WO2007082379A2 - Method to identify cd40-sensitive cells using gene expression - Google Patents

Method to identify cd40-sensitive cells using gene expression Download PDF

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WO2007082379A2
WO2007082379A2 PCT/CA2007/000073 CA2007000073W WO2007082379A2 WO 2007082379 A2 WO2007082379 A2 WO 2007082379A2 CA 2007000073 W CA2007000073 W CA 2007000073W WO 2007082379 A2 WO2007082379 A2 WO 2007082379A2
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cells
protein
genes
expression
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WO2007082379A3 (en
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C. Annette Hollmann
Robert Sladek
Trevor Owens
Thomas J. Hudson
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Mcgill University
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • 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
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6863—Cytokines, i.e. immune system proteins modifying a biological response such as cell growth proliferation or differentiation, e.g. TNF, CNF, GM-CSF, lymphotoxin, MIF or their receptors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30 CD40 or CD95
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2510/00—Detection of programmed cell death, i.e. apoptosis

Definitions

  • CD40 promotes survival, proliferation, and differentiation of normal B-cells, but can cause activation-induced cell death in malignant B-lymphocytes.
  • CD40 ligand and anti-CD40 antibodies have been used successfully to induce apoptosis in lymphoma lines both in vitro and in xenograft tumor models. While this makes CD40 an attractive target for anti-tumor therapies, the response of malignant B-cells to CD40 signaling is variable and CD40 stimulation can enhance proliferation and increase chemoresistance in some cell lines.
  • CD40 is first expressed prior to the rearrangement of immunoglobulin heavy chain genes in early B-cell development; its expression is maintained through all subsequent stages of B-cell development and is not lost during malignant transformation (2).
  • Malignant B-lymphocytes and other CD40-positive tumor cells differ from normal B-cells in that they undergo apoptosis following CD40 stimulation (3).
  • CD40 stimulation shows promise as an anti-tumor therapy in murine models of B-cell lymphoma and breast cancer (4, 5).
  • CD40 ligand has also been tested in phase I clinical trials (6); however, the use of CD40-directed therapy remains controversial because CD40 signaling can enhance cell proliferation and survival as well as induce resistance to chemotherapeutic agents in some B-cell malignancies (7, 8).
  • the invention is a method of determining whether first cells respond to CD40 stimulation by undergoing apoptosis, said method comprising testing said first cells for their profile of gene expression, and comparing said profile with a second profile of gene expression of second cells known to respond to CD40 stimulation by undergoing apoptosis. If the profile of gene expression of the first cells shows expression levels of genes characteristic of the second profile, said first cells respond to CD40 stimulation by undergoing apoptosis.
  • the method can be performed by analyzing RNA from the first cells and the second cells on one or more arrays prepared for detection and/or quantitation of RNA purified or partially purified from cells.
  • the invention is a method of determining whether first cells respond to CD40 stimulation by undergoing apoptosis, said method comprising testing said first cells for levels of expression of one or more genes, and comparing a first set of levels of expression of said one or more genes to a second set of levels of expression of said one or more genes in second cells known to respond to CD40 stimulation by undergoing apoptosis; wherein, if the first set of levels of expression of said one or more genes in said first cells is characteristic of said second set of levels of the second cells, said first cells respond to CD40 stimulation by undergoing apoptosis.
  • Methods for quantitating levels of gene expression and/or providing means to compare levels of expression of selected genes are known in the art, and any such method previously described can be used where a step of a method requires such quantitation and/or comparison.
  • Methods that rely on nucleic acid hybridization or hybridizable analogs thereof are particularly useful. They can include, for example, analysis by oligonucleotide (or hybridizable analogs thereof) arrays or microarrays, commercially available or custom-made.
  • Other methods that can be used for quantitating and comparing gene expression are RT-PCR, western blotting or immunostaining methods.
  • the invention is a method for determining whether a population of cells is CD40-sensitive, said method comprising quantitating expression of one or more genes in a sample of cells from the population, wherein said one or more genes in diffuse large-cell B-lymphoma (DLCBL) cell lines are differentially regulated between CD40-sensitive DLCBL cell lines and CD40-resistant DLCBL cell lines, and comparing quantities of expression of said one or more genes in said sample to quantities of expression of said one or more genes in CD40-resistant DLCBL cell lines, wherein if said one or more genes are differentially regulated between the cells in the sample and the CD40-resistant DLCBL cell lines, then the population of cells is CD40-sensitive.
  • DLCBL diffuse large-cell B-lymphoma
  • the genes to be examined for gene expression can be one or more of any of a number of genes described herein that were found to be expressed constitutively at significantly different levels in CD40-resistant cells as compared to expression of those genes in CD40-sensitive cells.
  • the genes can be one or any number of genes selected from B-cell maturation specific genes and members of the CD40/BCR signaling pathway (see Tables 7A, 7B, 1OA and 10B).
  • Preferred genes to examine are RAGl, RAG2, IGLLl, CD9, VPREBl, CD22, CD38, Bruton's tyrosine kinase, VAVl, LYN, LCK and MEK1/MAP2K1.
  • the gene to be examined can be RAGl or VAVl or both.
  • RT-PCR reverse transcription polymerase chain reaction
  • Another method that allows quantitating gene expression and comparing levels of expression among or between genes is analysis on arrays.
  • a further method to quantitate expression of a gene is immunohistochemistry, which employs antibodies that can be added to a sample of cells prepared for immunohistochemical testing. The antibodies bind specifically to the protein product of the gene.
  • Yet another embodiment of the invention is a method for determining whether a population of cells is CD40-sensitive or CD40-resistant, said method comprising testing a sample of cells from said population for the presence or absence of phosphorylated ERK, whereby, if phosphorylated ERK is present, the population of cells is CD40-sensitive, and if phosphorylated ERK is absent, population of cells is CD40-resistant.
  • the method can be carried out by testing the sample of cells by immunohistochemical methods, such as immunoblot of non-denatured lysates from the sample of cells using anti-phospho-ERK antibodies, or immunostaining with immunofluorescent labeled anti-phospho-ERK antibodies or with anti-phospho-ERK antibodies conjugated to a reactive label that can be readily visualized, for example.
  • immunohistochemical methods such as immunoblot of non-denatured lysates from the sample of cells using anti-phospho-ERK antibodies, or immunostaining with immunofluorescent labeled anti-phospho-ERK antibodies or with anti-phospho-ERK antibodies conjugated to a reactive label that can be readily visualized, for example.
  • any of the above methods can be carried out on a sample of cells wherein the sample is a tissue biopsy or a fluid sample from a human or animal. Any of the methods can be carried out on a population of cells or a portion of a population of cells wherein the population of cells is a primary culture of cells from a human or animal, or the population of cells is a cell line.
  • the population of cells can comprise B-cell lymphoma cells, diffuse large-cell B -lymphoma cells, cancer cells, for example cancer cells derived from endothelial cells, epithelial cells, fibroblasts, or breast cancer cells, prostate cancer cells, lung cancer cells, or colon cancer cells, for instance.
  • a further method can be used to identify CD40-sensitive cells, performed by treating said cells to activate CD40, and testing said cells for an increase in the quantity of phosphorylated ERK, whereby if an increase in the quantity of phosphorylated ERK is observed, said cells are CD40-sensitive cells.
  • Cells in a population of cells, following one or more generations of cell divisions, may change in phenotype and/or genotype relative to the original population of cells.
  • Cells may have been grown in culture for one or more generations or they may have undergone mutation(s) at their normal site in a human or animal.
  • Cancer cells are widely recognized as cells that have undergone genotypic and phenotypic changes so that they differ from their cell of origin. Cells that are derived from a specific cell type means that the original population of cells some generations ago were of that cell type.
  • Arrays or microarrays for detection and quantitation of RNA are not limited to the use of oligonucleotides as probes.
  • Arrays can include as probes oligonucleotides, peptide nucleic acids, locked nucleic acids, phosphorothioate analogs of oligonucleotides and other analogs or mimics of oligonucleotides that can hybridize to RNA.
  • probes can also be used in other methods based on hybridization.
  • CD40 signaling differ among DLCBL lines.
  • OCI-LyI, OCI-Ly7, OCI-Ly 8 or Su-DHL4 cells were seeded at 100,000 cells per mL in supplemented RPMI containing 10 ⁇ g/mL anti-CD40 antibody and 10 ⁇ g/mL crosslinking secondary antibody (anti-CD40; filled squares), or secondary antibody alone (control; open circles).
  • anti-CD40 10 ⁇ g/mL anti-CD40; filled squares
  • secondary antibody alone control; open circles.
  • aliquots were removed at 24-hour intervals, stained with propidium iodide without prior permeabilization, and analyzed by flow cytometry using a fixed-time setting of 30 seconds to quantitate the number of viable cells per unit volume. Results of two experiments of three replicates each were combined.
  • Error bars represent standard deviations; where these are not visible they are covered by the overlying symbol. Growth of OCI-Ly7 and Su-DHL4 cells was inhibited by crosslinked anti-CD40. For quantitation of apoptosis, cells were stimulated for 48 hours with anti-CD40 or control antibody as described above, and then permeabilized with ethanol prior to staining with propidium iodide. Intracellular DNA content was analyzed by flow cytometry. Figure 2 is a bar graph showing the percentage of cells with sub-Gl DNA. Cells containing less DNA than the Gl fraction, representing apoptotic cells, were quantitated. Results from two experiments of three replicates each are shown. Error bars indicate standard deviations; asterisks indicate statistically significant differences between control and anti-CD40 treated cells. The fraction of cells with sub-Gl DNA content increased in OCI-Ly7 and Su-DHL4 cells.
  • Figures 3 A-3D are profiles of fluorescence from cells sorted by flow cytometry.
  • CD40 could be detected on all four DLCBL cell lines by flow cytometry.
  • Open profiles indicate fluorescence from phycoerythrin-conjugated anti-CD40 antibody and shaded profiles represent similarly conjugated isotype control antibody. Cells were not permeabilized prior to staining, thereby restricting staining to antigens exposed on the cell surface.
  • Figures 4A and 4B are gene expression profiles of CD40-sensitive and CD40- resistant DLCBL: B-cell markers and CD40 signaling. mRNA from unstimulated DLCBL lines was analyzed on Affymetrix HG-U133A v 2.0 Gene Chips as described in the
  • B-cell differentiation markers and genes in the CD40/BCR signaling pathway were compared in triplicate samples of each of the four cell lines. Brackets indicate hierarchical clustering performed with Genesis software (23). The vertical bar indicates a group of co-segregating pre-B cell markers (pre-B). See also Tables 2A, 2B, 3 A, 3B, 4A, 4B, 5 A, 5B, 6A, 6B, 7A, 7B, 8A, 8B, 9A, 9B, 1OA and 1OB.
  • Figures 5A-5E are bar graphs showing relative expression levels of genes in the CD40 signaling pathway. Expression of several genes which had shown differential expression by oligonucleotide array analysis was verified by RT-PCR. PCR products were analyzed by gel electrophoresis and photographed with a Syngene gel documentation system. Relative levels of expression were quantitated with GeneTools software by comparison with a standard curve generated by amplification of PCR product from serially diluted cDNA. Results from triplicate samples are shown. Error bars indicate standard deviations. Where these are not visible variations between samples were very small. N. D. indicates not detectable.
  • Figure 6 is a diagram illustrating the sites of action of two kinase inhibitors. Two genes involved in CD40-mediated ERK signaling are differentially expressed among CD40-sensitive and CD40-resistant cell lines. Differences in expression levels based on oligonucleotide array analysis are indicated. Fold difference in expression could not be calculated for VAV, as this mRNA was not detectable in CD40-resistant cells.
  • FIGS 7A and 7B are images of immunoblots. Activity of LCK and ERK was analyzed with phosphorylation-specific antibodies. LCK was immunoprecipitated from nondenatured cell lysates and detected by Western blotting with phospho-src-family antibody (phospho-src). The blot was stripped and reprobed with an antibody against LCK (LCK). A commercially available Jurkat cell lysate was used as a positive control. This sample was used without prior immunoprecipitation, allowing distinction of LCK from the slightly lower mobility band representing the antibody used in immunoprecipitation.
  • LCK phospho-src-family antibody
  • FIGS. 8 A and 8B are graphs of absorbance of cells, as a measure of viability, following the addition of PPl or UO 126. Sensitivity of the cell lines to inhibition of LCK and ERK activity was tested by addition of the src family kinase inhibitor PPl or the MEK1/2 inhibitor U0126.
  • FIG. 10 is a bar graph showing the effect of ERK inhibition on CD40-mediated apoptosis.
  • Cells were subjected to CD40 stimulation for 96 hours in the presence of the MEK1/2 inhibitors U0126 (10 ⁇ M) or PD98059 (50 ⁇ M), or the p38 inhibitor SB2O358O (10 ⁇ M).
  • Cell viability was quantitated by staining nonpermeabilized cells with propidium iodide, and counting the number of unstained (live) cells per unit volume using a Becton- Dickinson FACScan flow cytometer set to count for 30 seconds.
  • the number of viable cells in anti-CD40-treated samples was expressed as a percentage of the number of viable cells incubated in secondary antibody only. Results from three experiments of four replicates each are shown. Error bars represent standard deviations.
  • the number of viable OCI-Ly7 and Su- DHL4 cells was reduced by CD40 ligation, p ⁇ 0.01.
  • the MEK1/2 inhibitors U0126 and PD98059 prevented CD40-mediated reduction in viability. Constitutive ERK phosphorylation is correlated with CD40-mediated cell death.
  • CD40-resistant cells expressed high levels of CD9, the recombination activating genes RAGl and RAG2, and the pre-B cell receptor genes IGLLl and VPREBl , which are characteristic of pre-B cells at the stage of immunoglobulin rearrangement (36-39), and have also been detected in B- lymphocytes in germinal centers (40).
  • the CD40-sensitive OCI-Ly7 and Su-DHL4 cell lines may be derived from mature, activated B-cells whereas the CD40- resistant OCI-LyI and OCI-Ly8 lines resemble immature B-cells.
  • Expression of members of the CD40 signaling pathway was investigated to determine the underlying mechanism of CD40-mediated cell death.
  • LCK and VAV have been previously shown to maintain constitutive activation of ERK via stimulation of the RAS pathway (31) which is consistent with our observation that ERK was constitutively phosphorylated in CD40-sensitive DLCBL cell lines but permanently inactive in VAV-deficient CD40-resistant lines.
  • the SRC family inhibitor PPl was more effective at reducing proliferation of OCI-Ly7 and Su-DHL4 cells. Differential sensitivity to PPl could result from inhibition of other SRC family kinases or from the differential function of downstream effectors such as VAV, RAS, and ERK.
  • ERK inhibitors prior to CD40 stimulation blocked activation-induced cell death, which indicates that overexpression or aberrant activation of a protein in the ERK signaling cascade may sensitize DLCBL cell lines to CD40.
  • ERK has been implicated in apoptosis in other systems of activation-induced cell death, both directly and as a predisposing factor.
  • TCR-mediated activation-induced cell death in a TCR hybridoma cell line was shown to be mediated by activation of VAV and ERK (42).
  • ERK may function in a similar way in DLCBL cell lines, rendering cells susceptible to a second signal caused by CD40 stimulation. However, the signal is unlikely to be calcium-mediated, as treatment of the cells with the calcium ionophore ionomycin induced cell death in Su-DHL4 but not OCI-Ly7 cells.
  • DLCBL has been shown to segregate into two subtypes with distinct gene expression patterns, one resembling germinal center cells (germinal center type) and the other similar to mature B-cells that have been subjected to CD40 and B-cell receptor stimulation (activated B-cell type) (45).
  • the prognosis was shown to differ significantly, with five-year survival being 76% for germinal center and 34% for activated type DLCBL (46).
  • Neither the prevalence of constitutive ERK activation in either subtype of DLCBL nor correlation with CD40 sensitivity has yet been investigated in tumor tissue. This area may be fruitful for future investigation based not only on our observations, but also on recent development of inhibitors which modulate relevant signal transduction pathways.
  • the SRC-VAV-ERK signal transduction pathway is activated by both CD40 and B-cell receptor signaling (12), and been implicated in proliferation of B-cell malignancies (41).
  • CD40 proteins in this pathway, including CD40, SRC family kinases, RAS, and MEK are being investigated as targets for anti-tumor therapies (47-50).
  • the studies herein show that increased expression of genes involved CD40/BCR signal transduction coincided with constitutive ERK activation and susceptibility to CD40-mediated cell death in DLCBL cell lines.
  • a constitutively active phenotype has previously been associated with reduced survival in DLCBL (45).
  • activated type DLCBL may be the result of one or more overactive proteins in the CD40 signal transduction pathway.
  • An interesting but as yet untested hypothesis is that the mechanism underlying the aggressive nature of activated DLCBL may also be its Achilles heel, leaving it vulnerable to therapies targeting the CD40 signal transduction pathway.
  • Epstein AL Kaplan HS. Feeder layer and nutritional requirements for the establishment and cloning of human malignant lymphoma cell lines. Cancer Res 1979;39:1748-1759.
  • Clark EA Yip TC, Ledbetter JA, et al. CDw40 and BLCa-specific monoclonal antibodies detect two distinct molecules which transmit progression signals to human B lymphocytes. Eur J Immunol 1988; 18:451-457.
  • TNF receptor-associated factor-3 signaling mediates activation of p38 and Jun N- terminal kinase, cytokine secretion, and Ig production following ligation of CD40 on human B cells. J Immunol 1998;161 : 1183-1 193.
  • Membrane CD22 defines circulating myeloma-related cells as mature or later B cells. Lab Invest 1997;77:333-344.
  • Diffuse large-cell lymphoma lines OCI-LyI , OCI-Ly7, OCI-Ly8, and Su-DHL4 were provided by Dr. Neil Berinstein, Ontario Cancer Institute, Toronto, ON, Canada.
  • a hybridoma line producing anti-human CD40 (clone G28.5) (15) was provided by Dr. Bruce Mazer, McGiIl University, Montreal, PQ, Canada.
  • the cell lines were maintained in RPMI 1640 medium (Sigma, Oakville, ON, Canada) supplemented with 10% bovine growth serum (VWR Canlab, Montreal, PQ, Canada), 0.2 mM glutamine, 0.05 mM ⁇ -mercaptoethanol, 100 U/mL penicillin andlOO ⁇ g/mL streptomycin in a 5% CO 2 atmosphere at 37°C.
  • Antibodies against human CD40 (clone G28.5) and murine IgG (clone HB58) were purified from hybridoma supernatants with a Protein G sepharose column as described by the manufacturer (Amersham, Baie d'Urfe, PQ, Canada).
  • Cells were resuspended at 1x10 5 cells / mL in RPMI 1640 medium supplemented as described above.
  • Anti-CD40 antibody G28.5 and secondary crosslinking antibody HB58 were added to a final concentration of 10 ⁇ g/mL each, and the cells were incubated at 37 0 C.
  • At 24 hour intervals aliquots of cells were harvested by centrifugation, washed once in phosphate buffered saline, and resuspended in FACS buffer.
  • Non-permeabilized cells were stained by addition of 1 ⁇ g/mL propidium iodide, and the density of viable cells was determined using a FACScan flow cytometer and CellQuest software (Becton Dickinson, Mississauga, ON, Canada) set to count for a fixed 30-second time interval. To determine the fraction of cells that had undergone apoptosis, total intracellular DNA content was measured by propidium iodide staining of ethanol-permeabilized cells as previously described (16).
  • CD40 on the cell surface was confirmed by staining non- permeabilized cells with a phycoerythrin-linked anti-CD40 antibody (clone 5C3, Becton- Dickinson) as per the manufacturer's directions, followed by flow cytometry.
  • a phycoerythrin-linked anti-CD40 antibody (clone 5C3, Becton- Dickinson) as per the manufacturer's directions, followed by flow cytometry.
  • the src family kinase inhibitor PPl and the MEK inhibitor UO 126 were purchased from Biomol (Plymouth Meeting, PA, USA), and from Cell Signaling Technology (Beverly, MA, USA) respectively.
  • Kinase inhibition assays were performed using cells seeded at a density of 5x10 4 per mL in 96- well plates, to which kinase inhibitors were added to final concentrations of 10 "4 to 10 "8 M. The treated cells were incubated at 37 0 C for 96 hours and cell viability was quantitated by MTT assay as previously described (17).
  • the MEK inhibitors UOl 26 (10 ⁇ M) and PD98059 (50 ⁇ M) as well as the p38 inhibitor SB203580 (10 ⁇ M) (Cell Signaling Technologies) were added 30 minutes prior to CD40 stimulation.
  • the dose of kinase inhibitors used in this study have been previously shown to mediate target-specific effects in lymphocytes (18).
  • Nondenatured whole cell lysates were prepared by sonicating cells in nondenaturing lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, ImM EDTA, 1 mM EGTA, 1% Triton-X 100, 1 mM Na 3 VO 4 ) containing a protease inhibitor cocktail (Roche Diagnostics, Laval, PQ, Canada).
  • Cytoplasmic-enriched extracts were prepared by lysing cells in hypotonic lysis buffer (10 mM Hepes pH 7.9, 1.5 mM MgCl 2 , 100 mM KCl, ImM DTT, 1% protease inhibitor cocktail (Sigma, P8340)) followed by shearing through a 23G needle to release the nuclei.
  • the nuclei were pelleted at 450xg and the supernatant (cytoplasmic-enriched cell extract) was removed and stored at -8O 0 C. Protein concentration was determined using the BCA protein assay (Pierce, Rockford, IL, USA).
  • LCK was immunoprecipitated from nondenatured cell lysate with a polyclonal rabbit antibody (Cell Signaling Technology #2752) as recommended by the manufacturer. Proteins were separated by SDS-PAGE on a 14% polyacrylamide gel at 180V for Ih and transferred to a nitrocellulose membrane by electrophoretic transfer at 100V for 1 h. Western blots were performed as previously described (16).
  • RNA was prepared from cultured cells using Trizol reagent according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). The integrity of the purified RNA was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Probes for microarray analysis were prepared using 10 micrograms of total RNA and hybridized to Affymetrix HG-Ul 13A Gene Chips (Affymetrix, Santa Clara, CA) as previously described (19). In order to minimize technical variability, RNA processing steps (RNA extraction, probe labeling and chip hybridization) were performed in parallel for each set of four RNA samples. The hybridized arrays were scanned and raw data extracted using the Microarray
  • RNA isolation and cDNA synthesis was performed as for the microarray analyses.
  • Primers were designed to span introns to ensure specificity for cDNA as opposed to genomic DNA sequences. Intron/exon junctions were identified by use of the UCSC genome browser (http://www.genome.ucsc.edu) (24). Primers were designed using Primer3 software (http://frodo.wi. mit.edu/cgi-bin/primer3/primer3 www.cgi) (25) and their specificity was verified by performing a BLAST search (http://www.ncbi.nlm.nih.gov/BLAST/) of the NCBI "nr" nucleotide sequence database
  • GAPDH 5'GAAGGTGAAGGTCGGAGTCA SEQ ID NO:5;
  • VAVl 5 'CACCTGCTGTGAGAAGTTCG (SEQ ID NO: 11);
  • PCR amplification was performed with 0.01 U / ⁇ L Taq DNA polymerase (Sigma) in PCR buffer (Sigma) containing 2 raM MgCl 2 , 0.25 ⁇ g/ ⁇ L bovine serum albumin (New England
  • PCR products were detected by gel electrophoresis and ethidium bromide staining. Images were acquired with a Syngene gel documentation system and GeneSnap software. Gene expression was quantitated with GeneTools software, using PCR products amplified from a cDNA dilution series as a standard curve.
  • RNA from unstimulated OCI-LyI, OCI-Ly8, 0CI-Ly7, and Su- DHL4 cells was analyzed on Affymetrix U133A oligonucleotide arrays.
  • 304 genes were differentially expressed among CD40-sensitive and CD40-resistant cells ( Figures 4A and 4B; Tables 2A, 2B, 3 A and 3B. Further analysis was restricted to subsets of genes likely to be involved in CD40 signaling, including regulators of apoptosis, B-cell specific genes, and NF ⁇ B-regulated genes.
  • CD40-sensitive cells also expressed higher levels of several genes in the CD40 signaling pathway, including Bruton's tyrosine kinase, VAV, LYN, LCK, and MEK1/MAP2K1. Differential expression of several genes was confirmed by RT-PCT ( Figures 5A-5E). Transcripts for two of these genes could only be detected in one group of cell lines: RAGl was easily detectable in CD40-resistant OCI-LyI and OCI-Ly8 cells but absent in CD40-sensitive OCI-Ly7 and Su-DHL4 cells, and VAVl was present in CD40-sensitive but undetectable in CD40- resistant cells.
  • CD86 antigen CD28 antigen ligand 2, B7-2 antigen
  • 200706 s_at 7 13 6 99 7 1 1 5 71 5 61 5 62 7 31 7 01 7 14 5 89 5 91 5 84
  • TAP2 Hs 502 transporter 2 ATP-binding cassette, subfamily B (MDR/TAP)

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Abstract

A method of differentiating between first diffuse large cell B lymphoma (DLCBL) cells and second DLCBL cells, known to respond to CD40 mediated apoptosis, based on differences in expression of one or more genes or a profile of genes and a method to differentiate between CD40 sensitive and CD40 resistant DLCBL cells based on the differences in gene expression of recombination activating gene 1(RAG 1), pre-B lymphocyte gene 1 (VPREB 1), lymphocyte specific protein tyrosine kinase (LCK) and VAV 1 oncogene (VAV 1).

Description

METHOD TO IDENTIFY CD40-SENSITIVE CELLS
RELATED APPLICATION
This application claims the benefit of U.S. Provisional Application No. 60/760,648, filed on January 20, 2006. The entire teachings of the above application are incorporated herein by reference.
BACKGROUND OF THE INVENTION
CD40 promotes survival, proliferation, and differentiation of normal B-cells, but can cause activation-induced cell death in malignant B-lymphocytes. CD40 ligand and anti-CD40 antibodies have been used successfully to induce apoptosis in lymphoma lines both in vitro and in xenograft tumor models. While this makes CD40 an attractive target for anti-tumor therapies, the response of malignant B-cells to CD40 signaling is variable and CD40 stimulation can enhance proliferation and increase chemoresistance in some cell lines.
