the substrate is preferably solid.
  • Microarrays have been generally described in the art in, for example, U.S. Pat. Nos. 5,143,854 (Pirrung), 5,424,186 (Fodor), 5,445,934 (Fodor), 5,677,195 (Winkler), 5,744,305 (Fodor), 5,800,992 (Fodor), 6,040,193 (Winkler), and Fodor et al. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science, 251:767-777. Each of these references is incorporated by reference herein in their entirety.
  • gene expression signature refers to a group of coordinately expressed genes.
  • the genes making up this signature may be expressed in a specific cell lineage, stage of differentiation, or during a particular biological response.
  • the genes can reflect biological aspects of the tumors in which they are expressed, such as the cell of origin of the cancer, the nature of the non-malignant cells in the biopsy, and the oncogenic mechanisms responsible for the cancer (Shaffer 2001).
  • Examples of gene expression signatures include lymph node (Shaffer 2001), proliferation (Rosenwald 2002), MHC class II, ABC DLBCL high, B-cell differentiation, T-cell, macrophage, immune response-1, immune response-2, and germinal center B cell.
  • survival predictor score refers to a score generated by a multivariate model used to predict survival based on gene expression. A subject with a higher survival predictor score is predicted to have poorer survival than a subject with a lower survival predictor score.
  • survival may refer to the probability or likelihood of a subject surviving for a particular period of time. Alternatively, it may refer to the likely term of survival for a subject, such as expected mean or median survival time for a subject with a particular gene expression pattern.
  • LPS linear predictor score
  • a linear predictor score may be generated by other methods including but not limited to linear discriminant analysis (Dudoit 2002), support vector machines (Furey 2000), or shrunken centroids (Tibshirani 2002)
  • scale factor refers to a factor that defines the relative difference in expression of a particular gene between two samples.
  • An example of a scale factor is a t-score generated by a Student's t-test.
  • lymphoma subject wherein “lymphoma” is a specific lymphoma type (e.g., “follicular lymphoma subject”), may refer to a subject that has been diagnosed with a particular lymphoma by any method known in the art or discussed herein. This phrase may also refer to a subject with a known or suspected predisposition or risk of developing a particular lymphoma type.
  • the pattern of expression of a particular gene is closely connected to the biological role and effect of its gene product. For this reason, the systematic study of variations in gene expression provides an alternative approach for linking specific genes with specific diseases and for recognizing heritable gene variations that are important for immune function. For example, allelic differences in the regulatory region of a gene may influence the expression levels of that gene. An appreciation for such quantitative traits in the immune system may help elucidate the genetics of autoimmune diseases and lymphoproliferative disorders.
  • Genes that encode components of the same multi-subunit protein complex are often coordinately regulated. Coordinate regulation is also observed among genes whose products function in a common differentiation program or in the same physiological response pathway. Recent application of gene expression profiling to the immune system has shown that lymphocyte differentiation and activation are accompanied by parallel changes in expression among hundreds of genes. Gene expression databases may be used to interpret the pathological changes in gene expression that accompany autoimmunity, immune deficiencies, cancers of immune cells and of normal immune responses.
  • Mathematical analysis of gene expression data is a rapidly evolving science based on a rich mathematics of pattern recognition developed in other contexts (Kohonen 1997).
  • Mathematical analysis of gene expression generally has three goals. First, it may be used to identify groups of genes that are coordinately regulated within a biological system. Second, it may be used to recognize and interpret similarities between biological samples on the basis of similarities in gene expression patterns. Third, it may be used to recognize and identify those features of a gene expression pattern that are related to distinct biological processes or phenotypes.
  • Mathematical analysis of gene expression data often begins by establishing the expression pattern for each gene on an array across n experimental samples.
  • the expression pattern of each gene can be represented by a point in n-dimensional space, with each coordinate specified by an expression measurement in one of the n samples (Eisen 1998).
  • a clustering algorithm that uses distance metrics can then be applied to locate clusters of genes in this n-dimensional space. These clusters indicate genes with similar patterns of variation in expression over a series of experiments.
  • Clustering methods that have been applied to microarray data in the past include hierarchical clustering (Eisen 1998), self-organizing maps (SOMs) (Tamayo 1999), k-means (Tavazoie 1999), and deterministic annealing (Alon 1999).
  • Hierarchical clustering begins by determining the gene expression correlation coefficients for each pair of the n genes studied. Genes with similar gene expression correlation coefficients are grouped next to one another in a hierarchical fashion. Generally, genes with similar expression patterns under a particular set of conditions encode protein products that play related roles in the physiological adaptation to those conditions. Novel genes of unknown function that are clustered with a large group of functionally related genes are likely to participate in the same biological process. Likewise, the other clustering methods mentioned herein may also group genes together that encode proteins with related biological function.
  • Gene expression maps may be constructed by organizing gene expression data from multiple samples using any of the various clustering algorithms outlined herein. The ordered tables of data may then be displayed graphically in a way that allows researchers and clinicians to assimilate both the choreography of gene expression on a broad scale and the fine distinctions in expression of individual genes.
  • genes that are clustered together reflect a particular biological function, and are termed gene expression signatures (Shaffer 2001).
  • One general type of gene expression signature includes genes that are characteristically expressed in a particular cell type or at a particular stage of cellular differentiation or activation.
  • Another general type of gene expression signature includes genes that are regulated in their expression by a particular biological process such as proliferation, or by the activity of a particular transcription factor or signaling pathway.
  • the pattern of gene expression in a biological sample provides a distinctive and accessible molecular picture of its functional state and identity (DeRisi 1997; Cho 1998; Chu 1998; Holstege 1998; Spellman 1998). Each cell transduces variations in its environment, internal state, and developmental state into readily measured and recognizable variations in its gene expression patterns. Two different samples that have related gene expression patterns are therefore likely to be biologically and functionally similar to one another. Some biological processes are reflected by the expression of genes in a specific gene expression signature, as described above. The expression of a specific gene expression signature in a sample can provide important biological insights into its cellular composition and the function of various intracellular pathways within those cells.
  • the present invention discloses a variety of gene expression signatures related to the clinical outcome of lymphoma patients. While several of these signatures share a name with a previously disclosed signature, each of the gene expression signatures disclosed herein comprises a novel combination of genes.
  • the lymph node signature disclosed herein includes genes encoding extracellular matrix components and genes that are characteristically expressed in macrophage, NK, and T cells (e.g., ⁇ -Actinin, collagen type III ⁇ 1, connective tissue growth factor, fibronectin, KIAA0233, urokinase plasminogen activator).
  • the proliferation signature includes genes that are characteristically expressed by cells that are rapidly multiplying or proliferating (e.g., c-myc, E21G3, NPM3, BMP6).
  • the MHC class II signature includes genes that interact with lymphocytes in order to allow the recognition of foreign antigens (e.g., HLA-DP ⁇ , HLA-DQ ⁇ , HLA-DR ⁇ , HLA-DR ⁇ ).
  • the immune response-1 signature includes genes encoding T cell markers (e.g., CD7, CD8B1, ITK, LEF1, STAT4), as well as genes that are highly expressed in macrophages (e.g., ACTN1, TNFSF13B).
  • the immune response-2 signature includes genes known to be preferentially expressed in macrophages and/or dendritic cells (e.g., TLR5, FCGR1A, SEPT10, LGMN, C3AR1).
  • the germinal center B cell signature includes genes known to be overexpressed at this stage of B cell differentiation (e.g., MME, MEF2C, BCL6, LMO2, PRSPAP2, MBD4, EBF, MYBL1).
  • genes from the germinal center B-cell signature in a lymphoma biopsy suggests that the lymphoma is derived from this stage of B cell differentiation.
  • the expression of genes from the T cell signature can be used to estimate the degree of infiltration of the tumor by host T cells, while the expression of genes from the proliferation signature can be used to quantitate the tumor cell proliferation rate.
  • gene expression signatures provide an “executive summary” of the biological properties of a tumor specimen. Gene expression signatures can also be helpful in interpreting the results of a supervised analysis of gene expression data.
  • Gene expression profiles can be used to create multivariate models for predicting survival.
  • the methods for creating these models are called “supervised” because they use clinical data to guide the selection of genes to be used in the prognostic classification.
  • a supervised method might identify genes with expression patterns that correlate with the length of overall survival following chemotherapy.
  • the general method used to create a multivariate model for predicting survival may utilize the following steps:
  • a first FL survival predictor was generated using gene expression data obtained using Affymetrix U133A and U133B microarrays. This predictor incorporated immune response-1 and immune response-2 gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:
  • Survival predictor score [(2.71*immune response-2 gene expression signature value)] ⁇ [(2.36 ⁇ immune response-1 gene expression signature value)].
  • a second FL survival predictor was generated using gene expression data obtained using Affymetrix U133A and U133B microarrays. This predictor incorporated macrophage, T-cell, and B-cell differentiation gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:
  • Survival predictor score [2.053*(macrophage gene expression signature value)] ⁇ [2.344*( T -cell gene expression signature value)] ⁇ [0.729*( B -cell differentiation gene expression signature value)].
  • a third FL survival predictor was generated using gene expression data obtained using the Lymph Dx microarray. This predictor incorporated macrophage, T-cell, and B-cell differentiation gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:
  • Survival predictor score [1.51*(macrophage gene expression signature value)] ⁇ [2.11*( T -cell gene expression signature value)] ⁇ [0.505*( B -cell differentiation gene expression signature value)].
  • a first DLBCL survival predictor was generated using gene expression data obtained using Affymetrix U133A and U133B microarrays. This predictor incorporated ABC DLBCL high, lymph node, and MHC class II gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:
  • Survival predictor score [0.586*(ABC DLBCL high gene expression signature value)] ⁇ [0.468*(lymph node gene expression signature value)] ⁇ 0.336*(MHC class II gene expression signature value)].
  • a second DLBCL survival predictor was generated using gene expression data obtained using the Lymph Dx microarray. This predictor incorporated lymph node, proliferation, germinal center B-cell, and MHC class II gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:
  • Survival predictor score [ ⁇ 0.4337*(lymph node gene expression signature value)]+[0.09*(proliferation gene expression signature value)] ⁇ [0.4144*(germinal center B -cell gene expression signature value)] ⁇ [0.2006*(MHC class II gene expression signature value)].
  • a third DLBCL survival predictor was generated using gene expression data obtained using the Lymph Dx microarray. This predictor incorporated lymph node, germinal center B cell, and MHC class II gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:
  • Survival predictor score [ ⁇ 0.32*(lymph node gene expression signature value)] ⁇ [0.176*(germinal center B -cell gene expression signature value)] ⁇ [0.206*(MHC class II gene expression signature value)].
  • An MCL survival predictor was generated using gene expression data obtained using Affymetrix U133A, Affymetrix U133B, and Lymph Dx microarrays. This predictor incorporated a proliferation gene expression signature. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:
  • Gene expression data can also be used to diagnose and identify lymphoma types.
  • a statistical method based on Bayesian analysis was developed to classify lymphoma specimens according to their gene expression profiles. This method does not merely assign a tumor to a particular lymphoma type, but also determines the probability that the tumor belongs to that lymphoma type.
  • Many different methods have been formulated to predict cancer subgroups (Golub 1999; Ramaswamy 2001; Dudoit 2002; Radmacher 2002). These methods assign tumors to one of two subgroups based on expression of a set of differentially expressed genes. However, they do not provide a probability of membership in a subgroup.
  • the method disclosed herein used Bayes' rule to estimate this probability, thus allowing one to vary the probability cut-off for assignment of a tumor to a particular subgroup.
  • the present method allows samples that do not meet the gene expression criteria of known subgroups to fall into an unclassified group with intermediate probability.
  • a cancer subgroup predictor of the type described herein may be used clinically to provide quantitative diagnostic information for an individual cancer patient. This information can in turn be used to provide a predictor of treatment outcome for a particular cancer patient.
  • Lymph Dx microarray A novel microarray termed the Lymph Dx microarray is disclosed herein for the identification and diagnosis of various lymphoma types.
  • the Lymph Dx microarray contains cDNA probes corresponding to approximately 2,653 genes, fewer than the number seen on microarrays that have been used previously for lymphoma diagnosis.
  • the reduced number of probes on the Lymph Dx microarray is the result of eliminating genes that are less useful for the identification of lymphoma types and predicting clinical outcome. This reduction allows for simplified analysis of gene expression data.
  • the genes represented on the Lymph Dx microarray can be divided into four broad categories: 1,101 lymphoma predictor genes identified previously using the Affymetrix U133 microarray, 171 outcome predictor genes, 167 new genes not found on the Affymetrix U133 microarray, and 1,121 named genes.
  • a list of the probe sets on the Lymph Dx microarray is presented in Table 2, contained in the file “Table — 0002_LymphDx_Probe_List.txt.”
  • Gene expression data obtained using the Lymph Dx microarray may be used to identify and classify lymphomas using Bayesian analysis using a strategy similar to that set forth above.
  • this strategy may include additional steps designed to optimize the number of genes used and the cut-off points between lymphoma types.
  • FIG. 1 A general overview of such a method is presented in FIG. 1 .
  • each gene represented on the Lymph Dx microarray was placed into one of three gene-list categories based on its correlation with the lymph node or proliferation gene expression signatures: lymph node, proliferation, or standard. These signatures were identified by clustering of the DLBCL cases using hierarchical clustering and centroid-correlation of 0.35.
  • Lymph Dx gene expression data was first used to identify samples as FL, MCL, SLL, FH, or DLBCL/BL, then to identify DLBCL/BL samples as ABC, GCB, PMBL, or BL.
  • a series of pair-wise models was created, with each model containing a different pair of lymphoma types (e.g., FL vs. MCL, SLL vs. FH, etc.).
  • the difference in expression of each gene on the microarray was measured, and a t-statistic was generated representing this difference.
  • Genes from each gene-list category were ordered based on their t-statistic, and those with the largest t-statistics were used to generate a series of LPSs for samples belonging to either lymphoma type.
  • the number of genes used to generate the LPSs was optimized by repeating the calculation using between five and 100 genes from each gene-list category.
  • the number of genes from each category used in the final LPS calculation was that which gave rise to the largest difference in LPS between the two lymphoma types. Once the number of genes in each gene-list category was optimized, four different LPSs were calculated for each sample.
  • the probability q that a sample X belongs to the first lymphoma type of a pair-wise model can then be calculated using an equation:
  • LPS(X) is the LPS for sample X
  • ⁇ (x; ⁇ , ⁇ ) is the normal density function with mean ⁇ and standard deviation ⁇
  • ⁇ circumflex over ( ⁇ ) ⁇ 1 and ⁇ circumflex over ( ⁇ ) ⁇ 1 are the mean and variance of the LPSs for samples belonging to the first lymphoma type
  • ⁇ circumflex over ( ⁇ ) ⁇ 2 and ⁇ circumflex over ( ⁇ ) ⁇ 2 are the mean and variance of the LPSs for samples belonging to the second lymphoma type.
  • Samples with high q values were classified as the first lymphoma type
  • samples with low q values were classified as the second lymphoma type
  • samples with middle range q values were deemed unclassified.
  • This equation was used to favor the assignment of a sample to an “unclassified” category rather than to an incorrect lymphoma type.
  • the final cut-off points were those which minimized this equation.
  • the coefficient of 3.99 was chosen arbitrarily to allow an additional classification error only if the adjustment resulted in four or more unclassified samples becoming correctly classified.
  • the coefficient can be varied to achieve a different set of trade-offs between the number of unclassified and misidentified samples.
  • each model was validated by leave-one-out cross-validation. This entailed removing each sample of known lymphoma type from the data one at a time, and then determining whether the model could predict the missing sample. This process confirmed the accuracy of the prediction method.
  • a lymphoproliferative disorder in accordance with embodiments of the present invention may be used in combination with any other effective classification feature or set of features.
  • a disorder may be classified by a method of the present invention in conjunction with WHO suggested guidelines, morphological properties, histochemical properties, chromosomal structure, genetic mutation, cellular proliferation rates, immunoreactivity, clinical presentation, and/or response to chemical, biological, or other agents.
  • Embodiments of the present invention may be used in lieu of or in conjunction with other methods for lymphoma diagnosis, such as immunohistochemistry, flow cytometry, FISH for translocations, or viral diagnostics.
  • lymphoma type in a subject allows for better selection and application of therapeutic methods.
  • Knowledge about the exact lymphoma affecting a subject allows a clinician to select therapies or treatments that are most appropriate and useful for that subject, while avoiding therapies that are nonproductive or even counterproductive.
  • CNS prophylaxis may be useful for treating BL but not DLBCL
  • CHOP treatment may be useful for treating DLBCL but not blastic MCL (Fisher 1993; Khouri 1998)
  • subjects with follicular lymphoma frequently receive treatment while subjects with follicular hyperplasia do not.
  • the lymphoma types or subtypes in question can be difficult to distinguish using prior art diagnostic methods.
  • the diagnostic and identification methods of the present invention allow for more precise delineation between these lymphomas, which simplifies the decision of whether to pursue a particular therapeutic option.
  • the survival prediction methods disclosed in the present invention also allow for better selection of therapeutic options.
  • a subject with a very low survival predictor score i.e., very good prognosis
  • survival predictor scores increase (i.e., prognosis gets worse)
  • subjects may receive more intensive treatments.
  • Those subjects with the highest survival predictor scores i.e., very poor prognosis
  • Accurate survival prediction using the methods disclosed herein provides an improved tool for selecting treatment options and for predicting the likely clinical outcome of those options.
  • gene expression data may be measured or estimated using one or more microarrays.
  • the microarrays may be of any effective type, including but not limited to nucleic acid based or antibody based.
  • Gene expression may also be measured by a variety of other techniques, including but not limited to PCR, quantitative RT-PCR, real-time PCR, RNA amplification, in situ hybridization, immunohistochemistry, immunocytochemistry, FACS, serial analysis of gene expression (SAGE) (Velculescu 1995), Northern blot hybridization, or western blot hybridization.
  • Nucleic acid microarrays generally comprise nucleic acid probes derived from individual genes and placed in an ordered array on a support.
  • This support may be, for example, a glass slide, a nylon membrane, or a silicon wafer.
  • Gene expression patterns in a sample are obtained by hybridizing the microarray with the gene expression product from the sample.
  • This gene expression product may be, for example, total cellular mRNA, rRNA, or cDNA obtained by reverse transcription of total cellular mRNA.
  • the gene expression product from a sample is labeled with a radioactive, fluorescent, or other label to allow for detection.
  • the microarray is washed, and hybridization of gene expression product to each nucleic acid probe on the microarray is detected and quantified using a detection device such as a phosphorimager or scanning confocal microscope.
  • cDNA arrays consist of hundreds or thousands of cDNA probes immobilized on a solid support. These cDNA probes are usually 100 nucleotides or greater in size.
  • nitrocellulose filter array which is generally prepared by robotic spotting of purified DNA fragments or lysates of bacteria containing cDNA clones onto a nitrocellulose filter (Southern 1992; Southern 1994; Gress 1996; Pietu 1996).
  • cDNA arrays The other commonly used cDNA arrays is fabricated by robotic spotting of PCR fragments from cDNA clones onto glass microscope slides (Schena 1995; DeRisi 1996; Schena 1996; Shalon 1996; DeRisi 1997; Heller 1997; Lashkari 1997). These cDNA microarrays are simultaneously hybridized with two fluorescent cDNA probes, each labeled with a different fluorescent dye (typically Cy3 or Cy5). In this format, the relative mRNA expression in two samples is directly compared for each gene on the microarray. Oligonucleotide arrays differ from cDNA arrays in that the probes are 20- to 25-mer oligonucleotides.
  • Oligonucleotide arrays are generally produced by in situ oligonucleotide synthesis in conjunction with photolithographic masking techniques (Pease 1994; Lipshutz 1995; Chee 1996; Lockhart 1996; Wodicka 1997).
  • the solid support for oligonucleotide arrays is typically a glass or silicon surface.
  • Microarrays may generally be produced using a variety of techniques, such as mechanical or light directed synthesis methods that incorporate a combination of photolithographic methods and solid phase synthesis methods. Techniques for the synthesis of microarrays using mechanical synthesis methods are described in, for example, U.S. Pat. Nos. 5,384,261 (Winkler) and 6,040,193 (Winkler). Although a planar array surface is preferred, the microarray may be fabricated on a surface of virtually any shape, or even on a multiplicity of surfaces. Microarrays may be nucleic acids on beads, gels, polymeric surfaces, fibers such as fiber optics, glass or any other appropriate substrate. See, for example, U.S. Pat. Nos. 5,708,153 (Dower); 5,770,358 (Dower); 5,789,162 (Dower); 5,800,992 (Fodor); and 6,040,193 (Winkler), each of which is incorporated by reference herein in its entirety.
  • Microarrays may be packaged in such a manner as to allow for diagnostic use, or they can be an all-inclusive device. See, for example, U.S. Pat. Nos. 5,856,174 (Lipshutz) and 5,922,591 (Anderson), both of which are incorporated by reference herein in their entirety.
  • Microarrays directed to a variety of purposes are commercially available from Affymetrix (Affymetrix, Santa Clara, Calif.). For instance, these microarrays may be used for genotyping and gene expression monitoring for a variety of eukaryotic and prokaryotic species.
  • DLBCL diffuse large B cell lymphomas
  • MCL mantle cell lymphoma
  • SLL small cell lymphocytic lymphomas
  • MALT mucosa-associated lymphoid tissue lymphomas
  • CD1negMCL 10 cyclin-D1 negative lymphomas with MCL morphology
  • LPC lymphoplasmacytic lymphomas
  • the 231 DLBCL samples were subdivided into the following lymphoma types based on gene expression (see below):
  • PMBL primary mediastinal B cell lymphoma
  • the 16 MALT samples were subdivided into the following four group based on tumor origin:
  • Each of the 568 cell samples was given a unique sample ID number consisting of the lymphoma type followed by a unique numerical identifier.
  • “ABC — 304” refers to an ABC DLBCL sample numbered 304.
  • Cells were purified and RNA was isolated from the purified cells according to known methods described in the literature.
  • RNA from each sample were applied to Affymetrix U133A and Affymetrix U133B microarrays according to standard Affymetrix protocol.
  • the U133A and U133B microarrays are divided into probe sets, with each probe set consisting of up to 69 oligonucleotide probes 25 nucleotides in length. Each probe set represents a distinct human gene. Information pertaining to these microarrays is available at the Affymetrix company web site. Each microarray was scanned using an Affymetrix scanner, which records signal intensity for every probe on the microarray.
  • This information can be transformed into summary signal values for each probe set using a number of different algorithms, including MAS 5.0, D-chip (Li 2001), or Bioconductor's RMA algorithms (Irizarry 2003).
  • the images produced by the scanner were evaluated by Affymetrix MAS 5.0 software and stored as tables in .txt format. Since each sample was scanned on both microarrays, there are two .txt files for each sample. Each .txt file was given a unique name consisting of the table number, sample ID number (discussed above), and a letter denoting the microarray used.
  • Table — 0588_ABC — 304A.txt is the .txt file for Table 588, which contains data for sample ID number ABC — 304 from the U133A array. The data for each sample tested is contained in Tables 3-1138.
  • the signal value for each probe on the U133A and U133B microarrays was normalized to a target value of 500, and the base-2 log of the normalized values was used for the following analyses.
  • Log-signal values for each probe set are presented in Tables 1139-1706, contained in files with the title format “Table_No._NAME_log_signal.txt,” where NAME refers to the sample ID number (e.g., ABC — 304).
  • the first column provides the UNIQID for the probe set, while the second column provides the log-signal value.
  • Log-signal files were statistically analyzed using S+ software and the S+ subtype predictor script contained in the file entitled “Subtype_Predictor.txt,” located in the computer program listing appendix contained on CD number 22 of 22. Although the log-signal values were analyzed using S+ software and the above algorithm, any effective software/algorithm combination may be used.
  • Tables 1707-1721 provide descriptive statistical characteristics for each of the lymphoma types tested except for CD1 negMCL, non-gastric MALT, and UC_DLBCL.
  • Table 1722 provides statistical characteristics for all MALT samples combined, while Table 1723 does likewise for all DLBCL samples.
  • Tables 1707-1723 have the title format “Table_No._TYPE_Stats.txt,” where TYPE refers to the lymphoma type.
  • Each row of these tables represents a particular probe set.
  • the first column of each table provides the UNIQID for the probe set, while the second column provides the average log-signal for the probe set over all samples of a particular lymphoma type.
  • the third column provides the log-fold change in expression of the probe set between the lymphoma type in question and a second lymphoma type.
  • Tables 1710, 1715, and 1723 (corresponding to FL, MCL, and DLBCL, respectively) contain two additional columns entitled “TYPE_Cox_coefficient” and “TYPE_Cox_P_value.” The content of these columns is discussed in the following examples.
  • the novel Lymph Dx microarray contains cDNA probes corresponding to approximately 2,734 genes. 174 of these are “housekeeping” genes present for quality control, since they represent genes that are most variably expressed across all lymphoma samples. Other genes represented on the microarray were selected for their utility in identifying particular lymphoma samples and predicting survival in those samples.
  • the genes represented on the Lymph Dx microarray can be divided into four broad categories: 1,101 lymphoma predictor genes identified previously using the Affymetrix U133 microarray, 171 outcome predictor genes identified using the Affymetrix 0133 microarray, 167 genes not found on the Affymetrix U133 microarray but represented on the Lymphochip microarray (Alizadeh 1999), and 1,121 named genes.
  • Each of the 634 samples was given a unique sample ID number consisting of the lymphoma type followed by a unique numerical identifier.
  • BL — 2032 — 52748 refers to a Burkitt lymphoma sample with the numerical identifier 2032 — 52748.
  • Cells were purified and RNA was isolated from the purified cells according to known methods described in the literature.
  • RNA samples were applied to the Lymph Dx microarrays according to standard Affymetrix microarray protocol. Each microarray was scanned on an Affymetrix scanner. This scanner produced an image of the microarray, which was then evaluated by Affymetrix MAS 5.0 software. This information was stored in tables in .txt format. Each of these .txt files was given a unique name consisting of the table number, the sample ID number (discussed above), and the UNIQID for identifying the array data in the National Cancer Institute Database. For example, Table — 1725_BL — 2032 — 52748.txt is the .txt file for Table 1725, which contains data for sample ID number BL — 2032.
  • the data for each sample analyzed is contained in Tables 1725-2358.
  • the signal intensity for each probe on the microarray can be transformed into summary signal values for each probe set through a number of different algorithms, including but not limited to MAS 5.0, D-chip (Li 2001), or Bioconductor's RMA algorithms (Irizarry 2003).
  • Survival Signature Analysis begins by identifying genes whose expression patterns are statistically associated with survival. A hierarchical clustering algorithm is then used to identify subsets of these genes with correlated expression patterns across the lymphoma samples. These subsets are operationally defined as “survival-associated signatures.” Evaluating a limited number of survival-associated signatures mitigates the multiple comparison problems that are inherent in the use of large-scale gene expression data sets to create statistical models of survival (Ransohoff 2004).
  • FL samples were divided into two equivalent groups: a training set (95 samples) for developing the survival prediction model, and a validation set (96 samples) for evaluating the reproducibility of the model.
  • the overall survival of this cohort is depicted in FIG. 3 .
  • the median age at diagnosis was 51 years (ranging from 23 to 81 years), and the patients had a median follow-up of 6.6 years (8.1 years for survivors, with a range of ⁇ 1 to 28.2 years).
  • Gene expression data from Affymetrix U133A and U133B microarrays was obtained for each sample.
  • a Cox proportional hazards model was used to identify “survival predictor” genes, which were genes whose expression levels were associated with long survival (good prognosis genes) or short survival (poor prognosis genes).
  • a hierarchical clustering algorithm (Eisen 1998) was used to identify gene expression signatures within the good and poor prognosis genes according to their expression pattern across all samples. Ten gene expression signatures were observed within either the good prognosis or poor prognosis gene sets ( FIG. 4 ). The expression level of every component gene in each of these ten gene expression signatures was averaged to create a gene expression signature value.
  • the immune response-1 gene expression signature included genes encoding T cell markers (e.g., CD7, CD8B1, ITK, LEF1, STAT4) and genes that are highly expressed in macrophages (e.g., ACTN1, TNFSF13B).
  • the immune response-1 signature is not merely a surrogate for the number of T cells in the FL biopsy sample because many other standard T cell genes (e.g., CD2, CD4, LAT, TRIM, SH2D1A) were not associated with survival.
  • the immune response-2 gene expression signature included genes known to be preferentially expressed in macrophages and/or dendritic cells (e.g., TLR5, FCGR1A, SEPT10, LGMN, C3AR1). Table 2359 lists the genes that were used to generate the gene expression signature values for the immune response-1 and immune response-2 signatures.
  • the Unigene ID Build database referenced in the following tables is hosted by the hosted by the National Center for Biotechnology Information (NCBI) web site
  • the third signature was removed from the model and the two-signature model was used to generate a survival predictor score using the following equation:
  • Survival predictor score [(2.71*immune response-2 gene expression signature value)] ⁇ [(2.36 ⁇ immune response-1 gene expression signature value)].
  • the two-signature model was associated with survival in a statistically significant fashion in both the training set (p ⁇ 0.001) and the validation set (p ⁇ 0.001), which demonstrated that the model was reproducible.
  • the survival predictor score had a mean of 1.6 and a standard deviation of 0.894, with each unit increase in the predictor score corresponding to a 2.5 fold increase in the relative risk of death. Data for all 191 samples is shown in Table 2361.
  • the FL samples were ranked according to their survival predictor scores and divided into four quartiles. Kaplan-Meier plots of overall survival showed clear differences in survival rate in the validation set ( FIG. 5 ). The median survival for each of the four quartiles is set forth in Table 2362.
  • the samples in the validation set were divided into three groups based on their IPI score, and the relationship between survival and IPI score was visualized by Kaplan-Meier plot ( FIG. 6 ).
  • the gene-expression-based survival predictor could stratify patients into groups differing by more than 5 years with regards to median survival ( FIG. 7 ).
  • the high-risk IPI group (IPI 4-5) comprised less than 5% of the samples, and was omitted from this analysis.
  • 191 FL were divided into two equivalent groups: a training set (95 samples) for developing the survival prediction model, and a validation set (96 samples) for evaluating the reproducibility of the model.
  • Gene expression data from Affymetrix U133A and U133B microarrays was obtained for each of the samples.
  • a Cox proportional hazards model was used to identify survival predictor genes whose expression levels were associated with long survival (good prognosis genes) or short survival (poor prognosis genes) in the training set.
  • the correlation between expression and survival for each gene on the microarrays is provided in the final two columns of Table 1710. The first of these two columns (“FL_Cox_coefficient”) provides a Cox coefficient indicating the extent to which a 2-fold increase in expression of a particular gene affects mortality.
  • a positive Cox coefficient indicates increasing mortality with increasing expression of the gene, while a negative Cox coefficient indicates decreasing mortality with increasing expression of the gene.
  • the second of these two columns provides a Cox p-value indicating the estimated probability that the increase or decrease in survival associated with the gene would occur by chance if there was no connection between the expression of the gene and survival.
  • a hierarchical clustering algorithm (Eisen 1998) was used to identify gene expression signatures within the good and poor prognosis genes according to their expression pattern across all samples. Eight clusters of coordinately regulated genes were observed within the good prognosis gene set and six clusters were observed in the poor prognosis gene sets. The expression level of every component gene in each of these gene expression signatures was averaged to create a gene expression signature value. After averaging, only ten of the gene expression signatures were found to be significantly associated with survival in the training set (p ⁇ 0.01). To create a multivariate model of survival, different combinations of these ten gene expression signature averages were generated and evaluated for their ability to predict survival within the training set.
  • T-cell and macrophage based on the biological function of certain genes within each signature.
  • the T-cell gene expression signature included genes that were typically expressed in T-cells, while the macrophage gene expression signature included a number of genes typically expressed in macrophages.
  • these two signatures taken individually were not the best predictors of survival, the binary model formed by combining the two was more predictive than any combination of three signatures that did not contain these two signatures. Using these two signatures as an anchor, other signatures were added to the model using a step up procedure (Drapner 1966).
  • the B-cell differentiation signature included a number of genes that appear to be involved in B-cell signal transduction. Table 2364 lists the genes that were used to generate the gene expression signature values for the T-cell, macrophage, and B-cell differentiation gene expression signatures.
  • Survival predictor score [2.053*(macrophage gene expression signature value)] ⁇ [2.344*( T -cell gene expression signature value)] ⁇ [0.729*( B -cell differentiation gene expression signature value)].
  • the FL samples were ranked according to their survival predictor scores and divided into four quartiles. Kaplan-Meier plots of overall survival showed clear differences in survival rate in the validation set ( FIG. 8 ). The median survival for each of the four quartiles is set forth in Table 2366.
  • 191 FL samples were divided into two equivalent groups: a training set for developing the survival prediction model, and a validation set for evaluating the reproducibility of the model.
  • Gene expression data from the Lymph Dx microarray was obtained for those genes listed in Table 2364, above. This gene expression data was used to calculate gene expression signature values for the macrophage, T-cell, and B-cell differentiation gene expression signatures, and these signature values were used to generate a survival predictor score using the following equation:
  • Survival predictor score [1.51*(macrophage gene expression signature value)] ⁇ [2.11*( T -cell gene expression signature value)] ⁇ [0.505*( B -cell differentiation gene expression signature value)].
  • the correlation between expression of each gene represented on the microarrays and survival was estimated using a Cox proportional hazards model.
  • the results of this survival analysis are provided in the final two columns of Table 1723.
  • the first of these two columns (“DLBCL_Cox_coefficient”) provides a Cox coefficient indicating the extent to which a 2-fold increase in expression of a particular gene affects mortality.
  • a positive Cox coefficient indicates increasing mortality with increasing expression of the gene, while a negative Cox coefficient indicates decreasing mortality with increasing expression of the gene.
  • the second of these two columns (“DLBCL_Cox_P_value”) provides a Cox p-value indicating the estimated probability that the increase or decrease in survival associated with the gene would occur by chance if there was no connection between the expression of the gene and survival.
  • Genes that were significantly correlated with survival were grouped into gene expression signatures using a hierarchical clustering algorithm. The expression level of every component gene in each of these gene expression signatures was averaged for each sample to create a gene expression signature value.
  • a step-up procedure (Drapner 1966) was applied to determine the optimal number of gene signatures to use in the survival predictor model. First, the gene expression signature that was most significantly associated with survival was included in the model. Next, the gene expression signature with the second highest association with survival was added to the model to form a two-component model. This procedure was repeated until there was no gene expression signature to add to the model with a p-value of ⁇ 0.05.
  • the final prediction model incorporated gene expression signature values from three gene expression signatures.
  • the first gene expression signature added to the model was termed “ABC DLBCL high,” because it included genes that were more highly expressed in ABC than in GCB (Rosenwald 2002).
  • the second gene expression signature added to the model was termed “lymph node,” because it reflected the response of non-tumor cells in the lymph node to the malignant lymphoma cells.
  • the final gene expression signature added to the model was termed “MHC class II,” because it included all of the genes encoding the MHC class II alpha and beta chains. Table 2369 shows the genes that were averaged to form each of these signatures.
  • Survival predictor score [0.586*(ABC DLBCL high gene expression signature value)] ⁇ [0.468*(lymph node gene expression signature value)] ⁇ [0.336*(MHC Class II gene expression signature value)].
  • a DLBCL survival model based on gene expression had been developed previously using proliferation, germinal center B-cell, lymph node, and MHC class II gene expression signatures and the expression of the single gene BMP-6 (Rosenwald 2002).
  • BMP-6 expression was poorly measured on the Lymph Dx microarray, but genes associated with each of these four gene expression signatures exhibited associations with survival similar to those observed using Lymphochip microarrays.
  • DLBCL samples were divided into two groups: a training set (100 samples) for developing the survival prediction model, and a validation set (100 samples) for evaluating the reproducibility of the model. Gene expressed in the training set samples were clustered, and lymph node, germinal center B-cell, MHC class II, and proliferation gene expression signatures were identified. Within each signature, expression of genes that were associated with survival (p ⁇ 0.01) was averaged to generate a gene expression signature value for each signature. Table 2371 lists the genes that were used to generate the gene expression signature value for each signature.
  • Table 2372 lists p-values for the association of each signature with survival in the training set, the validation set, and overall.
  • the four gene expression signatures were used to generate a survival predictor score using the following equation:
  • Survival predictor score [ ⁇ 0.4337*(lymph node gene expression signature value)]+[0.09*(proliferation gene expression signature value)] ⁇ [0.4144*(germinal center B -cell gene expression signature value)] ⁇ [0.2006*(MHC class II gene expression signature value)].
  • the survival predictor score had a mean of 5.7 and a standard deviation of 0.78, with each unit increase in the predictor score corresponding to an approximately 2.7 fold increase in the relative risk of death. Data for all 200 samples is presented in Table 2373.
  • the number of genes used to generate the DLBCL survival predictor in Example 7 was reduced in order to create a survival predictor compatible with RT-PCR.
  • the list of genes from the lymph node and germinal center B-cell gene expression signatures was narrowed to those three genes from each signature that were most closely correlated with the lymph node and germinal center B-cell gene expression signature values, respectively.
  • the genes from the proliferation gene expression signature did not add significantly to the reduced gene survival prediction model, so they were removed entirely.
  • the expression of the genes within each signature was averaged on the log 2 scale to generate a gene expression signature value for each signature.
  • Table 2374 lists the genes that were used to generate these gene expression signature values.
  • Table 2375 lists p-values for the association of each signature with survival in the training set, the validation set, and overall.
  • Survival predictor score [ ⁇ 0.32*(lymph node gene expression signature value)] ⁇ [0.176*(germinal center B -cell gene expression signature value)] ⁇ [0.206*(MHC class II gene expression signature value)].
  • the survival predictor score had a mean of 6.54 and a standard deviation of 0.69, with each unit increase in the predictor score corresponding to an approximately 2.7 fold increase in the relative risk of death. Data for all 200 samples is presented in Table 2376.
  • a survival predictor score for MCL was generated using the following equation:
  • the 21 MCL samples were divided into two equivalent groups based on their survival predictor scores. Those samples with survival predictor scores above the median were placed in the high proliferation group, while those with survival predictor scores below the median were placed in the low proliferation group.
  • FIG. 13 illustrates the Kaplan Meier survival estimates for these two groups. Median survival for the high proliferation group was 1.07 years, while median survival for the low proliferation group was 5.18 years.
  • FIG. 14 illustrates the Kaplan Meier survival estimates for these two groups.
  • a statistical method based on Bayesian analysis was developed to distinguish MCL samples from samples belonging to other lymphoma types based on gene expression profiling. This method was developed using the gene expression data obtained in Example 1 for the following lymphoma types: ABC, GCB, PMBL, BL, FH, FL, MALT, MCL, PTLD, SLL, and splenic marginal zone lymphoma (splenic).
  • Tables 1707-1741 (discussed in Example 1) provide gene expression data for samples within each of these lymphoma types, including the expression level of each gene and the difference in expression of each gene between types.
  • Tables 1710, 1715, and 1723 (corresponding to FL, MCL, and DLBCL, respectively) include the correlation between expression of each gene and survival.
  • Each predictor model calculates the probability that the sample belongs to a first lymphoma type rather than a second lymphoma type.
  • a method was developed to determine whether a sample was MCL, or one of the following lymphoma types: ABC, BL, FH, FL, GCB, MALT, PMBL, PTLD, SLL, or splenic. This method required ten different predictor models, each designed to determine whether the sample belonged to MCL or one of the other ten lymphoma types (e.g., MCL vs. ABC, MCL vs. BL, etc.).
  • lymphoma samples analyzed displayed a tendency towards elevated or reduced expression of genes from the lymph node and proliferation gene expression signatures. These genes are likely to be highly differentially expressed between the lymphoma types, but they do not serve as good predictor genes because they are often variably expressed within a single lymphoma type. For this reason, any gene that displayed a correlation with the proliferation or lymph node signatures was eliminated from consideration.
  • LPS linear predictor score
  • X j is the expression of gene j in sample X and t j is the t-statistic for the difference in expression of gene j between a first lymphoma type and a second lymphoma type.
  • This is merely one method for generating an LPS.
  • Others methods include linear discriminant analysis (Dudoit 2002), support vector machines (Furey 2000), or shrunken centroids (Tibshirani 2002).
  • Dudoit 2002 linear discriminant analysis
  • Support vector machines Feurey 2000
  • shrunken centroids Tibshirani 2002
  • Bayes' rule can be used to estimate the probability that the sample belongs to a first lymphoma type rather than a second lymphoma type ( FIG. 15 ).
  • Bayes' rule was used to calculate the probability q that sample X was MCL rather than a second lymphoma type using the following equation:
  • type 1 is MCL
  • type 2 is one of the other nine lymphoma types
  • ⁇ (x; ⁇ , ⁇ ) is the normal density function with mean ⁇ and standard deviation ⁇
  • ⁇ circumflex over ( ⁇ ) ⁇ 1 and ⁇ circumflex over ( ⁇ ) ⁇ 1 are the sample mean and variance of the LPS values for lymphoma type 1
  • ⁇ circumflex over ( ⁇ ) ⁇ 2 and ⁇ circumflex over ( ⁇ ) ⁇ 2 are the sample mean and variance of the LPS values for lymphoma type 2.
  • This method was used to develop ten predictor models, one for each pairing of MCL and a second lymphoma type.
  • a sample was classified as MCL if each of the ten predictors generated at least a 90% probability that the sample was MCL. If any of the ten predictors indicated a probability of less than 90%, the sample was classified as non-MCL.
  • PLXNB1 plexin B1 18.38081568 1109505 Homo sapiens , Similar to LOC168058, clone MGC: 39372 17.17812448 IMAGE: 5089466, mRNA, complete cds 1098840 C3orf6—chromosome 3 open reading frame 6 16.32703666 1130926 C5orf13—chromosome 5 open reading frame 13 15.34261878 1096396 SPG3A—spastic paraplegia 3A (autosomal dominant) 14.75437736 1132734 COL9A3—collagen, type IX, alpha 3 14.684583 113939393 OPN3—opsin 3 (encephalopsin, panopsin) 14.39118445 1115537 LOC84518—protein related with psoriasis 14.18446144 1102215 Homo sapiens cDNA FLJ11666 fis, clone HEMBA1004672.
  • DNMT3A DNA (cytosine-5-)-methyltransferase 3 alpha 15.22540494 1139393
  • OPN3 opsin 3 (encephalopsin, panopsin) 14.64030565 1127849
  • SNN stannin 14.28242206 1098156 Human HeLa mRNA isolated as a false positive in a two- 14.00049272 hybrid-screen.
  • 1128845 FLJ20174 hyperothetical protein FLJ20174 13.96064416 1129943 Homo sapiens , similar to Zinc finger protein 85 (Zinc finger 13.85404507 protein HPF4) (HTF1), clone IMAGE: 352451, mRNA 1140116 DKFZP564B116—hypothetical protein DKFZp564B1162 13.81464172 1106855 KIAA1909—KIAA1909 protein 13.74521849 1120900 EPHB6—EphB6 13.46567004 1127371 Homo sapiens cDNA FLJ14046 fis, clone HEMBA1006461.
  • TIA1 TIA1 cytotoxic granule-associated RNA binding protein
  • EDG1 endothelial differentiation
  • sphingolipid G-protein- 13.1047657 coupled receptor 1 1098277
  • PRICKLE1 prickle-like 1 ( Drosophila )
  • TRIM34 tripartite motif-containing 34
  • 12.66260609 1100581 Homo sapiens mRNA; cDNA DKFZp667A1115 (from clone ⁇ 12.81251689 DKFZp667A1115)
  • EDG1 endothelial differentiation, sphingolipid G-protein- 8.045872672 coupled receptor, 1 1102215 Homo sapiens cDNA FLJ11666 fis, clone HEMBA1004672. 8.032351578 1121739 ZNF135—zinc finger protein 135 (clone pHZ-17) 8.020919565 1096070 DNMT3A—DNA (cytosine-5-)-methyltransferase 3 alpha 7.964477216 1101211 Homo sapiens cDNA: FLJ21960 fis, clone HEP05517.
  • CHL1 cell adhesion molecule with homology to L1CAM 7.516130116 (close homolog of L1) 1099437 Homo sapiens mRNA; cDNA DKFZp667B1913 (from clone 7.209041652 DKFZp667B1913) 1096503 GL012—hypothetical protein GL012 7.171540413 1135927 LILRA2—leukocyte immunoglobulin-like receptor, 7.134470829 subfamily A (with TM domain), member 2 1120645 FADS3—fatty acid desaturase 3 7.039952979
  • Lymphoma samples with morphology consistent with MCL were identified by pathological review. Since t(11; 14) translocation and cyclin D1 overexpression have been consistently associated with MCL, cyclin D1 mRNA levels were measured in each sample by quantitative RT-PCR. Of the 101 samples analyzed, 92 expressed cyclin D1 mRNA. These 92 samples, which were deemed the “core group” of MCLs, were divided into a training set and a validation set. Gene expression was measured in all 101 samples using a Lymphochip microarray (Alizadeh 1999). For comparison, gene expression was measured in 20 samples identified as SLL.
  • MCL expression data was compared to expression data obtained previously for GCB (134 cases) and ABC (83 cases) (Rosenwald 2002).
  • Several thousand genes were differentially expressed between cyclin D1-positive MCL and the other lymphoma types with high statistical significance (p ⁇ 0.001).
  • MCL vs. SLL MCL vs. GCB
  • MCL vs. ABC MCL vs. ABC
  • X j is the expression of gene j in sample X and t j is the t-statistic for the difference in expression of gene j between the two lymphoma types in the pair.
  • Cyclin D1 was excluded from the calculation of LPS so that the model could be used to identify potential MCL cases that were cyclin D1 negative.
  • ⁇ (x; ⁇ , ⁇ ) is the normal density function with mean ⁇ and standard deviation ⁇
  • ⁇ circumflex over ( ⁇ ) ⁇ MCL and ⁇ circumflex over ( ⁇ ) ⁇ MCL are the sample mean and variance of the LPS values for MCL
  • ⁇ circumflex over ( ⁇ ) ⁇ 2 and ⁇ circumflex over ( ⁇ ) ⁇ 2 are the sample mean and variance of the LPS values for the second lymphoma type of the pair.
  • a cut-off point of 90% was selected for assigning a sample to a particular lymphoma type. Every sample in the training set was classified correctly using this model ( FIG. 16 ). When applied to the validation set, the model correctly classified 98% of the cyclin D1-positive MCL cases as MCL ( FIG. 16 ).
  • This diagnostic test was applied to nine lymphoma cases that were morphologically consistent with MCL, but negative for cyclin D1 expression. Seven of these samples were classified as MCL, one was classified as GCB, and one was not assigned to any lymphoma type because none of the pairs generated a probability of 90% or greater.
  • a statistical method to classify DLBCL samples based on Bayesian analysis was developed using gene expression data obtained using the Lymphochip cDNA microarray (Rosenwald 2002). This data is available at http://llmpp.nih.gov/DLBCL. The data was divided into two sets: a training set used to create and optimize the prediction model, and a validation set to evaluate the performance of the model.
  • the training set consisted of 42 ABC DLBCL samples and 67 GCB DLBCL samples, while the validation set consisted of 41 ABC DLBCL samples, 67 GCB DLBCL samples, and 57 type 3 DLBCL samples (Shipp 2002).
  • X j represents the expression level of gene j
  • t j is a scaling factor whose value depends on the difference in expression of gene j between the two lymphoma types.
  • the scaling factor used in this example was the t-statistic generated by at test of the difference in gene j expression between two lymphoma types. Only those genes with the largest t-statistics were included when calculating the LPS for each sample. The list of genes used to generate the LPS was narrowed further by including only those genes that were most variably expressed within the training set. Only genes in the top third with respect to variance were included. Genes that displayed a correlation with proliferation or lymph node signatures (Shaffer 2001; Rosenwald 2002) were eliminated from consideration, because these genes are often variably expressed within samples from a single lymphoma type (Rosenwald 2002).
  • the LPS is a linear combination of gene expression values
  • its distribution within each lymphoma type should be approximately normal, provided that it includes a sufficient number of genes and the correlation structure of those genes is not extreme.
  • the mean and variance of these normal distributions within a lymphoma type can then be estimated from the combined LPS's of all samples within the type.
  • the LPS distribution of two lymphoma types can be used to estimate the probability that a new sample belongs to one of the types using Bayes' rule.
  • the probability q that a sample Y belongs to lymphoma type 1 can be determined by an equation:
  • ⁇ (x; ⁇ , ⁇ ) is the normal density function with mean ⁇ and standard deviation ⁇
  • ⁇ circumflex over ( ⁇ ) ⁇ 1 and ⁇ circumflex over ( ⁇ ) ⁇ 1 are the sample mean and variance of the LPS values for lymphoma type 1
  • ⁇ circumflex over ( ⁇ ) ⁇ 2 and ⁇ circumflex over ( ⁇ ) ⁇ 2 are the sample mean and variance of the LPS values for lymphoma type 2.
  • the number of genes in the predictor model was optimized based on the accuracy with which the predictor classified samples into the ABC or GCB subtypes defined previously by hierarchical clustering (Rosenwald 2002).
  • the final predictor incorporated 27 genes, and correctly classified 87% of the training set samples into the subtype to which they had been assigned by hierarchical clustering ( FIG. 17 ).
  • the genes included in the predictor are listed in Table 2391.
  • ER endoplasmic reticulum
  • Golgi apparatus Eight of the 32 genes encode proteins that reside and function in the endoplasmic reticulum (ER) or Golgi apparatus, suggesting that ABCs have increased the intracellular machinery for protein secretion. These eight genes are denoted in the above list by the designation “ER” or “golgi” in parentheses.
  • Another gene on this list, XBP-1 transcription factor encodes a protein that is required for plasma cell differentiation (Reimold 2001) and is involved in the response to unfolded proteins in the ER (Calfon 2002). ABCs have not undergone full plasmacytic differentiation, however, because other key plasma cell genes such as Blimp-1 were not more highly expressed in ABC.
  • Example 14 The prediction method described in Example 14 above was applied to gene expression data from 58 DLBCL samples obtained using an Affymetrix HU6800 oligonucleotide microarray (Shipp 2002). This data is available at www.genome.wi.mit.edu/MPR/lymphoma. The first step in analyzing this data was to exclude all microarray features with a median signal value of ⁇ 200 across the samples. Multiple microarray features representing the same gene were then averaged. Of the 27 genes in the DLBCL subtype predictor developed using the Lymphochip data (above), only 14 were represented on the Affymetrix array and passed this filtering process. These 14 genes are listed in Table 2394.
  • lymphoma biopsy samples identified as DLBCL by a panel of hematopathologists were divided into a 36 sample training set and a 274 sample validation set, with the validation set consisting of the DLBCL samples classified previously in Example 14. All patients from whom the samples were derived had been treated with anthracycline-containing multiagent chemotherapy protocols, with some patients additionally receiving radiation therapy.
  • the training set was profiled for gene expression using Lymphochip microarrays comprising 15,133 cDNA elements as described previously (Alizadeh 2000). This data is available at the web site companion for Rosenwald et al., J. Exp.
  • a hierarchical clustering algorithm (Eisen 1998) was used to organize the genes by their expression patterns across the 36 samples in the training set.
  • This cluster of genes included two genes, MAL and FIG. 1 , previously shown to be highly expressed in PMBL (Copie-Bergman 2002; Copie-Bergman 2003).
  • Several of the lymphomas with mediastinal involvement did not express this set of putative PMBL signature genes, and it was suspected that these samples were more likely to be conventional DLBCL than PMBL.
  • Hierarchical clustering was used to organize the samples according to their expression of the PMBL signature genes, resulting in two major clusters of cases ( FIG. 20B ).
  • One cluster contained 21 samples designated “PMBL core” samples by virtue of their higher expression of PMBL signature genes.
  • the other cluster contained some samples that had virtually no expression of these genes, and other samples that did express these genes but at lower levels than the PMBL core samples.
  • a gene expression-based method for distinguishing PMBL core cases from GCB and ABC DLBCL cases based on Bayesian analysis was developed using the methods described in Examples 14 and 15.
  • a set of genes were selected that were differentially expressed between the PMBL core samples and both GCB and ABC (p ⁇ 0.001).
  • This set of genes included all of the PMBL signature genes identified by hierarchical clustering ( FIG. 20A ), as well as a large number of additional genes. Many of the genes in this set belonged to the lymph node gene expression signature (Alizadeh 2000; Rosenwald 2002). These genes were excluded from the final predictor because they might cause some DLBCL samples with higher expression of lymph node gene expression signature genes to be misclassified as PMBL.
  • the list of PMBL distinction genes was refined by adding a requirement that they also be differentially expressed between the PMBL core samples and a subgroup of six DLBCL samples with higher expression of lymph node gene expression signature genes (p ⁇ 0.001).
  • the resulting set of 46 genes included 35 genes that were more highly expressed in PMBL and 11 genes that were more highly expressed in DLBCL ( FIG. 21A ).
  • the 46 genes in this set were PDL2, SNFT, ILI 3RA1, FGFR1, FLJ10420, CCL17/TARC, TNFRSF8/CD30, E2F2, MAL, TNFSF4/OX40 ligand, IL411/ FIG.
  • a series of linear predictor scores were generated based on the expression of this gene set. Based on the distribution of linear predictor scores within a particular lymphoma type, Bayes' rule can be used to estimate the probability that a particular sample belongs to either of the two types. An arbitrary probability cut-off of 90% or greater was used to classify a sample as a particular lymphoma type. All of the PMBL core samples were classified as PMBL using this method, as were six of the other lymphoma samples with mediastinal involvement. However, nine of the lymphoma samples with mediastinal involvement were classified as a DLBCL, as were all of the GCB and ABC samples.
  • Table 2395 compares the clinical parameters of patients assigned to the PMBL, ABC, and GCB subgroups of DLBCL using this prediction method.
  • the PMBL subgroup defined by the PMBL predictor had a relatively favorable overall survival rate after therapy ( FIG. 22 ).
  • a cluster of “proliferation signature” genes and a cluster of “lymph node signature” genes were identified. The expression of these genes was averaged to form a proliferation signature and a lymph node signature.
  • Each gene represented on the Lymph Dx microarray was placed into one of three “gene-list categories” based on its correlation with the proliferation or lymph node gene signatures. “Proliferation” genes were defined as those genes for which the correlation between their expression and the proliferation signature was greater than 0.35. Lymph node genes were defined as those genes for which the correlation between their expression and the lymph node signature was greater than 0.35. The remaining genes on the array were classified as standard genes. This classification resulted in 323 proliferation genes and 375 lymph node genes.
  • the samples were divided into five types: FL, MCL, SLL, FH, and a class of aggressive lymphomas that included DLBCL and BL.
  • Samples obtained from subjects with other diagnoses e.g., MALT, LPC
  • Data from the Lymph Dx microarray was then used to compare gene expression in each possible lymphoma type pair (e.g., FH vs. FL, MCL vs. SLL, etc.). This resulted in the creation of ten “pair-wise models” (one for each possible lymphoma type pair) for predicting whether a sample fell into a particular lymphoma type.
  • LPS linear predictor score
  • LPS LPS
  • X j is the expression of gene j in the sample
  • t j is the t-statistic representing the difference in expression of gene j between the two lymphoma types.
  • This formulation of LPS known as the compound covariate predictor, has previously been used successfully (Radmacher 2002; Rosenwald 2003a; Wright 2003).
  • Other ways to formulate an LPS include Fisher linear discriminant analysis (Dudoit 2002), weighted voting (Golub 1999), linear support vector machines (Ramaswamy 2001), and nearest shrunken centroids (Tibshirani 2002).
  • the optimal number of genes is that number which generates a maximum t-statistic when comparing the LPS of two samples from different lymphoma types ( FIG. 23 ). This optimization procedure was repeated for every gene-list category in every pair-wise model, meaning that 30 optimizations were performed in all.
  • LPS's were calculated for each sample using four different combinations. In the first, LPS was calculated using the standard genes only. In the second, LPS's were calculated for both the standard and proliferation genes, but not the lymph node genes. In the third, LPS's were calculated for both the standard and lymph node genes, but not the proliferation genes. In the fourth, LPS's were calculated using all three gene-list categories.
  • each sample could be thought of as a vector in a space of between one and three dimensions. Since the LPS's were sums of individual expressions, it was reasonable to approximate the distributions as normal. Multivariate normal distributions are defined by two quantities: a mean vector, which indicates the average value of each of the models within a given lymphoma type, and a covariance matrix, which indicates the magnitude and orientation spread of points away from this center. Both of these quantities can be estimated empirically from the observed data.
  • FIG. 24 shows the Standard and Proliferation LPS's for the FL vs. DLBCL/BL pair-wise model. The dotted lines indicate the standard deviations from the fitted multivariate normal distributions.
  • Bayes' rule (Bayes 1763) can be used to estimate the probability that a given sample belongs to one lymphoma type or another. Bayesian analysis of an LPS has been successfully employed in the past to distinguish DLBCL subtypes (Rosenwald 2003a, Wright 2003). For a sample X, the probability q of the sample belonging to a first lymphoma type rather than a second lymphoma type can be calculated using the formula:
  • LPS(X) is the linear predictor score for sample X
  • ⁇ (x; ⁇ , ⁇ ) is the normal density function with mean ⁇ and standard deviation ⁇
  • ⁇ circumflex over ( ⁇ ) ⁇ 1 and ⁇ circumflex over ( ⁇ ) ⁇ 1 are the mean and variance of the LPS's for the first lymphoma type
  • ⁇ circumflex over ( ⁇ ) ⁇ 2 and ⁇ circumflex over ( ⁇ ) ⁇ 2 are the mean and variance of the LPS's for the second lymphoma type.
  • This q value can then be used to classify a sample as a first lymphoma type, a second lymphoma type, or unclassified. Samples with the highest q values are classified as the first lymphoma type, while samples with the lowest q values are classified as the second lymphoma type. Samples with middle range q values are deemed unclassified. Classifying the samples in this manner requires two cut-off points: a lower cut-off point between the second lymphoma type and unclassified, and an upper cut-off point between unclassified and the first lymphoma type. To develop these cut-off points, samples were ordered by their q values, and each possible cut-off point between adjacent samples was considered. To ensure that the cut-off points were reasonable, the lower cut-off point was restricted to between 0.01 and 0.5 and the upper cut-off point was restricted to between 0.5 and 0.99.
  • the cut-off point would be adjusted to allow an additional error only if this adjustment resulted in four or more unclassified samples becoming correctly classified.
  • the final model and cut-off point for a given pair-wise analysis was that which minimized this equation.
  • the equation utilizes percentages rather than the actual number of cases in order to account for the different number of samples in each class.
  • cut-off point optimality is defined in terms of dividing the data into subtypes, all cut-off points between a pair of borderline cases will be equally optimal.
  • values were chosen that would lead to a larger unclassified region.
  • a value would be chosen that was 1 ⁇ 5 of the way from the smallest borderline case to the largest.
  • a value would be chosen that was 4 ⁇ 5 of the way from the smallest borderline case to the largest.
  • FIG. 25 illustrates the q-results of optimizing the cut-point for the FL versus DLBCL/BL samples.
  • FIG. 26 indicates how this choice of cut-off points divided the space of LPS's.
  • each pair-wise model will produce one of three possible results: 1) the sample belongs to the first lymphoma type of the pair-wise model, 2) the sample belongs to the second lymphoma type of the pair-wise model, or 3) the sample is unclassified. If each of the n ⁇ 1 models agrees that the sample belongs to a particular lymphoma type, then the sample is designated as belonging to that type. If the n ⁇ 1 models do not all agree that the sample belongs to a particular lymphoma type, the sample is designated as unclassified.
  • Tables 2396 and 2397 The results of the leave-one-out predictions are set forth in Tables 2396 and 2397, below.
  • the rows in each table correspond to different sample groups, while the columns indicate the prediction results.
  • the standard to which the prediction results were compared in this stage was the diagnoses of a panel of eight expert hematopathologists who used histological morphology and immunohistochemistry to classify the samples.
  • Table 2396 provides classification results for the five lymphoma types tested (DLBCL/BL, FL, FH, MCL, SLL), while Table 2397 provides more specific results for classification of subtypes within these five lymphoma types.
  • the results set forth in Table 2396 are also summarized in FIG. 27 .
  • Example 17 Samples identified as DLBCL/BL in Example 17 were subdivided into four types: ABC, GCB, PMBL, and BL. These samples were then used to generate six pair-wise models using the same procedure described in Example 17. The results of the leave-one-out predictions using these pair-wise models are set forth in Table 2398, below. These results are also summarized in FIG. 28 . The rows in the table correspond to different sample groups, while the columns indicate the prediction results. In this stage, the ability of the prediction method to identify BL was again measured against the diagnoses of hematopathologists.
  • the above classification was implemented using S+ software and the S+ subtype predictor script contained in the file entitled “Subtype_Predictor.txt,” located in the computer program listing appendix contained on CD number 22 of 22.
  • This S+ script implements the lymphoma prediction algorithm.
  • this script is pasted into an S+ script window and run in a working directory containing the data set files discussed below, it will produce a text file entitled “PredictionResults.txt,” which indicates the results of the predictive algorithm.
  • the other files in the computer program listing appendix contain the required data sets, in their required format, for carrying out the lymphoma type identification described above.
  • the file entitled “GeneData.txt” contains the gene expression values for each sample analyzed.
  • the file entitled “GeneID.txt” contains information about the genes in the GeneData.txt file, and is also included in the working directory when the S+ subtype predictor script is run. This file indicates the UNIQID for each gene, as well as the extent to which the gene is associated with the lymph node and proliferation signatures (“LN.cor” and “pro.cor,” respectively). The contents of “GeneID.txt” are also set forth in Table 2415 below.
  • the file entitled “SampleID.txt” contains information about the samples included in the “GeneData.txt” file, specifically the original classification of all the samples. This file is also included in the working directory when the S+ subtype predictor script is run.
  • the file entitled “PredictionResults.txt” is an example of the productive output of the prediction algorithm.
  • Tables 2399-2414 indicate for each of the pair wise models the list of genes used, the weight given to each of those genes, the signature with which each gene was associated, the mean values and covariance matrices associated with the subtypes being compared, and the q-value cut-points of the pair-wise model.
  • ABC activated B-cell-like diffuse large B cell lymphoma
  • BL Burkitt lymphoma
  • CHOP cyclophosphamide, doxorubicine, vincristine, and prednisone
  • CI confidence interval
  • CNS central nervous system
  • DLBCL diffuse large B-cell lymphoma
  • ECOG Eastern Cooperative Oncology Group
  • EST expressed sequence tag
  • FACS fluorescence-activated cell sorting
  • FH follicular hyperplasia
  • FL follicular lymphoma
  • GCB germinal center B-cell-like diffuse large B cell lymphoma
  • GI gastrointestinal
  • IPI International Prognostic Index
  • LPC lymphoplasmacytic lymphoma
  • LPS linear predictor score
  • MALT mucosa-associated lymphoid tissue lymphomas
  • MCL mantle cell lymphoma
  • MHC major histocompatibility complex
  • NA not available or not applicable
  • 91 1097329 1097329 TEAD1 :: TEA domain family member 1 153408 0.609915504509915 ⁇ 0.330588741531368 (SV40 transcriptional enhancer factor) 92 1097334 1097334: FLJ10074 :: hypothetical protein FLJ10074 71573 0.148822099251370 ⁇ 0.036195940379043 93 1097359 1097359: :: Homo sapiens transcribed sequence with weak similarity to 518723 0.053800334461785 ⁇ 0.154524230021900 protein ref: NP_060312.1 ( H.
  • PSMB7 proteasome (prosome, macropain) subunit, 197071 0.311409341908515 ⁇ 0.205155556831752 beta type, 7 104 1097561 1097561: C20orf112 :: chromosome 20 open reading frame 112 19221 0.527162504741833 ⁇ 0.440301485246365 105 1097563 1097563: FLJ14743 :: hypothetical protein FLJ14743 169577 ⁇ 0.168921612398568 ⁇ 0.030167777542399 106 1097564 1097564: SKIL :: SKI-like 272108 ⁇ 0.048959117197389 0.045546934477234 107 1097600 1097600: SAT2 :: spermidine/spermine N1-acetyltransferase 2 10846 0.
  • 1098447 1098447 JDP2 :: jun dimerization protein 2 154095 ⁇ 0.141461142027089 0.099602291803127 170 1098459 1098459: SPUVE :: protease, serine, 23 25338 0.737264124009213 ⁇ 0.334058738986943 171 1098461 1098461: DNER :: delta-notch-like EGF repeat-containing 234074 0.041020174413569 ⁇ 0.067455662571597 transmembrane 172 1098476 1098476: pknbeta :: protein kinase PKNbeta 300485 ⁇ 0.194588649952929 0.049490469697965 173 1098495 1098495: TBRG1 :: likely ortholog of mouse transforming growth 443668 0.052385916360886 ⁇ 0.306318481977251 factor beta regulated gene 1 174 109 109
  • HTPAP HTPAP protein 437179 0.172952993194321 ⁇ 0.447010228881662 179 1098574 1098574: KIAA0233 :: KIAA0233 gene product 79077 ⁇ 0.341045883809633 0.355913888061517 180 1098592 1098592: FLJ38771 :: hypothetical protein FLJ38771 283707 ⁇ 0.370411569171726 0.240153206136564 181 1098604 1098604: SLC39A10 :: solute carrier family 39 (zinc transporter), 32793 ⁇ 0.356817082601293 0.039590884115228 member 10 182 1098607 1098607: MGC15887 :: hypothetical gene supported by BC009447 38516 ⁇ 0.202635383865497 0.273499931529896
  • 1100609 1100609: PPIL2 :: peptidylprolyl isomerase (cyclophilin)-like 2 447045 ⁇ 0.010033297668578 ⁇ 0.251624647902145 323 1100625: RORC :: RAR-related orphan receptor C 232803 ⁇ 0.017550954843166 ⁇ 0.115801492903445 324 1100721 1100721: :: Homo sapiens cDNA FLJ32207 fis, clone PLACE6003204.
  • 1100873 1100873 :: Homo sapiens transcribed sequences 445884 ⁇ 0.204883351763766 0.157721916475158 333
  • 1100879 1100879: MASP2 mannan-binding lectin serine protease 2 119983 ⁇ 0.112831783867775 ⁇ 0.290649076935063 334
  • 1100904 LOC119504 :: hypothetical protein LOC119504 ⁇ 25 ⁇ 0.099036342262842 ⁇ 0.256431195474163 335 1100911 1100911: C4orf7 :: chromosome 4 open reading frame 7 320147 0.060001350276090 ⁇ 0.084108354010684 336 1100916 1100916: PRKWNK4 :: protein kinase, lysine deficient 4 105448 0.108814731820795 ⁇ 0.01150
  • 434 1104373 1104373 :: Homo sapiens cDNA FLJ11709 fis, 295633 ⁇ 0.005756063382418 ⁇ 0.123990346935139 clone HEMBA1005133.
  • 436 1104552 1104552 LOC96597 :: hypothetical protein LOC96597 193857 ⁇ 0.294998056306420 0.136359195898485 437
  • 1104840 1104840 :: Homo sapiens cDNA FLJ20112 fis, clone COL05405 482250 ⁇ 0.057537557429858 ⁇ 0.243362980194851 438 1104870 1104870: KIAA1486 :: KIAA1486 protein 210958 ⁇ 0.07748824504
  • Beta-Galactosidase (Chains I-P) 721 1117977 1117977: ::: Unknown ⁇ 40 ⁇ 0.092034285015709 ⁇ 0.087991577681170 722 1118148 1118148: ZBP1 :: Z-DNA binding protein 1 ⁇ 2 0.152802746225995 ⁇ 0.384059831029427 723 1118228 1118228: :: Homo sapiens hypothetical 173679 ⁇ 0.201134297495305 ⁇ 0.035774496444703 LOC339541 (LOC339541), mRNA 724 1118286 1118286: :: Homo sapiens transcribed sequences 147381 ⁇ 0.379333390537201 0.451787557640792 725 1118347 1118347: ITGA4 :: integrin, alpha 4 (antigen CD49D, 145140 0.055639362171438 ⁇ 0.253900279097663
  • AMSH associated molecule with the SH3 domain of STAM 12479 ⁇ 0.212970492666360 0.177745673538672 876 1119939 1119939: AHR :: aryl hydrocarbon receptor 170087 0.256970446704131 ⁇ 0.173340326402877 877 1119946 1119946: AGT :: angiotensinogen (serine (or cysteine) 19383 ⁇ 0.083357114527211 0.115295274530192 proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 8) 878 1119950 1119950: TAF15 :: TAF15 RNA polymerase II, TATA box 402752 ⁇ 0.306440406993752 0.338606484125856 binding protein (TBP)-associated factor, 68 kDa 879 1119972 1119972: EPHB4 :: EphB4 4370
  • pombe 249441 ⁇ 0.173056305348263 0.447075281308176 1420 1124577 1124577: HPCAL1 :: hippocalcin-like 1 3618 0.135165512513168 ⁇ 0.299780255879962 1421 1124583 1124583: GDAP1L1 :: ganglioside-induced differentiation-associated 20977 0.367602161929472 ⁇ 0.305814749065091 protein 1-like 1 1422 1124594 1124594: STK38L :: serine/threonine kinase 38 like 184523 0.019320900966301 0.207490282567835 1423 1124606 1124606: PTPRC :: protein tyrosine phosphatase, receptor type, C 444324 0.045317285693567 ⁇ 0.221810375999856 1424 1124610 1124610: IGJ :: immunoglobulin J polypeptide,
  • 1132462 1132462: FOXO3A :: forkhead box O3A 14845 0.368591254754925 ⁇ 0.433764383288663 1903 1132468 1132468: TFDP1 :: transcription factor Dp-1 79353 ⁇ 0.281111016450068 0.587665041868591 1904 1132479 1132479: CKS2 :: CDC28 protein kinase regulatory subunit 2 83758 ⁇ 0.336131034183213 0.776594329768994 1905 1132485 1132485: ADRBK2 :: adrenergic, beta, receptor kinase 2 445563 0.026350082372157 0.212105726957152 1906 1132498 1132498: PRKR :: protein kinase, interferon-inducible double 4395
  • pombe 146329 ⁇ 0.397443511905394 0.548880091150802 2169 1135487 1135487: SCN3A :: sodium channel, voltage-gated, type III, alpha 300717 0.035229423784445 ⁇ 0.077879014673317 2170 1135489 1135489: SSA2 :: Sjogren syndrome antigen A2 (60 kDa, 288178 ⁇ 0.213090090407771 0.262043380399309 ribonucleoprotein autoantigen SS-A/Ro) 2171 1135492 1135492: P2RX5 :: purinergic receptor P2X, ligand-gated ion channel, 5 408615 ⁇ 0.492212038510146 0.364853473313676 2172 1135513 1135513: CD209L :: CD209 antigen-like 421437 ⁇ 0.269435883536644 0.024441295489601
  • pombe 2410 1139017 1139017: NANS :: N-acetylneuraminic acid synthase (sialic acid 274424 0.139351446215690 0.183979506976574 synthase) 2411 1139026 1139026: MKNK2 :: MAP kinase-interacting serine/threonine kinase 2 512094 ⁇ 0.060610570736422 0.129185990473453 2412 1139037 1139037: CKIP-1 :: CK2 interacting protein 1; HQ0024c protein 173380 0.184289444061499 ⁇ 0.394499906002833 2413 1139039 1139039: TNKS2 :: tankyrase, TRF1-interacting ankyrin-related ADP- 280776 ⁇ 0.153598065351604 0.099989367851187 ribose polymerase 2 2414 1139048 1139048: CN
  • 2604 1529313 1529313 :: Homo sapiens transcribed sequences 271998 0.004383347722577 0.265566854529143
  • 2605 1529314 1529314 :: Homo sapiens transcribed sequences 276342 ⁇ 0.006227323367580 0.045472523730890
  • 2606 1529315 1529315 :: Homo sapiens transcribed sequence with weak similarity to 445718 ⁇ 0.084112604384647 0.019415177758716 protein ref: NP_062553.1 ( H.
  • musculus L1 repeat, Tf subfamily, member 30 [ Mus musculus ] 2614 1529323 1529323: :: Homo sapiens transcribed sequences 345834 0.336779571590933 ⁇ 0.359684409503434 2615 1529324 1529324: GZMH :: granzyme H (cathepsin G-like 2, protein h-CCPX) 348264 0.239243227392061 ⁇ 0.419048485474577 2616 1529325 1529325: :: BQ003404 ⁇ 75 ⁇ 0.140464406043795 ⁇ 0.021462938104706 2617 1529326 1529326: HDAC7A :: histone deacetylase 7A 200063 ⁇ 0.109850414890401 0.080269797544815 2618 1529327 1529327: SMN2 :: survival of motor neuron 2, centromeric 288986 ⁇ 0.0423842
  • cytokine receptor- like factor 2 cytokine receptor CRL2 precusor [ Homo sapiens ] 2626 1529335 1529335: :: Homo sapiens mRNA; cDNA DKFZp586L141 (from clone 400872 ⁇ 0.379618839813305 0.435859102100720 DKFZp586L141) 2627 1529336 1529336: PTK2B :: PTK2B protein tyrosine kinase 2 beta 405474 0.064169101462340 ⁇ 0.102556747779252 2628 1529337 1529337: C6orf166 :: chromosome 6 open reading frame 166 201864 ⁇ 0.018977987327815 0.016953866594291 2629 1529338 1529338: PAK2 :: p21 (CDKN1A)-activated kinase 2 284275 ⁇ 0.39691129

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Abstract

The present invention discloses methods for identifying, diagnosing, and predicting survival in a lymphoma or lymphoproliferative disorder on the basis of gene expression patterns. The invention discloses a novel microarray, the Lymph Dx microarray, for obtaining gene expression data from a lymphoma sample. The invention also discloses a variety of methods for utilizing lymphoma gene expression data to determine the identity of a particular lymphoma and to predict survival in a subject diagnosed with a particular lymphoma. This information is useful in developing the appropriate therapeutic approach for use with a particular subject.

Description

    CROSS-REFERENCE TO RELATED APPLICATIONS
  • This patent application is a continuation-in-part of copending U.S. patent application Ser. No. 12/592,778, filed Dec. 2, 2009, which is a divisional of U.S. patent application Ser. No. 10/934,930, filed Sep. 3, 2004, issued as U.S. Pat. No. 7,711,492, which claims the benefit of U.S. Provisional Patent Application No. 60/500,377, filed Sep. 3, 2003, which are incorporated by reference in their entirety herein.
    • REFERENCE TO TABLES AND COMPUTER PROGRAM LISTING APPENDIX PREVIOUSLY SUBMITTED ON COMPACT DISC
  • Tables 2-1723 and 1725-2358 are contained on 21 CD-ROMs submitted with U.S. patent application Ser. No. 10/934,930, now issued as U.S. Pat. No. 7,711,492, and U.S. patent application Ser. No. 12/592,778, filed Dec. 2, 2009. These CD-ROMs are numbered 1-21 of 22. The name, size, and date of creation for each file is presented in the file entitled “Tableofcontents.txt,” located on CD number 21 of 22. The name of each file incorporates the number of the corresponding table. Any reference to a table or file should be considered an incorporation by reference of the contents of the table and/or file at that particular place in the specification.
  • A computer program listing appendix is contained on one CD-ROM numbered 22 of 22 submitted with U.S. patent application Ser. No. 10/934,930, now issued U.S. as U.S. Pat. No. 7,711,492, and U.S. patent application Ser. No. 12/592,778, filed Dec. 2, 2009. The computer program listing appendix contains files related to the implementation of an algorithm for determining lymphoma type. The name, size, and date of creation for each file in the computer program listing appendix is presented in the file entitled “Table_of_contents.txt,” located on CD-ROM 22. Any reference to a file contained in the computer program listing appendix should be considered an incorporation by reference of the contents of that file at that particular place in the specification.
    • BACKGROUND OF INVENTION
  • A variety of systems for identifying and classifying lymphomas have been proposed over the last 20 years. In the 1980's, the Working Formulation was introduced as a method of classifying lymphomas based on morphological and clinical characteristics. In the 1990's, the Revised European-American Lymphoma (REAL) system was introduced in an attempt to take into account immunophenotypic and genetic characteristics in classifying lymphomas (Harris 1994). The most recent standard, set forth by the World Health Organization (WHO), attempts to build on these previous systems (Jaffe 2001). The WHO classification of lymphomas is based on several factors, including tumor morphology, immunophenotype, recurrent genetic abnormalities, and clinical features. Table 1, below, contains a list of the B and T cell neoplasms that have been recognized by the WHO classification. Each malignancy is listed according to its WHO classification nomenclature, followed by a WHO classification number.
  • TABLE 1
    Category Name WHO ID #
    B-cell neoplasms
    Precursor B-cell Precursor B-cell lymphoblastic 9835/3
    neoplasms leukemia
    Precursor B-cell lymphoblastic 9728/3
    lymphoma
    Mature B-cell Chronic lymphocytic leukemia 9823/3
    neoplasms
    Small lymphocytic lymphoma 9670/3
    B-cell prolymphocytic leukemia 9833/3
    Lymphoplasmacytic lymphoma 9671/3
    Splenic marginal zone 9689/3
    lymphoma
    Hairy cell leukemia 9940/3
    Plasma cell myeloma 9732/3
    Solitary plasmacytoma of bone 9731/3
    Extraosseous plasmacytoma 9734/3
    Extranodal marginal zone B-cell 9699/3
    lymphoma of mucosa-
    associated lymphoid tissue
    (MALT lymphoma)
    Nodal marginal zone B-cell 9699/3
    lymphoma
    Follicular lymphoma (Grade 1, 9690/3
    2, 3a, 3b)
    Mantle cell lymphoma 9673/3
    Diffuse large B-cell lymphoma 9680/3
    Mediastinal (thymic) large B-cell 9679/3
    lymphoma
    Intravascular large B-cell 9680/3
    lymphoma
    Primary effusion lymphoma 9678/3
    Burkitt lymphoma 9687/3
    Burkitt leukemia 9826/3
    B-cell proliferations Lymphomatoid granulomatosis 9766/1
    of uncertain
    malignant potential
    Post-transplant 9970/1
    lymphoproliferative disorder,
    polymorphic
    T-cell and NK-cell neoplasms
    Precursor T-cell and Precursor T lymphoblastic 9837/3
    NK-cell neoplasms leukemia
    Precursor T lymphoblastic 9729/3
    lymphoma
    Elastic NK-cell lymphoma 9727/3
    Mature T-cell and T-cell prolymphocytic leukemia 9834/3
    NK-cell neoplasms
    T-cell large granular 9831/3
    lymphocytic leukemia
    Aggressive NK-cell leukemia 9948/3
    Adult T-cell leukemia/lymphoma 9827/3
    Extranodal NK-/T-cell 9719/3
    lymphoma, nasal type
    Enteropathy-type T-cell 9717/3
    lymphoma
    Hepatosplenic T-cell lymphoma 9716/3
    Subcutaneous panniculitis-like 9708/3
    T-cell lymphoma
    Mycosis fungoides 9700/3
    Sezary syndrome (9701/3) 9701/3
    Primary cutaneous anaplastic 9718/3
    large cell lymphoma (C-ALCL)
    Peripheral T-cell lymphoma, 9702/3
    unspecified
    Angioimmunoblastic T-cell 9705/3
    lymphoma
    Anaplastic large cell lymphoma 9714/3
    T-cell proliferation Lymphomatoid papulosis 9718/3
    of uncertain
    malignant potential
    Hodgkin lymphoma Nodular lymphocyte 9659/3
    predominant Hodgkin
    lymphoma
    Classical Hodgkin lymphoma 9650/3
    Classical Hodgkin lymphoma, 9663/3
    nodular sclerosis
    Classical Hodgkin lymphoma, 9651/3
    lymphocyte-rich
    Classical Hodgkin lymphoma, 9652/3
    mixed cellularity
    Classical Hodgkin lymphoma, 9653/3
    lymphocyte depleted

    Other diagnoses that have not been given WHO diagnostic numbers include HIV-associated lymphoma, germinal center B cell-like subtype of diffuse large B cell lymphoma, activated B cell-like subtype of diffuse large B-cell lymphoma, follicular hyperplasia (non-malignant), and infectious mononucleosis (non-malignant).
  • Although the WHO classification has proven useful in patient management and treatment, patients assigned to the same WHO diagnostic category often have noticeably different clinical outcomes. In many cases, these different outcomes appear to be due to molecular differences between tumors that cannot be readily observed by analyzing tumor morphology. More precise methods are needed for identifying and classifying lymphomas based on their molecular characteristics.
    • SUMMARY OF THE INVENTION
  • Accurate identification of lymphoma type or subtype in a subject suffering from a lymphoproliferative disorder is important for developing an appropriate therapeutic strategy. Previous attempts have been made to identify lymphomas using gene expression data obtained using a microarray. However, there is a need in the art for more accurate and predictive methods of analyzing this gene expression data. In addition, there is a need for more specific and efficient methods of obtaining gene expression data.
  • The present invention discloses a novel microarray for obtaining gene expression data to be used in identifying lymphoma types and predicting survival in a subject. The present invention further discloses a variety of methods for analyzing gene expression data obtained from a lymphoma sample, and specific algorithms for predicting survival and clinical outcome in a subject suffering from a lymphoma.
  • One embodiment of the present invention provides a composition comprising the set of probes listed in Table 2, which is set forth below and contained in the file entitled “Tableb.-0002_LymphDx_Probe_List.txt.” Preferably, this composition comprises a microarray.
  • In another embodiment, the present invention provides a method of generating a survival predictor for a particular lymphoma type. In this method, one or more biopsy samples that have been diagnosed as belonging to a particular lymphoma type are obtained. Gene expression data is obtained for these samples, and genes with expression patterns associated with longer or shorter survival are identified. Hierarchical clustering is performed to group these genes into gene expression signatures, and the expression of all genes within each signature are averaged to obtain a gene expression signature value for each signature. These gene expression signature values are then used to generate a multivariate survival predictor.
  • In another embodiment, the present invention provides a method for predicting survival in a follicular lymphoma (FL) subject. In this method, a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample. The expression level of those genes belonging to an immune response-1 or immune response-2 gene expression signature are averaged to generate gene expression signature values for each signature. A survival predictor score is then calculated using an equation: [2.71*(immune response-2 gene expression signature value)]−[2.36*(immune response-1 gene expression signature value)]. A higher survival predictor score is associated with a less favorable outcome. In one embodiment, the gene expression data used in this method is obtained using a microarray.
  • In another embodiment, the present invention provides another method for predicting survival in a follicular lymphoma (FL) subject. In this method, a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample. The expression level of those genes belonging to a B cell differentiation, T-cell, or macrophage gene expression signature are averaged to generate gene expression signature values for each signature. A survival predictor score is then calculated using an equation: [2.053*(macrophage gene expression signature value)]−[2.344*(T-cell gene expression signature value)]−[0.729*(B-cell gene expression signature value)]. A higher survival predictor score is associated with a less favorable outcome. In one embodiment, the gene expression data used in this method is obtained using a microarray.
  • In another embodiment, the present invention provides yet another method for predicting survival in a follicular lymphoma (FL) subject. In this method, a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample. The expression level of those genes belonging to a macrophage, T-cell, or B-cell differentiation gene expression signature are averaged to generate gene expression signature values for each signature. A survival predictor score is then calculated using an equation: [1.51*(macrophage gene expression signature value)]−[2.11*(T-cell gene expression signature value)]−[0.505*(B-cell differentiation gene expression signature value)]. A higher survival predictor score is associated with a less favorable outcome. In one embodiment, the gene expression data used in this method is obtained using a microarray.
  • In another embodiment, the present invention provides a method for predicting survival in a diffuse large B cell lymphoma (DLBCL) subject. In this method, a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample. The expression level of those genes belonging to an ABC DLBCL high, lymph node, or MHC class II gene expression signature are averaged to generate gene expression signature values for each signature. A survival predictor score is then calculated using an equation: [0.586*(ABC DLBCL high gene expression signature value)]−[0.468*(lymph node gene expression signature value)]−[0.336*(MHC class II gene expression signature value)]. A higher survival predictor score is associated with a less favorable outcome. In one embodiment, the gene expression data used in this method is obtained using a microarray.
  • In another embodiment, the present invention provides another method for predicting survival in a diffuse large B cell lymphoma (DLBCL) subject. In this method, a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample. The expression level of those genes belonging to a lymph node, germinal B cell, proliferation, or MHC class II gene expression signature are averaged to generate gene expression signature values for each signature. A survival predictor score is then calculated using an equation: [−0.4337*(lymph node gene expression signature)]+[0.09*(proliferation gene expression signature)]−[0.4144*(germinal center B-cell gene expression signature)]−[0.2006*(MHC class II gene expression signature)]. A higher survival predictor score is associated with a less favorable outcome. In one embodiment, the gene expression data used in this method is obtained using a microarray.
  • In another embodiment, the present invention provides yet another method for predicting survival in a diffuse large B cell lymphoma (DLBCL) subject. In this method, a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample. The expression level of those genes belonging to a lymph node, germinal B cell, or MHC class II gene expression signature are averaged to generate gene expression signature values for each signature. A survival predictor score is then calculated using an equation: [−0.32*(lymph node gene expression signature)]−[0.176*(germinal B cell gene expression signature)]−[0.206*(MHC class II gene expression signature)]. A higher survival predictor score is associated with a less favorable outcome. In one embodiment, the gene expression data used in this method is obtained using a microarray. In another embodiment, the gene expression data is obtained using RT-PCR.
  • In another embodiment, the present invention provides a method for predicting survival in a mantle cell lymphoma (MCL) subject. In this method, a biopsy sample is obtained from the subject and gene expression data is obtained from the biopsy sample. The expression level of those genes belonging to a proliferation gene expression signature are averaged to generate a gene expression signature value. A survival predictor score is then calculated using an equation: [1.66*(proliferation gene expression signature value)]. A higher survival predictor score is associated with a less favorable outcome. In one embodiment, the gene expression data used in this method is obtained using a microarray.
  • In another embodiment, the present invention provides a method for determining the probability that a sample X belongs to a first lymphoma type or a second lymphoma type. In this method, a set of genes is identified that is differentially expressed between the two lymphoma types in question, and a set of scale factors representing the difference in expression between the lymphoma types for each of these genes are calculated. A series of linear predictor scores are generated for samples belonging to either of the two lymphoma types based on expression of these genes. Gene expression data is then obtained for sample X, and a linear predictor score is calculated for this sample. The probability that sample X belongs to the first lymphoma type is calculated using an equation that incorporates the linear predictor score of sample X and the mean and variance of the linear predictor scores for the known samples of either lymphoma type.
  • In another embodiment, the present invention provides a method for determining the lymphoma type of a sample X In this method, a set of genes is identified that is differentially expressed between a first lymphoma type and a second lymphoma type, and a set of scale factors representing the difference in expression of each of these genes between the two lymphoma types are calculated. A series of linear predictor scores are generated for samples belonging to either of the two lymphoma types based on expression of these genes. Gene expression data is then obtained for sample X, and a linear predictor score is calculated for this sample. The probability that sample X belongs to the first lymphoma type is calculated using an equation that incorporates the linear predictor score of sample X and the mean and variance of the linear predictor scores for the known samples of either lymphoma type. This entire process is then repeated with various lymphoma types being substituted for the first lymphoma type, the second lymphoma type, or both.
  • In another embodiment, the present invention provides another method for determining the lymphoma type of a sample X. In this method, a series of lymphoma type pairs are created, with each pair consisting of a first lymphoma type and a second lymphoma type. For each type pair, gene expression data is obtained for a set of genes, and a series of scale factors representing the difference in expression of each of these genes between the two lymphoma types are calculated. A subset of z genes with the largest scale factors are identified, and a series of linear predictor scores are generated for samples belonging to either of the two lymphoma types. Linear predictor scores are calculated for anywhere from 1 to z of these genes. The number of genes from 1 to z that results in the largest difference in linear predictor scores between the two lymphoma types is selected, and gene expression data for these genes is obtained for sample X. A linear predictor score is generated for sample X, and the probability that the sample belongs to the first lymphoma type is calculated using an equation that incorporates the linear predictor score for sample X and the mean and variance of the linear predictor scores for the known samples of either lymphoma type.
  • In another embodiment, the present invention provides another method for determining the lymphoma type of a sample X. In this method, a series of lymphoma type pairs are created, with each pair consisting of a first lymphoma type and a second lymphoma type. For each type pair, gene expression data is obtained for a set of genes, and a series of scale factors representing the difference in expression of each of these genes between the two lymphoma types are calculated. The set of genes is divided into gene-list categories indicating correlation with a gene expression signature. Within each gene-list category, a subset of z genes with the largest scale factors are identified, and a series of linear predictor scores are generated for samples belonging to either of the two lymphoma types. Linear predictor scores are calculated for anywhere from 1 to z of these genes. The number of genes from 1 to z that results in the largest difference in linear predictor scores between the two lymphoma types is selected, and gene expression data for these genes is obtained for sample X. A linear predictor score is generated for sample X, and the probability q that the sample belongs to the first lymphoma type is calculated using an equation that incorporates the linear predictor score for sample X and the mean and variance of the linear predictor scores for the known samples of either lymphoma type. A high probability q indicates that sample X belongs to the first lymphoma type, a low probability q indicates that sample X belongs to the second lymphoma type, and a middle probability q indicates that sample X belongs to neither lymphoma type. The cut-off point between high, middle, and low probability values is determined by ranking samples of known lymphoma type according to their probability values, then analyzing every possible cut-off point between adjacent samples using the equation: 3.99*[(% of first lymphoma type misidentified as second lymphoma type)+(% of second lymphoma type misidentified as a first lymphoma type)]+[(% of first lymphoma type identified as belonging to neither lymphoma type)+(% of second lymphoma type identified as belonging to neither lymphoma type)]. The final cut-off points are those that minimize the value of this equation.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIG. 1: Method for identifying lymphoma type. Flow chart depicts a general method for identifying lymphoma type using gene expression data.
  • FIG. 2: Survival signature analysis. Flow chart depicts method for developing a lymphoma survival predictor based on gene expression patterns.
  • FIG. 3: FL survival data. Survival data for 191 subjects diagnosed with FL. Median age at diagnosis was 51 years (ranging from 23 to 81 years), and the subjects had a median follow-up of 6.6 years (8.1 years for survivors, with a range of <1 to 28.2 years).
  • FIG. 4: Hierarchical clustering of survival associated genes in FL samples. Each column represents a single FL sample, while each row represents a single gene. Relative gene expression is depicted according to the scale at the bottom of the figure. The dendrogram to the left indicates the degree to which the expression pattern of each gene is correlated with that of the other genes. The colored bars indicate sets of coordinately regulated genes defined as gene expression signatures. Genes comprising the immune response-1 and immune response-2 gene expression signature are listed on the right.
  • FIG. 5: Kaplan-Meier plot of survival in FL samples based on survival predictor scores. 191 FL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [(2.71*immune response-2 gene expression signature value)]−[(2.36×immune response-1 gene expression signature value)].
  • FIG. 6: Kaplan-Meier plot of survival in FL samples based on IPI score. 96 FL samples were divided into three groups based on their IPI scores.
  • FIG. 7: Kaplan-Meier plot of survival in FL samples with low or high risk IPI scores based on survival predictor scores. 96 FL samples with low risk (left panel) or intermediate risk (right panel) IPI scores were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [(2.71*immune response-2 gene expression signature value)]−[(2.36 x immune response-1 gene expression signature value)].
  • FIG. 8: Kaplan-Meier plot of survival in FL samples based on survival predictor scores. 191 FL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [2.053*(macrophage gene expression signature value)]−[2.344*(T-cell gene expression signature value)]−[0.729*(B-cell differentiation gene expression signature value)].
  • FIG. 9: Kaplan-Meier plot of survival in FL samples based on survival predictor scores. 191 FL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [1.51*(macrophage gene expression signature value)]−[2.11*(T-cell gene expression signature value)]−[0.505*(B-cell differentiation gene expression signature value)].
  • FIG. 10: Kaplan-Meier plot of survival in DLBCL samples based on survival predictor scores. 231 DLBCL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [0.586*(ABC DLBCL high gene expression signature value)]−[0.468*(lymph node gene expression signature value)]−[(0.336*MHC Class II gene expression signature value)].
  • FIG. 11: Kaplan-Meier plot of survival in DLBCL samples based on survival predictor scores. 200 DLBCL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [−0.4337*(lymph node gene expression signature value)]+[0.09*(proliferation gene expression signature value)]−[0.4144*(germinal center B-cell gene expression signature value)]−[0.2006*(MHC class II gene expression signature value)].
  • FIG. 12: Kaplan-Meier plot of survival in DLBCL samples based on survival predictor scores. 200 DLBCL samples were divided into quartiles based on their survival predictor scores. The survival predictor scores were calculated by: [−0.32*(lymph node gene expression signature value)]−[0.176*(germinal center B-cell gene expression signature value)]−[0.206*(MHC class II gene expression signature value)].
  • FIG. 13: Kaplan-Meier plot of survival in MCL samples based on survival predictor scores. 21 MCL samples were divided into two equivalent groups based on their survival predictor scores. The survival predictor scores were calculated by: 1.66*(proliferation gene expression signature value).
  • FIG. 14: Kaplan-Meier plot of survival in MCL samples based on survival predictor scores. 21 MCL samples were divided into two equivalent groups based on their survival predictor scores. The survival predictor scores were calculated by: 1.66*(proliferation gene expression signature value).
  • FIG. 15: Predicting lymphoma type using Bayesian analysis. Bayes' rule can be used to determine the probability that an unknown sample belongs to a first lymphoma type rather than a second lymphoma type. A linear predictor score is generated for the sample, and the probability that the sample belongs to the first lymphoma type is determined based on the distribution of linear predictor scores within the first and second lymphoma type.
  • FIG. 16: Performance of MCL predictor model. Results of the gene-expression based predictor model for MCL are shown for three models (MCL vs. ABC, MCL vs. GCB, MCL vs. SLL). Performance is shown for both the training set and the validation set.
  • FIG. 17: Gene expression-based identification of DLBCL. Expression levels for 27 genes in a subgroup predictor are shown for 274 DLBCL samples. Expression levels are depicted according to the scale shown at the left. The 14 genes used to predict the DLBCL subgroups in the Affymetrix data set are indicated with asterisks. The probabilities that the DLBCL samples belong to the ABC or GCB subtypes are graphed at the top, and the DLBCL cases are arranged accordingly. Cases belonging to either ABC or GCB with 90% or greater probability are indicated.
  • FIG. 18: Performance of DLBCL subtype predictor model. Assignments of DLBCL samples to the ABC or GCB subtypes based on hierarchical clustering vs. the predictor model disclosed herein are compared within the training, validation, and total set of samples.
  • FIG. 19: Relationship of gene expression in normal B cell subpopulations to DLBCL subtypes. Relative gene expression in the indicated purified B cell populations is depicted according to the scale in FIG. 17. The P value of the difference in expression of these genes between the GCB and ABC DLBCL subtypes is shown, and the subtype with the higher expression is indicated. A. DLBCL subtype distinction genes that are more highly expressed in germinal center B cells than at other B cell differentiation stages. B. DLBCL subtype distinction genes that are more highly expressed in plasma cells than at other B cell differentiation stages.
  • FIG. 20: Identification of a PMBL gene expression signature. A. Hierarchical clustering identified a set of 23 PMBL signature genes that were more highly expressed in most lymphomas with a clinical diagnosis of PMBL than in lymphomas assigned to the GCB or ABC subtypes. Each row presents gene expression measurements from a single Lymphochip microarray feature representing the genes indicated. Each column represents a single lymphoma biopsy sample. Relative gene expression is depicted according to the scale shown. B. Hierarchical clustering of the lymphoma biopsy samples based on expression of the PMBL signature genes identified in (A). A “core” cluster of lymphoma cases was identified that highly expressed the PMBL signature genes.
  • FIG. 21: Development of a gene expression-based molecular diagnosis of PMBL. A. A PMBL predictor was created based on expression of the 46 genes shown. Relative gene expression for each lymphoma biopsy sample is presented according to the color scale shown in FIG. 20. The probability that each sample is PMBL or DLBCL based on gene expression is shown at the top. B. The PMBL predictor was used to classify 274 lymphoma samples as PMBL or DLBCL. Prediction results are summarized on the right, and the relative gene expression for each case that was classified by the predictor as PMBL is shown on the left. Average expression of each gene in samples classified as DLBCL is also shown. The 20 genes listed are those represented on the Lymphochip that were more highly expressed in PMBL than in DLBCL. Not shown are eight genes from the PMBL predictor that were more highly expressed in DLBCL than in PMBL.
  • FIG. 22: Clinical characteristics of PMBL patients. Kaplan-Meier plot of overall survival in PMBL, GCB, and ABC patients after chemotherapy.
  • FIG. 23: Optimization of gene number in lymphoma predictor. The optimal number of genes for inclusion in the lymphoma type predictor model is that number which generates a maximum t-statistic when comparing the LPS of two samples from different lymphoma types.
  • FIG. 24: LPS distribution among FL and DLBCL/BL samples. Standard and proliferation LPSs for FL (x) and DLBCL/BL (+) samples. Dotted lines indicate standard deviations from the fitted multivariate normal distributions.
  • FIG. 25: Determination of cut-off points for lymphoma classification. The cut-off points between samples classified as DLBCL/BL, FL, or unclassified were optimized to minimize the number of samples classified as the wrong lymphoma type. The optimal lower cut-off point was at q=0.49, while the optimal upper cut-off point was at q=0.84.
  • FIG. 26: Division of LPSs among FL and DLBCL/FL samples. Illustration of how the cut-off points described in FIG. 25 divided the space between the LPSs of FL (x) and DLBCL/BL (+) samples.
  • FIG. 27: Lymphoma classification results. Results of lymphoma classification based on gene expression. 100% of SLL, MCL, and FH samples were classified correctly, and only 3% of DLBCL/BL and FL samples were classified incorrectly.
  • FIG. 28: DLBCL subtype classification based on gene expression. None of the ABC samples were classified as the wrong subtype, while only one of the BL samples was classified incorrectly. Of the GCB and PMBL samples, only 5% and 6%, respectively, were classified incorrectly.
    •  DETAILED DESCRIPTION
  • The following description is merely intended to illustrate various embodiments of the invention. As such, the specific modifications discussed are not to be construed as limitations on the scope of the invention. It will be apparent to one skilled in the art that various equivalents, changes, and modifications may be made without departing from the scope of the invention, and it is understood that such embodiments are to be included herein.
  • Gene expression profiling of a cancer cell or biopsy reflects the molecular phenotype of a cancer at the time of diagnosis. As a consequence, the detailed picture provided by the genomic expression pattern provides the basis for a new systematic classification of cancers and more accurate predictors of survival and response to treatment. The present invention discloses methods for identifying, diagnosing, and/or classifying a lymphoma, lymphoid malignancy, or lymphoproliferative disorder based on its gene expression patterns. The present invention also discloses methods for predicting survival in a subject diagnosed with a particular lymphoma type or subtype using gene expression data. The information obtained using these methods will be useful in evaluating the optimal therapeutic approach to be employed with regards to a particular subject.
  • The term “lymphoproliferative disorder” as used herein refers to any tumor of lymphocytes, and may refer to both malignant and benign tumors. The terms “lymphoma” and “lymphoid malignancy” as used herein refer specifically to malignant tumors derived from lymphocytes and lymphoblasts. Examples of lymphomas include, but are not limited to, follicular lymphoma (FL), Burkitt lymphoma (BL), mantle cell lymphoma (MCL), follicular hyperplasia (FH), small cell lymphocytic lymphoma (SLL), mucosa-associated lymphoid tissue lymphoma (MALT), splenic lymphoma, multiple myeloma, lymphoplasmacytic lymphoma, post-transplant lymphoproliferative disorder (PTLD), lymphoblastic lymphoma, nodal marginal zone lymphoma (NMZ), germinal center B cell-like diffuse large B cell lymphoma (GCB), activated B cell-like diffuse large B cell lymphoma (ABC) and primary mediastinal B cell lymphoma (PMBL).
  • The phrase “lymphoma type” (or simply “type”) as used herein refers to a diagnostic classification of a lymphoma. The phrase may refer to a broad lymphoma class (e.g., DLBCL, FL, MCL, etc.) or to a subtype or subgroup falling within a broad lymphoma class (e.g., GCB DLBCL, ABC DLBCL).
  • The phrase “gene expression data” as used herein refers to information regarding the relative or absolute level of expression of a gene or set of genes in a cell or group of cells. The level of expression of a gene may be determined based on the level of RNA, such as mRNA, encoded by the gene. Alternatively, the level of expression may be determined based on the level of a polypeptide or fragment thereof encoded by the gene. “Gene expression data” may be acquired for an individual cell, or for a group of cells such as a tumor or biopsy sample.
  • The term “microarray,” “array,” or “chip” refers to a plurality of nucleic acid probes coupled to the surface of a substrate in different known locations. The substrate is preferably solid. Microarrays have been generally described in the art in, for example, U.S. Pat. Nos. 5,143,854 (Pirrung), 5,424,186 (Fodor), 5,445,934 (Fodor), 5,677,195 (Winkler), 5,744,305 (Fodor), 5,800,992 (Fodor), 6,040,193 (Winkler), and Fodor et al. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science, 251:767-777. Each of these references is incorporated by reference herein in their entirety.
  • The term “gene expression signature” or “signature” as used herein refers to a group of coordinately expressed genes. The genes making up this signature may be expressed in a specific cell lineage, stage of differentiation, or during a particular biological response. The genes can reflect biological aspects of the tumors in which they are expressed, such as the cell of origin of the cancer, the nature of the non-malignant cells in the biopsy, and the oncogenic mechanisms responsible for the cancer (Shaffer 2001). Examples of gene expression signatures include lymph node (Shaffer 2001), proliferation (Rosenwald 2002), MHC class II, ABC DLBCL high, B-cell differentiation, T-cell, macrophage, immune response-1, immune response-2, and germinal center B cell.
  • The phrase “survival predictor score” as used herein refers to a score generated by a multivariate model used to predict survival based on gene expression. A subject with a higher survival predictor score is predicted to have poorer survival than a subject with a lower survival predictor score.
  • The term “survival” as used herein may refer to the probability or likelihood of a subject surviving for a particular period of time. Alternatively, it may refer to the likely term of survival for a subject, such as expected mean or median survival time for a subject with a particular gene expression pattern.
  • The phrase “linear predictor score” or “LPS” as used herein refers to a score that denotes the probability that a sample belongs to a particular lymphoma type. An LPS may be calculated using an equation such as:
  • LPS ( S ) = ∑ j ∈ G t j S j ,
  • where Sj is the expression of gene j from gene set G in a sample S, and tj is a scale factor representing the difference in expression of gene j between a first lymphoma type and a second lymphoma type. Alternatively, a linear predictor score may be generated by other methods including but not limited to linear discriminant analysis (Dudoit 2002), support vector machines (Furey 2000), or shrunken centroids (Tibshirani 2002)
  • The phrase “scale factor” as used herein refers to a factor that defines the relative difference in expression of a particular gene between two samples. An example of a scale factor is a t-score generated by a Student's t-test.
  • The phrase “lymphoma subject,” wherein “lymphoma” is a specific lymphoma type (e.g., “follicular lymphoma subject”), may refer to a subject that has been diagnosed with a particular lymphoma by any method known in the art or discussed herein. This phrase may also refer to a subject with a known or suspected predisposition or risk of developing a particular lymphoma type.
  • The pattern of expression of a particular gene is closely connected to the biological role and effect of its gene product. For this reason, the systematic study of variations in gene expression provides an alternative approach for linking specific genes with specific diseases and for recognizing heritable gene variations that are important for immune function. For example, allelic differences in the regulatory region of a gene may influence the expression levels of that gene. An appreciation for such quantitative traits in the immune system may help elucidate the genetics of autoimmune diseases and lymphoproliferative disorders.
  • Genes that encode components of the same multi-subunit protein complex are often coordinately regulated. Coordinate regulation is also observed among genes whose products function in a common differentiation program or in the same physiological response pathway. Recent application of gene expression profiling to the immune system has shown that lymphocyte differentiation and activation are accompanied by parallel changes in expression among hundreds of genes. Gene expression databases may be used to interpret the pathological changes in gene expression that accompany autoimmunity, immune deficiencies, cancers of immune cells and of normal immune responses.
  • Scanning and interpreting large bodies of relative gene expression data is a formidable task. This task is greatly facilitated by algorithms designed to organize the data in a way that highlights systematic features, and by visualization tools that represent the differential expression of each gene as varying intensities and hues of color (Eisen 1998). The development of microarrays, which are capable of generating massive amounts of expression data in a single experiment, has greatly increased the need for faster and more efficient methods of analyzing large-scale expression data sets. In order to effectively utilize microarray gene expression data for the identification and diagnosis of lymphoma and for the prediction of survival in lymphoma patients, new algorithms must be developed to identify important information and convert it to a more manageable format. In addition, the microarrays used to generate this data should be streamlined to incorporate probe sets that are useful for diagnosis and survival prediction. Disclosed herein are various methods and compositions that address both of these issues.
  • Mathematical analysis of gene expression data is a rapidly evolving science based on a rich mathematics of pattern recognition developed in other contexts (Kohonen 1997). Mathematical analysis of gene expression generally has three goals. First, it may be used to identify groups of genes that are coordinately regulated within a biological system. Second, it may be used to recognize and interpret similarities between biological samples on the basis of similarities in gene expression patterns. Third, it may be used to recognize and identify those features of a gene expression pattern that are related to distinct biological processes or phenotypes.
  • Mathematical analysis of gene expression data often begins by establishing the expression pattern for each gene on an array across n experimental samples. The expression pattern of each gene can be represented by a point in n-dimensional space, with each coordinate specified by an expression measurement in one of the n samples (Eisen 1998). A clustering algorithm that uses distance metrics can then be applied to locate clusters of genes in this n-dimensional space. These clusters indicate genes with similar patterns of variation in expression over a series of experiments. Clustering methods that have been applied to microarray data in the past include hierarchical clustering (Eisen 1998), self-organizing maps (SOMs) (Tamayo 1999), k-means (Tavazoie 1999), and deterministic annealing (Alon 1999). A variety of different algorithms, each emphasizing distinct orderly features of the data, may be required to glean the maximal biological insight from a set of samples (Alizadeh 1998). One such algorithm, hierarchical clustering, begins by determining the gene expression correlation coefficients for each pair of the n genes studied. Genes with similar gene expression correlation coefficients are grouped next to one another in a hierarchical fashion. Generally, genes with similar expression patterns under a particular set of conditions encode protein products that play related roles in the physiological adaptation to those conditions. Novel genes of unknown function that are clustered with a large group of functionally related genes are likely to participate in the same biological process. Likewise, the other clustering methods mentioned herein may also group genes together that encode proteins with related biological function.
  • Gene expression maps may be constructed by organizing gene expression data from multiple samples using any of the various clustering algorithms outlined herein. The ordered tables of data may then be displayed graphically in a way that allows researchers and clinicians to assimilate both the choreography of gene expression on a broad scale and the fine distinctions in expression of individual genes.
  • In such a gene expression map, genes that are clustered together reflect a particular biological function, and are termed gene expression signatures (Shaffer 2001). One general type of gene expression signature includes genes that are characteristically expressed in a particular cell type or at a particular stage of cellular differentiation or activation. Another general type of gene expression signature includes genes that are regulated in their expression by a particular biological process such as proliferation, or by the activity of a particular transcription factor or signaling pathway.
  • The pattern of gene expression in a biological sample provides a distinctive and accessible molecular picture of its functional state and identity (DeRisi 1997; Cho 1998; Chu 1998; Holstege 1998; Spellman 1998). Each cell transduces variations in its environment, internal state, and developmental state into readily measured and recognizable variations in its gene expression patterns. Two different samples that have related gene expression patterns are therefore likely to be biologically and functionally similar to one another. Some biological processes are reflected by the expression of genes in a specific gene expression signature, as described above. The expression of a specific gene expression signature in a sample can provide important biological insights into its cellular composition and the function of various intracellular pathways within those cells.
  • The present invention discloses a variety of gene expression signatures related to the clinical outcome of lymphoma patients. While several of these signatures share a name with a previously disclosed signature, each of the gene expression signatures disclosed herein comprises a novel combination of genes. For example, the lymph node signature disclosed herein includes genes encoding extracellular matrix components and genes that are characteristically expressed in macrophage, NK, and T cells (e.g., α-Actinin, collagen type III α 1, connective tissue growth factor, fibronectin, KIAA0233, urokinase plasminogen activator). The proliferation signature includes genes that are characteristically expressed by cells that are rapidly multiplying or proliferating (e.g., c-myc, E21G3, NPM3, BMP6). The MHC class II signature includes genes that interact with lymphocytes in order to allow the recognition of foreign antigens (e.g., HLA-DPα, HLA-DQα, HLA-DRα, HLA-DRβ). The immune response-1 signature includes genes encoding T cell markers (e.g., CD7, CD8B1, ITK, LEF1, STAT4), as well as genes that are highly expressed in macrophages (e.g., ACTN1, TNFSF13B). The immune response-2 signature includes genes known to be preferentially expressed in macrophages and/or dendritic cells (e.g., TLR5, FCGR1A, SEPT10, LGMN, C3AR1). The germinal center B cell signature includes genes known to be overexpressed at this stage of B cell differentiation (e.g., MME, MEF2C, BCL6, LMO2, PRSPAP2, MBD4, EBF, MYBL1).
  • Databases of gene expression signatures have proven quite useful in elucidating the complex gene expression patterns of various cancers. For example, expression of genes from the germinal center B-cell signature in a lymphoma biopsy suggests that the lymphoma is derived from this stage of B cell differentiation. In the same lymphoma biopsy, the expression of genes from the T cell signature can be used to estimate the degree of infiltration of the tumor by host T cells, while the expression of genes from the proliferation signature can be used to quantitate the tumor cell proliferation rate. In this manner, gene expression signatures provide an “executive summary” of the biological properties of a tumor specimen. Gene expression signatures can also be helpful in interpreting the results of a supervised analysis of gene expression data. Supervised analysis generates a long list of genes with expression patterns that are correlated with survival. Gene expression signatures can be useful in assigning these “predictive” genes to functional categories. In building a multivariate model of survival based on gene expression data, this functional categorization helps to limit the inclusion of multiple genes in the model that measure the same aspect of tumor biology.
  • Gene expression profiles can be used to create multivariate models for predicting survival. The methods for creating these models are called “supervised” because they use clinical data to guide the selection of genes to be used in the prognostic classification. For example, a supervised method might identify genes with expression patterns that correlate with the length of overall survival following chemotherapy. The general method used to create a multivariate model for predicting survival may utilize the following steps:
      • 1. Identify genes with expression patterns that are univariately associated with a particular clinical outcome using a Cox proportional hazards model. Generally, a univariate p-value of <0.01 is considered the cut-off for significance. These genes are termed “predictor” genes.
      • 2. Within a set of predictor genes, identify gene expression signatures.
      • 3. For each gene expression signature that is significantly associated with survival, average the expression of the component genes within this signature to generate a gene expression signature value.
      • 4. Build a multivariate Cox model of clinical outcome using the gene expression signature values.
      • 5. If possible, include additional genes in the model that do not belong to a gene expression signature but which add to the statistical power of the model.
        This approach has been utilized in the present invention to create novel survival prediction models for FL, DLBCL, and MCL. Each of these models generates a survival predictor score, with a higher score being associated with worse clinical outcome. Each of these models may be used separately to predict survival. Alternatively, these models may be used in conjunction with one or more other models, disclosed herein or in other references, to predict survival.
  • A first FL survival predictor was generated using gene expression data obtained using Affymetrix U133A and U133B microarrays. This predictor incorporated immune response-1 and immune response-2 gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:

  • Survival predictor score=[(2.71*immune response-2 gene expression signature value)]−[(2.36×immune response-1 gene expression signature value)].
  • A second FL survival predictor was generated using gene expression data obtained using Affymetrix U133A and U133B microarrays. This predictor incorporated macrophage, T-cell, and B-cell differentiation gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:

  • Survival predictor score=[2.053*(macrophage gene expression signature value)]−[2.344*(T-cell gene expression signature value)]−[0.729*(B-cell differentiation gene expression signature value)].
  • A third FL survival predictor was generated using gene expression data obtained using the Lymph Dx microarray. This predictor incorporated macrophage, T-cell, and B-cell differentiation gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:

  • Survival predictor score=[1.51*(macrophage gene expression signature value)]−[2.11*(T-cell gene expression signature value)]−[0.505*(B-cell differentiation gene expression signature value)].
  • A first DLBCL survival predictor was generated using gene expression data obtained using Affymetrix U133A and U133B microarrays. This predictor incorporated ABC DLBCL high, lymph node, and MHC class II gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:

  • Survival predictor score=[0.586*(ABC DLBCL high gene expression signature value)]−[0.468*(lymph node gene expression signature value)]−0.336*(MHC class II gene expression signature value)].
  • A second DLBCL survival predictor was generated using gene expression data obtained using the Lymph Dx microarray. This predictor incorporated lymph node, proliferation, germinal center B-cell, and MHC class II gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:

  • Survival predictor score=[−0.4337*(lymph node gene expression signature value)]+[0.09*(proliferation gene expression signature value)]−[0.4144*(germinal center B-cell gene expression signature value)]−[0.2006*(MHC class II gene expression signature value)].
  • A third DLBCL survival predictor was generated using gene expression data obtained using the Lymph Dx microarray. This predictor incorporated lymph node, germinal center B cell, and MHC class II gene expression signatures. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:

  • Survival predictor score=[−0.32*(lymph node gene expression signature value)]−[0.176*(germinal center B-cell gene expression signature value)]−[0.206*(MHC class II gene expression signature value)].
  • An MCL survival predictor was generated using gene expression data obtained using Affymetrix U133A, Affymetrix U133B, and Lymph Dx microarrays. This predictor incorporated a proliferation gene expression signature. Fitting the Cox proportional hazards model to the gene expression signature values obtained from these signatures resulted in the following model:

  • Survival predictor score=[1.66*(proliferation gene expression signature value)].
  • Gene expression data can also be used to diagnose and identify lymphoma types. In an embodiment of the present invention, a statistical method based on Bayesian analysis was developed to classify lymphoma specimens according to their gene expression profiles. This method does not merely assign a tumor to a particular lymphoma type, but also determines the probability that the tumor belongs to that lymphoma type. Many different methods have been formulated to predict cancer subgroups (Golub 1999; Ramaswamy 2001; Dudoit 2002; Radmacher 2002). These methods assign tumors to one of two subgroups based on expression of a set of differentially expressed genes. However, they do not provide a probability of membership in a subgroup. By contrast, the method disclosed herein used Bayes' rule to estimate this probability, thus allowing one to vary the probability cut-off for assignment of a tumor to a particular subgroup. In tumor types in which unknown additional subgroups may exist, the present method allows samples that do not meet the gene expression criteria of known subgroups to fall into an unclassified group with intermediate probability. A cancer subgroup predictor of the type described herein may be used clinically to provide quantitative diagnostic information for an individual cancer patient. This information can in turn be used to provide a predictor of treatment outcome for a particular cancer patient.
  • For any two lymphoma types A and B, there is a set of genes with significantly higher expression in type A than type B, and a set of genes with significantly lower expression in type A than in type B. By observing the expression of these genes in an unknown sample, it is possible to determine to which of the two types the sample belongs. Evaluating the likelihood that a particular sample belongs to one or the other lymphoma type by Bayesian analysis may be done using the following steps:
      • 1. Identify those genes that are most differentially expressed between the two lymphoma types. This can be done by selecting those genes with the largest t-statistic between the two lymphoma types. The genes in this step may be subdivided into gene expression signatures in certain cases, with genes from each signature analyzed separately.
      • 2. Create a series of linear predictor score (LPS) for samples belonging to either lymphoma type.
      • 3. Evaluate the LPS for each sample in a training set, and estimate the distribution of these scores within each lymphoma type according to a normal distribution.
      • 4. Use Bayes' rule to evaluate the probability that each subsequent sample belongs to one or the other lymphoma type.
        If only two types of lymphoma are being distinguished, then a single probability score is sufficient to discriminate between the two types. However, if more than two lymphoma types are being distinguished, multiple scores will be needed to highlight specific differences between the types.
  • A novel microarray termed the Lymph Dx microarray is disclosed herein for the identification and diagnosis of various lymphoma types. The Lymph Dx microarray contains cDNA probes corresponding to approximately 2,653 genes, fewer than the number seen on microarrays that have been used previously for lymphoma diagnosis. The reduced number of probes on the Lymph Dx microarray is the result of eliminating genes that are less useful for the identification of lymphoma types and predicting clinical outcome. This reduction allows for simplified analysis of gene expression data. The genes represented on the Lymph Dx microarray can be divided into four broad categories: 1,101 lymphoma predictor genes identified previously using the Affymetrix U133 microarray, 171 outcome predictor genes, 167 new genes not found on the Affymetrix U133 microarray, and 1,121 named genes. A list of the probe sets on the Lymph Dx microarray is presented in Table 2, contained in the file “Table—0002_LymphDx_Probe_List.txt.”
  • Gene expression data obtained using the Lymph Dx microarray may be used to identify and classify lymphomas using Bayesian analysis using a strategy similar to that set forth above. In certain embodiments, this strategy may include additional steps designed to optimize the number of genes used and the cut-off points between lymphoma types. A general overview of such a method is presented in FIG. 1. In one example of the method, each gene represented on the Lymph Dx microarray was placed into one of three gene-list categories based on its correlation with the lymph node or proliferation gene expression signatures: lymph node, proliferation, or standard. These signatures were identified by clustering of the DLBCL cases using hierarchical clustering and centroid-correlation of 0.35. Standard genes were those with expression patterns that did not correlate highly with expression of the lymph node or proliferation signatures. Lymph Dx gene expression data was first used to identify samples as FL, MCL, SLL, FH, or DLBCL/BL, then to identify DLBCL/BL samples as ABC, GCB, PMBL, or BL. For each stage, a series of pair-wise models was created, with each model containing a different pair of lymphoma types (e.g., FL vs. MCL, SLL vs. FH, etc.). For each pair, the difference in expression of each gene on the microarray was measured, and a t-statistic was generated representing this difference. Genes from each gene-list category were ordered based on their t-statistic, and those with the largest t-statistics were used to generate a series of LPSs for samples belonging to either lymphoma type. The number of genes used to generate the LPSs was optimized by repeating the calculation using between five and 100 genes from each gene-list category. The number of genes from each category used in the final LPS calculation was that which gave rise to the largest difference in LPS between the two lymphoma types. Once the number of genes in each gene-list category was optimized, four different LPSs were calculated for each sample. The first included genes from the standard gene-list category only, the second included genes from the proliferation and standard gene-list categories, the third included genes from the lymph node and standard gene-list categories, and the fourth included genes from all three categories. The probability q that a sample X belongs to the first lymphoma type of a pair-wise model can then be calculated using an equation:
  • q = φ ( LPS ( X ) ; μ ^ 1 , σ ^ 1 ) φ ( LPS ( X ) ; μ ^ 1 , σ ^ 1 ) + φ ( LPS ( X ) ; μ ^ 2 , σ ^ 2 )
  • LPS(X) is the LPS for sample X, φ(x; μ,σ) is the normal density function with mean μ and standard deviation σ, and {circumflex over (μ)}1 and {circumflex over (σ)}1 are the mean and variance of the LPSs for samples belonging to the first lymphoma type, and, {circumflex over (μ)}2 and {circumflex over (σ)}2 are the mean and variance of the LPSs for samples belonging to the second lymphoma type. Samples with high q values were classified as the first lymphoma type, samples with low q values were classified as the second lymphoma type, and samples with middle range q values were deemed unclassified. To determine the proper cut-off point between high, low, and middle q values, every possible cut-off point between adjacent samples was analyzed by an equation:

  • 3.99*[(% of type 1 misidentified as type 2)+(% of type 2 misidentified as type 1)]+[(% of type 1 unclassified)+(% of type 2 misidentified)].
  • This equation was used to favor the assignment of a sample to an “unclassified” category rather than to an incorrect lymphoma type. The final cut-off points were those which minimized this equation. The coefficient of 3.99 was chosen arbitrarily to allow an additional classification error only if the adjustment resulted in four or more unclassified samples becoming correctly classified. The coefficient can be varied to achieve a different set of trade-offs between the number of unclassified and misidentified samples.
  • To ensure that the accuracy of the model was not a result of overfitting, each model was validated by leave-one-out cross-validation. This entailed removing each sample of known lymphoma type from the data one at a time, and then determining whether the model could predict the missing sample. This process confirmed the accuracy of the prediction method.
  • The classification of a lymphoproliferative disorder in accordance with embodiments of the present invention may be used in combination with any other effective classification feature or set of features. For example, a disorder may be classified by a method of the present invention in conjunction with WHO suggested guidelines, morphological properties, histochemical properties, chromosomal structure, genetic mutation, cellular proliferation rates, immunoreactivity, clinical presentation, and/or response to chemical, biological, or other agents. Embodiments of the present invention may be used in lieu of or in conjunction with other methods for lymphoma diagnosis, such as immunohistochemistry, flow cytometry, FISH for translocations, or viral diagnostics.
  • Accurate determination of lymphoma type in a subject allows for better selection and application of therapeutic methods. Knowledge about the exact lymphoma affecting a subject allows a clinician to select therapies or treatments that are most appropriate and useful for that subject, while avoiding therapies that are nonproductive or even counterproductive. For example, CNS prophylaxis may be useful for treating BL but not DLBCL, CHOP treatment may be useful for treating DLBCL but not blastic MCL (Fisher 1993; Khouri 1998), and subjects with follicular lymphoma frequently receive treatment while subjects with follicular hyperplasia do not. In each of these situations, the lymphoma types or subtypes in question can be difficult to distinguish using prior art diagnostic methods. The diagnostic and identification methods of the present invention allow for more precise delineation between these lymphomas, which simplifies the decision of whether to pursue a particular therapeutic option. Likewise, the survival prediction methods disclosed in the present invention also allow for better selection of therapeutic options. A subject with a very low survival predictor score (i.e., very good prognosis) may not receive treatment, but may instead be subjected to periodic check-ups and diligent observation. As survival predictor scores increase (i.e., prognosis gets worse), subjects may receive more intensive treatments. Those subjects with the highest survival predictor scores (i.e., very poor prognosis) may receive experimental treatments or treatments with novel agents. Accurate survival prediction using the methods disclosed herein provides an improved tool for selecting treatment options and for predicting the likely clinical outcome of those options.
  • Any effective method of quantifying the expression of at least one gene, gene set, or group of gene sets may be used to acquire gene expression data for use in embodiments of the present invention. For example, gene expression data may be measured or estimated using one or more microarrays. The microarrays may be of any effective type, including but not limited to nucleic acid based or antibody based. Gene expression may also be measured by a variety of other techniques, including but not limited to PCR, quantitative RT-PCR, real-time PCR, RNA amplification, in situ hybridization, immunohistochemistry, immunocytochemistry, FACS, serial analysis of gene expression (SAGE) (Velculescu 1995), Northern blot hybridization, or western blot hybridization.
  • Nucleic acid microarrays generally comprise nucleic acid probes derived from individual genes and placed in an ordered array on a support. This support may be, for example, a glass slide, a nylon membrane, or a silicon wafer. Gene expression patterns in a sample are obtained by hybridizing the microarray with the gene expression product from the sample. This gene expression product may be, for example, total cellular mRNA, rRNA, or cDNA obtained by reverse transcription of total cellular mRNA. The gene expression product from a sample is labeled with a radioactive, fluorescent, or other label to allow for detection. Following hybridization, the microarray is washed, and hybridization of gene expression product to each nucleic acid probe on the microarray is detected and quantified using a detection device such as a phosphorimager or scanning confocal microscope.
  • There are two broad classes of microarrays: cDNA and oligonucleotide arrays. cDNA arrays consist of hundreds or thousands of cDNA probes immobilized on a solid support. These cDNA probes are usually 100 nucleotides or greater in size. There are two commonly used designs for cDNA arrays. The first is the nitrocellulose filter array, which is generally prepared by robotic spotting of purified DNA fragments or lysates of bacteria containing cDNA clones onto a nitrocellulose filter (Southern 1992; Southern 1994; Gress 1996; Pietu 1996). The other commonly used cDNA arrays is fabricated by robotic spotting of PCR fragments from cDNA clones onto glass microscope slides (Schena 1995; DeRisi 1996; Schena 1996; Shalon 1996; DeRisi 1997; Heller 1997; Lashkari 1997). These cDNA microarrays are simultaneously hybridized with two fluorescent cDNA probes, each labeled with a different fluorescent dye (typically Cy3 or Cy5). In this format, the relative mRNA expression in two samples is directly compared for each gene on the microarray. Oligonucleotide arrays differ from cDNA arrays in that the probes are 20- to 25-mer oligonucleotides. Oligonucleotide arrays are generally produced by in situ oligonucleotide synthesis in conjunction with photolithographic masking techniques (Pease 1994; Lipshutz 1995; Chee 1996; Lockhart 1996; Wodicka 1997). The solid support for oligonucleotide arrays is typically a glass or silicon surface.
  • Methods and techniques applicable to array synthesis and use have been described in, for example, U.S. Pat. Nos. 5,143,854 (Pirrung), 5,242,974 (Holmes), 5,252,743 (Barrett), 5,324,633 (Fodor), 5,384,261 (Winkler), 5,424,186 (Fodor), 5,445,934 (Fodor), 5,451,683 (Barrett), 5,482,867 (Barrett), 5,491,074 (Aldwin), 5,527,681 (Holmes), 5,550,215 (Holmes), 5,571,639 (Hubbell), 5,578,832 (Trulson), 5,593,839 (Hubbell), 5,599,695 (Pease), 5,624,711 (Sundberg), 5,631,734 (Stern), 5,795,716 (Chee), 5,831,070 (Pease), 5,837,832 (Chee), 5,856,101 (Hubbell), 5,858,659 (Sapolsky), 5,936,324 (Montagu), 5,968,740 (Fodor), 5,974,164 (Chee), 5,981,185 (Matson), 5,981,956 (Stern), 6,025,601 (Trulson), 6,033,860 (Lockhart), 6,040,193 (Winkler), 6,090,555 (Fiekowsky), and 6,410,229 (Lockhart), and U.S. Patent Application Publication No. 20030104411 (Fodor). Each of the above patents and applications is incorporated by reference herein in its entirety.
  • Microarrays may generally be produced using a variety of techniques, such as mechanical or light directed synthesis methods that incorporate a combination of photolithographic methods and solid phase synthesis methods. Techniques for the synthesis of microarrays using mechanical synthesis methods are described in, for example, U.S. Pat. Nos. 5,384,261 (Winkler) and 6,040,193 (Winkler). Although a planar array surface is preferred, the microarray may be fabricated on a surface of virtually any shape, or even on a multiplicity of surfaces. Microarrays may be nucleic acids on beads, gels, polymeric surfaces, fibers such as fiber optics, glass or any other appropriate substrate. See, for example, U.S. Pat. Nos. 5,708,153 (Dower); 5,770,358 (Dower); 5,789,162 (Dower); 5,800,992 (Fodor); and 6,040,193 (Winkler), each of which is incorporated by reference herein in its entirety.
  • Microarrays may be packaged in such a manner as to allow for diagnostic use, or they can be an all-inclusive device. See, for example, U.S. Pat. Nos. 5,856,174 (Lipshutz) and 5,922,591 (Anderson), both of which are incorporated by reference herein in their entirety.
  • Microarrays directed to a variety of purposes are commercially available from Affymetrix (Affymetrix, Santa Clara, Calif.). For instance, these microarrays may be used for genotyping and gene expression monitoring for a variety of eukaryotic and prokaryotic species.
  • The following examples are provided to better illustrate the claimed invention and are not to be interpreted as limiting the scope of the invention. To the extent that specific materials are mentioned, it is merely for purposes of illustration and is not intended to limit the invention. One skilled in the art may develop equivalent means or reactants without the exercise of inventive capacity and without departing from the scope of the invention. It will be understood that many variations can be made in the procedures herein described while still remaining within the bounds of the present invention. It is the intention of the inventors that such variations are included within the scope of the invention.
    • EXAMPLES Example 1 Collection and Analysis of Gene Expression Data Using Affymetrix U133A and U133B Microarrays
  • 568 cell samples representing various forms of human lymphoid malignancies were obtained by biopsy using known methods described in the literature. The samples were reviewed by a panel of hematopathologists and classified into the following lymphoma types based on current diagnostic criteria:
  • 231 diffuse large B cell lymphomas (DLBCL)
  • 191 follicular lymphomas (FL)
  • 26 Burkitt lymphomas (BL)
  • 21 mantle cell lymphoma (MCL)
  • 18 follicular hyperplasias (FH)
  • 17 small cell lymphocytic lymphomas (SLL)
  • 16 mucosa-associated lymphoid tissue lymphomas (MALT)
  • 13 splenic lymphomas (Splenic)
  • 10 cyclin-D1 negative lymphomas with MCL morphology (CD1negMCL)
  • 9 multiple myeloma (Mult_Myeloma)
  • 6 lymphoplasmacytic lymphomas (LPC)
  • 4 post-transplant lymphoproliferative disorders (PTLD)
  • 3 lymphoblastic lymphomas (Lymbl)
  • 3 nodal marginal zone lymphomas (NMZ)
  • The 231 DLBCL samples were subdivided into the following lymphoma types based on gene expression (see below):
  • 88 germinal center B cell-like (GCB)
  • 78 activated B cell-like (ABC)
  • 33 primary mediastinal B cell lymphoma (PMBL)
  • 32 samples for which the subtype could not be determined (UC_DLBCL)
  • The 16 MALT samples were subdivided into the following four group based on tumor origin:
  • 9 from the gastric region (MALT_gastric)
  • 1 from the salivary gland (MALT_salivary)
  • 1 from the lung (MALT_lung)
  • 1 from the tonsil (MALT_tonsil)
  • 4 of unknown origin (MALT_unk)
  • Each of the 568 cell samples was given a unique sample ID number consisting of the lymphoma type followed by a unique numerical identifier. For example, “ABC—304” refers to an ABC DLBCL sample numbered 304. Cells were purified and RNA was isolated from the purified cells according to known methods described in the literature.
  • Aliquots of RNA from each sample were applied to Affymetrix U133A and Affymetrix U133B microarrays according to standard Affymetrix protocol. The U133A and U133B microarrays are divided into probe sets, with each probe set consisting of up to 69 oligonucleotide probes 25 nucleotides in length. Each probe set represents a distinct human gene. Information pertaining to these microarrays is available at the Affymetrix company web site. Each microarray was scanned using an Affymetrix scanner, which records signal intensity for every probe on the microarray. This information can be transformed into summary signal values for each probe set using a number of different algorithms, including MAS 5.0, D-chip (Li 2001), or Bioconductor's RMA algorithms (Irizarry 2003). The images produced by the scanner were evaluated by Affymetrix MAS 5.0 software and stored as tables in .txt format. Since each sample was scanned on both microarrays, there are two .txt files for each sample. Each .txt file was given a unique name consisting of the table number, sample ID number (discussed above), and a letter denoting the microarray used. For example, Table—0588_ABC—304A.txt is the .txt file for Table 588, which contains data for sample ID number ABC—304 from the U133A array. The data for each sample tested is contained in Tables 3-1138.
  • The signal value for each probe on the U133A and U133B microarrays was normalized to a target value of 500, and the base-2 log of the normalized values was used for the following analyses. Log-signal values for each probe set are presented in Tables 1139-1706, contained in files with the title format “Table_No._NAME_log_signal.txt,” where NAME refers to the sample ID number (e.g., ABC—304). The first column provides the UNIQID for the probe set, while the second column provides the log-signal value.
  • Log-signal files were statistically analyzed using S+ software and the S+ subtype predictor script contained in the file entitled “Subtype_Predictor.txt,” located in the computer program listing appendix contained on CD number 22 of 22. Although the log-signal values were analyzed using S+ software and the above algorithm, any effective software/algorithm combination may be used. Tables 1707-1721 provide descriptive statistical characteristics for each of the lymphoma types tested except for CD1 negMCL, non-gastric MALT, and UC_DLBCL. Table 1722 provides statistical characteristics for all MALT samples combined, while Table 1723 does likewise for all DLBCL samples.
  • The files containing Tables 1707-1723 have the title format “Table_No._TYPE_Stats.txt,” where TYPE refers to the lymphoma type. Each row of these tables represents a particular probe set. The first column of each table provides the UNIQID for the probe set, while the second column provides the average log-signal for the probe set over all samples of a particular lymphoma type. The third column provides the log-fold change in expression of the probe set between the lymphoma type in question and a second lymphoma type. For example, if logfold.ABC.vs.GCB is −0.21 for gene X, expression of gene X in the ABC samples is, on average, 0.86 (i.e., 2−0.21) times greater than expression of gene X in the GCB samples. The fourth column provides a two-sided P-value derived from a t-test of the log signals of the two lymphoma types compared in column three. If, for example, P.value.ABC.vs.GCB was 0.00001 for gene X, this would indicate that the observed difference in expression of gene X between ABC and GCB would only occur approximately one time in 100,000 if there was no actual difference in gene X expression between the two lymphoma types. The remainder of the columns can be read as pairs that repeat the pattern of columns three and four, presenting the log-fold change and P-value of the difference in expression of the probe set for the lymphoma type in question versus all other lymphoma types being tested. Tables 1710, 1715, and 1723 (corresponding to FL, MCL, and DLBCL, respectively) contain two additional columns entitled “TYPE_Cox_coefficient” and “TYPE_Cox_P_value.” The content of these columns is discussed in the following examples.
    • Example 2 Collection of Gene Expression Data Using the Novel Lymph Dx Microarray
  • The novel Lymph Dx microarray contains cDNA probes corresponding to approximately 2,734 genes. 174 of these are “housekeeping” genes present for quality control, since they represent genes that are most variably expressed across all lymphoma samples. Other genes represented on the microarray were selected for their utility in identifying particular lymphoma samples and predicting survival in those samples. The genes represented on the Lymph Dx microarray can be divided into four broad categories: 1,101 lymphoma predictor genes identified previously using the Affymetrix U133 microarray, 171 outcome predictor genes identified using the Affymetrix 0133 microarray, 167 genes not found on the Affymetrix U133 microarray but represented on the Lymphochip microarray (Alizadeh 1999), and 1,121 named genes. The types of genes making up each of these broad categories are summarized in Table 1724, below, while the specific genes represented on the Lymph Dx microarray are listed in Table 2 and contained in the file “Table—0002_Lymph Dx_Probe_List.txt.”
  • TABLE 2
    Unigene ID Unigene
    UNIQID Probe Set Build 167 Symbol
    1119003 200004_at 183684 EIF4G2
    1119007 200009_at 56845 GDI2
    1119015 200024_at 378103 RPS5
    1130426 200039_s_at 432607 PSMB2
    1130429 200048_s_at 6396 JTB
    1130430 200052_s_at 75117 ILF2
    1130433 200058_s_at 246112 U5-200KD
    1130446 200076_s_at 369785 MGC2749
    1130447 200077_s_at 446427 OAZ1
    1119039 200084_at 447513 SMAP
    1130465 200098_s_at 7101 ANAPC5
    1130468 200594_x_at 166463 HNRPU
    1130472 200599_s_at 192374 TRA1
    1119046 200606_at 349499 DSP
    1130482 200616_s_at 181418 KIAA0152
    1130483 200622_x_at 334330 CALM3
    1119056 200633_at 356190 UBB
    1119061 200644_at 75061 MLP
    1130501 200650_s_at 2795 LDHA
    1119068 200660_at 417004 S100A11
    1119070 200663_at 445570 CD63
    1130509 200665_s_at 111779 SPARC
    1119071 200667_at 411826 UBE2D3
    1119072 200670_at 437638 XBP1
    1119074 200675_at 54457 CD81
    1130518 200679_x_at 434102 HMGB1
    1119076 200681_at 268849 GLO1
    1130527 200692_s_at 184233 HSPA9B
    1130533 200706_s_at 76507 LITAF
    1119090 200709_at 374638 FKBP1A
    1130588 200775_s_at 307544 HNRPK
    1130603 200797_s_at 86386 MCL1
    1119111 200804_at 35052 TEGT
    1130618 200822_x_at 83848 GRCC9
    1130622 200829_x_at 97128 ZNF207
    1130624 200832_s_at 119597 SCD
    1130629 200839_s_at 135226 CTSB
    1130631 200842_s_at 171292 EPRS
    1130645 200860_s_at 279949 KIAA1007
    1130653 200875_s_at 376064 NOL5A
    1119139 200880_at 388392 DNAJA1
    1130658 200886_s_at 447492 PGAM1
    1130668 200897_s_at 194431 KIAA0992
    1130674 200905_x_at 381008 HLA-E
    1130676 200907_s_at 194431 KIAA0992
    1130680 200912_s_at 511904 EIF4A2
    1130687 200924_s_at 79748 SLC3A2
    1119155 200934_at 110713 DEK
    1130704 200951_s_at 376071 CCND2
    1130707 200956_s_at 79162 SSRP1
    1130712 200965_s_at 442540 ABLIM1
    1119171 200974_at 208641 ACTA2
    1119173 200978_at 75375 MDH1
    1119183 200997_at 211203 RBM4
    1130732 201002_s_at 381025 UBE2V1
    1119186 201005_at 387579 CD9
    1130735 201009_s_at 179526 TXNIP
    1130744 201027_s_at 158688 EIF5B
    1130746 201029_s_at 283477 CD99
    1130747 201030_x_at 234489 LDHB
    1119202 201042_at 512708 TGM2
    1130755 201043_s_at 356089 ANP32A
    1119209 201063_at 167791 RCN1
    1130771 201068_s_at 61153 PSMC2
    1119212 201069_at 367877 MMP2
    1130799 201114_x_at 233952 PSMA7
    1130812 201131_s_at 194657 CDH1
    1119237 201141_at 389964 GPNMB
    1130820 201144_s_at 151777 EIF2S1
    1119239 201145_at 199625 HAX1
    1130835 201163_s_at 435795 IGFBP7
    1130839 201167_x_at 159161 ARHGDIA
    1119243 201171_at 440165 ATP6V0E
    1119245 201178_at 5912 FBXO7
    1130852 201184_s_at 74441 CHD4
    1130855 201189_s_at 77515 ITPR3
    1119251 201194_at 433941 SEPW1
    1119258 201209_at 88556 HDAC1
    1119260 201212_at 18069 LGMN
    1119263 201216_at 511762 C12orf8
    1130871 201222_s_at 159087 RAD23B
    1130879 201231_s_at 433455 ENO1
    1119268 201234_at 6196 ILK
    1130882 201236_s_at 75462 BTG2
    1130888 201244_s_at 257266 RAF1
    1130898 201260_s_at 80919 SYPL
    1130900 201262_s_at 821 BGN
    1130906 201277_s_at 81361 HNRPAB
    1130910 201284_s_at 221589 APEH
    1130911 201287_s_at 82109 SDC1
    1119294 201292_at 156346 TOP2A
    1130914 201294_s_at 315379 WSB1
    1130922 201305_x_at 459987 ANP32B
    1130923 201306_s_at 459987 ANP32B
    1130926 201310_s_at 508741 C5orf13
    1119300 201314_at 155206 STK25
    1130936 201331_s_at 437475 STAT6
    1130942 201338_x_at 445977 GTF3A
    1119311 201341_at 104925 ENC1
    1119317 201349_at 396783 SLC9A3R1
    1119325 201365_at 74563 OAZ2
    1119334 201389_at 149609 ITGA5
    1130972 201393_s_at 76473 IGF2R
    1130977 201401_s_at 83636 ADRBK1
    1119350 201425_at 331141 ALDH2
    1130994 201431_s_at 150358 DPYSL3
    1119361 201448_at 391858 TIA1
    1119365 201460_at 75074 MAPKAPK2
    1131012 201464_x_at 78465 JUN
    1119369 201473_at 25292 JUNB
    1131019 201474_s_at 265829 ITGA3
    1119375 201489_at 381072 PPIF
    1131038 201502_s_at 81328 NFKBIA
    1119383 201508_at 1516 IGFBP4
    1119390 201518_at 77254 CBX1
    1119400 201536_at 181046 DUSP3
    1119401 201540_at 421383 FHL1
    1131068 201564_s_at 118400 FSCN1
    1131069 201565_s_at 180919 ID2
    1131074 201572_x_at 76894 DCTD
    1119417 201579_at 166994 FAT
    1131081 201586_s_at 180610 SFPQ
    1131082 201587_s_at 182018 IRAK1
    1119424 201599_at 75485 OAT
    1131107 201628_s_at 432330 RRAGA
    1131110 201631_s_at 76095 IER3
    1119438 201641_at 118110 BST2
    1131119 201647_s_at 349656 SCARB2
    1119443 201648_at 436004 JAK1
    1119445 201650_at 309517 KRT19
    1119448 201656_at 212296 ITGA6
    1131140 201684_s_at 194035 C14orf92
    1131149 201694_s_at 326035 EGR1
    1131150 201695_s_at 75514 NP
    1119460 201696_at 76122 SFRS4
    1119462 201700_at 83173 CCND3
    1119466 201710_at 179718 MYBL2
    1119467 201714_at 21635 TUBG1
    1119475 201739_at 296323 SGK
    1119477 201743_at 163867 CD14
    1131181 201744_s_at 406475 LUM
    1119479 201746_at 408312 TP53
    1119488 201761_at 154672 MTHFD2
    1131197 201778_s_at 269902 KIAA0494
    1119503 201803_at 149353 POLR2B
    1131218 201809_s_at 76753 ENG
    1131219 201810_s_at 109150 SH3BP5
    1119510 201820_at 433845 KRT5
    1119515 201833_at 3352 HDAC2
    1119516 201834_at 6061 PRKAB1
    1119519 201849_at 79428 BNIP3
    1131246 201853_s_at 153752 CDC25B
    1131260 201872_s_at 12013 ABCE1
    1131263 201877_s_at 249955 PPP2R5C
    1119533 201886_at 283976 WDR23
    1131268 201888_s_at 285115 IL13RA1
    1119537 201895_at 446641 TIMP1
    1131274 201897_s_at 374378 CKS1B
    1119541 201910_at 207428 FARP1
    1119546 201921_at 433898 GNG10
    1131290 201925_s_at 408864 DAF
    1119557 201939_at 398157 PLK2
    1119559 201941_at 5057 CPD
    1119561 201945_at 59242 FURIN
    1119564 201952_at 10247 ALCAM
    1119565 201953_at 135471 CIB1
    1119566 201954_at 433506 ARPC1B
    1119568 201957_at 269777 PPP1R12B
    1131321 201983_s_at 77432 EGFR
    1131325 201990_s_at 13313 CREBL2
    1119582 201998_at 2554 SIAT1
    1131336 202010_s_at 405945 ZNF410
    1131340 202018_s_at 437457 LTF
    1131342 202020_s_at 13351 LANCL1
    1131379 202075_s_at 439312 PLTP
    1119611 202076_at 289107 BIRC2
    1131395 202102_s_at 278675 BRD4
    1131401 202119_s_at 14158 CPNE3
    1131405 202123_s_at 446504 ABL1
    1131407 202125_s_at 154248 ALS2CR3
    1119633 202126_at 198891 PRPF4B
    1119636 202130_at 209061 RIOK3
    1131411 202135_s_at 2477 ACTR1B
    1119639 202136_at 145894 BS69
    1131414 202140_s_at 511790 CLK3
    1119647 202161_at 2499 PRKCL1
    1119652 202175_at 458374 CHPF
    1119655 202178_at 407181
    1131450 202200_s_at 369358 SRPK1
    1119667 202206_at 111554 ARL7
    1119680 202237_at 364345 NNMT
    1119683 202241_at 444947 C8FW
    1119684 202242_at 439586 TM4SF2
    1131473 202243_s_at 89545 PSMB4
    1131474 202246_s_at 95577 CDK4
    1119694 202265_at 380403 COMMD3
    1119699 202273_at 307783 PDGFRB
    1119706 202281_at 153227 GAK
    1119708 202283_at 173594 SERPINF1
    1131490 202284_s_at 370771 CDKN1A
    1119709 202288_at 338207 FRAP1
    1131497 202295_s_at 114931 CTSH
    1131503 202303_x_at 135705 SMARCA5
    1131507 202311_s_at 172928 COL1A1
    1119725 202329_at 77793 CSK
    1119729 202338_at 164457 TK1
    1131531 202350_s_at 153647 MATN2
    1119734 202351_at 436873 ITGAV
    1131541 202369_s_at 310230 TRAM2
    1119752 202391_at 511745 BASP1
    1131561 202403_s_at 232115 COL1A2
    1119765 202421_at 81234 IGSF3
    1119766 202423_at 93231 MYST3
    1131578 202431_s_at 202453 MYC
    1131584 202439_s_at 303154 IDS
    1131592 202450_s_at 83942 CTSK
    1131594 202454_s_at 306251 ERBB3
    1119775 202455_at 9028 HDAC5
    1119780 202472_at 75694 MPI
    1119782 202478_at 155418 TRB2
    1131614 202483_s_at 24763 RANBP1
    1119799 202518_at 408219 BCL7B
    1119802 202522_at 7370 PITPNB
    1131636 202524_s_at 436193 SPOCK2
    1131637 202527_s_at 75862 MADH4
    1119807 202530_at 79107 MAPK14
    1119808 202531_at 80645 IRF1
    1131640 202534_x_at 83765 DHFR
    1131645 202542_s_at 105656 SCYE1
    1119813 202545_at 155342 PRKCD
    1131654 202555_s_at 386078 MYLK
    1119817 202561_at 409194 TNKS
    1131663 202568_s_at 437625 MARK3
    1119820 202573_at 181390 CSNK1G2
    1119826 202589_at 87491 TYMS
    1131687 202606_s_at 369280 TLK1
    1119838 202615_at 469951 GNAQ
    1119841 202625_at 80887 LYN
    1119846 202634_at 351475 POLR2K
    1131705 202638_s_at 386467 ICAM1
    1131710 202644_s_at 211600 TNFAIP3
    1119860 202670_at 132311 MAP2K1
    1131733 202686_s_at 83341 AXL
    1119868 202688_at 387871 TNFSF10
    1131737 202693_s_at 9075 STK17A
    1119872 202696_at 95220 OSR1
    1119873 202697_at 446393 CPSF5
    1119876 202703_at 14611 DUSP11
    1119878 202705_at 194698 CCNB2
    1119880 202709_at 442844 FMOD
    1119884 202716_at 418004 PTPN1
    1131752 202724_s_at 170133 FOXO1A
    1131753 202727_s_at 180866 IFNGR1
    1131755 202729_s_at 241257 LTBP1
    1119889 202731_at 257697 PDCD4
    1131757 202736_s_at 76719 LSM4
    1119894 202740_at 334707 ACY1
    1119895 202741_at 156324 PRKACB
    1119903 202753_at 350939 p44S10
    1131767 202758_s_at 296776 RFXANK
    1119906 202762_at 58617 ROCK2
    1119907 202763_at 141125 CASP3
    1131778 202779_s_at 396393 UBE2S
    1119916 202780_at 177584 OXCT
    1119919 202786_at 199263 STK39
    1119920 202788_at 234521 MAPKAPK3
    1119924 202794_at 32309 INPP1
    1119928 202799_at 317335 CLPP
    1131786 202803_s_at 375957 ITGB2
    1119936 202811_at 407994 STAMBP
    1119939 202820_at 170087 AHR
    1119946 202834_at 19383 AGT
    1119950 202840_at 402752 TAF15
    1131806 202842_s_at 6790 DNAJB9
    1131808 202845_s_at 75447 RALBP1
    1131813 202853_s_at 285346 RYK
    1131815 202856_s_at 386678 SLC16A3
    1131816 202859_x_at 624 IL8
    1131827 202880_s_at 1050 PSCD1
    1131835 202888_s_at 1239 ANPEP
    1119972 202894_at 437008 EPHB4
    1131839 202899_s_at 405144 SFRS3
    1131845 202906_s_at 25812 NBS1
    1131847 202910_s_at 3107 CD97
    1119979 202911_at 445052 MSH6
    1119983 202920_at 409783 ANK2
    1131854 202923_s_at 414985 GCLC
    1131861 202933_s_at 194148 YES1
    1131863 202936_s_at 2316 SOX9
    1131868 202947_s_at 81994 GYPC
    1119995 202948_at 82112 IL1R1
    1119997 202951_at 367811 STK38
    1131870 202952_s_at 8850 ADAM12
    1119998 202953_at 8986 C1QB
    1131875 202965_s_at 169172 CAPN6
    1120008 202969_at 173135 DYRK2
    1120011 202983_at 3068 SMARCA3
    1120016 202991_at 77628 STARD3
    1120023 203005_at 1116 LTBR
    1120024 203006_at 408063 INPP5A
    1120026 203010_at 437058 STAT5A
    1131916 203035_s_at 435761 PIAS3
    1131918 203037_s_at 77694 MTSS1
    1120038 203044_at 110488 CHSY1
    1120044 203053_at 22960 BCAS2
    1131925 203054_s_at 250894 TCTA
    1120053 203073_at 82399 COG2
    1120055 203075_at 110741 MADH2
    1120059 203083_at 458354 THBS2
    1131940 203085_s_at 1103 TGFB1
    1120063 203090_at 118684 SDF2
    1120069 203104_at 174142 CSF1R
    1120072 203110_at 405474 PTK2B
    1131955 203112_s_at 21771 WHSC2
    1120079 203126_at 5753 IMPA2
    1131964 203130_s_at 6641 KIF5C
    1120081 203131_at 74615 PDGFRA
    1120082 203132_at 408528 RB1
    1120088 203138_at 13340 HAT1
    1120089 203139_at 244318 DAPK1
    1120090 203140_at 155024 BCL6
    1131972 203154_s_at 20447 PAK4
    1131975 203160_s_at 24439 RNF8
    1120108 203175_at 75082 ARHG
    1120120 203196_at 307915 ABCC4
    1120121 203198_at 150423 CDK9
    1131998 203210_s_at 443227 RFC5
    1120127 203213_at 334562 CDC2
    1132004 203217_s_at 415117 SIAT9
    1120128 203218_at 348446 MAPK9
    1120129 203221_at 406491 TLE1
    1132011 203229_s_at 73986 CLK2
    1132013 203232_s_at 434961 SCA1
    1120134 203233_at 75545 IL4R
    1132016 203238_s_at 8546 NOTCH3
    1120137 203240_at 111732 FCGBP
    1132022 203247_s_at 173911 ZNF24
    1120145 203256_at 191842 CDH3
    1132031 203266_s_at 134106 MAP2K4
    1132034 203271_s_at 410455 UNC119
    1132035 203272_s_at 8186 TUSC2
    1120152 203275_at 83795 IRF2
    1120153 203276_at 89497 LMNB1
    1120160 203288_at 436976 KIAA0355
    1120163 203302_at 709 DCK
    1132058 203313_s_at 161999 TGIF
    1120191 203373_at 405946 SOCS2
    1120194 203379_at 149957 RPS6KA1
    1120196 203386_at 173802 TBC1D4
    1132104 203387_s_at 173802 TBC1D4
    1120205 203405_at 5198 DSCR2
    1120214 203416_at 443057 CD53
    1120216 203418_at 85137 CCNA2
    1132122 203434_s_at 307734 MME
    1132132 203454_s_at 279910 ATOX1
    1120254 203485_at 99947 RTN1
    1120261 203499_at 171596 EPHA2
    1120266 203507_at 246381 CD68
    1120267 203508_at 256278 TNFRSF1B
    1120269 203510_at 419124 MET
    1120272 203514_at 29282 MAP3K3
    1120274 203517_at 31584 MTX2
    1132159 203521_s_at 147868 ZNF318
    1120278 203528_at 511748 SEMA4D
    1120288 203547_at 17483 CD4
    1120289 203552_at 246970 MAP4K5
    1132178 203554_x_at 350966 PTTG1
    1120299 203574_at 79334 NFIL3
    1120300 203575_at 82201 CSNK2A2
    1132196 203591_s_at 381027 CSF3R
    1120316 203611_at 63335 TERF2
    1120317 203612_at 106880 BYSL
    1120324 203627_at 239176 IGF1R
    1132220 203632_s_at 448805 GPRC5B
    1132223 203638_s_at 404081 FGFR2
    1132230 203649_s_at 76422 PLA2G2A
    1120335 203652_at 432787 MAP3K11
    1132236 203661_s_at 374849 TMOD1
    1120350 203679_at 446686 IL1RL1LG
    1120353 203685_at 79241 BCL2
    1120355 203687_at 80420 CX3CL1
    1120356 203688_at 458291 PKD2
    1120359 203697_at 128453 FRZB
    1132256 203702_s_at 169910 KIAA0173
    1132260 203706_s_at 173859 FZD7
    1120361 203708_at 188 PDE4B
    1120362 203709_at 196177 PHKG2
    1120366 203717_at 44926 DPP4
    1120370 203723_at 78877 ITPKB
    1120373 203728_at 93213 BAK1
    1120378 203738_at 151046 FLJ11193
    1120385 203755_at 36708 BUB1B
    1120387 203758_at 75262 CTSO
    1120389 203761_at 75367 SLA
    1132288 203767_s_at 79876 STS
    1132292 203771_s_at 435726 BLVRA
    1132294 203777_s_at 32156 RPS6KB2
    1120400 203787_at 152207 SSBP2
    1120402 203794_at 18586 CDC42BPA
    1132306 203795_s_at 371758 BCL7A
    1120417 203827_at 9398 FLJ10055
    1120419 203830_at 9800 NJMU-R1
    1120422 203835_at 151641 GARP
    1120423 203837_at 151988 MAP3K5
    1132329 203839_s_at 528296 ACK1
    1120425 203843_at 188361 RPS6KA3
    1132336 203853_s_at 30687 GAB2
    1120433 203856_at 422662 VRK1
    1132345 203868_s_at 109225 VCAM1
    1120438 203870_at 109268 USP46
    1132349 203881_s_at 169470 DMD
    1132353 203887_s_at 2030 THBD
    1132354 203890_s_at 153908 DAPK3
    1120465 203915_at 77367 CXCL9
    1120477 203934_at 12337 KDR
    1120478 203935_at 150402 ACVR1
    1132375 203942_s_at 157199 MARK2
    1132376 203944_x_at 169963 BTN2A1
    1120483 203947_at 180034 CSTF3
    1120484 203949_at 458272 MPO
    1120494 203967_at 405958 CDC6
    1120500 203979_at 82568 CYP27A1
    1132396 203988_s_at 118722 FUT8
    1120509 204000_at 155090 GNB5
    1132407 204005_s_at 406074 PAWR
    1120520 204023_at 35120 RFC4
    1120524 204033_at 436187 TRIP13
    1120529 204039_at 76171 CEBPA
    1132426 204049_s_at 102471 C6orf56
    1132428 204051_s_at 105700 SFRP4
    1120538 204057_at 14453 ICSBP1
    1132433 204059_s_at 14732 ME1
    1132434 204060_s_at 147996 PRKX
    1132435 204062_s_at 168762 ULK2
    1120544 204068_at 166684 STK3
    1120553 204086_at 30743 PRAME
    1120555 204090_at 444 STK19
    1132449 204092_s_at 250822 STK6
    1120562 204103_at 75703 CCL4
    1120564 204106_at 79358 TESK1
    1120572 204116_at 84 IL2RG
    1120574 204118_at 901 CD48
    1132460 204126_s_at 114311 CDC45L
    1120580 204127_at 115474 RFC3
    1120581 204129_at 415209 BCL9
    1132462 204131_s_at 14845 FOXO3A
    1120583 204133_at 153768 RNU3IP2
    1120588 204140_at 421194 TPST1
    1132468 204147_s_at 79353 TFDP1
    1120593 204150_at 301989 STAB1
    1120594 204154_at 442378 CDO1
    1120595 204156_at 444909 KIAA0999
    1120596 204159_at 4854 CDKN2C
    1120601 204166_at 441129 KIAA0963
    1132479 204170_s_at 83758 CKS2
    1120605 204171_at 86858 RPS6KB1
    1132485 204183_s_at 445563 ADRBK2
    1120615 204191_at 181315 IFNAR1
    1120616 204192_at 166556 CD37
    1120617 204193_at 439777 CPT1B
    1120625 204208_at 27345 RNGTT
    1132498 204211_x_at 439523 PRKR
    1120630 204218_at 38044 DKFZP564M082
    1132504 204222_s_at 511765 GLIPR1
    1120633 204225_at 222874 HDAC4
    1120637 204232_at 433300 FCER1G
    1132519 204247_s_at 166071 CDK5
    1132520 204249_s_at 283063 LMO2
    1120643 204252_at 19192 CDK2
    1132525 204255_s_at 2062 VDR
    1120645 204257_at 21765 FADS3
    1132529 204265_s_at 288316 GPSM3
    1132531 204267_x_at 77783 PKMYT1
    1120651 204269_at 80205 PIM2
    1132536 204285_s_at 96 PMAIP1
    1120673 204301_at 5333 KIAA0711
    1132545 204306_s_at 512857 CD151
    1132547 204310_s_at 78518 NPR2
    1120695 204352_at 385685 TRAF5
    1120697 204355_at 323462 DHX30
    1132572 204357_s_at 36566 LIMK1
    1120700 204362_at 410745 SCAP2
    1120703 204368_at 83974 SLCO2A1
    1132584 204379_s_at 1420 FGFR3
    1120716 204392_at 512804 CAMK1
    1120717 204394_at 444159 SLC43A1
    1132592 204396_s_at 211569 GRK5
    1120720 204401_at 10082 KCNN4
    1120730 204415_at 287721 G1P3
    1120743 204440_at 79197 CD83
    1132614 204446_s_at 89499 ALOX5
    1120750 204454_at 45231 LDOC1
    1132628 204468_s_at 78824 TIE
    1120755 204470_at 789 CXCL1
    1120765 204484_at 343329 PIK3C2B
    1132636 204490_s_at 306278 CD44
    1120770 204493_at 300825 BID
    1120779 204510_at 28853 CDC7
    1120780 204511_at 301283 FARP2
    1120785 204517_at 110364 PPIC
    1120789 204524_at 154729 PDPK1
    1132651 204529_s_at 439767 TOX
    1120792 204533_at 413924 CXCL10
    1120803 204549_at 321045 IKBKE
    1120808 204562_at 127686 IRF4
    1120809 204563_at 82848 SELL
    1120813 204568_at 414809 KIAA0831
    1120814 204569_at 417022 ICK
    1120818 204579_at 165950 FGFR4
    1120824 204589_at 200598 ARK5
    1120825 204591_at 388344 CRL1
    1120828 204600_at 2913 EPHB3
    1120832 204604_at 57856 PFTK1
    1120834 204606_at 57907 CCL21
    1120838 204612_at 433700 PKIA
    1120839 204613_at 512298 PLCG2
    1120846 204632_at 105584 RPS6KA4
    1132700 204633_s_at 109058 RPS6KA5
    1120847 204634_at 433008 NEK4
    1120853 204641_at 153704 NEK2
    1120854 204642_at 154210 EDG1
    1120858 204647_at 410683 HOMER3
    1120863 204655_at 489044 CCL5
    1120875 204674_at 124922 LRMP
    1120880 204682_at 105689 LTBP2
    1120881 204683_at 433303 ICAM2
    1132726 204707_s_at 433728 MAPK4
    1120900 204718_at 380089 EPHB6
    1132734 204724_s_at 126248 COL9A3
    1120918 204754_at 250692 HLF
    1120923 204765_at 334 ARHGEF5
    1120925 204773_at 204891 IL11RA
    1132762 204777_s_at 80395 MAL
    1132766 204781_s_at 82359 TNFRSF6
    1132768 204785_x_at 512211 IFNAR2
    1132775 204803_s_at 1027 RRAD
    1132780 204811_s_at 389415 CACNA2D2
    1120946 204813_at 25209 MAPK10
    1120952 204822_at 169840 TTK
    1120955 204825_at 184339 MELK
    1120958 204831_at 397734 CDK8
    1132787 204832_s_at 2534 BMPR1A
    1132799 204859_s_at 373575 APAF1
    1120976 204867_at 245644 GCHFR
    1120980 204872_at 494269 TLE4
    1132809 204878_s_at 291623 PSK
    1120986 204886_at 172052 PLK4
    1132818 204891_s_at 1765 LCK
    1132825 204900_x_at 512813 SAP30
    1132830 204908_s_at 31210 BCL3
    1120993 204912_at 327 IL10RA
    1132834 204914_s_at 432638 SOX11
    1121000 204924_at 519033 TLR2
    1121005 204932_at 81791 TNFRSF11B
    1121007 204936_at 440835 SF1
    1121012 204947_at 96055 E2F1
    1121013 204949_at 353214 ICAM3
    1132850 204954_s_at 130988 DYRK1B
    1121021 204958_at 153640 PLK3
    1132851 204961_s_at 1583
    1132852 204962_s_at 1594 CENPA
    1121028 204968_at 247323 APOM
    1121029 204971_at 412999 CSTA
    1121033 204975_at 356835 EMP2
    1132860 204986_s_at 291623 PSK
    1132862 204990_s_at 85266 ITGB4
    1132866 204998_s_at 9754 ATF5
    1132874 205013_s_at 197029 ADORA2A
    1121054 205016_at 170009 TGFA
    1121057 205026_at 434992 STAT5B
    1132883 205027_s_at 432453 MAP3K8
    1121061 205032_at 387725 ITGA2
    1121062 205034_at 408658 CCNE2
    1132890 205049_s_at 79630 CD79A
    1132892 205051_s_at 81665 KIT
    1121073 205052_at 81886 AUH
    1121076 205055_at 389133 ITGAE
    1121082 205067_at 126256 IL1B
    1121100 205098_at 301921 CCR1
    1121102 205101_at 126714 MHC2TA
    1132918 205114_s_at 73817 CCL3
    1132920 205119_s_at 753 FPR1
    1121115 205124_at 78881 MEF2B
    1121117 205126_at 82771 VRK2
    1121120 205130_at 104119 RAGE
    1121129 205159_at 285401 CSF2RB
    1121136 205168_at 440905 DDR2
    1132953 205180_s_at 86947 ADAM8
    1121143 205184_at 447973 GNG4
    1121149 205192_at 440315 MAP3K14
    1132959 205198_s_at 606 ATP7A
    1121159 205205_at 307905 RELB
    1121161 205207_at 512234 IL6
    1132961 205212_s_at 337242 CENTB1
    1121166 205214_at 88297 STK17B
    1121170 205220_at 458425 HM74
    1121186 205242_at 100431 CXCL13
    1121190 205247_at 436100 NOTCH4
    1121195 205253_at 408222 PBX1
    1132973 205255_x_at 169294 TCF7
    1121201 205263_at 193516 BCL10
    1121203 205266_at 2250 LIF
    1121205 205269_at 2488 LCP2
    1132979 205271_s_at 26322 CCRK
    1121217 205291_at 75596 IL2RB
    1121220 205296_at 87 RBL1
    1132990 205297_s_at 89575 CD79B
    1132994 205301_s_at 380271 OGG1
    1132996 205306_x_at 409081 KMO
    1121228 205312_at 157441 SPI1
    1133004 205327_s_at 389846 ACVR2
    1121248 205345_at 54089 BARD1
    1133011 205347_s_at 56145 TMSNB
    1121265 205372_at 14968 PLAG1
    1133021 205377_s_at 154495 ACHE
    1133024 205383_s_at 436987 ZNF288
    1133030 205392_s_at 272493 CCL15
    1121276 205394_at 24529 CHEK1
    1121278 205399_at 21355 DCAMKL1
    1121281 205403_at 25333 IL1R2
    1121287 205411_at 35140 STK4
    1121290 205418_at 7636 FES
    1121291 205419_at 784 EBI2
    1133042 205422_s_at 311054 ITGBL1
    1133047 205434_s_at 528338 AAK1
    1133049 205436_s_at 147097 H2AFX
    1121301 205437_at 449971 ZNF134
    1121306 205443_at 179312 SNAPC1
    1121309 205449_at 23642 HSU79266
    1121315 205455_at 2942 MST1R
    1121316 205456_at 3003 CD3E
    1121322 205467_at 5353 CASP10
    1121326 205476_at 75498 CCL20
    1133065 205479_s_at 77274 PLAU
    1133068 205483_s_at 458485 G1P2
    1121329 205484_at 88012 SIT
    1121331 205486_at 8980 TESK2
    1121343 205504_at 159494 BTK
    1133076 205512_s_at 18720 PDCD8
    1133080 205526_s_at 440341 KATNA1
    1133091 205544_s_at 73792 CR2
    1133093 205546_s_at 75516 TYK2
    1121368 205551_at 8071 SV2B
    1133099 205554_s_at 88646 DNASE1L3
    1121371 205558_at 444172 TRAF6
    1133102 205565_s_at 360041 FRDA
    1121380 205569_at 10887 LAMP3
    1121383 205572_at 115181 ANGPT2
    1121387 205578_at 208080 ROR2
    1133111 205593_s_at 389777 PDE9A
    1121400 205599_at 223474 TRAF1
    1133117 205607_s_at 435560 PACE-1
    1121404 205609_at 2463 ANGPT1
    1121406 205611_at TNFSF12
    1121408 205613_at 258326 LOC51760
    1133119 205614_x_at 512587 MST1
    1121414 205621_at 94542 ALKBH
    1121436 205659_at 487662 HDAC9
    1121444 205668_at 153563 LY75
    1133138 205671_s_at 1802 HLA-DOB
    1133141 205677_s_at 344524 DLEU1
    1121452 205681_at 227817 BCL2A1
    1133148 205692_s_at 174944 CD38
    1133150 205698_s_at 256924 MAP2K6
    1121468 205707_at 129751 IL17R
    1133156 205713_s_at 1584 COMP
    1121473 205718_at 1741 ITGB7
    1121482 205729_at 238648 OSMR
    1121497 205758_at 85258 CD8A
    1121511 205780_at 155419 BIK
    1133184 205786_s_at 172631 ITGAM
    1121516 205789_at 1799 CD1D
    1121518 205792_at 194679 WISP2
    1133192 205801_s_at 24024 RASGRP3
    1133195 205805_s_at 274243 ROR1
    1121533 205821_at 387787 KLRK1
    1121542 205831_at 89476 CD2
    1133210 205842_s_at 434374 JAK2
    1121546 205844_at 12114 VNN1
    1121554 205854_at 437046 TULP3
    1121558 205858_at 415768 NGFR
    1121559 205859_at 184018 LY86
    1121560 205861_at 437905 SPIB
    1121564 205865_at 437783 ARID3A
    1133216 205872_x_at 502577 PDE4DIP
    1121572 205876_at 446501 LIFR
    1121573 205878_at 2815 POU6F1
    1133219 205879_x_at 350321 RET
    1121574 205880_at 2891 PRKCM
    1133227 205895_s_at 75337 NOLC1
    1121584 205898_at 78913 CX3CR1
    1121585 205899_at 417050 CCNA1
    1121587 205901_at 371809 PNOC
    1121589 205904_at 90598 MICA
    1133232 205910_s_at 406160 CEL
    1121629 205965_at 41691 BATF
    1133252 205977_s_at 89839 EPHA1
    1121643 205986_at 514575 AATK
    1121645 205988_at 398093 CD84
    1133260 205992_s_at 528402 IL15
    1121650 206002_at 421137 GPR64
    1121655 206009_at 222 ITGA9
    1133272 206028_s_at 306178 MERTK
    1133275 206036_s_at 44313 REL
    1121680 206049_at 73800 SELP
    1133296 206070_s_at 123642 EPHA3
    1133299 206075_s_at 446484 CSNK2A1
    1121689 206076_at 155586 B7
    1121693 206080_at 170156 KIAA0450
    1121695 206082_at 511759 HCP5
    1133300 206085_s_at 19904 CTH
    1121711 206106_at 432642 MAPK12
    1121717 206114_at 73964 EPHA4
    1121720 206118_at 80642 STAT4
    1121722 206120_at 83731 CD33
    1121726 206126_at 113916 BLR1
    1121739 206142_at 85863 ZNF135
    1121743 206148_at 460433 IL3RA
    1121745 206150_at 355307 TNFRSF7
    1121757 206170_at 2551 ADRB2
    1121759 206172_at 336046 IL13RA2
    1121760 206176_at 285671 BMP6
    1121762 206181_at 32970 SLAMF1
    1121767 206187_at 458324 PTGIR
    1121780 206206_at 87205 LY64
    1121783 206211_at 89546 SELE
    1121788 206216_at 104865 STK23
    1121792 206222_at 119684 TNFRSF10C
    1121793 206223_at 122708 LMTK2
    1121809 206247_at 211580 MICB
    1121814 206255_at 389900 BLK
    1133355 206267_s_at 437808 MATK
    1121828 206271_at 29499 TLR3
    1121834 206279_at 183165 PRKY
    1133358 206283_s_at 73828 TAL1
    1121841 206291_at 80962 NTS
    1121844 206295_at 83077 IL18
    1121848 206301_at 278005 TEC
    1121853 206310_at 98243 SPINK2
    1121854 206312_at 171470 GUCY2C
    1121857 206315_at 114948 CRLF1
    1133376 206324_s_at 129208 DAPK2
    1121869 206336_at 164021 CXCL6
    1121870 206337_at 1652 CCR7
    1121874 206341_at 130058 IL2RA
    1133388 206362_x_at 435014 MAP3K10
    1121887 206363_at 134859 MAF
    1133389 206366_x_at 174228 XCL1
    1133392 206380_s_at 53155 PFC
    1133397 206390_x_at 81564 PF4
    1133400 206398_s_at 96023 CD19
    1133405 206407_s_at 414629 CCL13
    1133406 206411_s_at 159472 ABL2
    1121918 206412_at 121558 FER
    1133407 206413_s_at 144519 TCL6
    1133408 206414_s_at 12802 DDEF2
    1121947 206464_at 27372 BMX
    1133430 206467_x_at 348183 TNFRSF6B
    1121953 206478_at 38365 KIAA0125
    1121956 206482_at 51133 PTK6
    1121959 206486_at 409523 LAG3
    1121963 206493_at 411312 ITGA2B
    1121966 206498_at 82027 OCA2
    1133445 206499_s_at 196769 CHC1
    1121970 206508_at 99899 TNFSF7
    1133453 206518_s_at 117149 RGS9
    1121996 206545_at 1987 CD28
    1122007 206569_at 411311 IL24
    1133476 206571_s_at 3628 MAP4K4
    1122009 206575_at 50905 CDKL5
    1122021 206591_at 73958 RAG1
    1122036 206618_at 159301 IL18R1
    1122051 206637_at 2465 GPR105
    1122053 206641_at 2556 TNFRSF17
    1122065 206660_at 348935 IGLL1
    1122075 206674_at 385 FLT3
    1133515 206687_s_at 63489 PTPN6
    1122087 206693_at 72927 IL7
    1122091 206702_at 89640 TEK
    1122104 206718_at 1149 LMO1
    1122112 206729_at 1314 TNFRSF8
    1122131 206756_at 138155 CHST7
    1133538 206760_s_at 1416 FCER2
    1122139 206766_at 158237 ITGA10
    1122156 206794_at 1939 ERBB4
    1122165 206804_at 2259 CD3G
    1122181 206828_at 29877 TXK
    1133565 206846_s_at 6764 HDAC6
    1133568 206854_s_at 290346 MAP3K7
    1133569 206855_s_at 76873 HYAL2
    1133576 206864_s_at 87247 HRK
    1133577 206874_s_at 105751 SLK
    1133580 206881_s_at 113277 LILRA3
    1122215 206887_at 528317 CCBP2
    1122217 206890_at 223894 IL12RB1
    1122219 206892_at 437877 AMHR2
    1122230 206907_at 1524 TNFSF9
    1122241 206923_at 349611 PRKCA
    1133595 206926_s_at 1721 IL11
    1122253 206943_at 28005 TGFBR1
    1122274 206974_at 34526 CXCR6
    1122275 206975_at 36 LTA
    1122277 206978_at 511794 CCR2
    1122281 206983_at 46468 CCR6
    1122284 206988_at 310511 CCL25
    1133618 206991_s_at 511796 CCR5
    1122288 206999_at 413608 IL12RB2
    1122292 207008_at 846 IL8RB
    1133629 207011_s_at 90572 PTK7
    1122304 207029_at 1048 KITLG
    1122327 207061_at 137575 ERN1
    1122335 207073_at 143241 CDKL2
    1133652 207076_s_at 160786 ASS
    1122344 207094_at 194778 IL8RA
    1122353 207111_at 2375 EMR1
    1133672 207113_s_at 241570 TNF
    1133676 207121_s_at 271980 MAPK6
    1122380 207160_at 673 IL12A
    1133694 207163_s_at 368861 AKT1
    1122382 207165_at 72550 HMMR
    1133700 207173_x_at 443435 CDH11
    1133701 207176_s_at 838 CD80
    1133702 207178_s_at 89426 FRK
    1122388 207179_at 89583 TLX1
    1133704 207181_s_at 9216 CASP7
    1122394 207188_at 100009 CDK3
    1133708 207194_s_at 512159 ICAM4
    1122400 207199_at 439911 TERT
    1122412 207216_at 177136 TNFSF8
    1122420 207228_at 158029 PRKACG
    1133724 207239_s_at 171834 PCTK1
    1122428 207245_at 183596 UGT2B17
    1133731 207253_s_at 21479 UBN1
    1122449 207277_at 278694 CD209
    1122471 207312_at 512612 PHKG1
    1133753 207314_x_at 380156 KIR3DL1
    1133755 207318_s_at 404501 CDC2L5
    1133757 207320_x_at 6113 STAU
    1133766 207339_s_at 376208 LTB
    1122491 207354_at 10458 CCL16
    1133778 207375_s_at 12503 IL15RA
    1133786 207396_s_at 153591 ALG3
    1133801 207426_s_at 181097 TNFSF4
    1133802 207428_x_at 454861 CDC2L2
    1122537 207433_at 193717 IL10
    1122541 207442_at 2233 CSF3
    1133810 207445_s_at 225946 CCR9
    1122544 207446_at 366986 TLR6
    1133829 207497_s_at 386748 MS4A2
    1122581 207505_at 41749 PRKG2
    1133834 207509_s_at 43803 LAIR2
    1122596 207533_at 72918 CCL1
    1133846 207536_s_at 528403 TNFRSF9
    1122599 207538_at 73917 IL4
    1133848 207540_s_at 192182 SYK
    1122602 207550_at 82906 CDC20
    1122609 207568_at 103128 CHRNA6
    1122610 207569_at 1041 ROS1
    1133867 207571_x_at 10649 C1orf38
    1133869 207574_s_at 110571 GADD45B
    1133901 207633_s_at 156465 MUSK
    1122640 207634_at 158297 PDCD1
    1122645 207641_at 158341 TNFRSF13B
    1133904 207643_s_at 159 TNFRSF1A
    1133910 207655_s_at 167746 BLNK
    1122664 207681_at 198252 CXCR3
    1133931 207697_x_at 306230 LILRB2
    1122680 207709_at 256067 PRKAA2
    1122710 207766_at 380788 CDKL1
    1133998 207826_s_at 76884 ID3
    1122738 207840_at 81743 CD160
    1122740 207844_at 845 IL13
    1122743 207849_at 89679 IL2
    1122744 207850_at 89690 CXCL3
    1122749 207861_at 80420 CX3CL1
    1122763 207884_at 309958 GUCY2D
    1122767 207892_at 652 TNFSF5
    1122772 207900_at 66742 CCL17
    1122773 207901_at 674 IL12B
    1122774 207902_at 68876 IL5RA
    1122775 207906_at 694 IL3
    1122776 207907_at 129708 TNFSF14
    1122796 207952_at 2247 IL5
    1134069 207979_s_at 405667 CD8B1
    1134076 207988_s_at 83583 ARPC2
    1134083 207996_s_at 285091 C18orf1
    1134095 208018_s_at 89555 HCK
    1134109 208037_s_at 102598 MADCAM1
    1122824 208038_at 416814 IL1RL2
    1122834 208059_at 113222 CCR8
    1134133 208075_s_at 251526 CCL7
    1134145 208091_s_at 4750 DKFZP564K0822
    1134200 208161_s_at 90786 ABCC3
    1134212 208178_x_at 367689 TRIO
    1134220 208189_s_at 370421 MYO7A
    1122863 208193_at 960 IL9
    1122864 208195_at 434384 TTN
    1122865 208200_at 1722 IL1A
    1134230 208206_s_at 99491 RASGRP2
    1134233 208212_s_at 410680 ALK
    1134270 208284_x_at 352119 GGT1
    1134271 208286_x_at 249184 POU5F1
    1134280 208303_s_at 287729 CRLF2
    1122914 208304_at 506190 CCR3
    1134296 208335_s_at 183 FY
    1134316 208365_s_at 32959 GRK4
    1122939 208376_at 184926 CCR4
    1134361 208426_x_at 515605 KIR2DL4
    1134370 208438_s_at 1422 FGR
    1122956 208450_at 113987 LGALS2
    1134379 208451_s_at 150833 C4A
    1122983 208495_at 249125 TLX3
    1122994 208524_at 159900 GPR15
    1134422 208536_s_at 84063 BCL2L11
    1134424 208540_x_at S100A14
    1123026 208578_at 250443 SCN10A
    1134457 208605_s_at 406293 NTRK1
    1134480 208634_s_at 372463 MACF1
    1123038 208636_at 119000 ACTN1
    1123039 208638_at 212102 P5
    1134494 208657_s_at 288094 MSF
    1123052 208680_at 180909 PRDX1
    1123053 208683_at 350899 CAPN2
    1134517 208690_s_at 75807 PDLIM1
    1123055 208691_at 185726 TFRC
    1134523 208700_s_at 89643 TKT
    1134532 208711_s_at 371468 CCND1
    1134533 208716_s_at 93832 LOC54499
    1134542 208729_x_at 77961 HLA-B
    1123086 208774_at 378918 CSNK1D
    1134582 208794_s_at 78202 SMARCA4
    1134593 208812_x_at 274485 HLA-C
    1123105 208820_at 434281 PTK2
    1123108 208828_at 108112 POLE3
    1134615 208851_s_at 134643 THY1
    1134618 208854_s_at 168913 STK24
    1134647 208892_s_at 298654 DUSP6
    1123127 208894_at 409805 HLA-DRA
    1134653 208901_s_at 253536 TOP1
    1134665 208921_s_at 422340 SRI
    1134674 208937_s_at 410900 ID1
    1134676 208942_s_at 158193 TLOC1
    1123148 208944_at 82028 TGFBR2
    1134679 208946_s_at 12272 BECN1
    1134682 208949_s_at 411701 LGALS3
    1134687 208959_s_at 154023 TXNDC4
    1134699 208974_x_at 439683 KPNB1
    1123160 208982_at 78146 PECAM1
    1134706 208987_s_at 219614 FBXL11
    1123163 208991_at 421342 STAT3
    1134710 208993_s_at 77965 PPIG
    1134727 209018_s_at 439600 PINK1
    1134738 209033_s_at 75842 DYRK1A
    1134753 209053_s_at 110457 WHSC1
    1134778 209085_x_at 166563 RFC1
    1123188 209089_at 73957 RAB5A
    1123192 209100_at 315177 IFRD2
    1123193 209101_at 410037 CTGF
    1123198 209112_at 238990 CDKN1B
    1134797 209118_s_at 433394 TUBA3
    1123213 209154_at 12956 TIP-1
    1123223 209173_at 226391 AGR2
    1134837 209185_s_at 143648 IRS2
    1123231 209189_at 25647 FOS
    1123233 209193_at 81170 PIM1
    1123235 209196_at 436930 C6orf11
    1134843 209199_s_at 368950 MEF2C
    1134850 209210_s_at 270411 PLEKHC1
    1134852 209214_s_at 374477 EWSR1
    1134858 209226_s_at 405954 TNPO1
    1123250 209233_at 135643 C2F
    1123255 209239_at 160557 NFKB1
    1134865 209241_x_at 112028 MINK
    1134880 209265_s_at 168799 METTL3
    1134888 209278_s_at 438231 TFPI2
    1123278 209295_at 51233 TNFRSF10B
    1134903 209306_s_at 153026 SWAP70
    1123286 209311_at 410026 BCL2L2
    1123289 209317_at 5409 POLR1C
    1123293 209333_at 47061 ULK1
    1123298 209339_at 20191 SIAH2
    1134921 209341_s_at 413513 IKBKB
    1134928 209352_s_at 13999 SIN3B
    1123304 209354_at 279899 TNFRSF14
    1134933 209360_s_at 410774 RUNX1
    1123308 209364_at 76366 BAD
    1123310 209368_at 212088 EPHX2
    1134945 209379_s_at 81897 KIAA1128
    1123317 209386_at 351316 TM4SF1
    1123321 209392_at 23719 ENPP2
    1123331 209409_at 512118 GRB10
    1134961 209417_s_at 50842 IFI35
    1123346 209443_at 76353 SERPINA3
    1123358 209464_at 442658 AURKB
    1134988 209467_s_at 79516 MKNK1
    1134991 209474_s_at 444105 ENTPD1
    1123369 209481_at 79025 SNRK
    1123372 209487_at 195825 RBPMS
    1123376 209496_at 37682 RARRES2
    1135002 209500_x_at 54673 TNFSF13
    1123399 209541_at 308053 IGF1
    1135023 209543_s_at 374990 CD34
    1135024 209545_s_at 103755 RIPK2
    1123401 209550_at 50130 NDN
    1135028 209555_s_at 443120 CD36
    1123413 209575_at 418291 IL10RB
    1135042 209582_s_at 79015 MOX2
    1135047 209589_s_at 125124 EPHB2
    1123419 209590_at 170195 BMP7
    1135056 209604_s_at 169946 GATA3
    1123429 209619_at 446471 CD74
    1135068 209621_s_at 71719 PDLIM3
    1123430 209622_at 153003 STK16
    1123437 209636_at 73090 NFKB2
    1123439 209642_at 287472 BUB1
    1135080 209644_x_at 421349 CDKN2A
    1135085 209650_s_at 505862 C22orf4
    1135088 209656_s_at 8769 TM4SF10
    1135093 209666_s_at 198998 CHUK
    1135101 209680_s_at 20830 KIFC1
    1123455 209682_at 436986 CBLB
    1123457 209684_at 446304 RIN2
    1135102 209685_s_at 349845 PRKCB1
    1123459 209687_at 436042 CXCL12
    1123470 209704_at 31016 M96
    1123476 209711_at 82635 SLC35D1
    1123479 209716_at 173894 CSF1
    1123490 209732_at 85201 CLECSF2
    1123497 209747_at 2025 TGFB3
    1135130 209757_s_at 25960 MYCN
    1171502 209760_at 511944 KIAA0922
    1123507 209770_at 284283 BTN3A1
    1135138 209771_x_at 375108 CD24
    1135141 209774_x_at 75765 CXCL2
    1135151 209790_s_at 3280 CASP6
    1123529 209815_at 159526 PTCH
    1135164 209825_s_at 458360 UMPK
    1135165 209827_s_at 170359 IL16
    1123535 209829_at 389488 C6orf32
    1135168 209831_x_at 118243 DNASE2
    1135173 209841_s_at 3781 LRRN3
    1135186 209860_s_at 386741 ANXA7
    1135189 209863_s_at 137569 TP73L
    1123552 209879_at 423077 SELPLG
    1135209 209899_s_at 74562 SIAHBP1
    1123566 209906_at 155935 C3AR1
    1135214 209908_s_at 169300 TGFB2
    1123573 209924_at 16530 CCL18
    1135226 209929_s_at 43505 IKBKG
    1135227 209930_s_at 75643 NFE2
    1135229 209932_s_at 367676 DUT
    1123581 209941_at 390758 RIPK1
    1135234 209945_s_at 282359 GSK3B
    1123584 209946_at 79141 VEGFC
    1123586 209948_at 93841 KCNMB1
    1123587 209949_at 949 NCF2
    1135240 209955_s_at 436852 FAP
    1135251 209969_s_at 21486 STAT1
    1135253 209971_x_at 301613 JTV1
    1135267 209995_s_at 2484 TCL1A
    1135270 209999_x_at 50640 SOCS1
    1123608 210017_at 180566 MALT1
    1135285 210024_s_at 449501 UBE2E3
    1123611 210029_at 840 INDO
    1123613 210031_at 97087 CD3Z
    1123614 210038_at 408049 PRKCQ
    1135299 210044_s_at 46446 LYL1
    1123622 210051_at 8578 EPAC
    1123628 210058_at 178695 MAPK13
    1123634 210072_at 50002 CCL19
    1123635 210073_at 408614 SIAT8A
    1123643 210092_at 421576 MAGOH
    1135322 210095_s_at 450230 IGFBP3
    1135328 210105_s_at 390567 FYN
    1123663 210133_at 54460 CCL11
    1123671 210148_at 30148 HIPK3
    1135350 210151_s_at 164267 DYRK3
    1123672 210152_at 67846 LILRB4
    1123679 210163_at 103982 CXCL11
    1123680 210164_at 1051 GZMB
    1123682 210166_at 114408 TLR5
    1123690 210176_at 111805 TLR1
    1123694 210184_at 385521 ITGAX
    1135374 210214_s_at 53250 BMPR2
    1135379 210225_x_at 511766 LILRB3
    1135380 210229_s_at 1349 CSF2
    1135383 210240_s_at 435051 CDKN2D
    1123731 210258_at 17165 RGS13
    1135395 210260_s_at 17839 TNFAIP8
    1135399 210275_s_at 406096 ZNF216
    1123744 210279_at 88269 GPR18
    1123760 210313_at 406708 ILT7
    1123762 210316_at 415048 FLT4
    1123778 210349_at 440638 CAMK4
    1123780 210354_at 856 IFNG
    1135467 210404_x_at 321572 CAMK2B
    1135475 210416_s_at 146329 CHEK2
    1135487 210432_s_at 300717 SCN3A
    1135489 210438_x_at 288178 SSA2
    1123814 210439_at 56247 ICOS
    1123816 210442_at 66 IL1RL1
    1135492 210448_s_at 408615 P2RX5
    1135513 210481_s_at 421437 CD209L
    1123833 210487_at 397294 DNTT
    1123842 210506_at 457 FUT7
    1135526 210512_s_at 73793 VEGF
    1135529 210517_s_at 197081 AKAP12
    1123847 210523_at 87223 BMPR1B
    1135541 210538_s_at 127799 BIRC3
    1135549 210549_s_at 169191 CCL23
    1135550 210550_s_at 221811 RASGRF1
    1135571 210582_s_at 278027 LIMK2
    1135583 210606_x_at 41682 KLRD1
    1123875 210607_at 428 FLT3LG
    1135592 210621_s_at 758 RASA1
    1135593 210622_x_at 77313 CDK10
    1123889 210643_at 333791 TNFSF11
    1135606 210644_s_at 407964 LAIR1
    1123890 210654_at 129844 TNFRSF10D
    1123892 210659_at 159553 CMKLR1
    1135622 210671_x_at 445864 MAPK8
    1135645 210715_s_at 31439 SPINT2
    1135665 210749_x_at 423573 DDR1
    1135673 210759_s_at 82159 PSMA1
    1123938 210772_at 99855 FPRL1
    1135684 210775_x_at 329502 CASP9
    1135685 210776_x_at 371282 TCF3
    1135735 210838_s_at 410104 ACVRL1
    1135743 210847_x_at 299558 TNFRSF25
    1123954 210865_at 2007 TNFSF6
    1135755 210869_s_at 511397 MCAM
    1135773 210889_s_at 126384 FCGR2B
    1135778 210895_s_at 27954 CD86
    1135795 210933_s_at 55923 Lin10
    1135801 210943_s_at 130188 CHS1
    1135802 210944_s_at 439343 CAPN3
    1135826 210976_s_at 75160 PFKM
    1135830 210981_s_at 235116 GRK6
    1135835 210986_s_at 133892 TPM1
    1123988 211005_at 498997 LAT
    1135852 211008_s_at 302903 UBE2I
    1135858 211015_s_at 90093 HSPA4
    1135866 211026_s_at 409826 MGLL
    1135871 211031_s_at 104717 CYLN2
    1135899 211070_x_at 78888 DBI
    1135925 211100_x_at 149924 LILRB1
    1135929 211105_s_at 96149 NFATC1
    1135930 211107_s_at 98338 AURKC
    1135966 211155_s_at 1166 THPO
    1135968 211160_x_at 119000 ACTN1
    1135974 211168_s_at 388125 RENT1
    1135982 211178_s_at 129758 PSTPIP1
    1135994 211197_s_at 14155 ICOSL
    1136002 211208_s_at 288196 CASK
    1124049 211276_at 401835 my048
    1136048 211282_x_at 299558 TNFRSF25
    1136051 211286_x_at 520937 CSF2RA
    1136055 211296_x_at 183704 UBC
    1136056 211297_s_at 184298 CDK7
    1136087 211339_s_at 211576 ITK
    1136109 211370_s_at 436145 MAP2K5
    1136150 211432_s_at 381282 TYRO3
    1136152 211434_s_at 458436 CCRL2
    1136162 211453_s_at 326445 AKT2
    1136172 211470_s_at 38084 SULT1C1
    1136185 211488_s_at 355722 ITGB8
    1136193 211499_s_at 57732 MAPK11
    1136216 211528_x_at 512152 HLA-G
    1136269 211593_s_at 101474 MAST2
    1136273 211597_s_at 13775 HOP
    1136285 211615_s_at 182490 LRPPRC
    1124132 211658_at 432121 PRDX2
    1136329 211675_s_at 132739 HIC
    1136337 211685_s_at 90063 NCALD
    1136343 211692_s_at 87246 BBC3
    1124137 211693_at 366 MGC27165
    1136357 211709_s_at 512680 SCGF
    1136362 211714_x_at 356729 OK/SW-cl.56
    1136369 211724_x_at 387140 FLJ20323
    1136371 211726_s_at 361155 FMO2
    1136379 211734_s_at 897 FCER1A
    1136391 211748_x_at 446429 PTGDS
    1136393 211750_x_at 406578 TUBA6
    1136401 211761_s_at 27258 SIP
    1136408 211771_s_at 1101 POU2F2
    1136427 211795_s_at 276506 FYB
    1136430 211798_x_at 102950 IGLJ3
    1136459 211828_s_at 252550 KIAA0551
    1136464 211833_s_at 159428 BAX
    1136540 211924_s_at 179657 PLAUR
    1124176 211966_at 407912 COL4A2
    1124177 211967_at 172089 PORIMIN
    1124178 211969_at 446579 HSPCA
    1124187 211986_at 378738 MGC5395
    1124188 211987_at 282346 TOP2B
    1136573 211991_s_at 914 HLA-DPA1
    1124192 211992_at 275999 PRKWNK1
    1124195 211998_at 180877 H3F3B
    1136585 212022_s_at 80976 MKI67
    1124215 212037_at 409965 PNN
    1136595 212038_s_at 404814 VDAC1
    1136599 212046_x_at 861 MAPK3
    1136601 212048_s_at 322735 YARS
    1136605 212064_x_at 448398 MAZ
    1124237 212080_at 258855 MLL
    1136620 212091_s_at 415997 COL6A1
    1124254 212110_at 301743 SLC39A14
    1124266 212123_at 438991 DKFZP564D116
    1124283 212144_at 406612 UNC84B
    1124296 212158_at 1501 SDC2
    1124304 212168_at 166887 CPNE1
    1124316 212186_at 449863 ACACA
    1124318 212190_at 21858 SERPINE2
    1124321 212196_at 529772
    1136655 212218_s_at 388387 FBXO9
    1124342 212230_at 432840 PPAP2B
    1136662 212240_s_at 6241 PIK3R1
    1124357 212247_at 413636 NUP205
    1124362 212252_at 297343 CAMKK2
    1124365 212261_at 334871 TNRC15
    1124377 212282_at 199695 MAC30
    1124381 212288_at 440808 FNBP1
    1124384 212291_at 12259 HIPK1
    1124391 212299_at 7200 NEK9
    1136681 212303_x_at 91142 KHSRP
    1124400 212312_at 305890 BCL2L1
    1124411 212326_at 194737 VPS13D
    1124416 212331_at 283604 RBL2
    1124429 212344_at 409602 SULF1
    1136687 212345_s_at 59943 CREB3L2
    1124438 212358_at 7357 CLIPR-59
    1136692 212359_s_at 65135 KIAA0913
    1124456 212382_at 359289 TCF4
    1136702 212399_s_at 155584 KIAA0121
    1136710 212429_s_at 75782 GTF3C2
    1136712 212442_s_at 503941 LOC253782
    1136718 212459_x_at 446476 SUCLG2
    1136722 212481_s_at 250641 TPM4
    1136724 212491_s_at 433540 DNAJC8
    1124539 212494_at 6147 TENC1
    1124543 212500_at 99821 C10orf22
    1124549 212508_at 24719 MOAP1
    1124561 212530_at 24119 NEK7
    1124563 212533_at 249441 WEE1
    1124577 212552_at 3618 HPCAL1
    1124583 212558_at 20977 GDAP1L1
    1124594 212572_at 184523 STK38L
    1124606 212588_at 444324 PTPRC
    1124610 212592_at 381568 IGJ
    1124613 212599_at 296720 AUTS2
    1124616 212603_at 154655 MRPS31
    1136759 212605_s_at 188882
    1124620 212610_at 83572 PTPN11
    1136762 212624_s_at 380138 CHN1
    1136765 212629_s_at 69171 PRKCL2
    1124646 212646_at 436432 RAFTLIN
    1136774 212657_s_at 81134 IL1RN
    1124655 212658_at 79299 LHFPL2
    1124658 212663_at 522351 KIAA0674
    1136777 212671_s_at 387679 HLA-DQA1
    1124666 212672_at 526394 ATM
    1136781 212680_x_at 120197 PPP1R14B
    1136784 212689_s_at 321707 JMJD1
    1136786 212694_s_at 63788 PCCB
    1136788 212698_s_at 355455 9/10/2004
    1124692 212713_at 296049 MFAP4
    1124705 212730_at 381347 DMN
    1124712 212738_at 80305 ARHGAP19
    1124713 212740_at 306747 PIK3R4
    1124723 212753_at 435065 RNF3
    1124733 212771_at 66762 LOC221061
    1124734 212774_at 446677 ZNF238
    1124745 212789_at 438550 KIAA0056
    1136819 212798_s_at 112605 DKFZP564O043
    1124753 212801_at 528307 CIT
    1124755 212805_at 23311 KIAA0367
    1124760 212813_at 419149 JAM3
    1124768 212824_at 98751 FUBP3
    1124770 212827_at 153261 IGHM
    1136831 212841_s_at 12953 PPFIBP2
    1136832 212842_x_at 434959 RANBP2L1
    1124782 212843_at 78792 NCAM1
    1124786 212847_at 22370 NEXN
    1124798 212867_at 446678 NCOA2
    1124800 212871_at 413901 MAPKAPK5
    1136844 212875_s_at 16007 C21orf25
    1124806 212881_at 105779 PIASY
    1124820 212899_at 129836 CDK11
    1124830 212911_at 9059 KIAA0962
    1124831 212912_at 301664 RPS6KA2
    1124833 212914_at 356416 CBX7
    1136853 212922_s_at 66170 SMYD2
    1136859 212942_s_at 212584 KIAA1199
    1124862 212954_at 439530 DYRK4
    1136865 212959_s_at 412128 MGC4170
    1124864 212960_at 411317 KIAA0882
    1124875 212975_at 18166 KIAA0870
    1124889 212993_at 244847 BTBD14A
    1136876 212997_s_at 445078 TLK2
    1136877 212998_x_at 409934 HLA-DQB1
    1124893 213002_at 318603 MARCKS
    1124913 213027_at 288178 SSA2
    1124920 213039_at 6150 ARHGEF18
    1124921 213044_at 306307 ROCK1
    1124922 213045_at 173864 MAST3
    1124941 213068_at 80552 DPT
    1124942 213069_at 433452 HEG
    1124948 213075_at 357004 LOC169611
    1124953 213083_at 386278 SLC35D2
    1136902 213086_s_at 442592
    1136903 213087_s_at 334798 EEF1D
    1124967 213108_at 143535 CAMK2A
    1136913 213113_s_at 99962 SLC43A3
    1124972 213116_at 2236 NEK3
    1136925 213154_s_at 436939 BICD2
    1125001 213158_at 16193
    1125009 213169_at 27621
    1125010 213170_at 43728 GPX7
    1125013 213174_at 79170 TTC9
    1136938 213188_s_at 23294 MINA53
    1136939 213193_x_at 419777
    1125025 213196_at 301094
    1125027 213198_at 371974 ACVR1B
    1125058 213238_at 437241 ATP10D
    1125079 213264_at 211601 MAP3K12
    1125122 213324_at 436015 SRC
    1125124 213326_at 20021 VAMP1
    1136971 213330_s_at 257827 STIP1
    1136972 213331_s_at 414410 NEK1
    1125130 213338_at 35861 RIS1
    1125132 213341_at 47367 FEM1C
    1125136 213348_at 106070 CDKN1C
    1136983 213360_s_at 450237 LOC340318
    1136984 213364_s_at 498154 SNX1
    1136987 213370_s_at 21695 SFMBT1
    1136988 213373_s_at 243491 CASP8
    1136996 213397_x_at 283749 RNASE4
    1125181 213418_at 3268 HSPA6
    1125195 213438_at 7309
    1137022 213475_s_at 174103 ITGAL
    1125231 213489_at 446375 MAPRE2
    1137026 213490_s_at 366546 MAP2K2
    1125245 213517_at 132977 PCBP2
    1125246 213518_at 496511 PRKCI
    1125249 213523_at 244723 CCNE1
    1137042 213524_s_at 432132 G0S2
    1125279 213575_at 445652 TRA2A
    1125305 213627_at 376719 MAGED2
    1137097 213656_s_at 20107 KNS2
    1137109 213689_x_at 469653 RPL5
    1137112 213693_s_at 89603 MUC1
    1137137 213746_s_at 195464 FLNA
    1125377 213748_at 196966 KIAA0298
    1125397 213784_at 415172 RABL4
    1137158 213794_s_at 9043 C14orf120
    1137201 213877_x_at 433343 SRRM2
    1137202 213881_x_at 380973 SMT3H2
    1125456 213906_at 300592 MYBL1
    1125459 213909_at 288467 LRRC15
    1125462 213915_at 10306 NKG7
    1125485 213958_at 436949 CD6
    1137247 213975_s_at 234734 LYZ
    1137273 214020_x_at 149846 ITGB5
    1125516 214032_at 234569 ZAP70
    1125520 214038_at 271387 CCL8
    1137289 214049_x_at 36972 CD7
    1125527 214051_at 422848 MGC39900
    1137291 214055_x_at 446197 XTP2
    1125532 214058_at 437922 MYCL1
    1125546 214081_at 125036 PLXDC1
    1137308 214093_s_at 118962 FUBP1
    1137328 214130_s_at 502577 PDE4DIP
    1137332 214146_s_at 2164 PPBP
    1137343 214170_x_at 391168 FH
    1125593 214180_at 8910 MAN1C1
    1137360 214196_s_at 429658 CLN2
    1137378 214228_x_at 129780 TNFRSF4
    1125634 214265_at 171025 ITGA8
    1125658 214322_at 12436 CAMK2G
    1137439 214339_s_at 95424 MAP4K1
    1137447 214359_s_at 74335 HSPCB
    1137449 214363_s_at 223745 MATR3
    1125685 214371_at 103978 STK22B
    1137481 214428_x_at 150833 C4A
    1137486 214442_s_at 441069 MIZ1
    1137488 214448_x_at 9731 NFKBIB
    1137492 214459_x_at 274485 HLA-C
    1125742 214470_at 169824 KLRB1
    1137506 214501_s_at 75258 H2AFY
    1137512 214512_s_at 229641 PC4
    1137534 214551_s_at 36972 CD7
    1125789 214560_at 511953 FPRL2
    1137539 214567_s_at 458346 XCL2
    1125818 214607_at 152663 PAK3
    1125826 214617_at 2200 PRF1
    1137561 214639_s_at 67397 HOXA1
    1125852 214660_at 439320 ITGA1
    1125854 214663_at 6874 DustyPK
    1137582 214683_s_at 433732 CLK1
    1137583 214687_x_at 273415 ALDOA
    1125872 214696_at 417157 MGC14376
    1137594 214710_s_at 23960 CCNB1
    1137597 214721_x_at 3903 CDC42EP4
    1137601 214730_s_at 78979 GLG1
    1125901 214745_at 193143 KIAA1069
    1125916 214764_at 497770
    1125917 214769_at 417091 CLCN4
    1125919 214772_at 432369 G2
    1125921 214777_at 512003
    1125927 214787_at 511742 IRLB
    1125928 214790_at 435628 SUSP1
    1137626 214797_s_at 445402 PCTK3
    1137643 214864_s_at 155742 GRHPR
    1137663 214909_s_at 247362 DDAH2
    1126047 214969_at 437214 MAP3K9
    1137687 214974_x_at 89714 CXCL5
    1137698 215001_s_at 442669 GLUL
    1126081 215030_at 309763 GRSF1
    1137742 215111_s_at 114360 TSC22
    1126131 215117_at 159376 RAG2
    1137751 215127_s_at 241567 RBMS1
    1126148 215143_at 408264 FLJ36166
    1137760 215158_s_at 169681 DEDD
    1137771 215193_x_at 308026 HLA-DRB3
    1137782 215223_s_at 384944 SOD2
    1137806 215313_x_at 181244 HLA-A
    1137809 215332_s_at 405667 CD8B1
    1126293 215346_at 504816 TNFRSF5
    1137838 215411_s_at 437508 C6orf4
    1137868 215493_x_at 169963 BTN2A1
    1126387 215499_at 180533 MAP2K3
    1126408 215528_at 22689
    1137908 215603_x_at 454906
    1137955 215722_s_at 434901 SNRPA1
    1126540 215750_at 474916 KIAA1659
    1126554 215767_at 159528 LOC91752
    1126559 215776_at 248138 INSRR
    1138030 215925_s_at 116481 CD72
    1138048 215967_s_at 403857 LY9
    1138120 216178_x_at 287797 ITGB1
    1138128 216199_s_at 390428 MAP3K4
    1138132 216207_x_at 390427 IGKV1D-13
    1138136 216215_s_at 433574 RBM9
    1138147 216234_s_at 194350 PRKACA
    1138150 216237_s_at 77171 MCM5
    1138157 216251_s_at 82563 KIAA0153
    1126858 216261_at 87149 ITGB3
    1138192 216321_s_at 126608 NR3C1
    1126892 216331_at 74369 ITGA7
    1138244 216442_x_at 418138 FN1
    1138259 216484_x_at 89525 HDGF
    1138279 216520_s_at 374596 TPT1
    1138312 216598_s_at 303649 CCL2
    1138331 216640_s_at 212102 P5
    1138355 216705_s_at 407135 ADA
    1138379 216836_s_at 446352 ERBB2
    1127214 216837_at 201920 EPHA5
    1138392 216862_s_at 3548 MTCP1
    1138400 216876_s_at 41724 IL17
    1138417 216905_s_at 56937 ST14
    1138421 216913_s_at 434251 KIAA0690
    1138441 216945_x_at 397891 PASK
    1138443 216950_s_at 77424 FCGR1A
    1127290 217019_at 447032
    1127294 217028_at 421986 CXCR4
    1138507 217066_s_at 898 DMPK
    1138515 217080_s_at 93564 HOMER2
    1138532 217128_s_at 199068 CAMK1G
    1138537 217140_s_at
    1138538 217143_s_at 2014 TRD@
    1138541 217149_x_at 203420 TNK1
    1127371 217164_at 391858 TIA1
    1138555 217184_s_at 434481 LTK
    1138567 217200_x_at 355264 CYB561
    1138645 217373_x_at 212217 MDM2
    1138647 217377_x_at 171262 ETV6
    1138652 217388_s_at 444471 KYNU
    1138670 217422_s_at 262150 CD22
    1138671 217427_s_at 415735 HIRA
    1138677 217436_x_at 390440
    1127567 217529_at 440667 FLJ20013
    1127576 217544_at 529751
    1138721 217552_x_at 334019 CR1
    1138759 217707_x_at 396404 SMARCA2
    1138765 217716_s_at 306079 SEC61A1
    1138778 217736_s_at 434986 HRI
    1138780 217739_s_at 293464 PBEF1
    1138783 217742_s_at 370152 WAC
    1138789 217750_s_at 369120 FLJ13855
    1127720 217765_at 272736 NRBP
    1138801 217774_s_at 333579 HSPC152
    1127742 217814_at 8207 GK001
    1127744 217817_at 323342 ARPC4
    1138832 217829_s_at 12820 USP39
    1138845 217849_s_at 436985 CDC42BPB
    1127756 217850_at 313544 NS
    1127761 217863_at 75251 PIAS1
    1138858 217871_s_at 407995 MIF
    1127775 217886_at 79095 EPS15
    1138867 217892_s_at 10706 EPLIN
    1138874 217910_x_at 383019 TCFL4
    1138878 217917_s_at 100002 DNCL2A
    1138887 217937_s_at 200063 HDAC7A
    1127805 217947_at 380627 CKLFSF6
    1127807 217950_at 7236 NOSIP
    1127813 217962_at 14317 NOLA3
    1138905 217970_s_at 437844 KIAA1194
    1127822 217977_at 279623 SEPX1
    1138910 217982_s_at 374503 MORF4L1
    1127833 218001_at 382044 MRPS2
    1138920 218002_s_at 24395 CXCL14
    1127838 218012_at 136164 SE20-4
    1127849 218032_at 76691 SNN
    1138944 218051_s_at 84753 FLJ12442
    1127864 218066_at 172613 SLC12A7
    1138959 218076_s_at 203605 RICH1
    1127873 218089_at 11314 C20orf4
    1138973 218097_s_at 11270 C10orf66
    1127885 218113_at 160417 TMEM2
    1138994 218143_s_at 238030 SCAMP2
    1138995 218144_s_at 24956 FLJ22056
    1127901 218145_at 344378 C20orf97
    1139005 218168_s_at 273186 CABC1
    1139017 218189_s_at 274424 NANS
    1139026 218205_s_at 512094 MKNK2
    1127931 218208_at 288284 PQLC1
    1139037 218223_s_at 173380 CKIP-1
    1127940 218227_at 256549 NUBP2
    1139039 218228_s_at 280776 TNKS2
    1127943 218232_at 9641 C1QA
    1139048 218250_s_at 170553 CNOT7
    1139054 218263_s_at 25726 LOC58486
    1139076 218306_s_at 133411 HERC1
    1139100 218350_s_at 234896 GMNN
    1139105 218367_x_at 8015 USP21
    1139106 218368_s_at 355899 TNFRSF12A
    1139127 218409_s_at 13015 DNAJC1
    1128042 218436_at 297875 SIL1
    1128066 218475_at 63609 HTF9C
    1128070 218481_at 283741 RRP46
    1128079 218499_at 23643 MST4
    1128095 218520_at 432466 TBK1
    1128099 218529_at 333427 8D6A
    1128100 218530_at 95231 FHOD1
    1139185 218535_s_at 27021 RIOK2
    1128106 218542_at 14559 C10orf3
    1128111 218552_at 170915 FLJ10948
    1139196 218559_s_at 169487 MAFB
    1139202 218569_s_at 440695 KBTBD4
    1128125 218581_at 445665 ABHD4
    1139215 218597_s_at 43549 C10orf70
    1128144 218613_at 236438 DKFZp761K1423
    1128151 218625_at 103291 NRN1
    1128157 218631_at 23918 VIP32
    1139226 218633_x_at 266514 FLJ11342
    1139230 218640_s_at 29724 PLEKHF2
    1128164 218646_at 44344 FLJ20534
    1139235 218651_s_at 416755 FLJ11196
    1128167 218653_at 78457 SLC25A15
    1128174 218665_at 19545 FZD4
    1128192 218696_at 102506 EIF2AK3
    1128195 218699_at 115325 RAB7L1
    1139265 218722_s_at 187657 FLJ12436
    1139266 218723_s_at 76640 RGC32
    1128214 218734_at 408443 FLJ13848
    1139274 218740_s_at 20157 CDK5RAP3
    1139277 218747_s_at 267993 TAPBP-R
    1139280 218751_s_at 312503 FBXW7
    1128223 218753_at 55024 FLJ10307
    1128231 218764_at 315366 PRKCH
    1139301 218792_s_at 108502 BSPRY
    1139303 218794_s_at 134406 FLJ20511
    1128248 218802_at 234149 FLJ20647
    1139314 218831_s_at 111903 FCGRT
    1128283 218856_at 159651 TNFRSF21
    1128287 218862_at 300063 ASB13
    1128298 218887_at 55041 MRPL2
    1128311 218909_at 30352 RPS6KC1
    1128321 218921_at 433036 SIGIRR
    1139360 218947_s_at 173946 FLJ10486
    1128341 218955_at 274136 BRF2
    1128356 218983_at 415792 C1RL
    1128360 218988_at 445043 SLC35E3
    1128377 219014_at 371003 PLAC8
    1128386 219025_at 195727 CD164L1
    1128387 219028_at 397465 HIPK2
    1139393 219032_x_at 170129 OPN3
    1128395 219039_at 7188 SEMA4C
    1128401 219049_at 341073 ChGn
    1139411 219073_s_at 368238 OSBPL10
    1128418 219082_at 433499 CGI-14
    1128435 219109_at 6783 PF20
    1128439 219118_at 438695 FKBP11
    1128447 219130_at 40337 FLJ10287
    1128457 219148_at 104741 TOPK
    1139444 219151_s_at 355874 RABL2B
    1128469 219173_at 390817 FLJ22686
    1128471 219176_at 3592 FLJ22555
    1139461 219191_s_at 14770 BIN2
    1128494 219209_at 389539 MDA5
    1139466 219210_s_at 365655 RAB8B
    1128506 219226_at 416108 CRK7
    1139483 219249_s_at 3849 FKBP10
    1128535 219278_at 194694 MAP3K6
    1128536 219279_at 21126 DOCK10
    1139526 219356_s_at 415534 C9orf83
    1139528 219360_s_at 31608 TRPM4
    1139531 219365_s_at 145156 MGC8407
    1128585 219366_at 63168 AVEN
    1139542 219396_s_at 512732 NEIL1
    1128615 219410_at 104800 FLJ10134
    1128626 219424_at 501452 EBI3
    1139552 219441_s_at 413386 LRRK1
    1128648 219452_at 499331 DPEP2
    1139556 219457_s_at 413374 RIN3
    1128653 219461_at 21420 PAK6
    1128655 219463_at 22920 C20orf103
    1128660 219471_at 413071 C13orf18
    1128681 219500_at 191548 CLC
    1128688 219509_at 238756 MYOZ1
    1139572 219511_s_at 24948 SNCAIP
    1128694 219517_at 171466 ELL3
    1139575 219519_s_at 31869 SN
    1139579 219528_s_at 57987 BCL11B
    1128705 219535_at 109437 HUNK
    1128710 219542_at 159146 NEK11
    1128713 219545_at 17296 KCTD14
    1128733 219572_at 489847 CADPS2
    1128738 219581_at 335550 MGC2776
    1139603 219603_s_at 145956 ZNF226
    1128757 219618_at 142295 IRAK4
    1128781 219648_at 79741 FLJ10116
    1128786 219654_at 114062 PTPLA
    1128787 219655_at 114611 C7orf10
    1139623 219667_s_at 193736 BANK1
    1128801 219676_at 288539 ZNF435
    1128807 219686_at 58241 HSA250839
    1128845 219734_at 272416 FLJ20174
    1128860 219753_at 323634 STAG3
    1139645 219757_s_at 134051 C14orf101
    1139654 219787_s_at 293257 ECT2
    1139661 219806_s_at 416456 FN5
    1128900 219812_at 323634 STAG3
    1128901 219813_at 487239 LATS1
    1139663 219816_s_at 4997 RNPC4
    1128915 219831_at 105818 CDKL3
    1139669 219837_s_at 13872 C17
    1128965 219901_at 170623 FGD6
    1128969 219906_at 446590 FLJ10213
    1129024 220005_at 13040 GPR86
    1129026 220007_at 135146 FLJ13984
    1129043 220028_at 23994 ACVR2B
    1129049 220034_at 268552 IRAK3
    1129059 220054_at 98309 IL23A
    1129061 220056_at 110915 IL22RA1
    1129064 220059_at 121128 BRDG1
    1129071 220068_at 136713 VPREB3
    1129085 220088_at 2161 C5R1
    1129103 220118_at 99430 TZFP
    1139767 220127_s_at 12439 FBXL12
    1139774 220140_s_at 15827 SNX11
    1129120 220146_at 179152 TLR7
    1129151 220196_at 432676 MUC16
    1139805 220230_s_at 414362 CYB5R2
    1129203 220273_at 110040 IL17B
    1129223 220296_at 13785 GALNT10
    1129228 220302_at 148496 MAK
    1129232 220307_at 157872 CD244
    1129245 220322_at 211238 IL1F9
    1139830 220330_s_at 221851 SAMSN1
    1139831 220335_x_at 268700 FLJ21736
    1129265 220351_at 310512 CCRL1
    1139839 220357_s_at 62863 SGK2
    1129269 220358_at 62919 SNFT
    1139842 220367_s_at 133523 SAP130
    1129281 220377_at 395486 C14orf110
    1129310 220415_at 414091 TNNI3K
    1129336 220448_at 252617 KCNK12
    1129419 220565_at 278446 GPR2
    1139925 220643_s_at 173438 FAIM
    1129495 220684_at 272409 TBX21
    1129517 220712_at
    1139949 220725_x_at 528684 FLJ23558
    1139950 220731_s_at 437385 FLJ10420
    1129535 220737_at 368153 RPS6KA6
    1139955 220740_s_at 4876 SLC12A6
    1139957 220742_s_at 63657 NGLY1
    1129537 220745_at 71979 IL19
    1139962 220751_s_at 10235 C5orf4
    1139969 220761_s_at 12040 JIK
    1139971 220765_s_at 127273 LIMS2
    1140007 220865_s_at 279865 TPRT
    1140018 220917_s_at 438482 PWDMP
    1140027 220933_s_at 12742 ZCCHC6
    1140031 220937_s_at 3972 SIAT7D
    1129661 220971_at 302036 IL17E
    1140072 220984_s_at 199750 SLCO5A1
    1140075 220987_s_at 172012 SNARK
    1140088 221002_s_at 509050 DC-TM4F2
    1140127 221044_s_at 125300 TRIM34
    1140151 221080_s_at 236449 FAM31C
    1129681 221085_at 241382 TNFSF15
    1129694 221111_at 272350 IL26
    1129743 221191_at 429531 DKFZP434A0131
    1140214 221215_s_at 55565 ANKRD3
    1140236 221239_s_at 194976 SPAP1
    1140238 221241_s_at 11962 BCL2L14
    1129754 221271_at 302014 IL21
    1129760 221287_at 404277 RNASEL
    1129812 221355_at 248101 CHRNG
    1129821 221367_at 248146 MOS
    1129825 221371_at 248197 TNFSF18
    1129874 221463_at 247838 CCL24
    1129879 221468_at 248116 XCR1
    1140344 221479_s_at 132955 BNIP3L
    1129887 221485_at 107526 B4GALT5
    1140370 221520_s_at 48855 CDCA8
    1140378 221530_s_at 437282 BHLHB3
    1129907 221539_at 406408 EIF4EBP1
    1129911 221549_at 400625 GRWD1
    1140391 221558_s_at 44865 LEF1
    1129917 221560_at 118843 MARK4
    1129923 221571_at 297660 TRAF3
    1140399 221577_x_at 296638 GDF15
    1140404 221584_s_at 354740 KCNMA1
    1140416 221601_s_at 58831 TOSO
    1129943 221626_at 512828 ZNF506
    1140457 221658_s_at 210546 IL21R
    1140464 221667_s_at 111676 HSPB8
    1140473 221676_s_at 17377 CORO1C
    1140491 221696_s_at 24979 DKFZp761P1010
    1140497 221704_s_at 77870 FLJ12750
    1129967 221739_at 10927 C19orf10
    1140520 221741_s_at 11747 C20orf21
    1129978 221753_at 60377 SSH1
    1140524 221766_s_at 10784 C6orf37
    1129993 221777_at 412981 FLJ14827
    1140534 221790_s_at 184482 ARH
    1130007 221796_at 439109 NTRK2
    1130030 221834_at 301872 LONP
    1130040 221855_at 356460
    1130054 221872_at 82547 RARRES1
    1140565 221875_x_at 411958 HLA-F
    1140567 221881_s_at 25035 CLIC4
    1140570 221891_x_at 180414 HSPA8
    1140571 221893_s_at 210397 ADCK2
    1130072 221898_at 468675 T1A-2
    1130078 221905_at 386952 CYLD
    1140574 221912_s_at 17987 MGC1203
    1130088 221918_at 258536 PCTK2
    1130090 221922_at 278338 GPSM2
    1140584 221932_s_at 294083 C14orf87
    1140589 221942_s_at 433488 GUCY1A3
    1130114 221965_at 445084 MPHOSPH9
    1130117 221969_at 22030 PAX5
    1130121 221978_at 411958 HLA-F
    1140613 221998_s_at 443330 VRK3
    1140630 222033_s_at 347713 FLT1
    1140632 222036_s_at 460184 MCM4
    1130155 222043_at 436657 CLU
    1130168 222061_at 75626 CD58
    1130169 222062_at 132781 IL27RA
    1130201 222126_at 278502 HRBL
    1140729 222223_s_at 207224 IL1F5
    1140745 222245_s_at 72222 FER1L4
    1130293 222315_at 292853
    1130337 222368_at 491069
    1095985 222450_at 83883 TMEPAI
    1095996 222482_at 288801 SSBP3
    1114679 222503_s_at 16470 FLJ10904
    1096028 222557_at 285753 STMN3
    1114715 222565_s_at 434387 PRKCN
    1096035 222569_at 105794 UGCGL1
    1096038 222572_at 22265 PPM2C
    1114726 222590_s_at 3532 NLK
    1096054 222606_at 21331 FLJ10036
    1096070 222640_at 241565 DNMT3A
    1096077 222659_at 441043 IPO11
    1096078 222661_at 284216 HSU84971
    1114766 222666_s_at 113052 RCL1
    1096085 222674_at 224137 HSPC109
    1096108 222731_at 292871 ZDHHC2
    1114824 222762_x_at 193370 LIMD1
    1114853 222812_s_at 512618 ARHF
    1096149 222824_at 410205 NUDT5
    1096152 222828_at 288240 IL20RA
    1096158 222838_at 132906 SLAMF7
    1096163 222848_at 164018 FKSG14
    1114877 222862_s_at 18268 AK5
    1096172 222880_at 300642 AKT3
    1096180 222890_at 11614 HSPC065
    1114893 222891_s_at 314623 BCL11A
    1096182 222899_at 256297 ITGA11
    1114913 222920_s_at 33187 KIAA0748
    1096220 222974_at 287369 IL22
    1114967 223028_s_at 7905 SNX9
    1114970 223032_x_at 279529 PX19
    1096248 223040_at 109253 NAT5
    1096251 223044_at 409875 SLC40A1
    1114977 223052_x_at 30026 HSPC182
    1114981 223057_s_at 203206 XPO5
    1114988 223075_s_at 4944 C9orf58
    1115008 223117_s_at 441028 USP47
    1115012 223122_s_at 31386 SFRP2
    1096297 223141_at 9597 UCK1
    1096300 223151_at 74284 MGC2714
    1115034 223158_s_at 387222 NEK6
    1115052 223190_s_at 380021 MLL5
    1115071 223218_s_at 390476 MAIL
    1115073 223220_s_at 131315 BAL
    1096341 223241_at 12169 SNX8
    1096356 223266_at 259230 ALS2CR2
    1096357 223267_at 57898 FLJ20432
    1096362 223274_at 512706 TCF19
    1096364 223276_at 29444 NID67
    1096369 223286_at 417029 DERP6
    1096378 223303_at 180535 URP2
    1096379 223304_at 439590 SLC37A3
    1115128 223349_s_at 293753 BOK
    1096406 223361_at 238205 C6orf115
    1096429 223405_at 64896 NPL
    1115160 223413_s_at 425427 LYAR
    1096440 223423_at 231320 GPR160
    1096442 223430_at 306864 SIK2
    1096446 223434_at 92287 GBP3
    1115176 223451_s_at 15159 CKLF
    1096456 223454_at 82407 CXCL16
    1096460 223460_at 8417 CAMKK1
    1096466 223467_at 25829 RASD1
    1096469 223471_at 103267 RAB3IP
    1115186 223480_s_at 283734 MRPL47
    1115194 223502_s_at 270737 TNFSF13B
    1096499 223514_at 293867 CARD11
    1096503 223522_at 21379 C9orf45
    1115203 223534_s_at 414481 RPS6KL1
    1096530 223565_at 409563 PACAP
    1115226 223600_s_at 279718 KIAA1683
    1096570 223624_at 409813 ANUBL1
    1096579 223640_at 117339 HCST
    1115253 223664_x_at 310922 BCL2L13
    1096609 223696_at 528631 ARSD
    1115271 223705_s_at 71252 DKFZp761C169
    1096615 223707_at 356342 RPL27A
    1096616 223708_at 119302 C1QTNF4
    1096617 223710_at 131342 CCL26
    1096621 223715_at 170819 STK29
    1115286 223750_s_at 120551 TLR10
    1115290 223759_s_at 193666 GSG2
    1115303 223787_s_at 236257 LOC51244
    1115309 223804_s_at 443081 DKFZP434F091
    1096690 223827_at 334174 TNFRSF19
    1096693 223834_at 443271 PDCD1LG1
    1115329 223852_s_at 439658 MGC4796
    1096719 223874_at 250153 ARP3BETA
    1115338 223883_s_at 224355 STK31
    1096738 223903_at 87968 TLR9
    1115347 223909_s_at 112272 HDAC8
    1096742 223910_at 114905 ERN2
    1115360 223940_x_at 187199 PRO1073
    1096805 224027_at 334633 CCL28
    1096829 224071_at 272373 IL20
    1096834 224079_at 278911 IL17C
    1096877 224132_at 326732 MGC13008
    1115441 224156_x_at 5470 IL17RB
    1096903 224185_at 437460 FLJ10385
    1096936 224262_at 306974 IL1F10
    1115519 224302_s_at 408914 MRPS36
    1096965 224346_at 433466 PRO1853
    1115566 224369_s_at 163825 SP329
    1096981 224399_at 61929 PDCD1LG2
    1115587 224402_s_at 120260 IRTA1
    1115589 224406_s_at 415950 IRTA2
    1115591 224409_s_at 367871 SSTK
    1115607 224428_s_at 435733 CDCA7
    1115621 224450_s_at 437474 RIOK1
    1115646 224481_s_at 210850 HECTD1
    1115668 224509_s_at 155839 RTN4IP1
    1115673 224514_x_at 129959 IL17RC
    1115679 224523_s_at 8345 MGC4308
    1115695 224553_s_at 212680 TNFRSF18
    1115696 224555_x_at 166371 IL1F7
    1115704 224569_s_at 350268 IRF2BP2
    1097030 224574_at 511801
    1097065 224621_at 324473 MAPK1
    1097096 224659_at 8518 SEPN1
    1097107 224673_at 502378 LENG8
    1097109 224675_at 78871 MESDC2
    1097126 224694_at 274520 ANTXR1
    1097143 224716_at 74335 HSPCB
    1097156 224733_at 298198 CKLFSF3
    1097161 224740_at 5064
    1097172 224753_at 434886 CDCA5
    1097177 224761_at 9691 GNA13
    1097195 224785_at 149931 MGC29814
    1097202 224796_at 386779 DDEF1
    1097229 224830_at 446393 CPSF5
    1097236 224837_at 235860 FOXP1
    1115763 224839_s_at 355862 GPT2
    1097247 224851_at 388761 CDK6
    1097253 224859_at 77873 B7H3
    1097255 224861_at 380144
    1097271 224880_at 6906 RALA
    1097280 224891_at 423523
    1097281 224892_at 7037 PLDN
    1097282 224893_at 356719 LOC283241
    1097290 224903_at 151001 CIRH1A
    1097297 224917_at 166254 VMP1
    1097307 224929_at 379754 LOC340061
    1097310 224934_at 5672 SMAP-5
    1097325 224951_at 458450 LASS5
    1097329 224955_at 528675 TEAD1
    1097334 224960_at 71573 FLJ10074
    1097359 224990_at 518723
    1097365 224998_at 325825 CKLFSF4
    1097371 225005_at 7299 PHF13
    1097383 225019_at 111460 CAMK2D
    1097388 225024_at 278839 C20orf77
    1097395 225032_at 299883 FAD104
    1115800 225040_s_at 282260 RPE
    1097424 225067_at 7978 DKFZP434C131
    1097441 225086_at 6799 FLJ38426
    1097448 225093_at 250607 UTRN
    1115812 225164_s_at 412102 EIF2AK4
    1115813 225175_s_at 105509 CTL2
    1097540 225195_at 388087
    1097553 225214_at 197071 PSMB7
    1097561 225224_at 19221 DKFZP566G1424
    1097563 225226_at 169577 FLJ14743
    1097564 225227_at 272108 SKIL
    1115829 225253_s_at 433213 METTL2
    1097600 225272_at 10846 SAT2
    1097609 225283_at 6093 ARRDC4
    1097610 225284_at 6019 DNAJC3
    1097611 225285_at 438993 BCAT1
    1097614 225289_at 410491 MGC16063
    1115840 225308_s_at 437362 KIAA1728
    1097637 225317_at 63220 ACBD6
    1097665 225351_at 434241 HT011
    1097676 225366_at 23363 PGM2
    1097683 225373_at 132569 PP2135
    1097684 225374_at 368878 MGC45714
    1097704 225399_at 440663 C1orf19
    1097707 225402_at 440263 C20orf64
    1097717 225412_at 23317 FLJ14681
    1097735 225436_at 26765 LOC58489
    1097804 225519_at 446590 FLJ10213
    1097814 225529_at 21446 CENTB5
    1115876 225535_s_at 11866 TIMM23
    1097824 225540_at 167 MAP2
    1115877 225552_x_at 76239 MGC3047
    1097887 225611_at 212787 KIAA0303
    1097897 225622_at 266175 PAG
    1097899 225624_at 145047 LOC92017
    1097901 225626_at 266175 PAG
    1115888 225629_s_at 35096 ZBTB4
    1097902 225630_at 412318 KIAA1706
    1115892 225649_s_at 100057 STK35
    1097918 225650_at 140309 LOC90378
    1097928 225660_at 443012 SEMA6A
    1097930 225662_at 115175 ZAK
    1097940 225673_at 380906 MYADM
    1115895 225682_s_at 202505 RPC8
    1097948 225684_at 69476 LOC348235
    1097961 225699_at 25892
    1097966 225704_at 127270 KIAA1545
    1097976 225715_at 218017 raptor
    1098012 225756_at 355669 CSNK1E
    1115905 225757_s_at 301478 CLMN
    1098023 225773_at 181161 KIAA1972
    1098065 225817_at 10119 FLJ14957
    1098069 225823_at 356626
    1115916 225836_s_at 157148 MGC13204
    1115917 225849_s_at 284265 C6orf83
    1098095 225852_at 131059 ANKRD17
    1098103 225864_at 124951 NSE2
    1098145 225913_at 9587 KIAA2002
    1098152 225922_at 377588 KIAA1450
    1098156 225927_at 170610 MAP3K1
    1098168 225943_at 22151 NLN
    1098174 225949_at 274401 LOC340371
    1098179 225956_at 163725 LOC153222
    1098186 225964_at 288697 MGC11349
    1098195 225974_at 88594 DKFZp762C1112
    1098204 225984_at 43322 PRKAA1
    1098220 226002_at 80720 GAB1
    1098234 226016_at 446414 CD47
    1098235 226017_at 440494 CKLFSF7
    1098242 226025_at 273104 KIAA0379
    1098252 226035_at 16953 USP31
    1098256 226041_at 431871 SVH
    1098258 226043_at 239370 GPSM1
    1098268 226053_at 110299 MAP2K7
    1098271 226056_at 300670 CDGAP
    1098277 226065_at 6786 PRICKLE1
    1098278 226066_at 166017 MITF
    1098303 226096_at 15463 FNDC5
    1115953 226111_s_at 278422 ZNF385
    1115955 226132_s_at 7988 FLJ31434
    1098338 226136_at 269857 HRB2
    1115960 226145_s_at 15420 FRAS1
    1115965 226166_x_at 26996 STK36
    1098405 226218_at 362807 IL7R
    1098412 226225_at 409515 MCC
    1098415 226230_at 130900 KIAA1387
    1098433 226250_at 202577
    1098447 226267_at 154095 JDP2
    1098459 226279_at 25338 SPUVE
    1098461 226281_at 234074 DNER
    1098476 226299_at 300485 pknbeta
    1098495 226318_at 443668 TBRG1
    1098506 226333_at 193400 IL6R
    1098521 226350_at 170129 OPN3
    1098548 226377_at 436639 NFIC
    1098550 226381_at 355655
    1098553 226384_at 437179 HTPAP
    1098574 226410_at 79077 KIAA0233
    1098592 226431_at 283707 ALS2CR13
    1098604 226444_at 32793 SLC39A10
    1098607 226448_at 38516 MGC15887
    1098611 226452_at 433611 PDK1
    1098613 226454_at 388125 RENT1
    1098618 226459_at 374836 PIK3AP1
    1116001 226465_s_at 430541 SON
    1098629 226473_at 103305
    1116006 226491_x_at 172550 PTBP1
    1098658 226507_at 64056 PAK1
    1098668 226517_at 438993 BCAT1
    1098669 226518_at 302746 KCTD10
    1098678 226530_at 386140 BMF
    1098683 226535_at 57664 ITGB6
    1098694 226548_at 97837
    1098718 226574_at 16364 PSPC1
    1116022 226611_s_at 433422 p30
    1098771 226638_at 374446 KIAA1501
    1098784 226653_at 12808 MARK1
    1098809 226682_at 359394
    1098821 226694_at 42322 PALM2
    1098822 226695_at 443452 PRRX1
    1098832 226705_at 748 FGFR1
    1098840 226713_at 55098 C3orf6
    1098862 226737_at 303669 MGC26694
    1098865 226741_at 250905 LOC51234
    1098883 226760_at 412014 MBTPS2
    1098893 226771_at 43577 ATP8B2
    1098898 226777_at 8850 ADAM12
    1098909 226789_at 446408
    1098918 226799_at 170623 FGD6
    1098927 226811_at 356216 FLJ20202
    1116045 226828_s_at 23823 HEYL
    1098946 226834_at 135121 ASAM
    1098951 226840_at 75258 H2AFY
    1098952 226841_at 62264 KIAA0937
    1098954 226844_at 128905 MOBKL2B
    1098962 226853_at 20137 BMP2K
    1098978 226869_at 124863
    1098987 226879_at 412559 FLJ21127
    1098991 226884_at 126085 LRRN1
    1116056 226913_s_at 243678 SOX8
    1099028 226930_at 334838 FNDC1
    1099032 226936_at 35962
    1099040 226944_at 390421 HTRA3
    1116063 226957_x_at 75447 RALBP1
    1099053 226959_at 376041
    1099058 226964_at 425116
    1099072 226979_at 28827 MAP3K2
    1099088 226996_at 14355
    1099105 227013_at 78960 LATS2
    1099112 227020_at 368672
    1099120 227030_at 371680
    1099124 227034_at 355455 9/10/2004
    1099128 227039_at 350631 AKAP13
    1099135 227046_at 3402 SLC39A11
    1099140 227052_at 500350
    1099148 227060_at 434975 TNFRSF19L
    1099150 227062_at 240443
    1099152 227064_at 351247 MGC15396
    1099154 227066_at 97927 MOBKL2C
    1116071 227067_x_at 502564 FLJ20719
    1099167 227080_at 381105 MGC45731
    1116073 227103_s_at 146161 MGC2408
    1099204 227121_at 193784
    1116085 227173_s_at 88414 BACH2
    1099265 227193_at 375762
    1099291 227222_at 130774 FBXO10
    1099292 227223_at 282901 RNPC2
    1099299 227232_at 241471 EVL
    1099318 227255_at 29911 LOC149420
    1099328 227267_at 432726 FLJ35779
    1099332 227272_at 32433
    1099358 227300_at 93135
    1116103 227308_x_at 289019 LTBP3
    1099377 227324_at 130712 ADCK4
    1099388 227336_at 124024 DTX1
    1099396 227346_at 435949 ZNFN1A1
    1099403 227354_at 266175 PAG
    1099418 227370_at 172792 KIAA1946
    1099444 227407_at 434489 FLJ90013
    1116122 227408_s_at 42768 DKFZp761O0113
    1116126 227432_s_at 438669 INSR
    1099510 227482_at 15251 ADCK1
    1099526 227502_at 521240 LCHN
    1099539 227520_at 201624 CXorf15
    1099549 227533_at 446665
    1099563 227550_at 388347
    1099598 227590_at 511859
    1116150 227606_s_at 16229 AMSH-LP
    1099631 227624_at 367639 FLJ20032
    1099633 227627_at 380877 SGKL
    1099651 227646_at 120785 EBF
    1099669 227666_at 45057 MGC45428
    1099680 227677_at 210387 JAK3
    1099686 227684_at 117721
    1099699 227697_at 436943 SOCS3
    1099711 227713_at 243596
    1099734 227740_at 127310 KIS
    1099743 227750_at 162189 TRAD
    1099748 227755_at 356481
    1099760 227767_at 129206 CSNK1G3
    1099798 227811_at 411081 FGD3
    1099826 227842_at 445862 RAB30
    1099830 227847_at 28020 EPM2AIP1
    1099847 227867_at 36723 LOC129293
    1099857 227877_at 119768
    1116181 227891_s_at 402752 TAF15
    1099886 227917_at 511708
    1099900 227934_at 444508
    1099939 227983_at 488173 MGC7036
    1099951 227999_at 157728 LOC170394
    1099953 228001_at 433668 C21orf4
    1099960 228008_at 144583
    1099965 228014_at 71962 LOC138428
    1099978 228035_at 148135 STK33
    1116219 228056_s_at 322854 NAP1L
    1099995 228057_at 107515 DDIT4L
    1100005 228069_at 121536 DUFD1
    1100027 228094_at 16291 AMICA
    1100040 228109_at 410953 RASGRF2
    1100042 228113_at 351413 RAB37
    1116233 228128_x_at 440769 PAPPA
    1100054 228130_at 125353
    1100060 228139_at 268551 RIPK3
    1100071 228153_at 432653 IBRDC2
    1100130 228224_at 76494 PRELP
    1100136 228231_at 413078 NUDT1
    1100138 228234_at 278391 TIRP
    1100144 228240_at 436379
    1100150 228248_at 9343 MGC39830
    1100159 228258_at 32156 RPS6KB2
    1100161 228261_at 135805 LOC142678
    1100171 228273_at 528654 FLJ11029
    1100183 228286_at 180582 FLJ40869
    1100249 228367_at 388674 HAK
    1100258 228377_at 88442 KIAA1384
    1100263 228382_at 406335 LOC90268
    1116277 228384_s_at 118210 C10orf33
    1100288 228411_at 26981 ALS2CR19
    1100290 228414_at 4241
    1100301 228426_at 356250 LLT1
    1100311 228437_at 445890 HSPC163
    1100335 228464_at 268474
    1100339 228468_at 276905 MASTL
    1100384 228524_at 283374 ADCK5
    1100405 228549_at 119387 KIAA0792
    1100420 228565_at 50883 KIAA1804
    1100423 228568_at 50841 FLJ30973
    1100433 228580_at 390421 HTRA3
    1100443 228592_at 438040 MS4A1
    1100496 228654_at 111496 LOC139886
    1116317 228661_s_at 526415
    1100538 228709_at 432458 PRG4
    1100561 228736_at 194109 HEL308
    1100562 228737_at 26608 C20orf100
    1100581 228758_at 155024 BCL6
    1100585 228762_at 159142 LFNG
    1100591 228769_at 388162 HKR2
    1100598 228776_at 531058
    1100609 228788_at 447045 PPIL2
    1100625 228806_at 232803
    1100721 228918_at 18713
    1100750 228955_at 280387
    1100753 228958_at 512717 ZNF19
    1100770 228976_at 65578
    1100847 229070_at 97411 C6orf105
    1100849 229072_at 184430
    1100851 229074_at 55058 EHD4
    1100871 229101_at 48353
    1100873 229103_at 445884
    1100879 229111_at 119983 MASP2
    1100904 229145_at 426296 LOC119504
    1100911 229152_at 320147 C4orf7
    1100916 229158_at 105448 PRKWNK4
    1100977 229233_at 444783 NRG3
    1100995 229256_at 26612 PGM2L1
    1101004 229265_at 2969 SKI
    1101023 229288_at 73962 EPHA7
    1101054 229322_at 173328 PPP2R5E
    1116432 229356_x_at 409362 KIAA1259
    1101096 229373_at 527236
    1101119 229401_at 390823 IL17RE
    1101128 229411_at 436667 MGC45419
    1116445 229436_x_at 301927 C6.1A
    1101149 229437_at 517226 BIC
    1101211 229513_at 287659 STRBP
    1101272 229584_at 179089 DKFZp434H2111
    1101276 229588_at 1098 ERdj5
    1101291 229606_at 272458 PPP3CA
    1101295 229610_at 99807 FLJ40629
    1101305 229623_at 112742
    1101322 229645_at 227699
    1101354 229686_at 111377 P2RY8
    1101416 229764_at 338851 FLJ41238
    1101430 229779_at 418040
    1101439 229790_at 63335 TERF2
    1101477 229838_at 423095 NUCB2
    1101478 229839_at 146246 MGC45780
    1101514 229886_at 88801 FLJ32363
    1101566 229947_at 98558
    1101582 229967_at 195685 CKLFSF2
    1101586 229971_at 187884 GPR114
    1101628 230021_at 441708 MGC45866
    1101634 230028_at 510588
    1101687 230086_at 440808 FNBP1
    1101708 230110_at 459526 MCOLN2
    1101758 230170_at 248156 OSM
    1101775 230191_at 343820 TTBK1
    1101777 230193_at 359981 MGC33630
    1101829 230252_at 155538 GPR92
    1101892 230327_at 225948
    1116593 230329_s_at 422889 NUDT6
    1101905 230345_at 170843
    1101944 230391_at 439064
    1101948 230395_at 14411
    1101974 230425_at 272311 EPHB1
    1102027 230489_at 58685 CD5
    1102030 230494_at 110855 SLC20A1
    1102081 230551_at 506977
    1102165 230650_at 152460
    1102193 230680_at 22668
    1102282 230788_at 934 GCNT2
    1116666 230803_s_at 442801 DKFZP564B1162
    1102350 230864_at 25845 MGC42105
    1116676 230894_s_at 185084 MSI2
    1102408 230934_at 306327 RAB3GAP
    1102415 230942_at 99272 CKLFSF5
    1102437 230966_at 437023 IL4I1
    1102470 231007_at 292915
    1102471 231008_at 158357 UNC5CL
    1102479 231017_at 301772 STK11
    1102537 231087_at 202151
    1102540 231093_at 434881 FCRH3
    1116715 231149_s_at 123427 FLJ20574
    1102633 231198_at 511124
    1102652 231219_at 343717 CKLFSF1
    1102654 231221_at 380599 KIAA0350
    1102725 231303_at 234016 C21orf42
    1102744 231324_at 198671
    1102821 231412_at 202024
    1102859 231455_at 446195
    1102885 231481_at 130310 CCNB3
    1102898 231496_at 145519 FKSG87
    1102912 231514_at 194610 MGC15882
    1103054 231690_at 341531
    1103107 231759_at 247978 TAL2
    1103111 231763_at 436896 RPC155
    1103120 231775_at 401745 TNFRSF10A
    1103124 231779_at 424542 IRAK2
    1103134 231792_at 86092 MYLK2
    1103137 231796_at 283613 EPHA8
    1103139 231798_at 248201 NOG
    1116826 231823_s_at 26204 KIAA1295
    1116829 231840_x_at 115467 LOC90624
    1103224 231906_at 301963 HOXD8
    1116844 231920_s_at 405789 CSNK1G1
    1103264 231954_at 142307 DKFZP434I0714
    1103272 231964_at 137206
    1103284 231978_at 186655 TPCN2
    1116854 231992_x_at 438623
    1103303 232000_at 49605 C9orf52
    1103304 232001_at 46919
    1116863 232068_s_at 174312 TLR4
    1103390 232103_at 271752 BPNT1
    1103398 232112_at 220745 FLJ10244
    1103420 232138_at 372571 MBNL2
    1116879 232160_s_at 325630 TNIP2
    1103475 232204_at 120785 EBF
    1103497 232231_at 50115
    1103504 232239_at 142517
    1103540 232282_at 92423 PRKWNK3
    1103639 232399_at 388304 KIAA1765
    1103711 232478_at 288718
    1103766 232546_at 192132 TP73
    1103855 232645_at 259625 LOC153684
    1103858 232648_at 246240 PSMA3
    1116958 232693_s_at 27410 PBF
    1103921 232724_at 371612 MS4A6A
    1103932 232741_at 31330
    1116966 232744_x_at 301124
    1103982 232798_at 142926 MGC26226
    1104072 232906_at 287429
    1104175 233029_at 287383 KIAA1639
    1104195 233052_at 172101 DNAH8
    1117023 233110_s_at 289052 BCL2L12
    1104254 233121_at 492700
    1104373 233271_at
    1104545 233476_at 254477
    1104552 233483_at 193857 LOC96597
    1104840 233867_at 482250
    1104870 233916_at 210958 KIAA1486
    1117211 233955_x_at 356509 HSPC195
    1104905 233964_at 13453 FLJ14753
    1104910 233969_at 458262 IGL@
    1105001 234088_at 527386
    1117245 234107_s_at 527974 HARS2
    1105178 234284_at 283961 GNG8
    1117278 234312_s_at 14779 ACAS2
    1117298 234366_x_at 449586
    1105248 234403_at
    1117343 234643_x_at 306812 BUCS1
    1117350 234672_s_at 435982 FLJ10407
    1117373 234725_s_at 416077 SEMA4B
    1117394 234792_x_at
    1117403 234863_x_at 272027 FBXO5
    1105668 234954_at
    1105684 234973_at 195155 SLC38A5
    1105728 235022_at 13034 MGC24180
    1105732 235026_at 396626 FLJ32549
    1105751 235046_at 176376
    1105759 235056_at 171262 ETV6
    1105798 235099_at 154986 CKLFSF8
    1105814 235117_at 105223
    1105832 235136_at 306777 GSDML
    1105838 235142_at 129837 ZBTB8
    1105842 235146_at 173392 KIAA1145
    1105854 235158_at 267245 FLJ14803
    1105866 235170_at 9521 ZNF92
    1105900 235211_at 525015
    1105915 235229_at 332649
    1105935 235251_at 444290
    1105936 235252_at 276238 KSR
    1105959 235278_at 399982
    1105986 235310_at 49614 GCET2
    1106013 235341_at 6019 DNAJC3
    1106015 235343_at 96885 FLJ12505
    1106025 235353_at 49500 KIAA0746
    1106030 235359_at 162185 UNQ3030
    1106043 235372_at 266331 FREB
    1106053 235383_at 154578 MYO7B
    1106088 235421_at 499235
    1106110 235444_at 235860 FOXP1
    1106124 235458_at 155111 HAVCR2
    1106126 235460_at 434937 PPIB
    1106159 235496_at 208081
    1106196 235536_at 142074
    1106204 235545_at 445098 SDP35
    1106230 235572_at 381225 Spc24
    1106279 235626_at 130065 CAMK1D
    1106306 235657_at 14204
    1106317 235668_at 381140 PRDM1
    1106323 235674_at 442690
    1106394 235750_at 126932
    1106401 235758_at 11849 MGC15827
    1106415 235774_at 169071
    1117517 235816_s_at 148656 Rgr
    1106478 235843_at 119898
    1106522 235890_at 31903
    1106589 235965_at 22627 MIST1
    1106722 236109_at 150458 FLJ14494
    1106781 236172_at 445013 LTB4R
    1106855 236255_at 455101 KIAA1909
    1117555 236295_s_at 128357 NOD3
    1106908 236313_at 72901 CDKN2B
    1106935 236341_at 247824 CTLA4
    1106990 236401_at 369561
    1107044 236458_at 163426
    1107076 236491_at 283672 BCL2L10
    1107124 236543_at 130203
    1107190 236614_at 50601 MGC10986
    1107197 236621_at 40838
    1107329 236761_at 439124 LHFPL3
    1107348 236782_at 440508 SAMD3
    1107369 236805_at 512466
    1107457 236901_at 120330 ADAMTS2
    1117599 236918_s_at 120277 MGC27085
    1107527 236981_at 14706
    1107575 237033_at 424589 MGC52498
    1107637 237104_at
    1107762 237244_at 58597
    1107838 237322_at 355618
    1117644 237451_x_at 34174
    1107997 237493_at 126891 IL22RA2
    1108088 237591_at 441601
    1108200 237710_at 156135
    1108237 237753_at 126232
    1108323 237849_at 526982
    1108347 237880_at 121476
    1108467 238018_at 346333 LOC285016
    1108473 238025_at 119878 FLJ34389
    1108515 238071_at 98132 LCN6
    1108745 238323_at 528776 TEAD2
    1117747 238365_s_at 158272
    1108776 238376_at 513346
    1108910 238536_at 351848
    1108925 238552_at 136102 KIAA0853
    1108961 238593_at 292088 FLJ22531
    1108970 238604_at 140489
    1108988 238624_at 3532 NLK
    1117800 238701_x_at 125166
    1109058 238706_at 220277 FLJ38499
    1109107 238759_at 292925 KIAA1212
    1109188 238846_at 204044 TNFRSF11A
    1109195 238853_at 416155
    1109210 238870_at 117010 KCNK9
    1109220 238880_at 445977 GTF3A
    1109505 239186_at 8162 MGC39372
    1109519 239201_at 348711 ALS2CR7
    1117835 239205_s_at 89688 CR1L
    1109530 239214_at 123244
    1109545 239231_at 63187
    1109557 239243_at 444548 NP220
    1109560 239246_at 207428 FARP1
    1109603 239292_at
    1109732 239427_at 374124
    1109756 239453_at 530304
    1117853 239479_x_at 268724
    1109827 239533_at 127196 GPR155
    1109913 239629_at 355724 CFLAR
    1110019 239744_at
    1110070 239803_at
    1110099 239835_at 116665 TA-KRP
    1110198 239946_at 189046
    1110214 239964_at 144519 TCL6
    1110223 239973_at 212709
    1110284 240038_at 192221 ELL2
    1110309 240066_at 105623
    1110313 240070_at 421750 FLJ39873
    1110486 240260_at 445054
    1110608 240392_at 306227 CARD14
    1110610 240394_at 436906
    1110740 240538_at 416810
    1110852 240661_at 196026
    1110871 240681_at 431753
    1117977 240854_x_at
    1111070 240899_at 202201
    1111478 241357_at 133017 ERK8
    1111486 241365_at 33024
    1111494 241373_at 75432 IMPDH2
    1111503 241383_at 502910 KBRAS2
    1111694 241592_at 157302
    1111807 241751_at 6483 OFD1
    1111946 241928_at 280881
    1112019 242013_at 196484
    1118148 242020_s_at 302123 ZBP1
    1112052 242052_at 525361
    1112061 242064_at 43410
    1112256 242293_at 143198 ING3
    1112344 242406_at 163242
    1118228 242520_s_at 173679
    1112510 242595_at 314432 C14orf20
    1112521 242611_at 244818
    1112552 242650_at 89029
    1112674 242794_at 310320 MAML3
    1112689 242814_at 104879 SERPINB9
    1118286 242866_x_at 147381
    1112762 242901_at 208179
    1112764 242903_at 180866 IFNGR1
    1112837 242994_at 4099 NRD1
    1112849 243006_at 208965
    1112871 243030_at 269493
    1112935 243099_at 436677 NFAM1
    1112981 243154_at 86650
    1113020 243198_at 373484 LOC161577
    1118347 243366_s_at 528404 ITGA4
    1113263 243467_at 435736
    1113435 243659_at 100636
    1113488 243717_at 129435
    1113500 243729_at 165900
    1113545 243780_at 435736
    1113555 243791_at 291993
    1113589 243829_at 162967 BRAF
    1118414 243968_x_at 415473 FCRH1
    1113730 243993_at 293771
    1113769 244035_at 46996
    1113783 244052_at 71616 FLJ14431
    1113930 244214_at 24725 MGC35521
    1113972 244261_at 386334 IL28RA
    1113993 244286_at 131811
    1114017 244313_at 133255
    1114064 244364_at 148228 MYO3A
    1114109 244413_at 203041 DCAL1
    1114162 244467_at 526942
    1114351 244677_at 445534 PER1
    1114503 244845_at 170577
    1114543 244887_at 156189
    1118612 32625_at
    1118621 33307_at
    1130354 33323_r_at 184510 SFN
    1118659 35617_at
    1118681 36711_at
    1118684 36830_at
    1118708 37408_at
    1118736 38340_at
    1118772 40420_at
    1130378 44783_s_at 234434 HEY1
    1118835 47069_at
    1118861 49878_at
    1130387 50314_i_at 274422 C20orf27
    1130393 58780_s_at 22451 FLJ10357
    1118939 60528_at
    1118573 632_at
    1118949 64064_at
    1118963 65472_at
    1130400 74694_s_at 170253 FRA
    1140788 AFFX-DapX-3_at
    1140834 AFFX-HSAC07/X00351_3_at 426930 ACTB
    1140835 AFFX-HSAC07/X00351_5_at 426930 ACTB
    1140836 AFFX-HSAC07/X00351_M_at 426930 ACTB
    1140842 AFFX-HUMGAPDH/M33197_3_at 169476 GAPD
    1140843 AFFX-HUMGAPDH/M33197_5_at 169476 GAPD
    1140844 AFFX-HUMGAPDH/M33197_M_at 169476 GAPD
    1140845 AFFX-HUMISGF3A/M97935_3_at 21486 STAT1
    1140846 AFFX-HUMISGF3A/M97935_5_at 21486 STAT1
    1140847 AFFX-HUMISGF3A/M97935_MA_at 21486 STAT1
    1140848 AFFX-HUMISGF3A/M97935_MB_at 21486 STAT1
    1140837 AFFX-HUMRGE/M10098_3_at
    1140838 AFFX-HUMRGE/M10098_5_at
    1140839 AFFX-HUMRGE/M10098_M_at
    1140791 AFFX-LysX-3_at
    1140792 AFFX-LysX-5_at
    1140793 AFFX-LysX-M_at
    1140806 AFFX-M27830_3_at
    1140807 AFFX-M27830_5_at
    1140808 AFFX-M27830_M_at
    1140794 AFFX-PheX-3_at
    1140795 AFFX-PheX-5_at
    1140796 AFFX-PheX-M_at
    1140797 AFFX-ThrX-3_at
    1140798 AFFX-ThrX-5_at
    1140799 AFFX-ThrX-M_at
    1140802 AFFX-TrpnX-3_at
    1140803 AFFX-TrpnX-5_at
    1140804 AFFX-TrpnX-M_at
    1140805 AFFX-hum_alu_at
    1140809 AFFX-r2-Bs-dap-3_at
    1140810 AFFX-r2-Bs-dap-5_at
    1140811 AFFX-r2-Bs-dap-M_at
    1140812 AFFX-r2-Bs-lys-3_at
    1140813 AFFX-r2-Bs-lys-5_at
    1140814 AFFX-r2-Bs-lys-M_at
    1140815 AFFX-r2-Bs-phe-3_at
    1140816 AFFX-r2-Bs-phe-5_at
    1140817 AFFX-r2-Bs-phe-M_at
    1140827 AFFX-r2-Bs-thr-3_s_at
    1140828 AFFX-r2-Bs-thr-5_s_at
    1140829 AFFX-r2-Bs-thr-M_s_at
    1140820 AFFX-r2-Ec-bioB-3_at
    1140821 AFFX-r2-Ec-bioB-5_at
    1140822 AFFX-r2-Ec-bioB-M_at
    1140823 AFFX-r2-Ec-bioC-3_at
    1140824 AFFX-r2-Ec-bioC-5_at
    1140825 AFFX-r2-Ec-bioD-3_at
    1140826 AFFX-r2-Ec-bioD-5_at
    1140818 AFFX-r2-P1-cre-3_at
    1140819 AFFX-r2-P1-cre-5_at
    1529284 Lymph_Dx_001_at 409515 MCC
    1529285 Lymph_Dx_002_at 348929 KIAA1219
    1529286 Lymph_Dx_003_at 167700 MADH5
    1529287 Lymph_Dx_004_s_at 212787 KIAA0303
    1529288 Lymph_Dx_005_at 13291 CCNG2
    1529443 Lymph_Dx_006_at 88886
    1529289 Lymph_Dx_007_at 96557
    1529290 Lymph_Dx_008_at 101761 N4BP3
    1529291 Lymph_Dx_009_at 104450
    1529292 Lymph_Dx_010_at
    1529293 Lymph_Dx_011_at 113117
    1529294 Lymph_Dx_011_s_at 113117
    1529295 Lymph_Dx_012_at 116441
    1529296 Lymph_Dx_013_at 122428
    1529444 Lymph_Dx_014_at 126905
    1529297 Lymph_Dx_015_at 132335
    1529298 Lymph_Dx_016_at 136707
    1529299 Lymph_Dx_017_at 444290
    1529300 Lymph_Dx_018_at 449608
    1529301 Lymph_Dx_019_at
    1529445 Lymph_Dx_020_at
    1529302 Lymph_Dx_021_at 67928 ELF3
    1529303 Lymph_Dx_022_at
    1529304 Lymph_Dx_022_s_at
    1529305 Lymph_Dx_023_at 173957
    1529306 Lymph_Dx_024_at 190043 MGC26706
    1529446 Lymph_Dx_025_at 190626
    1529307 Lymph_Dx_026_at 435736
    1529308 Lymph_Dx_027_x_at 193014
    1529309 Lymph_Dx_028_at 512797 HSH2
    1529310 Lymph_Dx_029_x_at 3136 PRKAG1
    1529311 Lymph_Dx_030_at 251214
    1529312 Lymph_Dx_031_s_at 255809
    1529313 Lymph_Dx_032_at 271998
    1529314 Lymph_Dx_033_at
    1529315 Lymph_Dx_034_at 530912
    1529316 Lymph_Dx_035_at 315241 ZNF198
    1529447 Lymph_Dx_036_at 291886
    1529317 Lymph_Dx_037_at
    1529318 Lymph_Dx_038_at 291954
    1529319 Lymph_Dx_039_at 103329 KIAA0970
    1529320 Lymph_Dx_040_at 309149
    1529321 Lymph_Dx_041_s_at 411311 IL24
    1529322 Lymph_Dx_042_x_at 514291
    1529323 Lymph_Dx_043_at
    1529324 Lymph_Dx_044_at 348264 GZMH
    1529325 Lymph_Dx_045_at
    1529326 Lymph_Dx_046_s_at 200063 HDAC7A
    1529327 Lymph_Dx_047_s_at 288986 SMN2
    1529328 Lymph_Dx_048_s_at 369056
    1529448 Lymph_Dx_049_at 369101
    1529329 Lymph_Dx_049_s_at 369101
    1529330 Lymph_Dx_050_at 259625 LOC153684
    1529331 Lymph_Dx_051_s_at 374126
    1529332 Lymph_Dx_052_at 140443 LOC134492
    1529333 Lymph_Dx_053_at 378849
    1529334 Lymph_Dx_054_at 529494
    1529335 Lymph_Dx_055_s_at 400872
    1529336 Lymph_Dx_056_at 405474 PTK2B
    1529337 Lymph_Dx_057_at 201864 C6orf166
    1529338 Lymph_Dx_058_s_at 284275 PAK2
    1529339 Lymph_Dx_059_s_at
    1529449 Lymph_Dx_060_s_at
    1529340 Lymph_Dx_061_at
    1529341 Lymph_Dx_062_at 153563 LY75
    1529342 Lymph_Dx_063_at
    1529343 Lymph_Dx_064_at 521948
    1529344 Lymph_Dx_065_at 317970 SERPINA11
    1529450 Lymph_Dx_066_at
    1529345 Lymph_Dx_067_s_at 443475
    1529346 Lymph_Dx_068_at 443935
    1529347 Lymph_Dx_069_at 444019
    1529348 Lymph_Dx_070_s_at 326392 SOS1
    1529349 Lymph_Dx_071_at 445500
    1529451 Lymph_Dx_072_at 396853 JMY
    1529350 Lymph_Dx_073_at 445884
    1529351 Lymph_Dx_074_s_at 445898
    1529352 Lymph_Dx_075_at 446195
    1529353 Lymph_Dx_076_at 446198
    1529354 Lymph_Dx_077_at 314623 BCL11A
    1529452 Lymph_Dx_078_at 422550 AIM1
    1529355 Lymph_Dx_079_at 370675
    1529356 Lymph_Dx_080_at 303775 C14orf170
    1529357 Lymph_Dx_081_at 444651
    1529358 Lymph_Dx_082_at 127178
    1529359 Lymph_Dx_083_at
    1529360 Lymph_Dx_084_at 443036
    1529453 Lymph_Dx_085_at 372679 FCGR3A
    1529361 Lymph_Dx_086_s_at 388681 HDAC3
    1529362 Lymph_Dx_087_at 329989 PLK1
    1529363 Lymph_Dx_088_at 311559 NOTCH1
    1529364 Lymph_Dx_089_at 526394 ATM
    1529365 Lymph_Dx_090_at 344088 TNFRSF13C
    1529366 Lymph_Dx_091_at
    1529367 Lymph_Dx_092_at
    1529368 Lymph_Dx_093_at
    1529369 Lymph_Dx_095_at
    1529370 Lymph_Dx_096_at
    1529371 Lymph_Dx_097_at
    1529372 Lymph_Dx_098_at
    1529373 Lymph_Dx_099_at
    1529374 Lymph_Dx_100_at
    1529454 Lymph_Dx_101_at
    1529375 Lymph_Dx_102_at
    1529376 Lymph_Dx_103_at
    1529377 Lymph_Dx_104_at
    1529378 Lymph_Dx_105_at
    1529455 Lymph_Dx_107_at
    1529379 Lymph_Dx_108_at
    1529380 Lymph_Dx_109_at
    1529381 Lymph_Dx_110_at
    1529382 Lymph_Dx_111_at 371468 CCND1
    1529383 Lymph_Dx_112_at 371468 CCND1
    1529456 Lymph_Dx_113_at 371468 CCND1
    1529384 Lymph_Dx_114_at 371468 CCND1
    1529385 Lymph_Dx_115_at 371468 CCND1
    1529386 Lymph_Dx_116_at 371468 CCND1
    1529387 Lymph_Dx_117_at 79241 BCL2
    1529388 Lymph_Dx_118_at 79241 BCL2
    1529389 Lymph_Dx_119_at 79241 BCL2
    1529390 Lymph_Dx_120_at 79241 BCL2
    1529391 Lymph_Dx_121_at 79241 BCL2
    1529392 Lymph_Dx_122_at 352338 ACVR1C
    1529393 Lymph_Dx_123_s_at 182081 KIAA1811
    1529394 Lymph_Dx_124_s_at 339846 LOC91807
    1529395 Lymph_Dx_125_at 403201
    1529396 Lymph_Dx_126_at 512897 MGC33182
    1529397 Lymph_Dx_127_s_at 406557 CLK4
    1529398 Lymph_Dx_128_at 293590 HSMDPKIN
    1529399 Lymph_Dx_129_at 256916 LOC203806
    1529457 Lymph_Dx_130_at 351818 GRK7
    1529400 Lymph_Dx_131_s_at 210697 HIPK4
    1529401 Lymph_Dx_132_at 399752 MAP4K3
    1529402 Lymph_Dx_133_at 375836 KSR2
    1529403 Lymph_Dx_134_s_at 511780 LMTK3
    1529404 Lymph_Dx_135_at 170610 MAP3K1
    1529405 Lymph_Dx_136_s_at 227489 SAST
    1529406 Lymph_Dx_137_s_at 409066 MYO3B
    1529458 Lymph_Dx_138_at 448468 NEK8
    1529407 Lymph_Dx_139_s_at 284275 PAK2
    1529408 Lymph_Dx_141_at 336929 PSKH2
    1529409 Lymph_Dx_142_s_at 351173 FLJ25006
    1529410 Lymph_Dx_143_s_at 380991 SNF1LK
    1529411 Lymph_Dx_144_at 80181 APEG1
    1529459 Lymph_Dx_145_at 411061 SRMS
    1529412 Lymph_Dx_146_at 512763 STK22C
    1529413 Lymph_Dx_147_at 232116 PRKWNK2
    1529414 Lymph_Dx_148_s_at 352370 MGC22688
    1529415 Lymph_Dx_149_at 369523 DKFZp686A17109
    1529416 Lymph_Dx_150_s_at 421349 CDKN2A
    1529417 Lymph_Dx_151_at 421349 CDKN2A
    1529418 Lymph_Dx_152_at 421349 CDKN2A
    1529419 Lymph_Dx_153_s_at 104182
    1529420 Lymph_Dx_154_at 272295 IL17F
    1529421 Lymph_Dx_156_at 375043 IL27
    1529422 Lymph_Dx_157_s_at 375184 IL23R
    1529423 Lymph_Dx_158_at 381264 ITGAD
    1529424 Lymph_Dx_159_s_at 512683 CCL3L1
    1529425 Lymph_Dx_160_at 406228 IL9R
    1529426 Lymph_Dx_162_at 406744 IL28B
    1529427 Lymph_Dx_163_at 406745 IL29
    1529428 Lymph_Dx_164_at 415768 NGFR
    1529429 Lymph_Dx_165_at 434103 IL17D
    1529430 Lymph_Dx_166_at 444484 SPHK2
    1529431 Lymph_Dx_167_at
    1529432 Lymph_Dx_168_at
    1529433 Lymph_Dx_168_x_at
    1529434 Lymph_Dx_171_at 103995 FLJ27099
    1529435 Lymph_Dx_172_s_at
    1529436 Lymph_Dx_174_at
    1529437 Lymph_Dx_175_at 445162 BTLA
  • TABLE 1724
    Number of
    Gene type genes
    Lymphoma predictor genes 1101
    Subtype specific 763
    Lymph node signature 178
    Proliferation signature 160
    Outcome predictor genes 171
    DLBCL 79
    FL 81
    MCL 11
    New genes not on U133 167
    Lymphochip lymphoma predictor genes 84
    EBV and HHV8 viral genes 18
    BCL-2/cyclin D1/INK4a specialty probes 14
    Named genes missing from U133 51
    Named genes 1121
    Protein kinase 440
    Interleukin 35
    Interleukin receptor 29
    Chemokine 51
    Chemokine receptor 29
    TNF family 26
    TNF receptor family 51
    Adhesion 45
    Surface marker 264
    Oncogene/tumor suppressor 49
    Apoptosis 46
    Drug target 10
    Regulatory 46
  • Cell samples representing various forms of human lymphoid malignancy were obtained by biopsy using known methods described in the literature. These 634 biopsy samples were reviewed by a panel of hematopathologists and classified into the following lymphoma types based on current diagnostic criteria:
      • 201 diffuse large B-cell lymphomas (DLBCL)
      • 191 follicular lymphomas (FL)
      • 60 Burkitt lymphomas (BL)
      • 21 mantle cell lymphomas (MCL)
      • 30 primary mediastinal B cell lymphoma (PMBL)
      • 18 follicular hyperplasias (FH)
      • 18 small cell lymphocytic lymphomas (SLL)
      • 17 mucosa-associated lymphoid tissue lymphomas (MALT), including 9 gastric MALTs (GMALT)
      • 16 chronic lymphocytic leukemias (CLL)
      • 13 splenic lymphomas (SPL)
      • 11 lymphoplasmacytic lymphomas (LPC)
      • 11 transformed DLBCL (trDLBCL) (DLBCL that arose from an antecedent FL)
      • 10 cyclin D1 negative lymphomas with MCL morphology (CD1N)
      • 6 peripheral T-cell lymphoma (PTCL)
      • 4 post-transplant lymphoproliferative disorders (PTLD)
      • 4 nodal marginal zone lymphomas (NMZ)
      • 3 lymphoblastic lymphomas (LBL)
  • Each of the 634 samples was given a unique sample ID number consisting of the lymphoma type followed by a unique numerical identifier. For example, “BL—2032—52748” refers to a Burkitt lymphoma sample with the numerical identifier 2032—52748. Cells were purified and RNA was isolated from the purified cells according to known methods described in the literature.
  • Aliquots of purified RNA from each sample were applied to the Lymph Dx microarrays according to standard Affymetrix microarray protocol. Each microarray was scanned on an Affymetrix scanner. This scanner produced an image of the microarray, which was then evaluated by Affymetrix MAS 5.0 software. This information was stored in tables in .txt format. Each of these .txt files was given a unique name consisting of the table number, the sample ID number (discussed above), and the UNIQID for identifying the array data in the National Cancer Institute Database. For example, Table—1725_BL—2032—52748.txt is the .txt file for Table 1725, which contains data for sample ID number BL—2032. The data for each sample analyzed is contained in Tables 1725-2358. The signal intensity for each probe on the microarray can be transformed into summary signal values for each probe set through a number of different algorithms, including but not limited to MAS 5.0, D-chip (Li 2001), or Bioconductor's RMA algorithms (Irizarry 2003).
    • Example 3 Development of a First FL Survival Predictor Using Gene Expression Data from Affymetrix U133A and U133B Microarrays
  • An analytical method entitled Survival Signature Analysis was developed to create survival prediction models for lymphoma. This method is summarized in FIG. 2. The key feature of this method is the identification of gene expression signatures. Survival Signature Analysis begins by identifying genes whose expression patterns are statistically associated with survival. A hierarchical clustering algorithm is then used to identify subsets of these genes with correlated expression patterns across the lymphoma samples. These subsets are operationally defined as “survival-associated signatures.” Evaluating a limited number of survival-associated signatures mitigates the multiple comparison problems that are inherent in the use of large-scale gene expression data sets to create statistical models of survival (Ransohoff 2004).
  • FL samples were divided into two equivalent groups: a training set (95 samples) for developing the survival prediction model, and a validation set (96 samples) for evaluating the reproducibility of the model. The overall survival of this cohort is depicted in FIG. 3. The median age at diagnosis was 51 years (ranging from 23 to 81 years), and the patients had a median follow-up of 6.6 years (8.1 years for survivors, with a range of <1 to 28.2 years). Gene expression data from Affymetrix U133A and U133B microarrays was obtained for each sample. Within the training set, a Cox proportional hazards model was used to identify “survival predictor” genes, which were genes whose expression levels were associated with long survival (good prognosis genes) or short survival (poor prognosis genes). A hierarchical clustering algorithm (Eisen 1998) was used to identify gene expression signatures within the good and poor prognosis genes according to their expression pattern across all samples. Ten gene expression signatures were observed within either the good prognosis or poor prognosis gene sets (FIG. 4). The expression level of every component gene in each of these ten gene expression signatures was averaged to create a gene expression signature value.
  • To create a multivariate model of survival, different combinations of the ten gene expression signature values were generated and evaluated for their ability to predict survival within the training set. Among models consisting of two signatures, an exceptionally strong statistical synergy was observed between one signature from the good prognosis group and one signature from the poor prognosis group. These signatures were deemed “immune response-1” and “immune response-2,” respectively, based on the biological function of certain genes within each signature. The immune response-1 gene expression signature included genes encoding T cell markers (e.g., CD7, CD8B1, ITK, LEF1, STAT4) and genes that are highly expressed in macrophages (e.g., ACTN1, TNFSF13B). The immune response-1 signature is not merely a surrogate for the number of T cells in the FL biopsy sample because many other standard T cell genes (e.g., CD2, CD4, LAT, TRIM, SH2D1A) were not associated with survival. The immune response-2 gene expression signature included genes known to be preferentially expressed in macrophages and/or dendritic cells (e.g., TLR5, FCGR1A, SEPT10, LGMN, C3AR1). Table 2359 lists the genes that were used to generate the gene expression signature values for the immune response-1 and immune response-2 signatures. The Unigene ID Build database referenced in the following tables is hosted by the hosted by the National Center for Biotechnology Information (NCBI) web site
  • TABLE 2359
    Unigene ID
    Signature UNIQID Build 167 Gene symbol
    Immune response-1 1095985 83883 TMEPAI
    Immune response-1 1096579 117339 HCST
    Immune response-1 1097255 380144
    Immune response-1 1097307 379754 LOC340061
    Immune response-1 1097329 528675 TEAD1
    Immune response-1 1097561 19221 C20orf112
    Immune response-1 1098152 377588 KIAA1450
    Immune response-1 1098405 362807 IL7R
    Immune response-1 1098548 436639 NFIC
    Immune response-1 1098893 43577 ATP8B2
    Immune response-1 1099053 376041
    Immune response-1 1100871 48353
    Immune response-1 1101004 2969 SKI
    Immune response-1 1103303 49605 C9orf52
    Immune response-1 1107713 171806
    Immune response-1 1115194 270737 TNFSF13B
    Immune response-1 1119251 433941 SEPW1
    Immune response-1 1119838 469951 GNAQ
    Immune response-1 1119924 32309 INPP1
    Immune response-1 1120196 173802 TBC1D4
    Immune response-1 1120267 256278 TNFRSF1B
    Immune response-1 1121313 290432 HOXB2
    Immune response-1 1121406 NA TNFSF12
    Immune response-1 1121720 80642 STAT4
    Immune response-1 1122956 113987 LGALS2
    Immune response-1 1123038 119000 ACTN1
    Immune response-1 1123092 437191 PTRF
    Immune response-1 1123875 428 FLT3LG
    Immune response-1 1124760 419149 JAM3
    Immune response-1 1128356 415792 C1RL
    Immune response-1 1128395 7188 SEMA4C
    Immune response-1 1132104 173802 TBC1D4
    Immune response-1 1133408 12802 DDEF2
    Immune response-1 1134069 405667 CD8B1
    Immune response-1 1134751 106185 RALGDS
    Immune response-1 1134945 81897 KIAA1128
    Immune response-1 1135743 299558 TNFRSF25
    Immune response-1 1135968 119000 ACTN1
    Immune response-1 1136048 299558 TNFRSF25
    Immune response-1 1136087 211576 ITK
    Immune response-1 1137137 195464 FLNA
    Immune response-1 1137289 36972 CD7
    Immune response-1 1137534 36972 CD7
    Immune response-1 1139339 47099 GALNT12
    Immune response-1 1139461 14770 BIN2
    Immune response-1 1140391 44865 LEF1
    Immune response-1 1140524 10784 C6orf37
    Immune response-1 1140759 298530 RAB27A
    Immune response-2 1118755 127826 EPOR
    Immune response-2 1118966 19196 LOC51619
    Immune response-2 1121053 1690 FGFBP1
    Immune response-2 1121267 334629 SLN
    Immune response-2 1121331 8980 TESK2
    Immune response-2 1121766 396566 MPP3
    Immune response-2 1121852 421391 LECT1
    Immune response-2 1122624 126378 ABCG4
    Immune response-2 1122679 232770 ALOXE3
    Immune response-2 1122770 66578 CRHR2
    Immune response-2 1123767 1309 CD1A
    Immune response-2 1123841 389 ADH7
    Immune response-2 1126097 498015
    Immune response-2 1126380 159408
    Immune response-2 1126628 254321 CTNNA1
    Immune response-2 1126836 414410 NEK1
    Immune response-2 1127277 121494 SPAM1
    Immune response-2 1127519 NA
    Immune response-2 1127648 285050
    Immune response-2 1128483 444359 SEMA4G
    Immune response-2 1128818 115830 HS3ST2
    Immune response-2 1129012 95497 SLC2A9
    Immune response-2 1129582 272236 C21orf77
    Immune response-2 1129658 58356 PGLYRP4
    Immune response-2 1129705 289368 ADAM19
    Immune response-2 1129867 283963 G6PC2
    Immune response-2 1130003 432799
    Immune response-2 1130388 19196 LOC51619
    Immune response-2 1131837 156114 PTPNS1
    Immune resppnse-2 1133843 6682 SLC7A11
    Immune response-2 1133949 502092 PSG9
    Immune response-2 1134447 417628 CRHR1
    Immune response-2 1135117 512646 PSG6
    Immune response-2 1136017 1645 CYP4A11
    Immune response-2 1137478 315235 ALDOB
    Immune response-2 1137745 26776 NTRK3
    Immune response-2 1137768 479985
    Immune response-2 1138476 351874 HLA-DOA
    Immune response-2 1138529 407604 CRSP2
    Immune response-2 1138601 149473 PRSS7
    Immune response-2 1139862 251383 CHST4
    Immune response-2 1140189 287369 IL22
    Immune response-2 1140389 22116 CDC14B
  • Although the immune response-1 and immune response-2 gene expression signatures taken individually were not ideal predictors of survival, the binary model formed by combining the two was more predictive of survival in the training set than any other binary model (p<0.001). Using this binary model as an anchor, other signatures were added to the model using a step up procedure (Drapner 1966). Of the remaining eight signatures, only one signature contributed significantly to the model in the training set (p<0.01), resulting in a three-variable model for survival. This model was associated with survival in a highly statistically significant fashion in both the training (p<0.001) and validation sets (p=0.003). However, only the immune response-1 and immune response-2 gene expression signatures contributed to the predictive power of the model in both the training set and the validation set. The predictive power of each of these signatures is summarized in Table 2360.
  • TABLE 2360
    Contribution of Relative risk of death
    signature to model in among patients in Effect of increased
    Gene expression validation set validation set expression on
    signature (p-value) (95% C.I.) survival
    Immune response-1 <0.001 0.15 (0.05-0.46) Favorable
    Immune response-2 <0.001 9.35 (3.02-28.9) Poor
  • Based on this information, the third signature was removed from the model and the two-signature model was used to generate a survival predictor score using the following equation:

  • Survival predictor score=[(2.71*immune response-2 gene expression signature value)]−[(2.36×immune response-1 gene expression signature value)].
  • A higher survival predictor score was associated with worse outcome. The two-signature model was associated with survival in a statistically significant fashion in both the training set (p<0.001) and the validation set (p<0.001), which demonstrated that the model was reproducible. For the 187 FL samples with available clinical data, the survival predictor score had a mean of 1.6 and a standard deviation of 0.894, with each unit increase in the predictor score corresponding to a 2.5 fold increase in the relative risk of death. Data for all 191 samples is shown in Table 2361.
  • TABLE 2361
    Immune Immune
    Length of Status at response-1 response-2 Survival
    Sample follow-up follow- signature signature predictor
    ID # Set (years) up value value score
    FL_1073 Training 7.68 Dead 9.20 8.67 1.77
    FL_1074 Training 4.52 Dead 9.10 8.57 1.74
    FL_1075 Validation 4.52 Dead 8.97 8.69 2.38
    FL_1076 Training 3.22 Dead 9.20 8.55 1.44
    FL_1077 Training 7.06 Alive 9.80 8.46 −0.20
    FL_1078 Training 4.95 Alive 9.32 8.23 0.30
    FL_1080 Training 6.05 Alive 9.45 8.94 1.93
    FL_1081 Validation 6.61 Alive 9.00 8.22 1.05
    FL_1083 Training 10.01 Alive 9.82 8.72 0.47
    FL_1085 Validation 8.84 Alive 9.31 8.58 1.29
    FL_1086 Validation 1.98 Dead 9.49 9.09 2.22
    FL_1087 Training 8.19 Alive 9.98 9.27 1.57
    FL_1088 Validation 5.30 Alive 9.22 8.47 1.20
    FL_1089 Training 10.72 Alive 9.42 8.35 0.40
    FL_1090 Validation 10.20 Alive 9.27 8.37 0.82
    FL_1097 Validation 8.79 Dead 9.87 8.92 0.87
    FL_1098 Validation 5.34 Dead 9.33 8.81 1.87
    FL_1099 Training 7.65 Alive 9.73 9.04 1.54
    FL_1102 Validation 13.20 Dead 9.45 8.89 1.79
    FL_1104 Training 8.42 Dead 9.30 8.27 0.48
    FL_1106 Validation 7.94 Alive 9.13 9.19 3.36
    FL_1107 Training 5.01 Dead 9.41 9.32 3.07
    FL_1183 Training 11.56 Dead 9.31 8.53 1.16
    FL_1184 Training 6.93 Dead 9.66 8.83 1.13
    FL_1185 Validation 7.02 Dead 9.23 9.09 2.86
    FL_1186 Training 1.34 Dead 9.01 8.84 2.68
    FL_1416 Validation 6.21 Alive 9.50 8.67 1.08
    FL_1417 Training 2.40 Dead 8.47 8.39 2.73
    FL_1418 Validation 3.59 Alive 8.94 8.42 1.72
    FL_1419 Training 3.85 Alive 9.82 8.56 0.03
    FL_1422 Training 5.72 Alive 9.46 8.49 0.68
    FL_1425 Validation 4.26 Alive 8.93 8.50 1.98
    FL_1426 Training 7.32 Alive 9.08 8.26 0.97
    FL_1427 Training 5.22 Alive 8.57 8.28 2.22
    FL_1428 Validation 5.41 Dead 9.22 8.44 1.10
    FL_1432 Training 3.66 Alive 9.22 8.95 2.51
    FL_1436 Training 9.08 Dead 9.48 8.63 1.02
    FL_1440 Training 7.85 Alive 9.07 8.35 1.22
    FL_1445 Training 9.24 Dead 8.67 8.66 3.01
    FL_1450 Validation 0.65 Dead 9.83 9.99 3.86
    FL_1472 Validation 16.72 Alive 8.85 8.49 2.10
    FL_1473 Training 15.07 Alive 9.75 8.50 0.02
    FL_1474 Validation 2.75 Dead 9.34 9.10 2.62
    FL_1476 Validation 4.08 Dead 9.51 8.87 1.60
    FL_1477 Training 0.59 Dead 9.64 9.06 1.83
    FL_1478 Training 12.47 Dead 9.60 8.87 1.39
    FL_1479 Training 2.29 Dead 8.71 9.07 4.01
    FL_1480 Training 16.29 Alive 9.40 8.67 1.30
    FL_1579 Training 8.22 Dead 8.81 8.44 2.10
    FL_1580 Training 19.30 Alive 9.58 8.52 0.49
    FL_1581 Training 9.52 Dead 9.08 9.02 3.00
    FL_1582 Validation 1.30 Dead 8.40 8.18 2.36
    FL_1583 Training 15.26 Dead 9.47 8.79 1.48
    FL_1584 Training 15.73 Dead 9.44 8.55 0.89
    FL_1585 Validation 0.01 Alive 8.96 8.53 1.96
    FL_1586 Validation 3.11 Alive 9.38 8.55 1.03
    FL_1588 Training 0.49 Dead 9.52 9.06 2.08
    FL_1589 Training 3.15 Alive 9.72 8.74 0.72
    FL_1591 Training 11.22 Alive 9.49 8.62 0.97
    FL_1594 Validation 11.19 Alive 9.25 8.59 1.47
    FL_1595 Training 8.03 Alive 9.75 9.60 3.01
    FL_1598 Validation 2.80 Dead 8.81 8.33 1.79
    FL_1599 Validation 6.17 Alive 9.48 8.65 1.06
    FL_1603 Training 5.17 Dead 9.66 9.75 3.63
    FL_1604 Training 3.98 Dead 9.24 8.86 2.20
    FL_1606 Validation 4.22 Dead 9.45 9.18 2.57
    FL_1607 Validation 8.12 Alive 9.40 8.60 1.13
    FL_1608 Validation 9.70 Alive 8.92 8.41 1.72
    FL_1610 Validation 2.05 Dead 9.33 9.35 3.32
    FL_1611 Validation 10.15 Alive 9.42 8.69 1.31
    FL_1616 Training 2.36 Dead 9.38 8.82 1.78
    FL_1617 Validation 7.85 Alive 8.96 8.49 1.87
    FL_1619 Validation 9.24 Dead 9.43 8.56 0.94
    FL_1620 Validation 9.36 Dead 9.14 8.35 1.04
    FL_1622 Training 14.01 Alive 9.23 8.53 1.33
    FL_1623 Training 9.72 Alive 9.67 8.93 1.38
    FL_1624 Validation 3.98 Dead 9.05 8.50 1.70
    FL_1625 Validation 11.16 Alive 8.98 8.47 1.75
    FL_1626 Validation 6.47 Dead 8.59 8.14 1.76
    FL_1628 Validation 0.82 Dead 9.80 8.72 0.51
    FL_1637 Validation 18.81 Alive 9.95 9.58 2.48
    FL_1638 Validation 4.06 Alive 9.13 8.88 2.51
    FL_1639 Training 4.75 Alive 9.53 8.89 1.62
    FL_1643 Training 0.77 Dead 9.73 9.06 1.58
    FL_1644 Validation 3.84 Alive 9.55 8.68 0.98
    FL_1645 Training 3.56 Alive 9.49 8.70 1.18
    FL_1646 Training 1.97 Dead 9.25 8.61 1.50
    FL_1647 Training 1.22 Dead 9.12 8.89 2.55
    FL_1648 Training 11.01 Alive 9.13 8.12 0.46
    FL_1652 Training 3.72 Dead 9.50 9.14 2.35
    FL_1654 Validation 0.30 Dead 8.74 8.28 1.82
    FL_1655 Training 8.45 Alive 9.51 8.85 1.53
    FL_1656 Validation 9.36 Alive 9.06 8.58 1.87
    FL_1657 Training 10.09 Alive 9.53 8.46 0.44
    FL_1660 Training 2.32 Alive 8.81 8.38 1.91
    FL_1661 Validation 1.48 Alive 9.86 8.90 0.85
    FL_1662 Validation 0.74 Dead 9.57 9.15 2.21
    FL_1664 Validation 4.53 Dead 9.34 8.62 1.31
    FL_1669 Training 4.40 Dead 8.87 8.58 2.30
    FL_1670 Training 1.88 Alive 9.64 9.45 2.86
    FL_1675 Training 4.57 Alive 9.36 8.46 0.84
    FL_1681 Validation 4.23 Alive 9.52 8.63 0.91
    FL_1683 Validation 4.03 Dead 9.95 9.10 1.19
    FL_1684 Training 2.88 Dead 9.53 8.73 1.18
    FL_1716 Validation 9.69 Alive 8.95 8.35 1.50
    FL_1717 Validation 2.01 Dead 9.35 8.88 1.98
    FL_1718 Training 10.35 Alive 9.23 8.13 0.26
    FL_1719 Validation 7.70 Dead 9.13 8.50 1.49
    FL_1720 Training 3.91 Dead 8.78 8.88 3.33
    FL_1729 Training 8.06 Alive 9.35 8.65 1.39
    FL_1732 Validation 0.71 Dead 7.81 8.59 4.86
    FL_1761 Validation 10.83 Alive 9.31 8.55 1.22
    FL_1764 Training 0.42 Dead 9.25 8.87 2.21
    FL_1768 Training 13.04 Alive 9.42 8.47 0.72
    FL_1771 Training 9.26 Dead 9.09 8.67 2.06
    FL_1772 Validation 13.64 Dead 9.49 8.49 0.61
    FL_1788 Training 1.00 Dead 9.09 9.13 3.29
    FL_1790 Training 1.42 Alive 9.85 9.40 2.22
    FL_1792 Validation 2.01 Dead 9.33 8.72 1.61
    FL_1795 Training 0.71 Dead 10.19 9.27 1.08
    FL_1797 Validation 7.17 Alive 9.34 8.92 2.14
    FL_1799 Training 14.18 Alive 9.32 8.63 1.38
    FL_1810 Validation 9.91 Alive 8.66 8.41 2.35
    FL_1811 Validation 3.04 Alive 9.38 8.27 0.29
    FL_1825 Training 2.98 Alive 9.46 9.07 2.25
    FL_1827 Training 3.66 Alive 9.80 8.84 0.83
    FL_1828 Validation 11.51 Alive 8.99 8.09 0.72
    FL_1829 Validation 4.11 Alive 9.57 8.73 1.08
    FL_1830 Validation 5.65 Dead 9.01 8.68 2.25
    FL_1833 Training 11.95 Alive 9.74 8.67 0.51
    FL_1834 Validation 15.92 Alive 9.22 8.72 1.88
    FL_1835 Validation 12.49 Alive 9.26 8.83 2.10
    FL_1836 Validation 12.24 Alive 9.55 8.64 0.85
    FL_1837 Validation 0.55 Dead 9.47 8.84 1.62
    FL_1838 Validation 2.54 Alive 9.90 9.12 1.34
    FL_1839 Training 4.48 Alive 8.56 8.32 2.34
    FL_1841 Training 0.88 Dead 9.32 9.10 2.66
    FL_1842 Validation 4.56 Alive 9.73 8.87 1.07
    FL_1844 Validation 13.39 Alive 9.41 8.55 0.98
    FL_1845 Training 12.92 Dead 9.89 9.04 1.16
    FL_1846 Validation 1.80 Dead 9.79 9.61 2.93
    FL_1848 Training 12.52 Alive 9.76 8.81 0.82
    FL_1851 Training 4.08 Dead 9.43 9.01 2.18
    FL_1853 Validation 12.50 Alive 9.28 8.54 1.25
    FL_1854 Validation 13.81 Alive 9.32 8.84 1.98
    FL_1855 Validation 9.96 Dead 9.31 8.39 0.75
    FL_1857 Validation 8.39 Dead 9.80 9.14 1.65
    FL_1861 Validation 3.19 Dead 9.47 8.57 0.88
    FL_1862 Validation 7.22 Dead 8.96 8.33 1.44
    FL_1863 Validation 10.77 Dead 9.31 8.85 2.00
    FL_1864 Training 14.25 Alive 9.98 9.12 1.17
    FL_1866 Training 10.72 Dead 9.93 8.94 0.79
    FL_1870 Validation 6.41 Dead 10.01 9.22 1.36
    FL_1873 Training 7.78 Dead 9.39 8.66 1.30
    FL_1874 Validation 3.15 Dead 9.38 8.74 1.53
    FL_1876 Validation 15.07 Alive 9.59 8.72 0.98
    FL_1879 Training 7.13 Dead 9.25 8.62 1.53
    FL_1880 Validation 12.84 Dead 8.82 8.35 1.82
    FL_1882 Training 8.84 Dead 9.43 8.76 1.49
    FL_1884 Validation 11.92 Dead 9.48 9.14 2.41
    FL_1885 Validation 15.49 Alive 9.70 8.85 1.11
    FL_1887 Training 5.14 Dead 9.47 8.57 0.87
    FL_1888 Training 15.08 Alive 9.83 8.97 1.11
    FL_1890 Training 3.03 Dead 9.29 9.05 2.60
    FL_1894 Training 11.37 Dead 9.01 8.64 2.13
    FL_1896 Training 12.03 Alive 9.80 8.56 0.08
    FL_1897 Training 9.63 Alive 9.02 8.33 1.29
    FL_1898 Training 5.20 Alive 8.82 8.25 1.54
    FL_1900 Validation 7.38 Alive 9.13 8.26 0.85
    FL_1903 Validation 28.25 Alive 9.07 8.46 1.54
    FL_1904 Validation 7.36 Alive 9.16 8.53 1.50
    FL_1905 Validation 3.68 Dead 9.25 8.38 0.87
    FL_1906 Training 2.35 Dead 8.04 8.69 4.56
    FL_1907 Validation 2.35 Dead 8.11 8.21 3.11
    FL_1910 Training 13.84 Alive 9.36 8.72 1.56
    FL_1912 Validation 0.73 Dead 9.30 9.21 3.02
    FL_1913 Training 2.57 Alive 9.77 8.51 0.01
    FL_1916 Validation 11.61 Alive 9.22 8.49 1.24
    FL_1918 Validation 9.95 Dead 9.54 8.77 1.26
    FL_1919 Training 10.84 Dead 9.51 8.81 1.44
    FL_735 Validation 11.05 Dead 8.81 8.23 1.53
    FL_738 Validation 10.15 Dead 9.19 8.79 2.13
    FL_739 Training 10.80 Dead 9.29 8.77 1.85
    FL_878 Validation 3.87 Dead 8.85 8.54 2.26
    FL_879 Training 4.34 Dead 8.95 8.74 2.56
    FL_886 Validation 3.29 Alive 9.43 8.72 1.40
    FL_888 Validation 1.32 Dead 8.76 8.49 2.34
    FL_1627 Training NA NA 9.60 8.51 0.40
    FL_1429 Training NA NA 8.69 8.28 1.93
    FL_1850 Validation NA NA 9.75 8.83 0.92
    FL_1735 Validation NA NA 7.32 8.30 5.24
  • In order to visualize the predictive power of the model, the FL samples were ranked according to their survival predictor scores and divided into four quartiles. Kaplan-Meier plots of overall survival showed clear differences in survival rate in the validation set (FIG. 5). The median survival for each of the four quartiles is set forth in Table 2362.
  • TABLE 2362
    Quartile Median survival (years)
    1 13.6
    2 11.1
    3 10.8
    4 3.9
  • Various clinical variables were found to be significantly associated with survival, including the IPI and some of its components and the presence of B-symptoms. The gene expression-based model was independent of each of these variables at predicting survival. These clinical variables and the relative risk of death associated with each are summarized in Table 2363.
  • TABLE 2363
    Multivariate (clinical
    Univariate (clinical variable + survival
    variable only) predictor score)
    relative risk of death relative risk of death
    % of % of among patients in among patients in
    patients1 patients1 validation set validation set
    Clinical Training Validation RR2 (95% RR2 (95%
    variable Criteria set set C.I.) p-value C.I.) p-value
    Age
    60  64.5 70.2 1.90 0.044 2.21 <0.001
    >60  35.5 29.8 (1.02-3.56) (1.48-3.29)
    Stage I-II 33.3 25 1.31 0.447 2.31 <0.001
    III-IV 66.7 75 (0.65-2.64) (1.51-3.52)
    Extranodal 2 5.4 20.2 1.58 0.163 2.21 <0.001
    sites (#) <2   94.6 79.8 (0.83-2.99) (1.48-3.30)
    LDH Normal 77.1 66.2 1.77 0.065 2.40 <0.001
    Greater than 22.9 33.8 (0.97-3.24) (1.57-3.67)
    normal
    ECOG
    2 9.4 12.5 2.05 0.090 2.17 <0.001
    performance <2   90.6 87.5 (0.89-4.71) (1.40-3.35)
    status
    Gender Male
    42 65 1.62 0.105 2.17 <0.001
    Female 58 35 (0.90-2.90) (1.45-3.25)
    B-symptoms Present 17.2 21.3 2.05 0.029 2.10 <0.001
    Absent 82.8 78.7 (1.08-3.89) (1.37-3.23)
    Grade 3 1 45 43.4 N/A 0.118 2.55 <0.001
    2 34.8 33.3 2.03 (1.63-3.99)
    (1.04-3.96)
    3 20.2 23.3 1.39
    (0.65-2.98)
    Int'l. Scores 0-1 63.1 47.5 N/A 0.029 2.28 <0.001
    Prognostic (1.46-3.57)
    Index4 Scores 2-3 33.3 45 2.07
    (1.07-4.00)
    Scores 4-5 3.6 7.5 3.73
    (1.18-11.18)
    1Due to rounding, percentages may not total 100
    2Relative risk of death (RR) based on 2-fold increase in expression
    3RR for grades 2 and 3 calculated with respect to risk of death for grade 1. The p-value is calculated for all grades.
    4RR for scores 2-3 and 4-5 calculated with respect to risk of death for scores 0-1. The p-value is calculated for all grades.
  • The samples in the validation set were divided into three groups based on their IPI score, and the relationship between survival and IPI score was visualized by Kaplan-Meier plot (FIG. 6). Among validation set samples from the low-risk (IPI 0-1) and intermediate risk (IPI 2-3) IPI groups, the gene-expression-based survival predictor could stratify patients into groups differing by more than 5 years with regards to median survival (FIG. 7). The high-risk IPI group (IPI 4-5) comprised less than 5% of the samples, and was omitted from this analysis. These results demonstrate that the gene expression-based model is not merely acting as a surrogate for clinical variables that are known to predict survival in FL, but rather it identifies distinct biological attributes of the tumors that are associated with survival.
    • Example 4 Development of a Second FL Survival Predictor Using Gene Expression Data from Affymetrix U133A and U133B Microarrays
  • 191 FL were divided into two equivalent groups: a training set (95 samples) for developing the survival prediction model, and a validation set (96 samples) for evaluating the reproducibility of the model. Gene expression data from Affymetrix U133A and U133B microarrays was obtained for each of the samples. A Cox proportional hazards model was used to identify survival predictor genes whose expression levels were associated with long survival (good prognosis genes) or short survival (poor prognosis genes) in the training set. The correlation between expression and survival for each gene on the microarrays is provided in the final two columns of Table 1710. The first of these two columns (“FL_Cox_coefficient”) provides a Cox coefficient indicating the extent to which a 2-fold increase in expression of a particular gene affects mortality. A positive Cox coefficient indicates increasing mortality with increasing expression of the gene, while a negative Cox coefficient indicates decreasing mortality with increasing expression of the gene. The second of these two columns provides a Cox p-value indicating the estimated probability that the increase or decrease in survival associated with the gene would occur by chance if there was no connection between the expression of the gene and survival.
  • A hierarchical clustering algorithm (Eisen 1998) was used to identify gene expression signatures within the good and poor prognosis genes according to their expression pattern across all samples. Eight clusters of coordinately regulated genes were observed within the good prognosis gene set and six clusters were observed in the poor prognosis gene sets. The expression level of every component gene in each of these gene expression signatures was averaged to create a gene expression signature value. After averaging, only ten of the gene expression signatures were found to be significantly associated with survival in the training set (p<0.01). To create a multivariate model of survival, different combinations of these ten gene expression signature averages were generated and evaluated for their ability to predict survival within the training set. Among models consisting of two signatures, an exceptionally strong statistical synergy was noted between one signature from the good prognosis group and one from the poor prognosis group. These gene expression signatures were termed “T-cell” and “macrophage” based on the biological function of certain genes within each signature. The T-cell gene expression signature included genes that were typically expressed in T-cells, while the macrophage gene expression signature included a number of genes typically expressed in macrophages. Although these two signatures taken individually were not the best predictors of survival, the binary model formed by combining the two was more predictive than any combination of three signatures that did not contain these two signatures. Using these two signatures as an anchor, other signatures were added to the model using a step up procedure (Drapner 1966). Only one of the remaining eight signatures, termed the B-cell differentiation signature, contributed significantly to the model in the training set (p=0.054). The B-cell differentiation signature included a number of genes that appear to be involved in B-cell signal transduction. Table 2364 lists the genes that were used to generate the gene expression signature values for the T-cell, macrophage, and B-cell differentiation gene expression signatures.
  • TABLE 2364
    Unigene ID
    Signature UNIQID Build 167 Gene symbol
    B-cell differentiation 1119350 331141 ALDH2
    B-cell differentiation 1130922 459987 ANP32B
    B-cell differentiation 1130923 459987 ANP32B
    B-cell differentiation 1099291 130774 C9orf105
    B-cell differentiation 1102859 446195 FLJ42418
    B-cell differentiation 1120976 245644 GCHFR
    B-cell differentiation 1098862 303669 MGC26694
    B-cell differentiation 1111070 202201
    B-cell differentiation 1105935
    B-cell differentiation 1139017 274424 NANS
    B-cell differentiation 1108988 3532 NLK
    B-cell differentiation 1114726 3532 NLK
    B-cell differentiation 1097897 266175 PAG
    B-cell differentiation 1097901 266175 PAG
    B-cell differentiation 1119813 155342 PRKCD
    B-cell differentiation 1123298 20191 SIAH2
    B-cell differentiation 1101439 63335 TERF2
    B-cell differentiation 1120316 63335 TERF2
    B-cell differentiation 1096035 105794 UGCGL1
    T-cell 1134945 81897 KIAA1128
    T-cell 1134069 405667 CD8B1
    T-cell 1137809 405667 CD8B1
    T-cell 1119251 433941 SEPW1
    T-cell 1096579 117339 HCST
    T-cell 1101004 2969 SKI
    T-cell 1137137 195464 FLNA
    T-cell 1100871 48353
    T-cell 1139461 14770 BIN2
    T-cell 1128395 7188 SEMA4C
    T-cell 1119880 442844 FMOD
    T-cell 1130676 194431 KIAA0992
    T-cell 1130668 194431 KIAA0992
    T-cell 1135968 119000 ACTN1
    T-cell 1097329 528675 TEAD1
    T-cell 1098548 436639 NFIC
    T-cell 1123038 119000 ACTN1
    T-cell 1128356 415792 C1RL
    T-cell 1133408 12802 DDEF2
    T-cell 1140524 10784 C6orf37
    T-cell 1119838 469951 GNAQ
    T-cell 1097255 380144
    T-cell 1098152 377588 KIAA1450
    T-cell 1115194 270737 TNFSF13B
    T-cell 1124760 419149 JAM3
    T-cell 1120267 256278 TNFRSF1B
    T-cell 1137289 36972 CD7
    T-cell 1137534 36972 CD7
    T-cell 1097307 379754 LOC340061
    T-cell 1123613 97087 CD3Z
    T-cell 1121720 80642 STAT4
    T-cell 1120196 173802 TBC1D4
    T-cell 1136087 211576 ITK
    T-cell 1132104 173802 TBC1D4
    T-cell 1140391 44865 LEF1
    T-cell 1098405 362807 IL7R
    T-cell 1135743 299558 TNFRSF25
    T-cell 1136048 299558 TNFRSF25
    T-cell 1123875 428 FLT3LG
    T-cell 1098893 43577 ATP8B2
    T-cell 1097561 19221 C20orf112
    T-cell 1122956 113987 LGALS2
    T-cell 1121406 TNFSF12
    T-cell 1125532
    T-cell 1138538 2014 TRD
    T-cell 1103303 49605 C9orf52
    T-cell 1119924 32309 INPP1
    Macrophage 1123682 114408 TLR5
    Macrophage 1099124 355455 SEPT10
    Macrophage 1123401 50130 NDN
    Macrophage 1134379 150833 C4A
    Macrophage 1137481 150833 C4A
    Macrophage 1132220 448805 GPRC5B
    Macrophage 1119400 181046 DUSP3
    Macrophage 1131119 349656 SCARB2
    Macrophage 1123566 155935 C3AR1
    Macrophage 1138443 77424 FCGR1A
    Macrophage 1127943 9641 C1QA
    Macrophage 1119998 8986 C1QB
    Macrophage 1132433 14732 ME1
    Macrophage 1119260 18069 LGMN
    Macrophage 1098278 166017 MITF

    The three signatures were used to generate a survival predictor score using the following equation:

  • Survival predictor score=[2.053*(macrophage gene expression signature value)]−[2.344*(T-cell gene expression signature value)]−[0.729*(B-cell differentiation gene expression signature value)].
  • A higher survival predictor score was associated with worse outcome. According to a likelihood ratio test adjusted for the number of variables included, this model was significant in predicting survival in both the training set (p=1.8×10−8) and the validation set (p=2.0×10−5). For the 187 FL samples with available clinical data, the survival predictor score had a mean of −11.9 and a standard deviation of 0.9418, with each unit increase in the predictor score corresponding to a 2.5 fold increase in the relative risk of death. Data for all 191 samples is shown in Table 2365.
  • TABLE 2365
    B cell dif- Macro-
    ferentiation T-cell phage sig- Survival
    Sample signature signature nature predictor
    ID # Set value value value score
    FL_1073 Training 9.70 9.14 8.58 −10.89
    FL_1074 Training 11.11 9.06 8.52 −11.84
    FL_1075 Validation 11.23 8.92 8.75 −11.15
    FL_1076 Training 10.02 9.21 8.59 −11.25
    FL_1077 Training 9.94 9.77 8.44 −12.82
    FL_1078 Training 10.67 9.32 8.21 −12.76
    FL_1080 Training 10.62 9.44 8.88 −11.64
    FL_1081 Validation 10.38 9.00 8.09 −12.04
    FL_1083 Training 10.29 9.77 8.74 −12.47
    FL_1085 Validation 9.87 9.24 8.43 −11.55
    FL_1086 Validation 10.03 9.50 9.02 −11.06
    FL_1087 Training 9.83 9.98 9.37 −11.31
    FL_1088 Validation 10.57 9.21 8.29 −12.27
    FL_1089 Training 10.30 9.38 8.27 −12.53
    FL_1090 Validation 9.74 9.24 8.20 −11.93
    FL_1097 Validation 9.57 9.82 8.80 −11.93
    FL_1098 Validation 11.08 9.40 8.97 −11.69
    FL_1099 Training 10.23 9.70 9.12 −11.46
    FL_1102 Validation 9.66 9.46 8.90 −10.93
    FL_1104 Training 10.72 9.19 8.20 −12.53
    FL_1106 Validation 11.11 9.17 9.57 −9.96
    FL_1107 Training 9.70 9.42 9.55 −9.54
    FL_1183 Training 9.85 9.25 8.44 −11.54
    FL_1184 Training 10.12 9.57 8.86 −11.63
    FL_1185 Validation 10.75 9.21 9.13 −10.68
    FL_1186 Training 9.76 8.88 8.83 −9.80
    FL_1416 Validation 9.94 9.45 8.59 −11.77
    FL_1417 Training 10.12 8.53 8.43 −10.08
    FL_1418 Validation 9.35 8.86 8.27 −10.59
    FL_1419 Training 10.20 9.76 8.53 −12.81
    FL_1422 Training 10.22 9.48 8.40 −12.43
    FL_1425 Validation 9.61 8.89 8.58 −10.23
    FL_1426 Training 10.80 9.06 8.13 −12.41
    FL_1427 Training 10.27 8.56 8.13 −10.87
    FL_1428 Validation 10.76 9.25 8.38 −12.32
    FL_1432 Training 10.51 9.17 9.04 −10.59
    FL_1436 Training 9.69 9.40 8.61 −11.42
    FL_1440 Training 9.82 9.04 8.21 −11.50
    FL_1445 Training 9.24 8.69 8.62 −9.41
    FL_1450 Validation 9.70 9.88 10.37 −8.93
    FL_1472 Validation 10.78 8.96 8.51 −11.40
    FL_1473 Training 9.99 9.70 8.41 −12.75
    FL_1474 Validation 10.21 9.27 9.05 −10.59
    FL_1476 Validation 9.82 9.44 8.78 −11.27
    FL_1477 Training 9.32 9.61 9.03 −10.78
    FL_1478 Training 10.19 9.60 8.81 −11.83
    FL_1479 Training 10.69 8.78 9.09 −9.71
    FL_1480 Training 10.10 9.42 8.70 −11.57
    FL_1579 Training 10.15 8.82 8.24 −11.15
    FL_1580 Training 10.31 9.59 8.50 −12.54
    FL_1581 Training 9.91 8.96 9.05 −9.66
    FL_1582 Validation 9.73 8.31 8.06 −10.03
    FL_1583 Training 10.95 9.45 8.86 −11.95
    FL_1584 Training 9.98 9.38 8.46 −11.89
    FL_1585 Validation 10.53 8.88 8.46 −11.11
    FL_1586 Validation 10.00 9.30 8.42 −11.81
    FL_1588 Training 9.59 9.41 8.94 −10.68
    FL_1589 Training 10.29 9.68 8.73 −12.27
    FL_1591 Training 10.44 9.45 8.56 −12.18
    FL_1594 Validation 10.01 9.25 8.56 −11.41
    FL_1595 Training 9.61 9.75 9.65 −10.07
    FL_1598 Validation 11.18 8.80 8.31 −11.71
    FL_1599 Validation 10.55 9.48 8.60 −12.24
    FL_1603 Training 9.40 9.60 9.77 −9.31
    FL_1604 Training 9.92 9.21 8.90 −10.54
    FL_1606 Validation 9.87 9.45 9.17 −10.52
    FL_1607 Validation 9.76 9.37 8.50 −11.63
    FL_1608 Validation 9.92 8.90 8.39 −10.85
    FL_1610 Validation 10.02 9.38 9.74 −9.30
    FL_1611 Validation 10.18 9.41 8.69 −11.64
    FL_1616 Training 9.62 9.33 8.85 −10.71
    FL_1617 Validation 9.90 8.95 8.39 −10.98
    FL_1619 Validation 9.98 9.37 8.47 −11.85
    FL_1620 Validation 9.43 8.95 8.12 −11.19
    FL_1622 Training 9.84 9.15 8.31 −11.56
    FL_1623 Training 9.95 9.61 8.97 −11.37
    FL_1624 Validation 10.55 9.06 8.43 −11.61
    FL_1625 Validation 10.00 8.89 8.23 −11.22
    FL_1626 Validation 11.05 8.62 8.10 −11.62
    FL_1628 Validation 10.08 9.81 8.66 −12.57
    FL_1637 Validation 9.77 9.95 9.59 −10.76
    FL_1638 Validation 10.25 9.20 9.07 −10.41
    FL_1639 Training 10.29 9.52 8.99 −11.35
    FL_1643 Training 9.80 9.72 9.00 −11.46
    FL_1644 Validation 9.51 9.46 8.61 −11.43
    FL_1645 Training 9.39 9.46 8.70 −11.15
    FL_1646 Training 9.90 9.25 8.52 −11.42
    FL_1647 Training 9.51 9.12 8.95 −9.92
    FL_1648 Training 10.02 9.18 7.86 −12.67
    FL_1652 Training 9.62 9.39 9.19 −10.16
    FL_1654 Validation 10.32 8.59 8.10 −11.02
    FL_1655 Training 10.12 9.53 8.75 −11.74
    FL_1656 Validation 10.54 9.08 8.55 −11.42
    FL_1657 Training 10.53 9.53 8.55 −12.46
    FL_1660 Training 10.24 8.75 8.27 −10.99
    FL_1661 Validation 10.08 9.85 9.00 −11.97
    FL_1662 Validation 9.85 9.56 9.49 −10.11
    FL_1664 Validation 10.16 9.35 8.48 −11.92
    FL_1669 Training 9.48 8.76 8.28 −10.45
    FL_1670 Training 9.76 9.66 9.66 −9.92
    FL_1675 Training 10.57 9.28 8.41 −12.18
    FL_1681 Validation 10.48 9.52 8.66 −12.19
    FL_1683 Validation 9.88 9.92 9.07 −11.83
    FL_1684 Training 9.64 9.53 8.85 −11.20
    FL_1716 Validation 9.90 8.91 8.22 −11.23
    FL_1717 Validation 9.87 9.34 8.95 −10.71
    FL_1718 Training 10.00 9.21 7.98 −12.49
    FL_1719 Validation 9.87 9.06 8.42 −11.14
    FL_1720 Training 10.70 8.77 8.92 −10.05
    FL_1729 Training 10.50 9.23 8.65 −11.53
    FL_1732 Validation 9.91 7.68 8.54 −7.69
    FL_1761 Validation 9.81 9.22 8.39 −11.54
    FL_1764 Training 9.81 9.24 8.77 −10.80
    FL_1768 Training 10.12 9.36 8.50 −11.86
    FL_1771 Training 9.92 9.12 8.68 −10.79
    FL_1772 Validation 9.72 9.42 8.43 −11.87
    FL_1788 Training 9.65 9.05 9.12 −9.51
    FL_1790 Training 9.58 9.83 9.48 −10.56
    FL_1792 Validation 9.79 9.29 8.67 −11.11
    FL_1795 Training 9.58 10.18 9.33 −11.69
    FL_1797 Validation 9.93 9.26 8.79 −10.90
    FL_1799 Training 10.49 9.28 8.64 −11.65
    FL_1810 Validation 10.06 8.55 8.21 −10.52
    FL_1811 Validation 9.84 9.37 8.08 −12.56
    FL_1825 Training 10.49 9.44 9.03 −11.24
    FL_1827 Training 10.06 9.76 8.84 −12.08
    FL_1828 Validation 10.55 8.93 7.67 −12.87
    FL_1829 Validation 9.85 9.58 8.65 −11.87
    FL_1830 Validation 10.80 8.99 8.67 −11.15
    FL_1833 Training 10.41 9.83 8.82 −12.52
    FL_1834 Validation 10.81 9.25 8.63 −11.85
    FL_1835 Validation 9.36 9.25 8.91 −10.21
    FL_1836 Validation 10.58 9.58 8.61 −12.50
    FL_1837 Validation 10.22 9.47 8.76 −11.68
    FL_1838 Validation 10.51 9.89 9.19 −11.98
    FL_1839 Training 10.79 8.54 8.19 −11.09
    FL_1841 Training 10.32 9.31 9.18 −10.48
    FL_1842 Validation 10.36 9.69 8.92 −11.95
    FL_1844 Validation 10.92 9.43 8.49 −12.65
    FL_1845 Training 9.87 9.87 9.06 −11.73
    FL_1846 Validation 9.66 9.81 9.93 −9.63
    FL_1848 Training 9.82 9.74 8.70 −12.14
    FL_1851 Training 9.89 9.47 9.03 −10.87
    FL_1853 Validation 9.96 9.28 8.54 −11.49
    FL_1854 Validation 9.97 9.29 8.73 −11.12
    FL_1855 Validation 9.95 9.33 8.42 −11.85
    FL_1857 Validation 10.35 9.81 9.28 −11.50
    FL_1861 Validation 9.73 9.46 8.43 −11.96
    FL_1862 Validation 10.42 8.94 8.22 −11.69
    FL_1863 Validation 10.79 9.29 8.82 −11.54
    FL_1864 Training 9.67 9.97 9.07 −11.80
    FL_1866 Training 10.19 9.88 8.89 −12.33
    FL_1870 Validation 9.78 10.07 9.30 −11.63
    FL_1873 Training 10.09 9.41 8.77 −11.40
    FL_1874 Validation 10.05 9.33 8.69 −11.37
    FL_1876 Validation 10.15 9.59 8.67 −12.08
    FL_1879 Training 9.73 9.21 8.58 −11.06
    FL_1880 Validation 10.02 8.79 8.35 −10.77
    FL_1882 Training 9.59 9.44 8.80 −11.05
    FL_1884 Validation 9.76 9.51 9.26 −10.38
    FL_1885 Validation 10.48 9.66 8.75 −12.32
    FL_1887 Training 9.98 9.42 8.47 −11.96
    FL_1888 Training 9.73 9.83 8.99 −11.67
    FL_1890 Training 10.06 9.33 8.98 −10.76
    FL_1894 Training 9.85 8.99 8.75 −10.29
    FL_1896 Training 10.21 9.80 8.51 −12.94
    FL_1897 Training 10.67 8.99 8.26 −11.90
    FL_1898 Training 9.59 8.77 8.21 −10.68
    FL_1900 Validation 10.12 9.10 8.10 −12.08
    FL_1903 Validation 11.08 8.99 8.39 −11.93
    FL_1904 Validation 10.20 9.16 8.30 −11.87
    FL_1905 Validation 9.73 9.21 8.22 −11.80
    FL_1906 Training 9.95 8.15 8.44 −9.01
    FL_1907 Validation 10.12 7.95 7.99 −9.62
    FL_1910 Training 11.03 9.38 8.74 −12.10
    FL_1912 Validation 9.83 9.38 9.36 −9.95
    FL_1913 Training 9.81 9.75 8.43 −12.69
    FL_1916 Validation 9.83 9.18 8.40 −11.43
    FL_1918 Validation 9.86 9.52 8.79 −11.45
    FL_1919 Training 9.87 9.53 8.79 −11.48
    FL_735 Validation 10.48 8.73 8.23 −11.20
    FL_738 Validation 11.05 9.10 8.75 −11.43
    FL_739 Training 9.66 9.25 8.74 −10.78
    FL_878 Validation 10.61 8.92 8.65 −10.89
    FL_879 Training 9.92 8.94 8.78 −10.14
    FL_886 Validation 10.16 9.41 8.63 −11.73
    FL_888 Validation 9.35 8.76 8.38 −10.15
    FL_1627 Training 9.82 9.48 8.49 −11.94
    FL_1429 Training 10.06 8.70 8.14 −11.01
    FL_1850 Validation 9.58 9.73 8.70 −11.93
    FL_1735 Validation 9.60 7.46 8.42 −7.19
  • In order to visualize the predictive power of the model, the FL samples were ranked according to their survival predictor scores and divided into four quartiles. Kaplan-Meier plots of overall survival showed clear differences in survival rate in the validation set (FIG. 8). The median survival for each of the four quartiles is set forth in Table 2366.
  • TABLE 2366
    Median 5-year 10-year
    Quartile survival (yrs.) survival survival
    1 NR 94% 79%
    2 11.6 82% 62%
    3 8.8 69% 39%
    4 3.9 38% 22%
    • Example 5 Development of a Third FL Survival Predictor Using Gene Expression Data from the Lymph Dx Microarray
  • 191 FL samples were divided into two equivalent groups: a training set for developing the survival prediction model, and a validation set for evaluating the reproducibility of the model. Gene expression data from the Lymph Dx microarray was obtained for those genes listed in Table 2364, above. This gene expression data was used to calculate gene expression signature values for the macrophage, T-cell, and B-cell differentiation gene expression signatures, and these signature values were used to generate a survival predictor score using the following equation:

  • Survival predictor score=[1.51*(macrophage gene expression signature value)]−[2.11*(T-cell gene expression signature value)]−[0.505*(B-cell differentiation gene expression signature value)].
  • A higher survival predictor score was associated with worse outcome. For the 187 FL samples with available clinical data, the survival predictor score had a mean of −10.1 and a standard deviation of 0.69, with each unit increase in the predictor score corresponding to a 2.7 fold increase in the relative risk of death. Data for all 191 samples is shown in Table 2367.
  • TABLE 2367
    B cell dif- Macro-
    ferentiation T-cell phage sig- Survival
    Sample signature signature nature predictor
    ID # Set value value value score
    FL_1073 Training 8.26 8.17 7.36 −10.30
    FL_1074 Training 9.53 8.12 7.56 −10.53
    FL_1075 Validation 9.81 8.00 7.99 −9.77
    FL_1076 Training 8.46 8.10 7.62 −9.86
    FL_1077 Training 8.45 8.66 7.32 −11.49
    FL_1078 Training 9.23 8.32 7.32 −11.18
    FL_1080 Training 9.18 8.37 7.86 −10.42
    FL_1081 Validation 8.96 8.01 6.94 −10.96
    FL_1083 Training 8.72 8.65 7.89 −10.75
    FL_1085 Validation 8.34 8.17 7.54 −10.07
    FL_1086 Validation 8.50 8.35 7.94 −9.94
    FL_1087 Training 8.02 8.88 8.48 −10.00
    FL_1088 Validation 9.10 8.15 7.38 −10.65
    FL_1089 Training 8.76 8.31 7.35 −10.86
    FL_1090 Validation 8.18 8.23 7.43 −10.28
    FL_1097 Validation 8.07 8.81 7.90 −10.73
    FL_1098 Validation 9.53 8.30 8.09 −10.11
    FL_1099 Training 8.44 8.56 8.26 −9.86
    FL_1102 Validation 7.92 8.43 7.94 −9.80
    FL_1104 Training 9.17 8.07 7.21 −10.78
    FL_1106 Validation 9.71 8.15 8.77 −8.85
    FL_1107 Training 8.16 8.44 8.60 −8.95
    FL_1183 Training 8.49 8.15 7.23 −10.56
    FL_1184 Training 8.81 8.49 7.91 −10.43
    FL_1185 Validation 9.31 8.19 8.06 −9.80
    FL_1186 Training 8.43 7.87 7.83 −9.04
    FL_1416 Validation 8.42 8.34 7.63 −10.34
    FL_1417 Training 8.65 7.51 7.05 −9.58
    FL_1418 Validation 7.96 7.82 7.22 −9.62
    FL_1419 Training 8.80 8.71 7.55 −11.43
    FL_1422 Training 8.63 8.35 7.39 −10.83
    FL_1425 Validation 8.21 7.92 7.62 −9.36
    FL_1426 Training 9.39 8.09 7.15 −11.01
    FL_1427 Training 8.66 7.51 7.00 −9.65
    FL_1428 Validation 9.33 8.18 7.39 −10.81
    FL_1432 Training 8.98 8.17 7.93 −9.81
    FL_1436 Training 8.04 8.17 7.35 −10.20
    FL_1440 Training 8.29 7.82 7.15 −9.89
    FL_1445 Training 8.04 7.78 7.63 −8.94
    FL_1450 Validation 8.25 8.81 9.52 −8.39
    FL_1472 Validation 9.29 7.88 7.33 −10.26
    FL_1473 Training 8.49 8.57 7.52 −11.03
    FL_1474 Validation 8.59 8.09 8.53 −8.54
    FL_1476 Validation 8.25 8.39 7.71 −10.23
    FL_1477 Training 7.94 8.57 7.88 −10.21
    FL_1478 Training 8.57 8.40 7.88 −10.16
    FL_1479 Training 9.15 7.83 7.87 −9.27
    FL_1480 Training 8.25 8.38 7.44 −10.63
    FL_1579 Training 8.70 7.73 7.43 −9.48
    FL_1580 Training 8.86 8.46 7.64 −10.79
    FL_1581 Training 8.41 7.89 8.08 −8.69
    FL_1582 Validation 8.20 7.42 6.99 −9.24
    FL_1583 Training 9.34 8.34 7.94 −10.32
    FL_1584 Training 8.50 8.33 7.75 −10.17
    FL_1585 Validation 9.08 7.96 7.72 −9.72
    FL_1586 Validation 8.52 8.25 7.36 −10.61
    FL_1588 Training 7.97 8.35 7.73 −9.98
    FL_1589 Training 8.85 8.48 7.76 −10.66
    FL_1591 Training 8.92 8.36 7.77 −10.42
    FL_1594 Validation 8.54 8.22 7.74 −9.96
    FL_1595 Training 8.05 8.82 8.68 −9.57
    FL_1598 Validation 9.74 7.81 6.97 −10.88
    FL_1599 Validation 9.13 8.42 7.69 −10.77
    FL_1603 Training 7.97 8.66 8.90 −8.86
    FL_1604 Training 8.47 8.14 7.75 −9.75
    FL_1606 Validation 8.34 8.32 8.11 −9.51
    FL_1607 Validation 8.33 8.30 7.39 −10.57
    FL_1608 Validation 8.35 7.88 6.98 −10.31
    FL_1610 Validation 8.48 8.35 8.86 −8.52
    FL_1611 Validation 8.54 8.33 7.64 −10.37
    FL_1616 Training 8.03 8.39 7.67 −10.18
    FL_1617 Validation 8.30 7.85 7.52 −9.40
    FL_1619 Validation 8.53 8.31 7.64 −10.32
    FL_1620 Validation 8.09 7.99 7.17 −10.11
    FL_1622 Training 8.14 8.10 7.36 −10.09
    FL_1623 Training 8.45 8.52 8.15 −9.93
    FL_1624 Validation 9.13 8.12 7.46 −10.49
    FL_1625 Validation 8.53 7.94 7.17 −10.23
    FL_1626 Validation 9.63 7.67 7.17 −10.22
    FL_1628 Validation 8.63 8.76 7.95 −10.86
    FL_1637 Validation 8.07 8.81 8.79 −9.38
    FL_1638 Validation 8.52 8.18 8.19 −9.18
    FL_1639 Training 8.70 8.33 7.89 −10.06
    FL_1643 Training 8.26 8.62 8.01 −10.26
    FL_1644 Validation 8.28 8.33 7.77 −10.02
    FL_1645 Training 7.84 8.32 7.68 −9.91
    FL_1646 Training 8.40 8.26 7.71 −10.01
    FL_1647 Training 8.10 8.04 7.92 −9.10
    FL_1648 Training 8.33 8.08 6.87 −10.90
    FL_1652 Training 8.15 8.33 8.37 −9.07
    FL_1654 Validation 8.67 7.62 7.03 −9.85
    FL_1655 Training 8.53 8.41 7.75 −10.36
    FL_1656 Validation 9.09 8.09 7.62 −10.16
    FL_1657 Training 8.95 8.44 7.58 −10.89
    FL_1660 Training 8.82 7.79 7.26 −9.93
    FL_1661 Validation 8.56 8.79 8.17 −10.53
    FL_1662 Validation 8.30 8.47 8.69 −8.93
    FL_1664 Validation 8.62 8.23 7.56 −10.31
    FL_1669 Training 7.89 7.67 7.39 −9.02
    FL_1670 Training 8.01 8.54 8.64 −9.03
    FL_1675 Training 9.00 8.21 7.36 −10.76
    FL_1681 Validation 8.83 8.39 7.59 −10.72
    FL_1683 Validation 8.14 8.85 7.97 −10.74
    FL_1684 Training 7.99 8.42 7.84 −9.97
    FL_1716 Validation 8.28 7.90 7.26 −9.88
    FL_1717 Validation 8.27 8.21 7.89 −9.60
    FL_1718 Training 8.50 8.17 7.15 −10.75
    FL_1719 Validation 8.35 8.02 7.21 −10.26
    FL_1720 Training 9.03 7.65 8.01 −8.61
    FL_1729 Training 8.97 8.27 7.69 −10.37
    FL_1732 Validation 8.49 6.82 7.71 −7.02
    FL_1761 Validation 8.36 8.19 7.29 −10.49
    FL_1764 Training 8.52 8.24 7.94 −9.69
    FL_1768 Training 8.70 8.25 7.63 −10.28
    FL_1771 Training 8.55 8.19 7.65 −10.04
    FL_1772 Validation 8.30 8.38 7.41 −10.71
    FL_1788 Training 8.14 8.06 8.11 −8.87
    FL_1790 Training 7.95 8.69 8.36 −9.74
    FL_1792 Validation 8.16 8.20 7.64 −9.88
    FL_1795 Training 7.94 9.08 8.37 −10.54
    FL_1797 Validation 8.17 8.21 7.87 −9.57
    FL_1799 Training 9.02 8.21 7.77 −10.14
    FL_1810 Validation 8.43 7.52 7.06 −9.47
    FL_1811 Validation 8.33 8.24 7.07 −10.93
    FL_1825 Training 8.90 8.39 7.97 −10.18
    FL_1827 Training 8.47 8.77 7.96 −10.76
    FL_1828 Validation 9.13 7.87 6.76 −11.01
    FL_1829 Validation 8.34 8.51 7.59 −10.71
    FL_1830 Validation 9.26 8.04 7.62 −10.13
    FL_1833 Training 8.82 8.86 7.88 −11.26
    FL_1834 Validation 9.25 8.17 7.62 −10.39
    FL_1835 Validation 7.71 8.16 8.01 −9.02
    FL_1836 Validation 9.06 8.52 7.59 −11.09
    FL_1837 Validation 8.57 8.33 7.37 −10.79
    FL_1838 Validation 8.78 8.72 8.04 −10.69
    FL_1839 Training 9.27 7.36 7.37 −9.08
    FL_1841 Training 8.66 8.35 8.17 −9.64
    FL_1842 Validation 8.62 8.50 8.02 −10.19
    FL_1844 Validation 9.37 8.40 7.47 −11.18
    FL_1845 Training 8.33 8.84 8.30 −10.32
    FL_1846 Validation 8.11 8.75 9.06 −8.89
    FL_1848 Training 8.19 8.60 7.91 −10.33
    FL_1851 Training 8.37 8.50 8.15 −9.84
    FL_1853 Validation 8.37 8.14 7.43 −10.19
    FL_1854 Validation 8.50 8.29 7.96 −9.78
    FL_1855 Validation 8.63 8.34 7.54 −10.58
    FL_1857 Validation 8.73 8.82 8.45 −10.26
    FL_1861 Validation 8.21 8.50 7.50 −10.77
    FL_1862 Validation 8.98 7.96 7.31 −10.28
    FL_1863 Validation 9.30 8.22 7.86 −10.18
    FL_1864 Training 8.13 8.93 8.27 −10.46
    FL_1866 Training 8.62 8.78 7.91 −10.93
    FL_1870 Validation 8.16 8.97 8.52 −10.18
    FL_1873 Training 8.55 8.30 8.00 −9.74
    FL_1874 Validation 8.43 8.20 7.59 −10.10
    FL_1876 Validation 8.48 8.52 7.70 −10.64
    FL_1879 Training 8.29 8.21 7.66 −9.94
    FL_1880 Validation 8.56 7.76 7.34 −9.61
    FL_1882 Training 8.02 8.40 7.71 −10.14
    FL_1884 Validation 8.14 8.46 8.42 −9.24
    FL_1885 Validation 8.88 8.57 7.78 −10.81
    FL_1887 Training 8.38 8.39 7.38 −10.78
    FL_1888 Training 8.14 8.74 8.07 −10.37
    FL_1890 Training 8.45 8.24 8.11 −9.41
    FL_1894 Training 8.38 7.97 7.82 −9.25
    FL_1896 Training 8.63 8.71 7.52 −11.37
    FL_1897 Training 9.01 7.91 6.93 −10.78
    FL_1898 Training 8.08 7.75 7.09 −9.74
    FL_1900 Validation 8.61 7.94 6.84 −10.77
    FL_1903 Validation 9.63 7.96 7.30 −10.64
    FL_1904 Validation 8.79 8.14 7.15 −10.82
    FL_1905 Validation 8.22 8.24 7.36 −10.43
    FL_1906 Training 8.40 7.40 7.24 −8.93
    FL_1907 Validation 8.61 7.11 6.59 −9.40
    FL_1910 Training 9.47 8.28 7.63 −10.73
    FL_1912 Validation 8.32 8.45 8.52 −9.18
    FL_1913 Training 8.24 8.60 7.23 −11.41
    FL_1916 Validation 8.31 8.04 7.27 −10.19
    FL_1918 Validation 8.30 8.49 7.78 −10.37
    FL_1919 Training 8.05 8.42 8.00 −9.75
    FL_735 Validation 9.03 7.83 7.41 −9.88
    FL_738 Validation 9.54 8.07 7.65 −10.30
    FL_739 Training 8.14 8.09 7.69 −9.57
    FL_878 Validation 9.17 7.91 7.70 −9.69
    FL_879 Training 8.37 7.96 7.67 −9.45
    FL_886 Validation 8.59 8.38 7.67 −10.44
    FL_888 Validation 7.85 7.71 7.07 −9.56
    FL_1627 Training 8.26 8.17 7.36 −10.30
    FL_1429 Training 9.53 8.12 7.56 −10.53
    FL_1850 Validation 9.81 8.00 7.99 −9.77
    FL_1735 Validation 8.46 8.10 7.62 −9.86
  • In order to visualize the predictive power of the model, the FL samples were ranked according to their survival predictor scores and divided into four quartiles. Kaplan-Meier plots of overall survival showed clear differences in survival rate in the validation set (FIG. 9).
    • Example 6 Development of a First DLBCL Survival Predictor Using Gene Expression Data from Affymetrix U133A and U133B Microarrays
  • Gene expression data from Affymetrix U133A and U133B microarrays was obtained for 231 DLBCL samples. The follow-up time and status at follow-up for each of the subjects from whom these samples were acquired is listed in Table 2368. Table 2368 also indicates which samples were used in creating the survival predictor.
  • TABLE 2368
    Length of Used in creating
    Sample follow- Status at survival
    ID # up (years) follow-up predictor?
    ABC_1000 0.69 Dead Yes
    ABC_1002 0.28 Dead Yes
    ABC_1023 5.57 Dead Yes
    ABC_1027 0.25 Dead Yes
    ABC_1031 6.64 Dead Yes
    ABC_1034 2.31 Dead Yes
    ABC_1038 0.71 Dead Yes
    ABC_1043 2.31 Dead Yes
    ABC_1045 2.26 Dead Yes
    ABC_1055 7.81 Alive Yes
    ABC_1057 2.13 Dead Yes
    ABC_1059 2.00 Dead Yes
    ABC_1061 1.04 Dead Yes
    ABC_1946 0.68 Dead No
    ABC_1994 1.21 Dead No
    ABC_2001 1.32 Dead No
    ABC_304 1.31 Dead Yes
    ABC_305 0.82 Alive Yes
    ABC_309 2.80 Alive Yes
    ABC_413 0.60 Dead Yes
    ABC_428 11.38 Alive Yes
    ABC_432 0.38 Dead Yes
    ABC_446 2.82 Dead Yes
    ABC_462 7.49 Dead Yes
    ABC_477 1.70 Dead Yes
    ABC_481 10.75 Alive Yes
    ABC_482 7.72 Alive Yes
    ABC_538 0.34 Dead Yes
    ABC_541 4.11 Alive Yes
    ABC_544 1.31 Dead Yes
    ABC_547 0.05 Dead Yes
    ABC_577 1.65 Alive Yes
    ABC_616 0.99 Dead Yes
    ABC_626 2.49 Dead Yes
    ABC_633 2.02 Alive Yes
    ABC_642 0.34 Dead Yes
    ABC_644 0.31 Dead Yes
    ABC_645 6.08 Dead Yes
    ABC_646 2.59 Dead Yes
    ABC_651 2.34 Alive Yes
    ABC_652 0.01 Dead Yes
    ABC_660 0.20 Dead Yes
    ABC_663 0.62 Dead Yes
    ABC_668 6.44 Alive Yes
    ABC_676 1.00 Dead Yes
    ABC_678 0.06 Dead Yes
    ABC_687 0.94 Dead Yes
    ABC_689 2.54 Dead Yes
    ABC_692 10.53 Alive Yes
    ABC_694 4.83 Alive Yes
    ABC_700 5.40 Dead Yes
    ABC_702 4.13 Dead Yes
    ABC_704 9.67 Alive Yes
    ABC_709 0.47 Dead Yes
    ABC_712 3.26 Dead Yes
    ABC_714 2.45 Dead Yes
    ABC_717 0.42 Dead Yes
    ABC_725 0.96 Dead Yes
    ABC_726 7.62 Alive Yes
    ABC_730 1.03 Dead Yes
    ABC_753 0.04 Dead Yes
    ABC_756 7.21 Alive Yes
    ABC_771 6.80 Dead Yes
    ABC_779 0.35 Dead Yes
    ABC_800 0.33 Dead Yes
    ABC_807 0.31 Dead Yes
    ABC_809 0.51 Dead Yes
    ABC_816 1.86 Dead Yes
    ABC_820 1.59 Dead Yes
    ABC_823 0.16 Dead Yes
    ABC_835 1.22 Dead Yes
    ABC_839 0.29 Dead Yes
    ABC_841 10.14 Alive Yes
    ABC_858 3.58 Dead Yes
    ABC_872 5.00 Alive Yes
    ABC_875 8.45 Alive Yes
    ABC_912 16.79 Alive Yes
    ABC_996 0.21 Dead Yes
    GCB_1005 5.77 Alive Yes
    GCB_1008 6.46 Alive Yes
    GCB_1009 9.68 Alive Yes
    GCB_1021 14.59 Alive Yes
    GCB_1025 2.86 Dead Yes
    GCB_1026 6.94 Dead Yes
    GCB_1037 0.23 Dead Yes
    GCB_1039 2.05 Dead Yes
    GCB_1049 1.33 Dead Yes
    GCB_1051 0.12 Dead Yes
    GCB_1058 0.42 Dead Yes
    GCB_1060 6.45 Alive Yes
    GCB_1990 0.06 Dead No
    GCB_1991 1.01 Dead No
    GCB_2017 0.08 Dead No
    GCB_2018 0.17 Dead No
    GCB_2095 0.97 Alive No
    GCB_412 12.12 Alive Yes
    GCB_415 5.38 Dead Yes
    GCB_421 1.24 Dead Yes
    GCB_424 10.62 Dead Yes
    GCB_433 0.76 Dead Yes
    GCB_434 10.53 Alive Yes
    GCB_438 8.15 Alive Yes
    GCB_459 9.65 Alive Yes
    GCB_470 11.17 Alive Yes
    GCB_479 7.24 Alive Yes
    GCB_492 11.29 Alive Yes
    GCB_517 3.03 Dead Yes
    GCB_523 8.36 Alive Yes
    GCB_524 5.88 Alive Yes
    GCB_529 1.06 Dead Yes
    GCB_533 0.71 Dead Yes
    GCB_537 4.99 Dead Yes
    GCB_543 3.47 Alive Yes
    GCB_545 1.10 Dead Yes
    GCB_549 2.68 Dead Yes
    GCB_550 21.78 Alive Yes
    GCB_553 0.82 Dead Yes
    GCB_565 9.11 Dead Yes
    GCB_572 14.24 Alive Yes
    GCB_617 5.88 Alive Yes
    GCB_618 5.65 Alive Yes
    GCB_619 8.76 Alive Yes
    GCB_623 2.43 Alive Yes
    GCB_627 1.27 Dead Yes
    GCB_654 7.37 Alive Yes
    GCB_661 0.56 Alive Yes
    GCB_669 7.11 Alive Yes
    GCB_672 6.78 Alive Yes
    GCB_674 7.22 Alive Yes
    GCB_675 6.02 Alive Yes
    GCB_681 9.70 Alive Yes
    GCB_688 0.33 Dead Yes
    GCB_695 0.15 Dead Yes
    GCB_698 3.88 Alive Yes
    GCB_701 3.90 Alive Yes
    GCB_710 1.08 Dead Yes
    GCB_711 3.93 Dead Yes
    GCB_722 3.32 Alive Yes
    GCB_724 1.40 Dead Yes
    GCB_731 10.18 Alive Yes
    GCB_742 4.09 Alive Yes
    GCB_744 8.86 Alive Yes
    GCB_745 1.33 Dead Yes
    GCB_747 15.41 Alive Yes
    GCB_749 10.40 Alive Yes
    GCB_758 1.10 Dead Yes
    GCB_772 2.48 Alive Yes
    GCB_777 4.27 Dead Yes
    GCB_792 5.53 Alive Yes
    GCB_795 3.43 Alive Yes
    GCB_797 6.87 Dead Yes
    GCB_803 1.45 Dead Yes
    GCB_810 11.72 Alive Yes
    GCB_817 2.76 Dead Yes
    GCB_818 0.10 Dead Yes
    GCB_819 0.72 Dead Yes
    GCB_821 9.47 Alive Yes
    GCB_832 4.01 Alive Yes
    GCB_836 4.29 Alive Yes
    GCB_840 3.40 Alive Yes
    GCB_847 4.16 Alive Yes
    GCB_860 3.03 Dead Yes
    GCB_871 0.41 Dead Yes
    GCB_874 0.12 Dead Yes
    GCB_995 6.65 Alive Yes
    PMBL_1006 7.12 Alive Yes
    PMBL_1024 19.83 Alive Yes
    PMBL_1048 7.70 Alive Yes
    PMBL_1053 1.04 Dead Yes
    PMBL_1920 1.97 Alive No
    PMBL_1921 4.16 Alive No
    PMBL_1923 1.60 Alive No
    PMBL_1924 6.11 Alive No
    PMBL_1935 12.42 Alive No
    PMBL_1941 0.71 Alive No
    PMBL_1942 0.88 Alive No
    PMBL_1943 8.96 Alive No
    PMBL_1945 0.84 Dead No
    PMBL_1948 7.96 Alive No
    PMBL_1949 4.28 Alive No
    PMBL_1989 1.33 Dead No
    PMBL_1992 1.00 Dead No
    PMBL_1993 1.33 Dead No
    PMBL_2002 6.62 Alive No
    PMBL_2019 0.99 Dead No
    PMBL_2020 2.08 Alive No
    PMBL_2092 1.27 Alive No
    PMBL_484 1.40 Dead Yes
    PMBL_546 0.78 Dead Yes
    PMBL_570 14.40 Alive Yes
    PMBL_621 8.14 Alive Yes
    PMBL_638 0.70 Dead Yes
    PMBL_691 0.32 Dead Yes
    PMBL_791 1.33 Dead Yes
    PMBL_824 12.24 Alive Yes
    PMBL_906 16.80 Alive Yes
    PMBL_994 4.79 Alive Yes
    PMBL_998 9.11 Alive Yes
    UC_DLBCL_1001 0.33 Dead Yes
    UC_DLBCL_1004 6.72 Alive Yes
    UC_DLBCL_1007 2.26 Dead Yes
    UC_DLBCL_1018 0.03 Dead Yes
    UC_DLBCL_1041 3.13 Dead Yes
    UC_DLBCL_1054 12.34 Alive Yes
    UC_DLBCL_306 2.69 Alive Yes
    UC_DLBCL_310 0.97 Alive Yes
    UC_DLBCL_449 9.16 Alive Yes
    UC_DLBCL_452 9.17 Alive Yes
    UC_DLBCL_458 1.18 Dead Yes
    UC_DLBCL_460 9.02 Alive Yes
    UC_DLBCL_491 4.47 Dead Yes
    UC_DLBCL_528 1.64 Alive Yes
    UC_DLBCL_615 4.94 Alive Yes
    UC_DLBCL_625 5.24 Alive Yes
    UC_DLBCL_664 0.62 Dead Yes
    UC_DLBCL_671 3.35 Alive Yes
    UC_DLBCL_682 0.11 Dead Yes
    UC_DLBCL_683 7.42 Alive Yes
    UC_DLBCL_684 1.92 Dead Yes
    UC_DLBCL_748 1.01 Dead Yes
    UC_DLBCL_751 9.99 Alive Yes
    UC_DLBCL_808 0.37 Dead Yes
    UC_DLBCL_831 11.02 Dead Yes
    UC_DLBCL_834 1.64 Dead Yes
    UC_DLBCL_838 0.00 Dead Yes
    UC_DLBCL_851 0.05 Dead Yes
    UC_DLBCL_854 1.51 Dead Yes
    UC_DLBCL_855 1.67 Alive Yes
    UC_DLBCL_856 0.60 Dead Yes
  • The correlation between expression of each gene represented on the microarrays and survival was estimated using a Cox proportional hazards model. The results of this survival analysis are provided in the final two columns of Table 1723. The first of these two columns (“DLBCL_Cox_coefficient”) provides a Cox coefficient indicating the extent to which a 2-fold increase in expression of a particular gene affects mortality. A positive Cox coefficient indicates increasing mortality with increasing expression of the gene, while a negative Cox coefficient indicates decreasing mortality with increasing expression of the gene. The second of these two columns (“DLBCL_Cox_P_value”) provides a Cox p-value indicating the estimated probability that the increase or decrease in survival associated with the gene would occur by chance if there was no connection between the expression of the gene and survival.
  • Genes that were significantly correlated with survival (p<0.001) were grouped into gene expression signatures using a hierarchical clustering algorithm. The expression level of every component gene in each of these gene expression signatures was averaged for each sample to create a gene expression signature value. A step-up procedure (Drapner 1966) was applied to determine the optimal number of gene signatures to use in the survival predictor model. First, the gene expression signature that was most significantly associated with survival was included in the model. Next, the gene expression signature with the second highest association with survival was added to the model to form a two-component model. This procedure was repeated until there was no gene expression signature to add to the model with a p-value of <0.05.
  • The final prediction model incorporated gene expression signature values from three gene expression signatures. The first gene expression signature added to the model was termed “ABC DLBCL high,” because it included genes that were more highly expressed in ABC than in GCB (Rosenwald 2002). The second gene expression signature added to the model was termed “lymph node,” because it reflected the response of non-tumor cells in the lymph node to the malignant lymphoma cells. The final gene expression signature added to the model was termed “MHC class II,” because it included all of the genes encoding the MHC class II alpha and beta chains. Table 2369 shows the genes that were averaged to form each of these signatures.
  • TABLE 2369
    Signature UNIQID Gene symbol Survival p-value
    ABC DLBCL high 1134271 POU5F1 3.09E−05
    ABC DLBCL high 1121564 DRIL1 4.06E−05
    ABC DLBCL high 1119889 PDCD4 7.28E−05
    ABC DLBCL high 1133300 CTH 1.23E−04
    ABC DLBCL high 1106030 MGC: 50789 1.70E−04
    ABC DLBCL high 1139301 FLJ20150 4.49E−04
    ABC DLBCL high 1122131 CHST7 5.18E−04
    ABC DLBCL high 1114824 LIMD1 5.20E−04
    ABC DLBCL high 1100161 LOC142678 6.24E−04
    ABC DLBCL high 1120129 TLE1 6.95E−04
    Lymph node 1097126 TEM8 5.14E−09
    Lymph node 1120880 LTBP2 9.80E−07
    Lymph node 1098898 FLJ31066 1.09E−06
    Lymph node 1123376 RARRES2 1.68E−06
    Lymph node 1128945 SLC12A8 2.90E−06
    Lymph node 1130994 DPYSL3 3.37E−06
    Lymph node 1124429 SULF1 3.53E−06
    Lymph node 1099358 FLJ39971 4.09E−06
    Lymph node 1130509 SPARC 6.23E−06
    Lymph node 1095985 TMEPAI 7.07E−06
    Lymph node 1123038 ACTN1 7.90E−06
    Lymph node 1133700 CDH11 8.20E−06
    Lymph node 1122101 TFEC 9.66E−06
    Lymph node 1124296 SDC2 9.99E−06
    MHC Class II 1123127 HLA-DRA 1.21E−06
    MHC Class II 1136777 HLA-DQA1 3.45E−06
    MHC Class II 1137771 HLA-DRB1 3.95E−06
    MHC Class II 1134281 HLA-DRB4 2.70E−05
    MHC Class II 1136573 HLA-DPA1 2.92E−05
    MHC Class II 1132710 HLA-DRB3 7.09E−05
  • Fitting the Cox proportional hazards model to the three gene expression signature values resulted in the following model:

  • Survival predictor score=[0.586*(ABC DLBCL high gene expression signature value)]−[0.468*(lymph node gene expression signature value)]−[0.336*(MHC Class II gene expression signature value)].
  • A higher survival predictor score was associated with worse outcome. According to a likelihood ratio test adjusted for the number of variables included, this model was significant in predicting survival at p=2.13×10−13. In order to visualize the predictive power of the model, the 205 samples used to create the model were ranked according to their survival predictor scores and divided into four quartiles. Kaplan-Meier plots of overall survival probability show clear differences in survival rate between these four quartiles (FIG. 10). The five-year survival probabilities for each quartile are set forth in Table 2370.
  • TABLE 2370
    Quartile 5-year survival
    1 83%
    2 59%
    3 33%
    4 17%
    • Example 7 Development of a Second DLBCL Survival Predictor Using Gene Expression Data from the Lymph Dx Microarray
  • A DLBCL survival model based on gene expression had been developed previously using proliferation, germinal center B-cell, lymph node, and MHC class II gene expression signatures and the expression of the single gene BMP-6 (Rosenwald 2002). BMP-6 expression was poorly measured on the Lymph Dx microarray, but genes associated with each of these four gene expression signatures exhibited associations with survival similar to those observed using Lymphochip microarrays. DLBCL samples were divided into two groups: a training set (100 samples) for developing the survival prediction model, and a validation set (100 samples) for evaluating the reproducibility of the model. Gene expressed in the training set samples were clustered, and lymph node, germinal center B-cell, MHC class II, and proliferation gene expression signatures were identified. Within each signature, expression of genes that were associated with survival (p<0.01) was averaged to generate a gene expression signature value for each signature. Table 2371 lists the genes that were used to generate the gene expression signature value for each signature.
  • TABLE 2371
    Unigene ID
    Signature UNIQID Build 167 Gene symbol
    Germinal center B-cell 1099686 117721
    Germinal center B-cell 1099711 243596
    Germinal center B-cell 1103390 271752 BPNT1
    Germinal center B-cell 1106025 49500 KIAA0746
    Germinal center B-cell 1128287 300063 ASB13
    Germinal center B-cell 1132520 283063 LMO2
    Germinal center B-cell 1138192 126608 NR3C1
    Germinal center B-cell 1529318 291954
    Germinal center B-cell 1529344 317970 SERPINA11
    Germinal center B-cell 1529352 446195
    Germinal center B-cell 1096570 409813 ANUBL1
    Germinal center B-cell 1097897 266175 PAG
    Germinal center B-cell 1097901 266175 PAG
    Germinal center B-cell 1098611 433611 PDK1
    Germinal center B-cell 1100581 155024 BCL6
    Germinal center B-cell 1115034 387222 NEK6
    Germinal center B-cell 1120090 155024 BCL6
    Germinal center B-cell 1120946 25209 MAPK10
    Germinal center B-cell 1121248 54089 BARD1
    Germinal center B-cell 1123105 434281 PTK2
    Germinal center B-cell 1125456 300592 MYBL1
    Germinal center B-cell 1128694 171466 ELL3
    Germinal center B-cell 1128787 114611 C7orf10
    Germinal center B-cell 1132122 307734 MME
    Germinal center B-cell 1136269 101474 MAST2
    Germinal center B-cell 1136702 155584 KIAA0121
    Germinal center B-cell 1139230 29724 PLEKHF2
    Germinal center B-cell 1529292 NA
    Germinal center B-cell 1529295 116441
    Lymph node 1097126 274520 ANTXR1
    Lymph node 1099028 334838 FNDC1
    Lymph node 1099358 93135
    Lymph node 1101478 146246 MGC45780
    Lymph node 1103497 50115
    Lymph node 1121029 412999 CSTA
    Lymph node 1124429 409602 SULF1
    Lymph node 1135068 71719 PDLIM3
    Lymph node 1136051 520937 CSF2RA
    Lymph node 1136172 38084 SULT1C1
    MHC class II 1136777 387679 HLA-DQA1
    MHC class II 1136877 409934 HLA-DQB1
    Proliferation 1096903 437460 FLJ10385
    Proliferation 1120583 153768 RNU3IP2
    Proliferation 1123289 5409 POLR1C
    Proliferation 1131808 75447 RALBP1
    Proliferation 1133102 360041 FRDA
    Proliferation 1136595 404814 VDAC1
  • Table 2372 lists p-values for the association of each signature with survival in the training set, the validation set, and overall.
  • TABLE 2372
    Signature Training set Validation set Overall
    Lymph node 4.0 × 10−5 2.3 × 10−6  6.8 × 10−10
    Proliferation 8.1 × 10−5 3.4 × 10−3 2.1 × 10−6
    Germinal center B-cell 6.2 × 10−6 2.1 × 10−3 5.0 × 10−8
    MHC class II 2.4 × 10−2 2.7 × 10−3 3.1 × 10−4
  • The four gene expression signatures were used to generate a survival predictor score using the following equation:

  • Survival predictor score=[−0.4337*(lymph node gene expression signature value)]+[0.09*(proliferation gene expression signature value)]−[0.4144*(germinal center B-cell gene expression signature value)]−[0.2006*(MHC class II gene expression signature value)].
  • A higher survival predictor score was associated with worse outcome. For the 200 DLBCL samples used to generate the model, the survival predictor score had a mean of 5.7 and a standard deviation of 0.78, with each unit increase in the predictor score corresponding to an approximately 2.7 fold increase in the relative risk of death. Data for all 200 samples is presented in Table 2373.
  • TABLE 2373
    Germinal
    Lymph center B- MHC
    node Proliferation cell class II Survival
    Sample signature signature signature signature predictor
    ID # Set value value value value score
    ABC_1000 Validation 6.50 8.92 7.60 11.50 −5.08
    ABC_1002 Validation 7.00 8.58 7.27 12.54 −5.50
    ABC_1023 Validation 7.43 8.99 6.80 11.42 −5.05
    ABC_1027 Training 5.68 9.00 6.87 12.31 −4.70
    ABC_1031 Validation 8.02 9.00 7.17 11.68 −5.53
    ABC_1034 Validation 6.06 9.61 6.72 11.83 −4.58
    ABC_1038 Training 6.83 8.97 7.17 12.30 −5.23
    ABC_1043 Training 6.96 9.01 6.77 12.29 −5.11
    ABC_1045 Validation 8.18 8.21 6.77 12.07 −5.66
    ABC_1055 Validation 5.58 9.16 7.30 13.05 −4.76
    ABC_1057 Training 7.33 8.94 7.74 12.05 −5.53
    ABC_1059 Validation 9.02 8.46 7.15 11.35 −6.08
    ABC_1061 Training 7.13 9.18 7.09 12.28 −5.21
    ABC_304 Validation 5.92 8.80 6.76 12.76 −4.84
    ABC_305 Training 5.92 8.74 7.50 11.89 −4.91
    ABC_309 Validation 8.86 8.39 7.62 12.53 −6.46
    ABC_413 Validation 6.45 9.32 6.55 9.04 −4.16
    ABC_428 Training 7.52 9.19 7.98 10.25 −5.51
    ABC_432 Validation 6.48 9.33 7.45 9.56 −4.56
    ABC_446 Training 7.91 9.42 7.41 10.55 −5.46
    ABC_462 Validation 6.41 8.85 6.67 13.36 −5.03
    ABC_477 Validation 6.26 9.02 6.69 12.45 −4.89
    ABC_481 Training 8.18 8.30 7.35 11.98 −5.91
    ABC_482 Training 8.59 9.01 7.66 12.35 −6.16
    ABC_538 Validation 8.06 8.84 7.17 11.83 −5.69
    ABC_541 Training 6.14 8.52 7.42 10.59 −4.71
    ABC_544 Training 6.91 9.03 6.82 11.87 −4.89
    ABC_547 Validation 5.80 8.96 7.14 11.38 −4.60
    ABC_577 Validation 7.84 8.65 8.16 11.95 −5.94
    ABC_616 Validation 6.03 9.05 7.36 12.64 −4.84
    ABC_626 Validation 7.48 9.22 7.25 11.11 −5.27
    ABC_633 Training 7.74 8.35 7.39 12.45 −5.80
    ABC_642 Training 5.71 8.82 6.41 13.80 −4.62
    ABC_644 Validation 6.64 9.15 7.05 13.28 −5.20
    ABC_645 Training 8.44 8.81 7.93 13.39 −6.43
    ABC_646 Validation 5.94 9.11 6.71 11.60 −4.63
    ABC_652 Validation 5.87 8.85 6.88 12.73 −4.77
    ABC_660 Training 5.19 9.34 6.64 10.17 −3.86
    ABC_663 Training 5.69 9.02 7.33 12.82 −4.91
    ABC_668 Validation 7.12 9.28 7.03 10.57 −4.91
    ABC_676 Training 4.95 8.90 7.09 13.32 −4.61
    ABC_678 Training 5.84 9.11 7.34 11.26 −4.41
    ABC_687 Validation 5.15 9.89 6.56 10.46 −3.76
    ABC_689 Training 6.49 8.86 7.10 12.56 −4.88
    ABC_692 Validation 7.32 8.96 7.25 11.57 −5.32
    ABC_694 Validation 8.28 9.21 8.01 12.41 −6.23
    ABC_700 Training 7.29 8.97 7.55 12.10 −5.48
    ABC_702 Validation 7.60 8.66 6.86 12.55 −5.45
    ABC_704 Training 7.07 8.92 7.03 12.83 −5.35
    ABC_709 Validation 5.92 8.58 6.37 13.40 −4.66
    ABC_712 Validation 5.79 9.12 6.34 12.02 −4.23
    ABC_714 Training 7.49 8.88 7.49 11.97 −5.54
    ABC_717 Training 7.17 9.45 7.01 11.34 −5.05
    ABC_725 Training 6.71 9.01 6.52 12.76 −4.86
    ABC_726 Validation 6.91 8.72 6.71 11.91 −4.90
    ABC_730 Validation 6.28 9.22 7.28 12.14 −4.88
    ABC_753 Training 6.84 9.64 7.05 13.00 −5.22
    ABC_756 Training 7.67 8.45 7.59 12.48 −5.85
    ABC_771 Training 6.98 8.76 6.91 12.20 −5.18
    ABC_779 Training 6.73 9.32 6.78 9.82 −4.44
    ABC_800 Validation 8.75 8.31 7.45 11.91 −6.04
    ABC_807 Training 5.50 9.53 6.92 7.56 −3.79
    ABC_809 Training 7.40 8.70 7.68 10.83 −5.50
    ABC_816 Training 5.20 9.91 7.65 10.64 −4.14
    ABC_820 Training 6.71 8.94 6.55 11.98 −4.85
    ABC_823 Validation 5.58 9.26 6.44 10.09 −3.97
    ABC_835 Validation 6.95 8.68 8.04 12.31 −5.59
    ABC_839 Training 6.63 9.17 7.23 11.89 −5.04
    ABC_841 Validation 6.35 9.51 7.52 13.19 −5.28
    ABC_858 Training 7.63 8.51 7.12 11.74 −5.42
    ABC_872 Training 6.78 8.73 7.41 12.47 −5.44
    ABC_875 Training 7.59 8.81 7.20 11.26 −5.25
    ABC_912 Validation 7.01 8.55 7.45 12.79 −5.64
    ABC_996 Validation 5.00 9.53 6.70 10.02 −3.94
    GCB_1005 Validation 8.28 8.67 9.11 13.27 −6.98
    GCB_1008 Training 8.17 8.59 9.83 12.83 −7.06
    GCB_1009 Training 6.63 9.02 10.07 12.28 −6.19
    GCB_1021 Validation 6.44 8.83 9.34 13.20 −6.15
    GCB_1025 Validation 7.87 8.48 9.27 12.37 −6.57
    GCB_1026 Training 7.71 8.30 9.81 13.52 −6.85
    GCB_1037 Training 4.95 8.83 9.35 12.57 −5.22
    GCB_1039 Training 7.63 8.65 9.01 13.28 −6.47
    GCB_1049 Validation 8.54 8.61 8.12 12.60 −6.41
    GCB_1051 Validation 6.26 9.09 9.48 12.76 −5.97
    GCB_1058 Validation 7.12 8.89 8.34 12.80 −5.85
    GCB_1060 Validation 8.27 8.84 8.94 12.96 −6.75
    GCB_412 Training 7.22 8.33 8.50 13.09 −6.09
    GCB_415 Training 9.01 8.62 8.38 11.99 −6.47
    GCB_421 Training 7.59 7.89 7.49 12.20 −5.80
    GCB_424 Training 9.29 8.42 8.51 12.44 −6.79
    GCB_433 Training 8.45 8.34 8.02 12.64 −6.54
    GCB_434 Training 8.46 8.55 9.17 12.54 −6.98
    GCB_438 Validation 8.14 8.71 9.13 12.51 −6.67
    GCB_459 Validation 8.98 8.39 8.42 11.37 −6.49
    GCB_470 Validation 7.72 8.57 8.67 12.23 −6.12
    GCB_479 Validation 6.86 8.25 7.13 13.07 −5.35
    GCB_492 Training 8.01 8.61 9.51 12.34 −6.63
    GCB_517 Validation 8.57 8.73 7.99 12.76 −6.48
    GCB_523 Training 5.96 8.56 8.74 12.77 −5.72
    GCB_524 Training 8.51 8.09 8.76 12.51 −6.57
    GCB_529 Training 5.12 9.17 8.88 10.77 −4.86
    GCB_533 Training 8.88 8.81 8.36 12.44 −6.60
    GCB_537 Validation 7.42 8.19 9.73 13.29 −6.68
    GCB_543 Validation 8.49 8.02 8.66 12.06 −6.45
    GCB_545 Training 8.65 8.28 6.90 12.90 −6.13
    GCB_549 Validation 6.87 8.24 8.65 12.15 −6.00
    GCB_550 Validation 8.98 8.29 8.76 12.24 −6.94
    GCB_553 Validation 8.51 8.64 8.62 12.63 −6.69
    GCB_565 Validation 7.97 8.79 9.79 13.42 −6.98
    GCB_572 Training 7.61 8.60 9.39 12.58 −6.42
    GCB_617 Validation 8.31 7.89 7.54 13.17 −6.12
    GCB_618 Training 5.66 8.97 9.20 13.32 −5.54
    GCB_619 Validation 7.83 8.65 9.34 12.12 −6.36
    GCB_623 Training 7.16 8.88 9.26 12.35 −6.21
    GCB_627 Validation 8.13 8.83 8.62 11.85 −6.31
    GCB_654 Training 6.30 9.60 8.45 10.00 −4.88
    GCB_661 Validation 8.46 8.51 8.18 12.66 −6.33
    GCB_669 Training 7.88 8.65 8.59 12.32 −6.19
    GCB_672 Training 8.29 8.61 8.14 12.41 −6.21
    GCB_674 Validation 8.36 8.62 7.76 12.33 −6.14
    GCB_675 Validation 6.01 9.52 8.90 10.12 −5.09
    GCB_681 Training 9.25 8.72 8.72 12.59 −6.89
    GCB_688 Validation 6.97 9.01 9.90 9.94 −5.99
    GCB_695 Validation 8.80 8.73 9.23 12.45 −6.84
    GCB_698 Validation 9.27 8.35 8.85 11.99 −6.96
    GCB_701 Training 7.77 7.93 8.68 13.10 −6.33
    GCB_710 Validation 6.12 8.78 7.65 13.19 −5.24
    GCB_711 Training 7.57 8.80 8.43 11.44 −5.84
    GCB_722 Training 7.78 8.31 8.93 12.61 −6.51
    GCB_724 Training 7.88 9.08 8.74 11.53 −6.21
    GCB_731 Validation 7.72 8.92 9.08 12.20 −6.46
    GCB_742 Validation 8.33 8.55 8.58 12.95 −6.70
    GCB_744 Training 8.02 8.64 9.36 11.85 −6.52
    GCB_745 Training 8.47 8.34 8.93 11.95 −6.67
    GCB_747 Validation 7.64 8.48 8.32 13.06 −6.27
    GCB_749 Training 7.57 8.61 9.40 12.55 −6.56
    GCB_758 Validation 5.66 8.77 7.89 12.51 −4.63
    GCB_772 Validation 8.52 7.81 7.95 12.25 −6.34
    GCB_777 Validation 7.52 8.65 8.57 11.69 −6.10
    GCB_792 Training 8.14 8.64 9.21 12.08 −6.65
    GCB_795 Validation 9.19 8.17 8.81 11.60 −6.92
    GCB_797 Validation 7.50 8.62 8.08 12.84 −6.09
    GCB_803 Validation 6.19 8.65 9.49 13.18 −6.11
    GCB_810 Training 8.46 8.32 8.10 13.13 −6.50
    GCB_817 Training 6.93 8.51 9.49 11.09 −6.04
    GCB_818 Training 7.18 8.96 8.08 12.23 −5.76
    GCB_819 Validation 7.16 8.97 8.06 13.22 −5.79
    GCB_821 Validation 8.13 8.59 8.90 12.41 −6.61
    GCB_832 Training 7.83 8.35 8.71 12.47 −6.37
    GCB_836 Validation 7.84 8.99 8.50 11.46 −5.85
    GCB_840 Training 8.24 7.75 7.40 11.74 −5.77
    GCB_847 Training 7.82 8.17 8.97 12.55 −6.51
    GCB_860 Training 7.12 8.39 9.34 11.54 −6.10
    GCB_871 Training 5.59 9.60 7.28 11.16 −4.23
    GCB_874 Training 8.53 9.14 8.95 11.65 −6.47
    GCB_995 Validation 6.98 8.68 8.54 12.22 −5.76
    PMBL_1006 Validation 7.34 8.51 7.66 10.94 −5.33
    PMBL_1024 Validation 7.62 8.48 8.56 10.89 −5.96
    PMBL_1048 Validation 8.68 8.16 7.23 12.18 −6.08
    PMBL_1053 Training 7.02 8.28 8.24 11.12 −5.31
    PMBL_484 Training 7.15 8.45 7.01 13.62 −5.41
    PMBL_546 Validation 8.19 7.88 7.66 11.73 −6.06
    PMBL_570 Training 9.34 8.21 8.48 12.70 −6.86
    PMBL_621 Training 8.08 8.60 9.14 12.96 −6.72
    PMBL_638 Training 7.56 8.26 8.00 11.37 −5.75
    PMBL_691 Validation 6.48 8.92 8.40 10.17 −5.04
    PMBL_791 Validation 7.72 8.65 8.94 11.56 −6.16
    PMBL_824 Validation 8.06 8.01 7.76 13.28 −6.11
    PMBL_994 Training 9.15 8.36 7.46 12.43 −6.29
    PMBL_998 Training 6.70 8.35 9.24 13.19 −6.20
    UC_DLBCL_1001 Validation 6.74 8.43 7.10 12.76 −5.31
    UC_DLBCL_1004 Validation 7.54 8.75 8.01 13.09 −6.10
    UC_DLBCL_1007 Training 9.97 8.44 7.64 12.97 −6.85
    UC_DLBCL_1018 Training 6.42 8.38 6.97 12.71 −5.03
    UC_DLBCL_1041 Validation 5.76 8.69 6.78 13.38 −4.71
    UC_DLBCL_1054 Training 8.92 8.65 8.51 11.48 −6.59
    UC_DLBCL_306 Validation 7.85 8.90 8.31 12.36 −6.23
    UC_DLBCL_310 Training 8.14 8.80 7.63 12.27 −6.03
    UC_DLBCL_449 Validation 9.03 8.48 7.07 12.17 −6.01
    UC_DLBCL_458 Training 5.92 8.53 8.28 9.60 −4.96
    UC_DLBCL_460 Validation 7.92 9.08 8.30 12.29 −6.13
    UC_DLBCL_491 Training 7.65 8.33 7.35 12.39 −5.53
    UC_DLBCL_528 Validation 6.99 8.56 7.36 11.63 −5.35
    UC_DLBCL_615 Validation 7.11 8.32 8.77 12.80 −6.10
    UC_DLBCL_625 Training 8.93 7.78 7.85 12.62 −6.46
    UC_DLBCL_664 Training 7.62 8.15 8.17 12.72 −6.04
    UC_DLBCL_671 Training 8.09 8.48 7.61 11.53 −5.78
    UC_DLBCL_682 Training 7.38 8.35 7.14 12.33 −5.43
    UC_DLBCL_683 Training 7.91 8.36 7.78 12.57 −6.02
    UC_DLBCL_684 Validation 8.06 8.63 8.29 12.76 −6.29
    UC_DLBCL_748 Validation 5.38 8.57 7.45 9.55 −4.23
    UC_DLBCL_751 Training 6.33 8.65 8.88 13.14 −5.74
    UC_DLBCL_808 Training 7.42 9.01 7.44 13.09 −5.63
    UC_DLBCL_831 Validation 8.33 8.30 7.46 11.58 −5.84
    UC_DLBCL_834 Training 6.98 9.09 8.61 11.77 −5.66
    UC_DLBCL_838 Validation 7.25 8.40 7.23 12.56 −5.36
    UC_DLBCL_851 Validation 6.28 9.05 6.78 8.19 −4.10
    UC_DLBCL_854 Validation 7.36 8.50 7.39 12.59 −5.53
    UC_DLBCL_855 Training 8.31 7.94 7.49 12.08 −6.07
    UC_DLBCL_856 Validation 5.65 9.01 8.52 9.32 −4.68
  • In order to visualize the predictive power of the model, the 200 samples were ranked according to their survival predictor scores and divided into four quartiles. Kaplan-Meier plots of overall survival probability show clear differences in survival rate between these four quartiles (FIG. 11).
    • Example 8 Development of a Third DLBCL Survival Predictor Using Gene Expression Data from the Lymph Dx Microarray
  • The number of genes used to generate the DLBCL survival predictor in Example 7 was reduced in order to create a survival predictor compatible with RT-PCR. The list of genes from the lymph node and germinal center B-cell gene expression signatures was narrowed to those three genes from each signature that were most closely correlated with the lymph node and germinal center B-cell gene expression signature values, respectively. The genes from the proliferation gene expression signature did not add significantly to the reduced gene survival prediction model, so they were removed entirely. The expression of the genes within each signature was averaged on the log2 scale to generate a gene expression signature value for each signature. Table 2374 lists the genes that were used to generate these gene expression signature values.
  • TABLE 2374
    Unigene ID
    Signature UNIQID Build 167 Gene symbol
    Germinal center B-cell 1099686 117721
    Germinal center B-cell 1529318 291954
    Germinal center B-cell 1529344 317970 SERPINA11
    Lymph node 1097126 274520 ANTXR1
    Lymph node 1099358 93135
    Lymph node 1121029 412999 CSTA
    MHC class II 1136777 387679 HLA-DQA1
    MHC class II 1136877 409934 HLA-DQB1
  • Table 2375 lists p-values for the association of each signature with survival in the training set, the validation set, and overall.
  • TABLE 2375
    Signature Training set Validation set Overall
    Lymph node 6.1 × 10−6 0.0021 2.1 × 10−17
    Germinal center B-cell 3.5 × 10−4 0.0099 2.7 × 10−5  
    MHC class II 0.024 0.0026 0.00031
  • The three gene expression signatures were used to generate a survival predictor score using the following equation:

  • Survival predictor score=[−0.32*(lymph node gene expression signature value)]−[0.176*(germinal center B-cell gene expression signature value)]−[0.206*(MHC class II gene expression signature value)].
  • A higher survival predictor score was associated with worse outcome. For the 200 DLBCL samples used to generate the model, the survival predictor score had a mean of 6.54 and a standard deviation of 0.69, with each unit increase in the predictor score corresponding to an approximately 2.7 fold increase in the relative risk of death. Data for all 200 samples is presented in Table 2376.
  • TABLE 2376
    Lymph Germinal MHC class
    node center B- II Survival
    Sample signature cell signature signature predictor
    ID # Set value value value score
    ABC_1000 Validation 8.08 5.68 11.50 −5.96
    ABC_1002 Validation 8.32 6.06 12.54 −6.31
    ABC_1023 Validation 9.36 4.74 11.42 −6.18
    ABC_1027 Training 7.41 4.90 12.31 −5.77
    ABC_1031 Validation 9.40 5.23 11.68 −6.33
    ABC_1034 Validation 7.47 4.92 11.83 −5.69
    ABC_1038 Training 7.89 5.84 12.30 −6.09
    ABC_1043 Training 7.84 4.66 12.29 −5.86
    ABC_1045 Validation 9.31 4.66 12.07 −6.29
    ABC_1055 Validation 6.46 6.38 13.05 −5.88
    ABC_1057 Training 9.13 7.93 12.05 −6.80
    ABC_1059 Validation 10.93 4.82 11.35 −6.68
    ABC_1061 Training 8.18 5.04 12.28 −6.04
    ABC_304 Validation 7.31 6.47 12.76 −6.10
    ABC_305 Training 7.02 6.60 11.89 −5.86
    ABC_309 Validation 10.47 7.00 12.53 −7.16
    ABC_413 Validation 7.99 4.80 9.04 −5.26
    ABC_428 Training 9.43 7.59 10.25 −6.47
    ABC_432 Validation 7.29 8.16 9.56 −5.74
    ABC_446 Training 9.49 5.46 10.55 −6.17
    ABC_462 Validation 7.72 4.97 13.36 −6.10
    ABC_477 Validation 7.16 3.69 12.45 −5.51
    ABC_481 Training 9.75 6.89 11.98 −6.80
    ABC_482 Training 10.51 7.64 12.35 −7.25
    ABC_538 Validation 8.79 5.00 11.83 −6.13
    ABC_541 Training 7.70 5.80 10.59 −5.67
    ABC_544 Training 8.90 3.98 11.87 −5.99
    ABC_547 Validation 7.05 5.18 11.38 −5.51
    ABC_577 Validation 9.93 8.05 11.95 −7.06
    ABC_616 Validation 7.34 4.54 12.64 −5.75
    ABC_626 Validation 8.78 6.77 11.11 −6.29
    ABC_633 Training 9.63 5.02 12.45 −6.53
    ABC_642 Training 7.31 4.95 13.80 −6.05
    ABC_644 Validation 7.77 5.35 13.28 −6.15
    ABC_645 Training 9.77 6.21 13.39 −6.98
    ABC_646 Validation 7.39 3.75 11.60 −5.41
    ABC_652 Validation 7.51 4.53 12.73 −5.82
    ABC_660 Training 5.85 3.55 10.17 −4.59
    ABC_663 Training 7.04 5.06 12.82 −5.78
    ABC_668 Validation 8.00 5.65 10.57 −5.73
    ABC_676 Training 6.53 4.29 13.32 −5.59
    ABC_678 Training 6.87 7.48 11.26 −5.83
    ABC_687 Validation 6.39 3.78 10.46 −4.87
    ABC_689 Training 8.29 5.07 12.56 −6.13
    ABC_692 Validation 8.10 5.26 11.57 −5.90
    ABC_694 Validation 9.67 8.15 12.41 −7.09
    ABC_700 Training 8.37 6.75 12.10 −6.36
    ABC_702 Validation 8.44 4.59 12.55 −6.09
    ABC_704 Training 8.51 4.34 12.83 −6.13
    ABC_709 Validation 7.47 4.54 13.40 −5.95
    ABC_712 Validation 7.12 3.99 12.02 −5.46
    ABC_714 Training 9.57 7.03 11.97 −6.77
    ABC_717 Training 8.33 5.54 11.34 −5.98
    ABC_725 Training 8.04 4.40 12.76 −5.97
    ABC_726 Validation 7.79 4.18 11.91 −5.68
    ABC_730 Validation 8.13 7.36 12.14 −6.40
    ABC_753 Training 9.24 6.60 13.00 −6.80
    ABC_756 Training 9.51 5.21 12.48 −6.53
    ABC_771 Training 8.08 4.74 12.20 −5.93
    ABC_779 Training 8.11 4.09 9.82 −5.34
    ABC_800 Validation 10.34 4.83 11.91 −6.61
    ABC_807 Training 6.58 4.44 7.56 −4.44
    ABC_809 Training 9.29 5.72 10.83 −6.21
    ABC_816 Training 6.36 6.36 10.64 −5.35
    ABC_820 Training 8.10 4.79 11.98 −5.90
    ABC_823 Validation 6.63 4.85 10.09 −5.05
    ABC_835 Validation 9.17 7.78 12.31 −6.84
    ABC_839 Training 8.06 4.97 11.89 −5.90
    ABC_841 Validation 8.05 6.24 13.19 −6.39
    ABC_858 Training 9.02 4.86 11.74 −6.16
    ABC_872 Training 8.67 5.85 12.47 −6.37
    ABC_875 Training 9.60 5.59 11.26 −6.37
    ABC_912 Validation 7.99 7.74 12.79 −6.56
    ABC_996 Validation 6.89 6.23 10.02 −5.36
    GCB_1005 Validation 9.02 9.56 13.27 −7.30
    GCB_1008 Training 9.27 10.49 12.83 −7.46
    GCB_1009 Training 7.80 10.09 12.28 −6.80
    GCB_1021 Validation 8.73 9.20 13.20 −7.13
    GCB_1025 Validation 9.94 9.97 12.37 −7.49
    GCB_1026 Training 9.54 10.20 13.52 −7.63
    GCB_1037 Training 6.34 8.79 12.57 −6.17
    GCB_1039 Training 8.71 9.94 13.28 −7.27
    GCB_1049 Validation 10.53 8.18 12.60 −7.41
    GCB_1051 Validation 7.63 10.18 12.76 −6.86
    GCB_1058 Validation 8.61 9.04 12.80 −6.98
    GCB_1060 Validation 10.23 9.38 12.96 −7.59
    GCB_412 Training 8.79 7.92 13.09 −6.90
    GCB_415 Training 10.72 8.57 11.99 −7.41
    GCB_421 Training 9.23 5.26 12.20 −6.39
    GCB_424 Training 11.14 8.46 12.44 −7.62
    GCB_433 Training 9.26 8.52 12.64 −7.07
    GCB_434 Training 9.73 10.13 12.54 −7.48
    GCB_438 Validation 9.60 9.99 12.51 −7.41
    GCB_459 Validation 10.51 7.75 11.37 −7.07
    GCB_470 Validation 9.56 6.63 12.23 −6.74
    GCB_479 Validation 7.77 4.71 13.07 −6.01
    GCB_492 Training 8.82 9.52 12.34 −7.04
    GCB_517 Validation 9.92 6.96 12.76 −7.03
    GCB_523 Training 6.59 9.17 12.77 −6.35
    GCB_524 Training 10.00 7.83 12.51 −7.16
    GCB_529 Training 5.61 7.93 10.77 −5.41
    GCB_533 Training 9.55 5.54 12.44 −6.59
    GCB_537 Validation 8.25 10.25 13.29 −7.18
    GCB_543 Validation 9.92 8.85 12.06 −7.21
    GCB_545 Training 9.69 4.91 12.90 −6.62
    GCB_549 Validation 7.86 8.88 12.15 −6.58
    GCB_550 Validation 10.64 9.53 12.24 −7.60
    GCB_553 Validation 10.14 9.05 12.63 −7.44
    GCB_565 Validation 9.08 10.80 13.42 −7.57
    GCB_572 Training 8.93 10.03 12.58 −7.21
    GCB_617 Validation 9.27 7.80 13.17 −7.05
    GCB_618 Training 7.23 9.11 13.32 −6.66
    GCB_619 Validation 9.63 9.63 12.12 −7.27
    GCB_623 Training 8.94 9.07 12.35 −7.00
    GCB_627 Validation 9.72 8.33 11.85 −7.02
    GCB_654 Training 7.04 5.60 10.00 −5.30
    GCB_661 Validation 10.27 7.92 12.66 −7.29
    GCB_669 Training 9.15 9.29 12.32 −7.10
    GCB_672 Training 9.69 7.36 12.41 −6.95
    GCB_674 Validation 9.93 6.23 12.33 −6.81
    GCB_675 Validation 7.48 8.46 10.12 −5.97
    GCB_681 Training 10.77 9.52 12.59 −7.72
    GCB_688 Validation 8.01 10.17 9.94 −6.40
    GCB_695 Validation 10.58 9.38 12.45 −7.60
    GCB_698 Validation 10.44 9.00 11.99 −7.39
    GCB_701 Training 9.38 9.27 13.10 −7.33
    GCB_710 Validation 6.96 5.59 13.19 −5.93
    GCB_711 Training 9.28 8.49 11.44 −6.82
    GCB_722 Training 8.93 9.51 12.61 −7.13
    GCB_724 Training 9.51 8.39 11.53 −6.90
    GCB_731 Validation 8.82 9.19 12.20 −6.95
    GCB_742 Validation 9.95 9.37 12.95 −7.50
    GCB_744 Training 10.23 10.11 11.85 −7.49
    GCB_745 Training 10.29 9.71 11.95 −7.46
    GCB_747 Validation 9.83 9.79 13.06 −7.56
    GCB_749 Training 8.57 10.27 12.55 −7.14
    GCB_758 Validation 6.88 5.69 12.51 −5.78
    GCB_772 Validation 9.92 7.28 12.25 −6.98
    GCB_777 Validation 9.03 9.63 11.69 −6.99
    GCB_792 Training 9.49 9.06 12.08 −7.12
    GCB_795 Validation 11.12 9.02 11.60 −7.54
    GCB_797 Validation 8.42 5.90 12.84 −6.38
    GCB_803 Validation 7.33 10.11 13.18 −6.84
    GCB_810 Training 10.00 8.22 13.13 −7.35
    GCB_817 Training 8.60 10.16 11.09 −6.82
    GCB_818 Training 9.14 7.78 12.23 −6.81
    GCB_819 Validation 9.08 8.63 13.22 −7.15
    GCB_821 Validation 10.05 9.81 12.41 −7.50
    GCB_832 Training 8.83 6.91 12.47 −6.61
    GCB_836 Validation 9.49 7.86 11.46 −6.78
    GCB_840 Training 9.45 5.02 11.74 −6.33
    GCB_847 Training 9.41 8.77 12.55 −7.14
    GCB_860 Training 9.02 6.66 11.54 −6.43
    GCB_871 Training 6.60 4.46 11.16 −5.20
    GCB_874 Training 10.39 9.13 11.65 −7.33
    GCB_995 Validation 8.52 9.35 12.22 −6.89
    PMBL_1006 Validation 8.72 4.67 10.94 −5.86
    PMBL_1024 Validation 9.30 8.47 10.89 −6.71
    PMBL_1048 Validation 10.30 4.98 12.18 −6.68
    PMBL_1053 Training 8.75 9.78 11.12 −6.81
    PMBL_484 Training 8.25 4.96 13.62 −6.32
    PMBL_546 Validation 9.66 6.07 11.73 −6.57
    PMBL_570 Training 10.58 8.54 12.70 −7.50
    PMBL_621 Training 9.39 9.94 12.96 −7.43
    PMBL_638 Training 9.81 8.35 11.37 −6.95
    PMBL_691 Validation 8.37 7.51 10.17 −6.10
    PMBL_791 Validation 9.29 8.65 11.56 −6.88
    PMBL_824 Validation 9.87 7.19 13.28 −7.16
    PMBL_994 Training 11.27 6.73 12.43 −7.35
    PMBL_998 Training 7.92 8.34 13.19 −6.72
    UC_DLBCL_1001 Validation 8.25 5.63 12.76 −6.26
    UC_DLBCL_1004 Validation 9.01 7.01 13.09 −6.81
    UC_DLBCL_1007 Training 11.42 6.73 12.97 −7.51
    UC_DLBCL_1018 Training 7.77 4.58 12.71 −5.91
    UC_DLBCL_1041 Validation 7.90 4.33 13.38 −6.05
    UC_DLBCL_1054 Training 10.41 8.72 11.48 −7.23
    UC_DLBCL_306 Validation 9.42 6.54 12.36 −6.71
    UC_DLBCL_310 Training 9.97 5.50 12.27 −6.69
    UC_DLBCL_449 Validation 10.01 5.37 12.17 −6.65
    UC_DLBCL_458 Training 7.50 5.79 9.60 −5.40
    UC_DLBCL_460 Validation 10.26 8.27 12.29 −7.27
    UC_DLBCL_491 Training 9.43 4.73 12.39 −6.40
    UC_DLBCL_528 Validation 8.42 6.19 11.63 −6.18
    UC_DLBCL_615 Validation 8.44 9.01 12.80 −6.92
    UC_DLBCL_625 Training 10.43 8.27 12.62 −7.39
    UC_DLBCL_664 Training 9.80 8.74 12.72 −7.29
    UC_DLBCL_671 Training 9.42 5.26 11.53 −6.32
    UC_DLBCL_682 Training 9.01 4.73 12.33 −6.26
    UC_DLBCL_683 Training 8.85 8.23 12.57 −6.87
    UC_DLBCL_684 Validation 9.62 8.78 12.76 −7.25
    UC_DLBCL_748 Validation 7.60 5.79 9.55 −5.42
    UC_DLBCL_751 Training 6.40 9.91 13.14 −6.50
    UC_DLBCL_808 Training 9.44 7.01 13.09 −6.95
    UC_DLBCL_831 Validation 9.45 5.81 11.58 −6.43
    UC_DLBCL_834 Training 8.52 7.66 11.77 −6.50
    UC_DLBCL_838 Validation 8.49 4.60 12.56 −6.11
    UC_DLBCL_851 Validation 7.50 4.82 8.19 −4.94
    UC_DLBCL_854 Validation 8.35 5.82 12.59 −6.29
    UC_DLBCL_855 Training 9.56 5.44 12.08 −6.51
    UC_DLBCL_856 Validation 6.81 7.49 9.32 −5.42
  • In order to visualize the predictive power of the model, the 200 samples were ranked according to their survival predictor scores and divided into four quartiles. Kaplan-Meier plots of overall survival probability show clear differences in survival rate between these four quartiles (FIG. 12).
    • Example 9 Development of an MCL Survival Predictor Using Gene Expression Data from Affymetrix U133A and U133B Microarrays
  • The connection between higher expression of proliferation genes and worse survival in MCL had previously been documented and validated (Rosenwald 2003a). A cluster of proliferation genes had been identified in the DLBCL samples used to create the DLBCL survival predictor described in Example 7. By averaging the expression of these genes, a proliferation gene expression signature value had been developed for the DLBCL samples. The correlation of this signature with each probe set on the U133A and U133B microarrays was determined, and the 22 genes for which the correlation was greater than 0.5 were labeled proliferation genes. The correlation between expression of these proliferation genes and survival in 21 MCL samples was estimated using the Cox proportional hazards model. Table 2377 lists these 21 MCL samples.
  • TABLE 2377
    Length of Used in creating
    Sample follow- Status at survival
    ID # up (years) follow-up predictor?
    MCL_1012 3.19 Alive Yes
    MCL_1091 3.03 Alive Yes
    MCL_1114 0.59 Dead Yes
    MCL_1128 0.43 Dead Yes
    MCL_1150 3.21 Dead Yes
    MCL_1162 0.78 Alive Yes
    MCL_1166 0.53 Dead Yes
    MCL_1194 0.55 Alive Yes
    MCL_885 1.19 Alive Yes
    MCL_918 1.95 Dead Yes
    MCL_924 5.48 Dead Yes
    MCL_925 7.23 Alive Yes
    MCL_926 5.18 Dead Yes
    MCL_936 2.80 Alive Yes
    MCL_939 1.07 Dead Yes
    MCL_953 2.31 Dead Yes
    MCL_956 1.40 Dead Yes
    MCL_964 0.75 Alive Yes
    MCL_966 0.21 Dead Yes
    MCL_968 1.59 Dead Yes
    MCL_970 5.02 Dead Yes

    Out of the 22 proliferation genes, 11 were significant at a 0.001 level. The expression level of these 11 genes in each of the 21 MCL samples was averaged to generate a proliferation gene expression signature value. No other genes represented on the U133A or U133B microarrays correlated with MCL survival to an extent greater than would be expected by chance, so the final model included only proliferation genes. The 11 genes used to generate the model are presented in Table 2378.
  • TABLE 2378
    Signature UNIQID Gene Symbol
    Proliferation 1097290 CIRH1A
    Proliferation 1101295 FLJ40629
    Proliferation 1119729 TK1
    Proliferation 1120153 LMNB1
    Proliferation 1120494 CDC6
    Proliferation 1124745 KIAA0056
    Proliferation 1126148 DKFZp586E1120
    Proliferation 1130618 TPI1
    Proliferation 1134753 WHSC1
    Proliferation 1139654 ECT2
    Proliferation 1140632 IMAGE: 52707
  • A survival predictor score for MCL was generated using the following equation:

  • Survival predictor score=1.66*(proliferation gene expression signature value).
  • This model was associated with survival in a statistically significant manner (p=0.00018). To illustrate the significance of the model in predicting survival, the 21 MCL samples were divided into two equivalent groups based on their survival predictor scores. Those samples with survival predictor scores above the median were placed in the high proliferation group, while those with survival predictor scores below the median were placed in the low proliferation group. FIG. 13 illustrates the Kaplan Meier survival estimates for these two groups. Median survival for the high proliferation group was 1.07 years, while median survival for the low proliferation group was 5.18 years.
    • Example 10 Development of an MCL Survival Predictor Using Gene Expression Data from the Lymph Dx Microarray
  • A set of 21 genes associated with proliferation and poor prognosis in MCL had been identified previously (Rosenwald 2003a). Of these 21 genes, only four were represented on the Lymph Dx microarray. In order to find a larger set of genes on the Lymph Dx microarray associated with survival in MCL, Lymphochip expression data (Rosenwald 2003a) was re-analyzed and another set of proliferation genes whose expression levels were correlated with poor survival in MCL were identified. Thirteen of these genes were represented on the Lymph Dx microarray (median expression >6 on log2 scale). These 13 genes are listed in Table 2379.
  • TABLE 2379
    Unigene ID
    Signature UNIQID Build 167 Gene symbol
    Proliferation 1119294 156346 TOP2A
    Proliferation 1119729 164457 TK1
    Proliferation 1120153 89497 LMNB1
    Proliferation 1121276 24529 CHEK1
    Proliferation 1123358 442658 AURKB
    Proliferation 1124178 446579 HSPCA
    Proliferation 1124563 249441 WEE1
    Proliferation 1130799 233952 PSMA7
    Proliferation 1131274 374378 CKS1B
    Proliferation 1131778 396393 UBE2S
    Proliferation 1132449 250822 STK6
    Proliferation 1135229 367676 DUT
    Proliferation 1136585 80976 MKI67
  • The expression levels of the 13 genes listed in Table 2379 on the Lymph Dx microarray were transformed into the log2 scale and averaged to form a proliferation gene expression signature value. This was used to generate a survival predictor score using the following equation:

  • Survival predictor score=1.66*(proliferation gene expression signature value).
  • For the 21 MCL samples analyzed, the survival predictor score had a mean of 14.85 and a standard deviation of 1.13. Even in this limited sample set, the survival predictor score was significantly associated with prognosis (p=0.0049), with each unit increase in the score corresponding to a 2.7 fold increase in the relative risk of death. Data for all 21 samples is shown in Table 2380.
  • TABLE 2380
    Proliferation Survival predictor
    Sample ID # signature value score
    MCL_1012 8.83 14.658
    MCL_1091 8.81 14.625
    MCL_1114 10.39 17.247
    MCL_1128 10.12 16.799
    MCL_1150 8.33 13.828
    MCL_1162 8.15 13.529
    MCL_1166 9.40 15.604
    MCL_1194 7.44 12.350
    MCL_885 8.68 14.409
    MCL_918 9.33 15.488
    MCL_924 8.35 13.861
    MCL_925 8.86 14.708
    MCL_926 8.14 13.512
    MCL_936 8.56 14.21
    MCL_939 9.14 15.172
    MCL_953 9.25 15.355
    MCL_956 9.35 15.521
    MCL_964 9.74 16.168
    MCL_966 8.76 14.542
    MCL_968 9.10 15.106
    MCL_970 9.27 15.388
  • To illustrate the significance of the model in predicting survival, the 21 MCL samples were divided into two equivalent groups based on their survival predictor scores. Those samples with survival predictor scores above the median were placed in the high proliferation group, while those with survival predictor scores below the median were placed in the low proliferation group. FIG. 14 illustrates the Kaplan Meier survival estimates for these two groups.
    • Example 11 Identification of Lymphoma Samples as MCL Based on Bayesian Analysis of Gene Expression Data from Affymetrix U133A and U133B Microarrays
  • A statistical method based on Bayesian analysis was developed to distinguish MCL samples from samples belonging to other lymphoma types based on gene expression profiling. This method was developed using the gene expression data obtained in Example 1 for the following lymphoma types: ABC, GCB, PMBL, BL, FH, FL, MALT, MCL, PTLD, SLL, and splenic marginal zone lymphoma (splenic). Tables 1707-1741 (discussed in Example 1) provide gene expression data for samples within each of these lymphoma types, including the expression level of each gene and the difference in expression of each gene between types. Tables 1710, 1715, and 1723 (corresponding to FL, MCL, and DLBCL, respectively) include the correlation between expression of each gene and survival.
  • To determine the lymphoma type of a sample, a series of predictor models are generated. Each predictor model calculates the probability that the sample belongs to a first lymphoma type rather than a second lymphoma type. A method was developed to determine whether a sample was MCL, or one of the following lymphoma types: ABC, BL, FH, FL, GCB, MALT, PMBL, PTLD, SLL, or splenic. This method required ten different predictor models, each designed to determine whether the sample belonged to MCL or one of the other ten lymphoma types (e.g., MCL vs. ABC, MCL vs. BL, etc.).
  • Several of the lymphoma samples analyzed displayed a tendency towards elevated or reduced expression of genes from the lymph node and proliferation gene expression signatures. These genes are likely to be highly differentially expressed between the lymphoma types, but they do not serve as good predictor genes because they are often variably expressed within a single lymphoma type. For this reason, any gene that displayed a correlation with the proliferation or lymph node signatures was eliminated from consideration.
  • For each lymphoma type pair (e.g., MCL vs. ABC, MCL vs. FL, etc.), 20 genes were identified that exhibited the greatest difference in expression between MCL and the second lymphoma type according to a Student's t-test. The choice to use 20 genes was arbitrary. For each sample X, the 20 genes were used to generate a linear predictor score (LPS) according to the following formula:
  • LPS ( X ) = ∑ j = 1 20 t j X j ,
  • where Xj is the expression of gene j in sample X and tj is the t-statistic for the difference in expression of gene j between a first lymphoma type and a second lymphoma type. This is merely one method for generating an LPS. Others methods include linear discriminant analysis (Dudoit 2002), support vector machines (Furey 2000), or shrunken centroids (Tibshirani 2002). In addition, there is no requirement that a t-statistic be used as the scaling factor.
  • After an LPS had been formulated for each lymphoma sample, the mean and standard deviation of these LPS's was calculated for each lymphoma type. For a new sample X, Bayes' rule can be used to estimate the probability that the sample belongs to a first lymphoma type rather than a second lymphoma type (FIG. 15). In this example, Bayes' rule was used to calculate the probability q that sample X was MCL rather than a second lymphoma type using the following equation:
  • q ( X is type 1 ) = φ ( LPS ( X ) ; μ ^ 1 , σ ^ 1 ) φ ( LPS ( X ) ; μ ^ 1 , σ ^ 1 ) + φ ( LPS ( X ) ; μ ^ 2 , σ ^ 2 )
  • where type 1 is MCL, type 2 is one of the other nine lymphoma types, φ(x; μ,σ) is the normal density function with mean μ and standard deviation σ, {circumflex over (μ)}1 and {circumflex over (σ)}1 are the sample mean and variance of the LPS values for lymphoma type 1, and {circumflex over (μ)}2 and {circumflex over (σ)}2 are the sample mean and variance of the LPS values for lymphoma type 2.
  • This method was used to develop ten predictor models, one for each pairing of MCL and a second lymphoma type. A sample was classified as MCL if each of the ten predictors generated at least a 90% probability that the sample was MCL. If any of the ten predictors indicated a probability of less than 90%, the sample was classified as non-MCL.
  • The 10 sets of 20 genes that were included in these models and the t-statistics for each gene are presented in Tables 2381-2490.
  • TABLE 2381
    MCL vs. ABC predictor genes
    UNIQID Gene name Scale Factor
    1103711 Homo sapiens cDNA FLJ11833 fis, clone HEMBA1006579. 17.88496416
    1133111 PDE9A—phosphodiesterase 9A 17.61579873
    1137987 PLXNB1—plexin B1 17.47030156
    1132835 SOX11—SRY (sex determining region Y)-box 11 16.89404131
    1109505 Homo sapiens, Similar to LOC168058, clone MGC: 39372 15.78111902
    IMAGE: 5089466, mRNA, complete cds
    1139054 LOC58486—transposon-derived Buster1 transposase-like 15.77800815
    protein
    1119361 TIA1—TIA1 cytotoxic granule-associated RNA binding 15.68070962
    protein
    1115226 KIAA1683—KIAA1683 protein 15.67954057
    1101211 Homo sapiens cDNA: FLJ21960 fis, clone HEP05517. 15.4183527
    1118963 Homo sapiens cDNA FLJ35653 fis, clone SPLEN2013690. 15.36802586
    1096503 GL012—hypothetical protein GL012 14.64776335
    1127849 SNN—stannin 14.54859775
    1099204 Homo sapiens mRNA; cDNA DKFZp586K1922 (from clone 14.32724822
    DKFZp586K1922)
    1098840 C3orf6—chromosome 3 open reading frame 6 14.10346944
    1139444 RABL2B—RAB, member of RAS oncogene family-like 2B 14.10016196
    1106855 KIAA1909—KIAA1909 protein 13.9504946
    1126695 KIAA0484—KIAA0484 protein 13.92285415
    1120137 FCGBP—Fc fragment of IgG binding protein 13.86147896
    1133011 TMSNB—thymosin, beta, identified in neuroblastoma cells 13.74377784
    1133192 GRP3—guanine nucleotide exchange factor for Rap1 −17.09085725
  • TABLE 2382
    MCL vs. BL predictor genes
    UNIQID Gene name Scale Factor
    1120900 EPHB6—EphB6 13.43582327
    1112061 Homo sapiens cDNA FLJ90513 fis, clone NT2RP3004355. 12.73065392
    1109505 Homo sapiens, Similar to LOC168058, clone MGC: 39372 12.63674985
    IMAGE: 5089466, mRNA, complete cds
    1133099 DNASE1L3—deoxyribonuclease I-like 3 12.43333984
    1106855 KIAA1909—KIAA1909 protein 12.32623489
    1110070 ESTs 12.05416064
    1121739 ZNF135—zinc finger protein 135 (clone pHZ-17) 11.90460363
    1098840 C3orf6—chromosome 3 open reading frame 6 11.90309143
    1132833 SOX11—SRY (sex determining region Y)-box 11 11.60864812
    1121693 KIAA0450—KIAA0450 gene product 11.33634052
    1123760 ILT7—leukocyte immunoglobulin-like receptor, subfamily A 11.18744726
    (without TM domain), member 4
    1125964 KIAA0792—KIAA0792 gene product 11.14762675
    1112306 ESTs 11.02434114
    1096070 DNMT3A—DNA (cytosine-5-)-methyltransferase 3 alpha 10.98991879
    1129943 Homo sapiens, similar to Zinc finger protein 85 (Zinc finger 10.72494956
    protein HPF4) (HTF1), clone IMAGE: 3352451, mRNA
    1118749 PRKWNK1—protein kinase, lysine deficient 1 10.64623382
    1098954 FLJ13204—hypothetical protein FLJ13204 10.46164401
    1134749 PRKCBP1—protein kinase C binding protein 1 10.40948157
    1131860 BIN1—bridging integrator 1 10.31084561
    1123148 TGFBR2—transforming growth factor, beta receptor II 10.2956213
    (70/80 kDa)
  • TABLE 2383
    MCL vs. FH predictor genes
    UNIQID Gene name Scale Factor
    1132834 SOX11—SRY (sex determining region Y)-box 11 24.3531072
    1100873 ESTs 16.83342764
    1109603 ESTs 13.02401995
    1139411 OSBPL10—oxysterol binding protein-like 10 12.54369577
    1106855 KIAA1909—KIAA1909 protein 12.10316361
    1125193 CNR1—cannabinoid receptor 1 (brain) 12.070579
    1137450 ALOX5—arachidonate 5-lipoxygenase 11.74571823
    1100258 KIAA1384—KIAA1384 protein 11.60998697
    1133167 ZFD25—zinc finger protein (ZFD25) 11.52931491
    1136831 PPFIBP2—PTPRF interacting protein, binding protein 2 11.50062692
    (liprin beta 2)
    1138222 NA 10.99674674
    1099437 Homo sapiens mRNA; cDNA DKFZp667B1913 (from clone 10.90797288
    DKFZp667B1913)
    1140236 SPAP1—SH2 domain containing phosphatase anchor 10.77082801
    protein 1
    1114109 DCAL1—dendritic cell-associated lectin-1 10.65867119
    1098277 PRICKLE1—prickle-like 1 (Drosophila) 10.55457068
    1135138 CD24—CD24 antigen (small cell lung carcinoma cluster 4 10.41999962
    antigen)
    1103304 Homo sapiens clone CDABP0095 mRNA sequence −10.46625233
    1128460 RDGBB—retinal degeneration B beta −10.91106245
    1121953 KIAA0125—KIAA0125 gene product −11.22466255
    1129281 C14orf110—chromosome 14 open reading frame 110 −15.54465448
  • TABLE 2384
    MCL vs. FL predictor genes
    UNIQID Gene name Scale Factor
    1132835 SOX11—SRY (sex determining region Y)-box 11 22.14208817
    1096070 DNMT3A—DNA (cytosine-5-)-methyltransferase 3 alpha 20.53740132
    1103711 Homo sapiens cDNA FLJ11833 fis, clone HEMBA1006579. 20.49880004
    1137987 PLXNB1—plexin B1 18.38081568
    1109505 Homo sapiens, Similar to LOC168058, clone MGC: 39372 17.17812448
    IMAGE: 5089466, mRNA, complete cds
    1098840 C3orf6—chromosome 3 open reading frame 6 16.32703666
    1130926 C5orf13—chromosome 5 open reading frame 13 15.34261878
    1096396 SPG3A—spastic paraplegia 3A (autosomal dominant) 14.75437736
    1132734 COL9A3—collagen, type IX, alpha 3 14.684583
    1139393 OPN3—opsin 3 (encephalopsin, panopsin) 14.39118445
    1115537 LOC84518—protein related with psoriasis 14.18446144
    1102215 Homo sapiens cDNA FLJ11666 fis, clone HEMBA1004672. 14.16246426
    1124585 Homo sapiens cDNA: FLJ21930 fis, clone HEP04301, −14.33315955
    highly similar to HSU90916 Human clone 23815 mRNA sequence.
    1137561 HOXA1—homeo box A1 −15.38404642
    1100581 Homo sapiens mRNA; cDNA DKFZp667A1115 (from clone −15.91666634
    DKFZp667A1115)
    1124646 KIAA0084—KIAA0084 protein −16.40577696
    1114543 ESTs −17.60167863
    1120090 BCL6—B-cell CLL/lymphoma 6 (zinc finger protein 51) −17.63091181
    1123731 RGS13—regulator of G-protein signalling 13 −22.41602151
    1133192 GRP3—guanine nucleotide exchange factor for Rap1 −27.28308723
  • TABLE 2385
    MCL vs. GCB predictor genes
    UNIQID Gene name Scale Factor
    1098840 C3orf6—chromosome 3 open reading frame 6 22.26488562
    1132835 SOX11—SRY (sex determining region Y)-box 11 17.76179754
    1137987 PLXNB1—plexin B1 16.86845147
    1098954 FLJ13204—hypothetical protein FLJ13204 16.65023669
    1103711 Homo sapiens cDNA FLJ11833 fis, clone HEMBA1006579. 15.64719784
    1096070 DNMT3A—DNA (cytosine-5-)-methyltransferase 3 alpha 15.22540494
    1139393 OPN3—opsin 3 (encephalopsin, panopsin) 14.64030565
    1127849 SNN—stannin 14.28242206
    1098156 Human HeLa mRNA isolated as a false positive in a two- 14.00049272
    hybrid-screen.
    1128845 FLJ20174—hypothetical protein FLJ20174 13.96064416
    1129943 Homo sapiens, similar to Zinc finger protein 85 (Zinc finger 13.85404507
    protein HPF4) (HTF1), clone IMAGE: 352451, mRNA
    1140116 DKFZP564B116—hypothetical protein DKFZp564B1162 13.81464172
    1106855 KIAA1909—KIAA1909 protein 13.74521849
    1120900 EPHB6—EphB6 13.46567004
    1127371 Homo sapiens cDNA FLJ14046 fis, clone HEMBA1006461. 13.45735668
    1119361 TIA1—TIA1 cytotoxic granule-associated RNA binding protein 13.37376559
    1120854 EDG1—endothelial differentiation, sphingolipid G-protein- 13.1047657
    coupled receptor, 1
    1098277 PRICKLE1—prickle-like 1 (Drosophila) 13.04993076
    1140127 TRIM34—tripartite motif-containing 34 12.66260609
    1100581 Homo sapiens mRNA; cDNA DKFZp667A1115 (from clone −12.81251689
    DKFZp667A1115)
  • TABLE 2386
    MCL vs. MALT predictor genes
    UNIQID Gene name Scale Factor
    1132834 SOX11—SRY (sex determining region Y)-box 11 20.7489202
    1101987 KIAA1909—KIAA1909 protein 10.78991326
    1100873 ESTs 10.11845036
    1130764 HNRPA0—heterogeneous nuclear ribonucleoprotein A0 9.432459453
    1102178 Homo sapiens, Similar to thymosin, beta, identified in 9.035605572
    neuroblastoma cells, clone MGC: 39900 IMAGE: 5247537,
    mRNA, complete cds
    1098277 PRICKLE1—prickle-like 1 (Drosophila) 9.003360784
    1130926 C5orf13—chromosome 5 open reading frame 13 8.712830747
    1098694 LOC112868—hypothetical protein LOC112868 8.309789856
    1103711 Homo sapiens cDNA FLJ11833 fis, clone HEMBA1006579. 8.248526605
    1138099 NA 8.107440225
    1120854 EDG1—endothelial differentiation, sphingolipid G-protein- 8.045872672
    coupled receptor, 1
    1102215 Homo sapiens cDNA FLJ11666 fis, clone HEMBA1004672. 8.032351578
    1121739 ZNF135—zinc finger protein 135 (clone pHZ-17) 8.020919565
    1096070 DNMT3A—DNA (cytosine-5-)-methyltransferase 3 alpha 7.964477216
    1101211 Homo sapiens cDNA: FLJ21960 fis, clone HEP05517. 7.738742472
    1120825 CHL1—cell adhesion molecule with homology to L1CAM 7.516130116
    (close homolog of L1)
    1099437 Homo sapiens mRNA; cDNA DKFZp667B1913 (from clone 7.209041652
    DKFZp667B1913)
    1096503 GL012—hypothetical protein GL012 7.171540413
    1135927 LILRA2—leukocyte immunoglobulin-like receptor, 7.134470829
    subfamily A (with TM domain), member 2
    1120645 FADS3—fatty acid desaturase 3 7.039952979
  • TABLE 2387
    MCL vs. PMBL predictor genes
    UNIQID Gene name Scale Factor
    1132834 SOX11—SRY (sex determining region Y)-box 11 28.17593839
    1100873 ESTs 17.90004832
    1096503 GL012—hypothetical protein GL012 17.43982729
    1098840 C3orf6—chromosome 3 open reading frame 6 17.37421052
    1124734 NA 16.73821457
    1135102 PRKCB1—protein kinase C, beta 1 16.67436366
    1103711 Homo sapiens cDNA FLJ11833 fis, clone HEMBA1006579. 16.57202026
    1140416 TOSO—regulator of Fas-induced apoptosis 15.64802242
    1121757 ADRB2—adrenergic, beta-2-, receptor, surface 15.57336633
    1140236 SPAP1—SH2 domain containing phosphatase anchor 15.20264513
    protein 1
    1099140 ESTs, Moderately similar to hypothetical protein FLJ20378 15.11929571
    [Homo sapiens] [H. sapiens]
    1099549 ESTs 14.92883027
    1139054 LOC58486—transposon-derived Buster1 transposase-like 14.63422275
    protein
    1138818 ILF3—interleukin enhancer binding factor 3, 90 kDa 14.50621028
    1109444 ESTs, Highly similar to IL24_HUMAN Interleukin-24 14.20430672
    precursor (Suppression of tumorigenicity 16 protein)
    (Melanoma differentiation associated protein 7) (MDA-7)
    [H. sapiens]
    1124534 KIAA0553—KIAA0553 protein 14.18537487
    1098277 PRICKLE1—prickle-like 1 (Drosophila) 13.98526258
    1131687 TLK1—tousled-like kinase 1 13.97468703
    1125112 PLCL2—phospholipase C-like 2 13.85714318
    1125397 Homo sapiens cDNA FLJ33389 fis, clone BRACE2006871. 13.85049805
  • TABLE 2388
    MCL vs. PTLD predictor genes
    UNIQID Gene name Scale Factor
    1109603 ESTs 19.95553782
    1138222 NA 15.95397369
    1135138 CD24—CD24 antigen (small cell lung carcinoma cluster 4 15.89198725
    antigen)
    1134230 RASGRP2—RAS guanyl releasing protein 2 (calcium and 15.80452978
    DAG-regulated)
    1139411 OSBPL10—oxysterol binding protein-like 10 14.32818885
    1140416 TOSO—regulator of Fas-induced apoptosis 13.89685188
    1132834 SOX11—SRY (sex determining region Y)-box 11 13.78424818
    1121739 ZNF135—zinc finger protein 135 (clone pHZ-17) 13.02195529
    1098156 Human HeLa mRNA isolated as a false positive in a two- 12.95032505
    hybrid-screen.
    1099270 Homo sapiens cDNA FLJ30555 fis, clone 12.7877735
    BRAWH2003818.
    1139012 FLJ20373—hypothetical protein FLJ20373 12.70176225
    1120854 EDG1—endothelial differentiation, sphingolipid G-protein- 12.25264341
    coupled receptor, 1
    1120985 KIAA0053—KIAA0053 gene product 12.04626201
    1115952 LOC146517—hypothetical protein LOC146517 11.96299478
    1120825 CHL1—cell adhesion molecule with homology to L1CAM 11.82402907
    (close homolog of L1)
    1131636 SPOCK2—sparc/osteonectin, cwcv and kazal-like 11.80417657
    domains proteoglycan (testican) 2
    1136706 MYT1—myelin transcription factor 1 11.74962191
    1113560 Homo sapiens, clone IMAGE: 5725893, mRNA 11.72049882
    1133851 P4HA1—procollagen-proline, 2-oxoglutarate 4- −12.59876059
    dioxygenase (proline 4-hydroxylase), alpha polypeptide I
    1137459 BCAT1—branched chain aminotransferase 1, cytosolic −14.00465411
  • TABLE 2389
    MCL vs. SLL predictor genes
    UNIQID Gene name Scale Factor
    1132834 SOX11—SRY (sex determining region Y)-box 11 23.59602107
    1101987 KIAA1909—KIAA1909 protein 14.50254794
    1103711 Homo sapiens cDNA FLJ11833 fis, clone HEMBA1006579. 13.31375894
    1096070 DNMT3A—DNA (cytosine-5-)-methyltransferase 3 alpha 12.37453972
    1130926 C5orf13—chromosome 5 open reading frame 13 11.27840239
    1120645 FADS3—fatty acid desaturase 3 11.14057287
    1138099 NA 10.92729287
    1097887 KIAA0303—KIAA0303 protein 10.37913127
    1099941 ESTs 10.33953409
    1130373 KIAA0303—KIAA0303 protein 10.01524528
    1110957 SYNE2—spectrin repeat containing, nuclear envelope 2 9.865436185
    1130320 ESTs 9.807091644
    1124373 LPIN1—lipin 1 9.024985551
    1128813 KREMEN2—kringle containing transmembrane protein 2 8.903791941
    1131130 MARCKS—myristoylated alanine-rich protein kinase C 8.688979176
    substrate
    1120825 CHL1—cell adhesion molecule with homology to L1CAM 8.685132271
    (close homolog of L1)
    1119752 BASP1—brain abundant, membrane attached signal 8.663402838
    protein 1
    1131854 GCLC—glutamate-cysteine ligase, catalytic subunit −8.761521136
    1105801 Homo sapiens mRNA; cDNA DKFZp686H1529 (from clone −8.828675125
    DKFZp686H1529)
    1097824 MAP2—microtubule-associated protein 2 −9.345688564
  • TABLE 2390
    MCL vs. splenic predictor genes
    UNIQID Gene name Scale Factor
    1106855 KIAA1909—KIAA1909 protein 14.48278638
    1121739 ZNF135—zinc finger protein 135 (clone pHZ-17) 11.95918572
    1111850 Homo sapiens cDNA FLJ36977 fis, clone BRACE2006344. 11.13464157
    1098024 KIAA1972—KIAA1972 protein 10.10869886
    1130764 HNRPA0—heterogeneous nuclear ribonucleoprotein A0 10.06898534
    1135342 SHOX2—short stature homeobox 2 9.565884385
    1097218 MGC45400—hypothetical protein MGC45400 9.187725705
    1117193 RINZF—zinc finger protein RINZF 9.12522795
    1139564 PSMD10—proteasome (prosome, macropain) 26S 9.066714773
    subunit, non-ATPase, 10
    1132834 SOX11—SRY (sex determining region Y)-box 11 8.908574745
    1131130 MARCKS—myristoylated alanine-rich protein kinase C 8.732921026
    substrate
    1131756 PDCD4—programmed cell death 4 (neoplastic 8.441424593
    transformation inhibitor]
    1102187 DKFZp586C102—hypothetical protein DKFZp586C1021 8.391861029
    1098195 DKFZp762C111—hypothetical protein DKFZp762C1112 8.349839204
    1101211 Homo sapiens cDNA: FLJ21960 fis, clone HEP05517. 8.337208237
    1136673 GNAS—GNAS complex locus 8.254076655
    1139116 USP16—ubiquitin specific protease 16 8.179384251
    1098694 LOC112868—hypothetical protein LOC112868 7.935903681
    1120519 WWP2—Nedd-4-like ubiquitin-protein ligase −7.881202253
    1114916 FLJ13993—hypothetical protein FLJ13993 −8.33683119
  • With so many candidate predictor genes being utilized, it is possible to generate a predictor model that accurately predicts every element of a training set but fails to perform on an independent sample. This occurs because the model incorporates and “learns” the individual characteristics of each sample in the training set. Leave-one-out cross-validation was used to verify that the prediction models generated above would work on independent samples that the models had not encountered previously. In this cross-validation method, a single sample is removed from the training set, and the predictor is developed again using the remaining data. The resulting model is then used to predict the sample that was removed. This method is repeated with each individual sample taken out. Since no sample is predicted from a model that includes that sample, this method provides an unbiased estimate of predictor accuracy.
  • When the predictors developed above were evaluated by leave-one-out cross-validation, all but one of the 21 MCL samples were correctly identified as MCL and none of the 489 non-MCL samples were mistakenly identified as MCL.
    • Example 12 Identification of Lymphoma Samples as MCL Based on Bayesian Analysis of Gene Expression Data from a Lymphochip Microarray
  • Lymphoma samples with morphology consistent with MCL were identified by pathological review. Since t(11; 14) translocation and cyclin D1 overexpression have been consistently associated with MCL, cyclin D1 mRNA levels were measured in each sample by quantitative RT-PCR. Of the 101 samples analyzed, 92 expressed cyclin D1 mRNA. These 92 samples, which were deemed the “core group” of MCLs, were divided into a training set and a validation set. Gene expression was measured in all 101 samples using a Lymphochip microarray (Alizadeh 1999). For comparison, gene expression was measured in 20 samples identified as SLL. In addition, MCL expression data was compared to expression data obtained previously for GCB (134 cases) and ABC (83 cases) (Rosenwald 2002). Several thousand genes were differentially expressed between cyclin D1-positive MCL and the other lymphoma types with high statistical significance (p<0.001). A complete listing of these genes is available at Rosenwald et al., Cancer Cell, 3: 185-197 (2003), which is referenced therein at page 194 and which is hosted by the Lymphoma/Leukemia Molecular Profiling Project Gateways at the National Institute of Health web site.
  • Three different binary predictor models were developed: MCL vs. SLL, MCL vs. GCB, and MCL vs. ABC. Each of these models was designed to calculate the probability that a sample was MCL rather than the other lymphoma type in the pair. For each pair, the genes that were most differentially expressed between MCL and the other lymphoma type in the pair were identified, and the difference in expression between the lymphoma types was quantified using a Student's t-test. An LPS was then calculated for each sample using the following formula:
  • LPS ( X ) = ∑ j ∈ G t j X j ,
  • where Xj is the expression of gene j in sample X and tj is the t-statistic for the difference in expression of gene j between the two lymphoma types in the pair. Cyclin D1 was excluded from the calculation of LPS so that the model could be used to identify potential MCL cases that were cyclin D1 negative.
  • After an LPS had been formulated for each lymphoma sample, the mean and standard deviation of these LPS's was calculated for each lymphoma type. For a new sample X, Bayes' rule can be used to estimate the probability q that the sample belongs to MCL rather than the second lymphoma type in the pair using the following equation:
  • q ( X is MCL ) = φ ( LPS ( X ) ; μ ^ MCL , σ ^ MCL ) φ ( LPS ( X ) ; μ ^ MCL , σ ^ MCL ) + φ ( LPS ( X ) ; μ ^ 2 , σ ^ 2 )
  • where φ(x; μ,σ) is the normal density function with mean μ and standard deviation σ, {circumflex over (μ)}MCL and {circumflex over (σ)}MCL are the sample mean and variance of the LPS values for MCL, and {circumflex over (μ)}2 and {circumflex over (σ)}2 are the sample mean and variance of the LPS values for the second lymphoma type of the pair. A cut-off point of 90% was selected for assigning a sample to a particular lymphoma type. Every sample in the training set was classified correctly using this model (FIG. 16). When applied to the validation set, the model correctly classified 98% of the cyclin D1-positive MCL cases as MCL (FIG. 16).
  • This diagnostic test was applied to nine lymphoma cases that were morphologically consistent with MCL, but negative for cyclin D1 expression. Seven of these samples were classified as MCL, one was classified as GCB, and one was not assigned to any lymphoma type because none of the pairs generated a probability of 90% or greater.
    • Example 13 Classification of DLBCL Samples Based on Bayesian Analysis of Gene Expression Data from the Lymphochip Microarray
  • A statistical method to classify DLBCL samples based on Bayesian analysis was developed using gene expression data obtained using the Lymphochip cDNA microarray (Rosenwald 2002). This data is available at http://llmpp.nih.gov/DLBCL. The data was divided into two sets: a training set used to create and optimize the prediction model, and a validation set to evaluate the performance of the model. The training set consisted of 42 ABC DLBCL samples and 67 GCB DLBCL samples, while the validation set consisted of 41 ABC DLBCL samples, 67 GCB DLBCL samples, and 57 type 3 DLBCL samples (Shipp 2002).
  • Genes that were listed as present on >50% of the samples were identified, and the signal value for these genes on each microarray was normalized to 1,000. After normalization, all signal values under 50 were set to 50. A log2 transformation was then performed on all the signal values.
  • An LPS for distinguishing between two lymphoma types was calculated for each sample X in the training set using an equation:
  • LPS ( X ) = ∑ j t j X j ,
  • where Xj represents the expression level of gene j and tj is a scaling factor whose value depends on the difference in expression of gene j between the two lymphoma types. The scaling factor used in this example was the t-statistic generated by at test of the difference in gene j expression between two lymphoma types. Only those genes with the largest t-statistics were included when calculating the LPS for each sample. The list of genes used to generate the LPS was narrowed further by including only those genes that were most variably expressed within the training set. Only genes in the top third with respect to variance were included. Genes that displayed a correlation with proliferation or lymph node signatures (Shaffer 2001; Rosenwald 2002) were eliminated from consideration, because these genes are often variably expressed within samples from a single lymphoma type (Rosenwald 2002).
  • Since the LPS is a linear combination of gene expression values, its distribution within each lymphoma type should be approximately normal, provided that it includes a sufficient number of genes and the correlation structure of those genes is not extreme. The mean and variance of these normal distributions within a lymphoma type can then be estimated from the combined LPS's of all samples within the type. The LPS distribution of two lymphoma types can be used to estimate the probability that a new sample belongs to one of the types using Bayes' rule. The probability q that a sample Y belongs to lymphoma type 1 can be determined by an equation:
  • q ( Y is subtype 1 ) = φ ( LPS ( X ) ; μ ^ 1 , σ ^ 1 ) φ ( LPS ( Y ) ; μ ^ 1 , σ ^ 1 ) + φ ( LPS ( Y ) ; μ ^ 2 , σ ^ 2 )
  • where φ(x; μ,σ) is the normal density function with mean μ and standard deviation σ, {circumflex over (μ)}1 and {circumflex over (σ)}1 are the sample mean and variance of the LPS values for lymphoma type 1, and {circumflex over (μ)}2 and {circumflex over (σ)}2 are the sample mean and variance of the LPS values for lymphoma type 2. This calculation was used to determine the probability that each sample in the training set belonged to GCB or ABC. A sample was classified as a particular type if it had a 90% or greater probability of belonging to that type. The number of genes in the predictor model was optimized based on the accuracy with which the predictor classified samples into the ABC or GCB subtypes defined previously by hierarchical clustering (Rosenwald 2002). The final predictor incorporated 27 genes, and correctly classified 87% of the training set samples into the subtype to which they had been assigned by hierarchical clustering (FIG. 17). The genes included in the predictor are listed in Table 2391.
  • TABLE 2391
    Unigene ID
    UNIQID Build 167 Gene symbol
    19375 235860 FOXP1
    19346 109150 SH3BP5
    19227 193857 LOC96597
    16049 439852 IGHM
    32529 55098 C3orf6
    24729 127686 IRF4
    24899 81170 PIM1
    19348 NA NA
    27565 444105 ENTPD1
    17227 170359 IL16
    26919 118722 FUT8
    24321 171262 ETV6
    29385 167746 BLNK
    16858 376071 CCND2
    31801 386140 BMF
    19234 418004 PTPN1
    26385 307734 MME
    24361 388737 NA
    24570 446198 NA
    24904 18166 KIAA0870
    24429 155024 BCL6
    28224 387222 NEK6
    27673 124922 LRMP
    24376 317970 SERPINA11
    17496 300592 MYBL1
    17218 283063 LMO2
    28338 78877 ITPKB
  • Since the samples used to estimate the distribution of the LPS's were the same samples used to generate the model, there was a possibility of overfitting. Overfitting would result in a model that indicates a larger separation between the LPS's of two lymphoma types than would be found in independent data. To ensure that overfitting was not taking place, the model was tested on the validation set. The reproducibility of the predictor model was verified by its ability to correctly classify 88% of the samples in the validation set (FIG. 18). Interestingly, 56% of the DLBCL samples that had been placed in the type 3 subtype by hierarchical clustering were classified as either ABC or GCB using this Bayesian model.
  • In previous experiments, the genes that were used to distinguish GCB and ABC were deliberately selected to include those that were preferentially expressed in normal GC B cells (Alizadeh 2000; Rosenwald 2002). In the present analysis, the predictor model was not biased a priori to include such genes. The ABC and GCB lymphoma types as defined by the Bayesian model were analyzed for differential expression of GC B cell restricted genes. Thirty seven genes were found to be both more highly expressed in GC B cells than at other stages of differentiation (p<0.001) and differentially expressed between DLBCL subtypes (p<0.001) (FIG. 19A). These 37 genes are listed in Table 2392.
  • TABLE 2392
    Unigene ID
    UNIQID Build 167 Gene symbol
    28014 300592 MYBL1
    24376 317970 SERPINA11
    24429 155024 BCL6
    16886 124922 LRMP
    27374 283063 LMO2
    29912 446198
    24510 266175 PAG
    24854 439767 TOX
    32171 307734 MME
    24361 388737
    19365 171857 Cyorf15a
    27292 272251 KLHL5
    24822 283794 PCDHGC3
    30923 446195
    24825 88556 HDAC1
    31696 91139 SLC1A1
    26976 434281 PTK2
    19279 49614 GCET2
    17866 1765 LCK
    24386 437459 MYO1E
    33013 293130 VNN2
    25126
    30498 157441 SPI1
    26512 379414 MFHAS1
    26582 153260 SH3KBP1
    17840 132311 MAP2K1
    26000 25155 NET1
    24323 149342 AICDA
    30922 435904 C21orf107
    30641 79299 LHFPL2
    19308 179608 DHRS9
    24455 405387
    30034 300208 SEC23IP
    24977 169939 HS2ST1
    24449 206097 RRAS2
    30763 446198
    27987 73792 CR2

    All but two (AICDA and DHRS9) of these 37 genes were more highly expressed in GCB than in ABC. This demonstrates that the DLBCL subtypes defined by the Bayesian predictor seem to differ with respect to their cell of origin, with GCB retaining the gene expression program of normal GC B cells.
  • ABC, on the other hand, displayed higher expression of genes characteristic of plasma cells (FIG. 19B). Twenty four genes were found to be both more highly expressed in plasma cells than in B cells at earlier developmental stages (p<0.001) and differentially expressed between the DLBCL subtypes (p<0.001). These 24 genes are listed in Table 2393.
  • TABLE 2393
    Unigene ID
    UNIQID Build 167 Gene symbol
    16614 127686 IRF4
    26907 118722 FUT8
    31104 313544 NS
    19219 355724 CFLAR
    26174 28707 SSR3
    24566 169948 KCNA3
    34500 442808 B4GALT2
    26991 314828 UPP1
    30191 438695 FKBP11
    27402 259855 EEF2K
    26096 434937 PPIB
    15887 2128 DUSP5
    32440 512686 C20orf59
    34827 429975 PM5
    29232 437638 XBP1
    17763 76640 RGC32
    32163 445862 RAB30
    17814 5353 CASP10
    31460 409223 SSR4
    26693 83919 GCS1
    25130 409563 PACAP
    16436 267819 PPP1R2
    31610 76901 PDIR
    28961 212296 ITGA6

    The majority of these plasma cell-restricted genes were more highly expressed in ABC than in GCB. Eight of the 32 genes encode proteins that reside and function in the endoplasmic reticulum (ER) or Golgi apparatus, suggesting that ABCs have increased the intracellular machinery for protein secretion. These eight genes are denoted in the above list by the designation “ER” or “golgi” in parentheses. Another gene on this list, XBP-1 transcription factor, encodes a protein that is required for plasma cell differentiation (Reimold 2001) and is involved in the response to unfolded proteins in the ER (Calfon 2002). ABCs have not undergone full plasmacytic differentiation, however, because other key plasma cell genes such as Blimp-1 were not more highly expressed in ABC.
    • Example 14 Classification of DLBCL Samples Based on Bayesian Analysis of Gene Expression Data from the Affymetrix HU6800 Microarray
  • The prediction method described in Example 14 above was applied to gene expression data from 58 DLBCL samples obtained using an Affymetrix HU6800 oligonucleotide microarray (Shipp 2002). This data is available at www.genome.wi.mit.edu/MPR/lymphoma. The first step in analyzing this data was to exclude all microarray features with a median signal value of <200 across the samples. Multiple microarray features representing the same gene were then averaged. Of the 27 genes in the DLBCL subtype predictor developed using the Lymphochip data (above), only 14 were represented on the Affymetrix array and passed this filtering process. These 14 genes are listed in Table 2394.
  • TABLE 2394
    Unigene ID
    UNIQID Build 167 Gene symbol
    24729 127686 IRF4
    17227 170359 IL16
    26907 118722 FUT8
    27565 444105 ENTPD1
    16858 376071 CCND2
    24899 81170 PIM1
    16947 418004 PTPN1
    16049 439852 IGHM
    26385 307734 MME
    27673 124922 LRMP
    24429 155024 BCL6
    17218 283063 LMO2
    28338 78877 ITPKB
    17496 300592 MYBL1

    These 14 genes were used to create a new DLBCL subtype predictor in which the LPS scaling coefficients were again calculated based on the DLBCL subtype distinction in the Lymphochip data set (Rosenwald 2002). To account for systematic measuring differences between the Affymetrix and Lymphochip microarrays, the expression value of each gene on the Affymetrix microarray was shifted and scaled to match the mean and variance of the corresponding expression values on the Lymphochip. The adjusted expression values for each of the 14 genes were then used to calculate LPS's for each sample. DLBCL subtype membership was again assigned on a cut-off of 90% certainty. Several observations suggested that the predictor identified ABC and GCB samples within the Affymetrix data set that were comparable to those found in the Lymphochip data set. First, the relative proportions of ABC (29%) and GCB (53%) were very similar to the corresponding proportions in the Lymphochip data set (34% and 49%, respectively). Second, 43 genes were found to be differentially expressed between the two DLBCL subtypes with high significance (p<0.001) in the Affymetrix data. This number is substantially higher than would be expected by chance, given that the Affymetrix microarray measures the expression of approximately 5,720 genes. The symbols for these 43 genes were: IGHM; TCF4; IRF4; CCND2; SLA; BATF; KIAA0171; PRKCB1; P2RX5; GOT2; SPIB; CSNK1E; PIM2; MARCKS; PIM1; TPM2; FUT8; CXCR4; SP140; BCL2; PTPN1; KIAA0084; HLA-DMB; ACP1; HLA-DQA1; RTVP1; VCL; RPL21; ITPKB; SLAM; KRT8; DCK; PLEK; SCA1; PSIP2; FAM3C; GPR18; HMG14; CSTB; SPINK2; LRMP; MYBL1; and LMO2. Third, the 43 genes differentially expressed between the types included 22 genes that were not used in the predictor but were represented on Lymphochip arrays. Fourteen of these 22 genes were differentially expressed on the Lymphochip array with high statistical significance (p<0.001). Finally, the expression of the c-rel gene was previously found to correspond to amplification of the c-rel genomic locus in DLBCL tumor cells, and oncogenic event occurring in GCB but not ABC (Rosenwald 2002). In the Affymetrix data set, c-rel was differentially expressed between the two subtypes (p=0.0025), and was highly expressed only in a subset of GCB's.
    • Example 15 Identification of DLBCL Samples as PMBL Based on Bayesian Analysis of Gene Expression Data from the Lymphochip Microarray
  • 310 lymphoma biopsy samples identified as DLBCL by a panel of hematopathologists were divided into a 36 sample training set and a 274 sample validation set, with the validation set consisting of the DLBCL samples classified previously in Example 14. All patients from whom the samples were derived had been treated with anthracycline-containing multiagent chemotherapy protocols, with some patients additionally receiving radiation therapy. The training set was profiled for gene expression using Lymphochip microarrays comprising 15,133 cDNA elements as described previously (Alizadeh 2000). This data is available at the web site companion for Rosenwald et al., J. Exp. Med., 198: 851-862 (2003), which is referenced therein at page 852 and which is hosted by Lymphoma/Leukemia Molecular Profiling Project Gateway at the National Institute of Health web site. The validation set had previously been profiled using Lymphochip microarrays comprising 12,196 cDNA elements (Rosenwald 2002). This data is available at the web site companion for Rosenwald et al., New Eng. J. Med., 346: 1937-1947 (2002), which is referenced therein at page 1938 and which is hosted by the Lymphoma/Leukemia Molecular Profiling Project Gateway at the National Institute of Health web site.
  • A hierarchical clustering algorithm (Eisen 1998) was used to organize the genes by their expression patterns across the 36 samples in the training set. A large group of genes that were more highly expressed in lymphomas with mediastinal involvement than in other DLBCLs was shown to be tightly clustered in the resulting dendrogram (FIG. 20A). This cluster of genes included two genes, MAL and FIG. 1, previously shown to be highly expressed in PMBL (Copie-Bergman 2002; Copie-Bergman 2003). Several of the lymphomas with mediastinal involvement did not express this set of putative PMBL signature genes, and it was suspected that these samples were more likely to be conventional DLBCL than PMBL. Hierarchical clustering was used to organize the samples according to their expression of the PMBL signature genes, resulting in two major clusters of cases (FIG. 20B). One cluster contained 21 samples designated “PMBL core” samples by virtue of their higher expression of PMBL signature genes. The other cluster contained some samples that had virtually no expression of these genes, and other samples that did express these genes but at lower levels than the PMBL core samples.
  • A gene expression-based method for distinguishing PMBL core cases from GCB and ABC DLBCL cases based on Bayesian analysis was developed using the methods described in Examples 14 and 15. A set of genes were selected that were differentially expressed between the PMBL core samples and both GCB and ABC (p<0.001). This set of genes included all of the PMBL signature genes identified by hierarchical clustering (FIG. 20A), as well as a large number of additional genes. Many of the genes in this set belonged to the lymph node gene expression signature (Alizadeh 2000; Rosenwald 2002). These genes were excluded from the final predictor because they might cause some DLBCL samples with higher expression of lymph node gene expression signature genes to be misclassified as PMBL. The list of PMBL distinction genes was refined by adding a requirement that they also be differentially expressed between the PMBL core samples and a subgroup of six DLBCL samples with higher expression of lymph node gene expression signature genes (p<0.001). The resulting set of 46 genes included 35 genes that were more highly expressed in PMBL and 11 genes that were more highly expressed in DLBCL (FIG. 21A). The 46 genes in this set were PDL2, SNFT, ILI 3RA1, FGFR1, FLJ10420, CCL17/TARC, TNFRSF8/CD30, E2F2, MAL, TNFSF4/OX40 ligand, IL411/FIG. 1, IMAGE:686580, BST2, FLJ31131, FCER2/CD23, SAMSN1, JAK2, FLJ00066, MST1R, TRAF1, SLAM, LY75, TNFRSF6/Fas, FNBP1, TLR7, TNFRSF17/BCMA, CDKN1A/p21CIP1, RGS9, IMAGE:1340506, NFKB2, KIAA0339, ITGAM, IL23A, SPINT2, MEF2A, PFDN5, ZNF141, IMAGE:4154313, IMAGE:825382, DLEU1, ITGAE, SH3BP5, BANK, TCL1A, PRKAR1B, and CARD11. A series of linear predictor scores were generated based on the expression of this gene set. Based on the distribution of linear predictor scores within a particular lymphoma type, Bayes' rule can be used to estimate the probability that a particular sample belongs to either of the two types. An arbitrary probability cut-off of 90% or greater was used to classify a sample as a particular lymphoma type. All of the PMBL core samples were classified as PMBL using this method, as were six of the other lymphoma samples with mediastinal involvement. However, nine of the lymphoma samples with mediastinal involvement were classified as a DLBCL, as were all of the GCB and ABC samples.
  • In the validation set, 11 samples were identified on clinical grounds as being consistent with a diagnosis of PMBL, and the Bayesian model classified nine of these as PMBL (FIG. 21B). Interestingly, 12 of the remaining 263 DLBCL samples were classified as PMBL by the predictor. FIG. 21B shows that these cases were indistinguishable by gene expression from the nine cases diagnosed as PMBL on clinical grounds. As expected, the average expression of the PMBL predictor genes in the 249 samples classified as DLBCL was notably lower than in the 22 PMBL cases. Thus, PMBL represents a third subgroup of DLBCL than can be distinguished from ABC and GCB by gene expression profiling.
  • Table 2395 compares the clinical parameters of patients assigned to the PMBL, ABC, and GCB subgroups of DLBCL using this prediction method.
  • TABLE 2395
    PMBL PMBL PMBL
    ABC GCB Training Validation All
    DLBCL DLBCL set set cases P value
    Median age 66   61   33   33   33   4.4E−16
    Age <35  5% 10% 52% 56% 53% 7.2E−14
    Age 35-60 29% 38% 44% 28% 37%
    Age >60 66% 52%  4% 17%  9%
    Gender = male 59% 53% 44% 50% 47% 0.38
    Female <35  2%  3% 32% 39% 35% 1.1E−12
    Male <35  2%  7% 20% 17% 19%
    Female 35-60  6% 18% 24%  6% 16%
    Male 35-60 23% 19% 20% 22% 21%
    Female >60 33% 25%  0%  6%  2%
    Male >60 34% 27%  4% 11%  7%

    PMBL patients were significantly younger than other DLBCL patients, with a median age at diagnosis of 33 years compared with a median age of 66 and 61 years for ABC and GCB patients, respectively. Although there was no significant difference in gender distribution among the DLBCL subgroups, young women (<35 years) accounted for 35% of PMBL patients, more than any other DLBCL subgroup. Young men (<35 years) were also more frequently represented in the PMBL subgroup, accounting for 19% of the patients. Correspondingly, older men and women (age >60) were significantly underrepresented in the PMBL subgroup. These clinical characteristics were observed in both the training set and the validation set of PMBL cases, demonstrating that the PMBL predictor reproducibly identified a clinically distinct subgroup of DLBCL patients.
  • The PMBL subgroup defined by the PMBL predictor had a relatively favorable overall survival rate after therapy (FIG. 22). PMBL patients had a five-year survival rate of 64%, superior to the 46% rate seen in DLBCL patients as a whole (p=0.0067). The survival of the PMBL subgroup was significantly better than the 30% five-year survival rate of the ABC subgroup (FIG. 22; p=5.8E-5), but only marginally better than the 59% five-year survival rate of the GCB subgroup (p=0.18).
    • Example 16 Classification of Lymphomas into Types Based on Bayesian Analysis of Gene Expression Data from the Lymph Dx Microarray
  • Based on the clustering of the Lymph Dx microarray signals for the DLBCL samples, a cluster of “proliferation signature” genes and a cluster of “lymph node signature” genes were identified. The expression of these genes was averaged to form a proliferation signature and a lymph node signature. Each gene represented on the Lymph Dx microarray was placed into one of three “gene-list categories” based on its correlation with the proliferation or lymph node gene signatures. “Proliferation” genes were defined as those genes for which the correlation between their expression and the proliferation signature was greater than 0.35. Lymph node genes were defined as those genes for which the correlation between their expression and the lymph node signature was greater than 0.35. The remaining genes on the array were classified as standard genes. This classification resulted in 323 proliferation genes and 375 lymph node genes.
  • Two stages of lymphoma classification were performed using the gene expression data obtained for the above samples using the Lymph Dx microarray. The general procedure used to classify the samples is presented in flow chart form in FIG. 1.
  • For the first stage of expression analysis, the samples were divided into five types: FL, MCL, SLL, FH, and a class of aggressive lymphomas that included DLBCL and BL. Samples obtained from subjects with other diagnoses (e.g., MALT, LPC) were omitted from this analysis. Data from the Lymph Dx microarray was then used to compare gene expression in each possible lymphoma type pair (e.g., FH vs. FL, MCL vs. SLL, etc.). This resulted in the creation of ten “pair-wise models” (one for each possible lymphoma type pair) for predicting whether a sample fell into a particular lymphoma type.
  • For each lymphoma type pair, the difference in expression between the two types for every gene on the microarray was calculated, and a t-statistic was generated to represent this difference. Within each gene-list category (proliferation, lymph node, and standard), individual genes were ordered based on the absolute value of their t-statistic. Only those genes that displayed a statistically significant difference in expression between the two types were included in the model. Those genes with largest absolute t-statistics in each gene-list category were then used to generate a linear predictor score (LPS) for each sample. For a sample X and a set of genes G, the LPS was defined as:
  • LPS ( X ) = ∑ j ∈ G t j X j ,
  • where Xj is the expression of gene j in the sample and tj is the t-statistic representing the difference in expression of gene j between the two lymphoma types. This formulation of LPS, known as the compound covariate predictor, has previously been used successfully (Radmacher 2002; Rosenwald 2003a; Wright 2003). Other ways to formulate an LPS include Fisher linear discriminant analysis (Dudoit 2002), weighted voting (Golub 1999), linear support vector machines (Ramaswamy 2001), and nearest shrunken centroids (Tibshirani 2002).
  • In order to optimize the number of genes used to generate the LPS, a series of LPS's were generated for each sample using between five and 100 genes from each gene-list category. The optimal number of genes is that number which generates a maximum t-statistic when comparing the LPS of two samples from different lymphoma types (FIG. 23). This optimization procedure was repeated for every gene-list category in every pair-wise model, meaning that 30 optimizations were performed in all.
  • It was recognized that for some pair-wise models, it would be useful to calculate LPS's using different combinations of gene-list categories. LPS's were calculated for each sample using four different combinations. In the first, LPS was calculated using the standard genes only. In the second, LPS's were calculated for both the standard and proliferation genes, but not the lymph node genes. In the third, LPS's were calculated for both the standard and lymph node genes, but not the proliferation genes. In the fourth, LPS's were calculated using all three gene-list categories.
  • Depending on the number of gene-list categories included, between one and three LPS's were calculated for each sample in the pair-wise models. Thus, each sample could be thought of as a vector in a space of between one and three dimensions. Since the LPS's were sums of individual expressions, it was reasonable to approximate the distributions as normal. Multivariate normal distributions are defined by two quantities: a mean vector, which indicates the average value of each of the models within a given lymphoma type, and a covariance matrix, which indicates the magnitude and orientation spread of points away from this center. Both of these quantities can be estimated empirically from the observed data. FIG. 24 shows the Standard and Proliferation LPS's for the FL vs. DLBCL/BL pair-wise model. The dotted lines indicate the standard deviations from the fitted multivariate normal distributions.
  • Once the multidimensional distributions have been estimated, Bayes' rule (Bayes 1763) can be used to estimate the probability that a given sample belongs to one lymphoma type or another. Bayesian analysis of an LPS has been successfully employed in the past to distinguish DLBCL subtypes (Rosenwald 2003a, Wright 2003). For a sample X, the probability q of the sample belonging to a first lymphoma type rather than a second lymphoma type can be calculated using the formula:
  • q = φ ( LPS ( X ) ; μ ^ 1 , σ ^ 1 ) φ ( LPS ( X ) ; μ ^ 1 , σ ^ 1 ) + φ ( LPS ( X ) ; μ ^ 2 , σ ^ 2 )
  • where LPS(X) is the linear predictor score for sample X, φ(x; μ,σ) is the normal density function with mean μ and standard deviation σ, {circumflex over (μ)}1 and {circumflex over (σ)}1 are the mean and variance of the LPS's for the first lymphoma type, and {circumflex over (μ)}2 and {circumflex over (σ)}2 are the mean and variance of the LPS's for the second lymphoma type. Using this equation, a single probability q value can be developed for each sample and for each of the four LPS combinations. This q value can then be used to classify a sample as a first lymphoma type, a second lymphoma type, or unclassified. Samples with the highest q values are classified as the first lymphoma type, while samples with the lowest q values are classified as the second lymphoma type. Samples with middle range q values are deemed unclassified. Classifying the samples in this manner requires two cut-off points: a lower cut-off point between the second lymphoma type and unclassified, and an upper cut-off point between unclassified and the first lymphoma type. To develop these cut-off points, samples were ordered by their q values, and each possible cut-off point between adjacent samples was considered. To ensure that the cut-off points were reasonable, the lower cut-off point was restricted to between 0.01 and 0.5 and the upper cut-off point was restricted to between 0.5 and 0.99.
  • Every cut-off point and model combination was analyzed by the following equation:

  • 3.99*[(% of type 1 misidentified as type 2)+(% of type 2 misidentified as type 1)]+[(% of type 1 unclassified)+(% of type 2 misidentified)].
  • Using this equation, the cut-off point would be adjusted to allow an additional error only if this adjustment resulted in four or more unclassified samples becoming correctly classified. The final model and cut-off point for a given pair-wise analysis was that which minimized this equation. The equation utilizes percentages rather than the actual number of cases in order to account for the different number of samples in each class.
  • All cut-off points between a given pair of adjacent q-values will produce the same division of data. Since cut-off point optimality is defined in terms of dividing the data into subtypes, all cut-off points between a pair of borderline cases will be equally optimal. In choosing where to place the actual cut-off point values, values were chosen that would lead to a larger unclassified region. When the lower cut-off point was being defined, a value would be chosen that was ⅕ of the way from the smallest borderline case to the largest. When the upper cut-off point was being defined, a value would be chosen that was ⅘ of the way from the smallest borderline case to the largest. FIG. 25 illustrates the q-results of optimizing the cut-point for the FL versus DLBCL/BL samples. The optimal lower cut-off point for these samples was found at q=0.49, while the optimal upper cut-off point was found at q=0.84. FIG. 26 indicates how this choice of cut-off points divided the space of LPS's.
  • The above procedures resulted in a series of pair-wise models for comparing every lymphoma type to every other lymphoma type. If there are n types, then there will be n−1 pair-wise models for each type. Since there were five lymphoma types in the stage 1 analysis, each type was involved in 4 pair-wise models. For instance, there were four different pair-wise models for MCL: MCL vs. FH, MCL vs. FL, MCL vs. SLL, and MCL vs. DLBCL/BL. For each sample tested, each pair-wise model will produce one of three possible results: 1) the sample belongs to the first lymphoma type of the pair-wise model, 2) the sample belongs to the second lymphoma type of the pair-wise model, or 3) the sample is unclassified. If each of the n−1 models agrees that the sample belongs to a particular lymphoma type, then the sample is designated as belonging to that type. If the n−1 models do not all agree that the sample belongs to a particular lymphoma type, the sample is designated as unclassified.
  • To ensure that the above methods did not result in overfitting (i.e., models that fit particular idiosyncrasies of the training set but fail when applied to independent data), the models were validated by leave-one-out cross-validation fashion (Hills 1966). Each sample was removed from the data one at a time, and a predictive model was developed as described above using the remaining data. This model was then used to predict the sample that was removed. Since the model being used to predict a given sample was generated from data that did not include that sample, this method provided an unbiased estimate of the accuracy of the model.
  • The results of the leave-one-out predictions are set forth in Tables 2396 and 2397, below. The rows in each table correspond to different sample groups, while the columns indicate the prediction results. The standard to which the prediction results were compared in this stage was the diagnoses of a panel of eight expert hematopathologists who used histological morphology and immunohistochemistry to classify the samples. Table 2396 provides classification results for the five lymphoma types tested (DLBCL/BL, FL, FH, MCL, SLL), while Table 2397 provides more specific results for classification of subtypes within these five lymphoma types. The results set forth in Table 2396 are also summarized in FIG. 27.
  • TABLE 2396
    DLBCL/ % %
    BL FL FH MCL SLL Unclassified Total Correct Unclassified % Error
    DLBCL/BL 249 6 0 0 0 7 262  95% 2% 3%
    FL
    5 154 0 0 0 14 173  89% 8% 3%
    FH
    0 0 17 0 0 0 17 100% 0% 0%
    MCL
    0 0 0 22 0 0 22 100% 0% 0%
    SLL
    0 0 0 0 14 0 14 100% 0% 0%
  • TABLE 2397
    DLBCL/ % % %
    BL FL FH MCL SLL Unclassified Total Correct Unclassified Error
    ABC 78 0 0 0 0 0 78 100%  0% 0%
    GCB 77 4 0 0 0 4 85 91% 5% 5%
    PMBL 33 0 0 0 0 0 33 100%  0% 0%
    Unclassified 27 1 0 0 0 2 30 90% 7% 3%
    DLBCL
    DLBCL (not yet 14 0 0 0 0 1 15 93% 7% 0%
    subclassed)
    BL 20 1 0 0 0 0 21 95% 0% 5%
    FL grade
    1 1 78 0 0 0 3 82 95% 4% 1%
    FL grade
    2 2 58 0 0 0 3 63 92% 5% 3%
    FL grade 3A 2 18 0 0 0 8 28 64% 29%  7%
    Combined FL
    5 154 0 0 0 14 173 89% 8% 3 %
    grades
    1, 2, 3A
    FL grade 3B 2 1 0 0 0 4 7 14% 57%  29% 
    FL unknown grade 3 11 0 0 0 0 14 79% 0% 21% 
    FH
    0 0 17 0 0 0 17 100%  0% 0%
    MCL
    0 0 0 22 0 0 22 100%  0% 0%
    SLL
    0 0 0 0 14 0 14 100%  0% 0%
  • As seen in Table 2396, perfect prediction of SLL, MCL, and FH samples was obtained. The success rate for predicting FL and the aggressive lymphomas (DLBCL/BL) was also very good, with only 3% of the samples being classified incorrectly. As seen in Table 2397, perfect prediction was also obtained for ABC and PMBL samples within the DLBCL samples.
    • Example 17 Classification of DLBCL/BL Samples into Subtypes Based on Bayesian Analysis of Gene Expression Data from the Lymph Dx Microarray
  • Samples identified as DLBCL/BL in Example 17 were subdivided into four types: ABC, GCB, PMBL, and BL. These samples were then used to generate six pair-wise models using the same procedure described in Example 17. The results of the leave-one-out predictions using these pair-wise models are set forth in Table 2398, below. These results are also summarized in FIG. 28. The rows in the table correspond to different sample groups, while the columns indicate the prediction results. In this stage, the ability of the prediction method to identify BL was again measured against the diagnoses of hematopathologists. The ability of the prediction method to identify the various DLBCL subtypes, on the other hand, was measured against previous studies in which this distinction between subtypes was based on gene expression data from a Lymphochip microarray (Alizadeh 2000, Rosenwald 2002, Rosenwald 2003a, Wright 2003).
  • TABLE 2398
    % % %
    ABC GCB PMBL BL Unclassified Total Correct Unclassified Error
    ABC 76 0 0 0 2 78 97%  3% 0%
    GCB
    1 66 2 4 4 77 86%  9% 5%
    PMBL
    0 2 27 0 4 33 82% 12% 6%
    Unclassified DLBCL 5 9 1 1 11 27 NA 41% 4%
    DLBCL (not yet 5 5 0 1 3 14 NA 21% 7%
    subclassed)
    BL 0 1 0 18 1 20 90%  5% 5%
    FL grade
    1 0 1 0 0 0 1
    FL grade 2 0 1 0 0 1 2
    FL grade 3A 0 2 0 0 0 2
    Combined FL 0 4 0 0 1 5
    grades 1, 2, 3A
    FL grade 3B 0 1 0 0 1 2
    FL unknown grade 0 1 0 1 1 3
  • As seen in Table 2398, only 1 of the 20 BL lymphoma samples was classified incorrectly. The classification of DLBCL into subtypes was also quite effective. All previously identified ABC subtype samples were again assigned to the ABC subtype, while only 5% of the GCB samples and 6% of the PMBL samples were assigned to a different subtype than they were assigned to previously.
  • The above classification was implemented using S+ software and the S+ subtype predictor script contained in the file entitled “Subtype_Predictor.txt,” located in the computer program listing appendix contained on CD number 22 of 22. This S+ script implements the lymphoma prediction algorithm. When this script is pasted into an S+ script window and run in a working directory containing the data set files discussed below, it will produce a text file entitled “PredictionResults.txt,” which indicates the results of the predictive algorithm. The other files in the computer program listing appendix contain the required data sets, in their required format, for carrying out the lymphoma type identification described above. The file entitled “GeneData.txt” contains the gene expression values for each sample analyzed. This file is included in the working directory when the S+ subtype predictor script is run. The file entitled “GeneID.txt” contains information about the genes in the GeneData.txt file, and is also included in the working directory when the S+ subtype predictor script is run. This file indicates the UNIQID for each gene, as well as the extent to which the gene is associated with the lymph node and proliferation signatures (“LN.cor” and “pro.cor,” respectively). The contents of “GeneID.txt” are also set forth in Table 2415 below. The file entitled “SampleID.txt” contains information about the samples included in the “GeneData.txt” file, specifically the original classification of all the samples. This file is also included in the working directory when the S+ subtype predictor script is run. The file entitled “PredictionResults.txt” is an example of the productive output of the prediction algorithm.
  • After the above model was validated using leave-one-out cross-validation, the model was re-fit using all of the data to generate a final predictor that could be applied to a new set of data. Tables 2399-2414 indicate for each of the pair wise models the list of genes used, the weight given to each of those genes, the signature with which each gene was associated, the mean values and covariance matrices associated with the subtypes being compared, and the q-value cut-points of the pair-wise model.
  • TABLE 2399
    ABC vs. BL
    Unigene ID
    Signature Scale UNIQID Build 167 Probe set Gene symbol
    Standard −18.87 1101149 517226 229437_at BIC
    Standard −17.4 1121452 227817 205681_at BCL2A1
    Standard −16.42 1123163 421342 208991_at STAT3
    Standard −16.2 1121629 41691 205965_at BATF
    Standard −15 1134095 89555 208018_s_at HCK
    Standard −14.75 1132636 306278 204490_s_at CD44
    Standard −14.33 1119939 170087 202820_at AHR
    Standard −14.25 1100138 278391 228234_at TIRP
    Standard −14.02 1128626 501452 219424_at EB13
    Standard −13.89 1132883 432453 205027_s_at MAP3K8
    Standard −13.88 1134991 444105 209474_s_at ENTPD1
    Standard −13.37 1109913 355724 239629_at CFLAR
    Standard −13.25 1120389 75367 203761_at SLA
    Standard −12.99 1131497 114931 202295_s_at CTSH
    Standard −12.71 1115071 390476 223218_s_at MAIL
    Standard −12.46 1136329 132739 211675_s_at HIC
    Standard −12.41 1128195 115325 218699_at RAB7L1
    Standard −12.37 1124381 440808 212288_at FNBP1
    Standard −12.30 1100562 26608 228737_at C20orf100
    Standard −12.24 1101272 179089 229584_at DKFZp434
    Standard −12.18 1128536 21126 219279_at DOCK10
    Standard −11.64 1098271 300670 226056_at CDGAP
    Standard −11.41 1119566 433506 201954_at ARPC1B
    Standard −11.11 1120651 80205 204269_at PIM2
    Standard −10.89 1098952 62264 226841_at KIAA0937
    Standard −10.80 1099939 488173 227983_at MGC7036
    Standard −10.67 1134270 352119 208284_x_at GGT1
    Standard −10.44 1134145 4750 208091_s_at DKFZP564
    Standard −10.39 1123437 73090 209636_at NFKB2
    Standard −10.17 1119884 418004 202716_at PTPM1
    Standard −10.14 1129269 62919 220358_at SNFT
    Standard −10.13 1126293 504816 215346_at TNFRSF5
    Standard −10.12 1112344 163242 242406_at
    Standard −10.10 1135550 221811 210550_s_at RASGRF1
    Standard −10.08 1135165 170359 209827_s_at IL16
    Standard −10.05 1120808 127686 204562_at IRF4
    Standard −10.01 1122087 72927 206693_at IL7
    Standard −9.97 1132004 415117 203217_s_at SIAT9
    Standard −9.88 1114824 193370 222762_x_at LIMD1
    Standard −9.87 1132034 410455 203271_s_at UNC119
    Standard −9.87 1099680 210387 227677_at JAK3
    Standard −9.86 1132830 31210 204908_s_at BCL3
    Standard −9.79 1099631 367639 227624_at FLJ20032
    Standard −9.78 1120267 256278 203508_at TNFRSF1B
    Standard −9.77 1124187 378738 211986_at MGC5395
    Standard −9.73 1108970 140489 238604_at
    Standard −9.71 1136216 512152 211528_x_at HLA-G
    Standard −9.71 1120993 327 204912_at IL10RA
    Standard −9.68 1100847 97411 229070_at C6orf105
    Standard −9.64 1123413 418291 209575_at IL10RB
    Standard −9.62 1115704 350268 224569_s_at IRF2BP2
    Standard −9.58 1108237 126232 237753_at
    Standard −9.55 1121695 511759 206082_at HCP5
    Standard −9.48 1101905 170843 230345_at
    Standard −9.42 1119243 440165 201171_at ATP6V0E
    Standard −9.39 1140457 210546 221658_s_at IL21R
    Standard −9.32 1098506 193400 226333_at IL6R
    Standard −9.31 1139805 414362 220230_s_at CYB5R2
    Standard −9.30 1139037 173380 218223_s_at CKIP-1
    Standard −9.28 1130533 76507 200706_s_at LITAF
    Standard −9.15 1098678 386140 226530_at BMF
    Standard −9.04 1133210 434374 205842_s_at JAK2
    Standard 9.05 1116432 409362 229356_x_at KIAA1259
    Standard 9.17 1097281 7037 224892_at PLDN
    Standard 9.17 1140018 438482 220917_s_at PWDMP
    Standard 9.30 1119997 367811 202951_at STK38
    Standard 9.41 1119817 409194 202561_at TNKS
    Standard 9.55 1139842 133523 220367_s_at SAP130
    Standard 9.64 1132122 307734 203434_s_at MME
    Standard 9.77 1119258 88556 201209_at HDAC1
    Standard 9.80 1128248 234149 218802_at FLJ20647
    Standard 10.38 1101211 287659 229513_at STRBP
    Standard 10.52 1123419 170195 209590_at BMP7
    Standard 10.71 1133755 404501 207318_s_at CDC2L5
    Standard 10.80 1128192 102506 218696_at EIF2AK3
    Standard 10.85 1124786 22370 212847_at NEXN
    Standard 10.92 1130114 445084 221965_at MPHOSPH9
    Standard 11.00 1126081 309763 215030_at GRSF1
    Standard 11.17 1118736 96731 38340_at HIP1R
    Standard 11.26 1124613 296720 212599_at AUTS2
    Standard 11.43 1125456 300592 213906_at MYBL1
    Standard 11.60 1097177 9691 224761_at GNA13
    Standard 12.11 1120400 152207 203787_at SSBP2
    Standard 12.12 1139266 76640 218723_s_at RGC32
    Standard 12.22 1100770 65578 228976_at
    Standard 12.73 1131246 153752 201853_s_at CDC25B
    Standard 13.48 1096503 21379 223522_at C9orf45
    Standard 14.50 1124920 6150 213039_at ARHGEF1
    Standard 15.03 1128360 445043 218988_at SLC35E3
    Standard 15.24 1099444 434489 227407_at FLJ90013
    Standard 21.03 1134582 78202 208794_s_at SMARCA4
    Standard
    Mean ABC −4179.76 Cut 1 0.20
    Mean BL −1894.68 Cut 2 0.80
    Covariance ABC 53707.58
    Covariance BL 194887.5
  • TABLE 2400
    ABC vs. GCB
    Unigene ID
    Signature Scale UNIQID Build 167 Probe set Gene symbol
    Standard −15.31 1122645 158341 207641_at TNFRSF13B
    Standard −14.56 1120651 80205 204269_at PIM2
    Standard −14.18 1120808 127686 204562_at IRF4
    Standard −13.84 1114824 193370 222762_x_at LIMD1
    Standard −13.44 1136687 59943 212345_s_at CREB3L2
    Standard −13.12 1139805 414362 220230_s_at CYB5R2
    Standard −12.23 1104552 193857 233483_at LOC96597
    Standard −12.19 1097236 235860 224837_at FOXP1
    Standard −12.06 1121629 41691 205965_at BATF
    Standard −11.93 1128195 115325 218699_at RAB7L1
    Standard −11.72 1111503 502910 241383_at KBRAS2
    Standard −11.66 1134991 444105 209474_s_at ENTPD1
    Standard −11.27 1098678 386140 226530_at BMF
    Standard −10.9 1131074 76894 201572_x_at DCTD
    Standard −10.82 1135165 170359 209827_s_at IL16
    Standard −10.7 1132396 118722 203988_s_at FUT8
    Standard −10.54 1131541 310230 202369_s_at TRAM2
    Standard −10.47 1105759 171262 235056_at ETV6
    Standard −10.38 1121564 437783 205865_at ARID3A
    Standard −10.16 1130472 192374 200599_s_at TRA1
    Standard −10.04 1132058 161999 203313_s_at TGIF
    Standard −10.03 1105684 195155 234973_at SLC38A5
    Standard −9.95 1097735 26765 225436_at LOC58489
    Standard −9.94 1115071 390476 223218_s_at MAIL
    Standard −9.85 1101149 517226 229437_at BIC
    Standard −9.83 1119884 418004 202716_at PTPN1
    Standard −9.71 1134095 89555 208018_s_at HCK
    Standard −9.68 1135550 221811 210550_s_at RASGRF1
    Standard −9.61 1098927 356216 226811_at FLJ20202
    Standard −9.6 1120389 75367 203761_at SLA
    Standard −9.58 1133910 167746 207655_s_at BLNK
    Standard 9.56 1118736 96731 38340_at HIP1R
    Standard 9.58 1128860 323634 219753_at STAG3
    Standard 9.68 1134582 78202 208794_s_at SMARCA4
    Standard 9.7 1121853 98243 206310_at SPINK2
    Standard 10.14 1119258 88556 201209_at HDAC1
    Standard 10.19 1132122 307734 203434_s_at MME
    Standard 10.23 1120400 152207 203787_at SSBP2
    Standard 10.48 1529344 317970 Lymph_Dx_065_at SERPINA11
    Standard 10.64 1124613 296720 212599_at AUTS2
    Standard 10.72 1132159 147868 203521_s_at ZNF318
    Standard 10.98 1097901 266175 225626_at PAG
    Standard 11.1 1128287 300063 218862_at ASB13
    Standard 12.26 1099686 117721 227684_at
    Standard 12.45 1112674 310320 242794_at MAML3
    Standard 13.15 1120370 78877 203723_at ITPKB
    Standard 14.23 1125456 300592 213906_at MYBL1
    Lymph Node 6.8 1097202 386779 224796_at DDEF1
    Lymph Node 6.85 1131755 241257 202729_s_at LTBP1
    Lymph Node 7.27 1136273 13775 211597_s_at HOP
    Lymph Node 7.35 1119424 75485 201599_at OAT
    Lymph Node 7.86 1095985 83883 222450_at TMEPAI
    Lymph Node 8.02 1124875 18166 212975_at KIAA0870
    Lymph Node 8.32 1124655 79299 212658_at LHFPL2
    Lymph Node 8.62 1115034 387222 223158_s_at NEK6
    Proliferation −9.11 1120583 153768 204133_at RNU3IP2
    Proliferation −7.87 1135492 408615 210448_s_at P2RX5
    Proliferation −7.68 1127756 313544 217850_at NS
    Proliferation −7.57 1097195 149931 224785_at MGC29814
    Proliferation −7.31 1127813 14317 217962_at NOLA3
    Proliferation −7.24 1138944 84753 218051_s_at FLJ12442
    Proliferation −6.99 1139226 266514 218633_x_at FLJ11342
    Proliferation −6.7 1137486 441069 214442_s_at MIZ1
    Proliferation −6.51 1133786 153591 207396_s_at ALG3
    Proliferation −6.45 1131150 75514 201695_s_at NP
    Proliferation −6.45 1119076 268849 200681_at GLO1
    Proliferation −6.38 1115679 8345 224523_s_at MGC4308
    Proliferation −6.34 1110223 212709 239973_at
    Proliferation −6.3 1529338 284275 Lymph_Dx_058_s_at PAK2
    Proliferation −6.24 1135164 458360 209825_s_at UMPK
    Proliferation −6.24 1128738 335550 219581_at MGC2776
    Proliferation −6.01 1099088 14355 226996_at
    Proliferation −5.98 1123192 315177 209100_at IFRD2
    Proliferation −5.83 1116073 146161 227103_s_at MGC2408
    Proliferation 5.79 1097388 278839 225024_at C20orf77
    Proliferation 6.13 1124563 249441 212533_at WEE1
    Standard Lymph Node Proliferation
    Mean ABC −2226.57 476.67 −1096.34 Cut 1 0.50
    Mean GCB −1352.02 547.18 −1005.72 Cut 2 0.74
    Covariance ABC 33472.10 3418.91 4347.99
    3418.91 1296.05 846.32
    4347.99 846.32 1609.13
    Covariance GCB 53751.59 466.34 751.08
    466.34 777.74 249.29
    751.08 249.29 1708.67
  • TABLE 2401
    ABC vs. PMBL
    Unigene ID Gene
    Signature Scale UNIQID Build 167 Probe set symbol
    Standard −14.61 1097236 235860 224837_at FOXP1
    Standard −14.47 1104552 193857 233483_at LOC96597
    Standard −13.62 1122645 158341 207641_at TNFRSF13B
    Standard −12.05 1135102 349845 209685_s_at PRKCB1
    Standard −11.65 1096499 293867 223514_at CARD11
    Standard −11.26 1124770 153261 212827_at IGHM
    Standard −11.25 1125010 43728 213170_at GPX7
    Standard −11.13 1109545 63187 239231_at
    Standard −10.99 1109220 445977 238880_at GTF3A
    Standard −10.87 1131074 76894 201572_x_at DCTD
    Standard −10.68 1134517 75807 208690_s_at PDLIM1
    Standard −10.63 1098604 32793 226444_at SLC39A10
    Standard −10.56 1131219 109150 201810_s_at SH3BP5
    Standard −10.52 1120651 80205 204269_at PIM2
    Standard −10.39 1133910 167746 207655_s_at BLNK
    Standard −10.32 1099396 435949 227346_at ZNFN1A1
    Standard −10.25 1529297 132335 Lymph_Dx_015_at
    Standard −10.17 1107575 424589 237033_at MGC52498
    Standard −10.11 1117211 356509 233955_x_at HSPC195
    Standard 10.06 1129517 −33 220712_at
    Standard 10.29 1139950 437385 220731_s_at FLJ10420
    Standard 10.35 1097553 197071 225214_at PSMB7
    Standard 10.41 1119516 6061 201834_at PRKAB1
    Standard 10.47 1122772 66742 207900_at CCL17
    Standard 10.55 1132762 80395 204777_s_at MAL
    Standard 10.77 1099265 375762 227193_at
    Standard 10.81 1095996 288801 222482_at SSBP3
    Standard 11.14 1100770 65578 228976_at
    Standard 11.19 1133801 181097 207426_s_at TNFSF4
    Standard 11.61 1099154 97927 227066_at MOBKL2C
    Standard 11.63 1120370 78877 203723_at ITPKB
    Standard 11.8 1112674 310320 242794_at MAML3
    Standard 12.57 1105178 283961 234284_at GNG8
    Standard 12.63 1124613 296720 212599_at AUTS2
    Standard 13.28 1106415 169071 235774_at
    Standard 13.3 1121762 32970 206181_at SLAMF1
    Standard 13.6 1121853 98243 206310_at SPINK2
    Lymph Node 10.91 1105838 129837 235142_at ZBTB8
    Lymph Node 10.99 1136273 13775 211597_s_at HOP
    Lymph Node 11.02 1099418 172792 227370_at KIAA1946
    Lymph Node 11.46 1124875 18166 212975_at KIAA0870
    Lymph Node 11.99 1120299 79334 203574_at NFIL3
    Lymph Node 12.49 1135871 104717 211031_s_at CYLN2
    Lymph Node 13.33 1121767 458324 206187_at PTGIR
    Proliferation −13.17 1138944 84753 218051_s_at FLJ12442
    Proliferation −11.61 1116122 42768 227408_s_at DKFZp761O0113
    Proliferation −11.16 1110223 212709 239973_at
    Proliferation −9.93 1120717 444159 204394_at SLC43A1
    Proliferation −9.54 1110099 116665 239835_at TA-KRP
    Proliferation −9.49 1130942 445977 201338_x_at GTF3A
    Proliferation −9.28 1123192 315177 209100_at IFRD2
    Proliferation −9.14 1135492 408615 210448_s_at P2RX5
    Proliferation −9.03 1120011 3068 202983_at SMARCA3
    Proliferation −9.01 1096738 87968 223903_at TLR9
    Proliferation −8.91 1108961 292088 238593_at FLJ22531
    Standard Lymph Node Proliferation
    Mean ABC −849.47 531.79 −1027.48 Cut 1 0.20
    Mean PMBL 27.99 750.84 −872.43 Cut 2 0.80
    Covariance ABC 14028.46 3705.84 3118.60
    3705.84 2326.91 1083.37
    3118.60 1083.37 1589.42
    Covariance PMBL 19425.29 5109.98 2199.28
    5109.98 2084.28 620.86
    2199.28 620.86 1028.44
  • TABLE 2402
    BL vs. GCB
    Unigene ID Gene
    Signature Scale UNIQID Build 167 Probe set symbol
    Standard −12.78 1131246 153752 201853_s_at CDC25B
    Standard −11.35 1099444 434489 227407_at FLJ90013
    Standard −10.4 1116432 409362 229356_x_at KIAA1259
    Standard −10.3 1134582 78202 208794_s_at SMARCA4
    Standard −10.01 1133998 76884 207826_s_at ID3
    Standard −9.3 1126081 309763 215030_at GRSF1
    Standard −9.19 1096503 21379 223522_at C9orf45
    Standard −8.95 1529340 −99 Lymph_Dx_061_at
    Standard −8.88 1138128 390428 216199_s_at MAP3K4
    Standard −8.8 1099152 351247 227064_at MGC15396
    Standard −8.69 1133757 6113 207320_x_at STAU
    Standard −8.54 1116593 422889 230329_s_at NUDT6
    Standard −8.4 1130926 508741 201310_s_at C5orf13
    Standard −8.39 1135685 371282 210776_x_at TCF3
    Standard −8.39 1140520 11747 221741_s_at C20orf21
    Standard −8.34 1119802 7370 202522_at PITPNB
    Standard −8.31 1096149 410205 222824_at NUDT5
    Standard −8.23 1124786 22370 212847_at NEXN
    Standard −8.07 1098012 355669 225756_at CSNK1E
    Standard −7.89 1116317 526415 228661_s_at
    Standard −7.86 1109195 416155 238853_at
    Standard −7.71 1134880 168799 209265_s_at METTL3
    Standard −7.66 1529298 136707 Lymph_Dx_016_at
    Standard −7.55 1128660 413071 219471_at C13orf18
    Standard −7.55 1138973 11270 218097_s_at C10orf66
    Standard −7.46 1127294 421986 217028_at CXCR4
    Standard 7.47 1134270 352119 208284_x_at GGT1
    Standard 7.48 1120743 79197 204440_at CD83
    Standard 7.5 1098179 163725 225956_at LOC153222
    Standard 7.55 1121400 223474 205599_at TRAF1
    Standard 7.59 1114967 7905 223028_s_at SNX9
    Standard 7.6 1122087 72927 206693_at IL7
    Standard 7.64 1101905 170843 230345_at
    Standard 7.77 1120700 410745 204362_at SCAP2
    Standard 7.8 1120572 84 204116_at IL2RG
    Standard 7.84 1098271 300670 226056_at CDGAP
    Standard 7.9 1115073 131315 223220_s_at BAL
    Standard 7.9 1133210 434374 205842_s_at JAK2
    Standard 8 1129269 62919 220358_at SNFT
    Standard 8.01 1131940 1103 203085_s_at TGFB1
    Standard 8.07 1098506 193400 226333_at IL6R
    Standard 8.13 1120601 441129 204166_at KIAA0963
    Standard 8.21 1102540 434881 231093_at FCRH3
    Standard 8.24 1121695 511759 206082_at HCP5
    Standard 8.33 1136877 409934 212998_x_at HLA-DQB1
    Standard 8.37 1100138 278391 228234_at TIRP
    Standard 8.46 1126293 504816 215346_at TNFRSF5
    Standard 8.46 1127805 380627 217947_at CKLFSF6
    Standard 8.59 1136573 914 211991_s_at HLA-DPA1
    Standard 8.62 1119111 35052 200804_at TEGT
    Standard 8.7 1136329 132739 211675_s_at HIC
    Standard 8.74 1123690 111805 210176_at TLR1
    Standard 8.81 1138677 390440 217436_x_at
    Standard 8.89 1113993 131811 244286_at
    Standard 8.89 1132651 439767 204529_s_at TOX
    Standard 8.91 1119566 433506 201954_at ARPC1B
    Standard 9.01 1128626 501452 219424_at EBI3
    Standard 9.17 1101272 179089 229584_at DKFZp434H2111
    Standard 9.33 1136777 387679 212671_s_at HLA-DQA1
    Standard 9.33 1109756 530304 239453_at
    Standard 9.4 1136216 512152 211528_x_at HLA-G
    Standard 9.4 1124381 440808 212288_at FNBP1
    Standard 9.46 1099680 210387 227677_at JAK3
    Standard 9.49 1109913 355724 239629_at CFLAR
    Standard 9.55 1132636 306278 204490_s_at CD44
    Standard 9.59 1119243 440165 201171_at ATP6V0E
    Standard 9.72 1101149 517226 229437_at BIC
    Standard 9.8 1130674 381008 200905_x_at HLA-E
    Standard 10.34 1119939 170087 202820_at AHR
    Standard 10.44 1132883 432453 205027_s_at MAP3K8
    Standard 10.74 1121452 227817 205681_at BCL2A1
    Standard 10.84 1137360 429658 214196_s_at CLN2
    Standard 12.08 1132520 283063 204249_s_at LMO2
    Standard 12.33 1131497 114931 202295_s_at CTSH
    Standard 13.58 1123163 421342 208991_at STAT3
    Lymph Node −9.1 1138136 433574 216215_s_at RBM9
    Lymph Node 8.78 1130121 411958 221978_at HLA-F
    Lymph Node 9.22 1139830 221851 220330_s_at SAMSN1
    Lymph Node 9.23 1131705 386467 202638_s_at ICAM1
    Lymph Node 9.62 1130168 75626 222061_at CD58
    Lymph Node 9.66 1121844 83077 206295_at IL18
    Lymph Node 9.68 1121000 519033 204924_at TLR2
    Lymph Node 9.83 1102437 437023 230966_at IL4I1
    Lymph Node 10.71 1119475 296323 201739_at SGK
    Lymph Node 11.09 1131786 375957 202803_s_at ITGB2
    Proliferation −11.07 1133141 344524 205677_s_at DLEU1
    Proliferation −10.04 1138259 89525 216484_x_at HDGF
    Proliferation −9.74 1131578 202453 202431_s_at MYC
    Proliferation −9.45 1137449 223745 214363_s_at MATR3
    Proliferation −9.43 1130468 166463 200594_x_at HNRPU
    Proliferation −9.21 1138157 82563 216251_s_at KIAA0153
    Proliferation −9.15 1127756 313544 217850_at NS
    Proliferation −9 1130433 246112 200058_s_at U5-200KD
    Proliferation −8.76 1123108 108112 208828_at POLE3
    Proliferation −8.75 1128738 335550 219581_at MGC2776
    Proliferation −8.74 1122400 439911 207199_at TERT
    Proliferation −8.66 1097948 69476 225684_at LOC348235
    Proliferation −8.6 1119460 76122 201696_at SFRS4
    Proliferation −8.6 1136401 27258 211761_s_at SIP
    Proliferation −8.58 1099088 14355 226996_at
    Proliferation −8.51 1134653 253536 208901_s_at TOP1
    Proliferation −8.49 1140584 294083 221932_s_at C14orf87
    Proliferation −8.43 1121309 23642 205449_at HSU79266
    Proliferation −8.43 1120385 36708 203755_at BUB1B
    Proliferation −8.38 1136710 75782 212429_s_at GTF3C2
    Proliferation −8.36 1136605 448398 212064_x_at MAZ
    Proliferation −8.24 1120697 323462 204355_at DHX30
    Proliferation −8.19 1127833 382044 218001_at MRPS2
    Proliferation −8.11 1096903 437460 224185_at FLJ10385
    Proliferation −8.1 1120596 4854 204159_at CDKN2C
    Proliferation −8.1 1120779 28853 204510_at CDC7
    Standard Lymph Node Proliferation
    Mean BL 1098.69 576.05 −2392.12 Cut 1 0.09
    Mean GCB 2187.37 768.53 −2129.35 Cut 2 0.53
    Covariance BL 75263.67 12684.43 15734.77
    12684.43 2650.81 2358.05
    15734.77 2358.05 4653.00
    Covariance GCB 50548.22 9301.12 14182.83
    9301.12 2602.51 3028.21
    14182.83 3028.21 5983.04
  • TABLE 2403
    BL vs. PMBL
    Unigene ID
    Signature Scale UNIQID Build 167 Probe set Gene Symbol
    Standard −13.54 1099444 434489 227407_at FLJ90013
    Standard −13.42 1096503 21379 223522_at C9orf45
    Standard −13.36 1130114 445084 221965_at MPHOSPH9
    Standard −13.27 1124786 22370 212847_at NEXN
    Standard −13.27 1134582 78202 208794_s_at SMARCA4
    Standard −12.37 1096149 410205 222824_at NUDT5
    Standard −11.95 1130855 77515 201189_s_at ITPR3
    Standard −11.66 1529298 136707 Lymph_Dx_016_at
    Standard −11.35 1131246 153752 201853_s_at CDC25B
    Standard −11.17 1136925 436939 213154_s_at BICD2
    Standard −11.08 1124188 282346 211987_at TOP2B
    Standard −11.06 1133998 76884 207826_s_at ID3
    Standard −10.76 1139266 76640 218723_s_at RGC32
    Standard −10.74 1134880 168799 209265_s_at METTL3
    Standard −10.69 1140520 11747 221741_s_at C20orf21
    Standard −10.6 1109545 63187 239231_at
    Standard −10.55 1106043 266331 235372_at FREB
    Standard −10.52 1110214 144519 239964_at TCL6
    Standard −10.49 1098592 283707 226431_at ALS2CR13
    Standard −10.45 1109220 445977 238880_at GTF3A
    Standard −10.41 1131263 249955 201877_s_at PPP2R5C
    Standard 10.54 1122772 66742 207900_at CCL17
    Standard 10.59 1109913 355724 239629_at CFLAR
    Standard 10.82 1119884 418004 202716_at PTPN1
    Standard 10.83 1135189 137569 209863_s_at TP73L
    Standard 10.89 1123437 73090 209636_at NFKB2
    Standard 11.15 1124381 440808 212288_at FNBP1
    Standard 11.26 1108237 126232 237753_at
    Standard 11.34 1101149 517226 229437_at BIC
    Standard 11.77 1139774 15827 220140_s_at SNX11
    Standard 11.87 1123163 421342 208991_at STAT3
    Standard 11.93 1129269 62919 220358_at SNFT
    Standard 12.03 1132636 306278 204490_s_at CD44
    Standard 12.1 1138677 390440 217436_x_at
    Standard 12.2 1139950 437385 220731_s_at FLJ10420
    Standard 12.25 1134270 352119 208284_x_at GGT1
    Standard 12.27 1136216 512152 211528_x_at HLA-G
    Standard 12.79 1121400 223474 205599_at TRAF1
    Standard 12.82 1119939 170087 202820_at AHR
    Standard 13.12 1126293 504816 215346_at TNFRSF5
    Standard 13.44 1100138 278391 228234_at TIRP
    Standard 13.74 1132883 432453 205027_s_at MAP3K8
    Standard 13.94 1131497 114931 202295_s_at CTSH
    Standard 14.15 1121762 32970 206181_at SLAMF1
    Standard 14.51 1132520 283063 204249_s_at LMO2
    Standard 14.68 1121452 227817 205681_at BCL2A1
    Standard 15.24 1105178 283961 234284_at GNG8
    Lymph Node 10.95 1121205 2488 205269_at LCP2
    Lymph Node 11.22 1140845 21486 AFFX- STAT1
    HUMISGF3A/
    M97935_3_at
    Lymph Node 11.45 1131068 118400 201564_s_at FSCN1
    Lymph Node 11.92 1131705 386467 202638_s_at ICAM1
    Lymph Node 12.06 1131038 81328 201502_s_at NFKBIA
    Lymph Node 12.49 1121444 153563 205668_at LY75
    Lymph Node 13.01 1123457 446304 209684_at RIN2
    Lymph Node 13.19 1140404 354740 221584_s_at KCNMA1
    Lymph Node 13.26 1124875 18166 212975_at KIAA0870
    Lymph Node 14.06 1102437 437023 230966_at IL4I1
    Lymph Node 14.11 1132766 82359 204781_s_at TNFRSF6
    Lymph Node 15.31 1121767 458324 206187_at PTGIR
    Lymph Node 15.32 1135871 104717 211031_s_at CYLN2
    Lymph Node 15.34 1138652 444471 217388_s_at KYNU
    Lymph Node 16.01 1139830 221851 220330_s_at SAMSN1
    Standard Lymph Node
    Mean BL −66.97 1445.63 Cut 1 0.20
    Mean PMBL 1205.38 2041.25 Cut 2 0.80
    Covariance BL 35263.67 13424.88
    13424.88 7458.56
    Covariance PMBL 12064.38 5113.74
    5113.74 3216.53
  • TABLE 2404
    FH vs. DLBCL-BL
    Signature Scale UNIQID Unigene ID Build 167 Probe set Gene Symbol
    Standard −12.81 1104910 458262 233969_at IGL@
    Standard −11.54 1102898 145519 231496_at FKSG87
    Standard −11.46 1117298 449586 234366_x_at
    Standard −11.46 1132973 169294 205255_x_at TCF7
    Standard −11.22 1133099 88646 205554_s_at DNASE1L3
    Standard −10.76 1131531 153647 202350_s_at MATN2
    Standard −10.59 1124283 406612 212144_at UNC84B
    Standard −10.35 1099847 36723 227867_at LOC129293
    Standard −10.22 1136430 102950 211798_x_at IGLJ3
    Standard −10.05 1117394 −13 234792_x_at
    Standard −9.95 1133047 528338 205434_s_at AAK1
    Standard −9.95 1098865 250905 226741_at LOC51234
    Standard −9.82 1108515 98132 238071_at LCN6
    Standard −9.8 1131407 154248 202125_s_at ALS2CR3
    Standard −9.77 1128469 390817 219173_at FLJ22686
    Standard −9.7 1123875 428 210607_at FLT3LG
    Standard −9.69 1131875 169172 202965_s_at CAPN6
    Standard −9.69 1135173 3781 209841_s_at LRRN3
    Standard −9.48 1099798 411081 227811_at FGD3
    Standard −9.41 1119046 349499 200606_at DSP
    Standard −9.36 1122449 278694 207277_at CD209
    Standard −9.34 1114017 133255 244313_at
    Standard −9.34 1122767 652 207892_at TNFSF5
    Standard −9.24 1123369 79025 209481_at SNRK
    Standard −9.16 1098954 128905 226844_at MOBKL2B
    Standard −9.14 1135513 421437 210481_s_at CD209L
    Standard −9.08 1100904 426296 229145_at LOC119504
    Standard −8.99 1122738 81743 207840_at CD160
    Standard −8.94 1120925 204891 204773_at IL11RA
    Standard 9.09 1123055 185726 208691_at TFRC
    Standard 9.62 1134858 405954 209226_s_at TNPO1
    Standard 10.19 1123052 180909 208680_at PRDX1
    Standard 10.81 1124178 446579 211969_at HSPCA
    Lymph Node −10.59 1137597 3903 214721_x_at CDC42EP4
    Lymph Node −9.69 1119684 439586 202242_at TM4SF2
    Lymph Node −9.25 1125593 8910 214180_at MAN1C1
    Lymph Node −8.44 1124318 21858 212190_at SERPINE2
    Lymph Node −8.09 1119448 212296 201656_at ITGA6
    Lymph Node −8.07 1125546 125036 214081_at PLXDC1
    Lymph Node −7.7 1097683 132569 225373_at PP2135
    Lymph Node −7.56 1101305 112742 229623_at
    Lymph Node 7.45 1135240 436852 209955_s_at FAP
    Proliferation 6.97 1135101 20830 209680_s_at KIFC1
    Proliferation 7.03 1130426 432607 200039_s_at PSMB2
    Proliferation 7.04 1130501 2795 200650_s_at LDHA
    Proliferation 7.08 1130744 158688 201027_s_at EIF5B
    Proliferation 7.23 1137506 75258 214501_s_at H2AFY
    Proliferation 7.32 1131474 95577 202246_s_at CDK4
    Proliferation 7.39 1130871 159087 201222_s_at RAD23B
    Proliferation 7.42 1119375 381072 201489_at PPIF
    Proliferation 7.47 1136595 404814 212038_s_at VDAC1
    Proliferation 7.7 1135858 90093 211015_s_at HSPA4
    Proliferation 7.78 1130527 184233 200692_s_at HSPA9B
    Proliferation 7.78 1130820 151777 201144_s_at EIF2S1
    Proliferation 7.83 1115829 433213 225253_s_at METTL2
    Proliferation 7.84 1134699 439683 208974_x_at KPNB1
    Proliferation 7.87 1120274 31584 203517_at MTX2
    Proliferation 7.92 1136786 63788 212694_s_at PCCB
    Proliferation 7.95 1097172 434886 224753_at CDCA5
    Proliferation 8.4 1138537 −12 217140_s_at
    Proliferation 8.53 1119488 154672 201761_at MTHFD2
    Proliferation 8.58 1130799 233952 201114_x_at PSMA7
    Proliferation 8.72 1135673 82159 210759_s_at PSMA1
    Proliferation 9.4 1114679 16470 222503_s_at FLJ10904
    Standard Lymph Node Proliferation
    Mean FH −2193.59 −588.21 1571.78 Cut 1 0.50
    Mean DLBCL-BL −1448.27 −441.91 1735.00 Cut 2 0.92
    Covariance FH 6729.73 1223.99 2541.22
    1223.99 405.22 293.72
    2541.22 293.72 1797.58
    Covariance DLBCL-BL 17675.23 3642.41 4158.43
    3642.41 1379.81 1066.48
    4158.43 1066.48 2858.21
  • TABLE 2405
    FH vs. FL
    Unigene ID
    Signature Scale UNIQID Build 167 Probe set Gene Symbol
    Standard −11.23 1117298 449586 234366_x_at
    Standard −10.62 1121953 38365 206478_at KIAA0125
    Standard −10.6 1104910 458262 233969_at IGL@
    Standard −10.39 1136430 102950 211798_x_at IGLJ3
    Standard −9.96 1129281 395486 220377_at C14orf110
    Standard −9.73 1118835 102336 47069_at ARHGAP8
    Standard −9.21 1127807 7236 217950_at NOSIP
    Standard −9.05 1128377 371003 219014_at PLAC8
    Standard −8.85 1101004 2969 229265_at SKI
    Standard 9.06 1139411 368238 219073_s_at OSBPL10
    Standard 9.07 1120789 154729 204524_at PDPK1
    Standard 9.21 1136464 159428 211833_s_at BAX
    Standard 9.29 1125279 445652 213575_at TRA2A
    Standard 9.45 1529390 79241 Lymph_Dx_120_at BCL2
    Standard 9.52 1132022 173911 203247_s_at ZNF24
    Standard 9.57 1139645 134051 219757_s_at C14orf101
    Standard 9.64 1137561 67397 214639_s_at HOXA1
    Standard 9.66 1114893 314623 222891_s_at BCL11A
    Standard 10.38 1098095 131059 225852_at ANKRD17
    Standard 10.4 1134858 405954 209226_s_at TNPO1
    Standard 12.65 1101054 173328 229322_at PPP2R5E
    Standard 12.79 1124178 446579 211969_at HSPCA
    Standard 13.34 1135489 288178 210438_x_at SSA2
    Standard
    Mean FH 136.43 Cut 1 0.50
    Mean FL 640.38 Cut 2 0.99
    Covariance FH 10719.40
    Covariance FL 9373.11
  • TABLE 2406
    FH vs. MCL
    Unigene ID
    Signature Scale UNIQID Build 167 Probe set Gene Symbol
    Standard 13.05 1100258 88442 228377_at KIAA1384
    Standard 13.43 1529382 371468 Lymph_Dx_111_at CCND1
    Standard 13.54 1106855 455101 236255_at KIAA1909
    Standard 13.73 1529308 193014 Lymph_Dx_027_x_at
    Standard 14.56 1100873 445884 229103_at
    Standard 21.12 1132834 432638 204914_s_at SOX11
    Lymph Node −8.44 1130378 234434 44783_s_at HEY1
    Lymph Node −7.92 1123552 423077 209879_at SELPLG
    Lymph Node −7.7 1131218 76753 201809_s_at ENG
    Lymph Node −7.4 1097683 132569 225373_at PP2135
    Lymph Node −7.15 1136273 13775 211597_s_at HOP
    Lymph Node 14.16 1134532 371468 208711_s_at CCND1
    Standard Lymph Node
    Mean FH 451.68 −282.65 Cut 1 0.20
    Mean MCFL 863.16 −156.82 Cut 2 0.80
    Covariance FH 1617.92 222.89
    222.89 271.65
    Covariance MCL 3154.38 917.30
    917.30 659.94
  • TABLE 2407
    FH vs. SLL
    Signature Scale UNIQID Unigene ID Build 167 Probe set Gene Symbol
    Standard −13.14 1120765 343329 204484_at PIK3C2B
    Standard −12.9 1097897 266175 225622_at PAG
    Standard 12.72 1133195 274243 205805_s_at ROR1
    Standard 12.74 1140416 58831 221601_s_at TOSO
    Standard 13.53 1131687 369280 202606_s_at TLK1
    Standard 13.57 1107044 163426 236458_at
    Standard 14.43 1529389 79241 Lymph_Dx_119_at BCL2
    Standard 14.51 1129026 135146 220007_at FLJ13984
    Standard 14.77 1136987 21695 213370_s_at SFMBT1
    Standard 14.79 1137109 469653 213689_x_at RPL5
    Standard 15.37 1529308 193014 Lymph_Dx_027_x_at
    Standard 15.82 1120832 57856 204604_at PFTK1
    Standard 17.37 1135550 221811 210550_s_at RASGRF1
    Standard 18.98 1122864 434384 208195_at TTN
    Lymph Node −12.89 1123038 119000 208636_at ACTN1
    Lymph Node −12.8 1130378 234434 44783_s_at HEY1
    Lymph Node −11.59 1124875 18166 212975_at KIAA0870
    Lymph Node −11.47 1103497 50115 232231_at
    Lymph Node −10.31 1099358 93135 227300_at
    Lymph Node −10.27 1121129 285401 205159_at CSF2RB
    Lymph Node −10.23 1100249 388674 228367_at HAK
    Lymph Node −10.05 1132345 109225 203868_s_at VCAM1
    Lymph Node −9.93 1123401 50130 209550_at NDN
    Lymph Node −9.75 1120500 82568 203979_at CYP27A1
    Lymph Node −9.57 1124318 21858 212190_at SERPINE2
    Lymph Node −9.48 1120288 17483 203547_at CD4
    Lymph Node −9.45 1123372 195825 209487_at RBPMS
    Lymph Node −9.39 1123376 37682 209496_at RARRES2
    Lymph Node −9.29 1123213 12956 209154_at TIP-1
    Lymph Node −9.23 1098412 409515 226225_at MCC
    Lymph Node −9.23 1125593 8910 214180_at MAN1C1
    Lymph Node −9.17 1131786 375957 202803_s_at ITGB2
    Lymph Node −9.04 1097683 132569 225373_at PP2135
    Lymph Node −8.91 1097255 380144 224861_at
    Lymph Node −8.76 1131068 118400 201564_s_at FSCN1
    Lymph Node −8.7 1119074 54457 200675_at CD81
    Lymph Node −8.68 1125130 35861 213338_at RIS1
    Lymph Node −8.59 1139661 416456 219806_s_at FN5
    Standard Lymph Node
    Mean FH 1144.02 −2223.71 Cut 1 0.20
    Mean SLL 1592.27 −1798.11 Cut 2 0.80
    Covariance FH 902.56 442.69
    442.69 809.90
    Covariance SLL 2426.26 2938.58
    2938.58 9435.72
  • TABLE 2408
    FL vs. DLBCL-BL
    Signature Scale UNIQID Unigene ID Build 167 Probe set Gene Symbol
    Standard −23.03 1124833 356416 212914_at CBX7
    Standard −22.25 1099204 193784 227121_at
    Standard −22.2 1119766 93231 202423_at MYST3
    Standard −22.04 1099798 411081 227811_at FGD3
    Standard −22.01 1102898 145519 231496_at FKSG87
    Standard −21.79 1131197 269902 201778_s_at KIAA0494
    Standard −21.69 1098415 130900 226230_at KIAA1387
    Standard −21.57 1120834 57907 204606_at CCL21
    Standard −21.39 1130155 436657 222043_at CLU
    Standard −20.98 1100904 426296 229145_at LOC119504
    Standard −20.8 1131531 153647 202350_s_at MATN2
    Standard −20.72 1137582 433732 214683_s_at CLK1
    Standard −20.66 1119782 155418 202478_at TRB2
    Standard −20.59 1122767 652 207892_at TNFSF5
    Standard −20.58 1125001 16193 213158_at
    Standard −20.56 1134921 413513 209341_s_at IKBKB
    Standard −20.56 1132973 169294 205255_x_at TCF7
    Standard −20.53 1136984 498154 213364_s_at SNX1
    Standard −20.41 1115888 35096 225629_s_at ZBTB4
    Standard −20.37 1120160 436976 203288_at KIAA0355
    Standard −20.36 1139054 25726 218263_s_at LOC58486
    Standard −20.31 1130030 301872 221834_at LONP
    Standard −20.08 1133024 436987 205383_s_at ZNF288
    Standard −20.05 1124666 526394 212672_at ATM
    Standard −19.3 1529397 406557 Lymph_Dx_127_s_at CLK4
    Standard −19.16 1116056 243678 226913_s_at SOX8
    Standard −19.14 1098433 202577 226250_at
    Standard −19.1 1123635 408614 210073_at SIAT8A
    Standard −18.95 1138920 24395 218002_s_at CXCL14
    Standard −18.84 1133099 88646 205554_s_at DNASE1L3
    Standard −18.83 1098495 443668 226318_at TBRG1
    Standard −18.64 1100879 119983 229111_at MASP2
    Standard −18.59 1120695 385685 204352_at TRAF5
    Standard −18.55 1119983 409783 202920_at ANK2
    Standard −18.5 1101276 1098 229588_at ERdj5
    Standard −18.47 1099140 500350 227052_at
    Standard −18.46 1529331 374126 Lymph_Dx_051_s_at
    Standard −18.45 1131752 170133 202724_s_at FOXO1A
    Standard −18.45 1099265 375762 227193_at
    Standard −18.32 1098179 163725 225956_at LOC153222
    Standard −18.29 1119568 269777 201957_at PPP1R12B
    Standard −18.19 1099900 444508 227934_at
    Standard −18.17 1119361 391858 201448_at TIA1
    Standard −18.02 1121650 421137 206002_at GPR64
    Standard −17.91 1100911 320147 229152_at C4orf7
    Standard −17.86 1529285 348929 Lymph_Dx_002_at KIAA1219
    Standard −17.47 1529357 444651 Lymph_Dx_081_at
    Standard −17.42 1131863 2316 202936_s_at SOX9
    Standard −17.16 1129943 512828 221626_at ZNF506
    Standard −17.12 1121301 449971 205437_at ZNF134
    Standard −17.11 1131340 437457 202018_s_at LTF
    Standard −17.1 1124606 444324 212588_at PTPRC
    Standard −17.08 1131407 154248 202125_s_at ALS2CR3
    Standard −16.97 1118939 198161 60528_at PLA2G4B
    Standard −16.91 1134738 75842 209033_s_at DYRK1A
    Standard −16.9 1134083 285091 207996_s_at C18orf1
    Standard −16.89 1120925 204891 204773_at IL11RA
    Standard −16.86 1110070 −101 239803_at
    Standard −16.83 1100042 351413 228113_at RAB37
    Standard −16.82 1120134 75545 203233_at IL4R
    Standard −16.75 1124283 406612 212144_at UNC84B
    Standard −16.72 1109603 −100 239292_at
    Standard −16.71 1120509 155090 204000_at GNB5
    Standard −16.65 1133538 1416 206760_s_at FCER2
    Standard −16.64 1130735 179526 201009_s_at TXNIP
    Standard −16.59 1100150 9343 228248_at MGC39830
    Standard −16.54 1124237 258855 212080_at MLL
    Standard −16.51 1124416 283604 212331_at RBL2
    Standard −16.48 1133091 73792 205544_s_at CR2
    Standard −16.46 1131263 249955 201877_s_at PPP2R5C
    Standard −16.44 1118347 528404 243366_s_at ITGA4
    Standard −16.43 1529343 521948 Lymph_Dx_064_at
    Standard −16.43 1099549 446665 227533_at
    Standard 17.05 1529453 372679 Lymph_Dx_085_at FCGR3A
    Standard 17.41 1097540 388087 225195_at
    Standard 18.47 1140473 17377 221676_s_at CORO1C
    Standard 18.55 1121100 301921 205098_at CCR1
    Standard 20.07 1124254 301743 212110_at SLC39A14
    Standard 20.2 1130771 61153 201068_s_at PSMC2
    Standard 21.46 1137583 273415 214687_x_at ALDOA
    Standard 21.55 1098168 22151 225943_at NLN
    Standard 24.07 1123055 185726 208691_at TFRC
    Standard 24.09 1123052 180909 208680_at PRDX1
    Lymph Node −20.5 1137597 3903 214721_x_at CDC42EP4
    Lymph Node −18.52 1124318 21858 212190_at SERPINE2
    Lymph Node −18.5 1136762 380138 212624_s_at CHN1
    Lymph Node −18.07 1101305 112742 229623_at
    Lymph Node −17.75 1100249 388674 228367_at HAK
    Lymph Node −16.1 1098412 409515 226225_at MCC
    Lymph Node −15.51 1140464 111676 221667_s_at HSPB8
    Lymph Node −15.43 1136832 434959 212842_x_at RANBP2L1
    Lymph Node −15.37 1119684 439586 202242_at TM4SF2
    Lymph Node −15.02 1097448 250607 225093_at UTRN
    Lymph Node −14.83 1136844 16007 212875_s_at C21orf25
    Lymph Node −14.73 1135056 169946 209604_s_at GATA3
    Lymph Node −14.48 1097202 386779 224796_at DDEF1
    Lymph Node −14.44 1121278 21355 205399_at DCAMKL1
    Lymph Node −14.22 1125009 27621 213169_at
    Lymph Node −13.97 1100288 26981 228411_at ALS2CR19
    Lymph Node −13.51 1132462 14845 204131_s_at FOXO3A
    Lymph Node −13.37 1135322 450230 210095_s_at IGFBP3
    Lymph Node −13.35 1097280 423523 224891_at
    Lymph Node −12.86 1137097 20107 213656_s_at KNS2
    Lymph Node −12.85 1098809 359394 226682_at
    Lymph Node −12.28 1124875 18166 212975_at KIAA0870
    Lymph Node −12.18 1132345 109225 203868_s_at VCAM1
    Lymph Node −12 1097561 19221 225224_at DKFZP566G1424
    Lymph Node −11.71 1123401 50130 209550_at NDN
    Lymph Node −11.04 1136996 283749 213397_x_at RNASE4
    Lymph Node −10.77 1136788 355455 212698_s_at 36778
    Lymph Node −10.71 1098822 443452 226695_at PRRX1
    Lymph Node −10.63 1134200 90786 208161_s_at ABCC3
    Lymph Node −10.47 1136427 276506 211795_s_at FYB
    Lymph Node −10.46 1121186 100431 205242_at CXCL13
    Lymph Node −10.39 1099332 32433 227272_at
    Lymph Node −10.39 1098978 124863 226869_at
    Lymph Node −10.22 1103303 49605 232000_at C9orf52
    Lymph Node −10.16 1131325 13313 201990_s_at CREBL2
    Lymph Node −10.16 1098174 274401 225949_at LOC340371
    Lymph Node −9.93 1124733 66762 212771_at LOC221061
    Lymph Node −9.42 1123372 195825 209487_at RBPMS
    Lymph Node −9.36 1132220 448805 203632_s_at GPRC5B
    Lymph Node −9.29 1120703 83974 204368_at SLCO2A1
    Lymph Node −9.26 1132013 434961 203232_s_at SCA1
    Lymph Node −9.25 1097307 379754 224929_at LOC340061
    Lymph Node −9.18 1119251 433941 201194_at SEPW1
    Lymph Node −9.08 1097609 6093 225283_at ARRDC4
    Lymph Node −9.07 1136459 252550 211828_s_at KIAA0551
    Lymph Node −8.86 1132775 1027 204803_s_at RRAD
    Lymph Node −8.78 1098946 135121 226834_at ASAM
    Lymph Node −8.68 1140589 433488 221942_s_at GUCY1A3
    Lymph Node −8.44 1116966 301124 232744_x_at
    Lymph Node −8.39 1100130 76494 228224_at PRELP
    Lymph Node −8.36 1110019 −94 239744_at
    Lymph Node −8.3 1134647 298654 208892_s_at DUSP6
    Lymph Node −8.28 1125593 8910 214180_at MAN1C1
    Lymph Node 7.97 1134370 1422 208438_s_at FGR
    Lymph Node 8.05 1123566 155935 209906_at C3AR1
    Lymph Node 8.09 1131119 349656 201647_s_at SCARB2
    Lymph Node 8.11 1123586 93841 209948_at KCNMB1
    Lymph Node 8.13 1128615 104800 219410_at FLJ10134
    Lymph Node 8.21 1097297 166254 224917_at VMP1
    Lymph Node 8.23 1120299 79334 203574_at NFIL3
    Lymph Node 8.37 1128157 23918 218631_at VIP32
    Lymph Node 8.4 1130054 82547 221872_at RARRES1
    Lymph Node 8.41 1098152 377588 225922_at KIAA1450
    Lymph Node 8.53 1101566 98558 229947_at
    Lymph Node 8.59 1135251 21486 209969_s_at STAT1
    Lymph Node 8.84 1099167 381105 227080_at MGC45731
    Lymph Node 9.01 1132920 753 205119_s_at FPR1
    Lymph Node 9.26 1097253 77873 224859_at B7H3
    Lymph Node 9.29 1120500 82568 203979_at CYP27A1
    Lymph Node 9.36 1131507 172928 202311_s_at COL1A1
    Lymph Node 9.38 1096456 82407 223454_at CXCL16
    Lymph Node 9.49 1136172 38084 211470_s_at SULT1C1
    Lymph Node 10.03 1138244 418138 216442_x_at FN1
    Lymph Node 10.34 1134424 −17 208540_x_at S100A14
    Lymph Node 10.48 1136152 458436 211434_s_at CCRL2
    Lymph Node 10.51 1118708 7835 37408_at MRC2
    Lymph Node 10.6 1136540 179657 211924_s_at PLAUR
    Lymph Node 10.63 1098278 166017 226066_at MITF
    Lymph Node 10.76 1119477 163867 201743_at CD14
    Lymph Node 10.81 1096429 64896 223405_at NPL
    Lymph Node 11.58 1123672 67846 210152_at LILRB4
    Lymph Node 12 1096364 29444 223276_at NID67
    Lymph Node 12.16 1119070 445570 200663_at CD63
    Lymph Node 12.3 1133065 77274 205479_s_at PLAU
    Lymph Node 12.5 1135240 436852 209955_s_at FAP
    Lymph Node 13.09 1116826 26204 231823_s_at KIAA1295
    Lymph Node 13.32 1119068 417004 200660_at S100A11
    Lymph Node 13.45 1120266 246381 203507_at CD68
    Lymph Node 13.63 1133216 502577 205872_x_at PDE4DIP
    Lymph Node 13.67 1131815 386678 202856_s_at SLC16A3
    Lymph Node 14.38 1132132 279910 203454_s_at ATOX1
    Lymph Node 15.25 1134682 411701 208949_s_at LGALS3
    Lymph Node 15.46 1119237 389964 201141_at GPNMB
    Lymph Node 15.89 1137698 442669 215001_s_at GLUL
    Lymph Node 17.8 1137782 384944 215223_s_at SOD2
    Lymph Node 20.11 1130629 135226 200839_s_at CTSB
    Proliferation 21.02 1119375 381072 201489_at PPIF
    Proliferation 21.24 1119488 154672 201761_at MTHFD2
    Proliferation 21.31 1119467 21635 201714_at TUBG1
    Proliferation 21.68 1130820 151777 201144_s_at EIF2S1
    Proliferation 21.69 1131474 95577 202246_s_at CDK4
    Proliferation 22.2 1125249 244723 213523_at CCNE1
    Proliferation 22.97 1130501 2795 200650_s_at LDHA
    Proliferation 23.12 1136913 99962 213113_s_at SLC43A3
    Proliferation 24.05 1130426 432607 200039_s_at PSMB2
    Standard Lymph Node Proliferation
    Mean FL −11121.51 −1603.39 1890.60 Cut 1 0.34
    Mean DLBCL-BL −8760.65 −460.71 2101.10 Cut 2 0.94
    Covariance FL 246359.77 111505.42 28908.20
    111505.42 67036.17 13130.59
    28908.20 13130.59 4617.24
    Covariance DLBCL-BL 413069.12 178811.32 30151.89
    178811.32 106324.53 10877.26
    30151.89 10877.26 5180.68
  • TABLE 2409
    FL vs. MCL
    Signature Scale UNIQID Unigene ID Build 167 Probe set Gene Symbol
    Standard −24.56 1123731 17165 210258_at RGS13
    Standard −22.56 1133192 24024 205801_s_at RASGRP3
    Standard −21.12 1114543 156189 244887_at
    Standard −18.49 1120090 155024 203140_at BCL6
    Standard −18.07 1124646 436432 212646_at RAFTLIN
    Standard −17.24 1132122 307734 203434_s_at MME
    Standard −16.63 1105986 49614 235310_at GCET2
    Standard −15.09 1120134 75545 203233_at IL4R
    Standard −14.05 1132651 439767 204529_s_at TOX
    Standard 13.8 1098277 6786 226065_at PRICKLE1
    Standard 13.85 1109560 207428 239246_at FARP1
    Standard 13.86 1103504 142517 232239_at
    Standard 13.88 1132734 126248 204724_s_at COL9A3
    Standard 13.91 1115905 301478 225757_s_at CLMN
    Standard 14.89 1098840 55098 226713_at C3orf6
    Standard 14.97 1100873 445884 229103_at
    Standard 14.99 1139393 170129 219032_x_at OPN3
    Standard 16.13 1124864 411317 212960_at KIAA0882
    Standard 16.36 1106855 455101 236255_at KIAA1909
    Standard 16.43 1120858 410683 204647_at HOMER3
    Standard 17.38 1130926 508741 201310_s_at C5orf13
    Standard 18.3 1103711 288718 232478_at
    Standard 18.62 1109505 8162 239186_at MGC39372
    Standard 20.31 1132834 432638 204914_s_at SOX11
    Standard 22.61 1096070 241565 222640_at DNMT3A
    Standard 28.66 1529382 371468 Lymph_Dx_111_at CCND1
    Lymph Node −10.77 1097202 386779 224796_at DDEF1
    Lymph Node −10.22 1119546 433898 201921_at GNG10
    Lymph Node −9.89 1132766 82359 204781_s_at TNFRSF6
    Lymph Node −9.4 1138867 10706 217892_s_at EPLIN
    Lymph Node 9.65 1125025 301094 213196_at
    Lymph Node 10.44 1134797 433394 209118_s_at TUBA3
    Lymph Node 22.6 1529456 371468 Lymph_Dx_113_at CCND1
    Proliferation −7.36 1097948 69476 225684_at LOC348235
    Proliferation −7.31 1130747 234489 201030_x_at LDHB
    Proliferation −6.95 1130923 459987 201306_s_at ANP32B
    Proliferation −6.87 1120205 5198 203405_at DSCR2
    Proliferation −6.64 1132468 79353 204147_s_at TFDP1
    Proliferation −6.1 1119916 177584 202780_at OXCT
    Proliferation −6.08 1119873 446393 202697_at CPSF5
    Proliferation −6.08 1119488 154672 201761_at MTHFD2
    Proliferation −6.04 1130658 447492 200886_s_at PGAM1
    Proliferation −5.82 1132825 512813 204900_x_at SAP30
    Proliferation −5.53 1115607 435733 224428_s_at CDCA7
    Proliferation −5.44 1120316 63335 203611_at TERF2
    Proliferation −5.34 1114970 279529 223032_x_at PX19
    Proliferation −5.32 1140843 169476 AFFX- GAPD
    HUMGAPDH/M33197_5_at
    Proliferation −5.28 1131081 180610 201586_s_at SFPQ
    Proliferation −5.15 1121062 408658 205034_at CCNE2
    Proliferation 5.15 1120986 172052 204886_at PLK4
    Proliferation 5.16 1097195 149931 224785_at MGC29814
    Proliferation 5.2 1120011 3068 202983_at SMARCA3
    Proliferation 5.47 1100183 180582 228286_at FLJ40869
    Proliferation 5.67 1121012 96055 204947_at E2F1
    Proliferation 5.84 1115679 8345 224523_s_at MGC4308
    Proliferation 5.88 1135285 449501 210024_s_at UBE2E3
    Proliferation 5.92 1120520 35120 204023_at RFC4
    Proliferation 6.16 1529361 388681 Lymph_Dx_086_s_at HDAC3
    Proliferation 6.45 1096054 21331 222606_at FLJ10036
    Proliferation 6.45 1096738 87968 223903_at TLR9
    Proliferation 6.51 1136781 120197 212680_x_at PPP1R14B
    Proliferation 6.63 1119466 179718 201710_at MYBL2
    Proliferation 6.65 1136285 182490 211615_s_at LRPPRC
    Proliferation 6.67 1136853 66170 212922_s_at SMYD2
    Proliferation 7.45 1119390 77254 201518_at CBX1
    Proliferation 8.87 1116122 42768 227408_s_at DKFZp761O0113
    Proliferation 10.12 1119515 3352 201833_at HDAC2
    Standard Lymph Node Proliferation
    Mean FL −18.82 −33.90 23.53 Cut 1 0.14
    Mean MCL 1558.10 113.95 165.48 Cut 2 0.58
    Covariance FL 21302.14 1098.24 678.04
    1098.24 226.29 75.99
    678.04 75.99 315.67
    Covariance MCL 81008.29 5261.37 9185.20
    5261.37 2047.34 875.56
    9185.20 875.56 1447.43
  • TABLE 2410
    FL vs. SLL
    Signature Scale UNIQID Unigene ID Build 167 Probe set Gene Symbol
    Standard −21.04 1123731 17165 210258_at RGS13
    Standard −20.91 1124646 436432 212646_at RAFTLIN
    Standard −18.82 1099651 120785 227646_at EBF
    Standard −18.12 1114543 156189 244887_at
    Standard −17.85 1105986 49614 235310_at GCET2
    Standard −16.73 1100911 320147 229152_at C4orf7
    Standard −15.77 1132122 307734 203434_s_at MME
    Standard −15.12 1120090 155024 203140_at BCL6
    Standard −14.89 1097897 266175 225622_at PAG
    Standard −14.36 1529343 521948 Lymph_Dx_064_at
    Standard −14.32 1529318 291954 Lymph_Dx_038_at
    Standard −14.06 1128694 171466 219517_at ELL3
    Standard −13.61 1101586 187884 229971_at GPR114
    Standard −13.57 1119752 511745 202391_at BASP1
    Standard −13.13 1137561 67397 214639_s_at HOXA1
    Standard −12.85 1097247 388761 224851_at CDK6
    Standard −12.43 1529344 317970 Lymph_Dx_065_at SERPINA11
    Standard −12.4 1120765 343329 204484_at PIK3C2B
    Standard −12.33 1130155 436657 222043_at CLU
    Standard −12.07 1529292 −92 Lymph_Dx_010_at
    Standard −12.01 1119939 170087 202820_at AHR
    Standard −11.82 1119919 199263 202786_at STK39
    Standard −11.77 1099686 117721 227684_at
    Standard −11.63 1119782 155418 202478_at TRB2
    Standard 10.97 1529309 512797 Lymph_Dx_028_at HSH2
    Standard 10.97 1139393 170129 219032_x_at OPN3
    Standard 11.04 1131246 153752 201853_s_at CDC25B
    Standard 11.07 1140391 44865 221558_s_at LEF1
    Standard 11.16 1140416 58831 221601_s_at TOSO
    Standard 11.35 1127807 7236 217950_at NOSIP
    Standard 11.67 1529317 −98 Lymph_Dx_037_at
    Standard 11.81 1117343 306812 234643_x_at BUCS1
    Standard 11.82 1102081 506977 230551_at
    Standard 11.82 1135042 79015 209582_s_at MOX2
    Standard 11.96 1132734 126248 204724_s_at COL9A3
    Standard 12.09 1137109 469653 213689_x_at RPL5
    Standard 12.14 1099939 488173 227983_at MGC7036
    Standard 12.19 1129103 99430 220118_at TZFP
    Standard 12.47 1135592 758 210621_s_at RASA1
    Standard 12.78 1108970 140489 238604_at
    Standard 12.92 1097143 74335 224716_at HSPCB
    Standard 13.18 1136865 412128 212959_s_at MGC4170
    Standard 13.96 1098220 80720 226002_at GAB1
    Standard 14.06 1100847 97411 229070_at C6orf105
    Standard 14.39 1098865 250905 226741_at LOC51234
    Standard 15.57 1136687 59943 212345_s_at CREB3L2
    Standard 15.75 1107044 163426 236458_at
    Standard 16.52 1123622 8578 210051_at EPAC
    Standard 17.74 1136987 21695 213370_s_at SFMBT1
    Standard 19.15 1129026 135146 220007_at FLJ13984
    Standard 19.65 1131854 414985 202923_s_at GCLC
    Lymph Node −14.99 1124875 18166 212975_at KIAA0870
    Lymph Node −14.33 1099358 93135 227300_at
    Lymph Node −13.26 1121129 285401 205159_at CSF2RB
    Lymph Node −12.61 1119074 54457 200675_at CD81
    Lymph Node −12.52 1121029 412999 204971_at CSTA
    Lymph Node −11.48 1137247 234734 213975_s_at LYZ
    Lymph Node −10.97 1128781 79741 219648_at FLJ10116
    Lymph Node 11.79 1119880 442844 202709_at FMOD
    Lymph Node 14.4 1134370 1422 208438_s_at FGR
    Standard Lymph Node
    Mean FL −663.95 −730.08 Cut 1 0.20
    Mean SLL 1332.84 −484.93 Cut 2 0.80
    Covariance FL 37097.15 1710.73
    1710.73 663.78
    Covariance SLL 85989.25 17661.52
    17661.52 4555.06
  • TABLE 2411
    GCB vs. PMBL
    Unigene
    ID Build Gene
    Signature Scale UNIQID 167 Probe set Symbol
    Standard −8.39 1096440 231320 223423_at GPR160
    Standard −8.13 1096108 292871 222731_at ZDHHC2
    Standard −8.12 1125231 446375 213489_at MAPRE2
    Standard −8.02 1136759 188882 212605_s_at
    Standard −7.91 1096499 293867 223514_at CARD11
    Standard −7.8 1099388 124024 227336_at DTX1
    Standard −7.71 1139623 193736 219667_s_at BANK1
    Standard −7.68 1098592 283707 226431_at ALS2CR13
    Standard −7.67 1107575 424589 237033_at MGC52498
    Standard −7.63 1116829 115467 231840_x_at LOC90624
    Standard −7.42 1130114 445084 221965_at MPHOSPH9
    Standard −7.27 1098909 446408 226789_at
    Standard 7.34 1138759 396404 217707_x_at SMARCA2
    Standard 7.37 1120355 80420 203687_at CX3CL1
    Standard 7.4 1134270 352119 208284_x_at GGT1
    Standard 7.44 1115441 5470 224156_x_at IL17RB
    Standard 7.78 1103054 341531 231690_at
    Standard 7.91 1119765 81234 202421_at IGSF3
    Standard 7.92 1119438 118110 201641_at BST2
    Standard 8.09 1135645 31439 210715_s_at SPINT2
    Standard 8.15 1106015 96885 235343_at FLJ12505
    Standard 8.18 1121400 223474 205599_at TRAF1
    Standard 8.38 1139950 437385 220731_s_at FLJ10420
    Standard 8.73 1122112 1314 206729_at TNFRSF8
    Standard 8.77 1122772 66742 207900_at CCL17
    Standard 8.84 1132762 80395 204777_s_at MAL
    Standard 9.64 1139774 15827 220140_s_at SNX11
    Standard 10.53 1133801 181097 207426_s_at TNFSF4
    Standard 11.52 1106415 169071 235774_at
    Standard 12.09 1129269 62919 220358_at SNFT
    Standard
    Mean GCB 292.76 Cut 1 0.16
    Mean PMBL 725.28 Cut 2 0.50
    Covariance GCB 8538.86
    Covariance PMBL 11405.23
  • TABLE 2412
    MCL vs. DLBCL-BL
    Signature Scale UNIQID Unigene ID Build 167 Probe set Gene Symbol
    Standard −26.11 1529382 371468 Lymph_Dx_111_at CCND1
    Standard −18.35 1103711 288718 232478_at
    Standard −17.03 1106855 455101 236255_at KIAA1909
    Standard −16.49 1098840 55098 226713_at C3orf6
    Standard −15.41 1109505 8162 239186_at MGC39372
    Standard −15.11 1098954 128905 226844_at MOBKL2B
    Standard −14.96 1103504 142517 232239_at
    Standard −14.74 1096070 241565 222640_at DNMT3A
    Standard −13.81 1137663 247362 214909_s_at DDAH2
    Standard −13.8 1124864 411317 212960_at KIAA0882
    Standard −13.62 1140127 125300 221044_s_at TRIM34
    Standard −13.62 1119361 391858 201448_at TIA1
    Standard −13.37 1127849 76691 218032_at SNN
    Standard 13.72 1133192 24024 205801_s_at RASGRP3
    Standard 13.85 1137583 273415 214687_x_at ALDOA
    Standard 15.02 1123052 180909 208680_at PRDX1
    Standard 16.21 1097611 438993 225285_at BCAT1
    Lymph Node −19.18 1529456 371468 Lymph_Dx_113_at CCND1
    Lymph Node −10.71 1098978 124863 226869_at
    Lymph Node −9.17 1097448 250607 225093_at UTRN
    Lymph Node 8.84 1135240 436852 209955_s_at FAP
    Lymph Node 9.11 1119475 296323 201739_at SGK
    Lymph Node 9.22 1119237 389964 201141_at GPNMB
    Lymph Node 9.46 1130629 135226 200839_s_at CTSB
    Lymph Node 10.1 1130054 82547 221872_at RARRES1
    Standard Lymph Node
    Mean MCL −1417.55 −25.58 Cut 1 0.50
    Mean DLBCL-BL −756.07 202.29 Cut 2 0.88
    Covariance MCL 15347.98 3525.48
    3525.48 5420.31
    Covariance DLBCL-BL 5132.06 1007.64
    1007.64 991.38
  • TABLE 2413
    MCL vs. SLL
    Signature Scale UNIQID Unigene ID Build 167 Probe set Gene Symbol
    Standard −20.18 1132834 432638 204914_s_at SOX11
    Standard −15.17 1130926 508741 201310_s_at C5orf13
    Standard 13.44 1116150 16229 227606_s_at AMSH-LP
    Standard 14.44 1120134 75545 203233_at IL4R
    Standard 15.18 1529437 445162 Lymph_Dx_175_at BTLA
    Standard 15.19 1529317 −98 Lymph_Dx_037_at
    Standard 16.2 1135042 79015 209582_s_at MOX2
    Standard
    Mean MCL 181.38 Cut 1 0.20
    Mean SLL 564.92 Cut 2 0.80
    Covariance MCL 1734.42
    Covariance SLL 910.75
  • TABLE 2414
    SLL vs. DLBCL-BL
    Signature Scale UNIQID Unigene ID Build 167 Probe set Gene Symbol
    Standard −16.014498 1123622 8578 210051_at EPAC
    Standard −15.26356533 1102081 506977 230551_at
    Standard −14.82150028 1107044 163426 236458_at
    Standard −14.17813266 1098865 250905 226741_at LOC51234
    Standard −12.92844719 1110740 416810 240538_at
    Standard −12.86520757 1129026 135146 220007_at FLJ13984
    Standard −12.2702748 1135592 758 210621_s_at RASA1
    Standard −11.87309449 1117343 306812 234643_x_at BUCS1
    Standard −11.81789137 1136987 21695 213370_s_at SFMBT1
    Standard −11.78631706 1124830 9059 212911_at KIAA0962
    Standard −11.39454435 1133538 1416 206760_s_at FCER2
    Standard −11.39050362 1135802 439343 210944_s_at CAPN3
    Standard 11.72928644 1120770 300825 204493_at BID
    Lymph Node −12.21593247 1119880 442844 202709_at FMOD
    Lymph Node 9.514704847 1135240 436852 209955_s_at FAP
    Lymph Node 9.739298877 1096429 64896 223405_at NPL
    Lymph Node 10.05087645 1119475 296323 201739_at SGK
    Lymph Node 13.11985922 1119237 389964 201141_at GPNMB
    Proliferation 10.47525875 1128106 14559 218542_at C10orf3
    Proliferation 10.53295782 1132825 512813 204900_x_at SAP30
    Proliferation 11.93918891 1130501 2795 200650_s_at LDHA
    Proliferation 11.98738778 1123439 287472 209642_at BUB1
    Proliferation 11.99741644 1115607 435733 224428_s_at CDCA7
    Standard Lymph Node Proliferation
    Mean SLL −1383.640809 177.4452398 467.2463569 Cut 1 0.201266305
    Mean DLBCL-BL −926.7275468 329.6795845 582.9070266 Cut 2 0.799816116
    Covariance SLL 3591.384775 1789.7516 856.0703202
    1789.7516 1421.869535 663.4782048
    856.0703202 663.4782048 965.6470151
    Covariance DLBCL-BL 2922.643347 473.543487 634.3258773
    473.543487 931.9845277 −53.85584619
    634.3258773 −53.85584619 767.3545404
  • As stated above, the foregoing is merely intended to illustrate various embodiments of the present invention. The specific modifications discussed above are not to be construed as limitations on the scope of the invention. It will be apparent to one skilled in the art that various equivalents, changes, and modifications may be made without departing from the scope of the invention, and it is understood that such equivalent embodiments are to be included herein. All references cited herein are incorporated by reference as if fully set forth herein.
  • Abbreviations used herein: ABC, activated B-cell-like diffuse large B cell lymphoma; BL, Burkitt lymphoma; CHOP, cyclophosphamide, doxorubicine, vincristine, and prednisone; CI, confidence interval; CNS, central nervous system; DLBCL, diffuse large B-cell lymphoma; ECOG, Eastern Cooperative Oncology Group; EST, expressed sequence tag; FACS, fluorescence-activated cell sorting; FH, follicular hyperplasia; FL, follicular lymphoma; GCB, germinal center B-cell-like diffuse large B cell lymphoma; GI, gastrointestinal; IPI, International Prognostic Index; LPC, lymphoplasmacytic lymphoma; LPS, linear predictor score; MALT, mucosa-associated lymphoid tissue lymphomas; MCL, mantle cell lymphoma; MHC, major histocompatibility complex; NA, not available or not applicable; NK, natural killer; NMZ, nodal marginal zone lymphoma; PCR, polymerase chain reaction; PMBL, primary mediastinal B-cell lymphoma; PTLD, post-transplant lymphoproliferative disorder; REAL, Revised European-American Lymphoma; RPA, RNase protection assay; RR, relative risk of death; RT-PCR, reverse transcriptase polymerase chain reaction; SAGE, serial analysis of gene expression; SLL, small lymphocytic lymphoma; WHO, World Health Organization.
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  • TABLE 2415
    GeneID.txt
    Order UNIQID NAME GENEID LN.cor Pro.cor
    1 1095985 1095985: TMEPAI :: transmembrane, prostate androgen induced RNA 83883 0.765572912605858 −0.305829906881871
    2 1095996 1095996: SSBP3 :: single stranded DNA binding protein 3 288801 0.337878824571224 −0.246570833627667
    3 1096028 1096028: STMN3 :: stathmin-like 3 285753 0.247291930603322 −0.512359910432692
    4 1096035 1096035: UGCGL1 :: UDP-glucose ceramide glucosyltransferase-like 1 105794 −0.044857707563452 0.126915353662946
    5 1096038 1096038: PPM2C :: protein phosphatase 2C, magnesium-dependent, 22265 0.059429204462921 −0.188473830832503
    catalytic subunit
    6 1096054 1096054: FLJ10036 :: hypothetical protein FLJ10036 21331 −0.371427712016433 0.730940143905553
    7 1096070 1096070: DNMT3A :: DNA (cytosine-5-)-methyltransferase 3 alpha 241565 0.065715669272673 −0.156420432074750
    8 1096077 1096077: IPO11 :: importin 11 441043 −0.272220885257140 0.497353016437345
    9 1096078 1096078: HSU84971 :: fetal hypothetical protein 284216 −0.414916213421669 0.418061447763775
    10 1096085 1096085: HSPC109 :: hypothetical protein HSPC109 224137 −0.293990882168277 0.238351282285725
    11 1096108 1096108: ZDHHC2 :: zinc finger, DHHC domain containing 2 292871 −0.051768610245872 0.113517147008026
    12 1096149 1096149: NUDT5 :: nudix (nucleoside diphosphate linked moiety X)- 410205 −0.328630578583663 0.210623718410482
    type motif 5
    13 1096152 1096152: IL20RA :: interleukin 20 receptor, alpha 288240 −0.082760468199485 −0.000212236348592
    14 1096158 1096158: SLAMF7 :: SLAM family member 7 132906 0.141965675898601 −0.400637349397057
    15 1096163 1096163: FKSG14 :: leucine zipper protein FKSG14 164018 −0.302881859478226 0.709798806284115
    16 1096172 1096172: AKT3 :: v-akt murine thymoma viral oncogene homolog 3 300642 0.079018970053188 −0.070815586824077
    (protein kinase B, gamma)
    17 1096180 1096180: HSPC065 :: HSPC065 protein 11614 −0.248427935178953 0.244895501152730
    18 1096182 1096182: ITGA11 :: integrin, alpha 11 256297 0.484784321132005 −0.141574493942455
    19 1096220 1096220: IL22 :: interleukin 22 287369 −0.012202602288250 0.102513778017030
    20 1096248 1096248: NAT5 :: N-acetyltransferase 5 (ARD1 homolog, S. cerevisiae) 109253 −0.179981414304964 0.304665808254639
    21 1096251 1096251: SLC40A1 :: solute carrier family 40 (iron-regulated 409875 −0.350169148476026 −0.039724364810070
    transporter), member 1
    22 1096297 1096297: UCK1 :: uridine-cytidine kinase 1 9597 0.107276488247798 −0.131638659028410
    23 1096300 1096300: MGC2714 :: hypothetical protein MGC2714 74284 −0.293976225239911 0.702711029782148
    24 1096341 1096341: SNX8 :: sorting nexin 8 12169 0.143322315228953 −0.018039018612117
    25 1096356 1096356: ALS2CR2 :: amyotrophic lateral sclerosis 2 (juvenile) 259230 0.110280642995490 −0.020357388828095
    chromosome region, candidate 2
    26 1096357 1096357: FLJ20432 :: hypothetical protein FLJ20432 57898 −0.498064299913012 0.547207859146077
    27 1096362 1096362: TCF19 :: transcription factor 19 (SC1) 512706 −0.399070415427405 0.449227205058841
    28 1096364 1096364: NID67 :: putative small membrane protein NID67 29444 0.683874750520760 −0.414039064356815
    29 1096369 1096369: DERP6 :: S-phase 2 protein 417029 −0.344757531355776 0.376048402134116
    30 1096378 1096378: URP2 :: UNC-112 related protein 2 180535 0.201631483396441 −0.176115831847333
    31 1096379 1096379: SLC37A3 :: solute carrier family 37 (glycerol-3-phosphate 439590 0.381537720604309 −0.447728614022874
    transporter), member 3
    32 1096406 1096406: C6orf115 :: chromosome 6 open reading frame 115 238205 0.165024207205827 −0.097834654666083
    33 1096429 1096429: NPL :: N-acetylneuraminate pyruvate lyase 64896 0.521727444062009 −0.359471289677876
    (dihydrodipicolinate synthase)
    34 1096440 1096440: GPR160 :: G protein-coupled receptor 160 231320 −0.270973814036627 0.306462668135112
    35 1096442 1096442: SIK2 :: salt-inducible serine/threonine kinase 2 306864 −0.062856819831174 0.170832425890252
    36 1096446 1096446: GBP3 :: guanylate binding protein 3 92287 0.386684402604806 −0.494981443515261
    37 1096456 1096456: CXCL16 :: chemokine (C—X—C motif) ligand 16 82407 0.534265409104252 −0.494680174142867
    38 1096460 1096460: CAMKK1 :: calcium/calmodulin-dependent protein 8417 0.063944985869638 −0.228128654986856
    kinase kinase 1, alpha
    39 1096466 1096466: RASD1 :: RAS, dexamethasone-induced 1 25829 0.289870036740434 −0.219151800055010
    40 1096469 1096469: RAB3IP :: RAB3A interacting protein (rabin3) 103267 −0.332016102837598 0.464149286520712
    41 1096499 1096499: CARD11 :: caspase recruitment domain family, member 11 293867 −0.436883733442666 0.265844768784079
    42 1096503 1096503: C9orf45 :: chromosome 9 open reading frame 45 21379 −0.298819325021361 −0.023184197355755
    43 1096530 1096530: PACAP :: proapoptotic caspase adaptor protein 409563 −0.314448231660953 0.248763567467872
    44 1096570 1096570: ANUBL1 :: AN1, ubiquitin-like, homolog (Xenopus laevis) 409813 0.087244086284512 −0.114499206537960
    45 1096579 1096579: HCST :: hematopoietic cell signal transducer 117339 0.191275472761633 −0.323814264064461
    46 1096609 1096609: ARSD :: arylsulfatase D −35 0.501162661333468 −0.492064259946528
    47 1096615 1096615: RPL27A :: ribosomal protein L27a 356342 −0.284923968217501 0.414116756593771
    48 1096616 1096616: C1QTNF4 :: C1q and tumor necrosis factor related protein 4 119302 0.245717528496956 −0.066211741589717
    49 1096617 1096617: CCL26 :: chemokine (C-C motif) ligand 26 131342 0.139107804989950 −0.111244751036349
    50 1096621 1096621: STK29 :: serine/threonine kinase 29 170819 0.121643230282416 0.000022906837176
    51 1096690 1096690: TNFRSF19 :: tumor necrosis factor receptor superfamily, 334174 0.046446130012764 −0.106555400562260
    member 19
    52 1096693 1096693: PDCDILG1 :: programmed cell death 1 ligand 1 443271 0.256067109408327 −0.178200268373170
    53 1096719 1096719: ARP3BETA :: actin-related protein 3-beta 250153 0.245831877624803 −0.006615297551808
    54 1096738 1096738: TLR9 :: toll-like receptor 9 87968 −0.454086982168439 0.435099752153320
    55 1096742 1096742: ERN2 :: Homo sapiens hypothetical gene supported by 114905 −0.020800763316815 0.082977324102791
    NM_033266 (LOC374284), mRNA
    56 1096805 1096805: CCL28 :: chemokine (C-C motif) ligand 28 334633 −0.119965557753727 −0.076751767859586
    57 1096829 1096829: IL20 :: interleukin 20 272373 0.000592650321134 0.142312268819410
    58 1096834 1096834: IL17C :: interleukin 17C 278911 −0.085306904722356 −0.026275991743137
    59 1096877 1096877: MGC13008 :: hypothetical protein MGC13008 326732 −0.152752641907604 0.133576812781343
    60 1096903 1096903: FLJ10385 :: hypothetical protein FLJ10385 437460 −0.363962088997560 0.386488614725012
    61 1096936 1096936: IL1F10 :: interleukin 1 family, member 10 (theta) 306974 −0.088807796915772 0.147815256172852
    62 1096965 1096965: PRO1853 :: hypothetical protein PRO1853 433466 0.234905061259092 −0.151522525032889
    63 1096981 1096981: PDCD1LG2 :: programmed cell death 1 ligand 2 61929 0.411512700132525 −0.339724398106172
    64 1097030 1097030: :: Homo sapiens transcribed sequence with moderate 511801 0.084096291164457 −0.211349577111875
    similarity to protein pir: I60307 (E. coli) 160307 beta-galactosidase,
    alpha peptide - Escherichia coli
    65 1097065 1097065: MAPK1 :: mitogen-activated protein kinase 1 324473 −0.067419611001008 −0.077605763020246
    66 1097096 1097096: SEPN1 :: selenoprotein N, 1 8518 0.486311887679975 −0.324166091574385
    67 1097107 1097107: LENG8 :: leukocyte receptor cluster (LRC) member 8 −27 −0.367283482545225 0.117896751606288
    68 1097109 1097109: MESDC2 :: mesoderm development candidate 2 −23 −0.084057602411658 0.123691273481405
    69 1097126 1097126: ANTXR1 :: anthrax toxin receptor 1 274520 0.872281447063434 −0.360699565338566
    70 1097143 1097143: HSPCB :: heat shock 90 kDa protein 1, beta 74335 −0.329763699311407 0.161353868658910
    71 1097156 1097156: CKLFSF3 :: chemokine-like factor super family 3 298198 0.356521698413820 −0.224978670328984
    72 1097161 1097161: :: Homo sapiens cDNA clone IMAGE: 5270526, partial cds 5064 −0.283918984792974 0.245645271796048
    73 1097172 1097172: CDCA5 :: cell division cycle associated 5 434886 −0.327278444996126 0.823349285555297
    74 1097177 1097177: GNA13 :: guanine nucleotide binding protein (G protein), 9691 −0.037330227523842 0.164092697479536
    alpha 13
    75 1097195 1097195: MGC29814 :: hypothetical protein MGC29814 −22 −0.311093569811657 0.387394625596569
    76 1097202 1097202: DDEF1 :: development and differentiation enhancing factor 1 −33 0.404219688288097 −0.239957287582709
    77 1097229 1097229: CPSF5 :: cleavage and polyadenylation specific factor 5, 446393 −0.364448004904438 0.618328935053735
    25 kDa
    78 1097236 1097236: FOXP1 :: forkhead box P1 235860 −0.374613701666339 0.219940106264499
    79 1097247 1097247: :: Homo sapiens cDNA clone IMAGE: 4520413, partial cds 388761 0.078706536819919 0.079845030074853
    80 1097253 1097253: B7H3 :: B7 homolog 3 77873 0.509686941959052 −0.300155823803531
    81 1097255 1097255: :: Homo sapiens, clone IMAGE: 5289004, mRNA 380144 0.655182909405963 −0.480162974610710
    82 1097271 1097271: RALA :: v-ral simian leukemia viral oncogene homolog A 6906 0.233158496732894 0.116175646014776
    (ras related)
    83 1097280 1097280: :: Homo sapiens cDNA clone IMAGE: 4814010, partial cds 423523 0.425384591076580 −0.493447794310351
    84 1097281 1097281: PLDN :: pallidin homolog (mouse) 7037 0.173437680009131 −0.194314449880568
    85 1097282 1097282: LOC283241 :: hypothetical protein LOC283241 356719 −0.025407453597505 −0.131750092303776
    86 1097290 1097290: CIRH1A :: cirrhosis, autosomal recessive 1A (cirhin) 151001 −0.492530933582546 0.676549644346020
    87 1097297 1097297: VMP1 :: likely ortholog of rat vacuole membrane protein 1 166254 0.453085943117571 −0.244926367026450
    88 1097307 1097307: LOC340061 :: hypothetical protein LOC340061 379754 0.677089831326282 −0.583057243877707
    89 1097310 1097310: SMAP-5 :: golgi membrane protein SB140 5672 0.264429734648259 −0.148300598780685
    90 1097325 1097325: LASS5 :: LAG1 longevity assurance homolog 5 458450 0.077585149886997 −0.030530283585439
    (S. cerevisiae)
    91 1097329 1097329: TEAD1 :: TEA domain family member 1 153408 0.609915504509915 −0.330588741531368
    (SV40 transcriptional enhancer factor)
    92 1097334 1097334: FLJ10074 :: hypothetical protein FLJ10074 71573 0.148822099251370 −0.036195940379043
    93 1097359 1097359: :: Homo sapiens transcribed sequence with weak similarity to 518723 0.053800334461785 −0.154524230021900
    protein ref: NP_060312.1 (H. sapiens) hypothetical protein FLJ20489
    [Homo sapiens]
    94 1097365 1097365: CKLFSF4 :: chemokine-like factor super family 4 325825 0.519294317954343 −0.216309380198487
    95 1097371 1097371: PHF13 :: PHD finger protein 13 7299 −0.321720660373057 0.340367027876139
    96 1097383 1097383: CAMK2D :: calcium/calmodulin-dependent protein kinase 111460 −0.290642761065368 0.133360053100389
    (CaM kinase) II delta
    97 1097388 1097388: C20orf77 :: chromosome 20 open reading frame 77 278839 −0.197775027946280 0.376751974725969
    98 1097395 1097395: FAD104 :: FAD104 299883 0.736100200479402 −0.373635154671711
    99 1097424 1097424: DKFZP434C131 :: DKFZP434C131 protein 7978 −0.134018331816916 −0.109225857504428
    100 1097441 1097441: FLJ38426 :: hypothetical protein FLJ38426 6799 −0.402273189776746 0.543694221269586
    101 1097448 1097448: UTRN :: utrophin (homologous to dystrophin) 250607 0.360883799114271 −0.584276143462886
    102 1097540 1097540: :: Homo sapiens cDNA FLJ13141 fis, clone NT2RP3003210. 388087 −0.061066580853079 0.258721848569539
    103 1097553 1097553: PSMB7 :: proteasome (prosome, macropain) subunit, 197071 0.311409341908515 −0.205155556831752
    beta type, 7
    104 1097561 1097561: C20orf112 :: chromosome 20 open reading frame 112 19221 0.527162504741833 −0.440301485246365
    105 1097563 1097563: FLJ14743 :: hypothetical protein FLJ14743 169577 −0.168921612398568 −0.030167777542399
    106 1097564 1097564: SKIL :: SKI-like 272108 −0.048959117197389 0.045546934477234
    107 1097600 1097600: SAT2 :: spermidine/spermine N1-acetyltransferase 2 10846 0.349508117260322 −0.551195374259974
    108 1097609 1097609: LOC91947 :: hypothetical protein LOC91947 6093 0.698019824770373 −0.413944744306518
    109 1097610 1097610: DNAJC3 :: DnaJ (Hsp40) homolog, subfamily C, member 3 6019 0.354942495910287 −0.301478249730580
    110 1097611 1097611: BCAT1 :: branched chain aminotransferase 1, cytosolic 438993 0.231503275940178 0.054391439403167
    111 1097614 1097614: MGC16063 :: hypothetical protein MGC16063 410491 0.046334195779423 −0.052886978168640
    112 1097637 1097637: ACBD6 :: acyl-Coenzyme A binding domain containing 6 63220 −0.455371733025381 0.588517058172155
    113 1097665 1097665: HT011 :: uncharacterized hypothalamus protein HT011 434241 0.302114923194357 −0.218617058012615
    114 1097676 1097676: PGM2 :: phosphoglucomutase 2 23363 −0.105211493496590 0.411367274902218
    115 1097683 1097683: PP2135 :: PP2135 protein 132569 0.438652292433518 −0.531837589765522
    116 1097684 1097684: MGC45714 :: hypothetical protein MGC45714 368878 −0.262573752576479 0.186215149748326
    117 1097704 1097704: C1orf19 :: chromosome 1 open reading frame 19 440663 −0.299851016612681 0.328280021104323
    118 1097707 1097707: C20orf64 :: chromosome 20 open reading frame 64 440263 −0.208966762154304 0.237923731267286
    119 1097717 1097717: FLJ14681 :: hypothetical protein FLJ14681 23317 0.125057120164488 −0.094075705262804
    120 1097735 1097735: LOC58489 :: hypothetical protein from EUROIMAGE 26765 −0.152766753795439 0.150760192399265
    588495
    121 1097804 1097804: FLJ10213 :: hypothetical protein FLJ10213 446590 −0.232974145960649 0.385796656610468
    122 1097814 1097814: CENTB5 :: centaurin, beta 5 21446 0.025599591925261 −0.077279249251246
    123 1097824 1097824: MAP2 :: microtubule-associated protein 2 167 0.117548992931937 −0.120439543060478
    124 1097887 1097887: KIAA0303 :: KIAA0303 protein 212787 0.092960318117084 −0.116573446206172
    125 1097897 1097897: PAG :: phosphoprotein associated with glycosphingolipid- 266175 0.191577241800621 −0.085455707264803
    enriched microdomains
    126 1097899 1097899: LOC92017 :: similar to RIKEN cDNA 4933437K13 145047 0.096634326522832 −0.342206059804613
    127 1097901 1097901: PAG :: phosphoprotein associated with glycosphingolipid- 266175 0.204617854117621 −0.117013400778641
    enriched microdomains
    128 1097902 1097902: KIAA1706 :: KIAA1706 protein 412318 0.203615260815970 −0.140541494164973
    129 1097918 1097918: LOC90378 :: atherin 140309 −0.379406336299933 0.520098002520735
    130 1097928 1097928: SEMA6A :: sema domain, transmembrane domain (TM), and 443012 0.234759397668220 −0.219646366867697
    cytoplasmic domain, (semaphorin) 6A
    131 1097930 1097930: ZAK :: sterile alpha motif and leucine zipper containing 115175 0.108699289989043 0.073998196964394
    kinase AZK
    132 1097940 1097940: LOC91663 :: hypothetical protein BC013995 380906 0.706870503069227 −0.502093351185603
    133 1097948 1097948: LOC348235 :: hypothetical protein LOC348235 69476 −0.269699076470008 0.529419096597393
    134 1097961 1097961: :: Homo sapiens ACA9 snoRNA gene 25892 −0.429719438748216 0.625988904538759
    135 1097966 1097966: KIAA1545 :: KIAA1545 protein 127270 0.027173493843938 −0.400522062454424
    136 1097976 1097976: raptor :: raptor 218017 −0.148308861940539 0.120470330039901
    137 1098012 1098012: CSNK1E :: casein kinase 1, epsilon 355669 −0.342068884130279 0.262100628123216
    138 1098023 1098023: KIAA1972 :: KIAA1972 protein 181161 −0.129150683371564 0.086536959397880
    139 1098065 1098065: FLJ14957 :: hypothetical protein FLJ14957 10119 0.609772948330722 −0.373661396100191
    140 1098069 1098069: :: Homo sapiens mRNA similar to QIL1 (cDNA clone 356626 −0.282366680428328 0.222535690878294
    MGC: 57483 IMAGE: 5288954), complete cds
    141 1098095 1098095: ANKRD17 :: ankyrin repeat domain 17 131059 −0.102008011290600 0.114467644297043
    142 1098103 1098103: NSE2 :: breast cancer membrane protein 101 124951 0.223410146111536 −0.418382440606729
    143 1098145 1098145: KIAA2002 :: KIAA2002 protein 9587 −0.043305517146293 −0.071453322767335
    144 1098152 1098152: KIAA1450 :: KIAA1450 protein 377588 0.582609629394882 −0.401088162485662
    145 1098156 1098156: MAP3K1 :: mitogen-activated protein kinase kinase kinase 1 170610 −0.393164723370577 0.064183682917463
    146 1098168 1098168: NLN :: neurolysin (metallopeptidase M3 family) 22151 −0.086110889605484 0.266365022083743
    147 1098174 1098174: LOC340371 :: hypothetical protein LOC340371 274401 0.371605420749830 −0.378069656516585
    148 1098179 1098179: LOC153222 :: adult retina protein 163725 0.113653935807107 −0.578870218791412
    149 1098186 1098186: MGC11349 :: hypothetical protein MGC11349 288697 −0.411774761515353 0.252798351125526
    150 1098195 1098195: DKFZp762C1112 :: hypothetical protein DKFZp762C1112 88594 −0.162948668373984 0.064023508939311
    151 1098204 1098204: PRKAA1 :: protein kinase, AMP-activated, alpha 1 catalytic 43322 0.082481444229336 −0.126559120661099
    subunit
    152 1098220 1098220: GAB1 :: GRB2-associated binding protein 1 80720 −0.270353808866967 0.129171526797500
    153 1098234 1098234: CD47 :: CD47 antigen (Rh-related antigen, integrin-associated 446414 −0.204808859254960 −0.130670945404961
    signal transducer)
    154 1098235 1098235: CKLFSF7 :: chemokine-like factor super family 7 440494 −0.003820637227097 −0.213943192132446
    155 1098242 1098242: KIAA0379 :: KIAA0379 protein 273104 −0.146990537817309 0.382995758727720
    156 1098252 1098252: KIAA1203 :: ubiquitin-specific protease KIAA1203 16953 −0.006618002834239 0.046833591332181
    157 1098256 1098256: SVH :: SVH protein 431871 −0.452504903187901 0.363026813249536
    158 1098258 1098258: AGS3 :: activator of G-protein signaling 3 239370 0.310744715383991 −0.322355508448668
    159 1098268 1098268: MAP2K7 :: mitogen-activated protein kinase kinase 7 110299 −0.298346850539865 0.241278514570550
    160 1098271 1098271: CDGAP :: KIAA1204 protein 300670 0.173495129742519 −0.257241770812174
    161 1098277 1098277: PRICKLE1 :: prickle-like 1 (Drosophila) 6786 −0.273817683372350 0.064132444418075
    162 1098278 1098278: MITF :: microphthalmia-associated transcription factor 166017 0.618314859385319 −0.387872278743441
    163 1098303 1098303: FRCP2 :: likely ortholog of mouse fibronectin type III repeat 15463 0.010448057045878 −0.100537311719435
    containing protein 2
    164 1098338 1098338: HRB2 :: HIV-1 rev binding protein 2 269857 0.310283160362659 −0.307858826824513
    165 1098405 1098405: IL7R :: interleukin 7 receptor 362807 0.549494110248763 −0.263717657392419
    166 1098412 1098412: MCC :: mutated in colorectal cancers −24 0.454236696826577 −0.310591183271143
    167 1098415 1098415: KIAA1387 :: KIAA1387 protein 130900 −0.116869481419355 −0.122838250620999
    168 1098433 1098433: :: Homo sapiens cDNA FLJ10158 fis, clone 202577 0.136410689468839 −0.299039669796789
    HEMBA1003463.
    169 1098447 1098447: JDP2 :: jun dimerization protein 2 154095 −0.141461142027089 0.099602291803127
    170 1098459 1098459: SPUVE :: protease, serine, 23 25338 0.737264124009213 −0.334058738986943
    171 1098461 1098461: DNER :: delta-notch-like EGF repeat-containing 234074 0.041020174413569 −0.067455662571597
    transmembrane
    172 1098476 1098476: pknbeta :: protein kinase PKNbeta 300485 −0.194588649952929 0.049490469697965
    173 1098495 1098495: TBRG1 :: likely ortholog of mouse transforming growth 443668 0.052385916360886 −0.306318481977251
    factor beta regulated gene 1
    174 1098506 1098506: IL6R :: interleukin 6 receptor 193400 0.299704358316571 −0.483797688597999
    175 1098521 1098521: OPN3 :: opsin 3 (encephalopsin, panopsin) 170129 −0.309674653956075 0.290933486492843
    176 1098548 1098548: NFIC :: nuclear factor I/C (CCAAT-binding transcription 436639 0.577838108495008 −0.573059285395985
    factor)
    177 1098550 1098550: :: Homo sapiens cDNA FLJ36584 fis, clone TRACH2013450. 355655 −0.090479408634668 −0.005454207841183
    178 1098553 1098553: HTPAP :: HTPAP protein 437179 0.172952993194321 −0.447010228881662
    179 1098574 1098574: KIAA0233 :: KIAA0233 gene product 79077 −0.341045883809633 0.355913888061517
    180 1098592 1098592: FLJ38771 :: hypothetical protein FLJ38771 283707 −0.370411569171726 0.240153206136564
    181 1098604 1098604: SLC39A10 :: solute carrier family 39 (zinc transporter), 32793 −0.356817082601293 0.039590884115228
    member 10
    182 1098607 1098607: MGC15887 :: hypothetical gene supported by BC009447 38516 −0.202635383865497 0.273499931529896
    183 1098611 1098611: PDK1 :: pyruvate dehydrogenase kinase, isoenzyme 1 433611 0.011464972668250 0.218494255827149
    184 1098613 1098613: RENT1 :: regulator of nonsense transcripts 1 388125 −0.409061726498054 0.340688285828164
    185 1098618 1098618: PIK3AP1 :: phosphoinositide-3-kinase adaptor protein 1 374836 −0.256727551852790 0.025741438982940
    186 1098629 1098629: :: Homo sapiens mRNA; cDNA DKFZp434B0425 (from 103305 −0.188649329326843 0.425239786821600
    clone DKFZp434B0425)
    187 1098658 1098658: PAK1 :: p21/Cdc42/Rac1-activated kinase 1 (STE20 64056 0.012658587060208 −0.114254490164613
    homolog, yeast)
    188 1098668 1098668: BCAT1 :: branched chain aminotransferase 1, cytosolic 438993 0.198467154785237 0.101188582172517
    189 1098669 1098669: KCTD10 :: potassium channel tetramerisation domain 302746 −0.054505167679050 0.005953626629536
    containing 10
    190 1098678 1098678: BMF :: Bcl-2 modifying factor 386140 −0.340027764754526 0.107012841951926
    191 1098683 1098683: ITGB6 :: integrin, beta 6 57664 0.254592203414043 −0.200152902993317
    192 1098694 1098694: :: Homo sapiens mRNA; cDNA DKFZp547J047 (from clone 97837 0.128247191609226 −0.269181101036406
    DKFZp547J047)
    193 1098718 1098718: PSPC1 :: paraspeckle component 1 16364 −0.320538780285753 0.522732450579130
    194 1098771 1098771: KIAA1501 :: KIAA1501 protein 374446 0.328061924477626 −0.168759177690866
    195 1098784 1098784: MARK1 :: MAP/microtubule affinity-regulating kinase 1 12808 0.088534795440517 −0.093360079546100
    196 1098809 1098809: :: Homo sapiens hypothetical protein LOC283666, mRNA 359394 0.447370410855574 −0.496179620225829
    (cDNA clone IMAGE: 4415549), partial cds
    197 1098821 1098821: PALM2 :: paralemmin 2 42322 0.179862598270706 −0.187856000103763
    198 1098822 1098822: PRRX1 :: paired related homeobox 1 443452 0.774883481649142 −0.543483135789053
    199 1098832 1098832: FGFR1 :: fibroblast growth factor receptor 1 (fms-related 748 0.543603649322806 −0.330357417669066
    tyrosine kinase 2, Pfeiffer syndrome)
    200 1098840 1098840: C3orf6 :: chromosome 3 open reading frame 6 55098 −0.146221260881764 −0.090592943233251
    201 1098862 1098862: MGC26694 :: hypothetical protein MGC26694 303669 −0.034863463975044 −0.146817360127211
    202 1098865 1098865: LOC51234 :: hypothetical protein LOC51234 250905 0.159594910624286 −0.309933221730095
    203 1098883 1098883: MBTPS2 :: membrane-bound transcription factor protease, 412014 0.360729355144278 0.015238352387109
    site 2
    204 1098893 1098893: ATP8B2 :: ATPase, Class I, type 8B, member 2 43577 0.159404272308497 −0.298738852653094
    205 1098898 1098898: ADAM12 :: a disintegrin and metalloproteinase domain 12 −36 0.763097942064200 −0.294746482348485
    (meltrin alpha)
    206 1098909 1098909: MGC71745 :: similar to embigin 446408 −0.262428029790519 −0.053305715167356
    207 1098918 1098918: FGD6 :: FYVE, RhoGEF and PH domain containing 6 170623 0.156113760591959 0.048524812619013
    208 1098927 1098927: FLJ20202 :: FLJ20202 protein 356216 −0.081190091806277 −0.118355192853442
    209 1098946 1098946: :: Homo sapiens transcribed sequence with moderate 135121 0.645970747276803 −0.478233290280070
    similarity to protein sp: P39195 (H. sapiens) ALU8_HUMAN
    Alu subfamily SX sequence contamination warning entry
    210 1098951 1098951: H2AFY :: H2A histone family, member Y 75258 −0.105148799565054 0.000183905271443
    211 1098952 1098952: KIAA0937 :: KIAA0937 protein 62264 −0.155610228904124 −0.112321975971408
    212 1098954 1098954: MOB3B :: MOB3B protein 128905 0.141136508773827 −0.149504432709389
    213 1098962 1098962: BMP2K :: BMP2 inducible kinase 20137 0.286170948451110 −0.181990310332082
    214 1098978 1098978: :: Homo sapiens full length insert cDNA clone ZD77F06 124863 0.619336132796843 −0.505050387984609
    215 1098987 1098987: FLJ21127 :: hypothetical protein FLJ21127 412559 0.062127070347666 −0.441644144559995
    216 1098991 1098991: LRRN1 :: leucine rich repeat neuronal 1 126085 0.069832627264346 −0.114738890765678
    217 1099028 1099028: FNDC1 :: fibronectin type III domain containing 1 334838 0.631435118754401 −0.300213120295103
    218 1099032 1099032: :: Homo sapiens cDNA clone IMAGE: 4448513, partial cds 35962 −0.258137643029524 0.696628339145868
    219 1099040 1099040: HTRA3 :: serine protease HTRA3 390421 0.507829674693844 −0.252934339568439
    220 1099053 1099053: :: Homo sapiens mRNA; cDNA DKFZp761D1624 (from 376041 −0.147877893008140 −0.132787590083425
    clone DKFZp761D1624)
    221 1099058 1099058: :: Homo sapiens, clone IMAGE: 5267224, mRNA 425116 −0.152727193720123 0.086705174421553
    222 1099072 1099072: MAP3K2 :: mitogen-activated protein kinase kinase kinase 2 28827 0.326012687586492 −0.341129976548376
    223 1099088 1099088: :: Homo sapiens mRNA; cDNA DKFZp686N20218 (from 14355 −0.339066628811356 0.384877728106452
    clone DKFZp686N20218)
    224 1099105 1099105: LATS2 :: LATS, large tumor suppressor, homolog 2 78960 0.495842158034742 −0.343366651347192
    (Drosophila)
    225 1099112 1099112: :: Homo sapiens cDNA FLJ39934 fis, clone SPLEN2021458, 368672 0.271313775607110 −0.552177849009380
    weakly similar to Mus musculus mdgl-1 mRNA.
    226 1099120 1099120: :: Homo sapiens cDNA FLJ46579 fis, clone THYMU3042758 371680 −0.188611271416496 0.122311426949034
    227 1099124 1099124: FLJ21870 :: hypothetical protein FLJ21870 396161 0.519619700424312 −0.453311608748159
    228 1099128 1099128: AKAP13 :: A kinase (PRKA) anchor protein 13 350631 −0.013033876971250 −0.132909940435626
    229 1099135 1099135: SLC39A11 :: solute carrier family 39 (metal ion transporter), 3402 0.326183693547397 −0.243872317095855
    member 11
    230 1099140 1099140: :: Homo sapiens cDNA FLJ26764 fis, clone PRS02668 500350 0.065600037256185 −0.226915577288523
    231 1099148 1099148: TNFRSF19L :: tumor necrosis factor receptor superfamily, 434975 0.188804128027844 −0.086049656003445
    member 19-like
    232 1099150 1099150: :: Homo sapiens mRNA; cDNA DKFZp686L01105 240443 0.440961016035862 −0.370874002114838
    (from clone DKFZp686L01105
    233 1099152 1099152: MGC15396 :: hypothetical protein MGC15396 351247 −0.310898020091843 0.293673968871125
    234 1099154 1099154: MOB3C :: MOB3C protein 97927 0.205447190901989 −0.397428894897845
    235 1099167 1099167: MGC45731 :: hypothetical protein MGC45731 381105 0.510485627999948 −0.199429872177220
    236 1099204 1099204: :: Homo sapiens mRNA; cDNA DKFZp586K1922 193784 0.208527885951095 −0.331184935715711
    (from clone DKFZp586K1922)
    237 1099265 1099265: :: Homo sapiens,clone IMAGE: 4828750, mRNA 375762 0.191460172021332 −0.292819027251602
    238 1099291 1099291: FBXO10 :: F-box only protein 10 130774 −0.241213003745553 0.140643790486120
    239 1099292 1099292: RNPC2 :: RNA-binding region (RNP1, RRM) containing 2 282901 −0.011512027826638 −0.146104933503048
    240 1099299 1099299: EVL :: Enah/Vasp-like 241471 0.217471121189110 −0.497486588999731
    241 1099318 1099318: LOC149420 :: casein kinase 29911 −0.031451620931163 0.032273607550190
    242 1099328 1099328: FLJ35779 :: hypothetical protein FLJ35779 432726 −0.254822688277176 0.160319358394402
    243 1099332 1099332: :: Homo sapiens cDNA FLJ44521 fis, clone UTERU3002786 32433 0.353038975004276 −0.376426689684681
    244 1099358 1099358: LOC338773 :: hypothetical protein LOC338773 449718 0.813232650418064 −0.319504511328730
    245 1099377 1099377: ADCK4 :: aarF domain containing kinase 4 130712 −0.050763139906985 0.004763238452783
    246 1099388 1099388: DTX1 :: deltex homolog 1 (Drosophila) 124024 −0.194780161074778 0.313061833581174
    247 1099396 1099396: ZNFN1A1 :: zinc finger protein, subfamily 1A, 1 (Ikaros) 435949 −0.480396437660557 0.241771812595989
    248 1099403 1099403: PAG :: phosphoprotein associated with 266175 0.157815263023168 −0.138144351639275
    glycosphingolipid-enriched microdomains
    249 1099418 1099418: KIAA1946 :: KIAA1946 protein 172792 0.352518727172842 −0.221041836869096
    250 1099444 1099444: FLJ90013 :: hypothetical protein FLJ90013 434489 −0.154725204627076 0.144181046064220
    251 1099510 1099510: ADCK1 :: aarF domain containing kinase 1 15251 0.036823049790738 −0.189535081209326
    252 1099526 1099526: LCHN :: LCHN protein 521240 0.059814201915876 −0.318229548955097
    253 1099539 1099539: CXorf15 :: chromosome X open reading frame 15 201624 −0.159971879950874 0.335150972693171
    254 1099549 1099549: :: Homo sapiens transcribed sequences −45 −0.384484470966513 0.213030278389421
    255 1099563 1099563: :: Homo sapiens mRNA; cDNA DKFZp686J0156 (from clone 388347 0.091030785211341 −0.163765026275539
    DKFZp686J0156)
    256 1099598 1099598: MGC2452 :: hypothetical protein MGC2452 275711 −0.347670787807501 0.173371242361433
    257 1099631 1099631: FLJ20032 :: hypothetical protein FLJ20032 367639 −0.105513306302497 −0.093592194250014
    258 1099633 1099633: SGKL :: serum/glucocorticoid regulated kinase-like 380877 0.366469483816619 −0.401250676057012
    259 1099651 1099651: EBF :: early B-cell factor −31 −0.137184837781477 0.247346085114095
    260 1099669 1099669: MGC45428 :: hypothetical protein MGC45428 45057 −0.094311296476672 −0.134670571453547
    261 1099680 1099680: JAK3 :: Janus kinase 3 (a protein tyrosine kinase, leukocyte) 210387 0.158713315773940 −0.344236607885679
    262 1099686 1099686: :: Homo sapiens transcribed sequence with weak similarity to 117721 0.339760641299220 −0.126834793111279
    protein ref: NP_060312.1 (H. sapiens) hypothetical protein FLJ20489
    [Homo sapiens]
    263 1099699 1099699: SOCS3 :: suppressor of cytokine signaling 3 436943 0.458674229868194 −0.269705172389045
    264 1099711 1099711: :: Homo sapiens mRNA; cDNA DKFZp686I21166 243596 0.139055481628475 0.201358145780389
    (from clone DKFZp686I21166)
    265 1099734 1099734: KIS :: kinase interacting with leukemia-associated 127310 0.002341421127241 −0.061937188018310
    gene (stathmin)
    266 1099743 1099743: TRAD :: serine/threonine kinase with Dbl- and 162189 0.130663684870377 −0.073102099734362
    pleckstrin homology domains
    267 1099748 1099748: :: Homo sapiens cDNA FLJ42435 fis, clone BLADE2006849 356481 0.085730011981031 −0.405219346399157
    268 1099760 1099760: CSNK1G3 :: casein kinase 1, gamma 3 129206 −0.007660349798916 −0.109292619399866
    269 1099798 1099798: FGD3 :: FGD1 family, member 3 411081 −0.015909131360829 −0.501064586770852
    270 1099826 1099826: RAB30 :: RAB30, member RAS oncogene family 445862 −0.294473360458321 0.412965834268278
    271 1099830 1099830: EPM2AIP1 :: EPM2A (laforin) interacting protein 1 28020 −0.358690409532099 0.237419003752701
    272 1099847 1099847: LOC129293 :: hypothetical protein LOC129293 36723 −0.029109229364516 −0.268448964730217
    273 1099857 1099857: :: Homo sapiens annexin II receptor mRNA, complete cds 119768 0.049788466833904 −0.291863614075693
    274 1099886 1099886: :: Homo sapiens mRNA; cDNA DKFZp434N2116 −49 0.148774754361664 −0.263395075051385
    (from clone DKFZp434N2116)
    275 1099900 1099900: :: Homo sapiens transcribed sequences 444508 −0.104446381462296 −0.145223660017070
    276 1099939 1099939: MGC7036 :: hypothetical protein MGC7036 488173 −0.099560227175285 −0.171318365358415
    277 1099951 1099951: LOC170394 :: hypothetical protein BC011630 157728 0.274596536409081 −0.347843922255294
    278 1099953 1099953: C21orf4 :: chromosome 21 open reading frame 4 433668 0.047645355151766 −0.294401060293225
    279 1099960 1099960: :: Homo sapiens cDNA clone IMAGE: 3462401, partial cds 144583 −0.127871935602877 −0.010821560153853
    280 1099965 1099965: LOC138428 :: hypothetical protein LOC138428 71962 0.091962882474027 −0.091249651864211
    281 1099978 1099978: STK33 :: serine/threonine kinase 33 148135 −0.179708365440309 0.235587009064294
    282 1099995 1099995: LOC115265 :: similar to Smhs1 protein 107515 0.007329815357109 −0.132004117518270
    283 1100005 1100005: DUFD1 :: DUF729 domain containing 1 121536 −0.135976170321747 0.601059023563389
    284 1100027 1100027: AMICA :: adhesion molecule AMICA 16291 0.300925302822323 −0.551597607471469
    285 1100040 1100040: RASGRF2 :: Ras protein-specific guanine 410953 0.147596960954750 −0.215628806283083
    nucleotide-releasing factor 2
    286 1100042 1100042: RAB37 :: RAB37, member of RAS oncogene family 351413 0.165978306204715 −0.447611162228477
    287 1100054 1100054: :: Homo sapiens cDNA FLJ10641 fis, clone NT2RP2005748. 125353 −0.093387430515190 −0.046922285279186
    288 1100060 1100060: RIPK3 :: receptor-interacting serine-threonine kinase 3 268551 −0.080673891292211 −0.183740301156722
    289 1100071 1100071: IBRDC2 :: IBR domain containing 2 432653 −0.096139559105640 0.021910530191750
    290 1100130 1100130: PRELP :: proline arginine-rich end leucine-rich repeat protein 76494 0.448903531773197 −0.427716260301673
    291 1100136 1100136: NUDT1 :: nudix (nucleoside diphosphate linked 413078 0.056972383642216 −0.056702588166804
    moiety X)-type motif 1
    292 1100138 1100138: CGI-109 :: CGI-109 protein 278391 0.075525386230414 −0.015196240931810
    293 1100144 1100144: :: Homo sapiens transcribed sequence with 436379 0.342120616958852 −0.305881511542112
    moderate similarity to protein ref: NP_004563.1 (H. sapiens)
    plakophilin 2 [Homo sapiens]
    294 1100150 1100150: KIAA1999 :: KIAA1999 protein 9343 0.043922323292873 −0.262547992538478
    295 1100159 1100159: FLJ00332 :: FLJ00332 protein 123164 −0.175114276904071 −0.151251745398630
    296 1100161 1100161: LOC142678 :: skeletrophin 135805 −0.268803408286193 0.043074199399014
    297 1100171 1100171: FLJ11029 :: hypothetical protein FLJ11029 274448 −0.315599369534162 0.776632148727844
    298 1100183 1100183: FLJ40869 :: hypothetical protein FLJ40869 180582 −0.319113707524938 0.407258049070190
    299 1100249 1100249: HAK :: heart alpha-kinase 388674 0.405202029528982 −0.422914576572978
    300 1100258 1100258: KIAA1384 :: KIAA1384 protein 88442 −0.482927417502683 0.245462430738922
    301 1100263 1100263: LOC90268 :: hypothetical protein BC007706 406335 0.061549164584574 0.052439579303132
    302 1100288 1100288: ALS2CR19 :: amyotrophic lateral sclerosis 2 26981 0.428889792428239 −0.320712838583390
    (juvenile) chromosome region, candidate 19
    303 1100290 1100290: :: Homo sapiens cDNA FLJ30800 fis, clone FEBRA2001197. 4241 0.136196171503417 −0.229576669665241
    304 1100301 1100301: LLT1 :: lectin-like NK cell receptor 356250 −0.001129259036374 −0.099966890057848
    305 1100311 1100311: HSPC163 :: HSPC163 protein 445890 0.105307377070741 −0.165266726365081
    306 1100335 1100335: :: Homo sapiens transcribed sequence with moderate 268474 −0.125278649387652 0.316598617445776
    similarity to protein pir: I60307 (E. coli) I60307 beta-galactosidase,
    alpha peptide - Escherichia coli
    307 1100339 1100339: FLJ14813 :: hypothetical protein FLJ14813 276905 −0.222316026912740 0.607673448698899
    308 1100384 1100384: ADCK5 :: aarF domain containing kinase 5 283374 0.020059370587246 0.007329091610762
    309 1100405 1100405: KIAA0792 :: KIAA0792 gene product 119387 0.252199782581926 −0.442247983365885
    310 1100420 1100420: KIAA1804 :: mixed lineage kinase 4 50883 −0.165851676757938 0.231232139369928
    311 1100423 1100423: FLJ30973 :: hypothetical protein FLJ30973 50841 0.159003371714792 −0.138588437250525
    312 1100433 1100433: HTRA3 :: serine protease HTRA3 390421 0.163178704381462 −0.118871240794897
    313 1100443 1100443: MS4A1 :: membrane-spanning 4-domains, 438040 −0.105067576170844 0.035186610667903
    subfamily A, member 1
    314 1100496 1100496: LOC139886 :: hypothetical protein LOC139886 111496 −0.124735215994899 0.440981805278388
    315 1100538 1100538: PRG4 :: proteoglycan 4, (megakaryocyte 432458 −0.021487630294264 −0.194800347586334
    stimulating factor, articular superficial zone protein, camptodactyly,
    arthropathy, coxa vara, pericarditis syndrome)
    316 1100561 1100561: HEL308 :: DNA helicase HEL308 194109 −0.185491511987517 0.129409778871118
    317 1100562 1100562: C20orf100 :: chromosome 20 open reading frame 100 26608 0.059305525501118 −0.237095028247775
    318 1100581 1100581: :: Homo sapiens mRNA; cDNA 356307 0.165135933716527 0.026126858437344
    DKFZp667A1115 (from clone DKFZp667A1115)
    319 1100585 1100585: LFNG :: lunatic fringe homolog (Drosophila) 159142 0.308152082775067 −0.295830383149056
    320 1100591 1100591: HKR2 :: GLI-Kruppel family member HKR2 388162 −0.281373260470838 0.142310651962664
    321 1100598 1100598: :: Homo sapiens cDNA FLJ40955 fis, clone UTERU2011199. 438749 −0.081272856483147 0.389541653250864
    322 1100609 1100609: PPIL2 :: peptidylprolyl isomerase (cyclophilin)-like 2 447045 −0.010033297668578 −0.251624647902145
    323 1100625 1100625: RORC :: RAR-related orphan receptor C 232803 −0.017550954843166 −0.115801492903445
    324 1100721 1100721: :: Homo sapiens cDNA FLJ32207 fis, clone PLACE6003204. 18713 0.320178262906959 −0.294600821446125
    325 1100750 1100750: :: Homo sapiens,clone IMAGE: 4753714, mRNA 280387 −0.220418967314602 0.334098240571130
    326 1100753 1100753: ZNF19 :: zinc finger protein 19 (KOX 12) 512717 −0.096315574634547 −0.073564313338261
    327 1100770 1100770: :: Homo sapiens transcribed sequences 65578 0.126400491381177 −0.124140490500188
    328 1100847 1100847: C6orf105 :: chromosome 6 open reading frame 105 97411 0.101671461597607 −0.160154386139487
    329 1100849 1100849: :: Homo sapiens cDNA FLJ34866 fis, clone NT2NE2014113. 184430 −0.409355182450365 0.352909174326550
    330 1100851 1100851: EHD4 :: EH-domain containing 4 55058 0.321339038108403 −0.287001767216924
    331 1100871 1100871: :: Homo sapiens cDNA FLJ32274 fis, clone PROST2000036. 48353 0.435206681695438 −0.544521387799030
    332 1100873 1100873: :: Homo sapiens transcribed sequences 445884 −0.204883351763766 0.157721916475158
    333 1100879 1100879: MASP2 :: mannan-binding lectin serine protease 2 119983 −0.112831783867775 −0.290649076935063
    334 1100904 1100904: LOC119504 :: hypothetical protein LOC119504 −25 −0.099036342262842 −0.256431195474163
    335 1100911 1100911: C4orf7 :: chromosome 4 open reading frame 7 320147 0.060001350276090 −0.084108354010684
    336 1100916 1100916: PRKWNK4 :: protein kinase, lysine deficient 4 105448 0.108814731820795 −0.011505711122245
    337 1100977 1100977: NRG3 :: neuregulin 3 −8 0.107540349948529 −0.052860133552450
    338 1100995 1100995: FLJ32029 :: hypothetical protein FLJ32029 26612 0.222494929393081 −0.247794549127664
    339 1101004 1101004: SKI :: v-ski sarcoma viral oncogene homolog (avian) 2969 0.300578623845209 −0.357871271240017
    340 1101023 1101023: EPHA7 :: EphA7 73962 −0.081992625701500 −0.012091224764700
    341 1101054 1101054: PPP2R5E :: protein phosphatase 2, regulatory 173328 −0.142239905250465 0.091911875646825
    subunit B (B56), epsilon isoform
    342 1101096 1101096: :: Homo sapiens transcribed sequences 457403 0.393655668577862 −0.355743747889559
    343 1101119 1101119: IL17RE :: interleukin 17 receptor E 390823 0.039586216405584 0.044022252281821
    344 1101128 1101128: MGC45419 :: Similar to calcium/calmodulin- 436667 −0.241815550224320 0.169113348318235
    dependent protein kinase 1, beta
    345 1101149 1101149: :: Homo sapiens BIC noncoding mRNA, complete sequence 517226 0.029858079836277 −0.090026984564981
    346 1101211 1101211: STRBP :: spermatid perinuclear RNA binding protein 287659 −0.250696465092268 0.025159511937388
    347 1101272 1101272: DKFZp434H2111 :: hypothetical protein DKFZp434H2111 179089 0.009706674301822 −0.269133228709153
    348 1101276 1101276: ERdj5 :: ER-resident protein ERdj5 1098 0.006940542351402 0.036655849606570
    349 1101291 1101291: PPP3CA :: protein phosphatase 3 (formerly 2B), 272458 −0.133666602302100 0.284183973397199
    catalytic subunit, alpha isoform (calcineurin A alpha)
    350 1101295 1101295: FLJ40629 :: hypothetical protein FLJ40629 99807 −0.205479511626541 0.628330940348730
    351 1101305 1101305: :: Homo sapiens cDNA clone IMAGE: 6301163, 112742 0.473043674581829 −0.340194063635630
    containing frame- shift errors
    352 1101322 1101322: :: Homo sapiens similar 227699 −0.115836732640888 0.157977457392334
    to RIKEN cDNA 2900024C23 (LOC125704), mRNA
    353 1101354 1101354: P2RY8 :: purinergic receptor P2Y, G-protein coupled, 8 111377 0.121615764539941 −0.111489709331474
    354 1101416 1101416: FLJ41238 :: FLJ41238 protein 338851 0.215337920108734 −0.112373898517407
    355 1101430 1101430: :: Homo sapiens transcribed sequences 418040 0.232052953728175 −0.060942343084998
    356 1101439 1101439: TERF2 :: telomeric repeat binding factor 2 63335 −0.043553911594881 0.235168237858145
    357 1101477 1101477: NUCB2 :: nucleobindin 2 423095 0.160097042319521 −0.161034301134445
    358 1101478 1101478: MGC45780 :: hypothetical protein MGC45780 146246 0.560131166008654 −0.244033724256484
    359 1101514 1101514: FLJ32363 :: FLJ32363 protein 88801 −0.213358324410450 0.584456949856772
    360 1101566 1101566: :: Homo sapiens cDNA FLJ26876 fis, clone PRS09003 98558 0.547923586173589 −0.120576676385804
    361 1101582 1101582: CKLFSF2 :: chemokine-like factor super family 2 195685 −0.164617883959410 0.163800631985653
    362 1101586 1101586: GPR114 :: G protein-coupled receptor 114 187884 0.106771558157668 −0.040640551768368
    363 1101628 1101628: LOC374654 :: similar to kinesin family 441708 −0.330140484955472 0.649432137236986
    member 21A; N-5 kinesin
    364 1101634 1101634: :: Homo sapiens transcribed sequences 510588 −0.187767924798762 0.150456533036268
    365 1101687 1101687: FNBP1 :: formin binding protein 1 440808 0.094301262952051 −0.183143704416937
    366 1101708 1101708: MCOLN2 :: mucolipin 2 459526 −0.206286880737142 0.089733971257195
    367 1101758 1101758: OSM :: oncostatin M 248156 0.427679944948121 −0.134414873641202
    368 1101775 1101775: TTBK1 :: tau tubulin kinase 1 343820 −0.106506268653088 0.070427043729278
    369 1101777 1101777: MGC33630 :: hypothetical protein MGC33630 359981 0.095553061289930 0.052525796095336
    370 1101829 1101829: GPR92 :: G protein-coupled receptor 92 155538 −0.170716626765422 0.053271309080346
    371 1101892 1101892: CCL27 :: chemokine (C-C motif) ligand 27 225948 0.090149523471370 0.082897675676425
    372 1101905 1101905: :: Homo sapiens transcribed sequence with weak similarity to 170843 0.191141074226577 −0.112946854380485
    protein pir: I60307 (E. coli) I60307 beta-galactosidase, alpha peptide -
    Escherichia coli
    373 1101944 1101944: :: Homo sapiens transcribed sequences 439064 0.511312767121963 −0.502590781948196
    374 1101948 1101948: :: Homo sapiens mRNA full length insert cDNA 14411 0.109781853161187 −0.205413488978966
    clone EUROIMAGE 2138357
    375 1101974 1101974: EPHB1 :: EphB1 272311 −0.151333397001395 −0.109778957757325
    376 1102027 1102027: CD5 :: CD5 antigen (p56-62) 58685 0.051477533952002 −0.356234543694019
    377 1102030 1102030: SLC20A1 :: solute carrier family 20 (phosphate 110855 0.320766322780251 −0.218010866476956
    transporter), member 1
    378 1102081 1102081: :: Homo sapiens mRNA; cDNA DKFZp686L0948 506977 −0.014999088235277 −0.142774708354838
    (from clone DKFZp686L0948)
    379 1102165 1102165: :: Homo sapiens cDNA FLJ12909 fis, clone NT2RP2004400. 152460 0.286428236301455 −0.254747456654948
    380 1102193 1102193: :: Homo sapiens transcribed sequences 22668 0.225058272151899 0.014961101827526
    381 1102282 1102282: GCNT2 :: glucosaminyl (N-acetyl) transferase 2, 934 0.048762986298498 −0.034020100922042
    I-branching enzyme
    382 1102350 1102350: MGC42105 :: hypothetical protein MGC42105 25845 −0.026228919079674 −0.028985150162382
    383 1102408 1102408: RAB3GAP :: RAB3 GTPase-ACTIVATING PROTEIN 306327 −0.084819962049070 0.075341563718927
    384 1102415 1102415: CKLFSF5 :: chemokine-like factor super family 5 99272 0.082819335162941 −0.159143215400658
    385 1102437 1102437: NUP62 :: nucleoporin 62 kDa 437023 0.418912844259920 −0.394203628829545
    386 1102470 1102470: :: Homo sapiens transcribed sequence with weak similarity to 292915 0.105172178085776 −0.079629308072535
    protein ref: NP_060265.1 (H. sapiens) hypothetical protein
    FLJ20378 [Homo sapiens]
    387 1102471 1102471: UNC5CL :: unc-5 homolog C (C. elegans)-like 158357 −0.094907736964586 −0.227754093321577
    388 1102479 1102479: STK11 :: serine/threonine kinase 11 (Peutz-Jeghers syndrome) 301772 0.037690452961669 −0.137459558533489
    389 1102537 1102537: :: Homo sapiens transcribed sequences 202151 0.108853907619606 −0.170270299488847
    390 1102540 1102540: FCRH3 :: Fc receptor-like protein 3 434881 −0.153114207986084 0.059006826674309
    391 1102633 1102633: :: Homo sapiens transcribed sequences 511124 −0.038532708435624 0.067743723935813
    392 1102652 1102652: CKLFSF1 :: chemokine-like factor super family 1 343717 0.147463476236581 −0.107172237917063
    393 1102654 1102654: KIAA0350 :: KIAA0350 protein 380599 −0.099657744074508 0.234041359355527
    394 1102725 1102725: C21orf42 :: chromosome 21 open reading frame 42 234016 0.122651922822787 −0.047341180286403
    395 1102744 1102744: :: Homo sapiens transcribed sequences 198671 −0.161033129852380 0.020948786809089
    396 1102821 1102821: :: Homo sapiens mRNA; cDNA DKFZp686L14188 202024 0.118625008373993 0.023472946360875
    (from clone DKFZp686L14188)
    397 1102859 1102859: :: Homo sapiens cDNA FLJ42418 fis, clone BLADE2001987 446195 −0.065690917989146 0.168415178725098
    398 1102885 1102885: CCNB3 :: cyclin B3 130310 −0.092278455245970 0.067527659533562
    399 1102898 1102898: FKSG87 :: FKSG87 protein 145519 −0.013747221559531 −0.070588363385651
    400 1102912 1102912: MGC15882 :: hypothetical protein MGC15882 194610 −0.011672180281967 0.144165981071462
    401 1103054 1103054: :: Homo sapiens transcribed sequences 341531 0.223445105771884 −0.188710045144392
    402 1103107 1103107: TAL2 :: T-cell acute lymphocytic leukemia 2 247978 −0.092171941247663 0.081590292816983
    403 1103111 1103111: RPC155 :: polymerase (RNA) III (DNA directed) (155 kD) 436896 −0.300266776102017 0.238379729664432
    404 1103120 1103120: TNFRSF10A :: tumor necrosis factor receptor 401745 −0.021792053857555 0.031738694361568
    superfamily, member 10a
    405 1103124 1103124: IRAK2 :: interleukin-1 receptor-associated kinase 2 424542 0.339830393625871 −0.235298214260479
    406 1103134 1103134: MYLK2 :: myosin light chain kinase 2, skeletal muscle 86092 0.018064833082290 −0.026257429266506
    407 1103137 1103137: EPHA8 :: EphA8 283613 −0.127428747463846 0.109096457119722
    408 1103139 1103139: NOG :: noggin 248201 0.112737761541130 −0.019607674631529
    409 1103224 1103224: HOXD8 :: homeo box D8 301963 0.288364072940970 −0.201074068135796
    410 1103264 1103264: DKFZP434I0714 :: hypothetical protein DKFZP434I0714 142307 −0.322975964968122 0.264079373684896
    411 1103272 1103272: :: Homo sapiens,clone IMAGE: 5312754, mRNA 137206 −0.100994707504263 0.025377105393344
    412 1103284 1103284: TPCN2 :: two pore segment channel 2 186655 0.345601083093747 −0.227937096818758
    413 1103303 1103303: C9orf52 :: chromosome 9 open reading frame 52 49605 0.399198464844216 −0.466790651317946
    414 1103304 1103304: :: Homo sapiens clone CDABP0095 mRNA sequence 46919 0.065720206673849 −0.204868670295576
    415 1103390 1103390: BPNT1 :: 3′(2′), 5′-bisphosphate nucleotidase 1 271752 0.136442060214909 0.191250282764510
    416 1103398 1103398: FLJ10244 :: Ral-A exchange factor RalGPS2 220745 −0.361204561848680 0.406852093691962
    417 1103420 1103420: MBNL2 :: muscleblind-like 2 (Drosophila) 372571 0.124346374266239 −0.191222651743482
    418 1103475 1103475: EBF :: early B-cell factor 120785 −0.141391424615001 0.266048426373043
    419 1103497 1103497: :: Homo sapiens mRNA; cDNA DKFZp761J1112 (from clone 50115 0.602843374034205 −0.450380110586192
    DKFZp761J1112)
    420 1103504 1103504: :: Homo sapiens mRNA; cDNA DKFZp434P0810 (from clone 142517 0.038565684752532 −0.192091997201980
    DKFZp434P0810)
    421 1103540 1103540: PRKWNK3 :: protein kinase, lysine deficient 3 92423 0.079917307313713 −0.146365124023944
    422 1103639 1103639: KIAA1765 :: KIAA1765 protein 388304 −0.021903689889921 −0.015706254591252
    423 1103711 1103711: :: Homo sapiens cDNA FLJ11833 fis, 288718 −0.117756771697465 0.060550901815652
    clone HEMBA1006579.
    424 1103766 1103766: TP73 :: tumor protein p73 192132 −0.202367662929968 0.151460270224789
    425 1103855 1103855: LOC153684 :: hypothetical protein LOC153684 259625 0.089916530004118 −0.401249389389032
    426 1103858 1103858: PSMA3 :: proteasome (prosome, macropain) 246240 0.036320631564259 −0.110232856407265
    subunit, alpha type, 3
    427 1103921 1103921: MS4A6A :: membrane-spanning 4-domains, 371612 0.079553258539825 −0.373450772906280
    subfamily A, member 6A
    428 1103932 1103932: :: Homo sapiens clone HQ0319 31330 0.132220773211356 −0.148815074748484
    429 1103982 1103982: MGC26226 :: beta cysteine string protein 142926 0.343337538439363 −0.063435983118753
    430 1104072 1104072: :: Homo sapiens cDNA FLJ11586 fis, 287429 −0.084275585872729 −0.086488630731059
    clone HEMBA1003720.
    431 1104175 1104175: KIAA1639 :: KIAA1639 protein 287383 0.240417880903839 −0.271486553982473
    432 1104195 1104195: DNAH8 :: dynein, axonemal, heavy polypeptide 8 172101 0.125358396983583 −0.167980969699610
    433 1104254 1104254: :: Homo sapiens cDNA FLJ12299 fis, 492700 −0.151297255208119 0.081019729886145
    clone MAMMA1001851.
    434 1104373 1104373: :: Homo sapiens cDNA FLJ11709 fis, 295633 −0.005756063382418 −0.123990346935139
    clone HEMBA1005133.
    435 1104545 1104545: :: Homo sapiens cDNA FLJ20182 fis, clone COLF0190 254477 −0.180198148895551 0.014637656197947
    436 1104552 1104552: LOC96597 :: hypothetical protein LOC96597 193857 −0.294998056306420 0.136359195898485
    437 1104840 1104840: :: Homo sapiens cDNA FLJ20112 fis, clone COL05405 482250 −0.057537557429858 −0.243362980194851
    438 1104870 1104870: KIAA1486 :: KIAA1486 protein 210958 −0.077488245043722 −0.071174044111354
    439 1104905 1104905: FLJ14753 :: hypothetical protein F1114753 13453 0.046259333205597 −0.072272236986864
    440 1104910 1104910: IGL@ :: immunoglobulin lambda locus −28 −0.021591390579858 0.046363051743828
    441 1105001 1105001: :: Homo sapiens transcribed sequence with moderate 296695 −0.014192107773996 −0.089068020278894
    similarity to protein sp: P39193 (H. sapiens) ALU6_HUMAN Alu
    subfamily SP sequence contamination warning entry
    442 1105178 1105178: GNG8 :: guanine nucleotide binding protein 283961 0.242480929979626 −0.272541916184894
    (G protein), gamma 8
    443 1105248 1105248: :: Homo sapiens similar to Olfactory receptor 111 (Olfactory −47 0.105352411032661 −0.084585315483932
    receptor 19-20) (OR19-20) (LOC126370), mRNA
    444 1105668 1105668: :: Genomic sequence on chromosome 6q23 −62 −0.123114691799488 0.460907242218706
    445 1105684 1105684: SLC38A5 :: solute carrier family 38, member 5 195155 −0.215379417617045 0.165637048268766
    446 1105728 1105728: MGC24180 :: hypothetical protein MGC24180 13034 −0.273706962285229 0.476949972442765
    447 1105732 1105732: FLJ32549 :: hypothetical protein FLJ32549 396626 −0.185773660713166 0.331821807671563
    448 1105751 1105751: :: Homo sapiens transcribed sequences 176376 0.282674447127367 −0.540879875488500
    449 1105759 1105759: ETV6 :: ets variant gene 6 (TEL oncogene) 171262 −0.063219469536356 −0.109967146172245
    450 1105798 1105798: CKLFSF8 :: chemokine-like factor super family 8 154986 −0.226202356526156 0.078083683806646
    451 1105814 1105814: :: Homo sapiens cDNA clone MGC: 61554 105223 −0.299247057499614 0.681904708275970
    IMAGE: 6174351, complete cds
    452 1105832 1105832: GSDML :: gasdermin-like 306777 −0.030059243970236 −0.173576690137134
    453 1105838 1105838: ZBTB8 :: zinc finger and BTB domain containing 8 129837 0.350149587738349 −0.241921665436000
    454 1105842 1105842: KIAA1145 :: KIAA1145 protein 173392 0.181381965671083 −0.293334666502675
    455 1105854 1105854: FLJ14803 :: hypothetical protein FLJ14803 267245 −0.289009334412393 0.391432538881942
    456 1105866 1105866: ZNF92 :: zinc finger protein 92 (HTF12) 9521 −0.217503504116412 0.242431438313012
    457 1105900 1105900: :: Homo sapiens transcribed sequence with weak similarity to 525015 −0.039954870700039 0.063846335693864
    protein ref: NP_060312.1 (H. sapiens) hypothetical protein
    FLJ20489 [Homo sapiens]
    458 1105915 1105915: :: Homo sapiens similar to seven transmembrane 332649 0.355873471451831 −0.549616497728459
    helix receptor (LOC346170), mRNA
    459 1105935 1105935: :: Homo sapiens cDNA FLJ42786 fis, clone BRAWH3006761 444290 −0.004981640577809 0.009313018150590
    460 1105936 1105936: KSR :: kinase suppressor of ras 276238 0.402034241649637 −0.508523150659365
    461 1105959 1105959: :: Homo sapiens cDNA FLJ43911 fis, clone TEST14010928 −52 0.045923922873497 −0.170316061302771
    462 1105986 1105986: GCET2 :: germinal center expressed transcript 2 49614 −0.086493932869463 0.206833859689091
    463 1106013 1106013: DNAJC3 :: DnaJ (Hsp40) homolog, subfamily C, member 3 6019 0.151020336613047 −0.095724381670206
    464 1106015 1106015: FLJ12505 :: hypothetical protein FLJ12505 96885 0.003443352514749 −0.152871957172409
    465 1106025 1106025: KIAA0746 :: KIAA0746 protein 49500 0.096092302067900 0.172477760689875
    466 1106030 1106030: UNQ3030 :: ELLP3030 162185 −0.141195502114527 −0.119993933340636
    467 1106043 1106043: FREB :: Fc receptor homolog expressed in B cells 266331 −0.332541268340366 0.343043552564271
    468 1106053 1106053: MYO7B :: myosin VIIB 154578 0.020701117764110 −0.030706574277501
    469 1106088 1106088: :: Homo sapiens, clone IMAGE: 4689481, mRNA 499235 0.232626061986162 −0.237498779839844
    470 1106110 1106110: FOXP1 :: forkhead box P1 235860 −0.337961967073500 0.177654717311019
    471 1106124 1106124: HAVCR2 :: hepatitis A virus cellular receptor 2 155111 0.433718618157491 −0.387490674695267
    472 1106126 1106126: PPIB :: peptidylprolyl isomerase B (cyclophilin B) 434937 0.089296594603901 −0.151245276102718
    473 1106159 1106159: :: Homo sapiens clone DNA49141 208081 0.175796277722861 −0.190528520520377
    LGLL338 (UNQ338) mRNA, complete cds
    474 1106196 1106196: :: Homo sapiens cDNA FLJ44273 fis, clone TOVAR2001281 142074 0.260032888023746 −0.248582710869995
    475 1106204 1106204: SDP35 :: cell cycle control protein SDP35 445098 −0.281476076882118 0.762743730546786
    476 1106230 1106230: FLJ90806 :: hypothetical protein FLJ90806 381225 −0.344498084563556 0.748294017497618
    477 1106279 1106279: CAMK1D :: calcium/calmodulin-dependent protein kinase ID 130065 −0.131837900700824 −0.026370539273523
    478 1106306 1106306: :: Homo sapiens transcribed sequence with weak similarity to 14204 0.222510499735753 −0.057963784683797
    protein pir: JC1405 (H. sapiens) JC1405
    6-pyruvoyltetrahydropterin synthase -
    human
    479 1106317 1106317: PRDM1 :: PR domain containing 1, with ZNF domain 381140 0.202422907441878 −0.278012993914435
    480 1106323 1106323: :: Homo sapiens transcribed sequence with 442690 −0.316314328384987 0.085395654673848
    moderate similarity to protein ref: NP_056011.1
    (H. sapiens) KIAA0922 protein [Homo sapiens]
    481 1106394 1106394: :: Homo sapiens transcribed sequence with 126932 0.022214815501423 −0.037232237149913
    moderate similarity to protein ref: NP_060265.1
    (H. sapiens) hypothetical protein FLJ20378 [Homo
    sapiens]
    482 1106401 1106401: MGC15827 :: hypothetical protein MGC15827 11849 −0.187511903901925 0.040102924392511
    483 1106415 1106415: :: Homo sapiens cDNA FLJ42409 fis, clone BLADE2000866 169071 0.211976489947730 −0.154318192993322
    484 1106478 1106478: :: Homo sapiens transcribed sequences 119898 −0.094232371717217 0.225662520964665
    485 1106522 1106522: :: Homo sapiens transcribed sequences 31903 −0.283587160786216 0.127680579514931
    486 1106589 1106589: MIST1 :: class II bHLH protein MIST1 22627 −0.047877525130132 −0.002404261340158
    487 1106722 1106722: FLJ14494 :: hypothetical protein FLJ14494 150458 −0.060926027646147 −0.002462635331184
    488 1106781 1106781: LTB4R :: leukotriene B4 receptor 445013 0.007134788675039 −0.190509701181572
    489 1106855 1106855: KIAA1909 :: KIAA1909 protein 455101 −0.112998501100632 −0.036068093105841
    inhibits CDK4)
    490 1106908 1106908: CDKN2B :: cyclin-dependent kinase inhibitor 2B (p15, 72901 0.338895194330555 −0.124572813650838
    491 1106935 1106935: CTLA4 :: cytotoxic T-lymphocyte-associated protein 4 247824 0.242155855304133 −0.478880430951650
    492 1106990 1106990: :: Homo sapiens transcribed sequences 369561 0.325855303432119 −0.572765753817467
    493 1107044 1107044: :: Homo sapiens transcribed sequences 163426 −0.248956419132601 −0.074083786735442
    494 1107076 1107076: BCL2L10 :: BCL2-like 10 (apoptosis facilitator) 283672 −0.174263409358457 0.142807702201562
    495 1107124 1107124: :: Homo sapiens transcribed sequences 130203 0.032157877924701 −0.055754120038729
    496 1107190 1107190: MGC10986 :: hypothetical protein MGC10986 50601 −0.227953163675436 0.145694856605193
    497 1107197 1107197: :: Homo sapiens transcribed sequence with strong similarity to 40838 0.001673335706470 −0.094560326284670
    protein pir: A48045 (H. sapiens) A48045 ribosomal protein
    S27, cytosolic - (reprolysin type)
    human
    498 1107329 1107329: LHFPL3 :: lipoma HMGIC fusion partner-like 3 439124 0.049458571639358 0.016357240588240
    499 1107348 1107348: SAMD3 :: sterile alpha motif domain containing 3 440508 0.383635070918944 −0.539687643012946
    500 1107369 1107369: :: Homo sapiens similar to kinase, Germline helicase-Binding, 512466 −0.113783226530150 0.145555603342058
    mitogen/stress activated protein kinase, c-jun N-terminal kinase (kgb-2)
    (LOC375783), mRNA
    501 1107457 1107457: ADAMTS2 :: a disintegrin-like and metalloprotease 120330 0.311369108148620 −0.287615459819004
    (reprolysin type) with thrombospondin type 1
    motif, 2
    502 1107527 1107527: :: Homo sapiens clone DNA57836 GLPG464 14706 0.214235142595632 −0.115893542930530
    (UNQ464) mRNA, complete cds
    503 1107575 1107575: MGC52498 :: hypothetical protein MGC52498 424589 −0.256404584752245 0.133592527736628
    504 1107637 1107637: :: Homo sapiens transcribed sequences 135491 0.216865140113354 −0.301114146422204
    505 1107762 1107762: :: Homo sapiens transcribed sequences 58597 −0.026249400695137 0.105000264860588
    506 1107838 1107838: :: Homo sapiens cDNA FLJ45323 fis, clone BRHIP3006390 −51 0.259677601688845 −0.248521794709865
    507 1107997 1107997: IL22RA2 :: interleukin 22 receptor, alpha 2 126891 0.425997734470218 −0.065713810429864
    508 1108088 1108088: :: Homo sapiens cDNA FLJ42957 fis, clone BRSTN2010500 441601 0.224696354704615 −0.357079341494018
    509 1108200 1108200: :: Homo sapiens transcribed sequences 156135 0.122650831349266 −0.127800809316600
    510 1108237 1108237: :: Homo sapiens transcribed sequence with weak similarity to 126232 0.150006719613133 −0.176773524991788
    protein sp: P39189 (H. sapiens) ALU2_HUMAN Alu subfamily
    SB sequence contamination warning entry
    511 1108323 1108323: :: Homo sapiens transcribed sequence with 520353 −0.056559071242791 −0.017831032028604
    moderate similarity to protein ref: NP_005898.1
    (H. sapiens) mannosidase, alpha, class 1A, member
    1; Man9-mannosidase [Homo sapiens]
    512 1108347 1108347: :: Homo sapiens transcribed sequences 121476 0.042929515389297 0.180791027467577
    513 1108467 1108467: LOC285016 :: hypothetical protein LOC285016 346333 0.077616196801139 −0.053502666868708
    514 1108473 1108473: FLJ34389 :: hypothetical protein FLJ34389 119878 0.154316813062797 −0.310176893404700
    515 1108515 1108515: LCN6 :: lipocalin 6 98132 −0.052695347232417 −0.116970698134434
    516 1108745 1108745: TEAD2 :: TEA domain family member 2 166556 −0.076084681856776 0.034540377111740
    517 1108776 1108776: :: Homo sapiens cDNA FLJ30967 fis, clone 513346 0.008924647334006 −0.176389651304266
    HEART2000309, weakly similar to
    PTB-ASSOCIATED SPLICING FACTOR.
    518 1108910 1108910: :: Homo sapiens transcribed sequence with strong similarity to 351848 0.098503999737852 −0.107340932053734
    protein ref: NP_542398.1 (H. sapiens) hypothetical
    protein MGC15407 [Homo sapiens]
    519 1108925 1108925: KIAA0853 :: KIAA0853 136102 −0.067377606440520 −0.082618534020208
    520 1108961 1108961: FLJ22531 :: hypothetical protein FLJ22531 292088 −0.420239196092467 0.357243765247241
    521 1108970 1108970: :: Homo sapiens cDNA FLJ25559 fis, clone JTH02834 140489 −0.190988477846490 −0.089199166803974
    522 1108988 1108988: NLK :: nemo-like kinase 3532 −0.030608793253581 0.089882597947955
    523 1109058 1109058: FLJ38499 :: hypothetical protein FLJ38499 220277 −0.089335338277617 −0.065610169727742
    524 1109107 1109107: FLJ10392 :: hypothetical protein FLJ10392 292925 −0.222666311239519 0.361324446901530
    525 1109188 1109188: TNFRSF11A :: tumor necrosis factor receptor 204044 0.280812133971682 −0.079369288251375
    superfamily, member 11a, activator of NFKB
    526 1109195 1109195: :: Homo sapiens cDNA FLJ41734 fis, clone HLUNG2018029 416155 −0.397342842842403 0.280143126653589
    527 1109210 1109210: KCNK9 :: potassium channel, subfamily K, member 9 117010 −0.017281359417599 −0.083690216430606
    528 1109220 1109220: GTF3A :: general transcription factor IIIA 445977 −0.429250063896662 0.332595945727056
    529 1109505 1109505: MGC39372 :: hypothetical protein MGC39372 8162 0.075357807105408 −0.258052753389713
    530 1109519 1109519: ALS2CR7 :: amyotrophic lateral sclerosis 2 348711 0.119836847940248 −0.019289786238779
    (juvenile) chromosome region, candidate 7
    531 1109530 1109530: :: Homo sapiens transcribed sequences 123244 −0.393536865160815 0.467473280881231
    532 1109545 1109545: :: Homo sapiens cDNA FLJ41910 fis, clone PEBLM2007834 63187 −0.397583692461428 0.257403431395117
    533 1109557 1109557: NP220 :: NP220 nuclear protein 444548 −0.135367039008095 −0.087433086257880
    534 1109560 1109560: FARP1 :: FERM, RhoGEF (ARHGEF) and pleckstrin 207428 0.033336743092972 −0.086075002105908
    domain protein 1 (chondrocyte-derived)
    535 1109603 1109603: :: Homo sapiens transcribed sequences 317740 −0.351537059310986 0.129233831238711
    536 1109732 1109732: :: Homo sapiens transcribed sequences 374124 0.300165387297213 −0.442390304962831
    537 1109756 1109756: FNBP1 :: formin binding protein 1 191534 0.061372936344349 −0.209804169980805
    538 1109827 1109827: GPR155 :: G protein-coupled receptor 154 127196 0.242983476822492 −0.418280288872407
    539 1109913 1109913: CFLAR :: CASP8 and FADD-like apoptosis regulator 355724 0.207532726896619 −0.403624127184567
    540 1110019 1110019: :: Homo sapiens transcribed sequences 31444 0.360190305256616 −0.350732887975507
    541 1110070 1110070: :: Homo sapiens transcribed sequences 122464 0.271451755158904 −0.436226517954694
    542 1110099 1110099: TA-KRP :: T-cell activation ketch repeat protein 116665 −0.445325720625770 0.477608651819287
    543 1110198 1110198: :: Homo sapiens transcribed sequences 189046 −0.298393216431026 0.206436758539511
    544 1110214 1110214: TCL6 :: T-cell leukemia/lymphoma 6 144519 −0.228315826191486 0.241502528970347
    545 1110223 1110223: :: Homo sapiens transcribed sequence with 212709 −0.430615107958902 0.454780809992101
    moderate similarity to protein ref: NP_060265.1
    (H. sapiens) hypothetical protein FLJ20378 [Homo
    sapiens]
    546 1110284 1110284: ELL2 :: elongation factor, RNA polymerase II, 2 192221 0.191540498442880 −0.196150765305570
    547 1110309 1110309: :: Homo sapiens transcribed sequences 105623 −0.215474752721580 0.156976932842674