CD40 is first expressed prior to the rearrangement of immunoglobulin heavy chain genes in early B-cell development; its expression is maintained through all subsequent stages of B-cell development and is not lost during malignant transformation (2). Malignant B-lymphocytes and other CD40-positive tumor cells differ from normal B-cells in that they undergo apoptosis following CD40 stimulation (3). CD40 stimulation shows promise as an anti-tumor therapy in murine models of B-cell lymphoma and breast cancer (4, 5). CD40 ligand has also been tested in phase I clinical trials (6); however, the use of CD40-directed therapy remains controversial because CD40 signaling can enhance cell proliferation and survival as well as induce resistance to chemotherapeutic agents in some B-cell malignancies (7, 8). Consequently, elucidation of the mechanisms involved in CD40-mediated apoptosis may help to identify markers for susceptibility to CD40- mediated cell death and reveal proteins that specifically control the apoptotic arm of CD40 signaling. It would be useful to have a method to use to predict whether a specific cell line or tumor will undergo apoptosis when stimulated with CD40, and to identify targets downstream of CD40 which affect only the apoptotic arm of CD40 signaling. SUMMARY OF THE INVENTION
In one embodiment, the invention is a method of determining whether first cells respond to CD40 stimulation by undergoing apoptosis, said method comprising testing said first cells for their profile of gene expression, and comparing said profile with a second profile of gene expression of second cells known to respond to CD40 stimulation by undergoing apoptosis. If the profile of gene expression of the first cells shows expression levels of genes characteristic of the second profile, said first cells respond to CD40 stimulation by undergoing apoptosis. The method can be performed by analyzing RNA from the first cells and the second cells on one or more arrays prepared for detection and/or quantitation of RNA purified or partially purified from cells.
In another embodiment, the invention is a method of determining whether first cells respond to CD40 stimulation by undergoing apoptosis, said method comprising testing said first cells for levels of expression of one or more genes, and comparing a first set of levels of expression of said one or more genes to a second set of levels of expression of said one or more genes in second cells known to respond to CD40 stimulation by undergoing apoptosis; wherein, if the first set of levels of expression of said one or more genes in said first cells is characteristic of said second set of levels of the second cells, said first cells respond to CD40 stimulation by undergoing apoptosis.
Methods for quantitating levels of gene expression and/or providing means to compare levels of expression of selected genes are known in the art, and any such method previously described can be used where a step of a method requires such quantitation and/or comparison. Methods that rely on nucleic acid hybridization or hybridizable analogs thereof are particularly useful. They can include, for example, analysis by oligonucleotide (or hybridizable analogs thereof) arrays or microarrays, commercially available or custom-made. Other methods that can be used for quantitating and comparing gene expression are RT-PCR, western blotting or immunostaining methods.
In a further embodiment, the invention is a method for determining whether a population of cells is CD40-sensitive, said method comprising quantitating expression of one or more genes in a sample of cells from the population, wherein said one or more genes in diffuse large-cell B-lymphoma (DLCBL) cell lines are differentially regulated between CD40-sensitive DLCBL cell lines and CD40-resistant DLCBL cell lines, and comparing quantities of expression of said one or more genes in said sample to quantities of expression of said one or more genes in CD40-resistant DLCBL cell lines, wherein if said one or more genes are differentially regulated between the cells in the sample and the CD40-resistant DLCBL cell lines, then the population of cells is CD40-sensitive.
The genes to be examined for gene expression can be one or more of any of a number of genes described herein that were found to be expressed constitutively at significantly different levels in CD40-resistant cells as compared to expression of those genes in CD40-sensitive cells. The genes can be one or any number of genes selected from B-cell maturation specific genes and members of the CD40/BCR signaling pathway (see Tables 7A, 7B, 1OA and 10B). Preferred genes to examine are RAGl, RAG2, IGLLl, CD9, VPREBl, CD22, CD38, Bruton's tyrosine kinase, VAVl, LYN, LCK and MEK1/MAP2K1. In other methods, the gene to be examined can be RAGl or VAVl or both.
Methods to quantitate gene expression are known by persons of skill in the art. One such suitable method is reverse transcription polymerase chain reaction (RT-PCR). Another method that allows quantitating gene expression and comparing levels of expression among or between genes is analysis on arrays. A further method to quantitate expression of a gene is immunohistochemistry, which employs antibodies that can be added to a sample of cells prepared for immunohistochemical testing. The antibodies bind specifically to the protein product of the gene.
Yet another embodiment of the invention is a method for determining whether a population of cells is CD40-sensitive or CD40-resistant, said method comprising testing a sample of cells from said population for the presence or absence of phosphorylated ERK, whereby, if phosphorylated ERK is present, the population of cells is CD40-sensitive, and if phosphorylated ERK is absent, population of cells is CD40-resistant. The method can be carried out by testing the sample of cells by immunohistochemical methods, such as immunoblot of non-denatured lysates from the sample of cells using anti-phospho-ERK antibodies, or immunostaining with immunofluorescent labeled anti-phospho-ERK antibodies or with anti-phospho-ERK antibodies conjugated to a reactive label that can be readily visualized, for example.
Any of the above methods can be carried out on a sample of cells wherein the sample is a tissue biopsy or a fluid sample from a human or animal. Any of the methods can be carried out on a population of cells or a portion of a population of cells wherein the population of cells is a primary culture of cells from a human or animal, or the population of cells is a cell line. The population of cells can comprise B-cell lymphoma cells, diffuse large-cell B -lymphoma cells, cancer cells, for example cancer cells derived from endothelial cells, epithelial cells, fibroblasts, or breast cancer cells, prostate cancer cells, lung cancer cells, or colon cancer cells, for instance.
A further method can be used to identify CD40-sensitive cells, performed by treating said cells to activate CD40, and testing said cells for an increase in the quantity of phosphorylated ERK, whereby if an increase in the quantity of phosphorylated ERK is observed, said cells are CD40-sensitive cells.
Cells in a population of cells, following one or more generations of cell divisions, may change in phenotype and/or genotype relative to the original population of cells. Cells may have been grown in culture for one or more generations or they may have undergone mutation(s) at their normal site in a human or animal. Cancer cells are widely recognized as cells that have undergone genotypic and phenotypic changes so that they differ from their cell of origin. Cells that are derived from a specific cell type means that the original population of cells some generations ago were of that cell type.
Arrays or microarrays for detection and quantitation of RNA are not limited to the use of oligonucleotides as probes. Arrays can include as probes oligonucleotides, peptide nucleic acids, locked nucleic acids, phosphorothioate analogs of oligonucleotides and other analogs or mimics of oligonucleotides that can hybridize to RNA. Such probes can also be used in other methods based on hybridization.
BRIEF DESCRIPTION OF THE DRAWINGS Figures IA- ID are graphs showing that antiproliferative and apoptotic effects of
CD40 signaling differ among DLCBL lines. OCI-LyI, OCI-Ly7, OCI-Ly 8 or Su-DHL4 cells were seeded at 100,000 cells per mL in supplemented RPMI containing 10 μg/mL anti-CD40 antibody and 10 μg/mL crosslinking secondary antibody (anti-CD40; filled squares), or secondary antibody alone (control; open circles). For assessment of cell viability, aliquots were removed at 24-hour intervals, stained with propidium iodide without prior permeabilization, and analyzed by flow cytometry using a fixed-time setting of 30 seconds to quantitate the number of viable cells per unit volume. Results of two experiments of three replicates each were combined. Error bars represent standard deviations; where these are not visible they are covered by the overlying symbol. Growth of OCI-Ly7 and Su-DHL4 cells was inhibited by crosslinked anti-CD40. For quantitation of apoptosis, cells were stimulated for 48 hours with anti-CD40 or control antibody as described above, and then permeabilized with ethanol prior to staining with propidium iodide. Intracellular DNA content was analyzed by flow cytometry. Figure 2 is a bar graph showing the percentage of cells with sub-Gl DNA. Cells containing less DNA than the Gl fraction, representing apoptotic cells, were quantitated. Results from two experiments of three replicates each are shown. Error bars indicate standard deviations; asterisks indicate statistically significant differences between control and anti-CD40 treated cells. The fraction of cells with sub-Gl DNA content increased in OCI-Ly7 and Su-DHL4 cells.
Figures 3 A-3D are profiles of fluorescence from cells sorted by flow cytometry. CD40 could be detected on all four DLCBL cell lines by flow cytometry. Open profiles indicate fluorescence from phycoerythrin-conjugated anti-CD40 antibody and shaded profiles represent similarly conjugated isotype control antibody. Cells were not permeabilized prior to staining, thereby restricting staining to antigens exposed on the cell surface.
Figures 4A and 4B are gene expression profiles of CD40-sensitive and CD40- resistant DLCBL: B-cell markers and CD40 signaling. mRNA from unstimulated DLCBL lines was analyzed on Affymetrix HG-U133A v 2.0 Gene Chips as described in the
Materials and Methods section of the Examples. B-cell differentiation markers and genes in the CD40/BCR signaling pathway were compared in triplicate samples of each of the four cell lines. Brackets indicate hierarchical clustering performed with Genesis software (23). The vertical bar indicates a group of co-segregating pre-B cell markers (pre-B). See also Tables 2A, 2B, 3 A, 3B, 4A, 4B, 5 A, 5B, 6A, 6B, 7A, 7B, 8A, 8B, 9A, 9B, 1OA and 1OB.
Figures 5A-5E are bar graphs showing relative expression levels of genes in the CD40 signaling pathway. Expression of several genes which had shown differential expression by oligonucleotide array analysis was verified by RT-PCR. PCR products were analyzed by gel electrophoresis and photographed with a Syngene gel documentation system. Relative levels of expression were quantitated with GeneTools software by comparison with a standard curve generated by amplification of PCR product from serially diluted cDNA. Results from triplicate samples are shown. Error bars indicate standard deviations. Where these are not visible variations between samples were very small. N. D. indicates not detectable.
Figure 6 is a diagram illustrating the sites of action of two kinase inhibitors. Two genes involved in CD40-mediated ERK signaling are differentially expressed among CD40-sensitive and CD40-resistant cell lines. Differences in expression levels based on oligonucleotide array analysis are indicated. Fold difference in expression could not be calculated for VAV, as this mRNA was not detectable in CD40-resistant cells.
Figures 7A and 7B are images of immunoblots. Activity of LCK and ERK was analyzed with phosphorylation-specific antibodies. LCK was immunoprecipitated from nondenatured cell lysates and detected by Western blotting with phospho-src-family antibody (phospho-src). The blot was stripped and reprobed with an antibody against LCK (LCK). A commercially available Jurkat cell lysate was used as a positive control. This sample was used without prior immunoprecipitation, allowing distinction of LCK from the slightly lower mobility band representing the antibody used in immunoprecipitation. ERK was detected by immunoblotting with an antibody recognizing phosphorylated ERK 1/2 (phospho) and the blot was reprobed with a pan-specific anti-ERKl/2 antibody (total). Figures 8 A and 8B are graphs of absorbance of cells, as a measure of viability, following the addition of PPl or UO 126. Sensitivity of the cell lines to inhibition of LCK and ERK activity was tested by addition of the src family kinase inhibitor PPl or the MEK1/2 inhibitor U0126. Cells were incubated for 96 hours in inhibitor concentrations ranging from 10"4 to 10~8 M, and viability was assessed by MTT [3-(4, 5 - dimethylthiazol- 2-yl)-2, 5-diphenyltetrazolium bromide] assay. Viability is expressed as a percentage of the absorbance at 570 nm as compared to untreated samples. Results of two experiments with quadruplicate samples each were combined. Error bars indicate standard deviations. Figure 9 consists of images of stained Western blots. Cytoplasmic cell extracts were prepared from cells stimulated with crosslinked anti-CD40 antibody for 0 to 180 minutes. Total and phosphorylated ERK was detected by Western blot. Blots were first probed with the phospho-specific antibody, then the same membrane was re-probed for total protein with the pan-specific antibody. Figure 10 is a bar graph showing the effect of ERK inhibition on CD40-mediated apoptosis. Cells were subjected to CD40 stimulation for 96 hours in the presence of the MEK1/2 inhibitors U0126 (10 μM) or PD98059 (50 μM), or the p38 inhibitor SB2O358O (10 μM). Cell viability was quantitated by staining nonpermeabilized cells with propidium iodide, and counting the number of unstained (live) cells per unit volume using a Becton- Dickinson FACScan flow cytometer set to count for 30 seconds. The number of viable cells in anti-CD40-treated samples was expressed as a percentage of the number of viable cells incubated in secondary antibody only. Results from three experiments of four replicates each are shown. Error bars represent standard deviations. In the presence of DMSO (control) or the p38 inhibitor SB203580, the number of viable OCI-Ly7 and Su- DHL4 cells was reduced by CD40 ligation, p<0.01. The MEK1/2 inhibitors U0126 and PD98059 prevented CD40-mediated reduction in viability. Constitutive ERK phosphorylation is correlated with CD40-mediated cell death.
DETAILED DESCRIPTION OF THE INVENTION Differences in the effects elicited by CD40 stimulation in B-cell lines suggest that different signal transduction pathways may be expressed in CD40-sensitive and CD40- resistant cells. To assess this, expression microarray studies were performed on CD40- sensitive and CD40-resistant DLCBL cell lines. The data showing that CD40-sensitive and resistant cells display different gene expression profiles suggests that these lines may be derived from two distinct B-cell populations. CD40-sensitive cells overexpressed CD22 and CD38, which are found on mature, activated B-cells (35). CD40-resistant cells expressed high levels of CD9, the recombination activating genes RAGl and RAG2, and the pre-B cell receptor genes IGLLl and VPREBl , which are characteristic of pre-B cells at the stage of immunoglobulin rearrangement (36-39), and have also been detected in B- lymphocytes in germinal centers (40). This suggests that the CD40-sensitive OCI-Ly7 and Su-DHL4 cell lines may be derived from mature, activated B-cells whereas the CD40- resistant OCI-LyI and OCI-Ly8 lines resemble immature B-cells. Expression of members of the CD40 signaling pathway was investigated to determine the underlying mechanism of CD40-mediated cell death. Failure of OCI-LyI and OCI-Ly8 cells to undergo apoptosis upon CD40 stimulation may be the result of defects in the CD40 signal transduction pathway. These two cell lines showed reduced expression of several genes involved in CD40 signaling, including LCK, VAV, and MEKl. Analysis of LCK by RT-PCR and Western blot revealed that although RNA levels differed among CD40-sensitive and CD40-resistant lines, all four cell lines expressed significant amounts of active LCK. This suggests that differences in LCK mRNA levels may not have any functional consequences. However, differences in VAV, a phosphorylation target of LCK, were striking, with strong mRNA expression in CD40-sensitive lines and undetectable levels in CD40-resistant lines. LCK and VAV have been previously shown to maintain constitutive activation of ERK via stimulation of the RAS pathway (31) which is consistent with our observation that ERK was constitutively phosphorylated in CD40-sensitive DLCBL cell lines but permanently inactive in VAV-deficient CD40-resistant lines. Although all four cell lines expressed active LCK, the SRC family inhibitor PPl was more effective at reducing proliferation of OCI-Ly7 and Su-DHL4 cells. Differential sensitivity to PPl could result from inhibition of other SRC family kinases or from the differential function of downstream effectors such as VAV, RAS, and ERK. Lack of VAV and inactive ERK in OCI-LyI and OCI-Ly8 cells is consistent with a dead-end in the SRC signal transduction pathway. This could render the cells resistant to SRC family kinase inhibitors even if the targeted kinase itself is active. ERK activation has often been reported to be anti-apoptotic in both lymphoid and non-lymphoid malignancies (34, 41); however, the effect of ERK phosphorylation varies, even among different stimuli in the same cell line (12). Two different ERK inhibitors did not affect the growth of DLCBL cell lines containing activated ERK, which suggests that these lines are not dependent on ERK signaling for survival or proliferation. Addition of ERK inhibitors prior to CD40 stimulation blocked activation-induced cell death, which indicates that overexpression or aberrant activation of a protein in the ERK signaling cascade may sensitize DLCBL cell lines to CD40. The observation reported herein that ERK is constitutively active in these cell lines suggests that the actual death signal must be initiated by a second pathway when CD40 signaling occurs. ERK has been implicated in apoptosis in other systems of activation-induced cell death, both directly and as a predisposing factor. TCR-mediated activation-induced cell death in a TCR hybridoma cell line was shown to be mediated by activation of VAV and ERK (42). Transfection of RAT- 1 fibroblasts or MCF-7 human breast cancer cells with the ERK-regulated transcription factor elk-1 did not induce apoptosis directly, but rendered the cells susceptible to killing by a calcium ionophore (38). ERK may function in a similar way in DLCBL cell lines, rendering cells susceptible to a second signal caused by CD40 stimulation. However, the signal is unlikely to be calcium-mediated, as treatment of the cells with the calcium ionophore ionomycin induced cell death in Su-DHL4 but not OCI-Ly7 cells.
The observations herein on two pairs of cell lines are insufficient to determine whether differential expression of maturation-specific genes outside of the LCK-ERK pathway plays a role in determining susceptibility to CD40-mediated cell death; however, they are consistent with a previous report that B-cells at different stages of development differ in the protein phosphorylation patterns elicited by CD40 stimulation (43). As CD40 signaling can promote proliferation and resistance to apoptosis in normal B-cells (44), it is possible that constitutive activation of this pathway in a tumor may lead to a more aggressive phenotype. DLCBL has been shown to segregate into two subtypes with distinct gene expression patterns, one resembling germinal center cells (germinal center type) and the other similar to mature B-cells that have been subjected to CD40 and B-cell receptor stimulation (activated B-cell type) (45). The prognosis was shown to differ significantly, with five-year survival being 76% for germinal center and 34% for activated type DLCBL (46). Neither the prevalence of constitutive ERK activation in either subtype of DLCBL nor correlation with CD40 sensitivity has yet been investigated in tumor tissue. This area may be fruitful for future investigation based not only on our observations, but also on recent development of inhibitors which modulate relevant signal transduction pathways. The SRC-VAV-ERK signal transduction pathway is activated by both CD40 and B-cell receptor signaling (12), and been implicated in proliferation of B-cell malignancies (41). Several proteins in this pathway, including CD40, SRC family kinases, RAS, and MEK are being investigated as targets for anti-tumor therapies (47-50). The studies herein show that increased expression of genes involved CD40/BCR signal transduction coincided with constitutive ERK activation and susceptibility to CD40-mediated cell death in DLCBL cell lines. A constitutively active phenotype has previously been associated with reduced survival in DLCBL (45). This raises the question whether the poor prognosis of activated type DLCBL may be the result of one or more overactive proteins in the CD40 signal transduction pathway. An interesting but as yet untested hypothesis is that the mechanism underlying the aggressive nature of activated DLCBL may also be its Achilles heel, leaving it vulnerable to therapies targeting the CD40 signal transduction pathway.
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EXAMPLES
Materials & Methods
Lymphoma and hybridoma cell lines
Diffuse large-cell lymphoma lines OCI-LyI , OCI-Ly7, OCI-Ly8, and Su-DHL4 (13, 14) were provided by Dr. Neil Berinstein, Ontario Cancer Institute, Toronto, ON, Canada. A hybridoma line producing anti-human CD40 (clone G28.5) (15) was provided by Dr. Bruce Mazer, McGiIl University, Montreal, PQ, Canada. The cell lines were maintained in RPMI 1640 medium (Sigma, Oakville, ON, Canada) supplemented with 10% bovine growth serum (VWR Canlab, Montreal, PQ, Canada), 0.2 mM glutamine, 0.05 mM β-mercaptoethanol, 100 U/mL penicillin andlOO μg/mL streptomycin in a 5% CO2 atmosphere at 37°C. Antibodies against human CD40 (clone G28.5) and murine IgG (clone HB58) were purified from hybridoma supernatants with a Protein G sepharose column as described by the manufacturer (Amersham, Baie d'Urfe, PQ, Canada).
CD40 stimulation and assessment of viability
Cells were resuspended at 1x105 cells / mL in RPMI 1640 medium supplemented as described above. Anti-CD40 antibody G28.5 and secondary crosslinking antibody HB58 were added to a final concentration of 10 μg/mL each, and the cells were incubated at 370C. At 24 hour intervals aliquots of cells were harvested by centrifugation, washed once in phosphate buffered saline, and resuspended in FACS buffer. Non-permeabilized cells were stained by addition of 1 μg/mL propidium iodide, and the density of viable cells was determined using a FACScan flow cytometer and CellQuest software (Becton Dickinson, Mississauga, ON, Canada) set to count for a fixed 30-second time interval. To determine the fraction of cells that had undergone apoptosis, total intracellular DNA content was measured by propidium iodide staining of ethanol-permeabilized cells as previously described (16). Expression of CD40 on the cell surface was confirmed by staining non- permeabilized cells with a phycoerythrin-linked anti-CD40 antibody (clone 5C3, Becton- Dickinson) as per the manufacturer's directions, followed by flow cytometry.
Growth inhibition by kinase inhibitors
The src family kinase inhibitor PPl and the MEK inhibitor UO 126 were purchased from Biomol (Plymouth Meeting, PA, USA), and from Cell Signaling Technology (Beverly, MA, USA) respectively. Kinase inhibition assays were performed using cells seeded at a density of 5x104 per mL in 96- well plates, to which kinase inhibitors were added to final concentrations of 10"4 to 10"8 M. The treated cells were incubated at 370C for 96 hours and cell viability was quantitated by MTT assay as previously described (17). For inhibition of CD40-mediated apoptosis, the MEK inhibitors UOl 26 (10 μM) and PD98059 (50 μM) as well as the p38 inhibitor SB203580 (10 μM) (Cell Signaling Technologies) were added 30 minutes prior to CD40 stimulation. The dose of kinase inhibitors used in this study have been previously shown to mediate target-specific effects in lymphocytes (18).
Detection of intracellular phosphorylated ERK by flow cytometry Cells were permeabilized in Cytofix/Cytoperm (Becton-Dickinson) for 20 minutes, and stained with anti-phospho-ERK antibody (Cell Signaling Technology #9101) and FITC-conjugated anti-rabbit secondary antibody (Cedarlane Laboratories, Hornby, ON, CA) following the manufacturers' instructions. The stained cells were analyzed by flow cytometry with a FACScan flow cytometer and CellQuest software.
Preparation of cell extracts Nondenatured whole cell lysates were prepared by sonicating cells in nondenaturing lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, ImM EDTA, 1 mM EGTA, 1% Triton-X 100, 1 mM Na3VO4) containing a protease inhibitor cocktail (Roche Diagnostics, Laval, PQ, Canada). Cytoplasmic-enriched extracts were prepared by lysing cells in hypotonic lysis buffer (10 mM Hepes pH 7.9, 1.5 mM MgCl2, 100 mM KCl, ImM DTT, 1% protease inhibitor cocktail (Sigma, P8340)) followed by shearing through a 23G needle to release the nuclei. The nuclei were pelleted at 450xg and the supernatant (cytoplasmic-enriched cell extract) was removed and stored at -8O0C. Protein concentration was determined using the BCA protein assay (Pierce, Rockford, IL, USA).
Immunoprecipitation and Western blot: LCK was immunoprecipitated from nondenatured cell lysate with a polyclonal rabbit antibody (Cell Signaling Technology #2752) as recommended by the manufacturer. Proteins were separated by SDS-PAGE on a 14% polyacrylamide gel at 180V for Ih and transferred to a nitrocellulose membrane by electrophoretic transfer at 100V for 1 h. Western blots were performed as previously described (16). Primary antibodies against total and phosphorylated ERK, JNK, and p38 (Cell Signaling Technology #9101 , #9102, #9151, #9152, #921 1 and #9212) were used at a dilution of 1 : 100, primary antibodies against LCK and activated src family kinases (Cell Signaling Technology #2752 and #2101) were diluted 1 :500, and peroxidase-conjugated goat anti-mouse or donkey anti- rabbit secondary antibodies (BioCan Scientific, Mississauga, ON, Canada) were used at a dilution of 1 : 10000. The compositions of blocking and antibody dilution solutions were as specified by the manufacturer. Blots were immersed in Femto West ECL staining solution (Pierce) for 30 seconds and photographed with a Syngene chemiluminescence imaging system and GeneSnap software. Image size and contrast was adjusted using Canvas software. Expression microarrays
Total RNA was prepared from cultured cells using Trizol reagent according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). The integrity of the purified RNA was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Probes for microarray analysis were prepared using 10 micrograms of total RNA and hybridized to Affymetrix HG-Ul 13A Gene Chips (Affymetrix, Santa Clara, CA) as previously described (19). In order to minimize technical variability, RNA processing steps (RNA extraction, probe labeling and chip hybridization) were performed in parallel for each set of four RNA samples. The hybridized arrays were scanned and raw data extracted using the Microarray
Analysis Suite 5.0 (MAS5, Affymetrix, Santa Clara, CA). The raw data were normalized using RMAExpress (20) (http://stat-www.berkeley.edu/users/bolstad/ RMAExpress/RMAExpress.html) and filtered to exclude genes that MAS5 did not identify as "Present" in any expression profile. Differentially expressed genes were identified by performing a t-test between each pair of CD40-sensitive and CD40-resistant lines. False positive error correction was performed to maintain a 10% false discovery rate (FDR) (21). Genes whose expression differed significantly and showed the same direction of change in all four comparisons were considered to be differentially regulated between sensitive and resistant lines. Functional assessment of these expression differences was performed using contingency table analysis, based on hand-curated lists of NFKB targets ((22) and references obtained from http://people.bu.edu/gilmore/nf-kb)) genes involved in CD40 and BCR signal transduction, B-cell maturation markers and the Gene Ontology classification of proteins implicated in apoptosis (Affymetrix, Santa Clara, CA). See Tables 4A, 4B, 5 A, 5B, 6A, 6B, 7A, 7B, 8A, 8B, 9A, 9B, 1OA and 1OB. Figures 4A and 4B illustrating relevant expression profiles were prepared using Genesis (http://genome.tugraz.at/Software/GenesisCenter.html) (23).