    548 1110313 1110313: FLJ39873 :: hypothetical protein FLJ39873 421750 0.069702715608045 −0.402411470521682
    549 1110486 1110486: :: Homo sapiens transcribed sequences 445054 0.041319461801742 −0.116877614471182
    550 1110608 1110608: CARD14 :: caspase recruitment domain family, member 14 306227 0.331483074884149 −0.441101824343302
    551 1110610 1110610: :: Homo sapiens transcribed sequences 436906 0.028013446240267 −0.137363692502881
    552 1110740 1110740: :: Homo sapiens transcribed sequences 416810 −0.195991680240688 0.007835013134266
    553 1110852 1110852: :: Homo sapiens cDNA FLJ44885 fis, clone BRAMY2039630 196026 0.195262191447797 −0.125057253667954
    554 1110871 1110871: :: Homo sapiens transcribed sequences 431753 0.138463783532811 −0.121059247114496
    555 1111070 1111070: :: Homo sapiens transcribed sequence with 202201 −0.050110477343771 −0.034250369213883
    moderate similarity to protein sp: P39192 (H. sapiens)
    ALU5_HUMAN Alu subfamily SC sequence
    contamination warning entry
    556 1111478 1111478: ERK8 :: extracellular signal-regulated kinase 8 133017 −0.120955857697857 −0.022637205903073
    557 1111486 1111486: :: Homo sapiens cDNA FLJ42259 fis, clone TKIDN2011289 33024 0.187010000009634 −0.440447209346948
    558 1111494 1111494: IMPDH2 :: IMP (inosine monophosphate) dehydrogenase 2 75432 −0.153973066560439 0.069775805472499
    559 1111503 1111503: KBRAS2 :: I-kappa-B-interacting Ras-like protein 2 502910 −0.291172996398988 0.201225423261566
    560 1111694 1111694: :: Homo sapiens transcribed sequences 157302 0.134965621816156 −0.064733017359634
    561 1111807 1111807: OFD1 :: oral-facial-digital syndrome 1 6483 0.150829248997032 −0.253651952300585
    562 1111946 1111946: :: Homo sapiens transcribed sequences 280881 −0.159828571994911 −0.162813334629172
    563 1112019 1112019: :: Homo sapiens hypothetical LOC148280 196484 0.071877889993013 −0.048827289854263
    (LOC148280), mRNA
    564 1112052 1112052: :: Homo sapiens cDNA FLJ31445 fis, clone NT2NE2000864. 525361 −0.072204408405921 0.020806399380158
    565 1112061 1112061: :: Homo sapiens cDNA FLJ90513 fis, clone NT2RP3004355. 43410 0.261039034660754 −0.299416343840340
    566 1112256 1112256: ING3 :: inhibitor of growth family, member 3 143198 −0.125562046082355 0.143701534203396
    567 1112344 1112344: :: Homo sapiens transcribed sequences 163242 −0.146713182348301 0.093803692880128
    568 1112510 1112510: C14orf20 :: chromosome 14 open reading frame 20 314432 0.104763882180010 −0.081623532083441
    569 1112521 1112521: :: Homo sapiens transcribed sequence with weak similarity to 244818 0.186313001167652 −0.195394559688516
    protein ref: NP_009032.1 (H. sapiens) sarcosine dehydrogenase;
    dimethylglycine dehydrogenase-like 1 [Homo sapiens]
    570 1112552 1112552: :: Homo sapiens transcribed sequences 89029 0.113342903534869 −0.150103125377604
    571 1112674 1112674: MAML3 :: mastermind-like 3 (Drosophila) 310320 0.342597737627672 −0.164070058630283
    572 1112689 1112689: SERPINB9 :: serine (or cysteine) proteinase 104879 0.143780170116893 −0.201560350725374
    inhibitor, Glade B (ovalbumin), member 9
    573 1112762 1112762: :: Homo sapiens mRNA; cDNA DKFZp686G24244 208179 0.150233483486388 −0.257040066964479
    (from clone DKFZp686G24244)
    574 1112764 1112764: IFNGR1 :: interferon gamma receptor 1 180866 0.374189546225726 −0.308519391383641
    575 1112837 1112837: NRD1 :: nardilysin (N-arginine dibasic convertase) 4099 −0.128229223629686 0.093232911170115
    576 1112849 1112849: :: Homo sapiens cDNA FLJ30333 fis, clone BRACE2007262. 208965 0.195240136859781 −0.389576368956041
    577 1112871 1112871: :: Homo sapiens transcribed sequences 269493 −0.168246902555918 −0.116751272574924
    578 1112935 1112935: NFAM1 :: NFAT activation molecule 1 436677 0.349529061115025 −0.429878706483203
    579 1112981 1112981: :: Homo sapiens transcribed sequences 86650 −0.347953389898022 0.075874931243046
    580 1113020 1113020: LOC161577 :: LOC161577 protein 373484 0.135613302187717 0.036736840045959
    581 1113263 1113263: :: Homo sapiens cDNA FLJ46553 fis, clone THYMU3038879 435736 −0.148749974226581 0.101621280353679
    582 1113435 1113435: :: Homo sapiens cDNA F1136210 fis, clone THYMU2000155 100636 0.034825029929201 −0.041626982844820
    583 1113488 1113488: :: Homo sapiens, Similar to Eph receptor A7, 129435 0.009080742764582 0.044988996497229
    clone IMAGE: 5273054, mRNA
    584 1113500 1113500: :: Homo sapiens cDNA FLJ37931 fis, clone CTONG2004397. 165900 0.272078126902990 −0.472804242511080
    585 1113545 1113545: :: Homo sapiens cDNA FLJ46553 fis, clone THYMU3038879 435736 −0.008456873734778 0.007667610676891
    586 1113555 1113555: :: Homo sapiens transcribed sequences 291993 −0.139176879567708 −0.125987425138451
    587 1113589 1113589: BRAF :: v-raf murine sarcoma viral oncogene homolog B1 162967 −0.121772870570279 0.253077019731888
    588 1113730 1113730: :: Homo sapiens transcribed sequences 293771 0.114063697377525 −0.237457649248006
    589 1113769 1113769: :: Homo sapiens full length insert cDNA clone YZ11B11 46996 −0.393658244074914 0.080473352209481
    590 1113783 1113783: FLJ14431 :: hypothetical protein FLJ14431 512793 −0.222799826904987 0.358817889836136
    591 1113930 1113930: MGC35521 :: pellino 3 alpha 24725 −0.055846303583161 0.210056043718661
    lambda receptor)
    592 1113972 1113972: IL28RA :: interleukin 28 receptor, 386334 −0.185314697287965 0.230148638275733
    alpha (interferon,
    593 1113993 1113993: :: Homo sapiens transcribed sequence with moderate 131811 0.173371210700442 −0.239300750059210
    similarity to protein ref: NP_060265.1 (H. sapiens)
    hypothetical protein FLJ20378 [Homo sapiens]
    594 1114017 1114017: :: Homo sapiens transcribed sequences 133255 0.308724526786620 −0.310188543930668
    595 1114064 1114064: MYO3A :: myosin IIIA 148228 −0.300520026473458 0.088707148385397
    596 1114109 1114109: DCAL1 :: dendritic cell-associated lectin-1 203041 −0.191231948777420 0.183023497372357
    597 1114162 1114162: :: Homo sapiens transcribed sequences 435736 0.258730255563098 −0.182285726467478
    598 1114351 1114351: PER1 :: period homolog 1 (Drosophila) 514664 0.065700609177559 −0.158512640752179
    599 1114503 1114503: :: Homo sapiens transcribed sequences 170577 −0.049779313136241 −0.022799815868667
    600 1114543 1114543: :: Homo sapiens transcribed sequences 156189 0.089727575328993 0.087415478817855
    601 1114679 1114679: FLJ10904 :: hypothetical protein FLJ10904 16470 −0.313418247196259 0.568840722644661
    602 1114715 1114715: PRKCN :: protein kinase C, nu 434387 −0.130103404630746 0.271352489418930
    603 1114726 1114726: NLK :: nemo-like kinase 3532 −0.003199898057120 0.151365565219048
    604 1114766 1114766: RCL1 :: RNA terminal phosphate cyclase-like 1 113052 −0.087555464003998 0.217546838114269
    605 1114824 1114824: LIMD1 :: LIM domains containing 1 193370 −0.148463864832943 −0.033916294109501
    606 1114853 1114853: ARHF :: ras homolog gene family, member F (in filopodia) 512618 0.016180684058318 0.014510688794040
    607 1114877 1114877: AK5 :: adenylate kinase 5 18268 0.232192378472237 −0.050181060405945
    608 1114893 1114893: BCL11A :: B-cell CLL/lymphoma 11A (zinc finger protein) 314623 −0.285216070613527 0.316813819176734
    609 1114913 1114913: KIAA0748 :: KIAA0748 gene product 33187 −0.210416126426711 −0.027114426717208
    610 1114967 1114967: SNX9 :: sorting nexin 9 7905 0.297577356714608 −0.280214852748554
    611 1114970 1114970: PX19 :: px19-like protein 279529 −0.259951401409926 0.398931866897413
    612 1114977 1114977: HSPC182 :: HSPC182 protein 30026 −0.026093693057321 0.046619049116212
    613 1114981 1114981: XPO5 :: exportin 5 203206 −0.414069207073602 0.452995936587216
    614 1114988 1114988: IBA2 :: ionized calcium binding adapter molecule 2 4944 0.122190372505081 −0.254155885467689
    615 1115008 1115008: USP47 :: ubiquitin specific protease 47 441028 0.061008496955961 −0.051040281866044
    616 1115012 1115012: SFRP2 :: secreted frizzled-related protein 2 31386 0.562213196556748 −0.283291904250779
    617 1115034 1115034: NEK6 :: NIMA (never in mitosis gene a)-related kinase 6 387222 0.387672292810071 −0.139523546421676
    618 1115052 1115052: MLL5 :: myeloid/lymphoid or mixed-lineage 380021 0.039758974918423 −0.107953085916089
    leukemia 5 (trithorax homolog, Drosophila)
    619 1115071 1115071: MAIL :: molecule possessing ankyrin repeats induced by 390476 −0.110817987747237 −0.026034205682165
    lipopolysaccharide (MAIL), homolog of mouse
    620 1115073 1115073: BAL :: B aggressive lymphoma gene 131315 0.175136379072991 −0.372997453296061
    621 1115128 1115128: BOK :: BCL2-related ovarian killer 293753 0.453574167307278 −0.255947563977460
    622 1115160 1115160: LYAR :: hypothetical protein FLJ20425 425427 −0.406888533093173 0.586797819139025
    623 1115176 1115176: CKLF :: chemokine-like factor 15159 0.192788341170135 0.046619194874123
    624 1115186 1115186: MRPL47 :: mitochondrial ribosomal protein L47 283734 −0.420230779755538 0.571199396674772
    625 1115194 1115194: TNFSF13B :: tumor necrosis factor 270737 0.475174704917625 −0.577483430130737
    (ligand) superfamily, member 13b
    626 1115203 1115203: RPS6KL1 :: ribosomal protein S6 kinase-like 1 414481 0.015390697806082 0.003703623518892
    627 1115226 1115226: KIAA1683 :: KIAA1683 protein 279718 −0.006255737442234 −0.282909576455325
    628 1115253 1115253: BCL2L13 :: BCL2-like 13 (apoptosis facilitator) 310922 −0.183634412043605 0.327528714656041
    629 1115271 1115271: DKFZp761C169 :: vasculin 71252 −0.368758470490713 0.067050568022970
    630 1115286 1115286: TLR10 :: toll-like receptor 10 120551 −0.259024464746980 0.325663372291740
    631 1115290 1115290: GSG2 :: haspin 193666 −0.482306139325171 0.619212145708754
    632 1115303 1115303: LOC51244 :: hypothetical protein LOC51244 236257 −0.249657257281461 0.132172351643750
    633 1115309 1115309: DKFZP434F091 :: DKFZP434F091 protein 443081 −0.240319754851193 0.324212477679077
    634 1115329 1115329: MGC4796 :: Ser/Thr-like kinase 439658 0.040208198815129 −0.018704127839472
    635 1115338 1115338: STK31 :: serine/threonine kinase 31 224355 −0.053536185139454 −0.107899047198573
    636 1115347 1115347: HDAC8 :: histone deacetylase 8 112272 −0.028339713769977 0.390069214505358
    637 1115360 1115360: PRO1073 :: PRO1073 protein 187199 0.015150578049290 −0.241074918363573
    638 1115441 1115441: IL17RB :: interleukin 17 receptor B 5470 −0.063434193422993 −0.014102884885889
    639 1115519 1115519: MRPS36 :: mitochondrial ribosomal protein S36 408914 −0.297069852346310 0.396251982430131
    640 1115566 1115566: SP329 :: hypothetical protein SP329 −5 −0.118697538219683 −0.012110621854279
    641 1115587 1115587: IRTA1 :: immunoglobulin superfamily receptor translocation 120260 −0.052595986636235 0.142155752703307
    associated 1
    642 1115589 1115589: IRTA2 :: immunoglobulin superfamily receptor translocation 415950 −0.265747517495947 0.086115378248171
    associated 2
    643 1115591 1115591: SSTK :: serine/threonine protein kinase SSTK 367871 −0.128216622193601 0.059300320623737
    644 1115607 1115607: CDCA7 :: cell division cycle associated 7 435733 −0.262295427951373 0.573434589773844
    645 1115621 1115621: RIOK1 :: RIO kinase 1 (yeast) 437474 −0.229738976454067 0.447251600358189
    646 1115646 1115646: HECTD1 :: HECT domain containing 1 210850 −0.167037011541555 0.128780114293504
    647 1115668 1115668: RTN4IP1 :: reticulon 4 interacting protein 1 155839 −0.320652767737175 0.306593126968738
    648 1115673 1115673: IL17RC :: interleukin 17 receptor C 129959 0.311147392581012 −0.307735752432534
    649 1115679 1115679: MGC4308 :: hypothetical protein MGC4308 8345 −0.482150529158383 0.656200427232135
    650 1115695 1115695: TNFRSF18 :: tumor necrosis factor receptor 212680 0.126824051069217 −0.342995126764104
    superfamily, member 18
    651 1115696 1115696: IL1F7 :: interleukin 1 family, member 7 (zeta) 166371 0.135412621405814 −0.163355627129065
    652 1115704 1115704: IRF2BP2 :: interferon regulatory factor 2 binding protein 2 350268 0.258469364814320 −0.344047490615961
    653 1115763 1115763: GPT2 :: glutamic pyruvate transaminase (alanine 355862 −0.262333353369976 0.306381008609851
    aminotransferase) 2
    654 1115800 1115800: RPE :: ribulose-5-phosphate-3-epimerase 282260 −0.040365629363253 0.244729456838177
    655 1115812 1115812: EIF2AK4 :: eukaryotic translation initiation 412102 0.045588510962448 −0.074238327120572
    factor 2 alpha kinase 4
    656 1115813 1115813: CTL2 :: CTL2 gene 105509 −0.221292272952100 −0.028168066606459
    657 1115829 1115829: FLJ12760 :: hypothetical protein FLJ12760 381204 −0.369293215780449 0.627808556684385
    658 1115840 1115840: KIAA1728 :: KIAA1728 protein 437362 0.589217883938435 −0.416684777312541
    659 1115876 1115876: TIMM23 :: translocase of inner mitochondrial 11866 −0.381689052923779 0.668903617669604
    membrane 23 homolog (yeast)
    660 1115877 1115877: AKIP :: aurora-A kinase interacting protein 76239 −0.207980996336103 0.344080166383221
    661 1115888 1115888: ZBTB4 :: zinc finger and BTB domain containing 4 35096 0.298080578428648 −0.657393520135917
    662 1115892 1115892: STK35 :: serine/threonine kinase 35 100057 0.153696425328605 −0.057444650366930
    663 1115895 1115895: RPC8 :: RNA polymerase III subunit RPC8 202505 −0.354708569266870 0.493832792496113
    664 1115905 1115905: CLMN :: calmin (calponin-like, transmembrane) 301478 0.091056873434158 −0.184176927851473
    665 1115916 1115916: MGC13204 :: hypothetical protein MGC13204 157148 −0.291511838717354 0.401615662719805
    666 1115917 1115917: C6orf83 :: chromosome 6 open reading frame 83 284265 0.270658416402021 −0.224326090174219
    667 1115953 1115953: ZNF385 :: zinc finger protein 385 278422 0.309580141662476 −0.371867309369219
    668 1115955 1115955: FLJ31434 :: hypothetical protein FLJ31434 7988 −0.153394088626576 0.245407623813638
    669 1115960 1115960: FRAS1 :: Fraser syndrome 1 15420 0.273562188785241 −0.206947496325428
    (fused homolog, Drosophila)
    670 1115965 1115965: STK36 :: serine/threonine kinase 36 26996 0.076460376343936 −0.120715477463443
    671 1116001 1116001: SON :: SON DNA binding protein 430541 −0.038000317919225 −0.084548879882143
    672 1116006 1116006: PTBP1 :: polypyrimidine tract binding protein 1 172550 −0.116461984704372 0.168668607063908
    673 1116022 1116022: p30 :: nuclear protein p30 433422 −0.040984109576481 0.089035758253502
    with YRPW motif-like
    674 1116045 1116045: HEYL :: hairy/enhancer-of-split related 23823 0.298715739339798 −0.119650232859985
    675 1116056 1116056: SOX8 :: SRY (sex determining region Y)-box 8 243678 0.060190043795450 −0.181079858440255
    676 1116063 1116063: RALBP1 :: ralA binding protein 1 75447 −0.325857678019344 0.201375045992707
    677 1116071 1116071: :: Homo sapiens mRNA; cDNA DKFZp586O031 (from clone 502564 0.326268800212765 −0.248774088633798
    DKFZp586O031)
    678 1116073 1116073: MGC2408 :: hypothetical protein MGC2408 146161 −0.367109495613606 0.473361274829460
    679 1116085 1116085: BACH2 :: BTB and CNC homology 1, basic leucine zipper 88414 −0.246093347541336 0.093569752151740
    transcription factor 2
    680 1116103 1116103: LTBP3 :: latent transforming growth factor 289019 0.342939273133271 −0.369780572465803
    beta binding protein 3
    681 1116122 1116122: DKFZp761O0113 :: hypothetical protein DKFZp761O0113 42768 −0.426616095442673 0.454893774014263
    682 1116126 1116126: INSR :: insulin receptor 438669 0.454459408301310 −0.265298709888399
    683 1116150 1116150: AMSH-LP :: associated molecule with the SH3 16229 −0.266185991205955 0.083378166105849
    domain of STAM (AMSH) like protein
    684 1116181 1116181: TAF15 :: TAF15 RNA polymerase II, TATA box 402752 −0.062544122751392 0.006142039132744
    binding protein (TBP)-associated factor, 68 kDa
    685 1116219 1116219: NAP1L :: napsin B pseudogene 322854 −0.189162359230305 0.087037800792380
    686 1116233 1116233: PAPPA :: pregnancy-associated plasma protein A 455350 0.251466587847966 −0.234146528669534
    687 1116277 1116277: C10orf33 :: chromosome 10 open reading frame 33 118210 0.094135933623219 −0.201399654874422
    688 1116317 1116317: :: Homo sapiens cDNA clone IMAGE: 4821863, partial cds 440776 −0.349847858207637 0.196451295358354
    689 1116432 1116432: KIAA1259 :: hypothetical protein KIAA1259 525807 −0.153668990852911 −0.021062212586290
    690 1116445 1116445: C6.1A :: c6.1A 301927 −0.091951874829546 0.312024877401937
    691 1116593 1116593: NUDT6 :: nudix (nucleoside diphosphate linked 422889 −0.159193962550566 0.195466499750992
    moiety X)-type motif 6
    692 1116666 1116666: DKFZP564B1162 :: hypothetical protein DKFZp564B1162 442801 −0.383182496994710 0.271520439423627
    693 1116676 1116676: MSI2 :: musashi homolog 2 (Drosophila) 185084 −0.282699630935485 0.106190364019197
    694 1116715 1116715: FLJ20574 :: hypothetical protein FLJ20574 123427 −0.193791635217953 0.316655728293102
    695 1116826 1116826: KIAA1295 :: KIAA1295 protein 26204 0.721314629392213 −0.377963323366938
    696 1116829 1116829: LOC90624 :: hypothetical protein LOC90624 115467 −0.335027077607960 0.336788815470870
    697 1116844 1116844: CSNK1G1 :: casein kinase 1, gamma 1 405789 −0.058317444499632 0.048781994752368
    698 1116854 1116854: :: Homo sapiens cDNA FLJ14309 fis, clone PLACE3000221. 438623 −0.043460166463994 −0.054723733397946
    699 1116863 1116863: TLR4 :: toll-like receptor 4 174312 0.475472475469738 −0.300348466739063
    700 1116879 1116879: TNIP2 :: TNFAIP3 interacting protein 2 325630 0.312285624448172 −0.214671720019409
    701 1116958 1116958: PBF :: papillomavirus regulatory factor PRF-1 27410 −0.229333149413005 0.297027698820665
    702 1116966 1116966: :: Homo sapiens cDNA FLJ11681 fis, 301124 0.430855116758033 −0.468612200509693
    clone HEMBA1004865.
    703 1117023 1117023: BCL2L12 :: BCL2-like 12 (proline rich) 289052 −0.470242230711918 0.673594400951872
    704 1117211 1117211: HSPC195 :: hypothetical protein HSPC195 356509 −0.350305805203319 0.246811696581929
    705 1117245 1117245: HARS2 :: histidyl-tRNA synthetase 2 444706 −0.175279674549348 0.324254247578305
    706 1117278 1117278: ACAS2 :: acetyl-Coenzyme A synthetase 2 (ADP forming) 14779 0.360381976214154 −0.450784610189096
    707 1117298 1117298: :: Homo sapiens clone H3 anti-mucin1 light chain 449586 0.190383103967389 −0.163373239822681
    variable region mRNA, partial cds
    708 1117343 1117343: BUCS1 :: butyryl Coenzyme A synthetase 1 306812 0.002627195859024 −0.128596603481639
    709 1117350 1117350: FLJ10407 :: hypothetical protein FLJ10407 435982 −0.321428599824394 0.748139228339341
    710 1117373 1117373: SEMA4B :: sema domain, immunoglobulin domain (Ig), 416077 0.070054264582924 −0.127801110560990
    transmembrane domain (TM) and short cytoplasmic
    domain, (semaphorin) 4B
    711 1117394 1117394: :: immunoglobulin heavy chain V region −37 0.077318881358942 0.037375816090329
    712 1117403 1117403: FBXO5 :: F-box only protein 5 272027 −0.270275521248700 0.472830182511296
    713 1117517 1117517: Rgr :: Ral-GDS related protein Rgr 148656 0.085023272566783 −0.339585977561694
    714 1117555 1117555: NOD3 :: NOD3 protein 128357 0.017413352126443 −0.259854083394416
    715 1117599 1117599: MGC27085 :: hypothetical protein MGC27085 120277 −0.297300511558719 0.294857589419262
    716 1117644 1117644: :: Homo sapiens transcribed sequence with 34174 −0.043891472376770 −0.046176754319814
    moderate similarity to protein ref: NP_060312.1 (H. sapiens)
    hypothetical protein FLJ20489 [Homo sapiens]
    717 1117747 1117747: :: Homo sapiens hypothetical LOC256686 158272 −0.156604323316062 −0.033451106438867
    (LOC256686), mRNA
    718 1117800 1117800: :: Homo sapiens LOH11CR1F gene, loss 125166 −0.265166847772953 −0.035683423757495
    of heterozygosity, 11, chromosomal region 1 gene F product
    719 1117835 1117835: CR1L :: complement component (3b/4b) receptor 1-like 89688 0.276367621813185 −0.053572671658412
    720 1117853 1117853: :: Homo sapiens transcribed sequence with strong similarity to 268724 −0.098130731820168 −0.212694005004947
    protein pdb: 1BGM (E. coli) O Chain O,
    Beta-Galactosidase (Chains I-P)
    721 1117977 1117977: :: Unknown −40 −0.092034285015709 −0.087991577681170
    722 1118148 1118148: ZBP1 :: Z-DNA binding protein 1 −2 0.152802746225995 −0.384059831029427
    723 1118228 1118228: :: Homo sapiens hypothetical 173679 −0.201134297495305 −0.035774496444703
    LOC339541 (LOC339541), mRNA
    724 1118286 1118286: :: Homo sapiens transcribed sequences 147381 −0.379333390537201 0.451787557640792
    725 1118347 1118347: ITGA4 :: integrin, alpha 4 (antigen CD49D, 145140 0.055639362171438 −0.253900279097663
    alpha 4 subunit of VLA-4 receptor)
    726 1118414 1118414: FCRH1 :: Fc receptor-like protein 1 415473 −0.092952084806830 0.080500778588061
    727 1118573 1118573: GSK3A :: glycogen synthase kinase 3 alpha 435970 −0.351134088845212 0.325972671457629
    728 1118612 1118612: NPR1 :: natriuretic peptide receptor A/guanylate cyclase A 438864 0.155477087321411 −0.159267282520294
    (atrionatriuretic peptide receptor A)
    729 1118621 1118621: CGI-96 :: CGI-96 protein 239934 −0.292642395717393 0.473939710525280
    730 1118659 1118659: MAPK7 :: mitogen-activated protein kinase 7 150136 −0.051883863404460 −0.141266790241099
    731 1118681 1118681: MAFF :: v-maf musculoaponeurotic 460889 0.647665560383226 −0.362054883818999
    fibrosarcoma oncogene homolog F (avian)
    732 1118684 1118684: MIPEP :: mitochondrial intermediate peptidase 68583 −0.328213532979876 0.407014917128267
    733 1118708 1118708: MRC2 :: mannose receptor, C type 2 7835 0.754467580767100 −0.424450710158145
    734 1118736 1118736: HIP1R :: huntingtin interacting protein-1-related 96731 0.039974764124592 0.066130790515351
    735 1118772 1118772: STK10 :: serine/threonine kinase 10 16134 0.030402652799298 −0.421006508321850
    736 1118835 1118835: ARHGAP8 :: Rho GTPase activating protein 8 102336 0.311235535095650 −0.396387124788783
    737 1118861 1118861: PEX16 :: peroxisomal biogenesis factor 16 100915 0.029858540970158 −0.043179604561765
    738 1118939 1118939: PLA2G4B :: phospholipase A2, group IVB (cytosolic) 198161 0.217116959349918 −0.409971040705761
    739 1118949 1118949: IAN4L1 :: immune associated nucleotide 4 like 1 (mouse) 412331 0.142206792172366 −0.512656283348152
    740 1118963 1118963: :: Homo sapiens cDNA FLJ42818 fis, clone BRCAN2015371 −53 −0.064431805022853 −0.171638599308421
    741 1119003 1119003: EIF4G2 :: eukaryotic translation initiation factor 4 gamma, 2 183684 −0.133347112654528 0.112848239923822
    742 1119007 1119007: GDI2 :: GDP dissociation inhibitor 2 56845 −0.382242002371530 0.470849494659261
    743 1119015 1119015: RPS5 :: ribosomal protein S5 378103 −0.384887386329798 0.343492082296666
    744 1119039 1119039: SMAP :: small acidic protein 447513 −0.301459283715944 0.321366636007445
    745 1119046 1119046: DSP :: desmoplakin 349499 0.323961715872806 −0.285977303076169
    746 1119056 1119056: UBB :: ubiquitin B 356190 0.028334739217252 −0.196600028796086
    747 1119061 1119061: MLP :: MARCKS-like protein 75061 0.003502916223950 0.225174791526797
    748 1119068 1119068: S100A11 :: S100 calcium binding protein A11 (calgizzarin) 417004 0.629923256421890 −0.515428592835300
    749 1119070 1119070: CD63 :: CD63 antigen (melanoma 1 antigen) 445570 0.600681920968223 −0.477615687123999
    750 1119071 1119071: UBE2D3 :: ubiquitin-conjugating enzyme E2D 3 411826 −0.152909102348063 0.188214633454210
    (UBC4/5 homolog, yeast)
    751 1119072 1119072: XBP1 :: X-box binding protein 1 437638 −0.073072023747563 0.071992250474592
    752 1119074 1119074: CD81 :: CD81 antigen (target of antiproliferative antibody 1) 54457 0.460590309714153 −0.316306331329744
    753 1119076 1119076: GLO1 :: glyoxalase I 268849 −0.485600996113581 0.560563431563709
    754 1119090 1119090: FKBP1A :: FK506 binding protein 1A, 12 kDa 374638 −0.167154087365112 0.256238003053443
    755 1119111 1119111: TEGT :: testis enhanced gene transcript (BAX inhibitor 1) 35052 0.117050432650685 −0.195242199439661
    756 1119139 1119139: DNAJA1 :: DnaJ (Hsp40) homolog, subfamily A, member 1 388392 −0.106484916885441 0.145147017992332
    757 1119155 1119155: DEK :: DEK oncogene (DNA binding) 110713 −0.246967603602159 0.515244500061071
    758 1119171 1119171: ACTA2 :: actin, alpha 2, smooth muscle, aorta 208641 0.761340632898360 −0.452825423217664
    759 1119173 1119173: MDH1 :: malate dehydrogenase 1, NAD (soluble) 75375 −0.127094708879037 0.258023826328223
    760 1119183 1119183: RBM4 :: RNA binding motif protein 4 211203 −0.428472864406565 0.396021571030955
    761 1119186 1119186: CD9 :: CD9 antigen (p24) 387579 0.381081618660027 −0.168246859132740
    762 1119202 1119202: TGM2 :: transglutaminase 2 (C polypeptide, 512708 0.435342892077885 −0.323641082136671
    protein-glutamine-gamma-glutamyltransferase)
    763 1119209 1119209: RCN1 :: reticulocalbin 1, EF-hand calcium binding domain 167791 0.571093261465677 −0.388503774716019
    764 1119212 1119212: MMP2 :: matrix metalloproteinase 2 (gelatinase A, 367877 0.910359724823026 −0.353773466993166
    72 kDa gelatinase, 72 kDa type IV collagenase)
    765 1119237 1119237: GPNMB :: glycoprotein (transmembrane) nmb 389964 0.610412926960347 −0.312611665779815
    766 1119239 1119239: HAX1 :: HS1 binding protein 199625 −0.465663098537398 0.508445219571895
    767 1119243 1119243: ATP6V0E :: ATPase, H+ transporting, lysosomal 440165 0.250369153999525 −0.272868162874347
    9 kDa, V0 subunit e
    768 1119245 1119245: FBXO7 :: F-box only protein 7 5912 −0.231979379939439 0.094393580671121
    769 1119251 1119251: SEPW1 :: selenoprotein W, 1 433941 0.410533826180220 −0.461863162528100
    770 1119258 1119258: HDAC1 :: histone deacetylase 1 88556 −0.067200590610105 0.310238210060964
    771 1119260 1119260: LGMN :: legumain 18069 −0.000745128042019 −0.229008754509885
    772 1119263 1119263: C12orf8 :: chromosome 12 open reading frame 8 511762 −0.476397099487274 0.260114831651188
    773 1119268 1119268: ILK :: integrin-linked kinase 6196 0.333491562996737 −0.117810222588527
    774 1119294 1119294: TOP2A :: topoisomerase (DNA) II alpha 170 kDa 156346 −0.344066595023870 0.821915015867740
    775 1119300 1119300: STK25 :: serine/threonine kinase 25 (STE20 homolog, yeast) 155206 −0.283256434250802 0.270411211177143
    776 1119311 1119311: ENC1 :: ectodermal-neural cortex (with BTB-like domain) 104925 0.258463564894777 −0.221825498871520
    777 1119317 1119317: SLC9A3R1 :: solute carrier family 9 396783 −0.014658638115010 −0.191639458116196
    (sodium/hydrogen exchanger), isoform 3 regulatory factor 1
    778 1119325 1119325: OAZ2 :: ornithine decarboxylase antizyme 2 74563 0.242847106449200 −0.195053295490539
    779 1119334 1119334: ITGA5 :: integrin, alpha 5 (fibronectin receptor, 149609 0.742369051797669 −0.374025974512821
    alpha polypeptide)
    780 1119350 1119350: ALDH2 :: aldehyde dehydrogenase 2 family (mitochondrial) 331141 0.608086049431527 −0.390151454914606
    781 1119361 1119361: TIA1 :: TIA1 cytotoxic granule-associated 391858 −0.026668805173817 −0.189784545154414
    RNA binding protein
    782 1119365 1119365: MAPKAPK2 :: mitogen-activated protein 75074 −0.059278973835078 −0.035574775797084
    kinase-activated protein kinase 2
    783 1119369 1119369: JUNB :: jun B proto-oncogene 400124 0.460486004055358 −0.369644781391790
    784 1119375 1119375: PPIF :: peptidylprolyl isomerase F (cyclophilin F) 381072 −0.116077021105342 0.359654077539207
    785 1119383 1119383: IGFBP4 :: insulin-like growth factor binding protein 4 1516 0.627827304350395 −0.357001758702634
    786 1119390 1119390: CBX1 :: chromobox homolog 1 (HP1 beta 77254 −0.286085532090585 0.535476131212779
    homolog Drosophila)
    787 1119400 1119400: DUSP3 :: dual specificity phosphatase 3 181046 0.384346199622817 −0.392842766782088
    (vaccinia virus phosphatase VH1-related)
    788 1119401 1119401: FHL1 :: four and a half LIM domains 1 421383 0.342758824589712 −0.226789376446408
    789 1119417 1119417: FAT :: FAT tumor suppressor homolog 1 (Drosophila) 166994 0.742466957569965 −0.454543207590739
    790 1119424 1119424: OAT :: ornithine aminotransferase (gyrate atrophy) 75485 0.460491519833347 −0.147080268886920
    791 1119438 1119438: BST2 :: bone marrow stromal cell antigen 2 118110 0.327211434111655 −0.338002355723367
    792 1119443 1119443: JAK1 :: Janus kinase 1 (a protein tyrosine kinase) 436004 −0.025586939182056 0.025836310250933
    793 1119445 1119445: KRT19 :: keratin 19 309517 0.265474647684479 −0.137484590496784
    794 1119448 1119448: ITGA6 :: integrin, alpha 6 212296 0.412797513436557 −0.255244929698541
    795 1119460 1119460: SFRS4 :: splicing factor, arginine/serine-rich 4 76122 −0.219899785493274 0.375669306197949
    796 1119462 1119462: CCND3 :: cyclin D3 83173 0.050395367966880 0.143613724160422
    797 1119466 1119466: MYBL2 :: v-myb myeloblastosis viral oncogene 179718 −0.410801274991122 0.741902823834935
    homolog (avian)-like 2
    798 1119467 1119467: TUBG1 :: tubulin, gamma 1 21635 −0.430720113786154 0.761998646900583
    799 1119475 1119475: SGK :: serum/glucocorticoid regulated kinase 296323 0.458464756569231 −0.179908409244619
    800 1119477 1119477: CD14 :: CD14 antigen 75627 0.374658686322277 −0.449833721869226
    801 1119479 1119479: TP53 :: tumor protein p53 (Li-Fraumeni syndrome) 426890 −0.273520348057380 0.189062886154923
    802 1119488 1119488: MTHFD2 :: methylene tetrahydrofolate 154672 −0.190082814208343 0.507122961206866
    dehydrogenase (NAD+ dependent),
    methenyltetrahydrofolate cyclohydrolase
    803 1119503 1119503: POLR2B :: polymerase (RNA) II (DNA directed) 149353 −0.276147772083673 0.452575668664126
    polypeptide B, 140 kDa
    804 1119510 1119510: KRT5 :: keratin 5 (epidermolysis bullosa simplex, Dowling- 433845 0.173908847805493 −0.148894839466960
    Meara/Kobner/Weber-Cockayne types)
    805 1119515 1119515: HDAC2 :: histone deacetylase 2 3352 −0.296163638102074 0.420133073064140
    806 1119516 1119516: PRKAB1 :: protein kinase, AMP-activated, 6061 −0.032255323397443 0.048963236579424
    beta 1 non-catalytic subunit
    807 1119519 1119519: BNIP3 :: BCL2/adenovirus E1B 19 kDa interacting protein 3 79428 0.070790959573082 0.034778072787655
    808 1119533 1119533: WDR23 :: WD repeat domain 23 283976 −0.176058140462130 0.021248719822432
    809 1119537 1119537: ARAF1 :: v-raf murine sarcoma 3611 viral 423807 −0.080692792057249 0.107243029276800
    oncogene homolog 1
    810 1119541 1119541: FARP1 :: FERM, RhoGEF (ARHGEF) and 207428 0.319164983800046 −0.239696774568353
    pleckstrin domain protein 1 (chondrocyte-derived)
    811 1119546 1119546: GNG10 :: guanine nucleotide binding protein 433898 0.366292039811560 −0.247632394673373
    (G protein), gamma 10
    812 1119557 1119557: SNK :: serum-inducible kinase 398157 0.703474357008969 −0.369781265328559
    813 1119559 1119559: CPD :: carboxypeptidase D 5057 0.477567634089383 −0.484691652037264
    814 1119561 1119561: FURIN :: furin (paired basic amino acid cleaving enzyme) 59242 0.203389107343861 −0.194260517260963
    815 1119564 1119564: ALCAM :: activated leukocyte cell adhesion molecule 10247 −0.174212933203010 −0.033522636800175
    816 1119565 1119565: CIB1 :: calcium and integrin binding 1 (calmyrin) 135471 0.077380378763426 −0.165969584136888
    817 1119566 1119566: ARPC1B :: actin related protein 2/3 complex, 433506 0.030123569365004 −0.044674445410727
    subunit 1B, 41 kDa
    818 1119568 1119568: PPP1R12B :: protein phosphatase 1, regulatory 130760 0.031485901809650 −0.198501575206590
    (inhibitor) subunit 12B
    819 1119582 1119582: SIAT1 :: sialyltransferase 1 (beta-galactoside alpha-2,6- 2554 −0.494168402771241 0.205936873075801
    sialyltransferase)
    820 1119611 1119611: BIRC2 :: baculoviral IAP repeat-containing 2 289107 0.153685965242011 −0.064993693037635
    821 1119633 1119633: PRPF4B :: PRP4 pre-mRNA processing factor 4 198891 −0.349211363145953 0.381772530527532
    homolog B (yeast)
    822 1119636 1119636: RIOK3 :: RIO kinase 3 (yeast) 209061 0.081817545037163 −0.207039528628000
    823 1119639 1119639: BS69 :: adenovirus 5 E1A binding protein 145894 0.220729171963144 −0.452502889318328
    824 1119647 1119647: PRKCL1 :: protein kinase C-like 1 2499 −0.359787604971237 0.315822728005629
    825 1119652 1119652: CHPF :: chondroitin polymerizing factor 458374 0.231475094432380 −0.103490870734691
    826 1119655 1119655: :: Homo sapiens hypothetical gene supported by NM_018065 407181 0.271438641659253 −0.320546868315670
    (LOC374293), mRNA
    827 1119667 1119667: ARL7 :: ADP-ribosylation factor-like 7 111554 0.344025040053841 −0.364460171367448
    828 1119680 1119680: NNMT :: nicotinamide N-methyltransferase 364345 0.849481601667150 −0.407473012706719
    829 1119683 1119683: C8FW :: phosphoprotein regulated by mitogenic pathways 444947 0.175976631640823 −0.225708506051835
    830 1119684 1119684: TM4SF2 :: transmembrane 4 superfamily member 2 439586 0.370013597929631 −0.285991368891065
    831 1119694 1119694: BMI1 :: B lymphoma Mo-MLV insertion region (mouse) 380403 −0.051029087019197 −0.238731608205694
    832 1119699 1119699: PDGFRB :: platelet-derived growth factor 307783 0.727905513250235 −0.426870326630435
    receptor, beta polypeptide
    833 1119706 1119706: GAK :: cyclin G associated kinase 153227 0.047312310573583 −0.212371832168573
    834 1119708 1119708: SERPINF1 :: serine (or cysteine) proteinase inhibitor, 173594 0.818127717962518 −0.494784353536062
    Clade F (alpha-2 antiplasmin, pigment epithelium
    derived factor), member 1
    835 1119709 1119709: FRAP1 :: FK506 binding protein 12-rapamycin 338207 −0.100924735319417 0.123840911452660
    associated protein 1
    836 1119725 1119725: CSK :: c-src tyrosine kinase 77793 −0.342193698499374 0.386680662501259
    837 1119729 1119729: TK1 :: thymidine kinase 1, soluble 164457 −0.178159168560846 0.621943500601026
    838 1119734 1119734: ITGAV :: integrin, alpha V (vitronectin receptor, 436873 0.880095069226405 −0.341583015797392
    alpha polypeptide, antigen CD51)
    839 1119752 1119752: BASP1 :: brain abundant, membrane attached signal protein 1 511745 0.039736680045055 0.128939385773097
    840 1119765 1119765: IGSF3 :: immunoglobulin superfamily, member 3 81234 0.043154074341915 −0.220966017200884
    841 1119766 1119766: MYST3 :: MYST histone acetyltransferase 93231 −0.201625331472481 0.020169749212703
    (monocytic leukemia) 3
    842 1119775 1119775: HDAC5 :: histone deacetylase 5 9028 −0.047258845589192 −0.144307812706093
    843 1119780 1119780: MPI :: mannose phosphate isomerase 75694 −0.249376705561104 0.265128946611980
    844 1119782 1119782: TRB2 :: tribbles homolog 2 155418 0.015840462162037 −0.057383709246075
    845 1119799 1119799: BCL7B :: B-cell CLL/lymphoma 7B 408219 −0.301353371006817 0.333515975123573
    846 1119802 1119802: PITPNB :: phosphotidylinositol transfer protein, beta 7370 −0.279346455254819 0.285255269810126
    847 1119807 1119807: MAPK14 :: mitogen-activated protein kinase 14 79107 −0.103247521829532 0.086030304232384
    848 1119808 1119808: IRF1 :: interferon regulatory factor 1 80645 0.214974139783435 −0.487005406874141
    849 1119813 1119813: PRKCD :: protein kinase C, delta 155342 −0.095881893640700 0.021482940393706
    850 1119817 1119817: TNKS :: tankyrase, TRF1-interacting 409194 −0.047999395366169 0.021277604032916
    ankyrin-related ADP-ribose polymerase
    851 1119820 1119820: CSNK1G2 :: casein kinase 1, gamma 2 181390 0.101155785845682 −0.029637775969762
    852 1119826 1119826: TYMS :: thymidylate synthetase 87491 −0.371762638989175 0.732371010652222
    853 1119838 1119838: GNAQ :: guanine nucleotide binding protein (G protein), q 469951 0.608858917985059 −0.451610474749559
    polypeptide
    854 1119841 1119841: LYN :: v-yes-1 Yamaguchi sarcoma viral 80887 −0.385987016514418 0.241969623986561
    related oncogene homolog
    855 1119846 1119846: POLR2K :: polymerase (RNA) II (DNA directed) 351475 −0.144645595994654 0.345426430436713
    polypeptide K, 7.0 kDa
    856 1119860 1119860: MAP2K1 :: mitogen-activated protein kinase kinase 1 132311 0.081523729635758 0.107249499092262
    857 1119868 1119868: TNFSF10 :: tumor necrosis factor (ligand) superfamily, 387871 0.361597221904698 −0.553123293632563
    member 10
    858 1119872 1119872: OSR1 :: oxidative-stress responsive 1 95220 −0.348692541889615 0.471254203040539
    859 1119873 1119873: CPSF5 :: cleavage and polyadenylation specific 446393 −0.235700347405962 0.584626529399289
    factor 5, 25 kDa
    860 1119876 1119876: DUSP11 :: dual specificity phosphatase 11 14611 −0.190844618983350 0.299994415193974
    (RNA/RNP complex 1-interacting)
    861 1119878 1119878: CCNB2 :: cyclin B2 194698 −0.291964604694904 0.784720009084587
    862 1119880 1119880: FMOD :: fibromodulin 442844 0.561780493586553 −0.548252797794380
    863 1119884 1119884: PTPN1 :: protein tyrosine phosphatase, non-receptor type 1 418004 −0.007199191487470 0.033799420525184
    864 1119889 1119889: PDCD4 :: programmed cell death 4 (neoplastic transformation 257697 −0.387457805191161 0.042363269173874
    inhibitor)
    865 1119894 1119894: ACY1 :: aminoacylase 1 334707 −0.350776535174252 0.264656076550105
    866 1119895 1119895: PRKACB :: protein kinase, cAMP-dependent, catalytic, beta 156324 −0.005364457034190 −0.120396590491985
    867 1119903 1119903: p44S10 :: proteasome regulatory particle subunit p44S10 350939 −0.492672600495662 0.540375320876622
    868 1119906 1119906: ROCK2 :: Rho-associated, coiled-coil containing 58617 −0.037457516068621 0.095524196892679
    protein kinase 2
    869 1119907 1119907: CASP3 :: caspase 3, apoptosis-related cysteine protease 141125 −0.261343210354826 0.147838406405152
    870 1119916 1119916: OXCT :: 3-oxoacid CoA transferase 177584 −0.420512115118106 0.570427247250647
    871 1119919 1119919: STK39 :: serine threonine kinase 39 199263 0.036380914794334 0.137316042469944
    (STE20/SPS1 homolog, yeast)
    872 1119920 1119920: MAPKAPK3 :: mitogen-activated protein 234521 0.033224901009291 −0.290845134954234
    kinase-activated protein kinase 3
    873 1119924 1119924: INPP1 :: inositol polyphosphate-1-phosphatase 32309 0.323225977540793 −0.354327057539113
    874 1119928 1119928: CLPP :: ClpP caseinolytic protease, 317335 −0.383473848217803 0.493264263215279
    ATP-dependent, proteolytic subunit homolog (E. coli)
    875 1119936 1119936: AMSH :: associated molecule with the SH3 domain of STAM 12479 −0.212970492666360 0.177745673538672
    876 1119939 1119939: AHR :: aryl hydrocarbon receptor 170087 0.256970446704131 −0.173340326402877
    877 1119946 1119946: AGT :: angiotensinogen (serine (or cysteine) 19383 −0.083357114527211 0.115295274530192
    proteinase inhibitor, clade A (alpha-1 antiproteinase,
    antitrypsin), member 8)
    878 1119950 1119950: TAF15 :: TAF15 RNA polymerase II, TATA box 402752 −0.306440406993752 0.338606484125856
    binding protein (TBP)-associated factor, 68 kDa
    879 1119972 1119972: EPHB4 :: EphB4 437008 0.213883588482106 −0.276537887742675
    880 1119979 1119979: MSH6 :: mutS homolog 6 (E. coli) 445052 −0.210797269834120 0.563006959737033
    881 1119983 1119983: ANK2 :: ankyrin 2, neuronal 409783 0.239718352750997 −0.362446515998409
    882 1119995 1119995: IL1R1 :: interleukin 1 receptor, type I 82112 0.880259393296759 −0.523750968501772
    883 1119997 1119997: STK38 :: serine/threonine kinase 38 367811 0.116255029911486 −0.270963700598019
    884 1119998 1119998: C1QB :: complement component 1, q subcomponent, beta 8986 −0.064997812238848 −0.308036422540148
    polypeptide
    885 1120008 1120008: DYRK2 :: dual-specificity tyrosine-(Y)-phosphorylation 173135 0.139680495957613 −0.138798127049231
    regulated kinase 2
    886 1120011 1120011: SMARCA3 :: SWI/SNF related, matrix associated, 3068 −0.393821573018423 0.440572225264925
    actin dependent regulator of chromatin, subfamily a,
    member 3
    887 1120016 1120016: STARD3 :: START domain containing 3 77628 0.197666440603128 −0.216926094278756
    888 1120023 1120023: LTBR :: lymphotoxin beta receptor (TNFR 1116 0.449547762265972 −0.391678588451956
    superfamily, member 3)
    889 1120024 1120024: INPP5A :: inositol polyphosphate-5-phosphatase, 40 kDa 408063 0.343186933129608 −0.211635679580085
    890 1120026 1120026: STAT5A :: signal transducer and activator of transcription 5A 437058 0.233594777682906 −0.490211434372936
    891 1120038 1120038: CHSY1 :: carbohydrate (chondroitin) synthase 1 110488 0.469412842283311 −0.278608622720236
    892 1120044 1120044: BCAS2 :: breast carcinoma amplified sequence 2 22960 −0.118171434304281 0.380613118455193
    893 1120053 1120053: COG2 :: component of oligomeric golgi complex 2 82399 −0.322127622203961 0.285853667630216
    894 1120055 1120055: MADH2 :: MAD, mothers against decapentaplegic homolog 2 110741 −0.198373862314482 0.151233465555872
    (Drosophila)
    895 1120059 1120059: THBS2 :: thrombospondin 2 458354 0.823561522648464 −0.307597847291106
    896 1120063 1120063: SDF2 :: stromal cell-derived factor 2 118684 −0.151141188451317 0.205246091448918
    897 1120069 1120069: CSF1R :: colony stimulating factor 1 receptor, 174142 0.586483471012455 −0.538330757879298
    formerly McDonough feline sarcoma viral
    (v-fms) oncogene homolog
    898 1120072 1120072: PTK2B :: PTK2B protein tyrosine kinase 2 beta 405474 0.025565694638970 −0.081698039331191
    899 1120079 1120079: IMPA2 :: inositol(myo)-1(or 4)-monophosphatase 2 5753 −0.142422649698462 0.380777710316534
    900 1120081 1120081: PDGFRA :: platelet-derived growth factor receptor, 74615 0.801797080306997 −0.363577157808831
    alpha polypeptide
    901 1120082 1120082: RB1 :: retinoblastoma 1 (including osteosarcoma) 408528 −0.092716888870664 0.307873154083231
    902 1120088 1120088: HAT1 :: histone acetyltransferase 1 13340 −0.233187350154903 0.685057151008412
    903 1120089 1120089: DAPK1 :: death-associated protein kinase 1 244318 0.466586398338559 −0.514289733675279
    904 1120090 1120090: BCL6 :: B-cell CLL/lymphoma 6 (zinc finger protein 51) 155024 0.144941230662303 0.048693731993595
    905 1120108 1120108: ARHG :: ras homolog gene family, member G (rho G) 75082 0.190899333887631 −0.071434473852746
    906 1120120 1120120: ABCC4 :: ATP-binding cassette, sub-family C 307915 0.227392907322269 −0.077875606978302
    (CFTR/MRP), member 4
    907 1120121 1120121: CDK9 :: cyclin-dependent kinase 9 (CDC2-related kinase) 150423 0.045051374703949 −0.071571722929467
    908 1120127 1120127: CDC2 :: cell division cycle 2, G1 to S and G2 to M 334562 −0.356711902630063 0.859586003083525
    909 1120128 1120128: MAPK9 :: mitogen-activated protein kinase 9 348446 0.053836424867107 0.050716859954676
    910 1120129 1120129: TLE1 :: transducin-like enhancer of split 1 (E(sp1) homolog, 406491 −0.147138605178005 0.004837891616427
    Drosophila)
    911 1120134 1120134: IL4R :: interleukin 4 receptor 75545 −0.046782309391954 −0.158009856362830
    912 1120137 1120137: FCGBP :: Fc fragment of IgG binding protein 111732 −0.021179847554413 0.084901186125138
    913 1120145 1120145: CDH3 :: cadherin 3, type 1, P-cadherin (placental) 191842 0.208811388283192 −0.196206998994574
    914 1120152 1120152: IRF2 :: interferon regulatory factor 2 83795 −0.245349312777798 −0.021862320330082
    915 1120153 1120153: LMNB1 :: lamin B1 89497 −0.349360475211000 0.567523295277270
    916 1120160 1120160: KIAA0355 :: KIAA0355 gene product 436976 −0.006389482890844 −0.147844881582699
    917 1120163 1120163: DCK :: deoxycytidine kinase 709 −0.262602853143119 0.474753625341165
    918 1120191 1120191: SOCS2 :: suppressor of cytokine signaling 2 405946 0.205081336164991 −0.120603880465586
    919 1120194 1120194: RPS6KA1 :: ribosomal protein S6 kinase, 149957 −0.172834971698563 0.110172857246101
    90 kDa, polypeptide 1
    920 1120196 1120196: TBC1D4 :: TBC1 domain family, member 4 173802 0.252268611353589 −0.365300630429192
    921 1120205 1120205: DSCR2 :: Down syndrome critical region gene 2 5198 −0.341638325826115 0.713407022486365
    922 1120214 1120214: CD53 :: CD53 antigen 443057 −0.152751764379210 −0.049590054715558
    923 1120216 1120216: CCNA2 :: cyclin A2 85137 −0.324160296081840 0.777319506164410
    924 1120254 1120254: RTN1 :: reticulon 1 99947 0.612541977651677 −0.539497884538483
    925 1120261 1120261: EPHA2 :: EphA2 171596 0.217934786713959 −0.365366022247552
    926 1120266 1120266: CD68 :: CD68 antigen 246381 0.451189190580461 −0.397687894156014
    927 1120267 1120267: TNFRSF1B :: tumor necrosis factor receptor superfamily, 256278 0.233418379708817 −0.357196376724822
    member 1B
    928 1120269 1120269: MET :: met proto-oncogene (hepatocyte growth factor 419124 0.095532546067821 0.070544177910803
    receptor)
    929 1120272 1120272: MAP3K3 :: mitogen-activated protein kinase kinase kinase 3 29282 0.044758338920690 −0.191842282997896
    930 1120274 1120274: MTX2 :: metaxin 2 31584 −0.329576839455756 0.527764199207566
    931 1120278 1120278: SEMA4D :: sema domain, immunoglobulin domain (Ig), 511748 0.224371642866400 −0.290878044536958
    transmembrane domain (TM) and short cytoplasmic domain,
    (semaphorin) 4D
    932 1120288 1120288: CD4 :: CD4 antigen (p55) 17483 0.453027496725459 −0.493671880192508
    933 1120289 1120289: MAP4K5 :: mitogen-activated protein kinase kinase kinase 246970 −0.101195827454930 0.110280186060386
    kinase 5
    934 1120299 1120299: NFIL3 :: nuclear factor, interleukin 3 regulated 79334 0.418150198365747 −0.353861915577026
    935 1120300 1120300: CSNK2A2 :: casein kinase 2, alpha prime polypeptide 82201 −0.447144828589450 0.441822317864757
    936 1120316 1120316: TERF2 :: telomeric repeat binding factor 2 63335 −0.223834288936832 0.378657341977871
    937 1120317 1120317: BYSL :: bystin-like 106880 −0.480611242448932 0.673114888210520
    938 1120324 1120324: IGF1R :: insulin-like growth factor 1 receptor 239176 0.486016697137607 −0.246282140833788
    939 1120335 1120335: MAP3K11 :: mitogen-activated protein kinase kinase 432787 0.167553983611871 −0.337924652268674
    kinase 11
    940 1120350 1120350: IL1RL1LG :: interleukin 1 receptor-like 1 ligand 446686 0.073526468292361 −0.142883449531743
    941 1120353 1120353: BCL2 :: B-cell CLL/lymphoma 2 79241 −0.350722162941236 −0.216689018753782
    942 1120355 1120355: CX3CL1 :: chemokine (C—X3—C motif) ligand 1 80420 0.096212197388840 −0.260021878158517
    943 1120356 1120356: PKD2 :: polycystic kidney disease 2 (autosomal dominant) 458291 0.604711621900698 −0.246336208434929
    944 1120359 1120359: FRZB :: frizzled-related protein 128453 0.089133553635861 −0.257184446624874
    945 1120361 1120361: PDE4B :: phosphodiesterase 4B, cAMP-specific 188 −0.084837939596466 −0.104428923019524
    (phosphodiesterase E4 dunce homolog, Drosophila)
    946 1120362 1120362: PHKG2 :: phosphorylase kinase, gamma 2 (testis) 196177 −0.077059000678308 −0.191291041020843
    947 1120366 1120366: DPP4 :: dipeptidylpeptidase 4 (CD26, adenosine deaminase 44926 0.297035769550426 −0.200947213073117
    complexing protein 2)
    948 1120370 1120370: ITPKB :: inositol 1,4,5-trisphosphate 3-kinase B 78877 0.190360802060295 −0.169751144548655
    949 1120373 1120373: BAK1 :: BCL2-antagonist/killer 1 93213 −0.200140816613802 0.113338862865570
    950 1120378 1120378: FLJ11193 :: hypothetical protein FLJ11193 151046 −0.272022865326159 0.234783123016162
    951 1120385 1120385: BUB1B :: BUB1 budding uninhibited by benzimidazoles 1 36708 −0.428733600165811 0.833405557024467
    homolog beta (yeast)
    952 1120387 1120387: CTSO :: cathepsin O 75262 0.374520964899448 −0.580832415098230
    953 1120389 1120389: SLA :: Src-like-adaptor 75367 −0.172426216404282 −0.127234467000589
    954 1120400 1120400: SSBP2 :: single-stranded DNA binding protein 2 152207 0.138133470457960 0.041953623299176
    955 1120402 1120402: CDC42BPA :: CDC42 binding protein kinase alpha 18586 0.342860793681219 −0.308950300777485
    (DMPK-like)
    956 1120417 1120417: FLJ10055 :: hypothetical protein FLJ10055 9398 0.458712245189916 −0.309562635887674
    957 1120419 1120419: NJMU-R1 :: protein kinase Njmu-R1 9800 −0.188537102796126 0.435261002773401
    958 1120422 1120422: GARP :: glycoprotein A repetitions predominant 151641 0.210134245590657 0.098618718300581
    959 1120423 1120423: MAP3K5 :: mitogen-activated protein kinase kinase kinase 5 151988 0.128014378546006 −0.414691971823296
    960 1120425 1120425: RPS6KA3 :: ribosomal protein S6 kinase, 90 kDa, 188361 0.280819408584904 −0.003327617440558
    polypeptide 3
    961 1120433 1120433: VRK1 :: vaccinia related kinase 1 422662 −0.298915556379366 0.717298406899907
    962 1120438 1120438: USP46 :: ubiquitin specific protease 46 109268 −0.301682893848221 0.251115921079262
    963 1120465 1120465: CXCL9 :: chemokine (C—X—C motif) ligand 9 77367 0.091216036037422 −0.424535324487160
    964 1120477 1120477: KDR :: kinase insert domain receptor (a type III 12337 0.473056670592013 −0.203310434691520
    receptor tyrosine kinase)
    965 1120478 1120478: ACVR1 :: activin A receptor, type I 150402 0.691949086102474 −0.523920470761015
    966 1120483 1120483: CSTF3 :: cleavage stimulation factor, 3′ pre-RNA, subunit 3, 180034 −0.518586670460773 0.446316197113926
    77 kDa
    967 1120484 1120484: MPO :: myeloperoxidase 458272 0.101960994023863 −0.054587543757020
    968 1120494 1120494: CDC6 :: CDC6 cell division cycle 6 homolog (S. cerevisiae) 405958 −0.416635429243115 0.842295577203676
    969 1120500 1120500: CYP27A1 :: cytochrome P450, family 27, subfamily A, 82568 0.653610023886872 −0.304787134639314
    polypeptide 1
    970 1120509 1120509: GNB5 :: guanine nucleotide binding protein (G protein), 155090 −0.267362638918031 0.200244247175214
    beta 5
    971 1120520 1120520: RFC4 :: replication factor C (activator 1) 4, 37 kDa 35120 −0.501231595987143 0.789659303959865
    972 1120524 1120524: TRIP13 :: thyroid hormone receptor interactor 13 436187 −0.368479048817546 0.832946538281856
    973 1120529 1120529: CEBPA :: CCAAT/enhancer binding protein (C/EBP), alpha 76171 0.603459145525783 −0.430431783000636
    974 1120538 1120538: ICSBP1 :: interferon consensus sequence binding protein 1 14453 −0.202713033551771 0.034802475287723
    975 1120544 1120544: STK3 :: serine/threonine kinase 3 (STE20 homolog, yeast) 166684 0.085584173231200 −0.034463191343131
    976 1120553 1120553: PRAME :: preferentially expressed antigen in melanoma 30743 0.096253753354037 0.013328837460755
    977 1120555 1120555: STK19 :: serine/threonine kinase 19 444 0.168786958397468 −0.247788203132821
    978 1120562 1120562: CCL4 :: chemokine (C-C motif) ligand 4 75703 0.281322248691298 −0.465719953116774
    979 1120564 1120564: TESK1 :: testis-specific kinase 1 79358 0.100723203368127 −0.228465660577298
    980 1120572 1120572: IL2RG :: interleukin 2 receptor, gamma (severe combined 84 0.235330936351446 −0.396807810508209
    immunodeficiency)
    981 1120574 1120574: CD48 :: CD48 antigen (B-cell membrane protein) 901 −0.194668752468389 −0.098819351341990
    982 1120580 1120580: RFC3 :: replication factor C (activator 1) 3, 38 kDa 115474 −0.307682737839499 0.789291151763360
    983 1120581 1120581: BCL9 :: B-cell CLL/lymphoma 9 415209 −0.190510681098454 0.148503187654638
    984 1120583 1120583: RNU3IP2 :: RNA, U3 small nucleolar interacting protein 2 153768 −0.526724070424994 0.500938051852095
    985 1120588 1120588: TPST1 :: tyrosylprotein sulfotransferase 1 421194 0.700554999280495 −0.302446735476920
    986 1120593 1120593: STAB1 :: stabilin 1 301989 0.315207523101052 −0.361469709646652
    987 1120594 1120594: CDO1 :: cysteine dioxygenase, type I 442378 0.096654329449506 −0.131902879792736
    988 1120595 1120595: KIAA0999 :: KIAA0999 protein 444909 −0.158743720518346 0.006339680783502
    989 1120596 1120596: CDKN2C :: cyclin-dependent kinase inhibitor 2C 4854 −0.277992134637003 0.464801755714349
    (p18, inhibits CDK4)
    990 1120601 1120601: KIAA0963 :: KIAA0963 protein 441129 0.115377312801900 −0.173467001738638
    991 1120605 1120605: RPS6KB1 :: ribosomal protein S6 kinase, 70 kDa, 86858 −0.049333332738750 0.272123372076907
    polypeptide 1
    992 1120615 1120615: IFNAR1 :: interferon (alpha, beta and omega) receptor 1 181315 0.109452635758577 −0.098788842929034
    993 1120616 1120616: CD37 :: CD37 antigen 153053 −0.532314280274716 0.308291940284235
    994 1120617 1120617: CPT1B :: carnitine palmitoyltransferase 1B (muscle) 439777 0.229122288389948 −0.467225308462803
    995 1120625 1120625: RNGTT :: RNA guanylyltransferase and 5′-phosphatase 27345 −0.060185273034959 −0.030566655399450
    996 1120630 1120630: DKFZP564M082 :: DKFZP564M082 protein 38044 −0.185687083825884 0.335258295065521
    997 1120633 1120633: HDAC4 :: histone deacetylase 4 222874 0.268465157579931 −0.393330515146740
    998 1120637 1120637: FCER1G :: Fc fragment of IgE, high affinity I, receptor for; 433300 0.331513918783418 −0.400800744737435
    gamma polypeptide
    999 1120643 1120643: CDK2 :: cyclin-dependent kinase 2 19192 −0.293669215593932 0.661617674173487
    1000 1120645 1120645: FADS3 :: fatty acid desaturase 3 21765 0.055507218063663 0.088445892207464
    1001 1120651 1120651: PIM2 :: pim-2 oncogene 80205 −0.281220927786929 0.185187824043508
    1002 1120673 1120673: KIAA0711 :: KIAA0711 gene product 5333 0.068811665106344 0.005641795833107
    1003 1120695 1120695: TRAF5 :: TNF receptor-associated factor 5 385685 −0.019131171585834 −0.161636874402010
    1004 1120697 1120697: DHX30 :: DEAN (Asp-Glu-Ala-His) box polypeptide 30 323462 −0.471181063703452 0.425078805218812
    1005 1120700 1120700: SCAP2 :: src family associated phosphoprotein 2 410745 −0.186747761610340 0.225356576750172
    1006 1120703 1120703: SLCO2A1 :: solute carrier organic anion transporter family, 83974 0.364711626940315 −0.247170134183657
    member 2A1
    1007 1120716 1120716: CAMK1 :: calcium/calmodulin-dependent protein kinase I 512804 0.168875956443599 −0.200055505150205
    1008 1120717 1120717: SLC43A1 :: solute carrier family 43, member 1 444159 −0.376807044586730 0.520626875405123
    1009 1120720 1120720: KCNN4 :: potassium intermediate/small conductance calcium- 10082 0.136091693845411 −0.076690223326382
    activated channel, subfamily N, member 4
    1010 1120730 1120730: G1P3 :: interferon, alpha-inducible protein (clone IFI-6-16) 287721 0.310445834508628 −0.358938894023986
    1011 1120743 1120743: CD83 :: CD83 antigen (activated B lymphocytes, 79197 0.016342520267471 −0.056434824824793
    immunoglobulin superfamily)
    1012 1120750 1120750: LDOC1 :: leucine zipper, down-regulated in cancer 1 45231 0.348398089655945 −0.373744732997425
    1013 1120755 1120755: CXCL1 :: chemokine (C—X—C motif) ligand 1 (melanoma 789 0.239712817378015 −0.227377568731226
    growth stimulating activity, alpha)
    1014 1120765 1120765: PIK3C2B :: phosphoinositide-3-kinase, class 2, beta 343329 0.099676443902521 −0.033239919662244
    polypeptide
    1015 1120770 1120770: BID :: BH3 interacting domain death agonist 300825 −0.168931051298000 0.231696940935265
    1016 1120779 1120779: CDC7 :: CDC7 cell division cycle 7 (S. cerevisiae) 28853 −0.364719870070187 0.702890401522440
    1017 1120780 1120780: FARP2 :: FERM, RhoGEF and pleckstrin domain protein 2 301283 0.218332541521728 −0.357639798743606
    1018 1120785 1120785: PPIC :: peptidylprolyl isomerase C (cyclophilin C) 110364 0.833250100411904 −0.364870410416830
    1019 1120789 1120789: PDPK1 :: 3-phosphoinositide dependent protein kinase-1 154729 0.036213766133773 −0.055311931358302
    1020 1120792 1120792: CXCL10 :: chemokine (C—X—C motif) ligand 10 413924 0.166606940060415 −0.407303162829402
    1021 1120803 1120803: IKBKE :: inhibitor of kappa light polypeptide gene enhancer 321045 0.173038590863187 −0.262684854061046
    in B-cells, kinase epsilon
    1022 1120808 1120808: IRF4 :: interferon regulatory factor 4 127686 −0.274522690905631 0.214443660765563
    1023 1120809 1120809: SELL :: selectin L (lymphocyte adhesion molecule 1) 82848 −0.034467098542711 −0.232667176371041
    1024 1120813 1120813: KIAA0831 :: KIAA0831 414809 0.140198507173410 −0.440539960257267
    1025 1120814 1120814: ICK :: intestinal cell (MAK-like) kinase 417022 0.185512034005136 −0.254094458847882
    1026 1120818 1120818: FGFR4 :: fibroblast growth factor receptor 4 165950 −0.173305192411460 0.170225481596070
    1027 1120824 1120824: ARK5 :: KIAA0537 gene product 200598 0.639988433549215 −0.342249782851512
    1028 1120825 1120825: CHL1 :: cell adhesion molecule with homology to L1CAM 388344 0.116148782379396 −0.093424425417522
    (close homolog of L1)
    1029 1120828 1120828: EPHB3 :: EphB3 2913 0.273313344428643 −0.065126563411831
    1030 1120832 1120832: PFTK1 :: PFTAIRE protein kinase 1 57856 0.168005950948601 −0.028716212628633
    1031 1120834 1120834: CCL21 :: chemokine (C-C motif) ligand 21 57907 −0.035804408078127 −0.204294856872407
    1032 1120838 1120838: PKIA :: protein kinase (cAMP-dependent, catalytic) inhibitor 433700 −0.146391280990281 0.187655861583021
    alpha
    1033 1120839 1120839: PLCG2 :: phospholipase C, gamma 2 (phosphatidylinositol- 512298 −0.460928399830360 0.522088964678862
    specific)
    1034 1120846 1120846: RPS6KA4 :: ribosomal protein S6 kinase, 90 kDa, 105584 0.045791529310886 −0.164030593362306
    polypeptide 4
    1035 1120847 1120847: NEK4 :: NIMA (never in mitosis gene a)-related kinase 4 433008 −0.162080158681806 0.363435471138679
    1036 1120853 1120853: NEK2 :: NIMA (never in mitosis gene a)-related kinase 2 153704 −0.257915260526437 0.773686557142882
    1037 1120854 1120854: EDG1 :: endothelial differentiation, sphingolipid G-protein- 154210 −0.122104475497316 −0.071633341557146
    coupled receptor, 1
    1038 1120858 1120858: HOMER3 :: homer homolog 3 (Drosophila) 410683 0.335496794625231 −0.271528013190748
    1039 1120863 1120863: CCL5 :: chemokine (C-C motif) ligand 5 489044 0.542336364272824 −0.582181977929694
    1040 1120875 1120875: LRMP :: lymphoid-restricted membrane protein 124922 0.003183268254248 0.168887881459636
    1041 1120880 1120880: LTBP2 :: latent transforming growth factor beta binding 105689 0.826255058669113 −0.434328882440352
    protein 2
    1042 1120881 1120881: ICAM2 :: intercellular adhesion molecule 2 433303 −0.213253074312284 −0.041517977663047
    1043 1120900 1120900: EPHB6 :: EphB6 380089 0.013945388707104 −0.198607193449715
    1044 1120918 1120918: HLF :: hepatic leukemia factor 250692 0.013775304997262 −0.055242216674679
    1045 1120923 1120923: ARHGEF5 :: Rho guanine nucleotide exchange factor 334 0.209882084442928 −0.150683350886678
    (GEF) 5
    1046 1120925 1120925: IL11RA :: interleukin 11 receptor, alpha 204891 0.273246691313366 −0.470149289804446
    1047 1120946 1120946: MAPK10 :: mitogen-activated protein kinase 10 25209 −0.002920323341900 0.154019887369059
    1048 1120952 1120952: TTK :: TTK protein kinase 169840 −0.236416169728487 0.593602839749024
    1049 1120955 1120955: MELK :: maternal embryonic leucine zipper kinase 184339 −0.208951798652608 0.724555523338905
    1050 1120958 1120958: CDK8 :: cyclin-dependent kinase 8 397734 −0.039317157762445 0.224625838601688
    1051 1120976 1120976: GCHFR :: GTP cyclohydrolase I feedback regulatory protein 245644 −0.035026457160826 0.213041780115649
    1052 1120980 1120980: TLE4 :: transducin-like enhancer of split 4 (E(sp1) homolog, 99824 −0.030677104931693 −0.067870579035081
    Drosophila)
    1053 1120986 1120986: STK18 :: serine/threonine kinase 18 172052 −0.272148311899732 0.739975084000157
    1054 1120993 1120993: IL10RA :: interleukin 10 receptor, alpha 327 0.047545601645909 −0.184922274295712
    1055 1121000 1121000: TLR2 :: toll-like receptor 2 519033 0.429492421868063 −0.480462743962837
    1056 1121005 1121005: TNFRSF11B :: tumor necrosis factor receptor superfamily, 81791 0.322049857523582 −0.151124812823603
    member 11b (osteoprotegerin)
    1057 1121007 1121007: MAP4K2 :: mitogen-activated protein kinase kinase kinase 512671 −0.234244240729329 0.375556542684312
    kinase 2
    1058 1121012 1121012: E2F1 :: E2F transcription factor 1 96055 −0.334386168154563 0.678410948823103
    1059 1121013 1121013: ICAM3 :: intercellular adhesion molecule 3 353214 −0.297026833246660 −0.013311917844355
    1060 1121021 1121021: CNK :: cytokine-inducible kinase 153640 −0.019398263377201 −0.088470692615038
    1061 1121028 1121028: APOM :: apolipoprotein M 247323 0.080461690727297 −0.173511617318374
    1062 1121029 1121029: CSTA :: cystatin A (stefin A) 412999 0.725032558235074 −0.312936257878748
    1063 1121033 1121033: EMP2 :: epithelial membrane protein 2 511911 0.712789461038450 −0.289956290195573
    1064 1121054 1121054: TGFA :: transforming growth factor, alpha 170009 0.070989900125764 −0.072416748854938
    1065 1121057 1121057: STAT5B :: signal transducer and activator of transcription 5B 434992 0.014885551405709 −0.076250115454824
    1066 1121061 1121061: ITGA2 :: integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 387725 −0.029030779750270 0.035897612258061
    receptor)
    1067 1121062 1121062: CCNE2 :: cyclin E2 408658 −0.210155943554150 0.646944545337192
    1068 1121073 1121073: AUH :: AU RNA binding protein/enoyl-Coenzyme A 81886 0.171546279035464 −0.332955161867336
    hydratase
    1069 1121076 1121076: ITGAE :: integrin, alpha E (antigen CD103, human mucosal 389133 −0.413199084125475 0.301133545375388
    lymphocyte antigen 1; alpha polypeptide)
    1070 1121082 1121082: IL1B :: interleukin 1, beta 126256 0.253565351329184 −0.274936908342392
    1071 1121100 1121100: CCR1 :: chemokine (C-C motif) receptor 1 301921 0.341955874946600 −0.274774576684184
    1072 1121102 1121102: MHC2TA :: MHC class II transactivator 126714 0.094969874201105 −0.250509581424846
    1073 1121115 1121115: MEF2B :: MADS box transcription enhancer factor 2, 78881 −0.260397502438443 0.457668819142024
    polypeptide B (myocyte enhancer factor 2B)
    1074 1121117 1121117: VRK2 :: vaccinia related kinase 2 82771 0.105930454706077 −0.045187449295500
    1075 1121120 1121120: RAGE :: renal tumor antigen 104119 0.011704601675353 −0.003336985459853
    1076 1121129 1121129: CSF2RB :: colony stimulating factor 2 receptor, beta, 285401 0.473407369637606 −0.474705087565604
    low-affinity (granulocyte-macrophage)
    1077 1121136 1121136: DDR2 :: discoidin domain receptor family, member 2 440905 0.497410432793414 −0.341535633908894
    1078 1121143 1121143: GNG4 :: guanine nucleotide binding protein (G protein), 447973 0.065124580945373 −0.114186071226629
    gamma 4
    1079 1121149 1121149: MAP3K14 :: mitogen-activated protein kinase kinase 440315 −0.045622884625820 −0.157979391580511
    kinase 14
    1080 1121159 1121159: RELB :: v-rel reticuloendotheliosis viral oncogene 307905 −0.014117999369713 0.054575676509177
    homolog B, nuclear factor of kappa light polypeptide gene enhancer in
    B-cells 3 (avian)
    1081 1121161 1121161: IL6 :: interleukin 6 (interferon, beta 2) 512234 0.270707514058880 −0.160285802317573
    1082 1121166 1121166: STK17B :: serine/threonine kinase 17b (apoptosis-inducing) 88297 0.135353436195562 0.076356575160992
    1083 1121170 1121170: HM74 :: putative chemokine receptor 458425 0.109820599871215 −0.169065883762500
    1084 1121186 1121186: CXCL13 :: chemokine (C—X—C motif) ligand 13 (B-cell 100431 0.378549805355286 −0.294764973487508
    chemoattractant)
    1085 1121190 1121190: NOTCH4 :: Notch homolog 4 (Drosophila) 436100 0.101751050016826 −0.006262723965488
    1086 1121195 1121195: PBX1 :: pre-B-cell leukemia transcription factor 1 408222 −0.059508030808216 −0.012690445881844
    1087 1121201 1121201: BCL10 :: B-cell CLL/ 193516 −0.097298819688125 0.262527744599808
    lymphoma 10
    1088 1121203 1121203: LIF :: leukemia inhibitory factor (cholinergic differentiation 2250 0.227708415345235 −0.237257236108422
    factor)
    1089 1121205 1121205: LCP2 :: lymphocyte cytosolic protein 2 (SH2 domain 2488 0.509256290000162 −0.616098101683677
    containing leukocyte protein of 76 kDa)
    1090 1121217 1121217: IL2RB :: interleukin 2 receptor, beta 75596 0.233728921730338 −0.367351838583743
    1091 1121220 1121220: RBL1 :: retinoblastoma-like 1 (p107) 87 −0.254718182068782 0.437740141713836
    1092 1121228 1121228: SPI1 :: spleen focus forming virus (SFFV) proviral integration 157441 0.101862646966026 −0.078795355216853
    oncogene spi1
    1093 1121248 1121248: BARD1 :: BRCA1 associated RING domain 1 54089 −0.332520033583970 0.540409719004797
    1094 1121265 1121265: PLAG1 :: pleiomorphic adenoma gene 1 14968 −0.055939614174796 0.094487218739530
    1095 1121276 1121276: CHEK1 :: CHK1 checkpoint homolog (S. pombe) 24529 −0.352853420627079 0.836388056331936
    1096 1121278 1121278: DCAMKL1 :: doublecortin and CaM kinase-like 1 21355 0.412883143697658 −0.298495227861876
    1097 1121281 1121281: IL1R2 :: interleukin 1 receptor, type II 25333 0.142459721447506 −0.302261496758997
    1098 1121287 1121287: STK4 :: serine/threonine kinase 4 35140 −0.141211379313466 0.140410355369261
    1099 1121290 1121290: FES :: feline sarcoma oncogene 7636 0.126479905402088 −0.115090374078902
    1100 1121291 1121291: EBI2 :: Epstein-Barr virus induced gene 2 (lymphocyte- 784 0.235439422364981 −0.105451694013327
    specific G protein-coupled receptor)
    1101 1121301 1121301: ZNF211 :: zinc finger protein 211 511749 −0.256995974326506 −0.116130479767648
    1102 1121306 1121306: SNAPC1 :: small nuclear RNA activating complex, 179312 −0.111148822811151 0.479702938197036
    polypeptide 1, 43 kDa
    1103 1121309 1121309: HSU79266 :: protein predicted by clone 23627 23642 −0.229837789455481 0.499904248128160
    1104 1121315 1121315: MST1R :: macrophage stimulating 1 receptor (c-met-related 2942 0.207517198765213 −0.192186835039801
    tyrosine kinase)
    1105 1121316 1121316: CD3E :: CD3E antigen, epsilon polypeptide (TiT3 complex) 3003 0.224738515046276 −0.499493301566731
    1106 1121322 1121322: CASP10 :: caspase 10, apoptosis-related cysteine protease 5353 0.089986731593722 −0.314526392551084
    1107 1121326 1121326: CCL20 :: chemokine (C-C motif) ligand 20 75498 0.215322214165972 −0.132606733260028
    1108 1121329 1121329: SIT :: SHP2 interacting transmembrane adaptor 88012 −0.210345828377640 0.102148279065859
    1109 1121331 1121331: TESK2 :: testis-specific kinase 2 8980 −0.039483229481418 0.033775496434037
    1110 1121343 1121343: BTK :: Bruton agammaglobulinemia tyrosine kinase 159494 −0.264292738475593 0.221493414593700
    1111 1121368 1121368: SV2B :: synaptic vesicle glycoprotein 2B 8071 0.141032356631520 −0.147797431288585
    1112 1121371 1121371: TRAF6 :: TNF receptor-associated factor 6 90957 0.075399751558709 −0.168875636897418
    1113 1121380 1121380: LAMP3 :: lysosomal-associated membrane protein 3 10887 0.570357891518240 −0.407916378045071
    1114 1121383 1121383: ANGPT2 :: angiopoietin 2 115181 0.217195685938879 −0.123710120323309
    1115 1121387 1121387: ROR2 :: receptor tyrosine kinase-like orphan receptor 2 208080 0.489331037769812 −0.053435946072310
    1116 1121400 1121400: TRAF1 :: TNF receptor-associated factor 1 438253 0.142917780292670 −0.296365843618807
    1117 1121404 1121404: ANGPT1 :: angiopoietin 1 2463 0.374587616111693 −0.287681985161262
    1118 1121406 1121406: TNFSF12 :: tumor necrosis factor (ligand) superfamily, −4 0.458155673630534 −0.447921783667761
    member 12
    1119 1121408 1121408: LOC51760 :: B/K protein 258326 0.108520226350273 −0.337094362419053
    1120 1121414 1121414: ALKBH :: alkB, alkylation repair homolog (E. coli) 94542 −0.519450896479011 0.507278510441829
    1121 1121436 1121436: HDAC9 :: histone deacetylase 9 116753 −0.062542813471143 0.051528289785797
    1122 1121444 1121444: LY75 :: lymphocyte antigen 75 153563 0.467870413003146 −0.334208325739869
    1123 1121452 1121452: BCL2A1 :: BCL2-related protein A1 227817 0.047073151548673 0.008784276860166
    1124 1121468 1121468: IL17R :: interleukin 17 receptor 129751 0.254701924480632 −0.250835608176983
    1125 1121473 1121473: ITGB7 :: integrin, beta 7 1741 0.050306964647293 −0.260994122489540
    1126 1121482 1121482: OSMR :: oncostatin M receptor 238648 0.287543499924824 −0.061525651754073
    1127 1121497 1121497: CD8A :: CD8 antigen, alpha polypeptide (p32) 85258 0.254383170803894 −0.508843134467300
    1128 1121511 1121511: BIK :: BCL2-interacting killer (apoptosis-inducing) 155419 −0.211383209660163 0.261057336302683
    1129 1121516 1121516: CD1D :: CD1D antigen, d polypeptide 1799 −0.172683395640843 0.187984153848567
    1130 1121518 1121518: WISP2 :: WNT1 inducible signaling pathway protein 2 194679 0.333528312498693 −0.211973809992181
    1131 1121533 1121533: KLRK1 :: killer cell lectin-like receptor subfamily K, 387787 0.170707791965083 −0.181208812511698
    member 1
    1132 1121542 1121542: CD2 :: CD2 antigen (p50), sheep red blood cell receptor 89476 0.302548346747810 −0.578942684928591
    1133 1121546 1121546: VNN1 :: vanin 1 12114 0.567093184662778 −0.186561364898219
    1134 1121554 1121554: TULP3 :: tubby like protein 3 437046 −0.056650771210584 0.127766542380693
    1135 1121558 1121558: NGFR :: nerve growth factor receptor (TNFR superfamily, 415768 0.195753701211791 −0.227262553501829
    member 16)
    1136 1121559 1121559: LY86 :: lymphocyte antigen 86 184018 −0.155376905904987 0.017075510540213
    1137 1121560 1121560: SPIB :: Spi-B transcription factor (Spi-1/PU.1 related) 437905 −0.289957995332695 0.340996439336590
    1138 1121564 1121564: DRIL1 :: dead ringer-like 1 (Drosophila) 437783 −0.163786854286590 0.046472888560482
    1139 1121572 1121572: LIFR :: leukemia inhibitory factor receptor 446501 0.067083275968437 −0.093351915656365
    1140 1121573 1121573: POU6F1 :: POU domain, class 6, transcription factor 1 2815 0.254499733231130 −0.448893257238791
    1141 1121574 1121574: PRKCM :: protein kinase C, mu 2891 0.439535360328520 −0.205359630656177
    1142 1121584 1121584: CX3CR1 :: chemokine (C—X3—C motif) receptor 1 78913 0.056642673180032 −0.293821160742612
    1143 1121585 1121585: CCNA1 :: cyclin A1 417050 0.132967965511067 −0.090551131678455
    1144 1121587 1121587: PNOC :: prepronociceptin 371809 −0.282566914984081 0.053468907476172
    1145 1121589 1121589: MICA :: MHC class I polypeptide-related sequence A 90598 0.099729225201395 −0.121123956711348
    1146 1121629 1121629: BATF :: basic leucine zipper transcription factor, ATF-like 41691 −0.163961627042657 0.058949273380032
    1147 1121643 1121643: AATK :: apoptosis-associated tyrosine kinase 514575 0.235022117248436 −0.174404212348862
    1148 1121645 1121645: CD84 :: CD84 antigen (leukocyte antigen) 398093 0.461177430829423 −0.431475417777315
    1149 1121650 1121650: GPR64 :: G protein-coupled receptor 64 421137 0.107743443918073 −0.167252293860867
    1150 1121655 1121655: ITGA9 :: integrin, alpha 9 222 −0.003296977642853 −0.030819207041264
    1151 1121680 1121680: SELP :: selectin P (granule membrane protein 140 kDa, 73800 0.185759516369856 −0.431934182574265
    antigen CD62)
    1152 1121689 1121689: B7 :: B7 gene 155586 0.026543717156240 −0.054949053008795
    1153 1121693 1121693: KIAA0450 :: KIAA0450 gene product 170156 0.196900710769728 −0.124900645118200
    1154 1121695 1121695: HCP5 :: HLA complex P5 511759 0.195273337988109 −0.381571715087991
    1155 1121711 1121711: MAPK12 :: mitogen-activated protein kinase 12 432642 −0.187453008816577 0.315641675037325
    1156 1121717 1121717: EPHA4 :: EphA4 73964 −0.095018154579005 0.154787074255348
    1157 1121720 1121720: STAT4 :: signal transducer and activator of transcription 4 80642 0.218763690606469 −0.502198054702293
    1158 1121722 1121722: CD33 :: CD33 antigen (gp67) 83731 0.276204494664653 −0.362551394460205
    1159 1121726 1121726: BLR1 :: Burkitt lymphoma receptor 1, GTP binding protein 113916 −0.189249439889998 0.258207310335521
    (chemokine (C—X—C motif) receptor 5)
    1160 1121739 1121739: ZNF135 :: zinc finger protein 135 (clone pHZ-17) 85863 0.068019769137243 −0.110406382804294
    1161 1121743 1121743: IL3RA :: interleukin 3 receptor, alpha (low affinity) 460433 0.418128176852651 −0.393074905406381
    1162 1121745 1121745: TNFRSF7 :: tumor necrosis factor receptor superfamily, 355307 −0.049393561288948 −0.199094753107042
    member 7
    1163 1121757 1121757: ADRB2 :: adrenergic, beta-2-, receptor, surface 2551 −0.123856836471263 −0.066380767065075
    1164 1121759 1121759: IL13RA2 :: interleukin 13 receptor, alpha 2 336046 0.096030075479116 −0.004610449857012
    1165 1121760 1121760: BMP6 :: bone morphogenetic protein 6 285671 −0.053975160456425 −0.004161001141957
    1166 1121762 1121762: SLAMF1 :: signaling lymphocytic activation molecule family 32970 0.321497941850406 −0.439833541268522
    member 1
    1167 1121767 1121767: PTGIR :: prostaglandin I2 (prostacyclin) receptor (IP) 458324 0.401404596559871 −0.371573726069884
    1168 1121780 1121780: LY64 :: lymphocyte antigen 64 homolog, radioprotective 87205 −0.166019615235407 0.174712903525339
    105 kDa (mouse)
    1169 1121783 1121783: SELE :: selectin E (endothelial adhesion molecule 1) 89546 0.501259144636438 −0.323622231877747
    1170 1121788 1121788: STK23 :: serine/threonine kinase 23 104865 0.096615237663810 −0.087773525250173
    1171 1121792 1121792: TNFRSF10C :: tumor necrosis factor receptor superfamily, 119684 0.015465407320874 −0.016309866660398
    member 10c, decoy without an intracellular domain
    1172 1121793 1121793: KPI2 :: kinase phosphatase inhibitor 2 122708 0.010013315668082 −0.019382995908031
    1173 1121809 1121809: MICB :: MHC class I polypeptide-related sequence B 211580 −0.140424139371804 0.239690343077825
    1174 1121814 1121814: BLK :: B lymphoid tyrosine kinase 389900 −0.311965481456666 0.229138774463185
    1175 1121828 1121828: TLR3 :: toll-like receptor 3 29499 0.342320705636510 −0.203784020011193
    1176 1121834 1121834: PRKY :: protein kinase, Y-linked 183165 0.060119302404676 −0.023441991964129
    1177 1121841 1121841: NTS :: neurotensin 80962 −0.147437100102581 0.037573389779696
    1178 1121844 1121844: IL18 :: interleukin 18 (interferon-gamma-inducing factor) 83077 0.681064645596460 −0.401312565491562
    1179 1121848 1121848: TEC :: tec protein tyrosine kinase 278005 0.007139144026899 0.077786277898995
    1180 1121853 1121853: SPINK2 :: serine protease inhibitor, Kazal type, 2 98243 0.231340981766496 −0.118178578456530
    (acrosin-trypsin inhibitor)
    1181 1121854 1121854: GUCY2C :: guanylate cyclase 2C (heat stable enterotoxin 171470 −0.166410484543226 0.015691903143909
    receptor)
    1182 1121857 1121857: CRLF1 :: cytokine receptor-like factor 1 114948 0.069617938465999 0.053913442948466
    1183 1121869 1121869: CXCL6 :: chemokine (C—X—C motif) ligand 6 (granulocyte 164021 0.144226064872636 −0.051053576857340
    chemotactic protein 2)
    1184 1121870 1121870: CCR7 :: chemokine (C-C motif) receptor 7 1652 −0.067933367028353 −0.306029747322952
    1185 1121874 1121874: IL2RA :: interleukin 2 receptor, alpha 130058 −0.051302661595226 0.043326548605735
    1186 1121887 1121887: MAF :: v-maf musculoaponeurotic fibrosarcoma oncogene 134859 0.291531644291303 −0.423330770602855
    homolog (avian)
    1187 1121918 1121918: FER :: fer (fps/fes related) tyrosine kinase 121558 −0.081261198422925 −0.022672401143613
    (phosphoprotein NCP94)
    1188 1121947 1121947: BMX :: BMX non-receptor tyrosine kinase 27372 −0.045807586018934 −0.042093914097017
    1189 1121953 1121953: KIAA0125 :: KIAA0125 38365 −0.074164934794289 0.093942617186532
    1190 1121956 1121956: PTK6 :: PTK6 protein tyrosine kinase 6 51133 −0.017027139910115 −0.158651344799207
    1191 1121959 1121959: LAG3 :: lymphocyte-activation gene 3 409523 0.193959621692431 −0.437806691232694
    1192 1121963 1121963: ITGA2B :: integrin, alpha 2b (platelet glycoprotein IIb of 411312 −0.279619286050182 0.284911304714724
    IIb/IIIa complex, antigen CD41B)
    1193 1121966 1121966: OCA2 :: oculocutaneous albinism II (pink-eye dilution 82027 −0.126556699537153 −0.138777934994851
    homolog, mouse)
    1194 1121970 1121970: TNFSF7 :: tumor necrosis factor (ligand) superfamily, 99899 −0.052884033648974 0.076289357833760
    member 7
    1195 1121996 1121996: CD28 :: CD28 antigen (Tp44) 1987 0.189150158821898 −0.444718988396679
    1196 1122007 1122007: IL24 :: interleukin 24 411311 −0.043959538709898 −0.038229511247943
    1197 1122009 1122009: CDKL5 :: cyclin-dependent kinase-like 5 50905 −0.110217563326053 0.038629974027743
    1198 1122021 1122021: RAG1 :: recombination activating gene 1 73958 0.003594546430902 −0.000989138304343
    1199 1122036 1122036: IL18R1 :: interleukin 18 receptor 1 159301 0.022775763687888 −0.206454025052186
    1200 1122051 1122051: GPR105 :: G protein-coupled receptor 105 2465 0.059326766092437 −0.376983837880304
    1201 1122053 1122053: TNFRSF17 :: tumor necrosis factor receptor superfamily, 2556 −0.118896791192488 −0.141169001959615
    member 17
    1202 1122065 1122065: IGLL1 :: immunoglobulin lambda-like polypeptide 1 348935 −0.101518631934236 0.138252188755721
    1203 1122075 1122075: FLT3 :: fms-related tyrosine kinase 3 385 −0.023290399924544 −0.134479118790636
    1204 1122087 1122087: IL7 :: interleukin 7 72927 −0.054663149358440 0.163686002792952
    1205 1122091 1122091: TEK :: TEK tyrosine kinase, endothelial (venous 89640 0.405019112365656 −0.229314036859117
    malformations, multiple cutaneous and mucosal)
    1206 1122104 1122104: LMO1 :: LIM domain only 1 (rhombotin 1) 1149 −0.088512856329657 0.001423124698225
    1207 1122112 1122112: TNFRSF8 :: tumor necrosis factor receptor superfamily, 1314 0.306311232422199 −0.257781706042048
    member 8
    1208 1122131 1122131: CHST7 :: carbohydrate (N-acetylglucosamine 6-O) 138155 0.017714188893945 −0.187857053179300
    sulfotransferase 7
    1209 1122139 1122139: ITGA10 :: integrin, alpha 10 158237 −0.126540289117975 −0.102013873270510
    1210 1122156 1122156: ERBB4 :: v-erb-a erythroblastic leukemia viral oncogene 1939 −0.201573406555134 0.167789413767230
    homolog 4 (avian)
    1211 1122165 1122165: CD3G :: CD3G antigen, gamma polypeptide (TiT3 complex) 2259 0.255114685310457 −0.501702664933897
    1212 1122181 1122181: TXK :: TXK tyrosine kinase 29877 0.116717796088994 −0.338924617001779
    1213 1122215 1122215: CCBP2 :: chemokine binding protein 2 24286 −0.095047926225869 0.017068598097254
    1214 1122217 1122217: IL12RB1 :: interleukin 12 receptor, beta 1 223894 −0.057505725481306 0.035649057057820
    1215 1122219 1122219: AMHR2 :: anti-Mullerian hormone receptor, type II 437877 −0.056887826816452 −0.019958969581757
    1216 1122230 1122230: TNFSF9 :: tumor necrosis factor (ligand) superfamily, 1524 −0.225333682313531 0.214293634736012
    member 9
    1217 1122241 1122241: PRKCA :: protein kinase C, alpha 349611 −0.004779534344590 0.129090253603676
    1218 1122253 1122253: TGFBR1 :: transforming growth factor, beta receptor I 28005 0.014232227032144 0.012676202549217
    (activin A receptor type II-like kinase, 53 kDa)
    1219 1122274 1122274: CXCR6 :: chemokine (C—X—C motif) receptor 6 34526 0.291116004542739 −0.538726060188242
    1220 1122275 1122275: LTA :: lymphotoxin alpha (TNF superfamily, member 1) 36 0.272859492127863 −0.052120311047222
    1221 1122277 1122277: CCR2 :: chemokine (C-C motif) receptor 2 511794 0.312042067191461 −0.414949503001742
    1222 1122281 1122281: CCR6 :: chemokine (C-C motif) receptor 6 46468 −0.003994610054083 −0.285880226053799
    1223 1122284 1122284: CCL25 :: chemokine (C-C motif) ligand 25 310511 −0.011468124459718 0.021672293312355
    1224 1122288 1122288: IL12RB2 :: interleukin 12 receptor, beta 2 413608 0.126082647687914 −0.226273945847826
    1225 1122292 1122292: IL8RB :: interleukin 8 receptor, beta 846 −0.024711905520565 −0.102623869064591
    1226 1122304 1122304: KITLG :: KIT ligand 1048 −0.055609736205835 0.138263983925332
    1227 1122327 1122327: ERN1 :: ER to nucleus signalling 1 137575 −0.081788789340055 0.000256455518645
    1228 1122335 1122335: CDKL2 :: cyclin-dependent kinase-like 2 143241 −0.064687268142039 −0.099486553801662
    (CDC2-related kinase)
    1229 1122344 1122344: IL8RA :: interleukin 8 receptor, alpha 194778 0.010181353539432 −0.043034622453406
    1230 1122353 1122353: EMR1 :: egf-like module containing, mucin-like, hormone 2375 0.070191511848735 −0.358463771479546
    receptor-like 1
    1231 1122380 1122380: IL12A :: interleukin 12A (natural killer cell stimulatory 673 −0.156980730012675 0.067544361254343
    factor 1, cytotoxic lymphocyte maturation factor 1, p35)
    1232 1122382 1122382: HMMR :: hyaluronan-mediated motility receptor (RHAMM) 72550 −0.364008235773999 0.783745372336510
    1233 1122388 1122388: TLX1 :: T-cell leukemia, homeobox 1 89583 −0.006028747857682 0.090819031432347
    1234 1122394 1122394: CDK3 :: cyclin-dependent kinase 3 100009 −0.109434076904651 0.005235741268251
    1235 1122400 1122400: TERT :: telomerase reverse transcriptase 439911 −0.305125651996366 0.360989824065773
    1236 1122412 1122412: TNFSF8 :: tumor necrosis factor (ligand) superfamily, 177136 −0.173470362237192 0.039366962226564
    member 8
    1237 1122420 1122420: PRKACG :: protein kinase, cAMP-dependent, catalytic, 158029 −0.042291694825976 0.107568347535975
    gamma
    1238 1122428 1122428: UGT2B17 :: UDP glycosyltransferase 2 family, 183596 −0.009708775277058 −0.154853580284755
    polypeptide B17
    1239 1122449 1122449: CD209 :: CD209 antigen 278694 −0.054065050435346 −0.148476591045507
    1240 1122471 1122471: PHKG1 :: phosphorylase kinase, gamma 1 (muscle) 512612 0.079932856062166 −0.081039280982416
    1241 1122491 1122491: CCL16 :: chemokine (C-C motif) ligand 16 10458 −0.182443367350429 0.080347048721680
    1242 1122537 1122537: IL10 :: interleukin 10 193717 0.084051369998383 −0.014477195723495
    1243 1122541 1122541: CSF3 :: colony stimulating factor 3 (granulocyte) 2233 0.023378070359723 −0.012578972648323
    1244 1122544 1122544: TLR6 :: toll-like receptor 6 366986 −0.034908792550942 −0.117727856389484
    1245 1122581 1122581: PRKG2 :: protein kinase, cGMP-dependent, type II 41749 0.032701567417012 0.012446649249384
    1246 1122596 1122596: CCL1 :: chemokine (C-C motif) ligand 1 72918 0.016785310093019 −0.118957054913180
    1247 1122599 1122599: IL4 :: interleukin 4 73917 0.018527418005221 −0.024997209419818
    1248 1122602 1122602: MPL :: myeloproliferative leukemia virus oncogene 84171 −0.028592483197097 0.035730086206858
    1249 1122609 1122609: CHRNA6 :: cholinergic receptor, nicotinic, alpha 103128 0.140757431162138 −0.089510942877138
    polypeptide 6
    1250 1122610 1122610: ROS1 :: v-ros UR2 sarcoma virus oncogene 1041 0.052118846272900 −0.039273113315543
    homolog 1 (avian)
    1251 1122640 1122640: PDCD1 :: programmed cell death 1 158297 0.037884799709331 −0.335541082139966
    1252 1122645 1122645: TNFRSF13B :: tumor necrosis factor receptor superfamily, 158341 −0.357072434096211 0.193042174649931
    member 13B
    1253 1122664 1122664: CXCR3 :: chemokine (C—X—C motif) receptor 3 198252 0.247485780222157 −0.455289533280340
    1254 1122680 1122680: PRKAA2 :: protein kinase, AMP-activated, alpha 2 catalytic 256067 0.129427414307946 −0.021680077911729
    subunit
    1255 1122710 1122710: CDKL1 :: cyclin-dependent kinase-like 1 (CDC2-related 380788 −0.130816816182024 0.037546570109463
    kinase)
    1256 1122738 1122738: CD160 :: CD160 antigen 81743 −0.080492304819797 −0.166670719053082
    1257 1122740 1122740: IL13 :: interleukin 13 845 −0.045698316016691 0.035475880600793
    1258 1122743 1122743: IL2 :: interleukin 2 89679 −0.018591226450345 −0.082394388827525
    1259 1122744 1122744: CXCL3 :: chemokine (C—X—C motif) ligand 3 89690 0.201982112102107 −0.162220923472979
    1260 1122749 1122749: CCL22 :: chemokine (C-C motif) ligand 22 97203 0.126129955425322 −0.113302826242635
    1261 1122763 1122763: GUCY2D :: guanylate cyclase 2D, membrane (retina-specific) 309958 0.092659149259446 −0.222285418267571
    1262 1122767 1122767: TNFSF5 :: tumor necrosis factor (ligand) superfamily, 652 0.094318123549143 −0.250910889088908
    member 5 (hyper-IgM syndrome)
    1263 1122772 1122772: CCL17 :: chemokine (C-C motif) ligand 17 66742 0.224016681721616 −0.157484933905442
    1264 1122773 1122773: IL12B :: interleukin 12B (natural killer cell stimulatory 674 0.157191653410742 −0.031305411933949
    factor 2, cytotoxic lymphocyte maturation factor 2, p40)
    1265 1122774 1122774: IL5RA :: interleukin 5 receptor, alpha 68876 0.033919120198367 0.031505076254719
    1266 1122775 1122775: IL3 :: interleukin 3 (colony-stimulating factor, multiple) 694 0.027509333831645 0.004526584546124
    1267 1122776 1122776: TNFSF14 :: tumor necrosis factor (ligand) superfamily, 129708 0.086682929814505 −0.077782141454216
    member 14
    1268 1122796 1122796: IL5 :: interleukin 5 (colony-stimulating factor, eosinophil) 2247 0.031894751519528 0.038555120526004
    1269 1122824 1122824: IL1RL2 :: interleukin 1 receptor-like 2 416814 0.150407278683836 −0.109242280419714
    1270 1122834 1122834: CCR8 :: chemokine (C-C motif) receptor 8 113222 −0.076673872782458 −0.054598693128587
    1271 1122863 1122863: IL9 :: interleukin 9 960 0.063436658685755 −0.069964371344722
    1272 1122864 1122864: TTN :: titin 434384 −0.079878461568367 0.057803856684836
    1273 1122865 1122865: IL1A :: interleukin 1, alpha 1722 −0.053194597179340 0.097988885553944
    1274 1122914 1122914: CCR3 :: chemokine (C-C motif) receptor 3 506190 0.067137799577373 −0.079789679856537
    1275 1122939 1122939: CCR4 :: chemokine (C-C motif) receptor 4 184926 0.000316877107091 −0.040959986051264
    1276 1122956 1122956: LGALS2 :: lectin, galactoside-binding, soluble, 2 (galectin 2) 113987 0.418472381199476 −0.449328556890785
    1277 1122983 1122983: TLX3 :: T-cell leukemia, homeobox 3 249125 −0.003266906586252 −0.023843091659097
    1278 1122994 1122994: GPR15 :: G protein-coupled receptor 15 159900 −0.062091251933203 −0.043311935732794
    1279 1123026 1123026: SCN10A :: sodium channel, voltage-gated, type X, alpha 250443 −0.116973597586132 0.070503156564898
    1280 1123038 1123038: ACTN1 :: actinin, alpha 1 119000 0.873550797366042 −0.478675322021290
    1281 1123039 1123039: P5 :: protein disulfide isomerase-related protein 212102 −0.033833903377211 0.140785743381923
    1282 1123052 1123052: PRDX1 :: peroxiredoxin 1 180909 0.191988590052824 0.162925830590233
    1283 1123053 1123053: CAPN2 :: calpain 2, (m/II) large subunit 350899 0.421280597945986 −0.436423248559518
    1284 1123055 1123055: TFRC :: transferrin receptor (p90, CD71) 185726 0.040046865678309 0.144813077262144
    1285 1123086 1123086: CSNK1D :: casein kinase 1, delta 378918 −0.155933500932564 −0.190171534622886
    1286 1123105 1123105: PTK2 :: PTK2 protein tyrosine kinase 2 434281 0.288913388096928 −0.065583389930882
    1287 1123108 1123108: POLE3 :: polymerase (DNA directed), epsilon 3 (p17 subunit) 108112 −0.436072096527712 0.682902758497920
    1288 1123127 1123127: HLA-DRA :: major histocompatibility complex, class II, 409805 0.047143225726272 −0.242770437918495
    DR alpha
    1289 1123148 1123148: TGFBR2 :: transforming growth factor, beta receptor II 82028 0.010273158752569 −0.246551848934111
    (70/80 kDa)
    1290 1123160 1123160: PECAM1 :: platelet/endothelial cell adhesion molecule (CD31 78146 0.369552095411465 −0.455742171741395
    antigen)
    1291 1123163 1123163: STAT3 :: signal transducer and activator of transcription 3 421342 0.088647677138997 −0.076284629745413
    (acute-phase response factor)
    1292 1123188 1123188: RAB5A :: RAB5A, member RAS oncogene family 73957 0.023479248710834 −0.110193635053030
    1293 1123192 1123192: IFRD2 :: interferon-related developmental regulator 2 315177 −0.486021348173979 0.488527458940548
    1294 1123193 1123193: CTGF :: connective tissue growth factor 410037 0.729609445971057 −0.281419391890177
    1295 1123198 1123198: CDKN1B :: cyclin-dependent kinase inhibitor 1B (p27, Kip1) 238990 0.042312425837938 −0.254204935247715
    1296 1123213 1123213: TIP-1 :: Tax interaction protein 1 12956 0.478214019444825 −0.210865933337574
    1297 1123223 1123223: AGR2 :: anterior gradient 2 homolog (Xenopus laevis) 226391 0.144465715233955 −0.064593480852986
    1298 1123231 1123231: FOS :: v-fos FBJ murine osteosarcoma viral oncogene 25647 0.457477092929620 −0.327994685230221
    homolog
    1299 1123233 1123233: PIM1 :: pim-1 oncogene 81170 −0.260781292717673 0.122887357920644
    1300 1123235 1123235: C6orf11 :: chromosome 6 open reading frame 11 436930 −0.301325588310411 0.312607703475414
    1301 1123250 1123250: C2F :: C2f protein 135643 −0.408607477799746 0.542558649958536
    1302 1123255 1123255: NFKB1 :: nuclear factor of kappa light polypeptide gene 160557 −0.247639376875525 0.307813059694491
    enhancer in B-cells 1 (p105)
    1303 1123278 1123278: TNFRSF10B :: tumor necrosis factor receptor superfamily, 51233 0.231916404010982 −0.133446996009752
    member 10b
    1304 1123286 1123286: BCL2L2 :: BCL2-like 2 410026 0.430813129995590 −0.256934797251460
    1305 1123289 1123289: POLR1C :: polymerase (RNA) I polypeptide C, 30 kDa 5409 −0.439470276015570 0.558476803814871
    1306 1123293 1123293: ULK1 :: unc-51-like kinase 1 (C. elegans) 47061 0.234598147527924 −0.243014710846460
    1307 1123298 1123298: SIAH2 :: seven in absentia homolog 2 (Drosophila) 20191 −0.020735974007859 0.251511790730967
    1308 1123304 1123304: TNFRSF14 :: tumor necrosis factor receptor superfamily, 279899 0.406281787477635 −0.640800528626002
    member 14 (herpesvirus entry mediator)
    1309 1123308 1123308: BAD :: BCL2-antagonist of cell death 76366 −0.055804103966625 0.200577209644432
    1310 1123310 1123310: EPHX2 :: epoxide hydrolase 2, cytoplasmic 212088 0.032733558863813 −0.191468518846761
    1311 1123317 1123317: TM4SF1 :: transmembrane 4 superfamily member 1 351316 0.511955936150185 −0.296195607797757
    1312 1123321 1123321: ENPP2 :: ectonucleotide pyrophosphatase/phosphodiesterase 2 23719 0.354323804583203 −0.253537585629660
    (autotaxin)
    1313 1123331 1123331: GRB10 :: growth factor receptor-bound protein 10 512118 0.546048470195960 −0.318504437702318
    1314 1123346 1123346: SERPINA3 :: serine (or cysteine) proteinase inhibitor, 76353 0.043287278241036 0.026601557579208
    clade A (alpha-1 antiproteinase, antitrypsin), member 3
    1315 1123358 1123358: AURKB :: aurora kinase B 442658 −0.383920119898266 0.752032680493908
    1316 1123369 1123369: SNRK :: SNF-1 related kinase 79025 0.063554265111443 −0.312500317456464
    1317 1123372 1123372: RBPMS :: RNA binding protein with multiple splicing 195825 0.729190743697357 −0.416042636778450
    1318 1123376 1123376: RARRES2 :: retinoic acid receptor responder (tazarotene 37682 0.767753207447146 −0.419368115432137
    induced) 2
    1319 1123399 1123399: IGF1 :: insulin-like growth factor 1 (somatomedin C) 308053 0.351339548125761 −0.181596238406175
    1320 1123401 1123401: NDN :: necdin homolog (mouse) 50130 0.666813744865187 −0.449821627439369
    1321 1123413 1123413: IL10RB :: interleukin 10 receptor, beta 418291 0.143751576129052 −0.265149372827460
    1322 1123419 1123419: BMP7 :: bone morphogenetic protein 7 (osteogenic protein 1) 170195 −0.025788274570143 0.099776284015714
    1323 1123429 1123429: CD74 :: CD74 antigen (invariant polypeptide of major 446471 −0.002859916045464 −0.296446042702963
    histocompatibility complex, class II antigen-associated)
    1324 1123430 1123430: STK16 :: serine/threonine kinase 16 153003 −0.161361543731864 0.064323356701808
    1325 1123437 1123437: NFKB2 :: nuclear factor of kappa light polypeptide gene 73090 0.219171220578543 −0.215739729198764
    enhancer in B-cells 2 (p49/p100)
    1326 1123439 1123439: BUB1 :: BUB1 budding uninhibited by benzimidazoles 1 287472 −0.257755664849282 0.734307550843963
    homolog (yeast)
    1327 1123455 1123455: CBLB :: Cas-Br-M (murine) ecotropic retroviral transforming 436986 −0.033290616456071 −0.205794640235363
    sequence b
    1328 1123457 1123457: RIN2 :: Ras and Rab interactor 2 446304 0.795227551186921 −0.522963551553488
    1329 1123459 1123459: CXCL12 :: chemokine (C—X—C motif) ligand 12 (stromal 436042 0.338116509418455 −0.536175354841238
    cell-derived factor 1)
    1330 1123470 1123470: M96 :: likely ortholog of mouse metal response element 31016 −0.246647928566614 0.509698649157703
    binding transcription factor 2
    1331 1123476 1123476: SLC35D1 :: solute carrier family 35 (UDP-glucuronic 82635 0.038691099915535 0.137047545122540
    acid/UDP-N-acetylgalactosamine dual transporter), member D1
    1332 1123479 1123479: CSF1 :: colony stimulating factor 1 (macrophage) 173894 0.565439363613831 −0.571152588046333
    1333 1123490 1123490: CLECSF2 :: C-type (calcium dependent, 85201 0.437423695658292 −0.418715249984207
    carbohydrate-recognition domain) lectin, superfamily member 2
    (activation-induced)
    1334 1123497 1123497: TGFB3 :: transforming growth factor, beta 3 2025 0.419181791755442 −0.341070014629490
    1335 1123502 1123502: KIAA0922 :: KIAA0922 protein 511944 −0.430991697827225 0.463134135573600
    1336 1123507 1123507: BTN3A1 :: butyrophilin, subfamily 3, member A1 284283 0.198254555831932 −0.590128827200630
    1337 1123529 1123529: PTCH :: patched homolog (Drosophila) 159526 −0.162582198261289 0.118247234101131
    1338 1123535 1123535: C6orf32 :: chromosome 6 open reading frame 32 389488 −0.248332319157757 0.033447287747404
    1339 1123552 1123552: SELPLG :: selectin P ligand 423077 0.480246751583851 −0.619068427619529
    1340 1123566 1123566: C3AR1 :: complement component 3a receptor 1 155935 0.371658703605566 −0.442232534412039
    1341 1123573 1123573: CCL18 :: chemokine (C-C motif) ligand 18 (pulmonary and 16530 −0.014202367476697 −0.100068061738832
    activation-regulated)
    1342 1123581 1123581: RIPK1 :: receptor (TNFRSF)-interacting serine-threonine 390758 0.136323407164192 −0.285283218731897
    kinase 1
    1343 1123584 1123584: VEGFC :: vascular endothelial growth factor C 79141 0.472324986740103 −0.294475802861250
    1344 1123586 1123586: KCNMB1 :: potassium large conductance calcium-activated 93841 0.508193311461163 −0.344403736032782
    channel, subfamily M, beta member 1
    1345 1123587 1123587: NCF2 :: neutrophil cytosolic factor 2 (65 kDa, chronic 949 0.283365445260573 −0.264421095224310
    granulomatous disease, autosomal 2)
    1346 1123608 1123608: MALT1 :: mucosa associated lymphoid tissue lymphoma 180566 0.047487079344585 −0.196154131449671
    translocation gene 1
    1347 1123611 1123611: INDO :: indoleamine- pyrrole 2,3 dioxygenase 840 0.253222128158468 −0.456068797135009
    1348 1123613 1123613: CD3Z :: CD3Z antigen, zeta polypeptide (TiT3 complex) 97087 0.153062526309775 −0.337757592132146
    1349 1123614 1123614: PRKCQ :: protein kinase C, theta 408049 0.305157145865210 −0.562196305322430
    1350 1123622 1123622: EPAC :: Rap1 guanine-nucleotide-exchange factor 8578 0.023864373661857 −0.205096809629451
    directly activated by cAMP
    1351 1123628 1123628: MAPK13 :: mitogen-activated protein kinase 13 178695 0.033235172641225 −0.074571795620075
    1352 1123634 1123634: CCL19 :: chemokine (C-C motif) ligand 19 50002 0.237018077209330 −0.370272180731036
    1353 1123635 1123635: SIAT8A :: sialyltransferase 8A (alpha-N- 408614 0.199110330196979 −0.415743690175678
    acetylneuraminate: alpha-2,8-sialyltransferase, GD3 synthase)
    1354 1123643 1123643: MAGOH :: mago-nashi homolog, proliferation-associated 421576 −0.355879676099144 0.581734359749056
    (Drosophila)
    1355 1123663 1123663: CCL11 :: chemokine (C-C motif) ligand 11 54460 0.264138545851733 −0.204563118558087
    1356 1123671 1123671: HIPK3 :: homeodomain interacting protein kinase 3 30148 0.047603483230918 0.055945015733371
    1357 1123672 1123672: LILRB4 :: leukocyte immunoglobulin-like receptor, 67846 0.478261377044532 −0.316050786052444
    subfamily B (with TM and ITIM domains), member 4
    1358 1123679 1123679: CXCL11 :: chemokine (C—X—C motif) ligand 11 103982 0.103429322264231 −0.363739751119532
    1359 1123680 1123680: GZMB :: granzyme B (granzyme 2, cytotoxic T-lymphocyte- 1051 0.089403932441954 −0.206108503310258
    associated serine esterase 1)
    1360 1123682 1123682: TLR5 :: toll-like receptor 5 114408 0.339045664045358 −0.420163322335381
    1361 1123690 1123690: TLR1 :: toll-like receptor 1 111805 0.315917942895492 −0.331871994933504
    1362 1123694 1123694: ITGAX :: integrin, alpha X (antigen CD11C (p150), alpha 385521 0.624065221290532 −0.401652202104813
    polypeptide)
    1363 1123731 1123731: RGS13 :: regulator of G-protein signalling 13 17165 0.094370061595793 0.059059084280978
    1364 1123744 1123744: GPR18 :: G protein-coupled receptor 18 88269 −0.051853832062774 −0.095369670056525
    1365 1123760 1123760: ILT7 :: leukocyte immunoglobulin-like receptor, subfamily A 406708 −0.202312173039078 −0.048154927899969
    (without TM domain), member 4
    1366 1123762 1123762: FLT4 :: fms-related tyrosine kinase 4 415048 0.007820470422523 0.029361292237663
    1367 1123778 1123778: CAMK4 :: calcium/calmodulin-dependent protein kinase IV 440638 −0.092561842977911 0.158012560576592
    1368 1123780 1123780: IFNG :: interferon, gamma 856 0.123476147166574 −0.362163213194207
    1369 1123814 1123814: ICOS :: inducible T-cell co-stimulator 56247 0.192515826351840 −0.464793820617578
    1370 1123816 1123816: IL1RL1 :: interleukin 1 receptor-like 1 66 0.186852010516034 −0.130615795169223
    1371 1123833 1123833: DNTT :: deoxynucleotidyltransferase, terminal −32 −0.056799193445582 −0.009669825386535
    1372 1123842 1123842: FUT7 :: fucosyltransferase 7 (alpha (1,3) fucosyltransferase) 457 0.137471775731450 −0.222998236604638
    1373 1123847 1123847: BMPR1B :: bone morphogenetic protein receptor, type IB 87223 0.025637318140648 −0.036872289193971
    1374 1123875 1123875: FLT3LG :: fms-related tyrosine kinase 3 ligand 428 0.156345539863462 −0.365585933772951
    1375 1123889 1123889: TNFSF11 :: tumor necrosis factor (ligand) superfamily, 333791 −0.074241864883289 −0.115086529686344
    member 11
    1376 1123890 1123890: TNFRSF10D :: tumor necrosis factor receptor superfamily, 129844 −0.031223526539161 −0.058937352170284
    member 10d, decoy with truncated death domain
    1377 1123892 1123892: CMKLR1 :: chemokine-like receptor 1 159553 0.322809856731336 −0.382060391333891
    1378 1123938 1123938: FPRL1 :: formyl peptide receptor-like 1 99855 0.137586060931396 −0.155416553108998
    1379 1123954 1123954: TNFSF6 :: tumor necrosis factor (ligand) superfamily, 2007 0.182530654744065 −0.397622965632797
    member 6
    1380 1123988 1123988: LAT :: linker for activation of T cells 498997 0.229116696368979 −0.579887127104931
    1381 1124049 1124049: my048 :: my048 protein −1 −0.037955390490940 −0.086367167725680
    1382 1124132 1124132: PRDX2 :: peroxiredoxin 2 432121 −0.125199234865877 0.288816173026307
    1383 1124137 1124137: MGC27165 :: hypothetical protein MGC27165 366 −0.128484811098311 0.100510215963241
    1384 1124176 1124176: COL4A2 :: collagen, type IV, alpha 2 407912 0.536118179940743 −0.067710785250196
    1385 1124177 1124177: PORIMIN :: pro-oncosis receptor inducing membrane 172089 0.018031256600808 0.028546874924655
    injury gene
    1386 1124178 1124178: HSPCA :: heat shock 90 kDa protein 1, alpha 446579 −0.115263936938935 0.214973051423235
    1387 1124187 1124187: MGC5395 :: hypothetical protein MGC5395 378738 0.349346778708932 −0.417635861357430
    1388 1124188 1124188: TOP2B :: topoisomerase (DNA) II beta 180 kDa 282346 −0.195346249007339 0.155878107050520
    1389 1124192 1124192: PRKWNK1 :: protein kinase, lysine deficient 1 275999 0.004140487461706 −0.055577533920845
    1390 1124195 1124195: H3F3B :: H3 histone, family 3B (H3.3B) 180877 0.095080814992035 −0.280306583417667
    1391 1124215 1124215: PNN :: pinin, desmosome associated protein 409965 −0.441382373300142 0.501531516295816
    1392 1124237 1124237: MLL :: myeloid/lymphoid or mixed-lineage leukemia 258855 −0.016966825088812 −0.249537844930093
    (trithorax homolog, Drosophila)
    1393 1124254 1124254: SLC39A14 :: solute carrier family 39 (zinc transporter), 301743 0.321139013957588 0.167246613564032
    member 14
    1394 1124266 1124266: DKFZP564D116 :: DKFZP564D116 protein 438991 −0.280125370200864 0.287120197674624
    1395 1124283 1124283: UNC84B :: unc-84 homolog B (C. elegans) 406612 0.315002331643639 −0.548815227035707
    1396 1124296 1124296: SDC2 :: syndecan 2 (heparan sulfate proteoglycan 1, cell 1501 0.693813172081440 −0.342258189120497
    surface-associated, fibroglycan)
    1397 1124304 1124304: CPNE1 :: copine I 166887 −0.504868086841360 0.680830591678959
    1398 1124316 1124316: ACACA :: acetyl-Coenzyme A carboxylase alpha 449863 −0.181134877886522 0.274185965541523
    1399 1124318 1124318: SERPINE2 :: serine (or cysteine) proteinase inhibitor, clade E 21858 0.370324342365429 −0.211095115024570
    (nexin, plasminogen activator inhibitor type 1), member 2
    1400 1124321 1124321: IL6ST :: interleukin 6 signal transducer (gp130, oncostatin M 71968 0.278059468191875 −0.396320310680725
    receptor)
    1401 1124342 1124342: PPAP2B :: phosphatidic acid phosphatase type 2B 432840 0.745344693498752 −0.321206737384094
    1402 1124357 1124357: C7orf14 :: chromosome 7 open reading frame 14 413636 −0.402085858524422 0.657812900111462
    1403 1124362 1124362: CAMKK2 :: calcium/calmodulin-dependent protein kinase 297343 0.082047941910144 0.012170322660202
    kinase 2, beta
    1404 1124365 1124365: TNRC15 :: trinucleotide repeat containing 15 334871 −0.146171232833643 0.129612912259863
    1405 1124377 1124377: MAC30 :: hypothetical protein MAC30 199695 −0.473824954763453 0.767955627108751
    1406 1124381 1124381: FNBP1 :: formin binding protein 1 440808 0.019230980336461 −0.207117033691842
    1407 1124384 1124384: HIPK1 :: homeodomain interacting protein kinase 1 12259 0.038569082287500 −0.073989736759850
    1408 1124391 1124391: NEK9 :: NIMA (never in mitosis gene a)-related kinase 9 7200 −0.285215409926676 0.158971093711156
    1409 1124400 1124400: BCL2L1 :: BCL2-like 1 305890 0.023976484721047 −0.056514291309960
    1410 1124411 1124411: FLJ10619 :: hypothetical protein FLJ10619 194737 −0.018902760490884 −0.337181044074577
    1411 1124416 1124416: RBL2 :: retinoblastoma-like 2 (p130) 283604 0.043711845509004 −0.322756914235943
    1412 1124429 1124429: SULF1 :: sulfatase 1 409602 0.756874827644649 −0.200326821232171
    1413 1124438 1124438: CLIPR-59 :: CLIP-170-related protein 7357 0.348844827581408 −0.173908788877715
    1414 1124456 1124456: TCF4 :: transcription factor 4 359289 −0.184783079390691 0.173790437828407
    1415 1124539 1124539: TENC1 :: tensin like C1 domain-containing phosphatase 6147 0.403712878533374 −0.395953899027013
    1416 1124543 1124543: C10orf22 :: chromosome 10 open reading frame 22 99821 −0.016931232646163 −0.133800710298489
    1417 1124549 1124549: MOAP1 :: modulator of apoptosis 1 24719 −0.176013780064857 0.084745406142491
    1418 1124561 1124561: NEK7 :: NIMA (never in mitosis gene a)-related kinase 7 24119 0.122442978195907 −0.209971856127309
    1419 1124563 1124563: WEE1 :: WEE1 homolog (S. pombe) 249441 −0.173056305348263 0.447075281308176
    1420 1124577 1124577: HPCAL1 :: hippocalcin-like 1 3618 0.135165512513168 −0.299780255879962
    1421 1124583 1124583: GDAP1L1 :: ganglioside-induced differentiation-associated 20977 0.367602161929472 −0.305814749065091
    protein 1-like 1
    1422 1124594 1124594: STK38L :: serine/threonine kinase 38 like 184523 0.019320900966301 0.207490282567835
    1423 1124606 1124606: PTPRC :: protein tyrosine phosphatase, receptor type, C 444324 0.045317285693567 −0.221810375999856
    1424 1124610 1124610: IGJ :: immunoglobulin J polypeptide, linker protein for 381568 0.056282104720538 −0.080088230864314
    immunoglobulin alpha and mu polypeptides
    1425 1124613 1124613: AUTS2 :: autism susceptibility candidate 2 296720 0.290104164160183 −0.197864543648102
    1426 1124616 1124616: MRPS31 :: mitochondrial ribosomal protein S31 154655 −0.254775558867050 0.431147918074326
    1427 1124620 1124620: PTPN11 :: protein tyrosine phosphatase, non-receptor type 11 83572 −0.287606650758719 0.434137390616062
    (Noonan syndrome 1)
    1428 1124646 1124646: RAFTLIN :: raft-linking protein 436432 0.219635297170966 −0.099887736967582
    1429 1124655 1124655: LHFPL2 :: lipoma HMGIC fusion partner-like 2 79299 0.364628032686042 −0.274907028091758
    1430 1124658 1124658: KIAA0674 :: KIAA0674 protein 522351 0.289946684284484 −0.325443854542448
    1431 1124666 1124666: ATM :: ataxia telangiectasia mutated (includes 504644 −0.214240439565213 −0.133443390905161
    complementation groups A, C and D)
    1432 1124692 1124692: MFAP4 :: microfibrillar-associated protein 4 296049 0.330287096674728 −0.408382477540657
    1433 1124705 1124705: DMN :: desmuslin 381347 0.311462686240068 −0.392006888364421
    1434 1124712 1124712: ARHGAP19 :: Rho GTPase activating protein 19 80305 −0.446305815524552 0.650257768410998
    1435 1124713 1124713: PIK3R4 :: phosphoinositide-3-kinase, regulatory subunit 4, 306747 −0.340750199021012 0.190039732116352
    p150
    1436 1124723 1124723: RNF3 :: ring finger protein 3 435065 0.226995185267053 −0.232885578590650
    1437 1124733 1124733: LOC221061 :: hypothetical protein LOC221061 66762 0.444250988609368 −0.296397457839185
    1438 1124734 1124734: ZNF238 :: zinc finger protein 238 446677 −0.344114190160318 0.037963727929040
    1439 1124745 1124745: KIAA0056 :: KIAA0056 protein 438550 −0.367377449201276 0.681944184031488
    1440 1124753 1124753: CIT :: citron (rho-interacting, serine/threonine kinase 21) 405932 −0.266684914532091 0.597601592399224
    1441 1124755 1124755: KIAA0367 :: KIAA0367 protein 23311 0.175438520231790 −0.161328615677927
    1442 1124760 1124760: JAM3 :: junctional adhesion molecule 3 419149 0.502500585815783 −0.322402807479759
    1443 1124768 1124768: FUBP3 :: far upstream element (FUSE) binding protein 3 98751 0.043535346616365 0.132673344353371
    1444 1124770 1124770: IGHM :: Homo sapiens transcribed sequence with moderate 439852 −0.264170929427200 0.171558583437037
    similarity to protein sp: P01871 (H. sapiens) MUC_HUMAN Ig MU
    chain C region
    1445 1124782 1124782: NCAM1 :: neural cell adhesion molecule 1 78792 0.067740345913373 −0.116287844761153
    1446 1124786 1124786: nexilin :: likely ortholog of rat F-actin binding protein nexilin 22370 −0.363619385660829 0.232945437352754
    1447 1124798 1124798: NCOA2 :: nuclear receptor coactivator 2 446678 0.236699642816994 −0.309047597110174
    1448 1124800 1124800: MAPKAPK5 :: mitogen-activated protein kinase-activated 413901 −0.193391449305070 0.467024572248984
    protein kinase 5
    1449 1124806 1124806: PIASY :: protein inhibitor of activated STAT protein PIASy 105779 −0.249365264160332 0.182499663961299
    1450 1124820 1124820: CDK11 :: cyclin-dependent kinase (CDC2-like) 11 129836 0.171715198585524 −0.189801012482926
    1451 1124830 1124830: KIAA0962 :: KIAA0962 protein 9059 −0.239108218809974 −0.071631456643250
    1452 1124831 1124831: RPS6KA2 :: ribosomal protein S6 kinase, 90 kDa, 301664 0.542423703800096 −0.359666198197007
    polypeptide 2
    1453 1124833 1124833: CBX7 :: chromobox homolog 7 356416 0.200522108417050 −0.597074769576343
    1454 1124862 1124862: DYRK4 :: dual-specificity tyrosine-(Y)-phosphorylation 439530 −0.185930582424260 0.107350511374489
    regulated kinase 4
    1455 1124864 1124864: KIAA0882 :: KIAA0882 protein 411317 0.230195362925492 −0.120226438072572
    1456 1124875 1124875: KIAA0870 :: KIAA0870 protein 18166 0.381004144174920 −0.317090511411673
    1457 1124889 1124889: BTBD14A :: BTB (POZ) domain containing 14A 244847 0.322548142484688 −0.483195482115568
    1458 1124893 1124893: MARCKS :: myristoylated alanine-rich protein kinase 318603 0.220998638177546 −0.233172073523505
    C substrate
    1459 1124913 1124913: SSA2 :: Sjogren syndrome antigen A2 (60 kDa, 288178 −0.317060278822500 0.353157816804561
    ribonucleoprotein autoantigen SS-A/Ro)
    1460 1124920 1124920: P114-RHO-GEF :: Rho-specific guanine nucleotide 6150 −0.017421135592496 −0.142182975239113
    exchange factor p114
    1461 1124921 1124921: ROCK1 :: Rho-associated, coiled-coil containing protein 306307 −0.219106199756838 0.167252552911467
    kinase 1
    1462 1124922 1124922: KIAA0561 :: KIAA0561 protein 173864 0.154513049267643 −0.226411686845406
    1463 1124941 1124941: DPT :: dermatopontin 80552 0.606288990238186 −0.334437688929020
    1464 1124942 1124942: KIAA1237 :: KIAA1237 protein 433452 0.544385475743196 −0.326311080060450
    1465 1124948 1124948: LOC169611 :: hypothetical protein LOC169611 357004 0.159693541113982 −0.213898050682879
    1466 1124953 1124953: SLC35D2 :: solute carrier family 35, member D2 386278 0.302215615930412 −0.532374546381988
    1467 1124967 1124967: CAMK2A :: calcium/calmodulin-dependent protein 143535 −0.044227814406713 0.135835028117236
    kinase (CaM kinase) II alpha
    1468 1124972 1124972: NEK3 :: NIMA (never in mitosis gene a)-related kinase 3 2236 −0.004668815670307 −0.018473350732855
    1469 1125001 1125001: :: Homo sapiens mRNA; cDNA DKFZp586B211 (from clone 16193 0.309877128137494 −0.394819111003227
    DKFZp586B211)
    1470 1125009 1125009: SEMA5A :: sema domain, seven thrombospondin repeats 27621 0.570335387773131 −0.238333322497496
    (type 1 and type 1-like), transmembrane domain (TM) and short
    cytoplasmic domain, (semaphorin) 5A
    1471 1125010 1125010: GPX6 :: glutathione peroxidase 6 43728 −0.406180476172999 0.329256599051926
    1472 1125013 1125013: TTC9 :: tetratricopeptide repeat domain 9 79170 0.203290284926991 −0.070305427994692
    1473 1125025 1125025: :: Homo sapiens, clone IMAGE: 5402962, mRNA 301094 0.373028589705817 −0.358455467318352
    1474 1125027 1125027: ACVR1B :: activin A receptor, type IB 371974 0.452094421087183 −0.406256554874994
    1475 1125058 1125058: ATP10D :: ATPase, Class V, type 10D 437241 0.239777925038262 −0.208589626023053
    1476 1125079 1125079: MAP3K12 :: mitogen-activated protein kinase kinase 211601 −0.023529974489696 0.097742384028628
    kinase 12
    1477 1125122 1125122: SRC :: v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene 436015 0.325821834875497 −0.281566755677791
    homolog (avian)
    1478 1125124 1125124: VAMP1 :: vesicle-associated membrane protein 1 20021 0.028033847060342 −0.030330298910767
    (synaptobrevin 1)
    1479 1125130 1125130: RIS1 :: Ras-induced senescence 1 35861 0.707291900474651 −0.304594771554232
    1480 1125132 1125132: FEM1C :: fem-1 homolog c (C. elegans) 47367 −0.178267778288773 0.251919721452546
    1481 1125136 1125136: CDKN1C :: cyclin-dependent kinase inhibitor 1C (p57, Kip2) 106070 0.205535321358345 −0.417689553546756
    1482 1125181 1125181: HSPA6 :: heat shock 70 kDa protein 6 (HSP70B′) 3268 0.218052146790839 −0.175456230712095
    1483 1125195 1125195: :: Homo sapiens cDNA FLJ34019 fis, clone FCBBF2002898. 7309 0.062351973383136 −0.242830127018530
    1484 1125231 1125231: MAPRE2 :: microtubule-associated protein, RP/EB family, 446375 −0.258250546492020 0.146207410520459
    member 2
    1485 1125245 1125245: DKFZP564J157 :: DKFZp564J157 protein 132977 −0.084163299925425 0.043797186647820
    1486 1125246 1125246: PRKCI :: protein kinase C, iota 496511 0.149649650776333 −0.029379048720556
    1487 1125249 1125249: CCNE1 :: cyclin E1 244723 −0.378533610256387 0.582611267644762
    1488 1125279 1125279: TRA2A :: transformer-2 alpha 445652 −0.039745460274163 −0.006496641958592
    1489 1125305 1125305: MAGED2 :: melanoma antigen, family D, 2 376719 0.279186046231037 −0.229412259186242
    1490 1125377 1125377: KIAA0298 :: KIAA0298 gene product 196966 0.043538773140655 −0.083535310053914
    1491 1125397 1125397: RABL4 :: RAB, member of RAS oncogene family-like 4 415172 −0.076074155660607 −0.152334780877398
    1492 1125456 1125456: MYBL1 :: v-myb myeloblastosis viral oncogene homolog 300592 0.085358543549403 0.119727077539206
    (avian)-like 1
    1493 1125459 1125459: CPN2 :: carboxypeptidase N, polypeptide 2, 83 kD 288467 0.753834612101326 −0.275359926533248
    1494 1125462 1125462: NKG7 :: natural killer cell group 7 sequence 10306 0.376390754863940 −0.440135617189111
    1495 1125485 1125485: CD6 :: CD6 antigen 436949 0.336912237115247 −0.602384838687388
    1496 1125516 1125516: ZAP70 :: zeta-chain (TCR) associated protein kinase 70 kDa 234569 0.095543492046246 −0.451426018665455
    1497 1125520 1125520: CCL8 :: chemokine (C-C motif) ligand 8 271387 0.121752040709514 −0.288077095465458
    1498 1125527 1125527: MGC39900 :: hypothetical protein MGC39900 422848 −0.180192646407023 0.262739415756805
    1499 1125532 1125532: MYCL1 :: v-myc myelocytomatosis viral oncogene −20 0.466507304726902 −0.557697249345758
    homolog 1, lung carcinoma derived (avian)
    1500 1125546 1125546: PLXDC1 :: plexin domain containing 1 125036 0.495153683434132 −0.378145766567478
    1501 1125593 1125593: MAN1C1 :: mannosidase, alpha, class 1C, member 1 8736 0.401795734231727 −0.364401736769574
    1502 1125634 1125634: ITGA8 :: integrin, alpha 8 171025 0.075527959445201 0.079267924222490
    1503 1125658 1125658: CAMK2G :: calcium/calmodulin-dependent protein 12436 −0.135367047257270 −0.093006589024883
    kinase (CaM kinase) II gamma
    1504 1125685 1125685: STK22B :: serine/threonine kinase 22B (spermiogenesis 103978 0.044261258588761 −0.051415134140489
    associated)
    1505 1125742 1125742: KLRB1 :: killer cell lectin-like receptor subfamily B, 169824 0.079711384000230 −0.301963846541283
    member 1
    1506 1125789 1125789: FPRL2 :: formyl peptide receptor-like 2 511953 0.380389682365687 −0.166148068940340
    1507 1125818 1125818: PAK3 :: p21 (CDKN1A)-activated kinase 3 152663 0.225596497818733 −0.244616982595961
    1508 1125826 1125826: PRF1 :: perforin 1 (pore forming protein) 2200 0.124824075540851 −0.389188823848422
    1509 1125852 1125852: ITGA1 :: integrin, alpha 1 439320 0.180842213274704 −0.117040332953727
    1510 1125854 1125854: KIAA0472 :: KIAA0472 protein 6874 0.110910134647931 −0.172998818690132
    1511 1125872 1125872: MGC14376 :: hypothetical protein MGC14376 417157 0.612329640905422 −0.552935361435317
    1512 1125901 1125901: KIAA1069 :: KIAA1069 protein 193143 −0.056011672384808 0.098707635358308
    1513 1125916 1125916: :: Homo sapiens mRNA, chromosome 1 specific transcript 497770 −0.163266668946423 0.152187955657425
    KIAA0507.
    1514 1125917 1125917: CLCN4 :: chloride channel 4 417091 −0.081086279636081 −0.031095539270792
    1515 1125919 1125919: G2 :: G2 protein 432369 0.118135844564772 −0.183475617606038
    1516 1125921 1125921: :: Homo sapiens immunoglobulin kappa light chain 512124 0.054181904837014 −0.063477080905441
    VKJ region mRNA, partial cds
    1517 1125927 1125927: IRLB :: c-myc promoter-binding protein 511742 0.007967940915944 0.004344525393029
    1518 1125928 1125928: SUSP1 :: SUMO-1-specific protease 435628 0.126140052656316 −0.187357956669395
    1519 1126047 1126047: MAP3K9 :: mitogen-activated protein kinase kinase kinase 9 437214 −0.123477928740905 0.090270515939190
    1520 1126081 1126081: GRSF1 :: G-rich RNA sequence binding factor 1 309763 −0.195427410459479 0.297879353203236
    1521 1126131 1126131: RAG2 :: recombination activating gene 2 159376 0.018198564132967 0.095689042169220
    1522 1126148 1126148: FLJ36166 :: hypothetical protein FLJ36166 408264 −0.341178035851254 0.550186976150584
    1523 1126293 1126293: TNFRSF5 :: tumor necrosis factor receptor superfamily, 504816 0.123994547059363 −0.098192969696021
    member 5
    1524 1126387 1126387: MAP2K3 :: mitogen-activated protein kinase kinase 3 180533 0.157473211343872 −0.097765784491014
    1525 1126408 1126408: :: Homo sapiens mRNA; cDNA DKFZp586O1318 22689 −0.068959872372587 0.053238627545519
    (from clone DKFZp586O1318)
    1526 1126540 1126540: KIAA1659 :: KIAA1659 protein 474916 0.081108591309987 −0.038577312232724
    1527 1126554 1126554: LOC91752 :: similar to C630007C17Rik protein 159528 −0.268188912986088 0.246488536495623
    1528 1126559 1126559: INSRR :: insulin receptor-related receptor 248138 −0.098379843482530 0.105773648371041
    1529 1126858 1126858: ITGB3 :: integrin, beta 3 (platelet glycoprotein IIIa, 87149 0.042983325871373 −0.144497681552225
    antigen CD61)
    1530 1126892 1126892: ITGA7 :: integrin, alpha 7 74369 0.083341738800239 −0.203924509390271
    1531 1127214 1127214: EPHA5 :: EphA5 201920 −0.013824470163245 −0.036690220251078
    1532 1127290 1127290: :: Homo sapiens ribosomal protein S4-like (RPS4L), mRNA −48 −0.144124961156077 0.225161668972163
    1533 1127294 1127294: CXCR4 :: chemokine (C—X—C motif) receptor 4 421986 −0.089364882672779 −0.133650582979350
    1534 1127371 1127371: TIA1 :: TIA1 cytotoxic granule-associated RNA 444689 −0.170709900312428 −0.069039973369378
    binding protein
    1535 1127567 1127567: FLJ20013 :: hypothetical protein FLJ20013 −29 −0.192452771538394 0.083618644652907
    1536 1127576 1127576: :: Homo sapiens, clone IMAGE: 4794941, mRNA 172998 0.025947000616036 −0.064411420957178
    1537 1127720 1127720: NRBP :: nuclear receptor binding protein 272736 0.242411931589308 −0.319823036043122
    1538 1127742 1127742: GK001 :: GK001 protein 8207 −0.175524415712497 0.253654275070550
    1539 1127744 1127744: ARPC4 :: actin related protein 2/3 complex, subunit 4, 20 kDa 323342 0.037191497103242 −0.033346100698264
    1540 1127756 1127756: NS :: nucleostemin 313544 −0.515885407863687 0.598986978423638
    1541 1127761 1127761: PIAS1 :: protein inhibitor of activated STAT, 1 75251 0.042686201903289 −0.222289998859397
    1542 1127775 1127775: EPS15 :: epidermal growth factor receptor pathway 79095 0.189507964126997 −0.127894991253663
    substrate 15
    1543 1127805 1127805: CKLFSF6 :: chemokine-like factor super family 6 380627 0.228996715729709 −0.226964695189832
    1544 1127807 1127807: NOSIP :: nitric oxide synthase interacting protein 7236 −0.247563970229520 0.168975022386913
    1545 1127813 1127813: NOLA3 :: nucleolar protein family A, member 3 14317 −0.267329642981471 0.382544204532760
    (H/ACA small nucleolar RNPs)
    1546 1127822 1127822: SEPX1 :: selenoprotein X, 1 279623 −0.043578471725612 −0.020427563338161
    1547 1127833 1127833: MRPS2 :: mitochondrial ribosomal protein S2 382044 −0.470025507537828 0.585205355806807
    1548 1127838 1127838: SE20-4 :: cutaneous T-cell lymphoma-associated tumor 136164 −0.103258781815064 −0.031095347592986
    antigen se20-4
    1549 1127849 1127849: SNN :: stannin 76691 0.021266526827127 −0.236719002607138
    1550 1127864 1127864: SLC12A7 :: solute carrier family 12 (potassium/chloride 172613 0.368860530480438 −0.359243502019673
    transporters), member 7
    1551 1127873 1127873: C20orf4 :: chromosome 20 open reading frame 4 11314 −0.275330975017113 0.241185315693476
    1552 1127885 1127885: TMEM2 :: transmembrane protein 2 160417 0.268288787080805 −0.265983709098421
    1553 1127901 1127901: C20orf97 :: chromosome 20 open reading frame 97 344378 −0.391732683018817 0.394691280966108
    1554 1127931 1127931: FLJ22378 :: hypothetical protein FLJ22378 288284 0.149298653587153 −0.194275386943659
    1555 1127940 1127940: NUBP2 :: nucleotide binding protein 2 (MinD 256549 −0.300885491703953 0.428992853698371
    homolog, E. coli)
    1556 1127943 1127943: C1QA :: complement component 1, q subcomponent, alpha 9641 −0.026333557586648 −0.341150779315542
    polypeptide
    1557 1128042 1128042: SIL1 :: endoplasmic reticulum chaperone SIL1, homolog 297875 0.393325385452913 −0.355463933112278
    of yeast
    1558 1128066 1128066: HTF9C :: Hpall tiny fragments locus 9C 63609 −0.338428568018676 0.192274782223654
    1559 1128070 1128070: RRP46 :: exosome component Rrp46 283741 −0.554229516123466 0.607715184909214
    1560 1128079 1128079: MST4 :: Mst3 and SOK1-related kinase 23643 −0.195204488353103 0.431778599814938
    1561 1128095 1128095: TBK1 :: TANK-binding kinase 1 432466 −0.035307688412218 0.050927269206120
    1562 1128099 1128099: 8D6A :: 8D6 antigen 333427 −0.338346262971788 0.398554942958158
    1563 1128100 1128100: FHOD1 :: formin homology 2 domain containing 1 95231 0.069172504045891 0.055506953252559
    1564 1128106 1128106: C10orf3 :: chromosome 10 open reading frame 3 14559 −0.301849657377729 0.772091150877424
    1565 1128111 1128111: FLJ10948 :: hypothetical protein FLJ10948 170915 0.136309727475261 −0.496737872614298
    1566 1128125 1128125: ABHD4 :: abhydrolase domain containing 4 445665 0.361732950699424 −0.356070410710610
    1567 1128144 1128144: DKFZp761K1423 :: hypothetical protein DKFZp761K1423 236438 0.320671799542360 −0.191688492385100
    1568 1128151 1128151: NRN1 :: neuritin 1 103291 −0.053655137752169 −0.122190847084027
    1569 1128157 1128157: VIP32 :: vasopressin-induced transcript 23918 0.450125317312805 −0.335255101074634
    1570 1128164 1128164: FLJ20534 :: hypothetical protein FLJ20534 44344 −0.136223990395658 0.499752179475021
    1571 1128167 1128167: SLC25A15 :: solute carrier family 25 (mitochondrial carrier; 78457 −0.292180964755755 0.464300618499445
    ornithine transporter) member 15
    1572 1128174 1128174: FZD4 :: frizzled homolog 4 (Drosophila) 19545 0.417791773620202 −0.227574007070855
    1573 1128192 1128192: EIF2AK3 :: eukaryotic translation initiation factor 2-alpha 102506 0.030022657950088 −0.105794931461638
    kinase 3
    1574 1128195 1128195: RAB7L1 :: RAB7, member RAS oncogene family-like 1 115325 −0.071449934839951 0.001712965210567
    1575 1128214 1128214: FLJ13848 :: hypothetical protein FLJ13848 408443 −0.389491187946975 0.393766423852120
    1576 1128223 1128223: FLJ10307 :: hypothetical protein FLJ10307 55024 −0.231713872811175 −0.036428732445300
    1577 1128231 1128231: PRKCH :: protein kinase C, eta 315366 0.291069538767355 −0.571782301191371
    1578 1128248 1128248: FLJ20647 :: hypothetical protein FLJ20647 234149 −0.131530675006671 0.267271954474071
    1579 1128283 1128283: TNFRSF21 :: tumor necrosis factor receptor 159651 0.338287130511519 −0.244101265027556
    superfamily, member21
    1580 1128287 1128287: ASB13 :: ankyrin repeat and SOCS box-containing 13 300063 0.278584506324044 −0.103554299642182
    1581 1128298 1128298: MRPL2 :: mitochondrial ribosomal protein L2 55041 −0.385624463595324 0.416247769862519
    1582 1128311 1128311: RPS6KC1 :: ribosomal protein S6 kinase, 52 kDa, 30352 0.017290660641073 −0.083949026713284
    polypeptide 1
    1583 1128321 1128321: SIGIRR :: single Ig IL-1R-related molecule 433036 0.155437434081317 −0.312639809674620
    1584 1128341 1128341: BRF2 :: BRF2, subunit of RNA polymerase III transcription 274136 −0.202955230211738 0.332040507811259
    initiation factor, BRF1-like
    1585 1128356 1128356: C1RL :: complement component 1, r subcomponent-like 415792 0.680615686054409 −0.570295986072283
    1586 1128360 1128360: SLC35E3 :: solute carrier family 35, member E2 445043 −0.080000685186761 0.123127675676569
    1587 1128377 1128377: PLAC8 :: placenta-specific 8 371003 −0.177981381447672 −0.090435241558140
    1588 1128386 1128386: CD164L1 :: CD164 sialomucin-like 1 195727 0.578953125706333 −0.242872939295295
    1589 1128387 1128387: HIPK2 :: homeodomain interacting protein kinase 2 397465 0.118459663415695 −0.299358008807702
    1590 1128395 1128395: SEMA4C :: sema domain, immunoglobulin domain (Ig), 7188 0.385224538166251 −0.358632797373520
    transmembrane domain (TM) and short cytoplasmic domain,
    (semaphorin) 4C
    1591 1128401 1128401: ChGn :: chondroitin beta1,4 341073 0.528070744382773 −0.289776027652708
    N-acetylgalactosaminyltransferase
    1592 1128418 1128418: CGI-14 :: CGI-14 protein 433499 −0.127373034363878 0.114200478146125
    1593 1128435 1128435: PF20 :: PF20 6783 0.092087102441032 0.063200995954978
    1594 1128439 1128439: FKBP11 :: FK506 binding protein 11, 19 kDa 438695 −0.246180835487664 0.168972167224322
    1595 1128447 1128447: FLJ10287 :: hypothetical protein FLJ10287 40337 −0.367947704342123 0.323692416170365
    1596 1128457 1128457: TOPK :: T-LAK cell-originated protein kinase 104741 −0.286232290714309 0.809770422276984
    1597 1128469 1128469: :: Homo sapiens similar to hypothetical protein FLJ22686 −46 0.317659021852908 −0.443676848604039
    (LOC374825), mRNA
    1598 1128471 1128471: FLJ22555 :: hypothetical protein FLJ22555 3592 −0.214459966486640 0.459159303116971
    1599 1128494 1128494: MDA5 :: melanoma differentiation associated protein-5 389539 0.381564813967180 −0.464350966920936
    1600 1128506 1128506: CRK7 :: CDC2-related protein kinase 7 416108 −0.171991120566355 0.362497043497882
    1601 1128535 1128535: MAP3K6 :: mitogen-activated protein kinase kinase kinase 6 194694 0.409909576040118 −0.416460864199563
    1602 1128536 1128536: DOCK10 :: dedicator of cytokinesis 10 21126 −0.091474581348913 −0.246286876471628
    1603 1128585 1128585: AVEN :: apoptosis, caspase activation inhibitor 63168 −0.185978318974428 0.287881726289107
    1604 1128615 1128615: FLJ10134 :: hypothetical protein FLJ10134 104800 0.750296824306779 −0.281205969297433
    1605 1128626 1128626: EBI3 :: Epstein-Barr virus induced gene 3 501452 0.153228999312480 −0.034410934349004
    1606 1128648 1128648: DPEP2 :: dipeptidase 2 499331 0.129320687206103 −0.345950212590144
    1607 1128653 1128653: PAK6 :: p21(CDKN1A)-activated kinase 6 21420 −0.267089728890750 0.211427597958234
    1608 1128655 1128655: C20orf103 :: chromosome 20 open reading frame 103 22920 −0.036922789176067 −0.017091313081673
    1609 1128660 1128660: C13orf18 :: chromosome 13 open reading frame 18 413071 −0.329977691323448 0.232152112413912
    1610 1128681 1128681: CLC :: cardiotrophin-like cytokine 191548 0.143956240585398 −0.053287848623373
    1611 1128688 1128688: MYOZ1 :: myozenin 1 238756 −0.032274730636254 0.068290273280881
    1612 1128694 1128694: ELL3 :: elongation factor RNA polymerase II-like 3 171466 −0.107780233344866 0.274777673936412
    1613 1128705 1128705: HUNK :: hormonally upregulated Neu-associated kinase 109437 −0.156244532976336 0.084177298832988
    1614 1128710 1128710: NEK11 :: NIMA (never in mitosis gene a)-related kinase 11 159146 −0.014339677064164 −0.057185262323488
    1615 1128713 1128713: KCTD14 :: potassium channel tetramerisation domain 17296 0.153126487439279 −0.305451178240051
    containing 14
    1616 1128733 1128733: CADPS2 :: Ca2+-dependent activator protein for secretion 2 489847 0.517597656273347 −0.367879062028602
    1617 1128738 1128738: MGC2776 :: hypothetical protein MGC2776 335550 −0.441569943886905 0.397227563725956
    1618 1128757 1128757: IRAK4 :: interleukin-1 receptor-associated kinase 4 142295 0.005480770877186 −0.089519474289808
    1619 1128781 1128781: FLJ10116 :: hypothetical protein FLJ10116 79741 0.593995376539243 −0.326248755475982
    1620 1128786 1128786: PTPLA :: protein tyrosine phosphatase-like (proline instead of 114062 −0.173989199888605 0.042407369155574
    catalytic arginine), member a
    1621 1128787 1128787: C7orf10 :: chromosome 7 open reading frame 10 114611 0.066883608916300 0.135633101298342
    1622 1128801 1128801: ZNF435 :: zinc finger protein 435 288539 0.095389848084550 −0.186965157005102
    1623 1128807 1128807: HSA250839 :: gene for serine/threonine protein kinase 58241 0.148179807102335 −0.027164856808638
    1624 1128845 1128845: FLJ20174 :: hypothetical protein FLJ20174 272416 −0.252855787139230 −0.168029598476545
    1625 1128860 1128860: STAG3 :: stromal antigen 3 323634 0.166435463482480 −0.080903410843672
    1626 1128900 1128900: STAG3 :: stromal antigen 3 323634 −0.126310620816102 −0.004486849116136
    1627 1128901 1128901: LATS1 :: LATS, large tumor suppressor, 487239 0.009763439382962 −0.024911702773039
    homolog 1 (Drosophila)
    1628 1128915 1128915: CDKL3 :: cyclin-dependent kinase-like 3 105818 −0.132291718442723 0.219964373254252
    1629 1128965 1128965: FGD6 :: FYVE, RhoGEF and PH domain containing 6 170623 0.109709621274018 0.168419208192988
    1630 1128969 1128969: FLJ10213 :: hypothetical protein FLJ10213 446590 −0.234154512640439 0.026794437866472
    1631 1129024 1129024: GPR86 :: G protein-coupled receptor 86 13040 0.305292619286846 −0.457485905772554
    1632 1129026 1129026: FLJ13984 :: hypothetical protein FLJ13984 135146 −0.309743417499126 −0.013237106043976
    1633 1129043 1129043: ACVR2B :: activin A receptor, type IIB 23994 0.068257334337018 −0.078869667492364
    1634 1129049 1129049: IRAK3 :: interleukin-1 receptor-associated kinase 3 268552 0.295844788432385 −0.096238995458166
    1635 1129059 1129059: IL23A :: interleukin 23, alpha subunit p19 98309 0.110558754830653 −0.172783710046595
    1636 1129061 1129061: IL22RA1 :: interleukin 22 receptor, alpha 1 110915 −0.049741735912372 0.102523209371207
    1637 1129064 1129064: BRDG1 :: BCR downstream signaling 1 121128 −0.052914098023446 0.083226377510035
    1638 1129071 1129071: VPREB3 :: pre-B lymphocyte gene 3 136713 −0.116559035957489 0.155319891626767
    1639 1129085 1129085: C5R1 :: complement component 5 receptor 1 (C5a ligand) 2161 0.431190714150359 −0.091961719019167
    1640 1129103 1129103: TZFP :: testis zinc finger protein 99430 −0.084913089830395 0.006324170944062
    1641 1129120 1129120: TLR7 :: toll-like receptor 7 179152 0.189943623624734 −0.353578222257396
    1642 1129151 1129151: MUC16 :: mucin 16 −21 0.088376628477854 −0.269336853755411
    1643 1129203 1129203: IL17B :: interleukin 17B 110040 −0.004171272880353 −0.001612024722616
    1644 1129223 1129223: GALNT10 :: UDP-N-acetyl-alpha-D- 512728 −0.024712521451973 −0.316144966589372