Semi-quantitative RT-PCR
RNA isolation and cDNA synthesis was performed as for the microarray analyses. Primers were designed to span introns to ensure specificity for cDNA as opposed to genomic DNA sequences. Intron/exon junctions were identified by use of the UCSC genome browser (http://www.genome.ucsc.edu) (24). Primers were designed using Primer3 software (http://frodo.wi. mit.edu/cgi-bin/primer3/primer3 www.cgi) (25) and their specificity was verified by performing a BLAST search (http://www.ncbi.nlm.nih.gov/BLAST/) of the NCBI "nr" nucleotide sequence database
(26). The following primer pairs were used:
BTK 5 'TGATGAAGGGCCTCTCTACG (SEQ ID NO:1);
3 'CGGTGAGAACTCCCAGGTTT (SEQ ID NO:2); CD9 5 'GACTATGGCTCCGATTCGAC (SEQ ID NO:3);
3'AGGAAGCCGAAGAACAGTCC (SEQ ID NO:4);
GAPDH 5'GAAGGTGAAGGTCGGAGTCA (SEQ ID NO:5);
3 'GACAAGCTTCCCGTTCTCAG (SEQ ID NO:6);
LCK 5'ATGAACTGGTCCGCCATTAC (SEQ ID NO:7); 3 'CCCGTTGTAGTACCCCATCC (SEQ ID NO:8);
RAGl 5' AGAGAGCAGAGAACACACTTTGC (SEQ ID NO:9);
3 'GATCTCACCCGGAACAGCTT (SEQ ID NO: 10);
VAVl 5 'CACCTGCTGTGAGAAGTTCG (SEQ ID NO: 11);
3 'GTCGGACAGGCCACTGTAGAT (SEQ ID NO: 12). PCR amplification was performed with 0.01 U /μL Taq DNA polymerase (Sigma) in PCR buffer (Sigma) containing 2 raM MgCl2, 0.25 μg/μL bovine serum albumin (New England
Biolabs), and 0.1 mM each dATP, DCTP, dGTP, and dTTP (Amersham). Amplification was performed with 25 cycles (GAPDH, BTK) or 35 cycles (all other primers) of 30 seconds each at 950C, 58°C, and 72°C. PCR products were detected by gel electrophoresis and ethidium bromide staining. Images were acquired with a Syngene gel documentation system and GeneSnap software. Gene expression was quantitated with GeneTools software, using PCR products amplified from a cDNA dilution series as a standard curve.
Images were transferred to Canvas software for adjustment of contrast and image size.
Example 1
Susceptibility of DLCBL cell lines to CD40-mediated cell death
Diffuse large-cell B-lymphoma cell lines were screened for susceptibility to CD40- mediated cell death. The number of viable OCI-Ly7 and Su-DHL4 cells was reduced after 72 hours of exposure to crosslinked anti-CD40 antibody, whereas the viability of OCI-LyI and OCI-Ly8 cells was unaffected (Figures IA- ID). CD40 stimulation also increased the proportion of cells with sub-Gl DNA content at 48 hours in OCI-Ly7 and Su-DHL4, but not OCI-LyI or OCI-Ly8 (Figure 2). Expression of CD40 on the cell surface was confirmed by flow cytometry for all four cell lines (Figures 3A-3D). Example 2
Gene expression profiling of CD40-sensitive and CD40-resistant DLCBL lines
To identify pre-existing gene expression patterns that may predict susceptibility to CD40-mediated cell death, RNA from unstimulated OCI-LyI, OCI-Ly8, 0CI-Ly7, and Su- DHL4 cells was analyzed on Affymetrix U133A oligonucleotide arrays. In total, 304 genes were differentially expressed among CD40-sensitive and CD40-resistant cells (Figures 4A and 4B; Tables 2A, 2B, 3 A and 3B. Further analysis was restricted to subsets of genes likely to be involved in CD40 signaling, including regulators of apoptosis, B-cell specific genes, and NFκB-regulated genes. Susceptibility to CD40-mediated apoptosis was not associated with differences in expression of pro-apoptotic or anti-apoptotic transcripts, and there was no statistically significant difference in expression of NFκB-regulated genes (Table 1). Differences in expression of transcripts encoding B-cell maturation-specific genes and members of the CD40 signaling pathway were statistically significant. CD40 resistant OCI-LyI and OCI-Ly8 cells expressed significantly higher levels of pre-B cell genes including RAGl, RAG2, IGLLl, CD9, and VPREBl, whereas CD40-sensitive OCI- Ly7 and Su-DHL4 cells expressed higher levels of CD22 and CD38. CD40-sensitive cells also expressed higher levels of several genes in the CD40 signaling pathway, including Bruton's tyrosine kinase, VAV, LYN, LCK, and MEK1/MAP2K1. Differential expression of several genes was confirmed by RT-PCT (Figures 5A-5E). Transcripts for two of these genes could only be detected in one group of cell lines: RAGl was easily detectable in CD40-resistant OCI-LyI and OCI-Ly8 cells but absent in CD40-sensitive OCI-Ly7 and Su-DHL4 cells, and VAVl was present in CD40-sensitive but undetectable in CD40- resistant cells.
Table 1 : Differences in gene expression among CD40-sensitive and CD40-resistant DLCBL lines
Group number differences of genes expected observed Chi Square p-value
Total unique markers 8003 N.A. 298 N.A. N.A.
Pre-B markers* 14 0.5 5.0 38.5 O.001
Mature, activated B-celf 18 0.7 3.0 8.1 O.005
Pan-B cell* 10 0.4 1 1.1 n.s.
CD40 / BCR signaling* 35 1.3 5.0 10.5 O.005
NFKB regulated 117 4.4 6.0 0.6 n.s.
Apoptosis 90 3.4 3 0.0 n.s.
Anti-apoptosis 56 1.1 0 1.1 n.s.
N.A. = not applicable, n.s. = not significant.
*Genes in these groups are listed in Tables 4A, 4B, 5A, 5B, 6A, 6B, 7A, 7B, 8A, 8B, 9A, 9B, 1OA and 1OB.
Table 2A: Genes With Increased Expression in CD40-Sensitive Cell Lines
Log2 fluorescence intensity
Probesets Ly1 (A1 ) Ly1 (A2) Ly1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
200011_s_at 9 37 9 43 9 33 9 70 9 59 9 63 9 31 9 23 9 40 10 31 10 30 10 42
200090_at 8 94 8 60 8 88 9 95 9 99 9 90 8 77 8 54 8 83 10 35 10 22 10 44
200625_s_at 9 62 9 46 9 54 10 25 10 12 10 13 9 77 9 77 9 66 10 06 10 22 10 15
200679 x at 10 87 11 27 11 16 12 13 12 00 12 04 10 97 11 15 11 22 12 13 12 12 12 32
200762_at 6 64 6 56 6 91 9 22 9 03 8 98 648 6 50 7 17 8 51 8 16 8 78
200833_s_at 9 81 9 59 9 83 10 35 10 24 10 47 9 82 9 74 9 92 10 57 10 57 10 79
200998_s_at 5 24 5 07 5 26 6 84 7 21 6 83 6 05 5 70 5 77 6 75 6 89 7 11
201029_s_at 7 24 7 18 7 18 9 63 9 66 9 37 8 31 7 88 8 11 10 81 11 04 10 86
201077_s_at 10 70 10 63 10 55 11 13 10 99 10 98 10 66 10 59 10 54 10 96 11 02 10 89
201089_at 8 18 7 80 7 79 8 87 8 64 8 84 7 96 7 78 7 97 9 21 9 21 9 51
201090_x_at 13 07 13 16 13 11 13 60 13 50 13 51 13 19 13 19 13 15 13 59 13 52 13 61
201209 at 960 9 38 9 66 1043 10 38 1040 9 67 9 39 9 63 1063 10 37 10 62
201260_s_at 7 65 7 59 8 15 9 44 9 34 9 55 7 62 7 59 7 99 9 62 9 64 9 71
201375_s at 8 03 7 78 8 17 9 52 9 38 9 56 8 15 7 75 8 23 9 53 9 37 9 73
O
201405_s_at 9 04 9 20 9 02 9 39 9 43 9 52 9 25 9 14 9 23 9 68 9 77 9 80
201422_at 9 85 9 47 9 78 10 90 10 97 10 90 9 76 9 64 9 53 11 91 12 37 12 03
201453 x at 9 97 9 88 10 00 10 55 10 55 10 60 9 92 9 73 9 87 10 44 10 53 10 49
201503_at 9 80 9 85 9 99 10 66 10 48 10 49 10 05 9 92 9 80 10 73 10 51 10 72
201561_s_at 7 98 7 71 7 60 8 68 846 8 34 7 96 7 83 7 68 8 67 848 8 73
201584_s_at 9 90 10 09 9 89 10 78 10 61 10 54 9 69 9 83 9 84 10 86 10 78 10 91
201663_s_at 8 95 9 05 8 91 10 27 10 06 9 98 8 91 8 97 9 13 10 37 10 52 10 36
201664 at 8 90 8 94 9 04 10 08 9 78 10 05 8 77 8 96 9 14 10 35 10 23 10 50
201764_at 8 92 9 00 8 74 9 51 9 54 9 37 8 84 8 84 8 92 10 18 10 15 10 12
201954 at 9 41 9 55 9 38 10 02 10 12 10 07 9 31 9 46 9 35 10 32 10 70 10 61
202016_at 4 54 4 76 4 78 7 52 7 49 7 74 4 73 4 52 4 58 10 41 9 58 10 29
202078 at 8 41 8 45 8 33 9 57 9 70 964 8 25 8 35 8 51 968 9 59 9 83
202154_x_at 9 80 9 90 9 50 10 89 10 65 10 62 10 00 9 93 9 66 10 68 10 82 10 71
202174_s_at 6 86 6 79 6 70 8 39 7 99 8 01 6 85 6 70 6 84 840 7 99 8 44
202263 at 5 45 5 37 5 14 6 30 6 29 6 18 5 51 5 50 5 50 6 18 6 12 6 00
202313_at 8 38 8 26 8 32 9 18 9 01 8 98 8 39 8 32 8 20 9 26 9 55 9 30
202355_s_at 7 17 7 16 7 06 7 80 7 59 7 67 7 21 7 08 7 28 7 81 8 14 8 09
202356_s_at 7 53 7 44 7 55 7 83 7 81 7 75 7 52 7 51 7 58 8 13 8 33 8 31
202415_s_at 8 09 8 36 7 98 9 19 9 13 8 92 8 28 8 33 8 23 9 03 9 32 9 14
202467 s at 8 94 8 88 9 18 10 05 9 89 10 07 8 87 8 86 9 12 9 82 9 58 9 89
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly 1 (A2) Ly 1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
202475_at 926 937 922 1027 1021 1023 926 925 931 986 997 1000 202484_s_at 888 910 928 1011 1008 1027 888 906 935 1094 1080 1122 202675_at 776 803 795 919 888 909 801 111 819 927 898 926 202691_at 845 855 862 926 900 922 838 837 861 908 907 933
202736_S_at 9 o u89s 9 σ o89s 9 a 7 I a8 1 i u0 u0t4 1 iu01 ι.2 1 i u01 it4 9 a 7/ o8 u 9σ61i 9 σ o8u0 1 i u0 J5O3 1 iu07 i o8 1 i u07 i s9
2028_s_at 6 69955 7 71166 6 68888 8 83311 8 80088 8 81144 6 68866 7 70022 7 70088 7 76644 7 79900 7 78855
202816_s_at 6 64400 6 61155 6 65533 8 86644 8 84444 8 86699 6 62255 5 59988 6 64499 7 71122 7 72277 7 76611
203046_s_at 839 849 845 902 901 887 838 842 839 899 911 917
203314_at 715 723 705 111 796 788 698 721 713 791 806 783
203534_at 865 860 847 958 943 948 861 835 861 1011 979 1020
203537_at 789 762 765 879 878 865 763 738 767 891 869 907
203605_at 759 747 111 882 864 877 779 767 795 839 850 874
203729_at 549 529 532 816 841 813 533 524 518 698 715 729
203905_at 859 868 876 941 951 946 872 867 874 994 1028 1013
203941_at 650 661 660 723 740 720 671 672 667 742 764 766
203972_s_at 6 68800 6 68800 6 69944 7 78855 7 78800 7 79955 6 68855 6 68855 7 71122 7 77700 7 78811 8 80066 ^
204057_at 768 744 769 900 895 881 714 739 721 943 964 929
204581_at 731 665 697 929 912 907 764 688 708 945 976 957
204604_at 547 543 571 858 855 814 564 556 523 911 942 948
204674_at 875 897 906 1026 1028 1009 884 922 924 1004 1032 1000
204867_at 738 659 696 886 885 845 755 694 712 985 1001 982
204891_s_at 682 623 668 1030 1026 1018 671 630 610 951 988 969
205022_s_at 608 578 602 704 725 680 603 595 609 662 679 694
205245_at 600 594 600 664 673 660 592 606 585 659 659 661
205356_at 794 807 796 908 884 899 779 802 815 864 860 884
205367_at 763 761 750 1059 1054 1027 714 760 742 1020 1020 1016
205412_at 928 928 938 995 1002 1009 947 938 963 1044 1045 1057
205457_at 541 547 553 614 637 623 549 536 555 597 606 584
205504 at o O 5008444 oo 5 yy9uu0 ob 6n1I1I a 8 O3Δ2 a O 8 ii1bb6 7 / / yy9tb6> bb 6ui0ni1 oo 5bb67// oo 5 »»8yy9 B B 8SO5JJ3 B B 84 44i11 Oo 8 oO5bb6
205685 at 6 6 6000666 55 5777777 55 5888999 66 6444000 66 6555888 66 6444999 55 5999333 55 5999555 66 6000333 77 7000666 77 7 333666 77 7222666
205692 s at 694 734 745 932 934 936 689 741 726 901 914 898
205748_s_at 881188 881100 880033 887733 886622 886600 882288 880088 882266 887799 889988 888822
205770_at 771111 772244 772266 883300 886622 883322 772233 772299 774422 887766 889911 887766
206060_s_at 552222 550099 552277 667799 772211 773333 551188 449900 551177 664477 666677 668877
206255 at 664466 667733 664488 888899 889955 888844 558888 660011 661122 992200 889911 992244
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
206296_x_at 863 805 815 980 953 924 832 787 785 999 1033 1005 206571_s_at 732 757 737 878 859 856 743 776 786 903 938 955
206976_s_at 9 93344 9 95599 9 98844 1 1006633 1 1002255 1 1005522 9 97733 9 99922 9 97733 1 1110066 1 1005588 1 1009966
207121_s_at 7 76600 7 78833 8 80066 1 1005522 1 1005544 1 1005599 7 77733 7 77744 8 81111 8 89900 9 91122 9 94499
207419_s_at 7 75588 7 72222 7 71166 8 85500 8 83311 8 82299 7 73399 7 70099 7 70000 8 87733 9 90011 8 86600
207480_s_at 4 46611 4 48833 5 50000 6 61177 6 61166 6 61122 4 48811 5 51122 4 49911 6 65544 6 65500 7 72200
207630_s_at 6 65500 6 64477 6 65599 7 78811 8 81122 7 79988 6 63399 6 67722 6 66600 9 93388 9 95533 9 95500
207760_s_at 704 714 699 865 832 816 736 699 735 866 893 906 208459_s_at 686 698 686 796 794 775 711 698 701 796 806 808 208642_s_at 989 1007 992 1091 1069 1079 992 1000 1011 1051 1059 1061 208643_s_at 927 953 957 1043 1045 1051 936 944 956 1005 1017 1024 208644_at 1085 1087 1077 1126 1117 1124 1085 1100 1088 1125 1132 1114 208679_s_at 1044 1029 1031 1105 1099 1089 1050 1022 1036 1088 1098 1108 208857_s_at 738 719 750 918 903 909 722 712 744 846 827 869 208875_s_at 773 771 790 879 883 868 774 763 789 892 907 921
209075_s_at 8 86633 8 87722 8 88877 9 97711 9 96611 9 96655 8 85533 8 87744 8 87799 9 95522 9 94422 9 97777 fcj
209229_s_at 766 788 754 859 836 856 770 783 786 868 884 891 209251jc_at 1304 1311 1310 1355 1352 1352 1316 1320 1317 1361 1354 1351 209316_s_at 747 735 753 828 826 853 751 758 788 862 855 881 209471_s_at 788 743 771 907 908 894 758 728 754 923 923 931 209517_s_at 871 856 847 966 938 959 864 848 885 979 967 985 209569_x_at 547 577 547 781 814 762 566 570 586 956 1022 975 209714_s_at 876 851 831 967 938 949 867 849 880 965 940 963 209765_at 548 562 600 700 732 723 561 586 578 680 714 704 209932_s_at 962 977 974 1106 1083 1098 947 958 983 1074 1057 1085 210981_s_at 638 652 657 753 763 735 648 663 660 762 773 757 211043_s_at 846 858 859 924 940 937 863 856 866 936 949 964 211066_x_at 688 696 712 878 896 877 669 725 647 843 877 894
211072_x_at 1 1228844 1 1229911 1 1228800 1 1333322 1 1332222 1 1332211 1 1228888 1 1228877 1 1229922 1 1332288 1 1332200 1 1332299
211593_s_at 6 67722 6 68833 6 64499 8 80011 7 78855 7 77799 6 69900 6 68899 6 67799 7 75500 7 76655 7 74433
211686_s_at 7 76633 7 76688 7 78877 8 85522 8 83366 8 84433 7 77766 7 78811 7 17171 8 83344 8 85522 8 85522
211945_s_at 8 86600 8 83388 8 86655 9 97722 9 97711 9 96633 8 87755 8 85599 8 86677 9 98811 9 97766 9 97744
212066_s_at 8 86655 8 81177 8 83355 9 98833 9 98800 9 98866 8 83366 8 82255 8 85544 9 96611 9 94477 9 97733
212085_at 1 1003377 9 99999 9 98822 1 1113377 1 1115599 1 1112211 1 1003355 9 98888 9 98844 1 1118877 1 1221100 1 1119955
212094 at 4 44400 4 45544 4 45511 8 82255 8 80011 7 78833 4 47766 4 45500 4 45555 7 72211 6 65533 6 69966
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly 1 (A2) Ly 1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
212313_at 683 682 657 768 737 744 670 650 660 805 818 808 212350_at 852 836 823 969 967 942 853 840 836 939 941 956
212372_at u 5 e2.7ι o 5 u5u0 o 5 ~ 1 \ έ2. 7 i j31 i 7 / J3Ό5 7 I o31 I a 5 J3U5 o 5 u5j3 o 5 o3o6 o 8o37/ 7 / 9a7/ o 8i41l
212443_at 6 62255 6 62200 6 60088 6 69977 6 67777 6 67722 6 63333 6 61188 6 62244 6 67766 6 69922 7 70011
212573_at 5 53322 5 54488 5 53399 7 78844 8 80000 7 76644 5 50055 5 55500 5 53355 6 68888 7 74477 7 72266
212587_s_at 6 65544 6 67755 7 72233 8 89955 9 92222 9 93322 6 69966 6 69911 7 72233 9 97755 9 98822 1 1003399
212588_at 6 60033 5 59999 6 66677 8 85577 8 88833 8 87777 5 59955 6 62222 6 65522 9 96677 9 94400 9 95566
212619_at 528 512 521 577 566 578 525 515 530 599 610 585
212646_at 894 908 933 1088 1091 1080 910 905 889 1146 1181 1152
212656_at 853 854 867 906 887 899 848 865 868 905 913 923
212735_at 678 662 658 735 723 722 648 660 656 748 767 769
212812_at 658 630 641 892 937 874 645 604 664 779 827 832
212826_s_at 1003 973 968 1113 1140 1098 993 975 970 1172 1184 1178
213093_at 663 666 670 838 808 816 671 640 659 859 836 880
213106_at 560 535 579 775 801 735 562 529 556 672 679 709
213476_x_at 1 1008822 1 1008822 1 1004433 1 1119944 1 1117755 1 1118800 1 1009944 1 1007711 1 1005599 1 1115566 1 1118800 1 1116699 &
213504_at 778 795 793 843 845 855 769 783 791 875 869 889
213603_s_at 964 937 935 1060 1055 1047 932 914 922 1071 1100 1086
213646_x_at 1320 1325 1309 1372 1359 1360 1316 1320 1324 1364 1360 1365
213906_at 488 460 466 817 748 746 453 449 472 837 821 860
214157_at 517 502 535 731 734 734 499 503 498 749 703 736
214219_x_at 830 785 789 941 921 889 823 762 757 952 1001 975
214339_s_at 779 744 778 909 883 874 792 733 721 917 958 955
214553_s_at 580 576 589 616 630 637 562 575 581 662 655 682
215023_s_at 508 503 518 582 594 609 516 490 504 593 627 627
215158_s_at 759 763 764 825 840 816 764 746 750 796 806 798
215836_s_at 690 650 693 793 844 790 664 687 693 790 812 799
216241_s_at 997 978 991 1050 1063 1050 975 966 975 1099 1098 1091
216321_s_at 5 58822 5 57766 6 61166 7 76655 7 75577 7 75588 5 52299 5 54444 5 57788 6 69988 7 73388 7 75577
217118_s_at 7 77744 7 79900 8 81155 9 92299 9 95522 9 94444 7 78822 8 81177 8 83300 9 90066 9 92233 9 94433
217898_at 7 77722 7 76699 7 73344 8 89999 9 90000 9 91100 7 76622 7 76611 7 78811 8 88855 8 89944 9 93322
217933_s_at 9 92277 9 92255 9 93399 1 1000044 9 99911 9 99922 9 95533 9 95533 9 96644 9 99900 9 98822 9 99922
218039_at 8 89922 8 89900 8 87777 1 1004400 1 1000044 1 1002211 8 87799 8 89922 9 90066 1 1004488 1 1001122 1 1004444
218096_at 7 74411 7 77755 8 80000 9 92233 8 89999 9 90055 7 78800 7 77733 8 80000 9 91133 9 90000 9 92255
218250 s at 8 87744 8 86600 8 87700 1 1000066 9 99999 9 99988 8 88833 8 85599 8 87733 9 99955 1 1000022 1 1001144
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
218287_s_at 657 661 665 711 712 707 664 669 667 723 732 720 218336_at 846 877 867 943 919 940 861 852 877 979 963 997
218404_at 5 58899 6 62200 5 59999 7 76677 7 76600 7 75599 6 61144 6 63388 6 66633 8 82233 8 82200 8 81144
218473_s_at 7 74488 7 74411 7 73377 7 79944 7 79900 7 79911 7 74444 7 74455 7 73322 8 82200 8 81133 8 81111
218640_s_at 6 65544 6 62299 6 67799 7 78800 8 81133 8 80022 6 63355 6 62255 6 66688 8 84411 8 88877 8 84400
218654_s_at 9 90066 9 91111 9 90099 9 98855 9 99900 9 98866 8 88877 8 87777 8 88800 9 99977 1 1000099 1 1001111
218680_x_at 6 62266 6 66600 6 68811 8 85566 8 86600 8 84488 6 65500 6 64477 6 67777 8 82288 8 80033 8 83300
218802_at 833 837 838 946 941 941 825 843 844 917 906 903 219220_x_at 786 792 775 876 875 876 788 784 790 884 886 895 219304_s_at 491 522 529 586 616 578 489 508 513 618 644 626 219428_s_at 672 690 674 750 744 741 654 661 676 783 766 771 219551_at 709 743 737 878 853 849 711 716 739 804 792 815 219911_s_at 655 705 673 815 804 793 682 712 679 827 845 830 220059_at 832 808 817 1014 1019 1019 809 795 795 989 972 993 221059_s_at 814 789 804 925 906 926 804 787 821 984 980 993
221080_s_at 6 67788 6 68822 6 66677 7 77700 7 74477 7 73399 6 69977 6 67766 6 68844 7 78833 8 80066 7 77766 £
221483_s_at 893 886 893 994 979 979 881 890 887 971 963 989 221558_s_at 750 750 764 1019 1030 1031 712 729 779 960 928 971 221692_s_at 780 795 807 903 902 882 785 789 785 877 873 872 221893_s_at 681 649 676 888 863 840 661 670 654 791 793 835 222065_s_at 615 617 602 743 723 715 628 621 601 690 711 691 222199_s_at 694 694 684 733 730 738 704 704 697 750 766 753 32541_at 463 449 460 561 546 568 453 434 447 552 582 589 35820_at 826 813 801 895 883 858 813 789 804 975 973 972 35974_at 111 803 834 968 975 956 779 825 840 931 972 942 36564_at 810 792 774 901 914 894 814 791 781 909 916 946 38521_at 875 860 851 972 986 976 871 854 842 989 1019 1005 39835_at 836 830 826 932 916 911 820 798 811 933 948 940 44120_at 728 712 718 852 855 858 701 697 710 832 828 841 200911 s at 734 720 719 969 963 963 765 742 782 932 941 969
201028_s_at 5 57788 5 55511 5 54499 8 80022 8 80000 7 78833 6 64455 6 60088 6 63355 9 93355 9 97744 9 94466