    galactosamine:polypeptide N-acetylgalactosaminyltransferase 10
    (GalNAc-T10)
    1645 1129228 1129228: MAK :: male germ cell-associated kinase 148496 0.079167291478789 0.015734627365448
    1646 1129232 1129232: CD244 :: CD244 natural killer cell receptor 2B4 157872 0.073453493038786 −0.377710109106282
    1647 1129245 1129245: IL1F9 :: interleukin 1 family, member 9 211238 −0.094915764294385 −0.121817602131821
    1648 1129265 1129265: CCRL1 :: chemokine (C-C motif) receptor-like 1 310512 −0.148880028528658 0.181608150889073
    1649 1129269 1129269: SNFT :: Jun dimerization protein p21SNFT 62919 0.196502835728553 −0.241893188568789
    1650 1129281 1129281: C14orf110 :: chromosome 14 open reading frame 110 395486 −0.027842501648286 0.029163772973386
    1651 1129310 1129310: CARK :: cardiac ankyrin repeat kinase 414091 −0.106755206423672 0.156920333732655
    1652 1129336 1129336: KCNK12 :: potassium channel, subfamily K, member 12 252617 0.256164419250147 −0.076661906553981
    1653 1129419 1129419: GPR2 :: G protein-coupled receptor 2 278446 −0.153560376153935 0.073266711206152
    1654 1129495 1129495: TBX21 :: T-box 21 272409 0.099926962762925 −0.206774112272127
    1655 1129517 1129517: :: FLJ12193 −63 0.268548338773064 −0.234272075916895
    1656 1129535 1129535: RPS6KA6 :: ribosomal protein S6 kinase, 90 kDa, 368153 −0.060691156845818 −0.112486779113327
    polypeptide 6
    1657 1129537 1129537: IL19 :: interleukin 19 71979 0.042032462904672 −0.082637131351126
    1658 1129661 1129661: IL17E :: interleukin 17E 302036 0.015759941561729 −0.147728639632796
    1659 1129681 1129681: TNFSF15 :: tumor necrosis factor (ligand) 241382 0.003868440543706 −0.085807864212777
    superfamily, member 15
    1660 1129694 1129694: IL26 :: interleukin 26 272350 0.014873438384474 −0.150408790090459
    1661 1129743 1129743: DKFZP434A0131 :: DKFZp434A0131 protein 429531 −0.053337181033571 −0.096738574513564
    1662 1129754 1129754: IL21 :: interleukin 21 302014 0.101034557454981 −0.028904887858268
    1663 1129760 1129760: RNASEL :: ribonuclease L (2′,5′-oligoisoadenylate synthetase- 404277 −0.076744614539946 0.041338871532864
    dependent)
    1664 1129812 1129812: CHRNG :: cholinergic receptor, nicotinic, gamma polypeptide 248101 −0.094659546499748 0.198887933475047
    1665 1129821 1129821: MOS :: v-mos Moloney murine sarcoma viral 248146 −0.077862620804062 0.125245212560540
    oncogene homolog
    1666 1129825 1129825: TNFSF18 :: tumor necrosis factor (ligand) 248197 −0.075226623664457 0.081966056961447
    superfamily, member 18
    1667 1129874 1129874: CCL24 :: chemokine (C-C motif) ligand 24 247838 −0.009869595016579 0.024069346953711
    1668 1129879 1129879: XCR1 :: chemokine (C motif) receptor 1 248116 −0.036265621695120 0.105554164155718
    1669 1129887 1129887: B4GALT5 :: UDP-Gal:betaGlcNAc beta 107526 0.380271891913627 −0.303897639472657
    1,4-galactosyltransferase, polypeptide 5
    1670 1129907 1129907: EIF4EBP1 :: eukaryotic translation initiation factor 4E 406408 0.036754064214461 0.115319060732266
    binding protein 1
    1671 1129911 1129911: GRWD1 :: glutamate-rich WD repeat containing 1 400625 −0.439357897736726 0.474210086029623
    1672 1129917 1129917: MARK4 :: MAP/microtubule affinity-regulating kinase 4 118843 −0.170633612286300 −0.010230271789505
    1673 1129923 1129923: TRAF3 :: TNF receptor-associated factor 3 297660 0.028090348976765 −0.086664596169330
    1674 1129943 1129943: ZNF506 :: zinc finger protein 506 512828 −0.101116534668903 −0.220361168950301
    1675 1129967 1129967: C19orf10 :: chromosome 19 open reading frame 10 10927 0.049070512080832 −0.032487526942485
    1676 1129978 1129978: SSH1 :: slingshot 1 60377 0.219169062430177 −0.289189938099277
    1677 1129993 1129993: FLJ14827 :: hypothetical protein FLJ14827 412981 −0.480749758772810 0.554011664313080
    1678 1130007 1130007: NTRK2 :: neurotrophic tyrosine kinase, receptor, type 2 494313 0.120279477549603 −0.243907629075211
    1679 1130030 1130030: LONP :: peroxisomal lon protease 301872 −0.072061292782188 −0.319264601727642
    1680 1130040 1130040: :: Homo sapiens, clone IMAGE: 3626627, mRNA 356460 −0.322229909790390 0.205828937779337
    1681 1130054 1130054: RARRES1 :: retinoic acid receptor responder 82547 0.685839603413505 −0.362689495840938
    (tazarotene induced) 1
    1682 1130072 1130072: T1A-2 :: lung type-I cell membrane-associated glycoprotein 468675 0.818831553703874 −0.294460779566936
    1683 1130078 1130078: CYLD :: cylindromatosis (turban tumor syndrome) 386952 0.183694775256214 −0.419576263991755
    1684 1130088 1130088: PCTK2 :: PCTAIRE protein kinase 2 258536 0.072152820235518 −0.107600969822367
    1685 1130090 1130090: LGN :: LGN protein 278338 0.004272301688512 0.479039312613795
    1686 1130114 1130114: MPHOSPH9 :: M-phase phosphoprotein 9 445084 −0.379537586983120 0.341620894714238
    1687 1130117 1130117: PAX5 :: paired box gene 5 (B-cell lineage specific 22030 −0.246528946838740 0.352341177052491
    activator protein)
    1688 1130121 1130121: HLA-F :: major histocompatibility complex, class I, F 411958 0.377839466682894 −0.570631345032229
    1689 1130155 1130155: CLU :: clusterin (complement lysis inhibitor, 436657 0.161844555045734 −0.283244372504117
    SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate
    message
    2, apolipoprotein J)
    1690 1130168 1130168: CD58 :: CD58 antigen, (lymphocyte function-associated 75626 0.364492432723028 −0.362266715730823
    antigen 3)
    1691 1130169 1130169: WSX1 :: class I cytokine receptor 132781 0.184454748443662 −0.424999376453384
    1692 1130201 1130201: HRBL :: HIV-1 Rev binding protein-like 278502 −0.075697663993041 −0.039821664399179
    1693 1130293 1130293: :: Homo sapiens partial mRNA, clone c4-1c6 292853 −0.155443177799334 0.095843890123974
    1694 1130337 1130337: :: Homo sapiens cDNA FLJ39459 fis, clone PROST2011439. 491069 −0.023896848401736 −0.224046963581455
    1695 1130354 1130354: SFN :: stratifin 184510 0.018070370867865 0.079139608113699
    1696 1130378 1130378: HEY1 :: hairy/enhancer-of-split related with YRPW motif 1 234434 0.395156586940864 −0.286377579116489
    1697 1130387 1130387: C20orf27 :: chromosome 20 open reading frame 27 274422 −0.419033206665522 0.532077072330916
    1698 1130393 1130393: FLJ10357 :: hypothetical protein FLJ10357 22451 0.634166877712643 −0.441880136419289
    1699 1130400 1130400: FRA :: Fos-related antigen 170253 −0.094009668900306 −0.063800779529085
    1700 1130426 1130426: PSMB2 :: proteasome (prosome, macropain) subunit, 432607 −0.206477681739062 0.544052744959488
    beta type, 2
    1701 1130429 1130429: JTB :: jumping translocation breakpoint 6396 −0.414145041883499 0.347678891334252
    1702 1130430 1130430: ILF2 :: interleukin enhancer binding factor 2, 45 kDa 75117 −0.551604865259108 0.730255055075483
    1703 1130433 1130433: U5-200KD :: U5 snRNP-specific protein, 200-KD 246112 −0.366436179521191 0.365690965936921
    1704 1130446 1130446: MGC2749 :: hypothetical protein MGC2749 369785 −0.162045856993512 0.204027835507349
    1705 1130447 1130447: OAZ1 :: ornithine decarboxylase antizyme 1 446427 −0.027334049396156 −0.125481385009298
    1706 1130465 1130465: ANAPC5 :: anaphase promoting complex subunit 5 7101 −0.188040952374909 0.335759442290327
    1707 1130468 1130468: HNRPU :: heterogeneous nuclear ribonucleoprotein U 166463 −0.414228315104379 0.449595813895559
    (scaffold attachment factor A)
    1708 1130472 1130472: TRA1 :: tumor rejection antigen (gp96) 1 192374 −0.058770406781845 0.008454200316347
    1709 1130482 1130482: KIAA0152 :: KIAA0152 gene product 181418 −0.013046088161047 0.140884826685794
    1710 1130483 1130483: CALM3 :: calmodulin 3 (phosphorylase kinase, delta) 334330 0.034506605516631 0.070747117402494
    1711 1130501 1130501: LDHA :: lactate dehydrogenase A 2795 −0.113416716689169 0.557153040616862
    1712 1130509 1130509: SPARC :: secreted protein, acidic, cysteine-rich (osteonectin) 111779 0.837304026622357 −0.223436112872554
    1713 1130518 1130518: HMGB1 :: high-mobility group box 1 434102 −0.304610144944285 0.589052869603598
    1714 1130527 1130527: HSPA9B :: heat shock 70 kDa protein 9B (mortalin-2) 184233 −0.405952252455406 0.580488234077170
    1715 1130533 1130533: LITAF :: lipopolysaccharide-induced TNF factor 76507 0.223648867635184 −0.307782200282530
    1716 1130588 1130588: HNRPK :: heterogeneous nuclear ribonucleoprotein K 307544 −0.404667709940553 0.444695456954984
    1717 1130603 1130603: MCL1 :: myeloid cell leukemia sequence 1 (BCL2-related) 86386 0.116326408892859 −0.411472574543256
    1718 1130618 1130618: GRCC9 :: likely ortholog of mouse gene rich cluster, C9 gene 83848 −0.105851503751508 0.515020841340678
    1719 1130622 1130622: ZNF207 :: zinc finger protein 207 97128 −0.352374085161843 0.668735280109416
    1720 1130624 1130624: SCD :: stearoyl-CoA desaturase (delta-9-desaturase) 119597 0.068466925131898 0.042110137344519
    1721 1130629 1130629: CTSB :: cathepsin B 135226 0.463103175029523 −0.332067792414087
    1722 1130631 1130631: EPRS :: glutamyl-prolyl-tRNA synthetase 171292 −0.242075805489007 0.343011789857582
    1723 1130645 1130645: KIAA1007 :: KIAA1007 protein 279949 −0.508883745098830 0.647834071617021
    1724 1130653 1130653: NOL5A :: nucleolar protein 5A (56 kDa with KKE/D repeat) 376064 −0.491441299595535 0.618358768431825
    1725 1130658 1130658: PGAM1 :: phosphoglycerate mutase 1 (brain) 447492 −0.225449863013289 0.594965205536490
    1726 1130668 1130668: KIAA0992 :: palladin 194431 0.738444323208338 −0.353184585890758
    1727 1130674 1130674: HLA-E :: major histocompatibility complex, class I, E 381008 0.316878271078233 −0.616553306253961
    1728 1130676 1130676: KIAA0992 :: palladin 194431 0.571670265195923 −0.239239604892387
    1729 1130680 1130680: EIF4A2 :: eukaryotic translation initiation factor 4A, 511904 −0.406851760364394 0.031928463084035
    isoform 2
    1730 1130687 1130687: SLC3A2 :: solute carrier family 3 (activators of dibasic 79748 0.005620687941009 0.221535198891908
    and neutral amino acid transport), member 2
    1731 1130704 1130704: CCND2 :: cyclin D2 376071 −0.086227213019376 −0.105185207044404
    1732 1130707 1130707: SSRP1 :: structure specific recognition protein 1 79162 −0.478812788644878 0.723198294147642
    1733 1130712 1130712: ABLIM1 :: actin binding LIM protein 1 442540 0.028989108097744 −0.024740365180999
    1734 1130732 1130732: UBE2V1 :: ubiquitin-conjugating enzyme E2 variant 1 381025 −0.365959820864458 0.273619600177731
    1735 1130735 1130735: TXNIP :: thioredoxin interacting protein 179526 0.147134141082822 −0.423880593075217
    1736 1130744 1130744: IF2 :: translation initiation factor IF2 158688 −0.436040464525393 0.549498651391074
    1737 1130746 1130746: CD99 :: CD99 antigen 283477 0.491775584257276 −0.301267508834440
    1738 1130747 1130747: LDHB :: lactate dehydrogenase B 234489 −0.474279747751518 0.634264298790119
    1739 1130755 1130755: ANP32A :: acidic (leucine-rich) nuclear phosphoprotein 356089 −0.531594087149504 0.564703678975089
    32 family, member A
    1740 1130771 1130771: PSMC2 :: proteasome (prosome, macropain) 26S subunit, 61153 −0.076342918509587 0.303662557781198
    ATPase, 2
    1741 1130799 1130799: PSMA7 :: proteasome (prosome, macropain) subunit, 233952 −0.183548593771997 0.433457258460047
    alpha type, 7
    1742 1130812 1130812: CDH1 :: cadherin 1, type 1, E-cadherin (epithelial) 194657 0.150350262021869 −0.310581185010029
    1743 1130820 1130820: EIF2S1 :: eukaryotic translation initiation factor 2, 151777 −0.248919180836398 0.645496589136077
    subunit 1 alpha, 35 kDa
    1744 1130835 1130835: IGFBP7 :: insulin-like growth factor binding protein 7 435795 0.694869060684746 −0.451635497409526
    1745 1130839 1130839: ARHGDIA :: Rho GDP dissociation inhibitor (GDI) alpha 159161 −0.287041819068728 0.319746037482479
    1746 1130852 1130852: CHD4 :: chromodomain helicase DNA binding protein 4 74441 −0.227607885519199 0.309877252850406
    1747 1130855 1130855: ITPR3 :: inositol 1,4,5-triphosphate receptor, type 3 77515 −0.090037163752447 0.246241985491480
    1748 1130871 1130871: RAD23B :: RAD23 homolog B (S. cerevisiae) 159087 −0.155432198525978 0.354647062606468
    1749 1130879 1130879: ENO1 :: enolase 1, (alpha) 433455 −0.103238523231766 0.472120612291936
    1750 1130882 1130882: BTG2 :: BTG family, member 2 75462 −0.401612459640219 0.215056573193418
    1751 1130888 1130888: RAF1 :: v-raf-1 murine leukemia viral oncogene homolog 1 257266 −0.316699264696602 0.210654762972939
    1752 1130898 1130898: SYPL :: synaptophysin-like protein 80919 −0.020322791403430 0.180749968332613
    1753 1130900 1130900: BGN :: biglycan 821 0.433491624346225 −0.034657560783871
    1754 1130906 1130906: HNRPAB :: heterogeneous nuclear ribonucleoprotein A/B 81361 −0.530041416930423 0.790305469314572
    1755 1130910 1130910: APEH :: N-acylaminoacyl-peptide hydrolase 221589 −0.396613250677159 0.314489748130245
    1756 1130911 1130911: SDC1 :: syndecan 1 82109 0.257574142041331 −0.110610745819271
    1757 1130914 1130914: WSB1 :: SOCS box-containing WD protein SWiP-1 315379 0.152566035413182 −0.130582325128830
    1758 1130922 1130922: ANP32B :: acidic (leucine-rich) nuclear phosphoprotein 459987 −0.268323023580090 0.586480999073766
    32 family, member B
    1759 1130923 1130923: ANP32B :: acidic (leucine-rich) nuclear phosphoprotein 459987 −0.356618082166821 0.545047027556475
    32 family, member B
    1760 1130926 1130926: C5orf13 :: chromosome 5 open reading frame 13 508741 −0.066893451027013 0.226117239200541
    1761 1130936 1130936: STAT6 :: signal transducer and activator of transcription 6, 437475 −0.187297336007257 0.021013107700686
    interleukin-4 induced
    1762 1130942 1130942: GTF3A :: general transcription factor IIIA 445977 −0.468852559402542 0.503393496496502
    1763 1130972 1130972: IGF2R :: insulin-like growth factor 2 receptor 76473 0.214658478470718 −0.361049786465530
    1764 1130977 1130977: ADRBK1 :: adrenergic, beta, receptor kinase 1 83636 −0.099523373504707 0.102662710355176
    1765 1130994 1130994: DPYSL3 :: dihydropyrimidinase-like 3 150358 0.809042808419035 −0.446523381134851
    1766 1131012 1131012: JUN :: v-jun sarcoma virus 17 oncogene homolog (avian) 78465 0.457086129845903 −0.354589691205210
    1767 1131019 1131019: ITGA3 :: integrin, alpha 3 (antigen CD49C, alpha 3 subunit 265829 0.053523581836060 −0.199397777676044
    of VLA-3 receptor)
    1768 1131038 1131038: NFKBIA :: nuclear factor of kappa light polypeptide gene 81328 0.462390024451032 −0.318458395207705
    enhancer in B-cells inhibitor, alpha
    1769 1131068 1131068: FSCN1 :: fascin homolog 1, actin-bundling protein 118400 0.536725531023657 −0.251210253863877
    (Strongylocentrotus purpuratus)
    1770 1131069 1131069: ID2 :: inhibitor of DNA binding 2, dominant negative 180919 0.247341922577442 −0.202808821943620
    helix-loop-helix protein
    1771 1131074 1131074: DCTD :: dCMP deaminase 76894 −0.248202975835252 0.038410672144689
    1772 1131081 1131081: SFPQ :: splicing factor proline/glutamine rich 180610 −0.473453393950819 0.738837614730302
    (polypyrimidine tract binding protein associated)
    1773 1131082 1131082: IRAK1 :: interleukin-1 receptor-associated kinase 1 182018 −0.020262248068331 0.232370997542063
    1774 1131107 1131107: RRAGA :: Ras-related GTP binding A 432330 0.325855382913029 −0.128821612464194
    1775 1131110 1131110: IER3 :: immediate early response 3 76095 0.516595624226035 −0.400848458725700
    1776 1131119 1131119: SCARB2 :: scavenger receptor class B, member 2 323567 0.355068180876334 −0.357222941974828
    1777 1131140 1131140: C14orf92 :: chromosome 14 open reading frame 92 194035 −0.175581522276715 0.264736273192001
    1778 1131149 1131149: EGR1 :: early growth response 1 326035 0.334773228743566 −0.223509421726847
    1779 1131150 1131150: NP :: nucleoside phosphorylase 75514 −0.354544451710958 0.542011939879683
    1780 1131181 1131181: LUM :: lumican 406475 0.892642895727236 −0.356076175533182
    1781 1131197 1131197: KIAA0494 :: KIAA0494 gene product 269902 0.137090820104737 −0.390038678127149
    1782 1131218 1131218: ENG :: endoglin (Osler-Rendu-Weber syndrome 1) 76753 0.656737413741246 −0.520955702540722
    1783 1131219 1131219: SH3BP5 :: SH3-domain binding protein 5 (BTK-associated) 109150 −0.312938579490861 0.164418197287064
    1784 1131246 1131246: CDC25B :: cell division cycle 25B 153752 −0.153291439533977 0.090249162613185
    1785 1131260 1131260: ABCE1 :: ATP-binding cassette, sub-family E (OABP), 12013 −0.388231075478314 0.595908004595403
    member 1
    1786 1131263 1131263: PPP2R5C :: protein phosphatase 2, regulatory 249955 −0.278824832021527 −0.010546616087432
    subunit B (B56), gamma isoform
    1787 1131268 1131268: IL13RA1 :: interleukin 13 receptor, alpha 1 285115 0.603655816737742 −0.426475715000783
    1788 1131274 1131274: CKS1B :: CDC28 protein kinase regulatory subunit 1B 374378 −0.472115050926466 0.804871568180769
    1789 1131290 1131290: DAF :: decay accelerating factor for complement 408864 −0.021713657405561 −0.031992085263801
    (CD55, Cromer blood group system)
    1790 1131321 1131321: EGFR :: epidermal growth factor receptor (erythroblastic 77432 0.260851077631343 −0.225904558910021
    leukemia viral (v-erb-b) oncogene homolog, avian)
    1791 1131325 1131325: CREBL2 :: cAMP responsive element binding protein-like 2 13313 0.554796719681771 −0.648770892709224
    1792 1131336 1131336: ZNF410 :: zinc finger protein 410 405945 −0.192207934621065 0.122792077578381
    1793 1131340 1131340: LTF :: lactotransferrin 437457 0.235576626054540 −0.261846903756942
    1794 1131342 1131342: LANCL1 :: LanC lantibiotic synthetase component C-like 1 13351 −0.017539774281155 0.118963845188131
    (bacterial)
    1795 1131379 1131379: PLTP :: phospholipid transfer protein 439312 0.233879501502951 −0.271204990365974
    1796 1131395 1131395: BRD4 :: bromodomain containing 4 278675 −0.010421483777346 0.015984797307132
    1797 1131401 1131401: CPNE3 :: copine III 14158 0.041142882609723 −0.055081905354774
    1798 1131405 1131405: ABL1 :: v-abl Abelson murine leukemia viral oncogene 446504 −0.221476283909564 0.182435762966943
    homolog 1
    1799 1131407 1131407: ALS2CR3 :: amyotrophic lateral sclerosis 2 (juvenile) 154248 0.338869376678187 −0.439596598652341
    chromosome region, candidate 3
    1800 1131411 1131411: ACTR1B :: ARP1 actin-related protein 1 homolog B, 2477 0.077923077119751 −0.079428496373113
    centractin beta (yeast)
    1801 1131414 1131414: CLK3 :: CDC-like kinase 3 511790 −0.269988760385229 0.082665928562320
    1802 1131450 1131450: SRPK1 :: SFRS protein kinase 1 369358 −0.461499682598341 0.660300221952223
    1803 1131473 1131473: PSMB4 :: proteasome (prosome, macropain) subunit, 89545 −0.520434353958541 0.484814019338330
    beta type, 4
    1804 1131474 1131474: CDK4 :: cyclin-dependent kinase 4 95577 −0.439683564755247 0.779895489372238
    1805 1131490 1131490: CDKN1A :: cyclin-dependent kinase inhibitor 1A (p21, Cip1) 370771 0.385643552030945 −0.301994028596566
    1806 1131497 1131497: CTSH :: cathepsin H 114931 0.330713175489614 −0.355002555291128
    1807 1131503 1131503: SMARCA5 :: SWI/SNF related, matrix associated, 135705 −0.387527664547821 0.543569727624998
    actin dependent regulator of chromatin, subfamily a, member 5
    1808 1131507 1131507: COL1A1 :: collagen, type I, alpha 1 172928 0.748114290829864 −0.207748584834290
    1809 1131531 1131531: MATN2 :: matrilin 2 153647 0.325141676021648 −0.307381647293302
    1810 1131541 1131541: TRAM2 :: translocation associated membrane protein 2 310230 −0.109763921862653 0.121260099038360
    1811 1131561 1131561: COL1A2 :: collagen, type I, alpha 2 232115 0.874692627775946 −0.334576284522396
    1812 1131578 1131578: MYC :: v-myc myelocytomatosis viral oncogene 202453 −0.473650493201987 0.439091538893661
    homolog (avian)
    1813 1131584 1131584: IDS :: iduronate 2-sulfatase (Hunter syndrome) 303154 0.409153834815565 −0.206704914490955
    1814 1131592 1131592: CTSK :: cathepsin K (pycnodysostosis) 83942 0.848850881019183 −0.369116963340649
    1815 1131594 1131594: ERBB3 :: v-erb-b2 erythroblastic leukemia viral oncogene 306251 −0.037028165004209 0.014125470226058
    homolog 3 (avian)
    1816 1131614 1131614: RANBP1 :: RAN binding protein 1 24763 −0.497718394256005 0.861673208863039
    1817 1131636 1131636: SPOCK2 :: sparc/osteonectin, cwcv and kazal-like domains 436193 0.163651135120878 −0.586216415254260
    proteoglycan (testican) 2
    1818 1131637 1131637: MADH4 :: MAD, mothers against decapentaplegic homolog 4 75862 −0.296122555295810 0.254301505485065
    (Drosophila)
    1819 1131640 1131640: DHFR :: dihydrofolate reductase 83765 −0.318925662013329 0.697984260974183
    1820 1131645 1131645: SCYE1 :: small inducible cytokine subfamily E, member 1 105656 −0.408590686241245 0.435284600019574
    (endothelial monocyte-activating)
    1821 1131654 1131654: MYLK :: myosin, light polypeptide kinase 506692 0.651782538418739 −0.499306112068076
    1822 1131663 1131663: MARK3 :: MAP/microtubule affinity-regulating kinase 3 437625 −0.127947033428119 0.128365431201822
    1823 1131687 1131687: TLK1 :: tousled-like kinase 1 369280 −0.479727631283518 0.180410183690407
    1824 1131705 1131705: ICAM1 :: intercellular adhesion molecule 1 (CD54), 386467 0.378982406710592 −0.337971803564004
    human rhinovirus receptor
    1825 1131710 1131710: TNFAIP3 :: tumor necrosis factor, alpha-induced protein 3 211600 0.463815458286967 −0.506090111158935
    1826 1131733 1131733: AXL :: AXL receptor tyrosine kinase 83341 0.378282997894475 −0.403851757655397
    1827 1131737 1131737: STK17A :: serine/threonine kinase 17a (apoptosis-inducing) 9075 0.130652258117317 −0.103978746190248
    1828 1131752 1131752: FOXO1A :: forkhead box O1A (rhabdomyosarcoma) 170133 −0.122578273317010 0.040350502997271
    1829 1131753 1131753: IFNGR1 :: interferon gamma receptor 1 180866 0.618517741082226 −0.417914352213948
    1830 1131755 1131755: LTBP1 :: latent transforming growth factor beta binding 241257 0.502355072705751 −0.139333692684381
    protein 1
    1831 1131757 1131757: LSM4 :: LSM4 homolog, U6 small nuclear RNA associated 76719 −0.338083430713762 0.555861490784508
    (S. cerevisiae)
    1832 1131767 1131767: RFXANK :: regulatory factor X-associated ankyrin-containing 296776 −0.298195363108909 0.396266516850386
    protein
    1833 1131778 1131778: E2-EPF :: ubiquitin carrier protein 396393 −0.444812770066341 0.811955135837133
    1834 1131786 1131786: ITGB2 :: integrin, beta 2 (antigen CD18 (p95), 375957 0.558038370974376 −0.444583848022385
    lymphocyte function-associated antigen 1; macrophage antigen 1
    (mac-1) beta subunit)
    1835 1131806 1131806: DNAJB9 :: DnaJ (Hsp40) homolog, subfamily B, member 9 6790 0.130968076956592 −0.292357967581071
    1836 1131808 1131808: RALBP1 :: ralA binding protein 1 75447 −0.431671598650297 0.449909231902008
    1837 1131813 1131813: RYK :: RYK receptor-like tyrosine kinase 285346 0.032808356450494 −0.176195154516543
    1838 1131815 1131815: SLC16A3 :: solute carrier family 16 (monocarboxylic acid 386678 0.595720282107956 −0.261951094065078
    transporters), member 3
    1839 1131816 1131816: IL8 :: interleukin 8 624 0.140264002040061 −0.022197751307439
    1840 1131827 1131827: PSCD1 :: pleckstrin homology, Sec7 and coiled-coil domains 1050 0.009086209334830 −0.326598876849318
    1(cytohesin 1)
    1841 1131835 1131835: ANPEP :: alanyl (membrane) aminopeptidase 1239 0.560675531752289 −0.319995337520616
    (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase,
    CD13, p150)
    1842 1131839 1131839: SFRS3 :: splicing factor, arginine/serine-rich 3 405144 −0.462771409363554 0.757901723793864
    1843 1131845 1131845: NBS1 :: Nijmegen breakage syndrome 1 (nibrin) 25812 0.187739986384909 −0.055487351990348
    1844 1131847 1131847: CD97 :: CD97 antigen 3107 0.470642638940702 −0.594528313613836
    1845 1131854 1131854: GCLC :: glutamate-cysteine ligase, catalytic subunit 414985 −0.229812122262907 0.033652611178791
    1846 1131861 1131861: YES1 :: v-yes-1 Yamaguchi sarcoma viral oncogene 194148 0.404068940647571 −0.352614969792935
    homolog 1
    1847 1131863 1131863: SOX9 :: SRY (sex determining region Y)-box 9 (campomelic 2316 0.023548359459035 0.008979903745464
    dysplasia, autosomal sex-reversal)
    1848 1131868 1131868: GYPC :: glycophorin C (Gerbich blood group) 81994 0.068679003500084 −0.169866880145741
    1849 1131870 1131870: ADAM12 :: a disintegrin and metalloproteinase domain 12 8850 0.672171616380497 −0.290298904712172
    (meltrin alpha)
    1850 1131875 1131875: CAPN6 :: calpain 6 169172 0.053625471376072 −0.113317658717737
    1851 1131916 1131916: PIAS3 :: protein inhibitor of activated STAT3 435761 0.060317360202652 −0.119267354100978
    1852 1131918 1131918: MTSS1 :: metastasis suppressor 1 77694 0.126594607748513 −0.215833828228631
    1853 1131925 1131925: TCTA :: T-cell leukemia translocation altered gene 250894 −0.140634086253037 −0.084263934757262
    1854 1131940 1131940: TGFB1 :: transforming growth factor, beta 1 (Camurati- 1103 0.077307306507790 −0.219635532756303
    Engelmann disease)
    1855 1131955 1131955: WHSC2 :: Wolf-Hirschhorn syndrome candidate 2 21771 −0.428553483194901 0.522335335717293
    1856 1131964 1131964: KIF5C :: kinesin family member 5C 6641 0.178798859283669 −0.000776060927303
    1857 1131972 1131972: PAK4 :: p21(CDKN1A)-activated kinase 4 20447 −0.184120285169395 0.182353309770624
    1858 1131975 1131975: RNF8 :: ring finger protein (C3HC4 type) 8 24439 −0.246051078343186 0.456159857346887
    1859 1131998 1131998: RFC5 :: replication factor C (activator 1) 5, 36.5 kDa 443227 −0.304105043276485 0.580015219267383
    1860 1132004 1132004: SIAT9 :: sialyltransferase 9 (CMP-NeuAc:lactosylceramide 415117 0.131829639089957 −0.357953062221225
    alpha-2,3-sialyltransferase; GM3 synthase)
    1861 1132011 1132011: CLK2 :: CDC-like kinase 2 73986 −0.433221154262639 0.333142142452891
    1862 1132013 1132013: SCA1 :: spinocerebellar ataxia 1 (olivopontocerebellar 434961 0.573011124237002 −0.558158560945881
    ataxia 1, autosomal dominant, ataxin 1)
    1863 1132016 1132016: NOTCH3 :: Notch homolog 3 (Drosophila) 8546 0.516342851051717 −0.283665731808773
    1864 1132022 1132022: ZNF24 :: zinc finger protein 24 (KOX 17) 173911 −0.132362253139443 0.019939786990243
    1865 1132031 1132031: MAP2K4 :: mitogen-activated protein kinase kinase 4 134106 −0.044326630951000 0.077057186977509
    1866 1132034 1132034: UNC119 :: unc-119 homolog (C. elegans) 410455 0.162674778479055 −0.152850646527214
    1867 1132035 1132035: PDAP2 :: PDGFA associated protein 2 8186 −0.351063634678681 0.341148418065009
    1868 1132058 1132058: TGIF :: TGFB-induced factor (TALE family homeobox) 161999 −0.089955439319608 0.012983428575114
    1869 1132104 1132104: TBC1D4 :: TBC1 domain family, member 4 173802 0.174716497125486 −0.303331906685459
    1870 1132122 1132122: MME :: membrane metallo-endopeptidase (neutral 307734 0.091058727833380 0.213585135607787
    endopeptidase, enkephalinase, CALLA, CD10)
    1871 1132132 1132132: ATOX1 :: ATX1 antioxidant protein 1 homolog (yeast) 279910 0.371746754962258 −0.235388977702808
    1872 1132159 1132159: ZNF318 :: zinc finger protein 318 147868 0.039152606400365 0.161742423454252
    1873 1132178 1132178: PTTG1 :: pituitary tumor-transforming 1 350966 −0.258893293711822 0.666347157955608
    1874 1132196 1132196: CSF3R :: colony stimulating factor 3 receptor (granulocyte) 381027 0.438613330885891 −0.418452605605811
    1875 1132220 1132220: GPRC5B :: G protein-coupled receptor, family C, group 5, 448805 0.366763832566919 −0.427970742931399
    member B
    1876 1132223 1132223: FGFR2 :: fibroblast growth factor receptor 2 (bacteria- 404081 0.317558427639917 −0.241289886185299
    expressed kinase, keratinocyte growth factor receptor, craniofacial
    dysostosis
    1, Crouzon syndrome, Pfeiffer syndrome, Jackson-
    Weiss syndrome)
    1877 1132230 1132230: PLA2G2A :: phospholipase A2, group IIA (platelets, 76422 0.279193056674363 −0.160817405939559
    synovial fluid)
    1878 1132236 1132236: TMOD1 :: tropomodulin 1 374849 0.324423040844218 −0.350644740562922
    1879 1132256 1132256: KIAA0173 :: KIAA0173 gene product 169910 0.031123896338403 0.336046918386896
    1880 1132260 1132260: FZD7 :: frizzled homolog 7 (Drosophila) 173859 0.462892817101932 −0.413817554150429
    1881 1132288 1132288: STS :: steroid sulfatase (microsomal), arylsulfatase C, 79876 0.134794043837710 0.081300346040601
    isozyme S
    1882 1132292 1132292: BLVRA :: biliverdin reductase A 435726 0.307210356182809 −0.329095748235412
    1883 1132294 1132294: RPS6KB2 :: ribosomal protein S6 kinase, 70 kDa, 103081 0.046867241876797 −0.031492411847754
    polypeptide 2
    1884 1132306 1132306: BCL7A :: B-cell CLL/lymphoma 7A −34 −0.145765239332859 0.288878301794857
    1885 1132329 1132329: ACK1 :: activated p21cdc42Hs kinase 128392 0.015481843347622 −0.205600218015162
    1886 1132336 1132336: GAB2 :: GRB2-associated binding protein 2 30687 0.279420865222956 −0.316921655907721
    1887 1132345 1132345: VCAM1 :: vascular cell adhesion molecule 1 109225 0.423122552434272 −0.521238250710401
    1888 1132349 1132349: DMD :: dystrophin (muscular dystrophy, Duchenne and 169470 0.015601524791194 0.155636775212336
    Becker types)
    1889 1132353 1132353: THBD :: thrombomodulin 2030 0.319336617488327 −0.304072866702818
    1890 1132354 1132354: DAPK3 :: death-associated protein kinase 3 153908 −0.087408304874834 0.165959747878693
    1891 1132375 1132375: MARK2 :: MAP/microtubule affinity-regulating kinase 2 157199 0.003817055906942 −0.029439031931299
    1892 1132376 1132376: BTN2A1 :: butyrophilin, subfamily 2, member A1 169963 0.269826752423953 −0.381922260724480
    1893 1132396 1132396: FUT8 :: fucosyltransferase 8 (alpha (1,6) fucosyltransferase) 118722 −0.244646243998852 0.231749952936851
    1894 1132407 1132407: PAWR :: PRKC, apoptosis, WT1, regulator 406074 −0.256402843713444 0.392482360907927
    1895 1132426 1132426: C6orf56 :: chromosome 6 open reading frame 56 102471 0.075623143391260 −0.263519720550745
    1896 1132428 1132428: SFRP4 :: secreted frizzled-related protein 4 105700 0.470112484475708 −0.289073301793498
    1897 1132433 1132433: ME1 :: malic enzyme 1, NADP(+)-dependent, cytosolic 14732 0.235924704818424 −0.341006938347295
    1898 1132434 1132434: PRKX :: protein kinase, X-linked 147996 0.082516439464899 −0.203822460383043
    1899 1132435 1132435: ULK2 :: unc-51-like kinase 2 (C. elegans) 168762 0.025216376306500 −0.043076970364662
    1900 1132449 1132449: STK6 :: serine/threonine kinase 6 250822 −0.342484271052208 0.854223977659442
    1901 1132460 1132460: CDC45L :: CDC45 cell division cycle 45-like (S. cerevisiae) 114311 −0.392694067278240 0.786127341984203
    1902 1132462 1132462: FOXO3A :: forkhead box O3A 14845 0.368591254754925 −0.433764383288663
    1903 1132468 1132468: TFDP1 :: transcription factor Dp-1 79353 −0.281111016450068 0.587665041868591
    1904 1132479 1132479: CKS2 :: CDC28 protein kinase regulatory subunit 2 83758 −0.336131034183213 0.776594329768994
    1905 1132485 1132485: ADRBK2 :: adrenergic, beta, receptor kinase 2 445563 0.026350082372157 0.212105726957152
    1906 1132498 1132498: PRKR :: protein kinase, interferon-inducible double 439523 0.066840579394694 −0.087904249908943
    stranded RNA dependent
    1907 1132504 1132504: GLIPR1 :: GLI pathogenesis-related 1 (glioma) 511765 0.332274083428259 −0.223315863333576
    1908 1132519 1132519: CDK5 :: cyclin-dependent kinase 5 166071 −0.047271288760870 0.233374203627911
    1909 1132520 1132520: LMO2 :: LIM domain only 2 (rhombotin-like 1) 283063 0.322555941970676 −0.133225258835905
    1910 1132525 1132525: VDR :: vitamin D (1,25-dihydroxyvitamin D3) receptor 2062 0.433864275074134 −0.287514297938507
    1911 1132529 1132529: C6orf9 :: chromosome 6 open reading frame 9 288316 0.020696537691352 −0.351700071982180
    1912 1132531 1132531: PKMYT1 :: membrane-associated tyrosine- and threonine- 77783 −0.326448359051311 0.770085323613511
    specific cdc2-inhibitory kinase
    1913 1132536 1132536: PMAIP1 :: phorbol-12-myristate-13-acetate-induced protein 1 96 −0.264821671020407 0.140274139633261
    1914 1132545 1132545: CD151 :: CD151 antigen 512857 0.484034201302057 −0.267724272339692
    1915 1132547 1132547: NPR2 :: natriuretic peptide receptor B/guanylate cyclase B 78518 0.146399574004803 −0.263444587844550
    (atrionatriuretic peptide receptor B)
    1916 1132572 1132572: LIMK1 :: LIM domain kinase 1 36566 0.134056222788714 0.042055189501082
    1917 1132584 1132584: FGFR3 :: fibroblast growth factor receptor 3 (achondroplasia, 1420 0.147516952526905 −0.119140751786612
    thanatophoric dwarfism)
    1918 1132592 1132592: GPRK5 :: G protein-coupled receptor kinase 5 211569 0.177329362173847 −0.033025403899686
    1919 1132614 1132614: ALOX5 :: arachidonate 5-lipoxygenase 89499 0.253272865281527 −0.158095339023624
    1920 1132628 1132628: TIE :: tyrosine kinase with immunoglobulin and 78824 0.235417471722526 −0.055952441856724
    epidermal growth factor homology domains
    1921 1132636 1132636: CD44 :: CD44 antigen (homing function and Indian 306278 0.170483625093136 −0.070535279463917
    blood group system)
    1922 1132651 1132651: TOX :: thymus high mobility group box protein TOX 439767 0.118932638076210 −0.079565463918791
    1923 1132700 1132700: RPS6KA5 :: ribosomal protein S6 kinase, 90 kDa, 109058 −0.017334567062377 −0.166266633063264
    polypeptide 5
    1924 1132726 1132726: MAPK4 :: mitogen-activated protein kinase 4 433728 0.009521048919827 −0.084175684705991
    1925 1132734 1132734: COL9A3 :: collagen, type IX, alpha 3 126248 −0.101320116382731 0.079697319215094
    1926 1132762 1132762: MAL :: mal, T-cell differentiation protein 80395 0.252541285182322 −0.443739008537555
    1927 1132766 1132766: TNFRSF6 :: tumor necrosis factor receptor superfamily, 82359 0.439880140313859 −0.246840312593953
    member 6
    1928 1132768 1132768: IFNAR2 :: interferon (alpha, beta and omega) receptor 2 512211 0.004319875316505 −0.106811200549353
    1929 1132775 1132775: RRAD :: Ras-related associated with diabetes 1027 0.382640243706838 −0.245069256965701
    1930 1132780 1132780: CACNA2D2 :: calcium channel, voltage-dependent, 389415 −0.008811475360416 −0.089903821942477
    alpha 2/delta subunit 2
    1931 1132787 1132787: BMPR1A :: bone morphogenetic protein receptor, type IA 2534 −0.115173969757864 0.228241887165543
    1932 1132799 1132799: APAF1 :: apoptotic protease activating factor 373575 0.108985290832645 0.033820592215645
    1933 1132809 1132809: PSK :: prostate derived STE20-like kinase PSK 122823 −0.084370387981083 0.063316707183397
    1934 1132818 1132818: LCK :: lymphocyte-specific protein tyrosine kinase 1765 0.166418049475020 −0.319367837467735
    1935 1132825 1132825: SAP30 :: sin3-associated polypeptide, 30 kDa 512813 0.064474665431520 0.408174220850057
    1936 1132830 1132830: BCL3 :: B-cell CLL/lymphoma 3 31210 0.012241396097884 −0.005770899349080
    1937 1132834 1132834: SOX11 :: SRY (sex determining region Y)-box 11 432638 −0.130130852086878 0.008934439925760
    1938 1132850 1132850: DYRK1B :: dual-specificity tyrosine-(Y)-phosphorylation 130988 −0.150245711405737 −0.064037848783788
    regulated kinase 1B
    1939 1132851 1132851: :: Homo sapiens cDNA FLJ46012 fis, clone SPLEN2007689, 1583 −0.105077219223237 −0.185727977850533
    highly similar to Neutrophil cytosol factor 1
    1940 1132852 1132852: CENPA :: centromere protein A, 17 kDa 1594 −0.330307054028778 0.834198009135619
    1941 1132860 1132860: PSK :: prostate derived STE20-like kinase PSK 122823 −0.140238455355596 0.075742960594935
    1942 1132862 1132862: ITGB4 :: integrin, beta 4 85266 −0.001397803543690 −0.006702616683621
    1943 1132866 1132866: ATF5 :: activating transcription factor 5 9754 −0.083740507309572 −0.030416622263988
    1944 1132874 1132874: ADORA2A :: adenosine A2a receptor 197029 −0.171103874940728 0.175530614350310
    1945 1132883 1132883: MAP3K8 :: mitogen-activated protein kinase kinase kinase 8 432453 0.220120953209822 −0.207562161908588
    1946 1132890 1132890: CD79A :: CD79A antigen (immunoglobulin-associated alpha) 79630 −0.337177451882671 0.299810735012318
    1947 1132892 1132892: KIT :: v-kit Hardy-Zuckerman 4 feline sarcoma viral 81665 0.346843052155709 −0.287525269110642
    oncogene homolog
    1948 1132918 1132918: CCL3 :: chemokine (C-C motif) ligand 3 73817 0.210200763463909 −0.379856191443791
    1949 1132920 1132920: FPR1 :: formyl peptide receptor 1 753 0.450668752553231 −0.271074665943058
    1950 1132953 1132953: ADAM8 :: a disintegrin and metalloproteinase domain 8 86947 0.090679204456041 −0.122432730144956
    1951 1132959 1132959: ATP7A :: ATPase, Cu++ transporting, alpha polypeptide 606 0.366616137158226 −0.278472771716937
    (Menkes syndrome)
    1952 1132961 1132961: CENTB1 :: centaurin, beta 1 337242 0.059851837494540 −0.386761070675942
    1953 1132973 1132973: TCF7 :: transcription factor 7 (T-cell specific, HMG-box) 169294 0.123121096136518 −0.447164392087382
    1954 1132979 1132979: CCRK :: cell cycle related kinase 26322 0.207844813354062 −0.131701392184582
    1955 1132990 1132990: CD79B :: CD79B antigen (immunoglobulin-associated beta) 89575 −0.344622456167376 0.358039114087407
    1956 1132994 1132994: OGG1 :: 8-oxoguanine DNA glycosylase 380271 −0.137099966252423 0.320169119840156
    1957 1132996 1132996: KMO :: kynurenine 3-monooxygenase (kynurenine 3- 409081 0.211990018555365 −0.291776582897728
    hydroxylase)
    1958 1133004 1133004: ACVR2 :: activin A receptor, type II 389846 0.279599795179747 −0.239731396808758
    1959 1133011 1133011: TMSNB :: thymosin, beta, identified in neuroblastoma cells 56145 −0.002520060395082 0.071841149776115
    1960 1133021 1133021: ACHE :: acetylcholinesterase (YT blood group) 154495 0.402482778770336 −0.155787254777042
    1961 1133024 1133024: ZNF288 :: zinc finger protein 288 436987 0.265865101259661 −0.396721785363083
    1962 1133030 1133030: CCL15 :: chemokine (C-C motif) ligand 15 272493 0.057379944824827 −0.281520577334817
    1963 1133042 1133042: ITGBL1 :: integrin, beta-like 1 (with EGF-like repeat 311054 0.622932591813418 −0.328959959392322
    domains)
    1964 1133047 1133047: AAK1 :: AP2 associated kinase 1 135941 0.348101012819978 −0.519349741936085
    1965 1133049 1133049: H2AFX :: H2A histone family, member X 147097 −0.194779401220227 0.611672944781315
    1966 1133065 1133065: PLAU :: plasminogen activator, urokinase 77274 0.783707351172337 −0.379451893760215
    1967 1133068 1133068: G1P2 :: interferon, alpha-inducible protein (clone IFI-15K) 458485 0.224134143117873 −0.313126229936884
    1968 1133076 1133076: PDCD8 :: programmed cell death 8 (apoptosis-inducing 18720 −0.157569526709521 0.402184728488840
    factor)
    1969 1133080 1133080: KATNA1 :: katanin p60 (ATPase-containing) subunit A 1 440341 −0.165970006007139 0.181023125522753
    1970 1133091 1133091: CR2 :: complement component (3d/Epstein Barr virus) 73792 0.030214844042362 0.092058217437685
    receptor 2
    1971 1133093 1133093: TYK2 :: tyrosine kinase 2 75516 −0.217551973397616 −0.002422536201704
    1972 1133099 1133099: DNASE1L3 :: deoxyribonuclease I-like 3 88646 −0.257980874817348 −0.166979927446227
    1973 1133102 1133102: FRDA :: Friedreich ataxia 360041 −0.335514224531287 0.492486823001609
    1974 1133111 1133111: PDE9A :: phosphodiesterase 9A 389777 0.133104476615309 −0.019862978252224
    1975 1133117 1133117: PACE-1 :: ezrin-binding partner PACE-1 435560 −0.016659594094386 −0.002954180593273
    1976 1133119 1133119: MST1 :: macrophage stimulating 1 (hepatocyte growth 512587 0.017059225812341 −0.167280765698926
    factor-like)
    1977 1133138 1133138: HLA-DOB :: major histocompatibility complex, class II, 1802 −0.150884123016589 −0.047034927110652
    DO beta
    1978 1133141 1133141: DLEU1 :: deleted in lymphocytic leukemia, 1 344524 −0.476295741441405 0.564225564362615
    1979 1133148 1133148: CD38 :: CD38 antigen (p45) 174944 −0.086274304083668 −0.258405804308845
    1980 1133150 1133150: MAP2K6 :: mitogen-activated protein kinase kinase 6 256924 −0.060625002575886 0.143053623586413
    1981 1133156 1133156: COMP :: cartilage oligomeric matrix protein 1584 0.441890669117056 −0.195814414026257
    1982 1133184 1133184: ITGAM :: integrin, alpha M (complement component 172631 0.753289632173116 −0.438207938207401
    receptor 3, alpha; also known as CD11b (p170), macrophage antigen
    alpha polypeptide)
    1983 1133192 1133192: RASGRP3 :: RAS guanyl releasing protein 3 (calcium 24024 −0.227545188050837 0.110767187589711
    and DAG-regulated)
    1984 1133195 1133195: ROR1 :: receptor tyrosine kinase-like orphan receptor 1 274243 0.211583482691962 −0.095352844765974
    1985 1133210 1133210: JAK2 :: Janus kinase 2 (a protein tyrosine kinase) 434374 0.211723154336484 −0.309565714170364
    1986 1133216 1133216: PDE4DIP :: phosphodiesterase 4D interacting protein 390449 0.469859143755927 −0.270025422668526
    (myomegalin)
    1987 1133219 1133219: RET :: ret proto-oncogene (multiple endocrine neoplasia and 350321 0.039216692256241 −0.113466892491905
    medullary thyroid carcinoma 1, Hirschsprung disease)
    1988 1133227 1133227: NOLC1 :: nucleolar and coiled-body phosphoprotein 1 75337 −0.467836599715920 0.605412542908700
    1989 1133232 1133232: CEL :: carboxyl ester lipase (bile salt-stimulated lipase) 406160 −0.047643754334538 0.004264213209241
    1990 1133252 1133252: EPHA1 :: EphA1 89839 0.291635532708424 −0.334277608203048
    1991 1133260 1133260: IL15 :: interleukin 15 168132 0.477661261402447 −0.545949137402680
    1992 1133272 1133272: MERTK :: c-mer proto-oncogene tyrosine kinase 306178 0.252944775766872 −0.308345262733304
    1993 1133275 1133275: REL :: v-rel reticuloendotheliosis viral oncogene 44313 −0.085309557979979 0.156958739161487
    homolog (avian)
    1994 1133296 1133296: EPHA3 :: EphA3 123642 0.158232174391835 −0.146669730921844
    1995 1133299 1133299: CSNK2A1 :: casein kinase 2, alpha 1 polypeptide 446484 −0.402393962409281 0.443591691051582
    1996 1133300 1133300: CTH :: cystathionase (cystathionine gamma-lyase) 19904 −0.174763128546197 0.309368945386643
    1997 1133355 1133355: MATK :: megakaryocyte-associated tyrosine kinase 437808 0.209013931316900 −0.223912921475326
    1998 1133358 1133358: TAL1 :: T-cell acute lymphocytic leukemia 1 73828 0.099663664736123 −0.092238236560719
    1999 1133376 1133376: DAPK2 :: death-associated protein kinase 2 129208 0.312209231371153 −0.375817373135772
    2000 1133388 1133388: MAP3K10 :: mitogen-activated protein kinase kinase 435014 −0.085980697049518 −0.084119677925152
    kinase 10
    2001 1133389 1133389: XCL1 :: chemokine (C motif) ligand 1 174228 −0.035790980270872 −0.263917654207473
    2002 1133392 1133392: PFC :: properdin P factor, complement 53155 0.101600551414248 −0.305806420968560
    2003 1133397 1133397: PF4 :: platelet factor 4 (chemokine (C—X—C motif) 81564 0.138980500020639 −0.024818220159783
    ligand 4)
    2004 1133400 1133400: CD19 :: CD19 antigen 96023 −0.142433949967589 0.163988190753814
    2005 1133405 1133405: CCL13 :: chemokine (C-C motif) ligand 13 414629 −0.083416470126778 −0.088402738547819
    2006 1133406 1133406: ABL2 :: v-abl Abelson murine leukemia viral oncogene 159472 0.022813711233182 0.032696347502914
    homolog 2 (arg, Abelson-related gene)
    2007 1133407 1133407: TCL1B :: T-cell leukemia/lymphoma 1B 512850 −0.174317478777086 0.242190379023676
    2008 1133408 1133408: DDEF2 :: development and differentiation enhancing factor 2 12802 0.540194218430208 −0.416938590146850
    2009 1133430 1133430: TNFRSF6B :: tumor necrosis factor receptor superfamily, 348183 0.269171054691013 −0.078298763058308
    member 6b, decoy
    2010 1133445 1133445: CHC1 :: chromosome condensation 1 196769 −0.388958919390715 0.590137912621854
    2011 1133453 1133453: RGS9 :: regulator of G-protein signalling 9 117149 0.120525989789610 −0.176381127128455
    2012 1133476 1133476: MAP4K4 :: mitogen-activated protein kinase kinase kinase 3628 0.186100449709661 0.138800618028371
    kinase 4
    2013 1133515 1133515: PTPN6 :: protein tyrosine phosphatase, non-receptor type 6 63489 0.012603181388466 −0.102763121939913
    2014 1133538 1133538: FCER2 :: Fc fragment of IgE, low affinity II, receptor 1416 0.106023153171250 −0.252188795472937
    for (CD23A)
    2015 1133565 1133565: HDAC6 :: histone deacetylase 6 6764 −0.192135925793860 0.026151793306868
    2016 1133568 1133568: MAP3K7 :: mitogen-activated protein kinase kinase kinase 7 290346 −0.068454670946960 0.068695359831212
    2017 1133569 1133569: HYAL2 :: hyaluronoglucosaminidase 2 76873 0.266854829641114 −0.217178690680440
    2018 1133576 1133576: HRK :: harakiri, BCL2 interacting protein (contains only 87247 −0.136002276499443 0.126882867488172
    BH3 domain)
    2019 1133577 1133577: SLK :: Ste20-related serine/threonine kinase 105751 0.130411355792943 −0.076955906871234
    2020 1133580 1133580: LILRA3 :: leukocyte immunoglobulin-like receptor, 113277 −0.251926329094464 −0.009994293775648
    subfamily A (without TM domain), member 3
    2021 1133595 1133595: IL11 :: interleukin 11 1721 0.030444042014686 −0.107584215640277
    2022 1133618 1133618: CCR5 :: chemokine (C-C motif) receptor 5 511796 0.412073449175704 −0.559429116658751
    2023 1133629 1133629: PTK7 :: PTK7 protein tyrosine kinase 7 90572 0.437358321386405 −0.235325422507285
    2024 1133652 1133652: ASS :: argininosuccinate synthetase 160786 0.299982247486773 −0.281306420532693
    2025 1133672 1133672: TNF :: tumor necrosis factor (TNF superfamily, member 2) 241570 0.229157733455114 −0.039984679710739
    2026 1133676 1133676: MAPK6 :: mitogen-activated protein kinase 6 271980 −0.053402388955127 0.156113673288142
    2027 1133694 1133694: AKT1 :: v-akt murine thymoma viral oncogene homolog 1 368861 −0.098441215455632 0.210637913631811
    2028 1133700 1133700: CDH11 :: cadherin 11, type 2, OB-cadherin (osteoblast) 443435 0.910273241078143 −0.447714717232453
    2029 1133701 1133701: CD80 :: CD80 antigen (CD28 antigen ligand 1, B7-1 antigen) 838 0.234271452338870 −0.123295283109379
    2030 1133702 1133702: FRK :: fyn-related kinase 89426 −0.088749786570166 0.145490673392961
    2031 1133704 1133704: CASP7 :: caspase 7, apoptosis-related cysteine protease 9216 0.150284681291938 −0.040276646079796
    2032 1133708 1133708: ICAM4 :: intercellular adhesion molecule 4, Landsteiner- 512159 0.072389666323349 −0.128178472781610
    Wiener blood group
    2033 1133724 1133724: PCTK1 :: PCTAIRE protein kinase 1 171834 −0.039172844280366 0.183412682054809
    2034 1133731 1133731: UBN1 :: ubinuclein 1 21479 −0.233103646285480 0.126011351317026
    2035 1133753 1133753: KIR3DL2 :: killer cell immunoglobulin-like receptor, 56328 0.057615719536991 0.021322335954838
    three domains, long cytoplasmic tail, 2
    2036 1133755 1133755: CDC2L5 :: cell division cycle 2-like 5 (cholinesterase- 404501 −0.171682635768532 −0.003512231465868
    related cell division controller)
    2037 1133757 1133757: STAU :: staufen, RNA binding protein (Drosophila) 6113 −0.285814369623812 0.192008922806710
    2038 1133766 1133766: LTB :: lymphotoxin beta (TNF superfamily, member 3) 376208 0.229636210128755 −0.178027816423099
    2039 1133778 1133778: IL15RA :: interleukin 15 receptor, alpha 12503 0.411529350916578 −0.384522006576836
    2040 1133786 1133786: ALG3 :: asparagine-linked glycosylation 3 homolog (yeast, 153591 −0.379755131485044 0.383219707931730
    alpha-1,3-mannosyltransferase)
    2041 1133801 1133801: TNFSF4 :: tumor necrosis factor (ligand) superfamily, 181097 0.137229819751181 −0.275883435383981
    member 4 (tax-transcriptionally activated glycoprotein
    1, 34 kDa)
    2042 1133802 1133802: CDC2L2 :: cell division cycle 2-like 2 402748 −0.137802379411402 0.057863977677410
    2043 1133810 1133810: CCR9 :: chemokine (C-C motif) receptor 9 225946 −0.117781028827656 0.124533083271088
    2044 1133829 1133829: MS4A2 :: membrane-spanning 4-domains, subfamily A, 386748 0.177404858682871 −0.054031419783302
    member 2 (Fc fragment of IgE, high affinity I, receptor for; beta
    polypeptide)
    2045 1133834 1133834: LAIR2 :: leukocyte-associated Ig-like receptor 2 43803 0.226784659149121 −0.267608718674007
    2046 1133846 1133846: TNFRSF9 :: tumor necrosis factor receptor superfamily, 193418 0.533030357422095 −0.338024239621130
    member 9
    2047 1133848 1133848: SYK :: spleen tyrosine kinase 192182 −0.311059247048826 0.343785891142310
    2048 1133867 1133867: C1orf38 :: chromosome 1 open reading frame 38 10649 0.307862904192117 −0.388823072767907
    2049 1133869 1133869: GADD45B :: growth arrest and DNA-damage-inducible, beta 110571 0.223306853942758 −0.339610292113472
    2050 1133901 1133901: MUSK :: muscle, skeletal, receptor tyrosine kinase 156465 0.045285571984218 0.076108036762733
    2051 1133904 1133904: TNFRSF1A :: tumor necrosis factor receptor superfamily, 159 0.643710808786366 −0.596010985742485
    member 1A
    2052 1133910 1133910: BLNK :: B-cell linker 167746 −0.446169388331319 0.329125198490164
    2053 1133931 1133931: LILRB2 :: leukocyte immunoglobulin-like receptor, 306230 0.189896565915764 −0.333536831009256
    subfamily B (with TM and ITIM domains), member 2
    2054 1133998 1133998: ID3 :: inhibitor of DNA binding 3, dominant negative helix- 76884 −0.231618348471321 0.102308599561213
    loop-helix protein
    2055 1134069 1134069: CD8B1 :: CD8 antigen, beta polypeptide 1 (p37) 405667 0.225901023201953 −0.484596706630053
    2056 1134076 1134076: ARPC2 :: actin related protein 2/3 complex, subunit 2, 34 kDa 83583 0.136046734918812 −0.005298188257533
    2057 1134083 1134083: C18orf1 :: chromosome 18 open reading frame 1 285091 0.346451715122800 −0.373477515568528
    2058 1134095 1134095: HCK :: hemopoietic cell kinase 89555 −0.014720188541950 0.038451469448641
    2059 1134109 1134109: MADCAM1 :: mucosal vascular addressin cell adhesion 102598 0.147538030038399 −0.064881411838308
    molecule 1
    2060 1134133 1134133: CCL7 :: chemokine (C-C motif) ligand 7 251526 0.166588295892007 −0.023081827233061
    2061 1134145 1134145: DKFZP564K0822 :: hypothetical protein DKFZp564K0822 4750 −0.071386477041643 −0.062712005236753
    2062 1134200 1134200: ABCC3 :: ATP-binding cassette, sub-family C (CFTR/MRP), 90786 0.559310932835367 −0.393423898786516
    member 3
    2063 1134212 1134212: TRIO :: triple functional domain (PTPRF interacting) 367689 0.207746847343388 −0.222959913655619
    2064 1134220 1134220: MYO7A :: myosin VIIA (Usher syndrome 1B (autosomal 370421 −0.017653358783537 −0.192603530737153
    recessive, severe))
    2065 1134230 1134230: RASGRP2 :: RAS guanyl releasing protein 2 (calcium and 99491 −0.154642991810068 0.051124540138756
    DAG-regulated)
    2066 1134233 1134233: ALK :: anaplastic lymphoma kinase (Ki-1) 410680 0.186575254434794 −0.189026699772156
    2067 1134270 1134270: GGT1 :: gamma-glutamyltransferase 1 352119 0.251750587831380 −0.349120537758305
    2068 1134271 1134271: POU5F1 :: POU domain, class 5, transcription factor 1 249184 −0.156623761238959 0.029995443126806
    2069 1134280 1134280: CRLF2 :: cytokine receptor-like factor 2 287729 −0.035287889475792 −0.057636116646176
    2070 1134296 1134296: FY :: Duffy blood group 183 0.217642615578632 −0.364345371369456
    2071 1134316 1134316: GPRK2L :: G protein-coupled receptor kinase 2-like 32959 0.033589097434719 −0.026724476713475
    (Drosophila )
    2072 1134361 1134361: KIR2DL4 :: killer cell immunoglobulin-like receptor, 515605 −0.064371839816714 −0.027523138295799
    two domains, long cytoplasmic tail, 4
    2073 1134370 1134370: FGR :: Gardner-Rasheed feline sarcoma viral (v-fgr) 1422 0.469900254155040 −0.371138296962091
    oncogene homolog
    2074 1134379 1134379: C4A :: complement component 4A 150833 0.153921754790563 −0.492982998610867
    2075 1134422 1134422: BCL2L11 :: BCL2-like 11 (apoptosis facilitator) 84063 −0.167169905260362 0.312275568218554
    2076 1134424 1134424: S100A14 :: LOC392086: similar to Putative S100 calcium- −6 0.577071499097494 −0.451549726315866
    binding protein A11 pseudogene
    2077 1134457 1134457: NTRK1 :: neurotrophic tyrosine kinase, receptor, type 1 406293 −0.051929755731206 −0.076605673516509
    2078 1134480 1134480: MACF1 :: microtubule-actin crosslinking factor 1 372463 0.385302560920052 −0.489132821439022
    2079 1134494 1134494: MSF :: MLL septin-like fusion 288094 −0.158164582532209 0.094745859172743
    2080 1134517 1134517: PDLIM1 :: PDZ and LIM domain 1 (elfin) 75807 −0.318932656287507 0.232330090652600
    2081 1134523 1134523: TKT :: transketolase (Wernicke-Korsakoff syndrome) 89643 −0.157519567091726 0.331118833432058
    2082 1134532 1134532: CCND1 :: cyclin D1 (PRAD1: parathyroid adenomatosis 1) 371468 0.357568571752350 −0.289354652996340
    2083 1134533 1134533: LOC54499 :: putative membrane protein 93832 0.027985409927586 0.065539358200285
    2084 1134542 1134542: HLA-B :: major histocompatibility complex, class I, B 77961 0.252413302304409 −0.486244623630763
    2085 1134582 1134582: SMARCA4 :: SWI/SNF related, matrix associated, actin 78202 −0.042161334059780 0.201113183134652
    dependent regulator of chromatin, subfamily a, member 4
    2086 1134593 1134593: HLA-C :: major histocompatibility complex, class I, C 274485 0.150604563084478 −0.372850743553715
    2087 1134615 1134615: THY1 :: Thy-1 cell surface antigen 134643 0.740295008324578 −0.289362396064258
    2088 1134618 1134618: STK24 :: serine/threonine kinase 24 (STE20 homolog, yeast) 168913 −0.302773915211256 0.366245931868612
    2089 1134647 1134647: DUSP6 :: dual specificity phosphatase 6 298654 0.506041172080515 −0.442864261312140
    2090 1134653 1134653: TOP1 :: topoisomerase (DNA) I 253536 −0.386004901157803 0.578538864529316
    2091 1134665 1134665: SRI :: sorcin 422340 0.070635339781393 0.014029892560073
    2092 1134674 1134674: ID1 :: inhibitor of DNA binding 1, dominant negative 410900 0.315979164228629 −0.295857070867065
    helix-loop-helix protein
    2093 1134676 1134676: TLOC1 :: translocation protein 1 158193 −0.382787060158885 0.187687539924563
    2094 1134679 1134679: BECN1 :: beclin 1 (coiled-coil, myosin-like BCL2 12272 0.105603493319489 −0.102323703391318
    interacting protein)
    2095 1134682 1134682: LGALS3 :: lectin, galactoside-binding, soluble, 3 (galectin 3) 411701 0.499705085052146 −0.365258666150658
    2096 1134687 1134687: TXNDC4 :: thioredoxin domain containing 4 (endoplasmic 154023 0.223571308720130 −0.241073271383677
    reticulum)
    2097 1134699 1134699: KPNB1 :: karyopherin (importin) beta 1 439683 −0.284720382004117 0.534018688023989
    2098 1134706 1134706: FBXL11 :: F-box and leucine-rich repeat protein 11 219614 0.044440338914973 −0.202122236667693
    2099 1134710 1134710: PPIG :: peptidyl-prolyl isomerase G (cyclophilin G) 77965 0.018281322001863 −0.014383939906630
    2100 1134727 1134727: PINK1 :: PTEN induced putative kinase 1 439600 0.312058012057399 −0.245134769222099
    2101 1134738 1134738: DYRK1A :: dual-specificity tyrosine-(Y)-phosphorylation 75842 −0.064568512991221 −0.100866986311723
    regulated kinase 1A
    2102 1134753 1134753: WHSC1 :: Wolf-Hirschhorn syndrome candidate 1 110457 −0.341151329387829 0.729975148861719
    2103 1134778 1134778: RFC1 :: replication factor C (activator 1) 1, 145 kDa 166563 −0.336733099289826 0.528235750344208
    2104 1134797 1134797: TUBA3 :: tubulin, alpha 3 433394 0.405096128352181 −0.125508822982315
    2105 1134837 1134837: IRS2 :: insulin receptor substrate 2 143648 0.449386774571679 −0.337887011456020
    2106 1134843 1134843: MEF2C :: MADS box transcription enhancer factor 2, 368950 0.073971584405973 0.121033219047677
    polypeptide C (myocyte enhancer factor 2C)
    2107 1134850 1134850: PLEKHC1 :: pleckstrin homology domain containing, 270411 0.727857421507228 −0.375542340871581
    family C (with FERM domain) member 1
    2108 1134852 1134852: EWSR1 :: Ewing sarcoma breakpoint region 1 374477 −0.370094949141491 0.556503015981440
    2109 1134858 1134858: KPNB2 :: karyopherin (importin) beta 2 405954 −0.133123256535390 0.344301361055445
    2110 1134865 1134865: MINK :: misshapen/NIK-related kinase 112028 −0.014360239308387 −0.031348981802659
    2111 1134880 1134880: METTL3 :: methyltransferase like 3 168799 −0.501356501976032 0.326720755408380
    2112 1134888 1134888: TFPI2 :: tissue factor pathway inhibitor 2 438231 0.308231647753657 −0.273918942666535
    2113 1134903 1134903: SWAP70 :: SWAP-70 protein 153026 0.029725397316418 0.226883023659028
    2114 1134921 1134921: IKBKB :: inhibitor of kappa light polypeptide gene enhancer 413513 0.101776675617754 −0.509485574811757
    in B-cells, kinase beta
    2115 1134928 1134928: SIN3B :: SIN3 homolog B, transcriptional regulator (yeast) 13999 −0.095326097028722 −0.220883061797362
    2116 1134933 1134933: RUNX1 :: runt-related transcription factor 1 (acute myeloid 410774 0.136721482617340 −0.286235830963271
    leukemia 1; aml1 oncogene)
    2117 1134945 1134945: KIAA1128 :: KIAA1128 protein 81897 0.307874711629927 −0.456973877209662
    2118 1134961 1134961: IFI35 :: interferon-induced protein 35 50842 0.138043455897837 −0.401306837995058
    2119 1134988 1134988: MKNK1 :: MAP kinase-interacting serine/threonine kinase 1 79516 0.226240988283301 −0.360081299039555
    2120 1134991 1134991: ENTPD1 :: ectonucleoside triphosphate diphosphohydrolase 1 444105 −0.067132377128918 0.006527793482675
    2121 1135002 1135002: TNFSF13 :: tumor necrosis factor (ligand) superfamily, 54673 0.660500070596942 −0.623176642780856
    member 13
    2122 1135023 1135023: CD34 :: CD34 antigen 374990 0.253442729839205 −0.043705876432332
    2123 1135024 1135024: RIPK2 :: receptor-interacting serine-threonine kinase 2 103755 0.283145198315740 −0.016099665131011
    2124 1135028 1135028: CD36 :: CD36 antigen (collagen type I receptor, 443120 0.021104930817611 0.007796830614863
    thrombospondin receptor)
    2125 1135042 1135042: MOX2 :: antigen identified by monoclonal antibody 79015 0.083289319982643 −0.213987775490654
    MRC OX-2
    2126 1135047 1135047: EPHB2 :: EphB2 125124 0.381665736064432 −0.280685437494666
    2127 1135056 1135056: GATA3 :: GATA binding protein 3 169946 0.372973462657120 −0.616704878063501
    2128 1135068 1135068: ALP :: alpha-actinin-2-associated LIM protein 71719 0.718732925951149 −0.283895978541139
    2129 1135080 1135080: CDKN2A :: cyclin-dependent kinase inhibitor 2A 421349 0.078828027642853 0.161587695324233
    (melanoma, p16, inhibits CDK4)
    2130 1135085 1135085: C22orf4 :: chromosome 22 open reading frame 4 505862 −0.026573621098559 0.016415427963998
    2131 1135088 1135088: TM4SF10 :: transmembrane 4 superfamily member 10 8769 0.788275799148947 −0.406065038614432
    2132 1135093 1135093: CHUK :: conserved helix-loop-helix ubiquitous kinase 198998 0.109586518187874 0.124991404895728
    2133 1135101 1135101: KIFC1 :: kinesin family member C1 20830 −0.215761248668721 0.596798091443639
    2134 1135102 1135102: PRKCB1 :: protein kinase C, beta 1 349845 −0.441119819917753 0.127447919616108
    2135 1135130 1135130: MYCN :: v-myc myelocytomatosis viral related oncogene, 25960 0.205396780967846 −0.132247221716585
    neuroblastoma derived (avian)
    2136 1135138 1135138: CD24 :: CD24 antigen (small cell lung carcinoma 375108 −0.224445750701083 0.047897690312253
    cluster 4 antigen)
    2137 1135141 1135141: CXCL2 :: chemokine (C—X—C motif) ligand 2 75765 0.216024020910474 −0.301155542846476
    2138 1135151 1135151: CASP6 :: caspase 6, apoptosis-related cysteine protease 3280 −0.029027422712854 0.022459532296497
    2139 1135164 1135164: UMPK :: uridine monophosphate kinase 458360 −0.281270374505862 0.508366629782454
    2140 1135165 1135165: IL16 :: interleukin 16 (lymphocyte chemoattractant factor) 170359 −0.352018704696172 0.134294035068052
    2141 1135168 1135168: DNASE2 :: deoxyribonuclease II, lysosomal 118243 0.356638133348548 −0.424972558101864
    2142 1135173 1135173: LRRN3 :: leucine rich repeat neuronal 3 3781 0.011132687277529 −0.007027834231566
    2143 1135186 1135186: ANXA7 :: annexin A7 386741 0.230842216449984 −0.125584578249155
    2144 1135189 1135189: TP73L :: tumor protein p73-like 137569 0.032938699487530 −0.029874965045244
    2145 1135209 1135209: SIAHBP1 :: fuse-binding protein-interacting repressor 74562 −0.298973092029240 0.426608855649514
    2146 1135214 1135214: TGFB2 :: transforming growth factor, beta 2 169300 −0.003837754874404 0.033518502051147
    2147 1135226 1135226: IKBKG :: inhibitor of kappa light polypeptide gene 43505 0.063215168889229 −0.006415810511503
    enhancer in B-cells, kinase gamma
    2148 1135227 1135227: NFE2 :: nuclear factor (erythroid-derived 2), 45 kDa 75643 0.023578319912982 −0.069183481854815
    2149 1135229 1135229: DUT :: dUTP pyrophosphatase 367676 −0.383694472826659 0.644465225193040
    2150 1135234 1135234: GSK3B :: glycogen synthase kinase 3 beta 282359 0.025939798183179 0.093409732601449
    2151 1135240 1135240: FAP :: fibroblast activation protein, alpha 436852 0.815662355251253 −0.281574290766028
    2152 1135251 1135251: STAT1 :: signal transducer and activator of 21486 0.378465896040287 −0.526929553625389
    transcription 1, 91 kDa
    2153 1135253 1135253: JTV1 :: JTV1 gene 301613 −0.464197830009685 0.642155481384349
    2154 1135267 1135267: TCL1A :: T-cell leukemia/lymphoma 1A 2484 −0.422456471874368 0.350212964400887
    2155 1135270 1135270: SOCS1 :: suppressor of cytokine signaling 1 50640 0.096514479095770 −0.088097434161321
    2156 1135285 1135285: UBE2E3 :: ubiquitin-conjugating enzyme E2E 3 449501 −0.299207238123007 0.432887460519918
    (UBC4/5 homolog, yeast)
    2157 1135299 1135299: LYL1 :: lymphoblastic leukemia derived sequence 1 46446 −0.060409506735203 0.127799805000889
    2158 1135322 1135322: IGFBP3 :: insulin-like growth factor binding protein 3 450230 0.451581199548195 −0.038586544922136
    2159 1135328 1135328: FYN :: FYN oncogene related to SRC, FGR, YES 390567 0.246626834451783 −0.483001893866662
    2160 1135350 1135350: DYRK3 :: dual-specificity tyrosine-(Y)-phosphorylation 164267 −0.130079797899979 0.204564836502494
    regulated kinase 3
    2161 1135374 1135374: BMPR2 :: bone morphogenetic protein receptor, type II 53250 0.021907823889001 −0.049583428001536
    (serine/threonine kinase)
    2162 1135379 1135379: LILRB3 :: leukocyte immunoglobulin-like receptor, −26 0.242300305886075 −0.328430462600683
    subfamily B (with TM and ITIM domains), member 3
    2163 1135380 1135380: CSF2 :: colony stimulating factor 2 (granulocyte-macrophage) 1349 0.067243088208555 −0.044335581523926
    2164 1135383 1135383: CDKN2D :: cyclin-dependent kinase inhibitor 2D 435051 −0.124512964427258 0.064707859522555
    (p19, inhibits CDK4)
    2165 1135395 1135395: GG2-1 :: TNF-induced protein 17839 −0.287358473815222 0.057585874019656
    2166 1135399 1135399: ZNF216 :: zinc finger protein 216 406096 0.562730843915336 −0.447012756023576
    2167 1135467 1135467: CAMK2B :: calcium/calmodulin-dependent protein kinase 321572 0.134875231463102 0.065771849282309
    (CaM kinase) II beta
    2168 1135475 1135475: CHEK2 :: CHK2 checkpoint homolog (S. pombe) 146329 −0.397443511905394 0.548880091150802
    2169 1135487 1135487: SCN3A :: sodium channel, voltage-gated, type III, alpha 300717 0.035229423784445 −0.077879014673317
    2170 1135489 1135489: SSA2 :: Sjogren syndrome antigen A2 (60 kDa, 288178 −0.213090090407771 0.262043380399309
    ribonucleoprotein autoantigen SS-A/Ro)
    2171 1135492 1135492: P2RX5 :: purinergic receptor P2X, ligand-gated ion channel, 5 408615 −0.492212038510146 0.364853473313676
    2172 1135513 1135513: CD209L :: CD209 antigen-like 421437 −0.269435883536644 0.024441295489601
    2173 1135526 1135526: VEGF :: vascular endothelial growth factor 73793 0.325113508581393 −0.029534731933042
    2174 1135529 1135529: AKAP12 :: A kinase (PRKA) anchor protein (gravin) 12 197081 0.327798628207461 −0.280667211293206
    2175 1135541 1135541: BIRC3 :: baculoviral IAP repeat-containing 3 127799 0.215026966456852 −0.008057017397116
    2176 1135549 1135549: CCL23 :: chemokine (C-C motif) ligand 23 169191 0.169612975596130 −0.255583009309114
    2177 1135550 1135550: RASGRF1 :: Ras protein-specific guanine nucleotide- 221811 −0.174032798373146 0.109815766607271
    releasing factor 1
    2178 1135571 1135571: LIMK2 :: LIM domain kinase 2 278027 0.228969728759419 −0.179979819712335
    2179 1135583 1135583: KLRD1 :: killer cell lectin-like receptor subfamily D, 41682 0.154767088293625 −0.291292436228335
    member 1
    2180 1135592 1135592: RASA1 :: RAS p21 protein activator (GTPase 758 −0.128504626836331 0.005951003511595
    activating protein) 1
    2181 1135593 1135593: CDK10 :: cyclin-dependent kinase (CDC2-like) 10 77313 −0.262720735278780 0.116299156451995
    2182 1135606 1135606: LAIR1 :: leukocyte-associated Ig-like receptor 1 407964 0.367419923397012 −0.504520192225527
    2183 1135622 1135622: MAPK8 :: mitogen-activated protein kinase 8 445864 −0.115106896338892 0.066131476924408
    2184 1135645 1135645: SPINT2 :: serine protease inhibitor, Kunitz type, 2 31439 0.037566720623906 −0.249380484239846
    2185 1135665 1135665: DDR1 :: discoidin domain receptor family, member 1 423573 0.230146680281770 −0.299775043520402
    2186 1135673 1135673: PSMA1 :: proteasome (prosome, macropain) subunit, 82159 −0.281720666174377 0.513064897309524
    alpha type, 1
    2187 1135684 1135684: CASP9 :: caspase 9, apoptosis-related cysteine protease 329502 −0.211300862040939 0.245352650816304
    2188 1135685 1135685: TCF3 :: transcription factor 3 (E2A immunoglobulin enhancer 371282 −0.132625532853511 0.339380670215153
    binding factors E12/E47)
    2189 1135735 1135735: ACVRL1 :: activin A receptor type II-like 1 410104 0.299065710574511 −0.308189802383384
    2190 1135743 1135743: TNFRSF25 :: tumor necrosis factor receptor superfamily, 299558 0.234872487618209 −0.471595034051215
    member 25
    2191 1135755 1135755: MCAM :: melanoma cell adhesion molecule 511397 0.269827609205101 0.050442231517023
    2192 1135773 1135773: FCGR2B :: Fc fragment of IgG, low affinity IIb, 126384 −0.094710034742556 0.074929655761349
    receptor for (CD32)
    2193 1135778 1135778: CD86 :: CD86 antigen (CD28 antigen ligand 2, B7-2 antigen) 27954 0.168916871462908 −0.289281311109271
    2194 1135795 1135795: Lin10 :: lin-10 protein homolog 55923 0.528293814614649 −0.217959944059237
    2195 1135801 1135801: CHS1 :: Chediak-Higashi syndrome 1 130188 0.115318364998609 −0.224257398564241
    2196 1135802 1135802: CAPN3 :: calpain 3, (p94) 439343 0.164155251202988 −0.418087129363220
    2197 1135826 1135826: PFKM :: phosphofructokinase, muscle 75160 −0.358643155033839 0.498879090538368
    2198 1135830 1135830: GPRK6 :: G protein-coupled receptor kinase 6 235116 −0.137147395547579 −0.066956658835406
    2199 1135835 1135835: TPM1 :: tropomyosin 1 (alpha) 133892 0.844500075257288 −0.400650137852855
    2200 1135852 1135852: UBE2I :: ubiquitin-conjugating enzyme E2I 302903 −0.055021621102330 0.012335299075447
    (UBC9 homolog, yeast)
    2201 1135858 1135858: HSPA4 :: heat shock 70 kDa protein 4 90093 −0.273737239778974 0.470740053479600
    2202 1135866 1135866: MGLL :: monoglyceride lipase 409826 −0.105545203381370 −0.152401403416860
    2203 1135871 1135871: CYLN2 :: cytoplasmic linker 2 104717 0.492247783576989 −0.405561899962111
    2204 1135899 1135899: DBI :: diazepam binding inhibitor (GABA receptor 78888 0.106730411631004 0.010913990066277
    modulator, acyl-Coenzyme A binding protein)
    2205 1135925 1135925: LILRB1 :: leukocyte immunoglobulin-like receptor, 149924 −0.022827469254302 −0.121870105927558
    subfamily B (with TM and ITIM domains), member 1
    2206 1135929 1135929: NFATC1 :: nuclear factor of activated T-cells, cytoplasmic, 512591 −0.230076225407584 0.015263924708268
    calcineurin-dependent 1
    2207 1135930 1135930: AURKC :: aurora kinase C 98338 −0.015602552109567 −0.050852618143140
    2208 1135966 1135966: THPO :: thrombopoietin (myeloproliferative leukemia 1166 −0.070240091216135 0.060929707028526
    virus oncogene ligand, megakaryocyte growth and development factor)
    2209 1135968 1135968: ACTN1 :: actinin, alpha 1 119000 0.803045210914051 −0.443427303702404
    2210 1135974 1135974: RENT1 :: regulator of nonsense transcripts 1 388125 −0.277013571071871 0.271498553157074
    2211 1135982 1135982: PSTPIP1 :: proline-serine-threonine phosphatase 129758 0.263915152962747 −0.498016545266176
    interacting protein 1
    2212 1135994 1135994: ICOSL :: inducible T-cell co-stimulator ligand 14155 0.095990130380820 −0.112046453556527
    2213 1136002 1136002: CASK :: calcium/calmodulin-dependent serine protein kinase 288196 0.101320852559842 −0.096367400453437
    (MAGUK family)
    2214 1136048 1136048: TNFRSF25 :: tumor necrosis factor receptor 299558 0.124716682297827 −0.408102750362765
    superfamily, member 25
    2215 1136051 1136051: CSF2RA :: colony stimulating factor 2 receptor, alpha, 520937 0.614522954701183 −0.281145422492197
    low-affinity (granulocyte-macrophage)
    2216 1136055 1136055: UBC :: ubiquitin C 183704 −0.017390939478490 −0.243810714198309
    2217 1136056 1136056: CDK7 :: cyclin-dependent kinase 7 (MO15 homolog, 184298 −0.204830293446290 0.441840876555980
    Xenopus laevis, cdk-activating kinase)
    2218 1136087 1136087: ITK :: IL2-inducible T-cell kinase 211576 0.211045649761843 −0.423904231475203
    2219 1136109 1136109: MAP2K5 :: mitogen-activated protein kinase kinase 5 436145 −0.270995770271572 0.045366180573479
    2220 1136150 1136150: TYRO3 :: TYRO3 protein tyrosine kinase 381282 0.069212714183531 −0.029671317117098
    2221 1136152 1136152: CCRL2 :: chemokine (C-C motif) receptor-like 2 458436 0.360883312741600 −0.375561473188188
    2222 1136162 1136162: AKT2 :: v-akt murine thymoma viral oncogene homolog 2 326445 −0.208297523200300 0.174642196469647
    2223 1136172 1136172: SULT1C1 :: sulfotransferase family, cytosolic, 1C, member 1 38084 0.650163073768228 −0.258621533863630
    2224 1136185 1136185: ITGB8 :: integrin, beta 8 355722 −0.039929578583942 −0.041458162075154
    2225 1136193 1136193: MAPK11 :: mitogen-activated protein kinase 11 57732 0.306565774763432 −0.328494812564979
    2226 1136216 1136216: HLA-G :: HLA-G histocompatibility antigen, class I, G 512152 0.332885800453946 −0.553560222998666
    2227 1136269 1136269: MAST205 :: microtubule associated testis specific 101474 0.223412342428654 0.138958768884101
    serine/threonine protein kinase
    2228 1136273 1136273: HOP :: homeodomain-only protein 13775 0.476703362822473 −0.307711782501049
    2229 1136285 1136285: LRPPRC :: leucine-rich PPR-motif containing 182490 −0.435679656870025 0.601290247138512
    2230 1136329 1136329: HIC :: I-mfa domain-containing protein 132739 −0.027288699750570 −0.117406065312260
    2231 1136337 1136337: NCALD :: neurocalcin delta 90063 0.338984738958917 −0.245462539985130
    2232 1136343 1136343: BBC3 :: BCL2 binding component 3 87246 −0.050405192310055 −0.036901688934723
    2233 1136357 1136357: SCGF :: stem cell growth factor; lymphocyte 512680 0.677947187540831 −0.298730690287187
    secreted C-type lectin
    2234 1136362 1136362: OK/SW-cl.56 :: beta 5-tubulin 356729 −0.408563420151110 0.742172430214216
    2235 1136369 1136369: FLJ20323 :: hypothetical protein FLJ20323 387140 −0.262683063661753 0.404486726869442
    2236 1136371 1136371: FMO2 :: flavin containing monooxygenase 2 361155 0.052259965061053 −0.122705355848300
    2237 1136379 1136379: FCER1A :: Fc fragment of IgE, high affinity I, 897 0.013936619697511 −0.013197557598909
    receptor for; alpha polypeptide
    2238 1136391 1136391: PTGDS :: prostaglandin D2 synthase 21 kDa (brain) 446429 0.511480233544877 −0.435655362037836
    2239 1136393 1136393: TUBA6 :: tubulin alpha 6 406578 −0.179227481381745 0.374710668827628
    2240 1136401 1136401: SIP :: Siah-interacting protein 27258 −0.379183284208103 0.535722487344917
    2241 1136408 1136408: POU2F2 :: POU domain, class 2, transcription factor 2 1101 −0.354137582792841 0.429728063769577
    2242 1136427 1136427: FYB :: FYN binding protein (FYB-120/130) 276506 0.357796609387918 −0.441555304919001
    2243 1136430 1136430: IGLJ3 :: immunoglobulin lambda joining 3 102950 0.109778160374844 −0.098831871658468
    2244 1136459 1136459: KIAA0551 :: Traf2 and NCK interacting kinase 252550 0.365508689849397 −0.430643879731062
    2245 1136464 1136464: BAX :: BCL2-associated X protein 159428 −0.106116191477644 0.042671340080830
    2246 1136540 1136540: PLAUR :: plasminogen activator, urokinase receptor 179657 0.666710687865820 −0.301093054608278
    2247 1136573 1136573: HLA-DPA1 :: major histocompatibility complex, 914 0.093919078766697 −0.282244466739273
    class II, DP alpha 1
    2248 1136585 1136585: MKI67 :: antigen identified by monoclonal antibody Ki-67 80976 −0.322784784394788 0.786209797714773
    2249 1136595 1136595: VDAC1 :: voltage-dependent anion channel 1 404814 −0.329398024691907 0.585972473136041
    2250 1136599 1136599: MAPK3 :: mitogen-activated protein kinase 3 861 0.079560238680393 0.110483410795923
    2251 1136601 1136601: KIAA1522 :: KIAA1522 protein 322735 −0.282563015525018 0.476574635966113
    2252 1136605 1136605: MAZ :: MYC-associated zinc finger protein (purine-binding 448398 −0.375211792940038 0.462155982376696
    transcription factor)
    2253 1136620 1136620: COL6A1 :: collagen, type VI, alpha 1 415997 0.752399713314935 −0.294498892879228
    2254 1136655 1136655: FBXO9 :: F-box only protein 9 388387 −0.340363407814236 0.444483352898254
    2255 1136662 1136662: PIK3R1 :: phosphoinositide-3-kinase, regulatory subunit, 6241 0.238423381122479 −0.289911768148796
    polypeptide 1 (p85 alpha)
    2256 1136681 1136681: KHSRP :: KH-type splicing regulatory protein 91142 −0.176274134948602 0.237953667245025
    (FUSE binding protein 2)
    2257 1136687 1136687: CREB3L2 :: cAMP responsive element binding 59943 −0.194398113086998 −0.060634386685776
    protein 3-like 2
    2258 1136692 1136692: KIAA0913 :: KIAA0913 protein 65135 0.157495567129249 −0.509878413292112
    2259 1136702 1136702: KIAA0121 :: KIAA0121 gene product 155584 0.054990929492512 0.085009319320804
    2260 1136710 1136710: GTF3C2 :: general transcription factor IIIC, 75782 −0.396439011974729 0.384390673177142
    polypeptide 2, beta 110 kDa
    2261 1136712 1136712: LOC253782 :: hypothetical protein LOC253782 503941 0.206133682187914 −0.355144643398998
    2262 1136718 1136718: SUCLG2 :: succinate-CoA ligase, GDP-forming, beta subunit 446476 −0.367316089248735 0.168181491783958
    2263 1136722 1136722: TPM4 :: tropomyosin 4 250641 0.032764759626493 0.117199289648095
    2264 1136724 1136724: DNAJC8 :: DnaJ (Hsp40) homolog, subfamily C, member 8 433540 −0.227564371595965 0.384799422123307
    2265 1136759 1136759: :: Homo sapiens clone 23872 mRNA sequence 188882 −0.246541834783006 0.118058054542888
    2266 1136762 1136762: CHN1 :: chimerin (chimaerin) 1 380138 0.531781776267429 −0.309684138139920
    2267 1136765 1136765: PRKCL2 :: protein kinase C-like 2 69171 −0.052449761989885 0.002703484644613
    2268 1136774 1136774: IL1RN :: interleukin 1 receptor antagonist 81134 0.198165705307058 −0.271282824734418
    2269 1136777 1136777: HLA-DQA1 :: major histocompatibility complex, 387679 0.095000643669076 −0.192356554908310
    class II, DQ alpha 1
    2270 1136781 1136781: PPP1R14B :: protein phosphatase 1, regulatory 120197 −0.350667785791036 0.599063986397151
    (inhibitor) subunit 14B
    2271 1136784 1136784: JMJD1 :: jumonji domain containing 1 321707 0.037507681795198 0.042300448176934
    2272 1136786 1136786: PCCB :: propionyl Coenzyme A carboxylase, 63788 −0.589479064855973 0.500462229668922
    beta polypeptide
    2273 1136788 1136788: SEPT10 :: septin 10 355455 0.743385086666469 −0.472469825174593
    2274 1136819 1136819: DKFZP564O043 :: hypothetical protein DKFZp564O043 112605 −0.108061343689995 0.015483574748141
    2275 1136831 1136831: PPFIBP2 :: PTPRF interacting protein, binding protein 2 12953 0.029792915483790 −0.007676278659483
    (liprin beta 2)
    2276 1136832 1136832: RANBP2L1 :: RAN binding protein 2-like 1 434959 0.482289022689679 −0.582659344585077
    2277 1136844 1136844: C21orf25 :: chromosome 21 open reading frame 25 16007 0.360004946699269 −0.421664849812932
    2278 1136853 1136853: SMYD2 :: SET and MYND domain containing 2 66170 −0.372211589853700 0.355510218953968
    2279 1136859 1136859: KIAA1199 :: KIAA1199 protein 212584 0.436417109927428 −0.218192786328106
    2280 1136865 1136865: MGC4170 :: MGC4170 protein 412128 0.282712755201433 −0.388421252788627
    2281 1136876 1136876: TLK2 :: tousled-like kinase 2 445078 −0.155319085898057 0.204103146968723
    2282 1136877 1136877: HLA-DQB2 :: major histocompatibility complex, 375115 0.192335314451624 −0.319281345548139
    class II, DQ beta 2
    2283 1136902 1136902: :: Homo sapiens mRNA; cDNA DKFZp779B1535 442592 0.037180838679762 0.027204468801935
    (from clone DKFZp779B1535)
    2284 1136903 1136903: EEF1D :: eukaryotic translation elongation factor 334798 −0.169515366664499 0.121701880331947
    1 delta (guanine nucleotide exchange protein)
    2285 1136913 1136913: EEG1 :: likely ortholog of mouse embryonic epithelial gene 1 99962 −0.120301577698138 0.418446911641021
    2286 1136925 1136925: BICD2 :: bicaudal D homolog 2 (Drosophila) 436939 −0.290814207335427 0.194781442202637
    2287 1136938 1136938: MINA53 :: myc-induced nuclear antigen, 53 kDa 23294 −0.417163002239899 0.308929563321094
    2288 1136939 1136939: :: Homo sapiens T cell receptor beta chain 419777 0.254956828947675 −0.564468551099593
    BV20S1 BJ1-5 BC1 mRNA, complete cds
    2289 1136971 1136971: STIP1 :: stress-induced-phosphoprotein 1 257827 −0.246439382578630 0.490417223621355
    (Hsp70/Hsp90-organizing protein)
    2290 1136972 1136972: NEK1 :: NIMA (never in mitosis gene a)-related kinase 1 414410 −0.231210263189500 0.204963384701897
    2291 1136983 1136983: :: Homo sapiens similar to Nuclear envelope pore 450237 −0.388641220178648 0.487819551534725
    membrane protein
    2292 1136984 1136984: SNX1 :: sorting nexin 1 498154 −0.040880352409561 −0.263364454525231
    2293 1136987 1136987: SFMBT1 :: Scm-like with four mbt domains 1 21695 −0.302266892109625 0.163781928286487
    2294 1136988 1136988: CASP8 :: caspase 8, apoptosis-related cysteine protease 243491 0.135637824443728 −0.336196763757261
    2295 1136996 1136996: RNASE4 :: ribonuclease, RNase A family, 4 283749 0.530666527925623 −0.397210146260416
    2296 1137022 1137022: ITGAL :: integrin, alpha L (antigen CD11A (p180), 174103 0.205038646441539 −0.397020451104670
    lymphocyte function-associated antigen 1; alpha polypeptide)
    2297 1137026 1137026: MAP2K2 :: mitogen-activated protein kinase kinase 2 366546 −0.262905023273146 0.252101699347407
    2298 1137042 1137042: G0S2 :: putative lymphocyte G0/G1 switch gene 432132 0.538116332321084 −0.276091529850567
    2299 1137097 1137097: KNS2 :: kinesin 2 60/70 kDa 512578 0.399642064990379 −0.453052638372648
    2300 1137109 1137109: RPL5 :: ribosomal protein L5 469653 −0.122252811851800 0.006080037924381
    2301 1137112 1137112: MUC1 :: mucin 1, transmembrane 89603 0.317119298256267 −0.312275797088170
    2302 1137137 1137137: FLNA :: filamin A, alpha (actin binding protein 280) 195464 0.567136331652304 −0.391193497147128
    2303 1137158 1137158: C14orf120 :: chromosome 14 open reading frame 120 9043 −0.282866289386583 0.413058262482048
    2304 1137201 1137201: SRRM2 :: serine/arginine repetitive matrix 2 433343 −0.272530261309250 0.320630860600962
    2305 1137202 1137202: SMT3H2 :: SMT3 suppressor of mif two 3 homolog 2 (yeast) 380973 −0.234617743279140 0.241957518841459
    2306 1137247 1137247: LYZ :: lysozyme (renal amyloidosis) 234734 0.608426386367492 −0.450067626480979
    2307 1137273 1137273: ITGB5 :: integrin, beta 5 149846 0.649262426877578 −0.271621269006555
    2308 1137289 1137289: CD7 :: CD7 antigen (p41) 36972 0.165984784499907 −0.465353463451909
    2309 1137291 1137291: XTP2 :: HBxAg transactivated protein 2 446197 0.078785114363620 −0.149442218814294
    2310 1137308 1137308: FUBP1 :: far upstream element (FUSE) binding protein 1 118962 −0.421138601237465 0.248985090248871
    2311 1137328 1137328: PDE4DIP :: phosphodiesterase 4D interacting protein 502577 0.240910452929125 −0.201889801334610
    (myomegalin)
    2312 1137332 1137332: PPBP :: pro-platelet basic protein (chemokine 2164 0.006793019489238 −0.121914777496122
    (C—X—C motif) ligand 7)
    2313 1137343 1137343: FH :: fumarate hydratase 391168 −0.259855496056412 0.452895074131933
    2314 1137360 1137360: CLN2 :: ceroid-lipofuscinosis, neuronal 2, late infantile 429658 0.086740222842950 −0.125808364812224
    (Jansky-Bielschowsky disease)
    2315 1137378 1137378: TNFRSF4 :: tumor necrosis factor receptor superfamily, 129780 0.371458297794605 −0.397187816049941
    member 4
    2316 1137439 1137439: MAP4K1 :: mitogen-activated protein kinase kinase kinase 95424 −0.303418341057957 0.261214531356896
    kinase 1
    2317 1137447 1137447: HSPCB :: heat shock 90 kDa protein 1, beta 74335 −0.458725739759769 0.604001646900960
    2318 1137449 1137449: MATR3 :: matrin 3 223745 −0.387281340518201 0.358637187063220
    2319 1137481 1137481: C4A :: complement component 4A 150833 0.182892012520496 −0.507231719813946
    2320 1137486 1137486: MIZ1 :: Msx-interacting-zinc finger 441069 −0.443002780855262 0.498631456766930
    2321 1137488 1137488: NFKBIB :: nuclear factor of kappa light polypeptide gene 9731 −0.222344495661454 0.244641154107860
    enhancer in B-cells inhibitor, beta
    2322 1137492 1137492: HLA-C :: major histocompatibility complex, class I, C 274485 0.197365260701921 −0.407821263356476
    2323 1137506 1137506: H2AFY :: H2A histone family, member Y 75258 −0.149835935606420 0.445133707052547
    2324 1137512 1137512: PC4 :: activated RNA polymerase II transcription cofactor 4 229641 −0.082525052793081 −0.145075136097169
    2325 1137534 1137534: CD7 :: CD7 antigen (p41) 36972 0.107180183166121 −0.365438064689284
    2326 1137539 1137539: XCL2 :: chemokine (C motif) ligand 2 458346 −0.053308591493161 −0.246840014028833
    2327 1137561 1137561: HOXA1 :: homeo box A1 67397 −0.150079735454765 0.253920313043797
    2328 1137582 1137582: CLK1 :: CDC-like kinase 1 433732 0.093677520704906 −0.366781439753622
    2329 1137583 1137583: ALDOA :: aldolase A, fructose-bisphosphate 273415 0.018724212498213 0.324301589252045
    2330 1137594 1137594: CCNB1 :: cyclin B1 23960 −0.375043781726022 0.836819695371722
    2331 1137597 1137597: CDC42EP4 :: CDC42 effector protein (Rho GTPase 3903 0.425898445808089 −0.369669790160663
    binding) 4
    2332 1137601 1137601: GLG1 :: golgi apparatus protein 1 78979 −0.035094612373837 0.009288993829497
    2333 1137626 1137626: PCTK3 :: PCTAIRE protein kinase 3 445402 0.603150172723823 −0.262769906333315
    2334 1137643 1137643: GRHPR :: glyoxylate reductase/hydroxypyruvate reductase 155742 −0.295435375518062 0.291585562608132
    2335 1137663 1137663: DDAH2 :: dimethylarginine dimethylaminohydrolase 2 247362 0.202876395419915 −0.290851646277916
    2336 1137687 1137687: CXCL5 :: chemokine (C—X—C motif) ligand 5 89714 0.150406826331083 0.017128841867423
    2337 1137698 1137698: GLUL :: glutamate-ammonia ligase (glutamine synthase) 442669 0.408287031744038 −0.261412315186599
    2338 1137742 1137742: TSC22 :: transforming growth factor beta-stimulated protein 433796 0.564778777615456 −0.406101020606446
    TSC-22
    2339 1137751 1137751: RBMS1 :: RNA binding motif, single stranded interacting 241567 0.433483960928137 −0.410155449387123
    protein 1
    2340 1137760 1137760: DEDD :: death effector domain containing 169681 −0.230491915465838 0.225693647285405
    2341 1137771 1137771: HLA-DRB3 :: major histocompatibility complex, class II, DR 308026 0.206113521293342 −0.346477434254079
    beta 3
    2342 1137782 1137782: SOD2 :: superoxide dismutase 2, mitochondrial 384944 0.418904407792592 −0.306800309295515
    2343 1137806 1137806: HLA-A :: major histocompatibility complex, class I, A 181244 0.201083967413937 −0.433287362783418
    2344 1137809 1137809: CD8B1 :: CD8 antigen, beta polypeptide 1 (p37) 405667 0.185618649145311 −0.524929307636060
    2345 1137838 1137838: C6orf4 :: chromosome 6 open reading frame 4 437508 −0.011993611215563 0.009969912053544
    2346 1137868 1137868: BTN2A1 :: butyrophilin, subfamily 2, member A1 169963 0.262408129037849 −0.396710767904983
    2347 1137908 1137908: :: Homo sapiens similar to Gamma-glutamyltranspeptidase 1 454906 0.210979969677693 −0.256296439980480
    precursor (Gamma-glutamyltransferase 1) (CD224 antigen)
    (LOC376813), mRNA
    2348 1137955 1137955: SNRPA1 :: small nuclear ribonucleoprotein polypeptide A′ 434901 −0.369156412146049 0.608254320273560
    2349 1138030 1138030: CD72 :: CD72 antigen 116481 −0.294390921816877 0.100908549519153
    2350 1138048 1138048: LY9 :: lymphocyte antigen 9 403857 0.073607730059501 −0.263186409754900
    2351 1138120 1138120: ITGB1 :: integrin, beta 1 (fibronectin receptor, beta 287797 0.160065610900893 −0.075596946134885
    polypeptide, antigen CD29 includes MDF2, MSK12)
    2352 1138128 1138128: MAP3K4 :: mitogen-activated protein kinase kinase kinase 4 390428 −0.049185143371545 −0.087852800223420
    2353 1138132 1138132: IGKV1D-13 :: immunoglobulin kappa variable 1D-13 390427 0.037120917614071 −0.136065857206246
    2354 1138136 1138136: RBM9 :: RNA binding motif protein 9 351478 0.378938518577512 −0.126082972595542
    2355 1138147 1138147: PRKACA :: protein kinase, cAMP-dependent, catalytic, alpha 194350 −0.053368491488809 0.041644135318140
    2356 1138150 1138150: MCM5 :: MCM5 minichromosome maintenance deficient 5, 77171 −0.444102278229523 0.638269533484216
    cell division cycle 46 (S. cerevisiae)
    2357 1138157 1138157: KIAA0153 :: KIAA0153 protein 82563 −0.391835266746382 0.547098931278669
    2358 1138192 1138192: NR3C1 :: nuclear receptor subfamily 3, group C, member 1 512414 0.118279477753652 −0.092009520189905
    (glucocorticoid receptor)
    2359 1138244 1138244: FN1 :: fibronectin 1 418138 0.813782327518728 −0.313203946687403
    2360 1138259 1138259: HDGF :: hepatoma-derived growth factor (high-mobility 89525 −0.214962450182430 0.470812643332632
    group protein 1-like)
    2361 1138279 1138279: TPT1 :: tumor protein, translationally-controlled 1 374596 −0.064219389358256 −0.167378055599220
    2362 1138312 1138312: CCL2 :: chemokine (C-C motif) ligand 2 303649 0.221948111535212 −0.350981175150463
    2363 1138331 1138331: P5 :: protein disulfide isomerase-related protein −7 −0.107207026289785 0.265506953156497
    2364 1138355 1138355: ADA :: adenosine deaminase 407135 0.040541203021177 −0.080197093953995
    2365 1138379 1138379: ERBB2 :: v-erb-b2 erythroblastic leukemia viral oncogene 446352 0.283250039386084 −0.286769120359251
    homolog 2, neuro/glioblastoma derived oncogene homolog (avian)
    2366 1138392 1138392: MTCP1 :: mature T-cell proliferation 1 3548 −0.004895350279116 0.276483111443163
    2367 1138400 1138400: IL17 :: interleukin 17 (cytotoxic T-lymphocyte-associated 41724 −0.032075332580235 −0.038773611235492
    serine esterase 8)
    2368 1138417 1138417: ST14 :: suppression of tumorigenicity 14 (colon carcinoma, 56937 −0.230448449478436 0.279346957925828
    matriptase, epithin)
    2369 1138421 1138421: KIAA0690 :: KIAA0690 protein 434251 −0.309133083322402 0.403967809571089
    2370 1138441 1138441: PASK :: PAS domain containing serine/threonine kinase 397891 0.144733774920620 −0.188242721745811
    2371 1138443 1138443: FCGR1A :: Fc fragment of IgG, high affinity Ia, receptor for 77424 0.207475205893738 −0.341850921762133
    (CD64)
    2372 1138507 1138507: DMPK :: dystrophia myotonica-protein kinase 898 0.021947645562805 −0.046183891035291
    2373 1138515 1138515: HOMER2 :: homer homolog 2 (Drosophila) 93564 −0.020645296163426 −0.133209561135918
    2374 1138532 1138532: CAMK1G :: calcium/calmodulin-dependent protein kinase IG 199068 −0.012177377955444 0.053516560538452
    2375 1138537 1138537: VDAC1P :: voltage-dependent anion channel 1 pseudogene −3 −0.324102650163308 0.516292454706352
    2376 1138538 1138538: TRD@ :: T cell receptor delta locus 2014 0.236980853252771 −0.340030980985647
    2377 1138541 1138541: TNK1 :: tyrosine kinase, non-receptor, 1 203420 −0.149408449223409 −0.017420119646561
    2378 1138555 1138555: LTK :: leukocyte tyrosine kinase 434481 −0.192632421203761 0.079999448729701
    2379 1138567 1138567: CYB561 :: cytochrome b-561 355264 0.218450857044390 −0.352832586952820
    2380 1138645 1138645: MDM2 :: Mdm2, transformed 3T3 cell double minute 2, p53 212217 −0.068650083946957 0.108796027856608
    binding protein (mouse)
    2381 1138647 1138647: ETV6 :: ets variant gene 6 (TEL oncogene) 171262 −0.010676070319985 −0.013258155419776
    2382 1138652 1138652: KYNU :: kynureninase (L-kynurenine hydrolase) 444471 0.465037916013166 −0.350613895243343
    2383 1138670 1138670: CD22 :: CD22 antigen 262150 −0.303837324203375 0.291639786954158
    2384 1138671 1138671: HIRA :: HIR histone cell cycle regulation defective 415735 −0.234356236620965 0.181811279669565
    homolog A (S. cerevisiae)
    2385 1138677 1138677: :: Homo sapiens cDNA clone MGC: 71446 IMAGE: −50 0.334871522054608 −0.565143538142995
    5420082, complete cds
    2386 1138721 1138721: CR1 :: complement component (3b/4b) receptor 1, including 334019 0.213185633461993 −0.167181676121616
    Knops blood group system
    2387 1138759 1138759: SMARCA2 :: SWI/SNF related, matrix associated, actin 396404 0.239912669361491 −0.356112384377712
    dependent regulator of chromatin, subfamily a, member 2
    2388 1138765 1138765: SEC61A1 :: Sec61 alpha 1 subunit (S. cerevisiae) 306079 −0.173564213544419 0.042950263600793
    2389 1138778 1138778: HRI :: heme-regulated initiation factor 2-alpha kinase 434986 −0.436150698025647 0.461973052646480
    2390 1138780 1138780: PBEF :: pre-B-cell colony-enhancing factor 293464 0.089301913080073 0.030231044097990
    2391 1138783 1138783: WAC :: WW domain-containing adapter with a coiled-coil 370152 −0.309940954918134 0.313859449051489
    region
    2392 1138789 1138789: FLJ13855 :: hypothetical protein FLJ13855 369120 0.086491087161513 −0.352846239711779
    2393 1138801 1138801: HSPC152 :: hypothetical protein HSPC152 333579 −0.483341541739176 0.490594109811054
    2394 1138832 1138832: USP39 :: ubiquitin specific protease 39 12820 −0.352268143901638 0.421581995099915
    2395 1138845 1138845: CDC42BPB :: CDC42 binding protein kinase beta 436985 0.425134584059284 −0.387183184478298
    (DMPK-like)
    2396 1138858 1138858: MIF :: macrophage migration inhibitory factor (glycosylation- 407995 −0.407665306199589 0.682825403279751
    inhibiting factor)
    2397 1138867 1138867: EPLIN :: epithelial protein lost in neoplasm beta 10706 0.464814747439025 −0.363469285796447
    2398 1138874 1138874: TCFL4 :: transcription factor-like 4 383019 −0.314256250926088 0.306346209499633
    2399 1138878 1138878: DNCL2A :: dynein, cytoplasmic, light polypeptide 2A 100002 −0.153830377554263 −0.051030556926909
    2400 1138887 1138887: HDAC7A :: histone deacetylase 7A 200063 −0.078208993612420 0.074601964005980
    2401 1138905 1138905: KIAA1194 :: KIAA1194 437844 −0.281406606938181 0.481911861505412
    2402 1138910 1138910: MORF4L1 :: mortality factor 4 like 1 374503 0.034752735498991 −0.015115740634790
    2403 1138920 1138920: CXCL14 :: chemokine (C—X—C motif) ligand 14 24395 0.272782188852422 −0.301011805560417
    2404 1138944 1138944: FLJ12442 :: hypothetical protein FLJ12442 84753 −0.388324622909977 0.572404037246780
    2405 1138959 1138959: RICH1 :: RhoGAP interacting with CIP4 homologs 1 203605 −0.433959401052288 0.126101372366550
    2406 1138973 1138973: MGC2491 :: hypothetical protein MGC2491 11270 −0.252406521349047 0.318256960904562
    2407 1138994 1138994: SCAMP2 :: secretory carrier membrane protein 2 238030 −0.048843627249750 −0.056347071925834
    2408 1138995 1138995: FLJ22056 :: hypothetical protein FLJ22056 24956 0.312239840661249 −0.155950823692214
    2409 1139005 1139005: CABC1 :: chaperone, ABC1 activity of bc1 complex like 273186 −0.132100329795946 −0.079271294569867
    (S. pombe)
    2410 1139017 1139017: NANS :: N-acetylneuraminic acid synthase (sialic acid 274424 0.139351446215690 0.183979506976574
    synthase)
    2411 1139026 1139026: MKNK2 :: MAP kinase-interacting serine/threonine kinase 2 512094 −0.060610570736422 0.129185990473453
    2412 1139037 1139037: CKIP-1 :: CK2 interacting protein 1; HQ0024c protein 173380 0.184289444061499 −0.394499906002833
    2413 1139039 1139039: TNKS2 :: tankyrase, TRF1-interacting ankyrin-related ADP- 280776 −0.153598065351604 0.099989367851187
    ribose polymerase 2
    2414 1139048 1139048: CNOT7 :: CCR4-NOT transcription complex, subunit 7 170553 −0.298252308752349 0.459920880578746
    2415 1139054 1139054: LOC58486 :: transposon-derived Buster1 transposase-like 25726 −0.222878320242169 −0.007560363161300
    protein
    2416 1139076 1139076: HERC1 :: hect (homologous to the E6-AP (UBE3A) carboxyl 133411 0.337597568585952 −0.434587953268159
    terminus) domain and RCC1 (CHC1)-like domain (RLD) 1
    2417 1139100 1139100: GMNN :: geminin, DNA replication inhibitor 234896 −0.318640932117085 0.797462309697701
    2418 1139105 1139105: USP21 :: ubiquitin specific protease 21 8015 −0.434624771827016 0.226787372995122
    2419 1139106 1139106: TNFRSF12A :: tumor necrosis factor receptor superfamily, 355899 0.499326017992532 −0.272857576593047
    member 12A
    2420 1139127 1139127: DNAJC1 :: DnaJ (Hsp40) homolog, subfamily C, member 1 13015 0.333008884215991 −0.255813893496613
    2421 1139185 1139185: RIOK2 :: RIO kinase 2 (yeast) 27021 −0.394717490147720 0.430516797716350
    2422 1139196 1139196: MAFB :: v-maf musculoaponeurotic fibrosarcoma oncogene 169487 0.439789287104131 −0.478712508849918
    homolog B (avian)
    2423 1139202 1139202: KBTBD4 :: kelch repeat and BTB (POZ) domain containing 4 440695 −0.139779161280927 0.186642624167192
    2424 1139215 1139215: MDS029 :: uncharacterized hematopoietic stem/progenitor 43549 −0.231448151224285 0.519061887050639
    cells protein MDS029
    2425 1139226 1139226: FLJ11342 :: hypothetical protein FLJ11342 266514 −0.505040308522747 0.354962950374504
    2426 1139230 1139230: PLEKHF2 :: pleckstrin homology domain containing, 29724 0.047925608046581 0.167450282579172
    family F (with FYVE domain) member 2
    2427 1139235 1139235: FLJ11196 :: acheron 416755 0.518138878363181 −0.428622150654900
    2428 1139265 1139265: FLJ12436 :: hypothetical protein FLJ12436 187657 −0.499034983187793 0.623313352401062
    2429 1139266 1139266: RGC32 :: RGC32 protein 76640 0.159027989824428 −0.087571314039428
    2430 1139274 1139274: CDK5RAP3 :: CDK5 regulatory subunit associated protein 3 20157 −0.323524477001354 −0.008936362298060
    2431 1139277 1139277: TAPBP-R :: TAP binding protein related 267993 0.175034517314223 −0.361681139356850
    2432 1139280 1139280: FBXW7 :: F-box and WD-40 domain protein 7 (archipelago 312503 −0.256428453680362 0.231741417406240
    homolog, Drosophila)
    2433 1139301 1139301: BSPRY :: B-box and SPRY domain containing 108502 −0.193830915039114 −0.024241326240483
    2434 1139303 1139303: FLJ20511 :: hypothetical protein FLJ20511 134406 −0.307110727683744 0.247243898936555
    2435 1139314 1139314: FCGRT :: Fc fragment of IgG, receptor, transporter, alpha 111903 0.263924260656374 −0.500814050113789
    2436 1139360 1139360: FLJ10486 :: hypothetical protein FLJ10486 173946 −0.403868709065567 0.512692327611680
    2437 1139393 1139393: OPN3 :: opsin 3 (encephalopsin, panopsin) 170129 0.076789396477269 −0.141913398593755
    2438 1139411 1139411: OSBPL10 :: oxysterol binding protein-like 10 368238 −0.417496181839488 0.261396462305931
    2439 1139444 1139444: RABL2B :: RAB, member of RAS oncogene family-like 2B 355874 0.063409117787863 −0.166237878791748
    2440 1139461 1139461: BIN2 :: bridging integrator 2 14770 0.256527759821467 −0.339692650263970
    2441 1139466 1139466: LOC51762 :: RAB-8b protein 365655 0.231557760181664 −0.095180733736222
    2442 1139483 1139483: FKBP10 :: FK506 binding protein 10, 65 kDa 3849 0.674153797219952 −0.221743793245193
    2443 1139526 1139526: HSPC177 :: hypothetical protein HSPC177 415534 0.163735980619122 −0.137102206317660
    2444 1139528 1139528: TRPM4 :: transient receptor potential cation channel, 31608 0.131053770432532 −0.044594419561590
    subfamily M, member 4
    2445 1139531 1139531: MGC8407 :: hypothetical protein MGC8407 145156 −0.078540256164261 0.151455641167260
    2446 1139542 1139542: NEIL1 :: nei endonuclease VIII-like 1 (E. coli) 512732 0.026893739120928 0.051569026919496
    2447 1139552 1139552: FLJ23119 :: hypothetical protein FLJ23119 413386 −0.003018803127220 −0.058250007576066
    2448 1139556 1139556: RIN3 :: Ras and Rab interactor 3 413374 0.295487317472535 −0.531059799897965
    2449 1139572 1139572: SNCAIP :: synuclein, alpha interacting protein (synphilin) 24948 0.148663268443581 −0.169804663179603
    2450 1139575 1139575: SN :: sialoadhesin 31869 −0.010823611694524 −0.347990816689990
    2451 1139579 1139579: BCL11B :: B-cell CLL/lymphoma 11B (zinc finger protein) 57987 0.269001973086771 −0.570933632618085
    2452 1139603 1139603: ZNF226 :: zinc finger protein 226 145956 0.112382635429707 −0.194688343434095
    2453 1139623 1139623: BANK1 :: B-cell scaffold protein with ankyrin repeats 1 193736 −0.166958172604313 0.185243160384443
    2454 1139645 1139645: C14orf101 :: chromosome 14 open reading frame 101 134051 −0.193861410475501 0.089892119649755
    2455 1139654 1139654: ECT2 :: epithelial cell transforming sequence 2 oncogene 293257 −0.204095198089242 0.656075928375559
    2456 1139661 1139661: FN5 :: FN5 protein 416456 0.567268031407027 −0.473817226590911
    2457 1139663 1139663: RNPC4 :: RNA-binding region (RNP1, RRM) containing 4 4997 −0.312001381814897 0.310598617201023
    2458 1139669 1139669: C17 :: cytokine-like protein C17 13872 0.224259916127251 −0.255436447025748
    2459 1139767 1139767: FBXL12 :: F-box and leucine-rich repeat protein 12 12439 −0.175973426526743 0.041273627872276
    2460 1139774 1139774: SNX11 :: sorting nexin 11 15827 0.021233224776666 −0.069044004608862
    2461 1139805 1139805: CYB5R2 :: cytochrome b5 reductase b5R.2 414362 −0.255806993410501 0.209851938563531
    2462 1139830 1139830: SAMSN1 :: SAM domain, SH3 domain and nuclear 221851 0.370981356457398 −0.381164453290482
    localisation signals, 1
    2463 1139831 1139831: FLJ21736 :: esterase 31 268700 −0.011968075306893 −0.016434297612474
    2464 1139839 1139839: SGK2 :: serum/glucocorticoid regulated kinase 2 62863 0.024109656506769 0.032626900537836
    2465 1139842 1139842: SAP130 :: mSin3A-associated protein 130 133523 −0.097742321655318 0.266312994370097
    2466 1139925 1139925: FAIM :: Fas apoptotic inhibitory molecule 173438 −0.124987151146701 0.328309523235883
    2467 1139949 1139949: DNAH3 :: dynein, axonemal, heavy polypeptide 3 375739 −0.169731374035577 0.074225125499242
    2468 1139950 1139950: FLJ10420 :: hypothetical protein FLJ10420 437385 0.236816945983053 −0.335727361898558
    2469 1139955 1139955: SLC12A6 :: solute carrier family 12 (potassium/chloride 4876 −0.020487054568829 −0.037480624844835
    transporters), member 6
    2470 1139957 1139957: NGLY1 :: N-glycanase 1 63657 −0.525638023143142 0.363478080938368
    2471 1139962 1139962: C5orf4 :: chromosome 5 open reading frame 4 10235 0.230250368247300 −0.233149594377572
    2472 1139969 1139969: JIK :: STE20-like kinase 12040 −0.197720240185810 0.063503215792743
    2473 1139971 1139971: LIMS2 :: LIM and senescent cell antigen-like domains 2 127273 −0.023501693605426 −0.081611153834008
    2474 1140007 1140007: TPT :: trans-prenyltransferase 279865 −0.267154068193449 0.678834620628513
    2475 1140018 1140018: PWDMP :: WD repeat membrane protein PWDMP 438482 −0.133214603635881 0.120024613326089
    2476 1140027 1140027: FLJ13409 :: hypothetical protein FLJ13409 −30 0.032352790493303 −0.421061800596014
    2477 1140031 1140031: SIAT7D :: sialyltransferase 7D ((alpha-N-acetylneuraminyl- 3972 −0.255702042856147 0.129661591849210
    2,3-betagalactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-
    sialyltransferase)
    2478 1140072 1140072: SLCO5A1 :: solute carrier organic anion transporter family, 199750 0.242253459635359 −0.221156982559850
    member 5A1
    2479 1140075 1140075: SNARK :: likely ortholog of rat SNF1/AMP-activated protein 172012 −0.047490349579645 −0.277054802560530
    kinase
    2480 1140088 1140088: DC-TM4F2 :: tetraspanin similar to TM4SF9 509050 0.226500769788379 −0.262234704475871
    2481 1140127 1140127: TRIM34 :: tripartite motif-containing 34 125300 −0.165828521151955 0.102914713660907
    2482 1140151 1140151: FLJ22757 :: hypothetical protein FLJ22757 236449 −0.089956291622834 −0.171243944377416
    2483 1140214 1140214: ANKRD3 :: ankyrin repeat domain 3 55565 −0.135384096304679 0.090538047157569
    2484 1140236 1140236: SPAP1 :: SH2 domain containing phosphatase anchor 194976 −0.437940303418959 0.326018914273141
    protein 1
    2485 1140238 1140238: BCLG :: apoptosis regulator BCL-G 11962 −0.042826609936427 −0.286603480568969
    2486 1140344 1140344: BNIP3L :: BCL2/adenovirus E1B 19 kDa interacting protein 132955 0.217814730487477 0.049767573763502
    3-like
    2487 1140370 1140370: CDCA8 :: cell division cycle associated 8 48855 −0.413518820286071 0.851402787359892
    2488 1140378 1140378: BHLHB3 :: basic helix-loop-helix domain containing, 437282 0.441953829397093 −0.128845498205439
    class B, 3
    2489 1140391 1140391: LEF1 :: lymphoid enhancer-binding factor 1 44865 −0.102669812122025 −0.218911457849257
    2490 1140399 1140399: PLAB :: prostate differentiation factor 296638 0.096863129825544 −0.118898412519241
    2491 1140404 1140404: KCNMA1 :: potassium large conductance calcium-activated 354740 0.587653373643620 −0.452387471739584
    channel, subfamily M, alpha member 1
    2492 1140416 1140416: TOSO :: regulator of Fas-induced apoptosis 58831 −0.227010373770165 −0.159494002878968
    2493 1140457 1140457: IL21R :: interleukin 21 receptor 210546 0.212002655160102 −0.176888063733686
    2494 1140464 1140464: H11 :: protein kinase H11 111676 0.562080363557665 −0.327453925079561
    2495 1140473 1140473: CORO1C :: coronin, actin binding protein, 1C 17377 0.173358377940601 −0.047338136392363
    2496 1140491 1140491: DKFZp761P1010 :: hypothetical protein DKFZp761P1010 24979 0.101756726051739 −0.183027999855880
    2497 1140497 1140497: FLJ12750 :: hypothetical protein FLJ12750 77870 0.339043501264461 −0.382487661946037
    2498 1140520 1140520: C20orf21 :: chromosome 20 open reading frame 21 11747 −0.439383490087482 0.339299186966798
    2499 1140524 1140524: C6orf37 :: chromosome 6 open reading frame 37 10784 0.464548931082200 −0.451242812457036
    2500 1140534 1140534: ARH :: LDL receptor adaptor protein 184482 0.219197513436446 −0.333907644050982
    2501 1140565 1140565: HLA-F :: major histocompatibility complex, class I, F 411958 0.384933870287039 −0.597355642875244
    2502 1140567 1140567: CLIC4 :: chloride intracellular channel 4 25035 0.087366213877805 0.196012165859917
    2503 1140570 1140570: HSPA8 :: heat shock 70 kDa protein 8 180414 −0.023139381570294 0.050939786779129
    2504 1140571 1140571: ADCK2 :: aarF domain containing kinase 2 210397 0.029868578992176 0.158934520479412
    2505 1140574 1140574: MGC1203 :: hypothetical protein MGC1203 17987 0.086226740004958 0.127077044778373
    2506 1140584 1140584: C14orf87 :: chromosome 14 open reading frame 87 294083 −0.335638395822406 0.547973957918325
    2507 1140589 1140589: GUCY1A3 :: guanylate cyclase 1, soluble, alpha 3 433488 0.456463431988372 −0.374874498826929
    2508 1140613 1140613: VRK3 :: vaccinia related kinase 3 443330 −0.380702233123925 0.211440380539557
    2509 1140630 1140630: FLT1 :: fms-related tyrosine kinase 1 (vascular endothelial 347713 0.192942882655688 −0.123277559696215
    growth factor/vascular permeability factor receptor)
    2510 1140632 1140632: MCM4 :: MCM4 minichromosome maintenance deficient 4 460184 −0.376728198824448 0.850172826162782
    (S. cerevisiae)
    2511 1140729 1140729: IL1F5 :: interleukin 1 family, member 5 (delta) 207224 −0.011674717854802 0.027823140475085
    2512 1140745 1140745: FER1L4 :: fer-1-like 4 (C. elegans) 72222 −0.172974560266972 0.044998775095322
    2513 1140781 1140781: NA −9 0.014530846048607 −0.103093007369487
    2514 1140782 1140782: NA −10 0.006268837628174 −0.083328907951826
    2515 1140783 1140783: NA −11 0.058336388513323 −0.094737922344377
    2516 1140784 1140784: NA −12 0.009386086273623 −0.065007336367840
    2517 1140785 1140785: NA −13 0.047643577567512 −0.140278204847852
    2518 1140786 1140786: NA −14 0.016786919443948 −0.174405991353998
    2519 1140787 1140787: NA −15 0.022891073012834 −0.155713264657076
    2520 1140788 1140788: :: Affy control −76 −0.117884908267157 0.200102966609546
    2521 1140789 1140789: NA −16 −0.053745102351612 0.056855755515683
    2522 1140790 1140790: NA −17 −0.002474950353002 0.146778154626489
    2523 1140791 1140791: :: Affy control −77 −0.044010031551127 0.103181030663411
    2524 1140792 1140792: :: Affy control −78 −0.170357382284597 0.155867721321911
    2525 1140793 1140793: :: Affy control −79 −0.094085257903303 0.015739455221676
    2526 1140794 1140794: :: Affy control −80 0.072047623150024 0.031475688587574
    2527 1140795 1140795: :: Affy control −81 0.019559904867390 −0.028763995255638
    2528 1140796 1140796: :: Affy control −82 −0.002597758314342 0.056810099843959
    2529 1140797 1140797: :: Affy control −83 −0.083637785960315 0.013226984835784
    2530 1140798 1140798: :: Affy control −84 −0.149412058607628 0.063774018243496
    2531 1140799 1140799: :: Affy control −85 −0.067949626733013 0.067189679174101
    2532 1140800 1140800: NA −18 0.004654423406066 −0.073603651584715
    2533 1140801 1140801: NA −19 0.007232174980560 −0.083719225734612
    2534 1140802 1140802: :: Affy control −86 −0.041429693151471 0.043909563253514
    2535 1140803 1140803: :: Affy control −87 −0.016514640117280 0.026369412380536
    2536 1140804 1140804: :: Affy control −88 −0.031829051168426 0.077781369765560
    2537 1140805 1140805: :: Affy control −89 0.020865760367817 −0.204408613047135
    2538 1140806 1140806: :: Affy control −90 −0.023926340232166 0.208878284785108
    2539 1140807 1140807: :: Affy control −91 0.113490613013508 −0.030826444609494
    2540 1140808 1140808: :: Affy control −92 0.012514982361291 0.075200735866390
    2541 1140809 1140809: :: Affy control −93 0.136504292454269 −0.119517051436108
    2542 1140810 1140810: :: Affy control −94 −0.057422781927538 0.086665252476037
    2543 1140811 1140811: :: Affy control −95 0.133189510202426 −0.101012852018164
    2544 1140812 1140812: :: Affy control −96 0.001223309520009 0.095793180622117
    2545 1140813 1140813: :: Affy control −97 −0.009371369059179 0.052514206556146
    2546 1140814 1140814: :: Affy control −98 −0.027062251510449 −0.029446918626741
    2547 1140815 1140815: :: Affy control −99 −0.019326891464828 0.082329569464007
    2548 1140816 1140816: :: Affy control −100 −0.016568107211094 0.097017805392993
    2549 1140817 1140817: :: Affy control −101 −0.006509426539146 0.128549591393422
    2550 1140818 1140818: :: Affy control −102 0.027938036404715 −0.189543315055064
    2551 1140819 1140819: :: Affy control −103 −0.021413730370109 −0.133918701719173
    2552 1140820 1140820: :: Affy control −104 0.001578324636409 −0.072457711989475
    2553 1140821 1140821: :: Affy control −105 −0.006400037365219 −0.059009456108435
    2554 1140822 1140822: :: Affy control −106 −0.023396144647357 −0.065693911773797
    2555 1140823 1140823: :: Affy control −107 0.011662567339774 −0.073288829281112
    2556 1140824 1140824: :: Affy control −108 0.012768276145964 −0.117644303599034
    2557 1140825 1140825: :: Affy control −109 −0.009563443665290 −0.042035406725848
    2558 1140826 1140826: :: Affy control −110 −0.000777025451842 −0.095436504049974
    2559 1140827 1140827: :: Affy control −111 −0.019671268603360 0.017149224395412
    2560 1140828 1140828: :: Affy control −112 −0.001327627906192 0.024569651878159
    2561 1140829 1140829: :: Affy control −113 −0.166625799047804 0.056909535950037
    2562 1140834 1140834: ACTB :: Affy control actin, beta 426930 0.036626782020363 −0.206629607105101
    2563 1140835 1140835: ACTB :: Affy control actin, beta 426930 −0.149602339907586 0.129812469536959
    2564 1140836 1140836: ACTB :: Affy control actin, beta 426930 −0.091647722342469 0.000432322929413
    2565 1140837 1140837: :: Affy control −114 0.094646356888252 0.037746051614047
    2566 1140838 1140838: :: Affy control −115 0.117242895542767 0.062821055865340
    2567 1140839 1140839: :: Affy control −116 0.089772638224071 0.092598810615234
    2568 1140842 1140842: GAPD :: Affy control glyceraldehyde-3-phosphate 169476 −0.081770293481056 0.122359836917701
    dehydrogenase
    2569 1140843 1140843: GAPD :: Affy control glyceraldehyde-3-phosphate 169476 −0.243924592429084 0.422918916154454
    dehydrogenase
    2570 1140844 1140844: GAPD :: Affy control glyceraldehyde-3-phosphate 169476 −0.205317596747236 0.311010631943087
    dehydrogenase
    2571 1140845 1140845: STAT1 :: Affy control signal transducer and activator of 21486 0.377358722885690 −0.541349128751760
    transcription 1, 91 kDa
    2572 1140846 1140846: STAT1 :: Affy control signal transducer and activator of 21486 0.097287175817027 −0.226153881821370
    transcription 1, 91 kDa
    2573 1140847 1140847: STAT1 :: Affy control signal transducer and activator of 21486 0.216947517172567 −0.391088029796798
    transcription 1, 91 kDa
    2574 1140848 1140848: STAT1 :: Affy control signal transducer and activator of 21486 0.222030839773439 −0.348450525763477
    transcription 1, 91 kDa
    2575 1529284 1529284: MCC :: mutated in colorectal cancers 409515 0.110972159568218 −0.072345229884740
    2576 1529285 1529285: KIAA1219 :: KIAA1219 protein 348929 −0.184556459472403 −0.049692544277234
    2577 1529286 1529286: MADH5 :: MAD, mothers against decapentaplegic homolog 5 167700 0.031685751568576 0.146378764529449
    (Drosophila)
    2578 1529287 1529287: KIAA0303 :: KIAA0303 protein 212787 0.051481011707667 0.042849436971698
    2579 1529288 1529288: CCNG2 :: cyclin G2 13291 0.077063799482395 0.059768352114886
    2580 1529289 1529289: :: Homo sapiens cDNA FLJ12727 fis, clone NT2RP2000027. 96557 −0.021365736556446 −0.015983700308380
    2581 1529290 1529290: N4BP3 :: Nedd4 binding protein 3 101761 −0.098254325850797 0.157368217757306
    2582 1529291 1529291: :: Homo sapiens transcribed sequences 104450 −0.076267577354527 −0.040509704775555
    2583 1529292 1529292: :: Homo sapiens transcribed sequences 105261 0.033769033555145 0.129433981816277
    2584 1529293 1529293: :: Homo sapiens hypothetical LOC284134 (LOC284134), 113117 0.156492425740869 −0.366194468589873
    mRNA
    2585 1529294 1529294: :: Homo sapiens hypothetical LOC284134 (LOC284134), 113117 0.182603122401687 −0.404979176023783
    mRNA
    2586 1529295 1529295: :: Homo sapiens transcribed sequences 116441 0.033705717151087 0.117633519020541
    2587 1529296 1529296: :: Homo sapiens transcribed sequences 122428 0.139091174867969 0.107806582080154
    2588 1529297 1529297: :: Homo sapiens mRNA; cDNA DKFZp686F08109 (from 132335 −0.297312324845849 0.119929613672577
    clone DKFZp686F08109)
    2589 1529298 1529298: :: Homo sapiens mRNA; cDNA DKFZp667B1520 (from 136707 −0.314207665564666 0.198327056016028
    clone DKFZp667B1520)
    2590 1529299 1529299: :: Homo sapiens cDNA FLJ42786 fis, clone 444290 −0.064690184926136 0.011327312833764
    2591 1529300 1529300: :: H. sapiens mRNA for immunoglobulin kappa light chain 449608 −0.204293297723690 0.145878170957971
    BRAWH3006761 VJ region (ID POM433)
    2592 1529301 1529301: :: AI281566 −117 0.071716279105228 −0.042503405899593
    2593 1529302 1529302: ELF3 :: E74-like factor 3 (ets domain transcription factor, 67928 0.029898524927091 0.032305158454658
    epithelial-specific)
    2594 1529303 1529303: :: W22811 −38 −0.128640352347951 −0.034389181844250
    2595 1529304 1529304: :: W22811 −38 −0.018858926497905 −0.156662687401548
    2596 1529305 1529305: :: Homo sapiens transcribed sequence with moderate 173957 0.045101000387545 −0.125823818297820
    similarity to protein ref: NP_060312.1 (H. sapiens) hypothetical protein
    FLJ20489 [Homo sapiens]
    2597 1529306 1529306: MGC26706 :: hypothetical protein MGC26706 190043 0.022863081364640 0.090864014434462
    2598 1529307 1529307: :: Homo sapiens cDNA FLJ46553 fis, clone 435736 −0.117004056094557 0.108321654537967
    THYMU3038879
    2599 1529308 1529308: :: Homo sapiens transcribed sequences 193014 −0.194608455512361 0.159131057131648
    2600 1529309 1529309: HSH2 :: hematopoietic SH2 protein 512797 −0.284514425855296 −0.009187563040830
    2601 1529310 1529310: PRKAG1 :: protein kinase, AMP-activated, gamma 1 non- 3136 0.084646768018470 −0.094185610330221
    catalytic subunit
    2602 1529311 1529311: :: Homo sapiens transcribed sequences 251214 −0.008562152181595 0.207360519494227
    2603 1529312 1529312: :: Homo sapiens cDNA FLJ34500 fis, clone 255809 −0.072056295484426 −0.259485982293033
    HLUNG2005479.
    2604 1529313 1529313: :: Homo sapiens transcribed sequences 271998 0.004383347722577 0.265566854529143
    2605 1529314 1529314: :: Homo sapiens transcribed sequences 276342 −0.006227323367580 0.045472523730890
    2606 1529315 1529315: :: Homo sapiens transcribed sequence with weak similarity to 445718 −0.084112604384647 0.019415177758716
    protein ref: NP_062553.1 (H. sapiens) hypothetical protein FLJ11267
    [Homo sapiens]
    2607 1529316 1529316: ZNF198 :: zinc finger protein 198 315241 −0.086336901114135 0.076958490701384
    2608 1529317 1529317: :: AA828425 −118 −0.224014424936674 −0.223856158514235
    2609 1529318 1529318: :: Homo sapiens transcribed sequences 291954 0.073854603491552 0.079840492528659
    2610 1529319 1529319: KIAA0970 :: KIAA0970 protein 103329 −0.004662599096684 0.007648241002329
    2611 1529320 1529320: :: Homo sapiens , clone IMAGE: 5222345, mRNA 309149 −0.023029642379006 −0.010624843950025
    2612 1529321 1529321: IL24 :: interleukin 24 411311 −0.109990803451750 0.025765040861020
    2613 1529322 1529322: :: Homo sapiens transcribed sequence with weak similarity to 514291 0.030436007092166 −0.175347477632027
    protein ref: NP_038605.1 (M. musculus) L1 repeat, Tf subfamily,
    member 30 [Mus musculus]
    2614 1529323 1529323: :: Homo sapiens transcribed sequences 345834 0.336779571590933 −0.359684409503434
    2615 1529324 1529324: GZMH :: granzyme H (cathepsin G-like 2, protein h-CCPX) 348264 0.239243227392061 −0.419048485474577
    2616 1529325 1529325: :: BQ003404 −75 −0.140464406043795 −0.021462938104706
    2617 1529326 1529326: HDAC7A :: histone deacetylase 7A 200063 −0.109850414890401 0.080269797544815
    2618 1529327 1529327: SMN2 :: survival of motor neuron 2, centromeric 288986 −0.042384278985820 0.248777434604123
    2619 1529328 1529328: :: Homo sapiens transcribed sequences 369056 0.056981262751925 −0.112051222335899
    2620 1529329 1529329: :: Homo sapiens transcribed sequences 369101 −0.135338205033608 0.159470087740367
    2621 1529330 1529330: LOC153684 :: hypothetical protein LOC153684 259625 −0.105755172392999 0.046487888216411
    2622 1529331 1529331: :: Homo sapiens transcribed sequence with weak similarity to 374126 −0.201436415316463 0.127028345378989
    protein ref: NP_060312.1 (H. sapiens) hypothetical protein FLJ20489
    [Homo sapiens ]
    2623 1529332 1529332: LOC134492 :: similar to RIKEN cDNA 2700047N05 140443 −0.300773106127023 0.228609503612335
    2624 1529333 1529333: :: Homo sapiens cDNA FLJ40549 fis, clone 378849 −0.016962900796743 0.032654218738799
    THYMU2001916
    2625 1529334 1529334: :: Homo sapiens transcribed sequence with moderate 380255 −0.073135831632244 −0.084277957239007
    similarity to protein ref: NP_071431.1 (H. sapiens) cytokine receptor-
    like factor 2; cytokine receptor CRL2 precusor [Homo sapiens ]
    2626 1529335 1529335: :: Homo sapiens mRNA; cDNA DKFZp586L141 (from clone 400872 −0.379618839813305 0.435859102100720
    DKFZp586L141)
    2627 1529336 1529336: PTK2B :: PTK2B protein tyrosine kinase 2 beta 405474 0.064169101462340 −0.102556747779252
    2628 1529337 1529337: C6orf166 :: chromosome 6 open reading frame 166 201864 −0.018977987327815 0.016953866594291
    2629 1529338 1529338: PAK2 :: p21 (CDKN1A)-activated kinase 2 284275 −0.396911297097266 0.365705541778953
    2630 1529339 1529339: :: Homo sapiens transcribed sequences 427710 −0.126611681377431 0.072949549681158
    2631 1529340 1529340: :: AA827872 −119 −0.119915444623348 0.179233924660731
    2632 1529341 1529341: LY75 :: lymphocyte antigen 75 153563 0.188892498067345 0.001326615372681
    2633 1529342 1529342: :: BQ026237 −74 0.158306373307698 −0.426400997795195
    2634 1529343 1529343: :: Homo sapiens transcribed sequence 521948 −0.039648581482154 0.106009965624923
    2635 1529344 1529344: SERPINA11 :: serine proteinase inhibitor A11 317970 0.238830242521113 0.051394835638056
    2636 1529345 1529345: :: Homo sapiens transcribed sequences 443475 −0.098204977598259 0.032635938575475
    2637 1529346 1529346: :: Homo sapiens transcribed sequences 443935 −0.133480744808980 −0.138767694000192
    2638 1529347 1529347: :: Homo sapiens transcribed sequences 444019 −0.261867960347880 0.063087517442791
    2639 1529348 1529348: SOS1 :: son of sevenless homolog 1 (Drosophila) 326392 −0.112147722903032 −0.017345761915274
    2640 1529349 1529349: :: Homo sapiens transcribed sequences 445500 0.004876940094089 −0.293504921159920
    2641 1529350 1529350: :: Homo sapiens transcribed sequences 445884 −0.196163065913620 0.239480017540847
    2642 1529351 1529351: :: Homo sapiens transcribed sequences 445898 −0.072117447206842 0.178173670478469
    2643 1529352 1529352: :: Homo sapiens cDNA FLJ42418 fis, clone BLADE2001987 446195 −0.006498231102315 0.089100493304306
    2644 1529353 1529353: :: Homo sapiens transcribed sequences 446198 −0.054986078590614 −0.011114342560876
    2645 1529354 1529354: BCL11A :: B-cell CLL/lymphoma 11A (zinc finger protein) 314623 −0.275920246770634 0.357053851248126
    2646 1529355 1529355: :: Homo sapiens transcribed sequences 370675 0.107276183111680 −0.141870873747761
    2647 1529356 1529356: C14orf170 :: chromosome 14 open reading frame 170 303775 −0.058235352127145 −0.001935868254300
    2648 1529357 1529357: :: Homo sapiens transcribed sequences 444651 −0.169332893572493 0.118609634840753
    2649 1529358 1529358: :: Homo sapiens transcribed sequence with moderate 127178 0.185280771017017 −0.002341003747225
    similarity to protein sp: P39195 (H. sapiens) ALU8_HUMAN Alu
    subfamily SX sequence contamination warning entry
    2650 1529359 1529359: :: AA832388 326173 0.185128908116345 −0.201485649206219
    2651 1529360 1529360: :: Homo sapiens transcribed sequences 443036 0.156862502241191 −0.359190734129611
    2652 1529361 1529361: HDAC3 :: histone deacetylase 3 388681 −0.361732180141791 0.391019787446920
    2653 1529362 1529362: PLK :: polo-like kinase (Drosophila) 329989 −0.388320346854452 0.833332607616786
    2654 1529363 1529363: NOTCH1 :: Notch homolog 1, translocation-associated 311559 0.259233913232295 −0.421434088005552
    (Drosophila)
    2655 1529364 1529364: ATM :: ataxia telangiectasia mutated (includes 504644 −0.118986043194098 −0.148365556666337
    complementation groups A, C and D)
    2656 1529365 1529365: TNFRSF13C :: tumor necrosis factor receptor superfamily, 344088 −0.057992715606171 0.052741212228336
    member 13C
    2657 1529366 1529366: :: EBV LMP1 unique −65 −0.082164264138660 0.018369754127342
    2658 1529367 1529367: :: EBV LMP1 3′ end −66 −0.064572311852911 −0.069680793133709
    2659 1529368 1529368: :: EBV EBNA2 3′ end −70 −0.173445974852027 0.205542104461719
    2660 1529369 1529369: :: EBV EBNA1 CDS −71 −0.071747968325640 0.065345583125480
    2661 1529370 1529370: :: EBV LPM2A −64 −0.001163089708170 −0.110956119752116
    2662 1529371 1529371: :: EBV BHRFA −73 −0.010090518075703 −0.076381918817641
    2663 1529372 1529372: :: EBV BZLF1 −72 −0.221272834194238 0.120180577006682
    2664 1529373 1529373: :: EBV EBNA3A −69 −0.161072632651006 0.055854607395513
    2665 1529374 1529374: :: EBV EBNA3C −67 0.059031065592265 −0.071187244369590
    2666 1529375 1529375: :: HHV8 K13 −59 −0.013666002623568 −0.085249642533594
    2667 1529376 1529376: :: HHV8 T0.7/P6 −57 −0.038217131973910 −0.030850737271204
    2668 1529377 1529377: :: HHV8 T1.1 −56 0.032597223400267 −0.067543040593593
    2669 1529378 1529378: :: HHV8 ORF73/LANA −58 −0.015664193006648 0.006139430844953
    2670 1529379 1529379: :: HHV8 vMIP1b ORFK4.2 KIE-3 −54 −0.015626336025217 −0.056403407873870
    2671 1529380 1529380: :: HHV8 vIL6 −55 −0.115982682592600 0.085106875588196
    2672 1529381 1529381: :: HHV8 K1-32 Bcb K1 protein −60 0.046823898274642 0.001406007567692
    2673 1529382 1529382: CCND1 :: Cyclin D1 coding region; by 498-1097 of 371468 0.094277437820395 −0.132713478377930
    NM_053056
    2674 1529383 1529383: CCND1 :: Cyclin D1 3′ end; by 3691-4290 of NM_053056 371468 0.555196850752576 −0.483293591801984
    2675 1529384 1529384: CCND1 :: Cyclin D1; bp 2491-3090 of NM_053056 371468 0.365173665475046 −0.261555570413604
    2676 1529385 1529385: CCND1 :: Cyclin D1; bp 1891-2490 of NM_054056 371468 0.281719638953775 −0.208410405004593
    2677 1529386 1529386: CCND1 :: Cyclin D1; bp 1291-1890 of NM_054056 371468 0.429543765430906 −0.281718193371932
    2678 1529387 1529387: BCL2 :: BCL-2 MBR by 2409-3009 of NM_000633 79241 −0.293554931269457 −0.116661021933823
    2679 1529388 1529388: BCL2 :: BCL-2 coding region end; bp 152-751 of 79241 −0.141729791902808 −0.017721784560266
    NM_000633
    2680 1529389 1529389: BCL2 :: BCL-2 3′ end; bp 5431-6030 of NM_000633 79241 −0.344617915920712 −0.207115780844928
    2681 1529390 1529390: BCL2 :: BCL-2; bp 1401-2000 of NM_000633 79241 −0.219032917773749 0.010350953136667
    2682 1529391 1529391: BCL2 :: BCL-2; bp 4431-5030 of NM_000633 79241 −0.403717253508751 −0.020031412999953
    2683 1529392 1529392: ACVR1C :: activin A receptor, type IC 352338 0.054521329510957 −0.065435713301877
    2684 1529393 1529393: KIAA1811 :: KIAA1811 protein 182081 0.333009117195884 −0.304901694858517
    2685 1529394 1529394: LOC91807 :: myosin light chain kinase (MLCK) 339846 −0.123907032755405 0.183602253317435
    2686 1529395 1529395: :: Homo sapiens similar to Serine/threonine-protein kinase 403201 0.028612792038585 0.028966275624666
    KKIALRE (Cyclin-dependent kinase-like 1) (LOC344387), mRNA
    2687 1529396 1529396: MGC33182 :: casein kinase I alpha S-like 512897 −0.038017413092940 −0.004616315101532
    2688 1529397 1529397: CLK4 :: CDC-like kinase 4 406557 0.086234150880245 −0.366605829522404
    2689 1529398 1529398: HSMDPKIN :: myotonic dystrophy protein kinase like protein 293590 −0.079557360480167 0.120197897136261
    2690 1529399 1529399: LOC203806 :: hypothetical protein LOC203806 256916 0.035952284333729 −0.030481696710319
    2691 1529400 1529400: FLJ32818 :: hypothetical protein FLJ32818 210697 −0.124775961566475 0.094567535746030
    2692 1529401 1529401: MAP4K3 :: mitogen-activated protein kinase kinase kinase 399752 0.277778965134787 −0.259253792231314
    kinase 3
    2693 1529402 1529402: KSR2 :: kinase suppressor of Ras-2 375836 −0.043546893836039 −0.006972792768919
    2694 1529403 1529403: KIAA1883 :: KIAA1883 protein 511780 −0.131034308134048 0.103925962598284
    2695 1529404 1529404: MAP3K1 :: mitogen-activated protein kinase kinase kinase 1 170610 −0.109948582091028 0.087977859649393
    2696 1529405 1529405: SAST :: syntrophin associated serine/threonine kinase 227489 0.126274276066276 −0.071352270643548
    2697 1529406 1529406: MYO3B :: myosin IIIB 409066 0.155629369566744 −0.026270257889408
    2698 1529407 1529407: PAK2 :: p21 (CDKN1A)-activated kinase 2 284275 −0.372590149141074 0.355639782047009
    2699 1529408 1529408: PSKH2 :: serine/threonine kinase PSKH2 336929 0.039376351837621 −0.003523691344492
    2700 1529409 1529409: FLJ25006 :: hypothetical protein FLJ25006 351173 −0.185470415631171 0.355295627732664
    2701 1529410 1529410: SNF1LK :: SNF1-like kinase 380991 0.310744319100462 −0.191354110343142
    2702 1529411 1529411: APEG1 :: aortic preferentially expressed protein 1 80181 −0.015090155827916 0.049326921582975
    2703 1529412 1529412: STK22C :: serine/threonine kinase 22C (spermiogenesis 512763 −0.152113151357401 0.144006256228092
    associated)
    2704 1529413 1529413: PRKWNK2 :: protein kinase, lysine deficient 2 232116 0.043707511124126 −0.024587852541792
    2705 1529414 1529414: MGC22688 :: hypothetical protein MGC22688 352370 0.129203581496830 −0.037058867228545
    2706 1529415 1529415: DKFZp686A17109 :: hypothetical protein DKFZp686A17109 369523 −0.148462736251386 0.034953320101641
    2707 1529416 1529416: CDKN2A :: p14ARF; unique 5O region from INK4a locus 421349 0.054323363043638 0.129218335773114
    2708 1529417 1529417: CDKN2A :: INK4a locus common sequence shared by 421349 0.042141777381482 0.177690611245249
    p14ARF and all p16 mRNA isoforms
    2709 1529418 1529418: CDKN2A :: p16INK4a; p16 unique sequence shared by 421349 −0.067908769750351 0.020087857642895
    p16INK4a transcript variants 1 and 3 but not p16INK4a transcript
    variant
    2 and variant 4 (p14ARF)
    2710 1529419 1529419: :: Homo sapiens transcribed sequences 104182 −0.097146163320226 0.131715317478596
    2711 1529420 1529420: IL17F :: interleukin 17F 272295 0.045525457266783 −0.009988757123239
    2712 1529421 1529421: IL27 :: interleukin 27 375043 −0.004883677033980 −0.115384956701855
    2713 1529422 1529422: IL23R :: interleukin-23 receptor 375184 0.094119854675173 0.044609962750620
    2714 1529423 1529423: ITGAD :: integrin, alpha D 381264 0.148605834731398 −0.198509767943520
    2715 1529424 1529424: CCL3L1 :: chemokine (C-C motif) ligand 3-like 1 512683 0.205301608020911 −0.340808318654676
    2716 1529425 1529425: IL9R :: interleukin 9 receptor 406228 −0.045519588598842 0.085600863168274
    2717 1529426 1529426: IL28B :: interleukin 28B (interferon, lambda 3) 406744 0.189355610681505 −0.165534213809855
    2718 1529427 1529427: IL29 :: interleukin 29 (interferon, lambda 1) 406745 −0.014392642430728 −0.070805657034640
    2719 1529428 1529428: NGFR :: nerve growth factor receptor (TNFR superfamily, 415768 0.035324253127484 −0.128267249447899
    member 16)
    2720 1529429 1529429: IL17D :: interleukin 17D 434103 −0.069810691656676 0.069997307160626
    2721 1529430 1529430: SPHK2 :: sphingosine kinase 2 444484 −0.321834026215950 0.170461543915022
    2722 1529431 1529431: :: Homo sapiens transcribed sequences 446193 −0.168353154209300 0.128224145113833
    2723 1529432 1529432: :: IgG1 constant region −41 0.076813190211455 −0.105760779150212
    2724 1529433 1529433: :: IgG1 constant region −41 0.070417647231205 −0.075267225590524
    2725 1529434 1529434: FLJ27099 :: IgG4 constant region 103995 0.018230596259647 −0.077214639544862
    2726 1529435 1529435: :: IgA1 constant region −44 0.186737460085977 −0.317208744354907
    2727 1529436 1529436: :: IgE constant region −43 0.101726014546358 −0.187640538570034
    2728 1529437 1529437: BTLA :: B and T lymphocyte associated 445162 −0.318763487600451 0.010989475889237
    2729 1529443 1529443: :: Homo sapiens transcribed sequences 88886 −0.026012720914063 0.076787080847203
    2730 1529444 1529444: :: Homo sapiens transcribed sequences 126905 0.010228055161144 0.032713206278291
    2731 1529445 1529445: :: BE675157 159050 −0.262325467861960 0.149553276873531
    2732 1529446 1529446: :: Homo sapiens transcribed sequences 190626 −0.025863059671753 −0.065797375687666
    2733 1529447 1529447: :: Homo sapiens transcribed sequences 291886 −0.035807248922759 0.126157477853033
    2734 1529448 1529448: :: Homo sapiens transcribed sequences 369101 −0.122448573444494 0.135610608469673
    2735 1529449 1529449: :: BQ710740 428762 −0.140372978110498 0.061475408728652
    2736 1529450 1529450: :: AA255658 −120 −0.077793575103323 −0.096601745707301
    2737 1529451 1529451: JMY :: junction-mediating and regulatory protein 396853 −0.070253972528956 0.001481500267825
    2738 1529452 1529452: AIM1 :: absent in melanoma 1 422550 −0.047576787628458 0.022144076488709
    2739 1529453 1529453: FCGR3A :: Fc fragment of IgG, low affinity IIIa, receptor for 372679 0.105750028795122 −0.221420850072347
    (CD16)
    2740 1529454 1529454: :: EBV EBNA3B −68 0.025237645629957 −0.049752634590638
    2741 1529455 1529455: :: HHV8 BCL2 homologue −61 −0.053831710598311 0.124768914047081
    2742 1529456 1529456: CCND1 :: Cyclin D1; bp 3091-3690 of NM_053056 371468 0.563476075442490 −0.453521864341999
    2743 1529457 1529457: GPRK7 :: G protein-coupled receptor kinase 7 351818 −0.113143362958157 0.050092066170263
    2744 1529458 1529458: NEK8 :: NIMA (never in mitosis gene a)-related kinase 8 448468 −0.258903564937414 0.040064079685056
    2745 1529459 1529459: SRMS :: src-related kinase lacking C-terminal regulatory 411061 −0.038227711901371 0.147063354283128
    tyrosine and N-terminal myristylation sites