201328_at 5 51166 4 49900 4 49977 6 62255 6 61144 6 62222 5 51122 4 49922 5 50044 7 73377 7 76666 8 80088
201425_at 5 56633 5 56677 5 54499 6 61122 6 61122 6 60044 5 55588 5 57788 5 56600 7 74466 7 71199 7 73399
201718 s at 6 65500 6 63344 6 64466 7 74411 7 72288 7 72222 6 67722 6 63366 6 66666 7 75522 7 74422 7 76688
201909 at 6 66611 6 65566 6 64499 1 1111155 1 1111155 1 1113322 6 65522 6 63355 6 66655 1 1113366 1 1115533 1 1114411
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly1 (A2) Ly 1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
202118_s_at 387 393 415 864 864 867 395 398 401 779 785 825
202119_s_at 466 450 469 1002 991 970 445 451 454 937 970 953
202359_s_at 416 426 421 482 463 470 414 425 410 459 462 470
202367_at 664 635 660 800 793 787 653 665 625 822 831 800
202391_at 587 592 516 831 814 781 590 561 569 988 1045 994
202729_s_at 592 614 619 839 859 834 592 596 607 778 783 797
202848_s_at 661 674 665 753 743 764 661 661 645 774 111 775
203072_at 505 489 518 589 576 587 509 490 496 615 652 635
203744_at 559 575 566 877 847 885 561 582 575 808 783 834
203805_s_at 639 653 644 809 796 788 657 669 659 694 702 708
203814_s_at 487 499 468 687 660 660 488 485 480 771 775 819
204081_at 547 558 548 619 648 631 537 541 544 700 737 721
204141_at 416 415 403 909 874 853 413 398 418 882 834 883
204197_s_at 543 537 562 843 838 825 543 564 542 773 837 847
204198_s_at 466 437 458 871 868 847 454 462 457 825 859 857
204529_s_at 400 407 394 526 493 513 404 393 368 761 739 785
204890_s_at 602 583 585 882 888 899 616 607 598 820 866 847
205000_at 426 434 426 837 729 803 379 409 439 790 762 788
205120_s_at 486 473 463 662 628 669 470 456 483 630 597 653
205718_at 575 551 513 862 880 815 574 583 567 780 783 787
205903_s_at 544 502 501 693 673 659 556 507 516 614 626 642
206219_s_at 609 619 590 823 818 801 640 615 604 844 886 903
206641_at 461 474 444 747 813 740 455 451 466 682 758 739
206700_s_at 530 546 533 652 667 656 511 519 522 624 642 658
207000_s_at 519 518 520 673 664 639 531 540 513 656 673 681
207238_s_at 636 631 645 813 855 818 665 658 659 905 922 911
207621_s_at 650 647 629 750 744 726 659 619 645 732 706 724
208119_s_at 540 542 549 586 582 590 533 538 521 687 670 677
208190_s_at 454 443 457 628 657 646 469 443 472 637 663 669
208502_s_at 678 726 731 828 898 845 653 702 634 868 952 922
209200_at 486 486 489 519 512 521 488 488 483 788 900 855
209372_x_at 772 776 747 844 832 846 786 769 769 836 843 850
209447_at 574 537 554 644 655 642 544 547 534 700 751 742
209570_s_at 524 500 492 655 683 652 515 509 510 840 896 877
209967 s at 579 549 541 734 727 706 562 555 545 883 913 901
Log2 fluorescence intensity
Probesets Ly 1 (A1 ) Ly1 (A2) Ly 1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
209980_s_at 644 629 619 731 748 728 638 615 631 709 721 717 210258_at 401 382 402 1027 1050 1068 384 374 386 1040 1022 1028
21 1 543 S 31 o 5 t4o8 « 5j £2.£2. u 6 u6u6 u 6 υ61 I u 6 o51 \ u 5 *4+*4+ 51 u3 5 c27t 680 7 i u0*4-t u 67 / σ9
212254_s_at 4 45566 4 45533 4 46644 6 66677 7 74488 7 71111 4 43344 4 49900 4 44455 6 60044 6 64455 6 61199
212592_at 4 44444 5 54433 4 45511 1 1005544 1 1007700 1 1005577 4 45577 4 46699 4 43377 1 1006666 9 99933 1 1004444
213029_at 4 46699 4 48833 4 48855 5 53355 5 55544 5 56666 4 48833 4 47766 4 49900 5 54488 5 56600 5 58833
213457_at 4 46666 5 50022 4 48844 7 76611 7 76666 7 73344 4 49933 4 49966 4 47733 8 89911 9 93377 9 95511
213533_at 547 569 595 671 700 683 545 605 561 815 826 846 214508_x_at 631 611 664 752 783 763 622 641 636 900 946 950 214669_x_at 577 573 575 990 995 997 578 535 615 942 951 916 214836_x_at 795 827 793 1054 1090 1046 748 803 798 1155 1168 1137 215016_x_at 419 420 433 645 717 673 424 453 441 578 604 628 215903_s_at 638 617 605 793 752 773 634 646 646 729 705 729 215967_s_at 579 565 583 641 624 621 561 560 576 693 685 676 217422_s_at 648 612 621 847 856 833 665 598 596 861 938 876
218017_s_at 6 60077 6 61199 6 62244 7 70088 7 72266 7 70077 6 60044 6 61155 5 59966 6 69999 7 70088 7 71100 ^
218412_s_at 537 565 548 749 755 721 563 593 549 698 691 676 218573_at 460 462 448 509 525 535 459 470 461 547 540 568 218723_s_at 498 498 460 842 904 841 467 474 482 779 808 744 218858_at 492 496 497 915 968 924 492 500 504 910 907 916 219165_at 497 468 469 634 630 631 517 510 482 728 780 792 219299_at 497 526 526 616 617 644 511 521 512 571 595 598 219855_at 644 655 621 917 923 897 618 629 633 748 759 768 220432_s_at 389 383 373 463 490 464 374 386 389 432 455 454 221003_s_at 552 557 572 636 638 620 576 564 568 695 733 697 221651_x_at 768 766 769 1288 1295 1292 792 745 817 1263 1262 1264 221671_x_at 773 773 773 1292 1299 1296 767 711 816 1259 1271 1261 222307_at 548 549 536 619 599 619 546 531 534 611 610 609
203722_at 5 58888 5 57766 5 57766 6 61155 6 60066 6 61188 5 57711 5 57700 5 57711 6 66677 6 66677 6 67788
219998_at 4 48866 4 48877 4 48811 5 51100 5 52200 5 52200 4 48811 4 48855 4 48844 5 50066 5 51144 5 51144
221487_s_at 6 60066 6 60077 6 62211 6 66622 6 68800 6 67766 6 61177 5 59900 6 61122 6 66677 6 65533 6 66677
Table 2B: Genes With Increased Expression in CD40-Sensitive Cell Lines t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene lD Gene Title Symbol
FDR Cutoff 1 OE-02 8 2E-03 1 2E-02 94E-03
200011_s_at 4 2E-03 8 2E-05 74E-03 1 1E-04 Yes ARF3 Hs 119177 ADP-πbosylation factor 3
200090_at 64E-03 7 4E-04 3 OE-03 2 0E-04 Yes FNTA Hs 356463 farnesyltransferase, CAAX box, alpha
200625_s_at 5 8E-04 7 3E-04 1 5E-03 2 4E-03 Yes CAP1 Hs 104125 CAP, adenylate cyclase-associated protein 1 (yeast)
200679_x_at 96E-03 3 7E-03 1 5E-03 4 5E-04 Yes HMGB1 Hs 434102 high-mobility group box 1
200762_at 1 3E-04 2 4E-03 54E-03 4 4E-03 Yes DPYSL2 Hs 173381 dihydropyrimidinase-like 2
200833_s_at 3 8E-03 1 OE-03 3 8E-03 1 3E-03 Yes RAP1B Hs 374418 RAP1B, member of RAS oncogene family
200998_s_at 1 2E-03 4 9E-04 2 6E-03 2 OE-03 Yes CKAP4 Hs 74368 cytoskeleton-associated protein 4
201029_s_at 94E-04 1 3E-04 1 1E-03 2 2E-04 Yes CD99 Hs 283477 CD99 antigen
201077_s_at 3 8E-03 4 8E-03 2 9E-03 2 2E-03 Yes NHP2L1 Hs 182255 NHP2 non-histone chromosome protein 2-lιke 1 (S cerevisiae)
201089 at 9 OE-03 1 4E-03 7 8E-04 6 4E-04 Yes ATP6V1 B2 Hs 295917 ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B, isoform 2 K)
201090 x_at 4 8E-04 2 4E-04 2 2E-03 1 OE-03 Yes K-ALPHA-1 Hs 446608 tubulin, alpha, ubiquitous
201209. "at 8 5E-03 1 2E-03 9 2E-03 1 3E-03 Yes HDAC1 Hs 88556 histone deacetylase 1
201260. _s_at 6 8E-03 7 9E-03 1 7E-03 3 2E-03 Yes SYPL Hs 80919 synaptophysin-like protein
201375. _s_at 1 6E-03 5 6E-04 5 6E-03 2 OE-03 Yes PPP2CB Hs 80350 protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform
201405. _s_at 9 2E-03 1 3E-03 8 7E-03 4 2E-04 Yes COPS6 Hs 15591 COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)
201422 .at 7 OE-03 2 OE-04 1 OE-03 5 5E-04 Yes IFI30 Hs 14623 interferon, gamma-inducible protein 30
201453 x_at 8 4E-04 4 8E-04 3 7E-03 2 8E-03 Yes RHEB Hs 279903 Ras homolog enriched in brain
201503. .at 1 3E-03 1 4E-03 2 8E-03 2 OE-03 Yes G3BP Hs 48549 Ras-GTPase-activating protein SH3-domaιn-bιndιng protein
201561 _s_at 8 8E-03 5 OE-03 6 8E-03 1 9E-03 Yes CLSTN 1 Hs 29665 calsyntenin 1
201584. _s_at 2 3E-03 9 9E-04 1 1E-03 1 2 E-04 Yes DDX39 Hs 311609 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39
201663 s at 1 9E-03 3 9E-05 7 7E-04 1 1E-04 Yes SMC4L1 Hs 50758 SMC4 structural maintenance of chromosomes 4-lιke
1 (yeast)
201664_at 3 1E-03 52E-04 2 2E-03 6 9E-04 Yes SMC4L1 Hs 50758 SMC4 structural maintenance of chromosomes 4-lιke
1 (yeast)
201764_at 4 2E-03 2 2E-03 2 1E-03 9 8E-06 Yes MGC5576 Hs 103834 hypothetical protein MGC5576 201954_at 1 4E-03 4 1E-03 5 1 E-04 4 2E-03 Yes ARPC1B Hs 433506 actin related protein 2/3 complex, subunit 1B, 41kDa 202016 at 1 4E-05 1 1E-03 1 3E-05 1 4E-03 Yes MEST Hs 440459 mesoderm specific transcript homolog (mouse)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene ID Gene Title
Symbol 202078_at 2 1 E-05 4 7E-04 6 4E-04 2 1 E-04 Yes COPS3 Hs 6076 COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)
202154_x_at 3 4E-03 7 3E-03 3 6E-03 6 7E-03 Yes TUBB4 Hs 511743 tubulin, beta, 4 202174_s_at 4 6E-03 4 7E-03 4 6E-03 4 7E-03 Yes PCM1 Hs 348501 pericentπolar material 1 202263_at 4 0E-03 4 OE-03 2 6E-03 84E-03 Yes CYB5R1 Hs 334832 cytochrome b5 reductase 1 (B5R 1) 202313_at 1 4E-03 3 1 E-03 8 5E-04 1 3E-03 Yes PPP2R2A Hs 512628 protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform
202355_s_at 3 2E-03 8 1 E-03 4 1 E-03 5 2E-03 Yes GTF2F1 Hs 68257 general transcription factor NF, polypeptide 1 , 74kDa
202356_s_at 2 9E-03 1 8E-03 1 OE-03 4 2E-03 Yes GTF2F1 Hs 68257 general transcription factor HF, polypeptide 1 , 74kDa
202415_s_at 3 6E-03 2 7E-03 5 3E-03 4 6E-03 Yes HSPBP1 Hs 53066 hsp70-ιnteractιng protein
202467_s_at 1 7E-03 4 2E-03 8 9E-04 2 9E-03 Yes TRIP15 Hs 30212 thyroid receptor interacting protein 15
202475_at 6 1 E-04 4 3E-04 3 2E-06 1 1 E-03 Yes NIFIE14 Hs 9234 seven transmembrane domain protein
202484_s_at 3 7E-03 3 4E-04 7 8E-03 5 3E-04 Yes MBD2 Hs 25674 methyl-CpG binding domain protein 2
202675_at 7 9E-04 6 6E-04 2 9E-03 2 OE-03 Yes SDHB Hs 64 succinate dehydrogenase complex, subunit B, iron sulfur (Ip) OO
202691 at 5 3E-03 7 OE-03 3 3E-03 3 8E-03 Y Yeess SNRPD1 Hs 86948 small nuclear πbonucleoprotein D1 polypeptide
16kDa
202736 s at 8 4E-03 3 5E-03 1 2E-02 1 1E-03 Y Yeess LSM4 Hs 76719 LSM4 homolog, U6 small nuclear RNA associated
(S cerevisiae)
2028_s_at 5 3E-04 2 4E-03 2 5E-04 1 6E-03 Yes E2F1 Hs 96055 E2F transcription factor 1
202816_s_at 1 9E-04 6 9E-03 7 OE-04 5 9E-03 Yes SS18 Hs 404263 synovial sarcoma translocation, chromosome 18
203046_s_at 1 8E-03 1 4E-03 5 3E-03 4 4E-03 Yes TIMELESS Hs 118631 timeless homolog (Drosophila)
203314_at 7 2E-04 9 7E-04 1 1 E-03 9 4E-04 Yes PGPL Hs 522840 pseudoautosomal GTP-binding protein-like
203534_at 2 4E-04 2 6E-03 2 2E-03 1 OE-03 Yes LSM1 Hs 425311 LSM1 homolog, U6 small nuclear RNA associated
(S cerevisiae)
203537_at 1 7E-03 1 5E-03 1 5E-03 8 9E-04 Yes PRPSAP2 Hs 13339 phosphoribosyl pyrophosphate synthetase- associated protein 2
203605_at 3 3E-04 2 6E-03 1 2E-03 5 7E-03 Yes SRP54 Hs 49346 signal recognition particle 54kDa 203729_at 2 9E-05 2 1 E-04 9 4E-05 4 5E-04 Yes EMP3 Hs 9999 epithelial membrane protein 3 203905 at 4 8E-04 1 1 E-03 9 2E-05 3 7E-03 Yes PARN Hs 43445 poly(A)-specιfιc ribonuclease (deadenylation nuclease)
203941_at 2 1 E-03 1 8E-03 8 7E-03 5 8E-03 Yes FLJ 10871 Hs 15562 hypothetical protein FLJ10871
203972_s_at 9 2E-05 4 9E-03 3 OE-03 3 2E-03 Yes PEX3 Hs 7277 peroxisomal biogenesis factor 3
204057_at 3 8E-04 1 9E-04 9 3E-05 1 2E-04 Yes ICSBP1 Hs 14453 interferon consensus sequence binding protein 1
204581 at 3 8E-03 1 4E-03 8 7E-03 3 9E-03 Yes CD22 Hs 262150 CD22 antigen
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene lD Gene Title
Symbol
204604_at 2 4E-04 2 4E-05 1 1E-04 2 4E-05 Yes PFTK1 Hs 57856 PFTAIRE protein kinase 1
204674_at 7 7E-04 1 OE-03 5 5E-03 4 1 E-03 Yes LRMP Hs 124922 lymphoid-restricted membrane protein
204867_at 5 7E-03 4 1 E-03 3 3E-03 2 2E-03 Yes GCHFR Hs 245644 GTP cyclohydrolase I feedback regulatory protein
204891_s_at 1 6E-03 3 6E-04 1 5E-03 3 3E-04 Yes LCK Hs 1765 lymphocyte-specific protein tyrosine kinase
205022_s_at 3 7E-03 3 1 E-03 1 OE-02 6 7E-03 Yes CHES1 Hs 211773 checkpoint suppressor 1
205245_at 6 6E-04 2 2E-04 1 3E-03 7 8E-03 Yes PARD6A Hs 112933 par-6 partitioning defective 6 homolog alpha
(C elegans)
205356_at 6 9E-04 3 2E-03 2 5E-03 7 OE-03 Yes USP13 Hs 85482 ubiquitin specific protease 13 (isopeptidase T-3) 205367_at 2 9E-04 7 2E-05 8 6E-05 2 1 E-03 Yes APS Hs 371366 adaptor protein with pleckstπn homology and src homology 2 domains
205412_at 2 4E-04 4 7E-05 7 OE-03 9 2E-04 Yes ACAT1 Hs 37 acetyl-Coenzyme A acetyltransferase 1 (acetoacetyl
Coenzyme A thiolase)
205457_at 1 9E-03 6 4E-03 9 9E-04 4 8E-03 Yes MGC4614 Hs 300691 hypothetical protein MGC4614
205504_at 1 2E-04 7 OE-05 9 4E-05 2 2E-04 Yes BTK Hs 159494 Bruton agammaglobulinemia tyrosine kinase
205685_at 7 1 E-03 4 1 E-04 2 8E-03 2 2E-03 Yes CD86 Hs 27954 CD86 antigen (CD28 antigen ligand 2, B7-2 antigen) to
205692_s_at 5 2E-03 4 2E-03 4 9E-03 3 9E-03 Yes CD38 Hs 174944 CD38 antigen (p45)
205748_s_at 8 2E-04 8 3E-04 7 3E-03 1 7E-03 Yes RNF126 Hs 69554 ring finger protein 126
205770_at 2 5E-03 1 9E-05 2 4E-03 3 7E-05 Yes GSR Hs 414334 glutathione reductase
206060_s_at 4 2E-03 2 OE-03 1 5E-03 5 7E-04 Yes PTPN22 Hs 87860 protein tyrosine phosphatase, non-receptor type 22
(lymphoid)
206255_at 3 6E-04 5 8E-05 5 6E-05 4 6E-05 Yes BLK Hs 389900 B lymphoid tyrosine kinase 206296 x at 6 8E-03 2 2E-03 2 5E-03 6 8E-04 Yes MAP4K1 Hs 95424 mitogen-activated protein kinase kinase kinase kinase 1
206571 s at 3 1 E-04 1 6E-03 6 8E-03 1 3E-03 Yes MAP4K4 Hs 3628 mitogen-activated protein kinase kinase kinase kinase 4
206976_s_at 9 8E-03 3 4E-03 1 2E-02 9 1 E-03 Yes HSPH1 Hs 36927 heat shock 105kDa/110kDa protein 1 207121_s_at 2 OE-03 4 2E-03 1 8E-03 4 6E-03 Yes MAPK6 Hs 271980 mitogen-activated protein kinase 6 207419 s at 6 1 E-03 1 3E-03 2 4E-03 6 7E-04 Yes RAC2 Hs 301175 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)
207480 s at 6 1 E-03 5 OE-03 4 6E-03 7 8E-03 Yes MEIS2 Hs 362805 Meιs1 , myeloid ecotropic viral integration site 1 homolog 2 (mouse)
207630. _s_ .at 1 1 E-03 1 6E-06 4 4E-04 1 4E-04 Yes CREM Hs 231975 cAMP responsive element modulator
207760 s_ .at 7 3E-03 1 7E-03 4 1 E-03 6 5E-04 Yes NCOR2 Hs 287994 nuclear receptor co-repressor 2
208459 S at 7 4E-04 3 2E-05 1 2E-03 4 9E-05 Yes XPO7 Hs 172685 exportin 7
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene ID Gene Title
Symbol 208642 S at 62E-04 2 OE-03 7 9E-04 2 8E-03 Yes XRCC5 Hs 257082 X-ray repair complementing defective repair in
Chinese hamster cells 5 (double-strand-break rejoining, Ku autoantigen, 8OkDa)
208643 s at 5 6E-03 5 9E-03 9 OE-04 9 7E-04 Yes XRCC5 Hs 257082 X-ray repair complementing defective repair in
Chinese hamster cells 5 (double-strand-break rejoining, Ku autoantigen, 8OkDa)
208644_at 5 8E-04 5 5E-03 8 3E-03 9 4E-03 Yes ADPRT Hs 177766 ADP-nbosyltransferase (NAD+, poly (ADP-nbose) polymerase)
208679_s_at 78E-04 1 3E-03 5 7E-03 4 7E-03 Yes ARPC2 Hs 83583 actin related protein 2/3 complex, subunit 2, 34kDa 208857_s_at 4 6E-04 2 6E-03 5 3E-04 1 9E-03 Yes PCMT1 Hs 79137 protein-L-isoaspartate (D-aspartate) O- methyltransferase
208875_s_at 3 2E-04 3 8E-04 1 2E-03 3 2E-04 Yes PAK2 Hs 284275 p21 (CDKNIA)-actιvated kinase 2 209075_s_at 2 3E-03 4 4E-03 2 9E-03 3 3E-03 Yes NIFU Hs 350702 nitrogen fixation cluster-like 209229_s_at 3 8E-03 1 3E-03 24E-03 5 OE-04 Yes KIAA1115 Hs 411875 KIAA1115 protein 209251_x_at 4 8E-04 3 OE-04 2 3E-05 2 6E-03 Yes TUBA6 Hs 406578 tubulin alpha 6 209316_s_at 2 1E-03 4 6E-04 9 OE-03 2 8E-03 Yes HBS1L Hs 221040 HBS1-lιke (S cerevisiae) O 209471_s_at 5 OE-03 5 2E-03 8 2E-04 1 4E-03 Yes FNTA Hs 356463 farnesyltransferase, CAAX box, alpha 209517_s_at 1 OE-03 2 8E-04 3 7E-03 3 2E-03 Yes ASH2L Hs 6856 ash2 (absent, small, or homeotιc)-lιke (Drosophila) 209569 x at 5 4E-04 3 OE-04 2 OE-03 1 OE-03 Yes D4S234E Hs 79404 DNA segment on chromosome 4 (unique) 234 expressed sequence
209714 s at 5 2E-03 4 8E-03 2 4E-03 1 9E-03 Yes CDKN3 Hs 84113 cyclin-dependent kinase inhibitor 3 (CDK2- associated dual specificity phosphatase)
209765_at 2 8E-03 4 OE-03 3 6E-04 8 3E-04 Yes ADAM 19 Hs 289368 a disintegrin and metalloproteinase domain 19
(meltπn beta)
209932_s_at 2 6E-04 1 5E-03 9 OE-04 1 5E-03 Yes DUT Hs 367676 dUTP pyrophosphatase 210981_s_at 1 1 E-03 1 1 E-04 1 9E-03 8 OE-05 Yes GPRK6 Hs 235116 G protein-coupled receptor kinase 6 211043_s_at 3 5E-04 2 3E-03 8 3E-04 4 5E-03 Yes CLTB Hs 380749 clathπn, light polypeptide (Lcb) 211066_x_at 4 7E-05 2 3E-03 9 1 E-03 4 1 E-03 Yes PCDHGC3 Hs 283794 protocadheπn gamma subfamily C, 3 211072_x_at 1 OE-03 5 9E-04 2 9E-03 7 OE-04 Yes K-ALPHA-1 Hs 446608 tubulin, alpha, ubiquitous 211593 s at 1 2E-03 3 8E-03 8 OE-04 2 5E-03 Yes MAST205 Hs 101474 microtubule associated testis specific serine/threonine protein kinase
211686_s_at 2 3E-03 1 7E-03 2 5E-03 5 2E-03 Yes LOC84549 Hs 77135 RNA binding protein 211945 s at 2 8E-03 2 8E-03 1 9E-04 2 4E-04 Yes ITGB1 Hs 287797 integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)
212066 s at 8 6E-03 4 6E-03 2 4E-03 4 4E-04 Yes USP34 Hs 507665 ubiquitin specific protease 34
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene ID Gene Title
Symbol 212085_at 4 OE-03 2 9E-03 3 7E-03 2 8E-03 Yes SLC25A6 Hs 350927 solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 6
212094_at 3 9E-04 5 OE-03 6 1 E-05 3 OE-03 Yes PEG10 Hs 137476 paternally expressed 10 212313_at 3 9E-03 9 8E-04 2 4E-03 6 7E-05 Yes MGC29816 Hs 5019 hypothetical protein MGC29816 212350_at 5 9E-04 9 5E-04 1 1 E-03 1 7E-04 Yes TBC1 D1 Hs 372659 TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1
212372_at 2 6E-03 1 1 E-04 5 4E-04 6 8E-04 Yes MYH 10 Hs 280311 myosin, heavy polypeptide 10, non-muscle
212443_at 4 OE-03 2 1 E-03 6 5E-03 3 3E-03 Yes KIAA0540 Hs 437043 KIAA0540 protein
212573_at 3 6E-04 6 2E-03 1 6E-04 1 3E-03 Yes KIAA0830 Hs 167115 KIAA0830 protein
212587_s_at 1 8E-03 3 9E-04 1 5E-04 1 1 E-03 Yes PTPRC Hs 444324 protein tyrosine phosphatase, receptor type, C
212588_at 3 9E-03 1 9E-03 1 1 E-03 4 5E-04 Yes PTPRC Hs 444324 protein tyrosine phosphatase, receptor type, C
212619_at 9 6E-04 1 6E-03 8 7E-04 2 OE-03 Yes KIAA0286 Hs 14912 KIAA0286 protein
212646_at 2 6E-03 9 7E-05 1 5E-04 1 6E-04 Yes RAFTLIN Hs 436432 raft-linking protein
212656_at 6 OE-03 1 4E-03 1 1 E-02 2 8E-03 Yes DKFZP586 Hs 435643 hepatocellularcarcinoma-associated antigen
D0919 HCA557a
212735_at 2 1 E-03 4 7E-04 2 1 E-04 7 OE-04 Yes KIAA0226 Hs 499355 KIAA0226 gene product 212812_at 1 6E-03 3 3E-03 5 1 E-04 2 OE-03 Yes Hs 288232 Homo sapiens cDNA FLJ22642 fis, clone HSI06970 212826_s_at 1 3E-03 1 4E-03 1 9E-03 1 6E-04 Yes SLC25A6 Hs 350927 solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 6
213093_at 2 3E-03 3 7E-03 2 OE-04 3 8E-04 Yes PRKCA Hs 349611 protein kinase C, alpha 213106_at 1 4E-03 1 8E-03 1 8E-03 8 5E-04 Yes ATP8A1 Hs 291385 ATPase, aminophospholipid transporter (APLT),
Class I1 type 8A, member 1
213476_x_at 5 9E-03 6 7E-03 2 1 E-03 2 5E-03 Yes TUBB4 Hs 511743 tubulin, beta, 4 213504 at 1 3E-03 4 7E-04 2 OE-03 4 OE-04 Yes COPS6 Hs 15591 COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)
213603 s at 3 1 E-03 3 8E-04 9 1 E-05 2 7 E-04 Yes RAC2 Hs 301175 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)
213646_x_at 2 1 E-03 6 8E-03 2 6E-03 2 8E-04 Yes K-ALPHA-1 Hs 446608 tubulin, alpha, ubiquitous 213906_at 2 8E-03 2 7E-05 3 2E-03 4 6E-05 Yes MYBL1 Hs 300592 v-myb myeloblastosis viral oncogene homolog
(avιan)-lιke 1
214157_at 1 8E-03 4 7E-04 2 6E-08 3 4E-03 Yes GNAS Hs 157307 GNAS complex locus 214219 x at 5 2E-03 1 OE-03 8 4E-03 2 7E-03 Yes MAP4K1 Hs 95424 mitogen-activated protein kinase kinase kinase kinase 1
214339 s at 1 5E-03 6 OE-04 1 2E-02 3 4E-03 Yes MAP4K1 Hs 95424 mitogen-activated protein kinase kinase kinase kinase 1
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene ID Gene Title Symbol
214553_s_at 5 7E-03 3 3E-03 2 8E-03 1 2 E-03 Yes ARPP-19 Hs 7351 cyclic AMP phosphoprotein, 19 kD 215023_s_at 2 2E-03 5 9E-03 1 1 E-03 2 2E-03 Yes PEX1 Hs 164682 peroxisome biogenesis factor 1 215158_s_at 8 7E-03 1 8E-03 1 3E-03 4 2E-03 Yes DEDD Hs 169681 death effector domain containing 215836_s_at 4 8E-03 5 1 E-03 7 5E-03 6 9E-04 Yes PCDHGC3 Hs 283794 protocadherin gamma subfamily C, 3 216241_s_at 1 1 E-03 7 6E-04 1 8E-04 7 2E-06 Yes TCEA1 Hs 78869 transcription elongation factor A (SII), 1 216321_s_at 4 2E-03 3 9E-03 3 8E-03 1 5E-03 Yes NR3C1 Hs 512414 nuclear receptor subfamily 3, group C, member 1
(glucocorticoid receptor)
217118_s_at 1 3E-03 1 3E-03 4 2E-03 3 9E-03 Yes KIAA0930 Hs 454533 KIAA0930 protein 217898_at 4 OE-03 1 7E-03 2 4E-04 4 4E-03 Yes LOC56851 Hs 4245 chromosome 15 hypothetical ATG/GTP binding protein
217933_s_at 3 9E-04 5 5E-04 2 4E-03 2 8E-03 Yes LAP3 Hs 182579 leucine aminopeptidase 3
218039_at 1 6E-03 2 1 E-03 7 7E-04 9 4E-04 Yes NUSAP1 Hs 279905 nucleolar and spindle associated protein 1
218096_at 7 1E-03 64E-03 3 8E-04 3 4E-04 Yes LPAAT-e Hs 281895 acid acyltransferase-epsilon
218250_s_at 4 5E-05 6 4E-05 1 1 E-03 1 7E-04 Yes CNOT7 Hs 170553 CCR4-NOT transcription complex, subunit 7
218287_s_at 1 3E-04 3 9E-04 5 3E-05 1 3E-03 Yes EIF2C1 Hs 309452 eukaryotic translation initiation factor 2C, 1 K)
218336_at 4 6E-03 9 8E-04 2 5E-03 94E-04 Yes PFDN2 Hs 298229 prefoldin 2
218404_at 1 8E-03 8 5E-04 1 1 E-02 5 OE-03 Yes SNX10 Hs 418132 sorting nexin 10
218473_s_at 2 1 E-03 7 9E-05 4 5E-03 2 7E-04 Yes FLJ22329 Hs 418795 hypothetical protein FLJ22329
218640_s_at 2 OE-03 6 9E-04 8 9E-04 5 2E-04 Yes PLEKHF2 Hs 29724 pleckstrin homology domain containing, family F
(with FYVE domain) member 2
218654_s_at 2 2E-06 8 7E-04 1 OE-04 4 7E-05 Yes MRPS33 Hs 83006 mitochondrial ribosomal protein S33
218680_x_at 46E-03 2 5E-03 7 9E-04 2 5E-04 Yes HYPK Hs 511978 Huntingtin interacting protein K
218802_at 9 1 E-07 1 7E-03 2 1 E-03 1 1 E-03 Yes FLJ20647 Hs 234149 hypothetical protein FLJ20647
219220_x_at 3 2E-03 2 2E-04 3 5E-04 1 OE-04 Yes MRPS22 Hs 512649 mitochondrial ribosomal protein S22
219304_s_at 84E-03 2 2E-03 4 8E-03 2 8E-04 Yes SCDGF-B Hs 112885 spinal cord-derived growth factor-B
219428_s_at 2 9E-03 3 OE-04 2 4E-03 2 3E-04 Yes PXM P4 Hs 436924 peroxisomal membrane protein 4, 24kDa
219551_at 8 1 E-04 6 8E-03 4 OE-04 2 1 E-03 Yes EAF2 Hs 383018 ELL associated factor 2
219911_s_at 5 7E-03 3 8E-03 1 9E-03 1 1E-03 Yes SLCO4A1 Hs 235782 solute carrier organic anion transporter family, member 4A1
220059_at 7 OE-04 6 3E-05 1 2 E-04 3 9E-05 Yes BRDG1 Hs 121128 BCR downstream signaling 1 221059_s_at 2 8E-04 1 6E-04 1 2E-03 9 6E-04 Yes CHST6 Hs 157439 carbohydrate (N-acetylglucosamine 6-0) sulfotransferase 6
221080_s_at 5 3E-03 1 8E-03 5 6E-03 1 3E-03 Yes FLJ22757 Hs 236449 hypothetical protein FLJ22757 221483 s at 6 8E-04 5 8E-03 3 3E-04 4 1 E-03 Yes ARPP-19 Hs 7351 cyclic AMP phosphoprotein, 19 kD
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene ID Gene Title
Symbol
221558_s_at 2 OE-06 1 8E-03 3 8E-03 1 8E-03 Yes LEF 1 Hs 44865 lymphoid enhancer-binding factor 1 221692_s_at 6 4E-04 7 5E-03 2 7E-03 2 OE-06 Yes MRPL34 Hs 238808 mitochondrial ribosomal protein L34 221893_s_at 5 7E-04 2 2E-03 2 3E-03 5 8E-03 Yes ADCK2 Hs 210397 aarF domain containing kinase 2 222065_s_at 8 6E-04 9 6E-04 6 5E-04 1 7E-03 Yes FLII Hs 445182 flightless I homolog (Drosophila) 222199_s_at 6 OE-04 8 4E-04 6 8E-04 2 8E-03 Yes BIN3 Hs 68090 bridging integrator 3 32541_at 4 8E-04 4 2E-03 2 2E-04 2 3E-03 Yes PPP3CC Hs 75206 protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineuπn A gamma)
35820_at 1 OE-02 1 8E-03 6 OE-03 1 5E-03 Yes GM2A Hs 387156 GM2 ganglioside activator protein
35974_at 5 6E-03 2 8E-03 9 1E-03 5 5E-03 Yes LRMP Hs 124922 lymphoid-restricted membrane protein
36564_at 2 OE-03 1 1 E-03 1 9E-03 1 1 E-03 Yes FLJ90005 Hs 511807 hypothetical protein FLJ90005
38521_at 4 5E-04 3 OE-04 1 3E-03 2 6E-04 Yes CD22 Hs 262150 CD22 antigen
39835_at 1 5E-03 1 1 E-04 2 6E-04 1 7E-04 Yes SBF1 Hs 112049 SET binding factor 1
44120_at 3 2E-04 5 3E-05 9 OE-05 1 9E-05 Yes ADC K2 Hs 210397 aarF domain containing kinase 2
200911_s_at 4 6E-05 6 9E-04 2 6E-03 3 4E-04 Yes TACC 1 Hs 279245 transforming, acidic coiled-coil containing protein 1
201028_s_at 8 6E-05 1 8E-05 7 4E-04 3 6E-05 Yes CD99 Hs 283477 CD99 antigen UJ UJ
201328_at 1 5E-03 2 6E-03 3 3E-04 3 7E-03 Yes ETS2 Hs 292477 v-ets erythroblastosis virus E26 oncogene homolog 2
(avian)
201425_at 3 9E-03 1 3E-04 1 OE-02 1 1 E-04 Yes ALDH2 Hs 331141 aldehyde dehydrogenase 2 family (mitochondrial)
201718_s_at 3 2E-04 5 5E-04 1 1 E-02 3 5E-03 Yes EPB41 L2 Hs 440387 erythrocyte membrane protein band 4 1 -like 2
201909_at 2 5E-06 7 2E-07 8 1 E-06 1 2E-05 Yes RPS4Y Hs 180911 ribosomal protein S4, Y-lιnked
202118_s_at 3 OE-04 1 OE-04 2 8E-07 1 2E-03 Yes CPNE3 Hs 14158 coprne III
202119_s_at 8 1 E-06 1 2E-05 1 4E-04 1 7E-04 Yes CPNE3 Hs 14158 copine III
202359_s_at 3 7E-03 8 2E-04 1 7E-03 1 5E-03 Yes SNX19 Hs 409862 sorting nexin 19
202367_at 1 5E-03 2 3E-04 3 8E-03 5 OE-04 Yes CUTL1 Hs 438974 cut-like 1 , CCAAT displacement protein (Drosophila)
202391_at 2 4E-03 2 3E-04 6 OE-04 2 8E-04 Yes BASP1 Hs 511745 brain abundant, membrane attached signal protein 1
202729_s_at 3 2E-05 1 4E-04 5 8E-05 2 1 E-05 Yes LTBP1 Hs 241257 latent transforming growth factor beta binding protein
1
202848_s_at 6 9E-04 6 7E-04 2 7E-04 1 4E-03 Yes GPRK6 Hs 235116 G protein-coupled receptor kinase 6
203072_at 3 8E-03 9 2E-04 4 OE-04 1 6E-03 Yes MYO1 E Hs 437459 myosin IE
203744_at 3 3E-04 1 7E-03 1 6E-04 1 2E-03 Yes HMGB3 Hs 19114 high-mobility group box 3
203805_s_at 8 2E-05 7 3E-04 1 8E-04 2 2E-03 Yes FANCA Hs 284153 Fanconi anemia, complementation group A
203814_s_at 1 3E-04 2 9E-04 1 3E-03 2 1 E-03 Yes NQO2 Hs 441039 NAD(P)H dehydrogenase, quinone 2
204081_at 4 3E-03 1 9E-03 5 6E-03 2 7E-03 Yes NRGN Hs 232004 neurogranin (protein kinase C substrate, RC3)
204141 at 6 7E-04 6 5E-04 3 7E-04 3 5E-04 Yes TUBB Hs 512712 tubulin, beta polypeptide
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene ID Gene Title
Symbol
204197_s_at 1 3E-05 4 OE-03 9 9E-06 4 3E-03 Yes RUNX3 Hs 170019 runt-related transcription factor 3
204198_s_at 4 8E-06 1 5E-05 1 2E-04 5 1 E-04 Yes RUNX3 Hs 170019 runt-related transcription factor 3
204529_s_at 3 5E-03 6 6E-04 1 1 E-03 3 9E-05 Yes TOX Hs 439767 thymus high mobility group box protein TOX
204890_s_at 4 OE-06 6 5E-04 2 6E-06 1 OE-03 Yes LCK Hs 1765 lymphocyte-specific protein tyrosine kinase
205000_at 74E-03 2 6E-04 1 6E-03 3 3E-04 Yes DDX3Y Hs 99120 DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-lιnked
205120_s_at 1 1 E-03 5 OE-03 7 1 E-04 3 7E-03 Yes SGCB Hs 438953 sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)
205718_at 3 3E-04 54E-03 3 2E-03 7 5E-05 Yes ITGB7 Hs 1741 integrin, beta 7 205903_s_at 1 3E-03 5 2E-03 2 1E-03 8 6E-03 Yes KCNN3 Hs 89230 potassium intermediate/small conductance calcium- activated channel, subfamily N, member 3
206219_s_at 6 2E-05 9 8E-04 2 9E-04 6 7E-04 Yes VAV1 Hs 116237 vav 1 oncogene 206641_at 2 4E-03 3 1E-03 4 3E-03 5 5E-03 Yes TNFRSF17 Hs 2556 tumor necrosis factor receptor superfamily, member
17
206700_s_at 6 0E-05 2 5E-03 2 6E-05 3 1E-03 Yes SMCY Hs 80358 Smcy homolog, Y-lιnked (mouse) 207000_s_at 5 2E-03 2 2E-03 7 2E-04 2 OE-04 Yes PPP3CC Hs 75206 protein phosphatase 3 (formerly 2B), catalytic UJ subunit, gamma isoform (calcineuπn A gamma)
207238_s_at 2 7E-03 2 5E-06 5 4E-03 4 6E-05 Yes PTPRC Hs 444324 protein tyrosine phosphatase, receptor type, C 207621_s_at 5 4E-04 1 6E-03 4 3E-03 7 7E-03 Yes PEMT Hs 15192 phosphatidylethanolamine N-methyltransferase 208119_s_at 4 4E-04 8 OE-05 2 8E-03 3 2E-05 Yes ZNF505 Hs 515284 zinc finger protein 505 208190_s_at 3 4E-04 62E-04 1 4E-04 1 4E-04 Yes LISCH7 Hs 312129 liver-specific bHLH-Zip transcription factor 208502_s_at 6 6E-03 3 7E-03 2 7E-03 1 6E-03 Yes PITX 1 Hs 84136 paired-like homeodomain transcription factor 1 209200 at 3 1 E-03 8 1 E-03 1 6E-03 8 OE-03 Yes MEF2C Hs 368950 MADS box transcription enhancer factor 2, polypeptide C (myocyte enhancer factor 2C)
209372_x_at 5 6E-03 5 2E-03 1 OE-03 9 2E-04 Yes TUBB Hs 512712 tubulin, beta polypeptide 209447_at 6 9E-03 1 4E-03 5 4E-05 4 6E-03 Yes SYN E 1 Hs 282117 spectrin repeat containing, nuclear envelope 1 209570 s at 3 3E-04 2 1E-04 3 2E-03 1 9E-03 Yes D4S234E Hs 79404 DNA segment on chromosome 4 (unique) 234 expressed sequence
209967_s_at 5 1 E-04 3 3E-05 2 9E-04 3 9E-05 Yes CREM Hs 231975 cAMP responsive element modulator
209980_s_at 4 1E-04 1 9E-03 3 1E-04 1 3E-03 Yes SHMT1 Hs 293636 serine hydroxymethyltransferase 1 (soluble)
210258_at 1 0E-05 4 1E-07 8 6E-05 2 6E-07 Yes RGS13 Hs 17165 regulator of G-protein signalling 13
211543_s_at 1 2E-03 2 2E-04 1 OE-03 2 OE-04 Yes GPRK6 Hs 235116 G protein-coupled receptor kinase 6
212254_s_at 7 8E-03 3 3E-03 1 4E-03 2 2E-03 Yes BPAG 1 Hs 443518 bullous pemphigoid antigen 1 , 230/24OkDa
212592_at 2 5E-03 2 9E-04 1 OE-05 2 9E-04 Yes IGJ Hs 381568 immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides
213029 at 5 2E-03 6 OE-03 7 5E-03 8 3E-03 Yes NFIB Hs 302690 nuclear factor I/B
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene UniGene ID Gene Title
Symbol
213457_at 4 9E-05 1 6E-04 5 5E-05 5 OE-04 Yes MFHAS1 Hs 379414 malignant fibrous histiocytoma amplified sequence 1 213533_at 4 2E-03 2 6E-04 1 2E-02 1 1 E-03 Yes D4S234E Hs 79404 DNA segment on chromosome 4 (unique) 234 expressed sequence
214508_x_at 4 2E-03 1 9E-04 5 7E-04 1 1 E-03 Yes CREM Hs 231975 cAMP responsive element modulator 214669 x at 6 1E-08 7 4E-04 2 8E-03 1 1 E-03 Yes Hs 525893 Homo sapiens cDNA FLJ26296 fis, clone
DMC07192, highly similar to Ig kappa chain V-III region HAH precursor
214836 x at 1 7E-04 2 2E-05 3 3E-04 3 5E-04 Yes Hs 525895 Homo sapiens cDNA FLJ39619 fis, clone
SMINT2000984, highly similar to IG KAPPA CHAIN
V-Il REGION GM607 PRECURSOR
215016_x_at 4 8E-03 3 6E-03 3 1E-03 1 8E-03 Yes BPAG 1 Hs 443518 bullous pemphigoid antigen 1 , 230/24OkDa 215903_s_at 6 9E-04 1 5E-03 4 5E-03 3 4E-03 Yes MAST205 Hs 101474 microtubule associated testis specific serine/threonine protein kinase
215967_s_at 2 9E-03 1 3E-04 1 5E-03 7 OE-05 Yes LY9 Hs 403857 lymphocyte antigen 9
217422_s_at 2 4E-04 2 7E-03 6 2E-03 1 2E-03 Yes CD22 Hs 262150 CD22 antigen
U)
218017_s_at 3 5E-04 2 7E-04 2 2E-04 3 OE-04 Yes FLJ32731 Hs 191320 hypothetical protein FLJ32731
218412_s_at 1 8E-04 2 3E-04 6 3E-04 3 9E-03 Yes GTF2IRD1 Hs 430854 GTF2I repeat domain containing 1
218573_at 4 4E-03 2 5E-03 7 6E-03 4 1 E-03 Yes MAGEH 1 Hs 279819 APR-1 protein
218723_s_at 3 5E-04 4 2E-04 2 OE-03 2 5E-03 Yes RGC32 Hs 76640 RGC32 protein
218858_at 1 3E-03 44E-07 9 6E-04 1 6E-07 Yes FLJ12428 Hs 87729 hypothetical protein FLJ 12428
219165_at 3 1 E-03 1 2E-03 6 1 E-03 1 2E-03 Yes PDLIM2 Hs 375560 PDZ and LIM domain 2 (mystique)
219299_at 1 1 E-03 4 9E-03 3 1 E-03 6 6E-03 Yes FLJ20772 Hs 9925 hypothetical protein FLJ20772
219855 at 4 OE-05 1 3E-03 4 OE-05 9 4E-05 Yes NUDT11 Hs 200016 nudix (nucleoside diphosphate linked moiety X)-type motif 11
220432_s_at 2 8E-03 3 8E-03 3 OE-03 4 1 E-03 Yes CYP39A1 Hs 387367 cytochrome P450, family 39, subfamily A, polypeptide 1
221003_s_at 1 1 E-03 1 8E-03 1 7E-03 4 5E-03 Yes FLJ12577 Hs 87159 hypothetical protein FLJ12577
221651_x_at 1 4E-06 1 2E-10 1 6E-03 1 9E-03 Yes
221671 x at 1 7E-05 5 7E-05 3 1 E-03 3 3E-03 Yes Hs 377975 Homo sapiens immunoglobulin kappa light chain mRNA, partial cds
222307 at 2 1E-03 3 6E-03 1 3E-03 3 6E-03 Yes Hs 293219 Homo sapiens cDNA FLJ40384 fis, clone
TESTI2035796
203722. .at 3 8E-03 8 4E-05 6 9E-03 1 4E-03 No ALDH4A1 Hs 77448 aldehyde dehydrogenase 4 family, member A1
219998. .at 3 OE-03 1 7E-03 4 3E-03 2 2E-03 No HSPC159 Hs 372208 HSPC159 protein
221487 S at 1 1 E-03 1 6E-03 4 2E-03 8 1E-03 No ENSA Hs 511916 endosulfine alpha
Table 3A: Genes With Reduced Expression in CD40-Sensitive Cell Lines
Log2 fluorescence intensity
Probesets Ly 1 (A1 ) Ly 1 (A2) Ly1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
200068_s_at 11 55 11 59 1 1 58 1 1 36 11 29 1 1 33 1 1 54 1 1 50 11 46 1 1 10 11 03 11 12
200670_at 9 90 9 51 10 05 7 15 7 18 6 83 10 00 9 39 9 51 7 84 8 10 7 97
200701_at 9 15 8 73 9 02 7 92 8 05 7 83 9 19 8 73 8 79 7 60 7 84 7 82
200736_s_at 10 16 9 88 9 93 9 46 9 47 9 25 10 48 10 24 10 32 9 01 9 19 9 02
200765_x_at 7 24 7 35 7 27 6 39 6 26 6 25 7 89 7 69 7 88 4 96 5 26 4 97
200814_at 1 1 23 1 1 07 1 1 11 10 08 10 1 1 9 72 11 39 11 31 11 15 9 27 9 52 9 31
200846_s_at 10 32 10 20 10 21 10 01 9 94 9 99 10 33 10 27 10 36 9 88 9 98 9 98
200887_s_at 8 85 8 58 8 62 7 98 7 58 7 65 8 68 8 76 8 89 7 28 7 06 7 32
200905_x_at 10 71 10 51 10 44 8 84 8 76 8 82 10 60 10 37 10 45 7 96 8 09 8 08
200936_at 13 09 13 10 13 08 12 67 12 70 12 72 13 12 13 07 13 17 12 87 12 92 12 89
200941_at 8 93 8 75 8 68 8 02 7 60 7 79 8 94 8 91 8 98 7 68 7 63 7 98
201011_at 8 78 8 70 8 80 8 43 8 50 8 39 8 85 8 88 9 00 8 55 8 44 8 52
201160_s_at 10 78 10 64 10 85 10 21 10 01 10 16 10 72 10 68 10 91 5 15 5 16 5 18
201 161_s_at 9 93 9 63 9 57 8 77 8 90 8 58 10 01 9 76 9 50 5 58 5 61 5 17 όo
201200_at 9 71 9 46 9 66 8 50 8 91 8 89 9 99 9 89 9 75 8 43 8 18 8 64 ^
201204_s_at 8 32 8 44 8 93 7 02 6 75 7 19 8 67 8 70 8 46 7 20 6 92 7 29
201206_s_at 8 01 8 19 8 16 6 60 6 77 6 20 8 28 8 39 8 02 6 49 6 91 6 67
201226_at 10 47 10 43 10 39 9 23 9 27 9 21 10 48 10 34 10 46 10 07 10 15 10 12
201263_at 9 79 9 91 9 59 8 72 8 90 8 55 10 22 9 92 9 87 7 74 8 00 8 28
201307_at 9 03 9 14 9 22 7 75 7 71 7 77 8 91 8 93 9 13 6 67 6 96 6 87
201398_s_at 10 71 10 97 10 99 9 80 9 77 9 93 10 77 10 90 10 84 9 34 9 30 9 55
201399_s_at 10 49 10 25 10 36 9 13 9 20 9 45 10 24 10 05 10 25 8 37 8 56 8 59
201470_at 10 34 10 47 10 20 5 78 5 46 5 80 10 52 10 53 10 57 8 93 8 75 8 96
201487_at 9 57 9 89 9 84 8 74 8 66 8 76 9 45 9 69 9 68 8 63 8 60 8 76
201499_s_at 10 04 9 96 10 06 9 43 9 25 9 29 10 00 9 92 10 1 1 9 35 9 30 9 52
201566_x_at 8 27 8 30 8 07 7 46 7 54 7 66 8 77 9 00 8 56 6 89 6 73 6 82
201590_x_at 9 41 9 46 9 20 7 12 6 89 6 92 9 49 9 28 9 26 7 00 6 97 6 73
201601_x_at 10 14 9 56 9 84 7 96 7 90 7 87 10 08 9 97 10 05 6 93 6 95 6 88
201649_at 9 26 9 15 9 06 8 16 8 54 8 32 9 34 9 24 9 18 5 72 5 44 5 23
201746_at 9 96 9 88 10 01 9 17 9 14 9 09 9 99 9 94 9 86 9 33 9 49 9 47
201874_at 8 65 8 67 8 51 7 63 7 84 7 49 8 49 8 47 8 33 7 32 7 26 7 28
201937_s_at 8 28 8 24 7 98 7 65 7 54 7 46 8 22 8 16 8 23 6 94 7 17 6 86
201968_s_at 9 90 9 45 9 75 8 53 8 30 8 34 10 01 9 60 9 89 7 28 7 59 7 56
202096_s_at 9 04 8 67 8 55 7 26 7 16 7 16 9 08 8 86 8 89 6 28 6 06 6 06
Log2 fluorescence intensity
Probesets Ly1 (A1 ) Ly1 (A2) Ly1 (A3; I Ly7 (Bi ; ) Ly7 (B2; I Ly7 (B3] I Ly8 (C1 ) Lyo (C2 ) Ly8 (C3 ) D4 (D1) D4 (D2) D4 (C
202123_s_at 8 35 8 27 8 44 7 06 6 75 7 09 8 21 8 19 8 37 7 72 7 78 7 90
202261 at 8 45 8 44 8 35 8 03 8 13 8 00 8 55 8 39 8 47 8 18 8 14 8 06
202279_at 10 46 10 39 10 33 9 96 9 87 9 78 10 83 10 78 10 84 9 96 9 96 10 09
202315_s_at 8 91 9 16 9 06 7 33 7 36 7 13 9 12 9 05 8 71 7 02 6 91 6 89
202382_s_at 7 66 7 40 7 34 6 90 6 62 6 74 1 11 7 58 7 46 4 95 5 16 4 96
202429_s_at 8 69 8 33 8 33 6 48 6 11 6 45 8 27 8 42 8 43 6 21 6 23 6 81
202443 x at 7 54 7 27 7 22 6 68 6 36 6 41 7 68 7 49 7 39 4 66 4 84 4 93
202447_at 8 94 8 90 8 98 8 55 8 46 8 40 8 90 8 88 8 92 7 41 7 41 7 73
202457 s at 8 98 8 52 8 87 7 08 6 82 7 34 8 70 8 42 8 94 7 48 7 32 7 74
202536_at 6 73 6 78 7 17 5 90 5 69 6 05 7 11 6 96 7 50 4 24 4 27 4 34
202696 at 8 63 8 47 8 57 8 33 8 21 8 18 8 64 8 55 8 62 8 10 8 25 8 24
202732_at 9 53 9 63 9 36 7 48 7 88 7 41 9 14 9 48 9 33 6 59 7 03 6 85
202811_at 7 98 7 82 8 04 6 68 6 70 6 49 7 80 7 93 7 98 6 91 6 98 7 18
202982_s_at 7 96 7 90 7 81 6 53 6 57 6 55 7 83 7 69 7 85 5 02 4 88 4 71
203031_s_at 9 17 8 91 8 84 7 06 7 05 6 71 8 96 8 80 8 66 7 53 7 72 7 73
203113 s at 11 40 11 29 11 21 10 75 10 77 10 75 11 45 11 23 11 34 10 48 10 71 10 76
203142_s_at 9 52 9 43 9 39 8 05 8 12 7 98 9 56 9 21 9 24 8 18 8 17 8 23
203217_s_at 8 27 7 88 8 31 6 1 1 6 53 6 65 8 29 8 06 8 15 6 39 6 59 6 34
203335_at 8 36 8 34 8 58 4 78 4 62 4 75 8 75 8 33 8 32 4 27 4 32 4 34
203343_at 7 22 7 64 7 64 6 30 6 60 6 64 7 23 7 44 7 64 5 30 5 93 5 96
203459_s_at 1 11 7 61 7 54 7 18 7 07 6 91 7 60 7 49 7 63 6 75 6 55 6 41
203659 s at 7 56 7 54 7 97 6 43 6 42 6 64 7 45 7 38 7 71 5 96 6 07 6 35
203825_at 8 10 8 25 7 95 6 94 6 97 6 96 7 96 8 06 7 95 6 94 6 99 6 99
203957_at 7 85 7 83 7 84 7 14 7 31 7 17 7 78 8 04 7 98 5 89 6 09 6 18
204003_s_at 8 03 8 12 8 04 7 55 7 34 7 41 7 76 7 89 7 93 7 07 7 02 7 19
204044_at 7 91 7 68 7 81 6 17 6 54 6 44 8 35 8 23 7 87 6 71 6 97 6 82
204168_at 7 91 7 98 7 95 6 83 6 90 6 87 8 16 8 21 8 29 7 16 7 21 7 20
204172 at 6 16 6 10 6 51 4 77 4 76 4 83 6 05 6 05 6 38 3 87 4 57 4 49
204220_at 9 58 9 35 9 28 8 69 8 23 847 944 9 14 941 7 38 7 13 7 52
204234 s at 7 75 7 48 7 28 6 52 6 42 6 36 7 61 7 16 7 42 6 00 6 33 6 29
204256_at 7 12 7 57 8 02 5 14 5 45 5 33 7 07 7 58 7 74 4 74 4 75 5 30
204279_at 10 03 10 03 10 06 8 83 9 06 8 96 10 09 9 94 10 06 5 49 5 88 5 75
204326_x_at 10 66 10 55 10 74 7 84 8 05 7 93 10 79 10 65 10 45 9 44 9 28 9 42
204386_s_at 10 92 11 04 11 05 10 20 10 07 10 03 11 00 11 07 11 02 10 41 10 21 10 42
204418 x at 7 57 7 57 742 6 44 666 6 67 7 37 7 35 7 12 6 77 6 50 647
Log2 fluorescence intensity
Probesets Ly 1 (A1 ) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
204565_at 9 31 9 15 9 07 7 55 7 59 7 51 9 18 8 84 9 12 6 36 6 31 6 69
204766_s_at 11 23 10 84 11 06 8 35 7 85 7 99 11 02 10 41 10 57 8 52 8 62 8 73
204769_s_at 7 91 8 05 7 79 6 83 7 05 7 05 7 76 7 84 7 87 6 10 6 19 6 19
204779_s_at 8 11 8 13 8 06 7 44 7 30 7 27 8 24 8 23 8 58 6 94 6 95 7 03