Claims (13)

1. A method for predicting survival in a follicular lymphoma (FL) subject comprising the steps of
a) isolating gene expression product from a biopsy sample from a subject;
b) obtaining gene expression data from the isolated gene expression product, wherein the gene expression data comprises data for genes in an immune response-1 gene expression signature and genes in an immune response-2 gene expression signature;
c) obtaining an average gene expression level for the genes in the immune response-1 gene expression signature to thereby obtain an immune response-1 gene expression signature value;
d) obtaining an average gene expression level for the genes in the immune response-2 gene expression signature to thereby obtain an immune response-2 gene expression signature value; and
f) calculating a survival predictor score using an equation: [2.71*(immune response-2 gene expression signature value)]−[2.36*(immune response-1 gene expression signature value)]; wherein a higher survival predictor score is associated with worse survival.
2. The method of claim 1 wherein the step of obtaining gene expression data comprises use of a microarray.
3. The method of claim 1 wherein the immune response-1 gene expression signature comprises at least one gene selected from the group consisting of (listed by UNIQID): 1095985, 1096579, 1097255, 1097307, 1097329, 1097561, 1098152, 1098405, 1098548, 1098893, 1099053, 1100871, 1120196, 1101004, 1103303, 1107713, 1115194, 1119251, 1119838, 1119924, 1120267, 1121313, 1121406, 1121720, 1122956, 1123038, 1123092, 1123875, 1124760, 1128356, 1128395, 1132104, 1133408, 1134069, 1134751, 1134945, 1135743, 1135968, 1136048, 1136087, 1137137, 1137289, 1137534, 1139339, 1139461, 11400391, 140524, and 1140759.
4. The method of claim 1 wherein the immune response-2 gene expression signature comprises at least one gene selected from the group consisting of (listed by UNIQID): 1118755, 1118966, 1121053, 1121267, 1121331, 1121766, 1121852, 1122624, 1122679, 1122770, 1123767, 1123841, 1126097, 1126380, 1126628, 1126836, 1127277, 1127519, 1127648, 1128483, 1128818, 1129012, 1129582, 1129658, 1129705, 1129867, 1130003, 1130388, 1131837, 1133843, 1133949, 1134447, 1135117, 1136017, 1137478, 1137745, 1137768, 1138476, 1138529, 1138601, 1139862, 1140189, and 1140389.
5. A method for predicting survival in a diffuse large B cell lymphoma (DLBCL) subject comprising the steps of:
a) isolating gene expression product from a biopsy sample from a subject;
b) obtaining gene expression data from the isolated gene expression product, wherein the gene expression data comprises data for genes in an ABC DLBCL high gene expression signature, a lymph node gene expression signature, and an MHC class II gene expression signature;
c) obtaining an average gene expression level for the genes in the ABC DLBCL high gene expression signature to thereby obtain an ABC DLBCL high gene expression signature value;
d) obtaining an average gene expression level for the genes in the lymph node gene expression signature to thereby obtain a lymph node gene expression signature value;
e) obtaining an average gene expression level for the genes in the MHC class II gene expression signature to thereby obtain an MHC class II gene expression signature value;
f) calculating a survival predictor score using an equation: [0.586*(ABC DLBCL high gene expression signature value)]−[0.468*(lymph node gene expression signature value)]−[0.336*(MHC class II gene expression signature)]−[0.2006*(MHC class II gene expression signature value)]; wherein a higher survival predictor score is associated with worse survival.
6. The method of claim 5 wherein the step of obtaining gene expression data comprises use of a micro array.
7. The method of claim 5 wherein the ABC DLBCL gene expression signature comprises at least one gene selected from the group consisting of (listed by UNIQID): 1134271, 1121564, 1119889, 1133300, 1106030, 1139301, 1122131, 1114824, 1100161, and 1120129.
8. The method of claim 5 wherein the lymph node gene expression signature comprises at least one gene selected from the group consisting of (listed by UNIQID): 1097126, 1120880, 1098898, 1123376, 1128945, 1130994, 1124429, 1099358, 1130509, 1095985, 1123038, 1133700, 1122101, and 1124296.
9. The method of claim 5 wherein the MHC class II gene expression signature comprises at least one gene selected from the group consisting of (listed by UNIQID): 1123127, 1136777, 1137771, 1134281, 1136573, and 1132710.
10. A method for predicting survival in a mantle cell lymphoma (MCL) subject comprising the steps of:
a) isolating gene expression product from a biopsy sample from a subject;
b) obtaining gene expression data from the isolated gene expression product, wherein the gene expression data comprises data for genes in a proliferation gene expression signature;
c) averaging the gene expression level of genes from the proliferation gene expression signature to thereby obtain a proliferation gene expression signature value;
d) calculating a survival predictor score using an equation: [1.66*(proliferation gene expression signature value)]; wherein a higher survival predictor score is associated with worse survival.
11. The method of claim 10 wherein the step of obtaining gene expression data comprises use of a microarray.
12. The method of claim 10 wherein the proliferation gene expression signature comprises at least one gene selected from the group consisting of (listed by UNIQID): 1097290, 1101295, 1119729, 1120153, 1120494, 1124745, 1126148, 1130618, 1134753, 1139654, and 1140632.
13. The method of claim 10 wherein the proliferation gene expression signature comprises at least one gene selected from the group consisting of (listed by UNIQID): 1119294, 1119729, 1120153, 1121276, 1123358, 1124178, 1124563, 1130799, 1131274, 1131778, 1132449, 1135229, and 1136585.
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