204806_x_at 10 73 10 67 10 38 8 83 8 96 8 54 10 45 10 30 10 31 7 67 7 82 7 49
204937_s_at 8 57 8 55 8 62 7 61 7 47 7 55 8 75 8 61 8 79 5 72 5 86 6 24
205048_s_at 8 88 8 65 8 92 6 13 6 37 6 19 9 07 9 15 8 77 6 33 5 82 6 60
205297_s_at 10 93 10 97 10 91 9 82 9 84 9 68 10 91 10 80 10 64 9 51 9 79 9 71
205659_at 6 94 7 23 7 38 6 06 6 40 6 44 7 24 7 56 7 73 6 08 6 31 6 27
206928_at 6 49 6 45 6 68 5 92 5 81 6 05 6 67 6 37 6 69 5 72 5 55 5 88
207181_s_at 6 65 664 6 83 6 24 6 01 6 12 6 78 6 80 6 81 5 49 5 27 5 07
207304_at 4 80 4 81 4 96 4 47 4 44 4 35 4 95 4 86 5 03 4 30 4 35 4 36
207585_s_at 11 22 11 31 11 37 10 89 10 90 10 84 11 28 11 29 11 46 10 67 10 73 10 80
207777_s_at 6 27 6 09 6 18 4 81 4 55 4 62 6 47 6 23 6 26 5 06 4 91 4 78
207809_s_at 8 69 8 51 8 58 8 01 8 05 8 04 8 73 8 63 8 75 8 13 8 02 8 25
208490_x_at 7 95 8 04 7 69 6 88 6 87 7 11 7 91 7 82 7 95 7 21 7 01 7 24 £
208527_x_at 6 57 6 46 6 47 5 60 5 62 5 52 6 69 6 57 6 44 5 51 5 81 5 64
208579_x_at 9 06 8 78 8 87 7 67 7 47 7 59 9 32 9 02 9 20 7 38 7 66 7 70
208581_x_at 10 94 1048 10 68 8 95 9 18 8 79 10 84 1043 1047 9 54 9 85 9 65
208690_s_at 10 01 9 98 9 74 7 90 7 94 7 68 10 10 10 26 10 33 6 86 6 99 6 98
208729_x_at 12 62 12 49 12 18 9 61 9 63 9 55 12 28 12 26 12 09 8 01 8 43 8 04
208812_x_at 12 57 12 47 12 47 11 36 11 55 11 37 12 49 12 38 12 41 7 97 8 09 8 03
208918_s_at 9 26 9 13 9 32 8 57 8 44 8 48 9 08 8 90 9 12 8 02 8 15 8 35
209040_s_at 10 14 10 23 10 31 9 50 9 61 9 63 10 20 10 16 10 31 7 41 762 7 86
209112_at 7 60 7 22 7 56 4 71 4 75 5 04 7 34 7 32 7 74 5 16 5 22 5 80
209124_at 9 60 9 57 9 51 9 16 8 93 9 01 9 72 9 82 9 83 9 34 9 22 9 27
209138_x_at 12 64 12 79 12 71 6 60 6 83 6 90 12 81 12 92 12 67 9 57 10 33 9 63
209140_x_at 13 05 12 93 13 01 10 68 10 95 10 64 13 05 12 96 12 89 8 24 8 59 8 46
209175_at 7 32 7 45 7 66 6 95 6 67 6 67 7 53 7 63 7 64 6 60 6 64 6 92
209201_x_at 11 47 11 31 11 07 9 68 9 77 9 27 11 34 11 22 10 55 9 32 9 43 8 91
209472_at 8 01 7 93 8 25 5 69 5 52 5 44 8 28 8 05 8 03 6 65 6 75 7 01
209476_at 1041 10 47 10 59 10 12 9 99 10 09 10 37 10 56 1045 10 00 9 76 10 02
209591_s_at 8 09 8 13 7 69 6 43 6 95 6 78 9 09 8 80 8 50 5 69 6 10 5 75
209970_x_at 7 75 8 08 7 53 5 51 5 56 5 28 7 44 7 98 7 85 5 44 5 42 5 20
209995_s_at 11 95 12 19 12 19 10 79 11 03 10 72 12 13 12 27 12 15 8 59 8 80 8 85
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (
210136_at 7 98 7 94 8 02 7 00 6 68 6 88 8 62 8 26 8 27 6 12 6 22 6 31
210844 x at 7 74 8 03 7 68 6 98 6 95 7 11 8 35 8 16 8 46 5 77 5 60 5 57
211061_s_at 9 41 9 28 9 69 8 10 8 51 8 23 9 55 9 38 9 15 7 45 8 20 7 71
211089 s at 6 09 6 08 6 26 546 5 35 5 56 5 96 6 16 6 19 5 37 5 54 5 58
211366_x_at 8 01 8 27 8 09 5 91 6 04 5 89 8 06 8 05 8 33 5 83 6 13 5 67
211528 x at 11 97 11 71 11 85 10 27 10 51 10 06 11 95 11 71 11 50 8 78 9 28 8 87
211529_x_at 12 05 11 67 11 65 10 28 10 45 10 02 11 73 11 63 11 48 8 67 9 12 8 55
211530 x at 10 43 10 30 10 28 9 19 9 49 9 38 10 13 10 25 9 97 8 63 8 77 8 66
211799_x_at 10 60 10 58 10 41 8 50 9 02 8 61 10 56 10 34 10 21 6 38 7 01 6 59
211911 x at 12 27 12 11 12 01 9 49 9 50 9 28 12 20 11 97 11 83 7 81 7 96 7 69
211919_s_at 11 52 11 20 11 09 9 77 9 75 9 40 11 31 11 17 10 58 9 44 9 42 9 03
211989 at 9 42 9 47 9 28 8 74 8 75 8 58 9 39 9 41 9 61 8 55 8 68 8 83
212057_at 9 16 9 14 9 32 7 09 6 77 7 02 9 35 9 32 8 96 6 97 7 41 7 48
212071 s at 10 87 11 02 10 95 8 73 8 62 8 74 10 80 10 94 10 89 4 78 5 45 5 25
212149_at 9 42 9 01 9 46 8 28 8 03 8 29 9 29 8 99 9 46 5 18 5 09 5 85
212382 at 7 45 7 94 8 47 5 20 5 31 5 62 7 72 8 13 8 50 4 76 4 97 5 23 W Ό
212385 at 7 45 7 66 7 79 6 43 6 27 6 42 7 57 7 66 8 04 6 03 6 36 6 17
212386 at 10 10 10 18 10 39 8 61 8 59 8 78 10 29 10 46 10 45 6 64 7 37 7 24
212387_at 8 77 8 61 8 89 7 31 7 19 7 22 8 93 9 01 9 06 6 07 6 29 6 34
212408 at 8 51 8 17 8 47 7 09 7 12 7 36 8 44 8 16 8 50 6 92 6 92 7 44
212446_s_at 5 54 5 36 5 36 3 63 3 80 3 86 5 39 5 46 5 89 3 80 3 82 3 78
212507 at 7 71 7 47 7 74 6 39 6 37 6 51 7 47 7 73 7 89 6 14 6 00 6 54
212547_at 7 80 7 94 7 89 6 72 6 52 6 58 7 83 7 92 8 09 6 52 6 74 6 91
212739 s at 10 60 10 47 10 47 8 69 8 86 8 60 10 57 10 38 10 27 6 39 5 60 6 02
212774_at 8 74 8 65 9 00 7 10 6 99 7 50 8 67 8 84 9 10 5 74 5 84 6 27
212792 at 6 10 6 37 6 29 5 46 5 49 5 56 6 53 6 54 6 45 5 68 5 62 5 35
212798_s_at 8 29 8 33 8 51 6 44 6 20 6 62 8 29 8 42 8 57 6 12 6 13 6 40
212946 at 8 76 8 42 8 49 7 22 7 56 7 47 8 67 8 22 8 59 6 28 6 15 6 40
213020 at 5 61 5 70 5 66 5 39 5 42 5 28 5 64 5 72 5 76 5 39 5 47 5 38
213116_at 7 40 7 52 7 74 5 87 6 02 5 88 7 47 7 53 7 72 5 68 5 54 5 62
213233 s at 8 79 8 57 8 74 7 14 7 45 7 12 8 78 8 90 8 56 7 11 7 30 7 16
213293_s_at 8 61 8 63 9 05 7 83 7 73 7 59 8 84 9 12 8 93 7 24 7 36 7 49
213357 at 8 43 8 33 8 64 8 03 7 79 7 90 8 72 8 40 8 60 7 00 6 87 7 26
213361_at 6 49 6 45 6 35 6 08 5 97 5 85 6 60 6 41 6 72 5 51 5 65 5 55
213435 at 6 68 6 84 7 27 5 62 5 52 5 94 7 01 7 31 7 28 5 24 4 63 5 11
Log2 fluorescence intensity
Probesets Ly1 (A1 ) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (C
213793_s_at 6 83 6 31 6 61 5 04 5 23 5 20 6 60 6 09 6 60 4 26 4 45 4 31
213891 s at 9 12 9 15 9 28 7 28 7 27 7 51 9 30 9 35 9 47 5 41 5 67 5 90
214022 s at 10 24 9 80 9 85 7 86 8 05 7 67 10 10 10 14 10 02 6 52 6 52 6 51
214032_at 7 58 7 49 7 36 5 75 5 83 5 79 7 78 7 52 7 54 5 55 5 87 5 53
214172_x_at 623 6 11 6 26 5 23 5 42 5 37 6 26 6 39 6 23 5 10 5 07 4 87
214369 s at 8 61 8 51 8 49 7 88 7 64 7 67 8 17 8 15 8 36 6 66 6 46 6 81
214394_x_at 11 62 11 69 11 68 11 30 11 30 11 37 11 78 11 70 11 82 11 37 11 31 11 37
214459 x at 12 47 12 49 12 46 11 42 11 67 11 41 12 54 12 37 12 26 8 26 8 86 8 86
214512_s_at 10 28 10 44 10 44 7 82 8 00 7 92 10 09 10 32 10 42 8 48 8 52 8 73
214677 x at 13 42 13 48 13 31 7 13 6 91 7 06 13 31 13 41 13 41 9 71 10 24 9 85
214749_s_at 9 55 946 9 57 8 76 8 74 8 72 9 38 9 30 9 31 6 99 6 52 6 89
214835 s at 7 93 7 92 8 33 6 59 6 67 6 29 1 11 8 21 8 07 6 84 6 94 7 07
214916 x at 8 71 8 55 8 48 7 93 8 06 7 82 8 51 8 37 8 28 4 96 5 53 5 27
215121_x_at 12 69 12 81 12 63 7 09 7 04 7 67 12 61 12 72 12 67 9 64 10 21 9 61
215516 at 4 64 4 43 4 42 4 05 3 91 4 02 4 32 4 35 4 46 4 09 3 94 4 00
215772_x_at 8 32 8 05 8 63 6 43 6 59 6 62 8 64 8 37 8 27 7 08 7 01 7 40 O
215946_x_at 9 45 10 25 10 15 6 14 6 52 6 35 9 37 9 73 9 78 7 00 7 41 6 77
216526 x_at 12 46 12 36 12 44 11 35 11 52 11 28 12 40 12 36 12 30 7 97 7 98 7 86
216733_s_at 8 74 8 51 8 97 5 02 5 17 5 35 8 26 8 11 8 29 5 34 5 38 5 41
216973_s_at 8 07 8 20 8 08 7 57 7 51 7 42 8 31 8 29 8 61 6 85 7 21 7 05
216976 s at 7 27 7 20 7 20 6 32 6 39 6 39 7 67 7 24 7 55 6 14 6 05 5 85
217028 at 10 94 11 03 11 08 9 61 9 69 9 31 10 99 10 98 10 65 9 27 9 15 9 06
217436 x at 9 84 9 56 9 53 7 91 8 38 8 22 9 78 9 39 9 37 7 30 7 54 7 52
217456_x_at 9 30 9 09 9 12 7 62 7 65 7 54 9 06 8 89 9 02 6 80 7 11 6 96
217809_at 11 42 11 35 11 46 10 34 10 24 10 27 11 37 11 33 11 45 10 99 10 96 11 10
217839 at 9 87 9 61 9 56 9 02 8 94 8 84 9 68 9 54 9 58 8 09 8 12 7 85
217911_s_at 7 04 7 17 741 5 54 4 84 5 01 8 02 7 90 7 53 4 87 4 90 4 80
217940_s_at 8 53 8 41 8 38 7 03 7 24 7 17 8 65 8 30 8 60 7 24 7 50 7 63
217950 at 9 21 8 99 9 06 8 31 8 06 8 19 9 21 8 87 9 11 8 01 8 00 8 21
217988_at 9 98 9 46 9 52 7 84 7 67 7 52 9 70 9 38 9 37 7 88 8 29 8 17
218026 at 9 30 9 33 929 8 59 8 50 8 61 9 44 9 39 9 61 8 57 849 8 71
218093_s_at 8 39 8 29 8 68 6 34 6 67 6 70 7 80 7 76 8 19 6 85 6 74 7 08
218100 s at 8 05 7 94 8 36 6 25 5 99 6 11 8 58 8 56 8 53 4 84 5 28 5 82
218187_s_at 845 8 39 8 39 7 56 7 31 7 34 8 31 8 31 8 40 7 48 7 17 7 34
218224 at 7 21 7 30 7 85 4 08 4 31 4 29 7 70 7 39 7 49 4 22 4 14 4 37
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (
218276 s at 6 55 6 49 6 39 5 84 5 61 5 66 7 26 7 03 7 00 5 24 5 20 5 39
218285 s at 7 37 7 59 7 68 5 86 5 86 5 95 7 44 7 46 1 11 6 01 6 02 6 32
218316 at 8 86 8 73 8 91 847 8 33 842 8 80 8 85 8 66 7 95 8 00 7 87
218343 s at 7 51 7 20 7 47 6 40 6 18 6 20 7 54 7 28 7 52 5 91 5 76 6 22
218358_at 9 73 9 86 10 01 8 58 8 32 8 67 9 64 9 66 9 51 8 64 8 35 8 65
218377_s_at 868 8 77 8 70 7 98 8 16 8 03 867 863 8 59 8 29 8 32 8 27
218490 s at 4 57 4 60 4 72 4 29 4 31 4 25 4 73 4 61 4 60 3 87 3 87 3 88
218491_s_at 9 04 9 02 8 74 8 32 8 14 8 08 8 90 8 69 8 80 7 96 7 66 8 08
218543 s at 7 65 7 40 1 11 6 47 6 27 645 7 87 7 65 7 73 5 96 564 5 98
218557 at 9 39 9 27 9 28 7 87 7 84 1 11 9 44 9 11 9 15 7 28 7 20 7 40
218633 x at 8 66 8 70 8 75 7 93 7 81 7 93 8 59 8 64 8 67 7 01 7 09 7 37
218648 at 7 91 7 89 1 11 5 87 6 13 6 37 7 75 7 88 7 87 6 37 6 08 6 29
218735 s at 7 74 8 04 8 29 6 75 7 00 6 67 8 00 8 13 8 28 6 16 6 40 6 59
218738 s at 9 42 9 35 9 63 8 74 8 59 8 59 9 37 9 53 9 59 8 71 8 65 8 82
218773_s_at 8 82 8 40 8 76 7 03 7 25 7 13 8 78 8 35 8 53 7 44 7 59 7 92
219008 at 6 90 6 61 7 27 5 37 4 92 4 79 7 03 6 61 7 10 5 60 5 25 5 32
219184_x_at 7 30 7 30 7 29 6 35 6 31 6 20 7 15 7 54 7 15 5 95 5 99 5 91
219209 at 5 38 5 30 5 58 4 82 4 53 4 76 5 59 5 76 5 92 4 30 4 49 4 27
219215_s_at 8 52 848 863 6 70 6 92 7 14 864 8 64 8 52 6 88 7 05 7 06
219248 at 6 96 7 16 7 31 5 92 6 06 6 24 6 98 7 17 7 02 6 27 6 51 6 38
219471_at 11 50 11 61 11 68 10 17 10 60 10 29 11 55 11 75 11 53 8 28 8 93 8 22
219489 s at 9 71 9 92 10 01 569 5 25 5 82 9 87 9 65 9 87 6 35 5 53 6 07
219563_at 8 96 9 27 9 42 4 98 5 11 4 79 8 37 8 48 8 29 4 74 4 36 4 28
219664 s at 10 37 9 75 9 82 8 06 8 06 7 70 10 36 9 93 9 82 8 33 8 14 7 88
219767_s_at 6 00 5 85 6 11 5 32 548 5 34 601 5 82 5 94 5 19 5 30 5 32
219822 at 6 85 6 89 7 03 5 44 5 43 5 48 6 92 6 83 7 04 5 36 5 43 5 87
220741 s at 9 37 9 31 9 37 7 72 7 54 7 45 9 31 9 21 9 45 8 13 8 06 8 18
221234 s at 9 73 9 80 9 57 8 75 8 81 865 9 76 9 86 9 53 8 08 8 27 7 91
221614_s_at 7 82 7 18 7 29 5 07 5 11 5 05 7 64 7 30 7 29 5 35 5 14 5 38
221847 at 7 49 7 26 7 35 5 94 5 92 5 94 7 47 7 15 7 71 6 14 6 05 6 40
221874_at 7 45 6 91 7 51 5 03 5 13 5 02 7 48 7 10 7 18 5 09 546 5 18
221875 x at 11 07 10 99 10 93 9 17 9 49 9 05 11 03 10 87 10 69 8 19 8 56 8 26
222146_s_at 7 71 7 86 7 40 5 84 6 21 5 70 7 60 7 66 1 11 4 92 5 50 5 26
35671_at 8 76 8 71 8 67 8 15 8 12 8 19 8 85 8 72 8 83 8 16 8 22 8 29
36830 at 7 17 742 7 37 5 98 6 04 6 24 6 93 7 22 7 48 5 91 6 07 6 30
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (Bi; ) Ly7 (B2; ) Ly7 (B3; ) Ly8 (C1 ) Ly8 (C2 ) Ly8 (C3 ) D4 (D1; I D4 (D2; ) D4 (
36936_at 8 33 8 35 8 35 7 73 7 52 7 55 8 16 8 14 8 08 7 56 7 59 7 56
37384 at 9 02 8 90 9 04 7 57 7 81 7 69 8 98 8 89 8 75 7 35 1 11 7 72
39318_at 12 14 12 32 12 26 11 06 11 18 10 93 12 27 12 49 12 25 8 75 8 94 8 48
40148 at 5 44 5 46 5 58 4 86 5 04 4 99 5 40 5 68 5 75 4 54 4 46 4 46
200660_at 8 56 849 8 21 540 5 06 5 36 8 56 8 51 8 45 5 81 5 38 540
200671_s_at 7 16 7 40 7 20 5 65 5 58 5 87 7 30 7 10 7 61 5 20 5 14 4 88
200672 x at 8 93 9 32 8 97 7 43 7 73 7 81 8 85 9 09 9 24 6 32 7 01 6 75
200704_at 8 62 8 23 8 24 5 83 6 09 5 91 8 96 8 80 8 50 6 19 6 29 6 00
200706 s_at 7 13 6 99 7 1 1 5 71 5 61 5 62 7 31 7 01 7 14 5 89 5 91 5 84
200782_at 7 51 7 44 7 83 4 72 5 12 5 13 8 78 8 85 9 29 5 09 5 33 5 65
200923_at 9 47 9 06 9 04 5 66 5 77 5 93 9 34 9 30 9 07 5 73 5 78 5 56
201005_at 10 54 10 55 10 64 4 88 4 53 4 83 10 91 10 82 10 60 5 25 4 95 4 80
201426_s_at 10 07 9 77 9 84 5 98 5 82 5 88 10 04 9 78 9 63 5 88 6 01 5 26
201485 s at 8 03 7 98 7 98 7 22 7 12 7 26 8 16 7 84 8 21 5 27 5 35 5 34
201792_at 8 18 849 8 69 5 99 542 5 82 8 50 8 77 8 58 6 36 5 74 5 91
202218 s at 7 55 7 32 7 86 5 92 5 77 5 88 7 89 7 50 7 42 6 24 6 24 5 88 K)
202283_at 10 43 9 33 10 17 5 54 5 28 5 59 10 37 9 42 9 62 6 16 5 84 6 11
202719 s at 6 49 6 41 6 60 5 41 5 13 5 38 6 53 6 63 6 58 5 99 5 89 6 01
202855_s_at 6 48 6 13 6 22 4 99 4 91 4 92 6 93 6 55 7 01 4 82 5 27 5 00
202856_s_at 6 18 6 07 6 32 4 75 4 26 4 55 6 63 6 50 6 34 4 61 4 59 4 65
203045_at 8 37 8 65 8 33 6 69 7 14 6 94 8 41 8 87 8 25 6 76 6 91 6 52
203063 at 844 8 27 8 60 7 11 7 32 6 95 845 8 23 8 17 7 02 7 34 7 16
203068_at 6 88 6 58 6 72 4 89 5 15 5 17 6 88 6 70 7 05 5 25 5 48 5 42
203211 s at 7 33 7 38 7 27 5 32 5 17 5 16 7 50 7 54 7 53 5 76 5 67 5 63
203212_s_at 8 24 7 99 7 83 6 21 5 74 6 36 8 16 8 03 8 27 7 00 6 69 7 03
203222_s_at 4 89 4 92 4 78 4 44 4 27 4 33 5 05 5 10 5 09 4 50 4 35 4 39
203305_at 841 8 31 8 36 542 5 67 5 90 9 17 9 07 9 21 5 76 6 22 5 83
203408 s at 8 28 7 85 7 91 6 70 6 31 6 54 8 22 7 73 7 95 6 76 6 46 6 62
203557_s_at 7 38 7 33 7 19 5 60 5 83 5 66 7 56 7 50 7 37 6 52 6 71 6 57
203708_at 7 61 8 10 8 86 5 13 5 50 5 1 1 8 10 8 38 8 07 5 15 5 45 5 00
203853_s_at 6 37 6 51 6 52 5 07 5 21 5 09 5 43 5 56 5 46 5 27 5 13 5 20
204305 at 7 97 8 06 7 69 6 50 6 67 6 50 7 74 7 90 7 91 6 65 6 73 6 81
204821_at 5 79 5 80 6 03 4 72 4 47 4 63 5 59 5 58 5 75 4 70 4 41 4 27
204994_at 8 12 8 07 8 25 5 34 5 86 5 54 8 38 8 15 8 19 5 51 6 15 5 79
205173 x at 5 53 5 47 5 79 4 41 4 57 4 51 5 59 5 60 5 70 4 47 4 64 4 38
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly 1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
205181_at 617 631 621 535 561 557 621 610 641 545 567 538
205366_s_at 565 553 557 473 499 496 546 569 579 515 499 490
205401_at 713 729 747 457 471 485 749 743 789 563 556 597
205668_at 646 660 707 414 466 469 629 660 666 475 462 451
205691_at 897 921 950 640 701 711 874 881 864 598 641 624
205790_at 804 791 779 572 568 579 788 753 792 637 602 605
205932_s_at 608 586 603 510 528 502 622 615 584 487 519 485
206082_at 766 732 779 536 584 545 755 768 732 538 520 517
206261_at 656 692 725 487 519 529 653 674 642 552 527 515
206437_at 810 840 814 654 639 605 792 785 800 634 649 607
206554_x_at 568 561 556 483 483 489 580 575 570 464 475 452
206591_at 755 815 876 439 415 425 834 884 868 423 400 432
206660_at 1068 1135 1055 541 482 494 907 1028 1032 510 493 530
206698_at 752 770 828 428 431 426 740 779 774 431 457 431
206866_at 671 683 667 557 533 527 660 643 625 562 555 533
208146_s_at 720 674 694 535 555 511 642 658 670 531 544 537
208964_s_at 775 757 771 582 630 596 798 788 741 608 648 593
209129_at 717 766 738 534 482 498 733 736 725 560 488 500
209310_s_at 706 666 729 521 480 495 661 644 684 508 493 497
209398_at 673 661 692 611 586 605 701 665 699 604 603 590
209590_at 734 781 751 630 617 636 810 852 792 614 621 594
209728_at 938 904 949 691 687 718 938 902 920 725 686 707
209790_s_at 667 685 671 530 523 519 699 704 733 629 619 640
210427_x_at 955 937 894 688 691 673 915 903 917 690 723 660
210715_s_at 921 881 923 601 582 574 888 872 919 587 652 570
210830_s_at 503 496 488 415 430 431 502 500 524 440 425 443
211367_s_at 599 623 616 432 402 413 612 625 663 438 441 414
211368_s_at 723 748 716 488 489 478 707 748 778 484 475 456
211812_s_at 554 576 609 423 426 443 531 566 558 446 437 423
212268_at 822 812 807 591 597 578 850 810 852 692 712 722
212442_s_at 875 885 852 588 573 627 876 872 897 611 574 582
212561_at 780 739 720 610 631 650 781 739 762 656 620 596
213147_at 784 800 780 632 658 651 734 765 754 614 627 634
213150_at 685 741 776 440 474 466 647 659 701 435 460 465
213371 at 696 696 689 458 493 461 743 711 702 495 478 459
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2; ) D4 (
213419 at 6 52 6 47 6 71 5 72 5 99 5 81 6 60 6 44 6 84 5 02 5 46 5 04
213502_x_at 9 93 10 40 9 72 6 52 6 78 6 55 9 60 9 86 9 68 7 01 7 06 7 30
213503 x at 9 33 9 29 9 11 6 93 6 99 6 80 9 21 9 20 9 24 7 11 7 21 6 83
213566_at 7 24 6 91 7 15 4 80 5 20 4 83 7 09 6 63 7 05 4 95 4 85 4 89
213568_at 4 82 4 76 4 79 4 11 4 16 4 22 4 81 4 88 4 92 4 10 4 02 4 05
213572 s at 7 30 6 68 7 22 4 48 4 52 4 44 7 15 7 00 7 42 5 55 5 32 5 72
213625_at 5 83 5 88 5 85 5 33 5 28 5 42 5 66 5 59 5 61 5 12 5 13 5 18
213788 s at 5 89 6 20 6 17 5 22 5 13 5 46 5 93 6 09 5 97 5 44 5 22 5 49
215071_s_at 9 91 8 89 8 75 5 01 5 37 5 26 10 11 8 63 9 06 5 62 5 24 5 58
215379 x at 11 62 11 63 11 58 5 86 5 97 5 95 11 58 11 63 11 46 8 05 8 92 8 29
216565 x at 7 47 7 34 7 50 6 52 6 71 6 39 7 57 7 50 7 37 6 85 6 88 6 74
217022_s_at 8 41 843 8 70 5 16 4 79 4 95 8 98 9 42 8 50 5 39 5 20 5 07
217360 x at 7 17 7 42 7 18 5 76 5 81 5 51 7 39 7 34 6 76 5 93 5 61 5 61
217759_at 9 36 9 34 9 61 4 88 5 28 5 17 9 17 9 18 9 34 5 68 5 82 6 07
217760 at 8 00 7 80 7 56 4 84 4 75 4 80 7 87 7 65 7 59 5 26 5 12 5 27
217977_at 8 24 8 28 8 29 7 97 7 98 7 91 8 26 8 26 8 33 8 08 8 13 8 07
218005 at 10 08 10 07 10 21 5 41 5 61 5 37 10 28 10 09 9 97 8 54 8 72 8 67
218006_s_at 7 90 8 08 8 61 4 67 4 71 4 65 8 13 8 23 8 03 5 82 6 15 6 21
218154_at 8 00 7 97 7 94 6 95 6 85 6 86 7 96 7 88 7 83 6 82 6 67 6 47
218457_s_at 5 49 5 36 5 56 4 85 4 93 5 03 5 53 5 41 5 53 5 15 5 03 4 92
218503 at 6 52 6 59 6 71 5 28 5 45 5 60 6 66 6 70 7 21 5 30 5 26 5 09
218618_s_at 6 53 6 15 6 50 5 16 5 45 5 49 6 83 6 83 6 60 4 91 4 90 5 08
218676 s at 7 89 7 44 7 50 5 73 5 52 5 71 7 79 7 35 7 87 5 10 5 28 4 85
218689_at 7 06 7 09 7 50 6 04 6 39 6 15 7 24 7 00 6 96 5 82 6 33 6 10
218729_at 7 33 7 31 6 98 4 88 4 70 5 13 7 17 6 85 7 03 5 29 5 49 5 35
219143_s_at 8 66 9 03 8 70 5 42 5 03 5 30 9 04 8 82 8 48 5 40 5 37 5 06
219362 at 5 71 5 62 5 66 5 22 5 02 5 19 5 66 5 81 5 94 4 83 4 60 4 92
219684_at 7 69 7 89 7 74 5 58 5 45 5 32 7 60 7 71 7 91 5 76 5 67 5 10
219734_at 4 89 4 56 4 89 3 82 4 01 4 00 4 66 4 66 4 87 3 87 3 81 4 01
219953_s_at 6 78 7 01 6 88 5 69 5 93 5 81 6 66 6 46 6 77 5 68 5 92 5 57
220104 at 5 56 5 64 5 78 4 91 5 12 4 87 5 74 6 13 5 92 4 84 4 90 4 76
220230_s_at 6 25 6 03 5 90 5 23 5 32 5 40 5 96 6 20 6 15 5 32 5 28 5 16
220235 s at 9 03 8 80 9 04 4 08 4 13 4 15 8 85 8 71 8 92 5 71 5 91 6 56
220784_s_at 6 05 5 80 6 04 4 49 4 31 4 65 5 86 5 58 5 90 4 74 4 35 4 55
221081 s at 7 68 7 82 8 21 5 48 5 55 5 38 7 35 7 55 7 25 6 27 6 33 6 14
Log2 fluorescence intensity
Probesets Ly1 (A1 ) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
221349_at 7 42 7 98 8 39 3 97 4 10 3 83 7 19 7 15 7 10 4 75 4 85 4 35
221641 s at 7 16 7 32 7 50 5 60 6 19 5 85 7 84 7 82 7 88 5 82 5 78 5 71
221666_s_at 8 11 8 25 8 15 5 95 5 54 5 61 8 25 7 98 8 13 549 5 41 5 20
221690_s_at 7 11 7 15 7 54 5 42 5 46 5 57 7 43 7 35 7 34 5 47 5 52 5 40
36030_at 7 98 8 10 8 39 6 83 7 22 7 17 8 18 8 13 8 20 7 40 7 19 7 49
51158 at 5 40 5 54 5 45 4 86 4 90 4 91 5 53 5 70 5 52 5 14 4 94 4 94
207714_s_at 7 38 7 55 7 30 6 27 6 32 6 51 7 61 7 56 7 33 6 76 6 88 6 67
208816 x at 7 91 7 98 8 01 6 91 6 96 6 75 8 01 7 87 7 89 7 15 7 11 7 26
211566 x_at 7 57 7 44 7 39 7 01 6 99 6 95 7 42 7 33 7 32 7 15 7 11 7 03
212235 at 5 90 5 93 5 80 4 96 5 24 5 01 6 19 6 33 6 14 4 83 5 00 4 98
Table 3B: Genes With Reduced Expression in CD40-Sensitive Cell Lines t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title 4-.
FDR Cutoff 1 OE-02 8 2E-03 1 2E-02 9 4E-03
200068_s_at 1 7E-03 1 OE-03 5 5 66EE--0033 5 5 22EE--0044 Yes CANX Hs 155560 calnexin
200670_at 3 2E-04 2 5E-03 9 9 OOEE--0044 6 6 11 EE--0033 Yes XBP1 Hs 437638 X-box binding protein 1
200701_at 4 7E-03 2 2E-03 1 1 11 EE--0022 5 5 66EE--0033 Yes NPC2 Hs 433222 Niemann-Pick disease, type C2
200736_s_at 6 2E-03 1 4E-03 7 7 77EE--0044 2 2 11 EE--0044 Yes GPX1 Hs 76686 glutathione peroxidase 1
200765_x_at 1 2E-04 7 OE-04 8 8 OOEE--0055 6 6 11 EE--0055 Yes CTNNA1 Hs 254321 catenin (cadherin-associated protein), alpha
1 , 102kDa
200814 at 5 5E-03 1 6E-04 2 2 22EE--0033 5 5 99EE--0055 Y Yeess PSME1 Hs 75348 proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)
200846 s at 9 4E-03 4 9E-03 6 9E-04 1 2 E-03 Yes PPP1CA Hs 183994 protein phosphatase 1 , catalytic subunit, alpha isoform
200887 s at 4 8E-03 2 4E-04 5 1 E-03 1 7E-04 Yes STAT1 Hs 21486 signal transducer and activator of transcription 1 , 91kDa
200905_x_at 1 1 E-03 9 5E-05 5 7E-04 2 8 E-05 Yes HLA-E Hs 381008 major histocompatibility complex, class I, E 200936_at 1 1 E-04 1 3E-03 1 2 E-03 6 6E-03 Yes RPL8 Hs 178551 ribosomal protein L8 200941_at 4 2E-03 2 5E-03 9 5E-03 7 2E-03 Yes HSBP1 Hs 250899 heat shock factor binding protein 1 201011_at 1 9E-03 4 3E-03 1 6E-03 2 6E-03 Yes RPN1 Hs 2280 ribophorin I 201160_s_at 1 9E-03 9 OE-05 2 7E-03 1 4E-04 Yes CSDA Hs 221889 cold shock domain protein A 201161_s_at 2 8E-03 3 1 E-05 7 3E-03 3 OE-05 Yes CSDA Hs 221889 cold shock domain protein A 201200 at 9 9E-03 3 5E-03 4 9E-03 2 2E-03 Yes CREG Hs 5710 cellular repressor of E1 A-stimulated genes
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene It Gene Title
201204_s_at 3 5E-03 5 5E-03 1 1 E-03 7 6E-04 Yes RRBP1 Hs 98614 ribosome binding protein 1 homolog 18OkDa (dog)
201206_s_at 6 1 E-03 2 2E-03 1 9E-03 7 3E-04 Yes RRBP1 Hs 98614 ribosome binding protein 1 homolog 18OkDa (dog)
201226_at 2 9E-06 5 8E-04 2 8E-04 7 7E-03 Yes NDUFB8 Hs 198273 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa
201263 at 1 8E-03 1 6E-03 1 OE-03 8 5E-04 Yes TARS Hs 84131 threonyl-tRNA synthetase
201307 at 6 6E-04 7 6E-05 2 OE-03 5 4E-05 Yes FLJ10849 Hs 386784 hypothetical protein FLJ 10849
201398_s_at 1 7E-03 2 7E-04 1 4E-04 6 OE-04 Yes TRAM1 Hs 4147 translocation associated membrane protein 1
201399 s at 1 2E-03 4 3E-05 2 3E-03 5 9E-05 Yes TRAM1 Hs 4147 translocation associated membrane protein 1
201470_at 1 3E-05 1 6E-04 4 5E-04 1 OE-03 Yes GSTO1 Hs 11465 glutathione S-transferase omega 1
201487 at 5 9E-03 2 7E-03 3 6E-03 1 2 E-03 Yes CTSC Hs 128065 cathepsin C
201499_s_at 1 1 E-03 4 3E-03 9 OE-04 2 3E-03 Yes USP7 Hs 386939 ubiquitin specific protease 7 (herpes virus- associated)
201566_x_at 2 6E-03 2 8E-04 3 9E-03 1 8 E-03 Yes ID2 Hs 180919 inhibitor of DNA binding 2, dominant negative hehx-loop-helix protein
201590 x at 2 6E-05 3 3E-05 2 1 E-05 3 4E-05 Yes ANXA2 Hs 462864 annexin A2
201601_x_at 6 5E-03 2 9E-03 2 OE-06 1 1 E-06 Yes IFITM1 Hs 458414 interferon induced transmembrane protein 1 (9-27)
201649 at 7 OE-03 3 6E-04 6 7E-03 5 3E-04 Yes UBE2L6 Hs 425777 ubiquitin-conjugating enzyme E2L 6
201746_at 2 2E-04 1 6E-03 2 5E-04 1 8E-03 Yes TP53 Hs 408312 tumor protein p53 (Li-Fraumeni syndrome)
201874 at 3 8E-03 4 6E-04 7 OE-03 6 OE-04 Yes FLJ21047 Hs 512729 hypothetical protein FLJ21047
201937_s_at 9 3E-03 8 5E-04 2 8E-03 4 1 E-03 Yes DNPEP Hs 258551 aspartyl aminopeptidase
201968 s at 3 3E-03 2 9E-04 1 4E-03 1 4E-04 Yes PGM 1 Hs 1869 phosphoglucomutase 1
202096_s_at 6 4E-03 6 2E-04 2 2E-04 1 OE-05 Yes BZRP Hs 202 benzodiazepine receptor (peripheral)
202123_s_at 2 OE-03 1 5E-03 1 9E-03 4 OE-03 Yes ABL1 Hs 446504 v-abl Abelson murine leukemia viral oncogene homolog 1
202261_at 2 6E-03 4 1 E-03 2 7E-03 5 2E-03 Yes TCFL1 Hs 2430 transcription factor-like 1
202279 at 2 OE-03 3 OE-03 1 4E-03 1 OE-03 Yes C14orf2 Hs 109052 chromosome 14 open reading frame 2
202315_s_at 6 9E-05 9 OE-05 9 9E-04 1 8E-03 Yes BCR Hs 446394 breakpoint cluster region
202382 s at 5 2E-03 6 7E-05 2 3E-03 3 8E-05 Yes GNPDA1 Hs 278500 glucosamιne-6-phosphate deaminase 1
202429_s_at 2 4E-04 2 1 E-03 1 OE-03 6 9E-03 Yes PPP3CA Hs 272458 protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)
202443_x_at 3 5E-03 5 1 E-05 1 4E-03 2 2E-05 Yes NOTCH2 Hs 8121 Notch homolog 2 (Drosophila)
202447 at 1 8E-03 3 8E-03 6 8E-03 5 4E-03 Yes DECR1 Hs 414754 2,4-dιenoyl CoA reductase 1 , mitochondrial
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title 202457 s at 1 1E-03 2 4E-03 1 6E-03 4 2E-03 Yes PPP3CA Hs 272458 protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)
202536_at 5 4E-03 1 9E-03 4 OE-03 2 3E-03 Yes DKFZP564O12 Hs 11449 DKFZP564O123 protein 3
202696_at 9 2E-03 5 8E-03 5 5E-03 4 2E-03 Yes OSR1 Hs 95220 oxidative-stress responsive 1 202732_at 1 3E-03 2 2E-04 1 2E-03 1 7E-04 Yes PKIG Hs 3407 protein kinase (cAMP-dependent, catalytic) inhibitor gamma
202811_at 1 5E-04 1 1E-03 1 6E-04 1 5E-03 Yes AMSH Hs 12479 associated molecule with the SH3 domain of
STAM
202982_s_at 4 2E-04 1 OE-04 1 OE-03 5 1 E-05 Yes ZAP128 Hs 446685 peroxisomal long-chain acyl-coA thioesterase
203031_s_at 2 1E-04 8 1E-04 3 3E-04 6 8E-04 Yes UROS Hs 75593 uroporphyrinogen III synthase (congenital erythropoietic porphyria)
203113_s_at 92E-03 5 6E-03 1 OE-02 4 1E-03 Yes EEF1D Hs 334798 eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein) J-.
203142_s_at 1 7E-05 1 5E-04 3 5E-03 8 OE-03 Yes AP3B1 Hs 446648 adaptor-related protein complex 3, beta 1 subunit
203217_s_at 1 5E-03 1 5E-03 4 OE-03 7 7E-05 Yes SIAT9 Hs 415117 sialyltransferase 9 (CMP-
NeuAc lactosylceramide alpha-2,3- sialyltransferase, GM3 synthase)
203335_at 1 2E-05 1 5E-04 44E-04 8 9E-04 Yes PHYH Hs 172887 phytanoyl-CoA hydroxylase (Refsum disease)
203343_at 6 3E-03 3 9E-03 4 9E-03 5 3E-03 Yes UGDH Hs 28309 UDP-glucose dehydrogenase
203459_s_at 5 OE-03 1 5E-03 9 OE-03 4 1E-03 Yes Hs 188838 vacuolar protein sorting protein 16
203659_s_at 4 7E-03 1 1E-03 1 8E-03 8 9E-04 Yes RFP2 Hs 436922 ret finger protein 2
203825_at 5 1E-03 4 2E-03 5 7E-04 1 3E-04 Yes BRD3 Hs 86896 bromodomain containing 3
203957_at 6 1E-03 2 2E-03 2 4E-03 8 6E-05 Yes E2F6 Hs 135465 E2F transcription factor 6
204003_s_at 3 5E-03 3 9E-04 6 5E-03 4 7E-04 Yes NUPL2 Hs 408241 nucleopoπn like 2
204044 at 9 2E-04 7 1E-04 9 1E-04 4 OE-03 Yes QPRT Hs 335116 quinolinate phosphoribosyltransferase
(πicotmate-nucleotide pyrophosphorylase
(carboxylating))
204168_at 3 OE-06 1 3E-05 5 OE-05 2 2E-04 Yes MGST2 Hs 81874 microsomal glutathione S-transferase 2 204172_at 6 1E-03 3 9E-03 4 9E-03 5 5E-03 Yes CPO Hs 89866 coproporphyrinogen oxidase
(coproporphyria, harderoporphyπa)
204220 at 6 7E-03 2 1E-04 8 6E-03 2 4E-04 Yes GMFG Hs 5210 gha maturation factor, gamma
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title
204234 s at 8 9E-03 2 OE-03 1 1 E-02 2 5E-03 Yes ZNF195 Hs 104382 zinc finger protein 195
204256_at 7 4E-03 1 8E-03 3 3E-03 8 OE-04 Yes ELOVL6 Hs 211556 ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3- I ike, yeast)
204279_at 3 2E-03 6 5E-04 3 8E-04 1 5E-04 Yes PSMB9 Hs 381081 proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2)
204326_x_ at 5 4E-06 7 7E-05 9 OE-05 1 5E-03 Yes MT1X Hs 374950 metallothionein 1X
204386 s at 2 1 E-04 3 OE-03 7 9E-04 6 OE-03 Yes MRP63 Hs 458367 mitochondrial ribosomal protein 63
204418_x_ at 8 7E-04 2 8E-03 3 4E-03 5 4E-03 Yes GSTM2 Hs 279837 glutathione S-transferase M2 (muscle)
204565 at 64E-04 2 1E-04 3 6E-03 9 8E-05 Yes THEM2 Hs 9676 thioesterase superfamily member 2
204766_s_ at 1 6E-04 3 2E-04 4 6E-04 4 4E-03 Yes NUDT1 Hs 413078 nudix (nucleoside diphosphate linked moiety X)-type motif 1
204769_s_ at 8 7E-04 4 7E-04 2 3E-03 3 9E-06 Yes TAP2 Hs 502 transporter 2, ATP-binding cassette, subfamily B (MDR/TAP)
204779 s at 2 1 E-03 1 6E-05 5 2E-03 4 8E-03 Yes HOXB7 Hs 436181 homeo box B7
OO
204806_x_ at 4 4E-04 3 5E-05 2 6E-03 1 5E-04 Yes HLA-F Hs 411958 major histocompatibility complex, class I, F
204937 s at 2 OE-04 2 9E-03 1 2E-04 1 2E-03 Yes ZNF274 Hs 83761 zinc finger protein 274
205048_s_ at 2 1E-05 3 7E-03 1 2E-04 1 7E-03 Yes — —
205297_s_ at 7 OE-04 3 1 E-03 1 1 E-03 6 3E-04 Yes CD79B Hs 89575 CD79B antigen (immunoglobulin-associated beta)
205659_at 7 2E-03 6 1 E-03 3 4E-03 4 6E-03 Yes HDAC9 Hs 487662 histone deacetylase 9
206928 at 3 2E-03 3 OE-03 9 9E-03 3 8E-03 Yes ZNF124 Hs 458362 zinc finger protein 124 (HZF-16)
207181_s_ at 3 2E-03 1 9E-03 9 OE-03 5 8E-03 Yes CAS P7 Hs 9216 caspase 7, apoptosis-related cysteine protease
207304_at 3 4E-03 4 5E-03 1 4E-03 2 4E-03 Yes ZNF45 Hs 381285 zinc finger protein 45 (a Kruppel-assoαated box (KRAB) domain polypeptide)
207585 s at 4 9E-03 8 OE-04 9 4E-03 1 7E-03 Yes RPL36AL Hs 444749 ribosomal protein L36a-lιke
207777 s at 2 4E-04 5 8E-04 1 1 E-04 2 4E-04 Yes SP140 Hs 399826 SP140 nuclear body protein
207809_s_ at 6 1 E-03 7 1 E-03 1 OE-03 4 8E-03 Yes ATP6AP1 Hs 6551 ATPase, H+ transporting, lysosomal accessory protein 1
208490_x_ at 2 7E-03 6 5E-03 2 3E-03 3 2E-03 Yes HIST1 H2BG Hs 182137 histone 1 , H2bg
208527 x at 4 7E-05 4 8E-03 1 9E-03 1 5E-03 Yes HIST1 H2BE Hs 182138 histone 1 , H2be
208579 x at 3 6E-04 6 3E-04 2 5E-04 3 1 E-04 Yes H2BFS Hs 473961 H2B histone family, member S
208581_x_ at 6 9E-04 4 9E-03 7 8E-04 6 3E-03 Yes MT1X Hs 374950 metallothionein 1X
208690 s at 6 OE-05 8 4E-05 3 OE-05 1 5E-05 Yes PDLIM1 Hs 75807 PDZ and LIM domain 1 (elfin)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title
208729_x_at 1 7E-03 2 2E-05 1 2E-04 1 8E-04 Yes HLA-B Hs 77961 major histocompatibility complex, class I, B
208812 x at 5 3E-04 8 6E-08 7 1 E-04 9 3E-08 Yes HLA-C Hs 274485 major histocompatibility complex, class I, C
208918_s_at 7 1 E-04 1 7E-03 5 5E-03 2 6E-03 Yes FLJ 13052 Hs 220324 NAD kinase
209040_s_at 6 1 E-04 8 3E-04 5 OE-04 9 3E-04 Yes PSMB8 Hs 180062 proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease
7)
209112_at 8 7E-05 2 3E-03 1 6E-04 1 9E-03 Yes CDKN 1 B Hs 238990 cyclin-dependent kinase inhibitor 1 B (p27,
Kιp1)
209124_at 8 2E-03 3 5E-03 1 9E-03 5 5E-04 Yes MYD88 Hs 82116 myeloid differentiation primary response gene (88)
209138_x_at 1 4E-05 5 8E-03 1 3E-06 4 OE-03 Yes IGL@ Hs 458262 immunoglobulin lambda locus
209140_x_at 6 OE-04 1 4E-04 3 6E-04 6 9E-05 Yes HLA-B Hs 77961 major histocompatibility complex, class I, B
209175 at 6 3E-03 5 9E-03 5 5E-03 7 1 E-03 Yes SEC23IP Hs 300208 SEC23 interacting protein
209201_x_at 1 2E-03 7 3E-04 1 1 E-02 5 6E-03 Yes CXCR4 Hs 421986 chemokine (C-X-C motif) receptor 4
209472 at 5 4E-05 9 6E-04 1 9E-05 8 5E-04 Yes LOC56267 Hs 134460 hypothetical protein 669
209476_at 3 7E-03 7 7E-03 5 3E-03 8 8E-03 Yes TXNDC Hs 125221 thioredoxin domain containing -P-
209591_s_at 4 1E-03 3 9E-04 8 9E-04 2 7E-04 Yes BMP7 Hs 170195 bone morphogenetic protein 7 (osteogenic protein 1)
209970_x_at 8 9E-04 1 OE-03 1 OE-03 1 2E-03 Yes CASP1 Hs 2490 caspase 1 , apoptosis-related cysteine protease (interleukin 1 , beta, convertase)
209995 s at 6 OE-04 7 8E-06 1 4E-03 2 9E-05 Yes TCL1A Hs 2484 T-cell leukemia/lymphoma 1A
210136_at 4 5E-03 2 OE-04 6 9E-04 6 6E-04 Yes MBP Hs 408543 myelin basic protein
210844_x_at 8 1 E-03 2 8E-04 8 OE-04 3 8E-05 Yes CTNNA1 Hs 254321 catenin (cadherin-associated protein), alpha
1 , 102kDa
211061_s_at 2 3E-03 6 OE-03 3 OE-03 7 5E-03 Yes MGAT2 Hs 93338 mannosyl (alpha-1 ,6-)-glycoproteιn beta-1 ,2-
N-acetylglucosamιnyltransferase
211089_s_at 1 3E-03 1 8E-03 2 6E-03 3 4E-03 Yes NEK3 Hs 2236 NIMA (never in mitosis gene a)-related kinase 3
211366_x_at 8 1 E-05 5 4E-04 2 4E-04 3 5E-04 Yes CASP1 Hs 2490 caspase 1 , apoptosis-related cysteine protease (interleukin 1 , beta, convertase)
211528_x_at 1 5E-03 5 1 E-04 1 4E-03 1 9E-04 Yes HLA-G Hs 512152 HLA-G histocompatibility antigen, class I, G
211529 x at 1 1 E-03 2 4E-04 1 7E-03 1 1 E-03 Yes HLA-G Hs 512152 HLA-G histocompatibility antigen, class I, G
211530_x_at 1 9E-03 1 5E-05 3 2E-03 7 OE-04 Yes HLA-G Hs 512152 HLA-G histocompatibility antigen, class I1 G
211799_x_at 3 5E-03 9 9E-04 1 9E-03 3 3E-04 Yes HLA-C Hs 274485 major histocompatibility complex, class I1 C
211911 x at 1 3E-05 2 4E-06 9 6E-05 1 3E-05 Yes HLA-B Hs 77961 major histocompatibility complex, class I, B
211919 s at 7 8E-04 4 6E-04 1 1 E-02 5 1 E-03 Yes CXCR4 Hs 421986 chemokine (C-X-C motif) receptor 4
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title
211989_at 8 8E-04 3 5E-03 1 3E-03 2 2E-03 Yes SMARCE1 Hs 437546 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1
212057 at 1 9E-04 34E-03 2 1E-04 9 OE-04 Yes KIAA0182 Hs 222171 KIAA0182 protein
212071_s_at 3 9E-06 7 OE-04 2 7E-06 7 8E-04 Yes SPTBN1 Hs 205401 spectrin, beta, non-erythrocytic 1
212149 at 5 6E-03 4 8E-04 5 2E-03 5 7E-04 Yes KIAA0143 Hs 84087 KIAA0143 protein
212382_at 5 7E-03 3 5E-03 1 4E-03 8 1E-04 Yes TCF4 Hs 359289 transcription factor 4
212385 at 1 5E-03 4 7E-04 5 5E-03 1 6E-03 Yes TCF4 Hs 359289 transcription factor 4
212386_at 2 1E-04 2 OE-03 34E-05 2 9E-03 Yes TCF4 Hs 359289 transcription factor 4
212387_at 5 9E-04 2 5E-05 5 OE-06 1 2E-04 Yes TCF4 Hs 359289 transcription factor 4
212408_at 1 2E-03 5 9E-03 1 1E-03 64E-03 Yes LAP1B Hs 234265 lamina-associated polypeptide 1 B
212446 s at 64E-05 96E-04 2 6E-03 7 5E-03 Yes LOC253782 Hs 503941 hypothetical protein LOC253782
212507_at 1 2E-03 4 3E-03 4 7E-03 2 6E-03 Yes RW1 Hs 318783 RW1 protein
212547 at 1 4E-04 4 7E-03 2 5E-04 1 4E-03 Yes — Hs 6580 Homo sapiens clone 23718 mRNA sequence
212739_s_at 1 7E-04 1 9E-03 1 4E-04 8 7E-04 Yes NME4 Hs 9235 non-metastatic cells 4, protein expressed in
212774 at 1 7E-03 3 OE-04 1 3E-03 2 OE-04 Yes ZNF238 Hs 446677 zinc finger protein 238 O
212792_at 6 2E-03 6 5E-03 1 5E-05 7 7E-03 Yes KIAA0877 Hs 408623 KIAA0877 protein
212798_s_at 6 6E-04 8 2E-05 3 8E-04 5 9E-05 Yes DKFZP564O04 Hs 112605 hypothetical protein DKFZp564O043
O
O
212946_at 1 4E-03 1 1E-04 44E-03 7 1E-04 Yes KIAA0564 Hs 405457 KIAA0564 protein
213020_at 8 5E-03 2 9E-03 4 1E-03 2 6E-03 Yes GOSR 1 Hs 124436 golgi SNAP receptor complex member 1
213116_at 6 7E-04 7 9E-04 1 5E-04 2 1E-04 Yes NEK3 Hs 2236 NIMA (never in mitosis gene a)-related kinase 3
213233 s at 7 7E-04 7 3E-05 4 9E-04 6 5E-04 Yes KIAA1354 Hs 147717 KIAA1354 protein
213293_s_at 8 1E-03 3 2E-03 3 9E-04 1 5E-04 Yes TRIM22 Hs 318501 tripartite motif-containing 22
213357_at 8 8E-03 7 4E-04 5 7E-03 5 6E-04 Yes — Hs 356224 Homo sapiens cDNA clone IMAGE 4446165, partial cds
213361_at 6 3E-03 1 5E-04 7 4E-03 2 7E-03 Yes PCTAIRE2BP Hs 416543 tudor repeat associator with PCTAIRE 2
213435_at 6 2E-03 1 6E-03 1 OE-03 1 8E-03 Yes SATB2 Hs 412327 SATB family member 2
213793_s_at 5 3E-03 1 8E-03 1 OE-02 3 2E-03 Yes HOMER1 Hs 129051 homer homolog 1 (Drosophila)
213891_s_at 1 6E-04 6 7E-04 9 5E-05 5 3E-04 Yes TCF4 Hs 359289 transcription factor 4
214022_s_at 3 8E-04 1 6E-03 1 1 E-03 9 OE-05 Yes IFITM1 Hs 458414 interferon induced transmembrane protein 1
(9-27)
214032_at 3 5E-04 5 5E-04 1 OE-03 2 2E-04 Yes ZAP70 Hs 234569 zeta-chain (TCR) associated protein kinase
7OkDa
214172 x at 4 OE-04 4 7E-04 2 6E-04 2 9E-04 Yes RYK Hs 285346 RYK receptor-like tyrosine kinase
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene IC Gene Title
214369_s_at 2 4E-03 1 OE-03 7 9E-03 4 4E-04 Yes RASGRP2 Hs 99491 RAS guanyl releasing protein 2 (calcium and
DAG-regulated)
214394_x_at 4 2E-04 4 9E-04 1 2E-03 2 OE-03 Yes EEF1 D Hs 334798 eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)
214459_x_at 7 3E-03 2 8E-03 1 7E-03 9 OE-04 Yes HLA-C Hs 274485 major histocompatibility complex, class I, C
214512_s_at 5 3E-06 9 6E-05 2 2E-04 2 3E-04 Yes PC4 Hs 229641 activated RNA polymerase Il transcription cofactor 4
214677_x_at 3 9E-07 9 9E-04 3 OE-06 1 5E-03 Yes IGLJ3 Hs 449601 immunoglobulin lambda joining 3
214749 s at 6 2E-04 1 8E-03 2 5E-04 2 6E-03 Yes FLJ20811 Hs 83530 hypothetical protein FLJ20811
214835_s_at 1 1E-03 5 6E-03 1 OE-03 5 3E-03 Yes SUCLG2 Hs 446476 succinate-CoA hgase, GDP-forming, beta subunit
214916_x_at 2 6E-03 6 5E-04 9 5E-03 7 9E-04 Yes — Hs 448957 Homo sapiens partial mRNA for IgM immunoglobulin heavy chain variable region
(IGHV gene), clone LIBPM376
215121_x_at 7 2E-04 2 7E-03 1 1E-03 3 9E-03 Yes — Hs 356861 Homo sapiens cDNA FLJ26905 fis, clone
RCT01427, highly similar to Ig lambda chain
C regions
215516_at 7 3E-03 7 7E-03 3 OE-03 4 OE-03 Yes LAM B4 Hs 62022 laminin, beta 4
215772_x_at 4 3E-03 6 3E-03 5 4E-04 1 6E-03 Yes SUCLG2 Hs 446476 succinate-CoA hgase, GDP-forming, beta subunit
215946_x_at 1 6E-03 1 1 E-03 4 8E-05 6 5E-04 Yes — Hs 272302 Homo sapiens, clone IMAGE 5728597, mRNA
216526_x at 1 7E-03 2 1E-07 2 2E-03 2 6E-07 Yes HLA-C Hs 274485 major histocompatibility complex, class I, C
216733_s_at 5 9E-05 1 2E-03 6 5E-05 5 6E-05 Yes GATM Hs 75335 glycine aminotransferase (L- argmine glycine aminotransferase)
216973_s at 6 3E-04 3 9E-03 5 5E-03 7 4E-04 Yes HOXB7 Hs 436181 homeo box B7
216976_s_at 1 2E-05 3 2E-03 1 1E-02 1 2E-03 Yes RYK Hs 285346 RYK receptor-like tyrosine kinase
217028_at 2 8E-03 4 OE-05 1 1E-03 8 6E-04 Yes — —
217436_x_at 1 6E-03 1 OE-04 2 2E-03 5 9E-04 Yes — —
217456 x at 2 5E-04 6 4E-05 6 9E-05 1 8E-04 Yes HLA-E Hs 381008 major histocompatibility complex, class I, E
217809_at 1 7E-05 2 2E-03 2 1E-05 3 OE-03 Yes BZW2 Hs 5216 basic leucine zipper and W2 domains 2
217839_at 5 6E-03 2 3E-04 8 8E-04 6 7E-04 Yes TFG Hs 446568 TRK-fused gene
217911_s_at 3 2E-03 1 1 E-03 8 4E-04 1 7E-03 Yes BAG3 Hs 15259 BCL2-assocιated athanogene 3
217940_s_at 1 4E-04 7 1E-03 1 4E-03 2 7E-03 Yes FLJ 10769 Hs 8083 hypothetical protein FLJ10769
217950_at 8 2E-04 4 5E-04 3 2E-03 2 3E-03 Yes NOSIP Hs 7236 nitric oxide synthase interacting protein
217988 at 1 4E-03 2 2E-03 2 4E-04 1 1 E-03 Yes C14orf18 Hs 107003 chromosome 14 open reading frame 18
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene l[ Gene Title
218026 at 1 1 E-03 6 6E-03 1 1 E-03 6 3E-04 Yes HSPC009 Hs 16059 HSPC009 protein
218093_s_at 3 3E-04 6 1 E-04 2 OE-03 5 2E-03 Yes ANKRD10 Hs 164969 ankyrin repeat domain 10
218100 s at 5 3E-04 3 9E-03 6 5E-04 7 3E-03 Yes ESRRBL1 Hs 170318 estrogen-related receptor beta like 1
218187_s_at 4 2E-03 4 8E-03 3 3E-03 4 OE-03 Yes FLJ20989 Hs 169615 hypothetical protein FLJ20989
218224 at 1 5E-03 1 7E-03 1 4E-05 1 8E-05 Yes PNMA1 Hs 194709 paraneoplastic antigen MA1
218276_s_at 1 3E-03 1 1 E-04 2 3E-04 1 1E-04 Yes SAV1 Hs 257341 Salvador homolog 1 (Drosophila)
218285_s_at 1 4E-03 5 OE-04 2 4E-03 6 3E-04 Yes DHRS6 Hs 124696 dehydrogenase/reductase (SDR family) member 6
218316_at 42E-03 3 OE-04 9 7E-03 6 2E-04 Yes TIMM9 Hs 440525 translocase of inner mitochondrial membrane
9 homolog (yeast)
218343_s_at 1 OE-03 1 5E-03 4 3E-04 1 7E-03 Yes GTF3C3 Hs 512838 general transcription factor INC, polypeptide
3, 102kDa
218358_at 7 9E-04 5 7E-04 3 7E-03 2 6E-03 Yes MGC11256 Hs 28029 hypothetical protein MGC11256
218377_s_at 1 5E-03 6 1 E-04 2 7E-03 8 OE-04 Yes C21orf6 Hs 34136 chromosome 21 open reading frame 6
218490_s_at 1 OE-02 3 7E-03 6 2E-03 2 9E-03 Yes ZNF302 Hs 436350 zinc finger protein 302
218491_s_at 4 4E-03 3 5E-03 3 1 E-03 8 4E-03 Yes THY28 Hs 13645 likely ortholog of the mouse thymocyte protein Thy28
218543 s at 1 1 E-03 3 4E-04 1 2E-04 4 5E-04 Yes ZC3HDC1 Hs 12646 zinc finger CCCH type domain containing 1
218557_at 1 1 E-05 3 OE-05 3 OE-03 3 9E-04 Yes NIT2 Hs 439152 Nit protein 2
218633 x at 2 1 E-04 3 3E-03 4 1 E-04 4 OE-03 Yes FLJ 11342 Hs 266514 hypothetical protein FLJ11342
218648_at 3 9E-03 5 3E-04 4 OE-03 5 4E-04 Yes FLJ21868 Hs 434956 hypothetical protein FLJ21868
218735_s_at 5 3E-03 1 6E-03 5 7E-04 6 6E-04 Yes AF020591 Hs 438994 zinc finger protein
218738_s_at 2 7E-03 3 8E-03 64E-04 9 5E-04 Yes RNF138 Hs 180403 ring finger protein 138
218773 s at 2 1 E-03 6 4E-03 2 3E-03 9 2E-03 Yes PILB Hs 461420 pilin-like transcription factor
219008_at 2 OE-03 5 2E-03 1 4E-03 1 9E-03 Yes FLJ21820 Hs 63300 hypothetical protein FLJ21820
219184_x_at 1 9E-03 2 3E-04 1 OE-02 7 9E-03 Yes TIMM22 Hs 87595 translocase of inner mitochondrial membrane
22 homolog (yeast)
219209_at 4 3E-03 7 4E-04 1 3E-03 4 4E-04 Yes MDA5 Hs 389539 melanoma differentiation associated protein-
5
219215_s_at 2 9E-03 5 OE-05 3 2E-03 6 7E-05 Yes SLC39A4 Hs 411274 solute carrier family 39 (zinc transporter), member 4
219248 at 1 5E-03 5 1E-03 1 7E-03 1 9E-03 Yes C2orf8 Hs 368545 chromosome 2 open reading frame 8
219471_at 4 7E-03 3 7E-03 3 OE-03 2 9E-03 Yes C13orf18 Hs 413071 chromosome 13 open reading frame 18
219489 s at 2 2E-04 1 5E-03 3 7E-04 2 OE-03 Yes RHBDL2 Hs 133999 rhomboid, veinlet-like 2 (Drosophila)
219563_at 3 9E-05 1 8E-05 3 4E-05 3 4E-04 Yes C14orf139 Hs 41502 chromosome 14 open reading frame 139
219664 s at 1 9E-03 2 4E-03 7 9E-04 1 OE-03 Yes DECR2 Hs 15898 2,4-dιenoyl CoA reductase 2, peroxisomal
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title
219767 _s_at 3 9E-03 3 3E-03 1 9E-03 1 OE-03 Yes CRYZL1 Hs 352671 crystallin, zeta (quinone reductase)-lιke 1
219822 _at 6 3E-04 7 5E-03 7 3E-04 7 1 E-03 Yes MTRF1 Hs 348472 mitochondrial translational release factor 1
220741 _s_at 1 OE-03 4 5E-05 7 8E-05 6 4E-04 Yes PPA2 Hs 421825 inorganic pyrophosphatase 2
221234 _s_at 5 9E-04 4 7E-04 3 2E-03 3 4E-04 Yes BACH2 Hs 88414 BTB and CNC homology 1, basic leucine zipper transcription factor 2
221614 _s_at 6 4E-03 3 8E-03 1 9E-03 2 6E-04 Yes RPH3AL Hs 437436 rabphihn 3A-lιke (without C2 domains)
221847 _at 2 OE-03 1 6E-03 1 1 E-02 5 OE-03 Yes TAS2R14 Hs 278469 taste receptor, type 2, member 14
221874 _at 6 OE-03 1 9E-03 1 4E-03 2 4E-04 Yes KIAA1324 Hs 104696 mabai
221875 _x_at 3 1 E-03 6 3E-04 8 5E-04 8 3E-05 Yes HLA-F Hs 411958 major histocompatibility complex, class I, F
222146 _s_at 1 1 E-03 4 3E-04 3 8E-03 2 4E-03 Yes TCF4 Hs 359289 transcription factor 4
35671_ at 1 3E-04 6 1E-04 6 OE-04 4 1E-04 Yes GTF3C1 Hs 331 general transcription factor IHC, polypeptide
1 , alpha 22OkDa
36830 at 3 5E-04 1 5E-03 9 OE-03 6 4E-03 Yes MIPEP Hs 68583 mitochondrial intermediate peptidase
36936_ at 7 6E-03 6 4E-06 1 OE-02 2 OE-04 Yes TSTA3 Hs 404119 tissue specific transplantation antigen P35B
37384_ at 3 1 E-04 4 9E-03 2 7E-04 3 5E-03 Yes PPM1 F Hs 278441 protein phosphatase 1 F (PP2C domain containing) 1>J
39318 at 3 2E-04 3 8E-04 2 7E-04 1 2E-04 Yes TCL1A Hs 2484 T-cell leukemia/lymphoma 1A
40148_ at 1 9E-03 1 6E-04 1 2E-02 5 8E-03 Yes APBB2 Hs 324125 amyloid beta (A4) precursor protein-binding, family B, member 2 (Fe65-lιke)
200660 _at 3 1 E-05 1 3E-04 4 7E-04 1 4E-03 Yes S100A11 Hs 417004 S100 calcium binding protein A11
(calgizzarin)
200671 _s_at 2 2E-04 1 1 E-04 1 8E-03 5 OE-04 Yes SPTBN1 Hs 205401 spectrin, beta, non-erythrocytic 1
200672 _x_at 1 2E-03 1 3E-03 9 7E-04 1 5E-03 Yes SPTBN 1 Hs 205401 spectrin, beta, non-erythrocytic 1
200704 _at 3 3E-04 3 3E-04 2 6E-04 2 4E-04 Yes LITAF Hs 76507 lipopolysaccharide-induced TNF factor
200706 _s_at 2 2E-05 1 8E-04 1 2E-03 3 1 E-03 Yes LITAF Hs 76507 lipopolysaccharide-induced TNF factor
200782 at 1 5E-04 5 9E-04 5 6E-05 9 4E-05 Yes ANXA5 Hs 145741 annexin A5
200923 _at 1 8E-04 2 7E-04 7 5E-06 7 5E-06 Yes LGALS3BP Hs 79339 lectin, galactoside-binding, soluble, 3 binding protein
201005 _at 1 1E-04 2 7E-04 2 4E-06 1 OE-05 Yes CD9 Hs 387579 CD9 antigen (p24)
201426 _s_at 3 3E-05 1 OE-03 2 2E-04 5 5E-04 Yes VIM Hs 435800 vimentin
201485 _s_at 9 7E-04 9 1E-07 1 OE-02 1 1 E-03 Yes RCN2 Hs 79088 reticulocalbin 2, EF-hand calcium binding domain
201792 _at 3 1 E-04 6 OE-04 8 2E-04 1 5E-03 Yes AEBP1 Hs 439463 AE binding protein 1
202218 s at 5 1 E-03 2 2E-03 4 1 E-03 1 6E-03 Yes FADS2 Hs 388164 fatty acid desaturase 2
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title 202283_at 3 1 E-03 4 1E-03 2 1E-03 2 9E-03 Yes SERPINF1 Hs 173594 serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1
202719 s at 84E-04 2 1E-03 2 4E-03 3 OE-04 Yes TES Hs 129129 testis derived transcript (3 LIM domains) 202855_s_at 4 OE-03 2 1 E-03 4 4E-03 7 7E-04 Yes SLC16A3 Hs 386678 solute carrier family 16 (monocarboxylic acid transporters), member 3
202856_s_at 2 OE-03 1 2E-03 8 7E-04 1 4E-03 Yes SLC16A3 Hs 386678 solute carrier family 16 (monocarboxylic acid transporters), member 3
203045_at 1 OE-03 3 8E-04 3 3E-03 2 7E-03 Yes NINJ1 Hs 11342 ninjuπn 1 203063_at 8 0E-04 6 8E-04 1 2E-03 8 9E-04 Yes PPM1 F Hs 278441 protein phosphatase 1 F (PP2C domain containing)
203068_at 2 OE-04 3 6E-04 1 9E-04 4 8E-04 Yes KIAA0469 Hs 7764 KIAA0469 gene product 203211_s_at 2 1 E-05 6 2E-06 2 8E-04 1 4E-04 Yes MTMR2 Hs 181326 myotubulaπn related protein 2 203212 s at 1 9E-03 2 5E-03 3 7E-03 1 4E-03 Yes MTMR2 Hs 181326 myotubularin related protein 2 203222_s_at 1 5E-03 2 OE-03 2 5E-03 2 4E-03 Yes TLE 1 Hs 406491 transduαn-like enhancer of split 1 (E(sp1) homolog, Drosophila)
203305 at 1 8E-03 2 5E-03 7 7E-04 1 OE-03 Yes F13A1 Hs 80424 coagulation factor XIII, A1 polypeptide 203408_s_at 1 1 E-03 1 7E-03 1 6E-03 2 7E-03 Yes SATB 1 Hs 416026 special AT-πch sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA's)
203557_s_at 6 9E-05 1 1E-03 4 7E-05 4 2E-04 Yes PCBD Hs 3192 6-pyruvoyl-tetrahydropteπn synthase/dimeπzation cofactor of hepatocyte nuclear factor 1 alpha (TCF1)
203708_at 8 7E-03 8 OE-03 8 6E-05 1 OE-04 Yes PDE4B Hs 188 phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)
203853_s_at 3 3E-05 4 2E-05 3 5E-03 7 4E-03 Yes GAB2 Hs 30687 GRB2-assocιated binding protein 2 204305 at 1 9E-03 3 9E-03 8 3E-05 1 3E-04 Yes MIPEP Hs 68583 mitochondrial intermediate peptidase 204821_at 3 OE-04 1 5E-03 4 7E-04 4 6E-03 Yes BTN3A3 Hs 167741 butyrophilin, subfamily 3, member A3 204994_at 1 4E-03 3 7E-03 8 1 E-04 2 5E-03 Yes MX2 Hs 926 myxovirus (influenza virus) resistance 2 (mouse)
205173_x_at 2 5E-03 1 2E-03 6 5E-05 1 1 E-03 Yes CD58 Hs 75626 CD58 antigen, (lymphocyte function- associated antigen 3)
205181_at 4 OE-03 5 5E-03 4 OE-03 4 2E-03 Yes ZNF193 Hs 100921 zinc finger protein 193 205366 s at 6 4E-03 7 4E-03 4 6E-03 8 3E-03 Yes HOXB6 Hs 98428 homeo box B6 205401 at 4 6E-05 8 5E-04 2 8E-04 6 4E-04 Yes AGPS Hs 407933 alkylglycerone phosphate synthase
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene IC Gene Title
205668 at 1 OE-03 3 6E-03 1 4E-03 4 6E-04 Yes LY75 Hs 153563 lymphocyte antigen 75
205691_at 1 5E-03 1 4E-04 1 1 E-02 7 7E-04 Yes SYNGR3 Hs 435277 synaptogyrin 3
205790_at 2 OE-04 4 4E-04 2 1 E-03 6 3E-04 Yes SCAP1 Hs 411942 src family associated phosphoprotein 1
205932_s_at 1 1E-03 2 8E-03 4 1 E-03 2 3E-03 Yes MSX1 Hs 424414 msh homeo box homolog 1 (Drosophila)
206082 at 5 5E-04 7 8E-04 6 9E-04 1 7E-04 Yes HCP5 Hs 511759 HLA complex P 5
206261 at 3 2E-03 5 4E-03 1 1 E-03 1 1 E-03 Yes ZNF239 Hs 25040 zinc finger protein 239
206437_at 8 6E-04 3 3E-04 5 OE-03 2 5E-03 Yes EDG6 Hs 159543 endothelial differentiation, G-protein-coupled receptor 6
206554_x_at 2 OE-04 8 7E-04 2 6E-05 1 OE-03 Yes SETMAR Hs 265855 SET domain and mariner transposase fusion gene
206591 at 6 2E-03 4 9E-03 1 5E-04 5 3E-05 Yes RAG1 Hs 73958 recombination activating gene 1
206660_at 8 7E-05 4 3E-04 2 5E-03 4 9E-03 Yes IGLL1 Hs 348935 immunoglobulin lambda-like polypeptide 1
206698_at 4 OE-03 1 8E-03 1 1E-03 6 1E-05 Yes XK Hs 78919 KeII blood group precursor (McLeod phenotype)
206866_at 9 8E-04 1 OE-03 1 6E-03 2 4E-03 Yes CDH4 Hs 376792 cadheπn 4, type 1 , R-cadherin (retinal)
208146 s at 9 3E-04 4 3E-03 2 5E-03 1 2 E-03 Yes CPVL Hs 95594 carboxypeptidase, vitellogenic-like
208964_s_at 3 OE-03 6 6E-03 1 9E-03 2 8E-03 Yes FADS1 Hs 503546 fatty acid desaturase 1
209129 at 3 5E-04 2 1E-03 3 2E-03 9 3E-03 Yes TRIP6 Hs 380230 thyroid hormone receptor interactor 6
209310_s_at 1 5E-03 6 OE-03 6 1 E-04 2 OE-03 Yes CASP4 Hs 74122 caspase 4, apoptosis-related cysteine protease
209398 at 3 6E-03 5 6E-03 5 2E-03 9 2E-03 Yes HIST1H1C Hs 7644 histone i , H1c
209590_at 5 1 E-03 2 OE-03 5 1 E-03 2 5E-03 Yes BMP7 Hs 170195 bone morphogenetic protein 7 (osteogenic protein 1 )
209728_at 2 7E-04 2 6E-04 1 OE-04 1 6E-04 Yes H LA-DR B3 Hs 308026 major histocompatibility complex, class II,
DR beta 3
209790_s_at 1 1 E-04 5 7E-03 1 7E-03 5 6E-03 Yes CAS P6 Hs 3280 caspase 6, apoptosis-related cysteine protease
210427_x_at 2 9E-03 7 4E-04 8 7E-06 4 6E-03 Yes ANXA2 Hs 462864 annexin A2
210715_s_at 1 7E-04 1 4E-03 1 9E-04 1 7E-03 Yes SPINT2 Hs 31439 serine protease inhibitor, Kunitz type, 2
210830_s_at 6 8E-04 1 5E-03 1 5E-03 2 2 E-03 Yes PON2 Hs 165598 paraoxonase 2
211367_s_at 8 7E-05 1 1E-04 8 7E-04 1 1E-03 Yes CASP1 Hs 2490 caspase 1 , apoptosis-related cysteine protease (interleukin 1 , beta, convertase)
211368_s_at 4 8E-04 3 8E-05 5 3E-03 2 2E-03 Yes CASP1 Hs 2490 caspase 1 , apoptosis-related cysteine protease (interleukin 1 , beta, convertase)
211812 s at 5 5E-03 5 7E-03 1 4E-03 1 5E-03 Yes B3GALT3 Hs 418062 UDP-GaI betaGlcNAc beta 1 ,3- galactosyltransferase, polypeptide 3
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title 212268_at 8 5E-06 1 9E-03 9 3E-04 2 5E-03 Yes SERPINB1 Hs 381167 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1
212442_s_at 4 OE-04 4 9E-05 6 5E-04 6 2E-05 Yes LOC253782 Hs 503941 hypothetical protein LOC253782
212561_at 84E-03 8 1 E-03 1 5E-03 4 4E-03 Yes RAB6IP1 Hs 26797 RAB6 interacting protein 1
213147_at 2 OE-04 4 4E-05 1 OE-03 6 5E-04 Yes HOXA10 Hs 110637 homeo box A10
213150_at 4 2E-03 4 7E-03 1 OE-03 1 2E-03 Yes HOXA10 Hs 110637 homeo box A10
213371_at 1 8E-03 1 5E-03 1 3E-04 1 4E-04 Yes LDB3 Hs 49998 LIM domain binding 3
213419_at 2 5E-03 34E-03 7 3E-03 1 7E-03 Yes
213502_x_at 1 1 E-03 1 4E-03 1 1 E-05 2 9E-05 Yes Hs 272302 Homo sapiens, clone IMAGE 5728597, mRNA
213503_x_at 1 7E-05 2 7E-04 3 5E-04 2 4E-03 Yes ANXA2 Hs 462864 annexin A2 213566_at 2 6E-04 8 3E-04 6 OE-04 4 OE-03 Yes RNASE6 Hs 23262 ribonuclease, RNase A family, k6 213568_at 2 8E-04 3 OE-05 1 2E-04 9 1E-05 Yes OSR2 Hs 152823 odd-skipped-related 2A protein 213572_s_at 5 2E-03 5 OE-03 1 6E-03 6 2E-04 Yes SERPINB1 Hs 381167 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1
213625_at 3 8E-03 4 1E-05 1 1E-02 8 7E-05 Yes P1 P373C6 Hs 44720 hypothetical protein P1 p373c6
213788_s_at 4 1 E-03 6 OE-03 7 5E-03 6 7E-03 Yes Hs 6580 Homo sapiens clone 23718 mRNA sequence
215071_s_at 5 1E-03 54E-03 8 6E-03 9 3E-03 Yes
215379_x_at 1 1 E-06 6 3E-03 6 8E-07 5 2E-03 Yes IGLJ3 Hs 449601 immunoglobulin lambda joining 3
216565_x_at 3 5E-03 74E-04 2 2E-03 1 3E-03 Yes
217022_s_at 1 9E-05 1 4E-05 1 6E-03 2 4E-03 Yes MGC27165 Hs 366 hypothetical protein MGC27165
217360_x_at 2 4E-04 4 5E-04 8 9E-03 7 9E-03 Yes
217759_at 1 8E-05 2 5E-05 1 2E-04 1 6E-04 Yes TRIM44 Hs 14512 tripartite motif-containing 44
217760_at 1 2E-03 8 1E-04 34E-04 9 5E-05 Yes TRIM44 Hs 14512 tripartite motif-containing 44
217977_at 7 5E-04 2 7E-03 5 OE-04 3 7E-03 Yes SEPX1 Hs 279623 selenoprotein X, 1
218005_at 4 2E-06 4 1E-05 3 5E-06 4 7E-04 Yes ZNF22 Hs 108642 zinc finger protein 22 (KOX 15)
218006_s_at 3 5E-03 2 6E-03 1 OE-04 7 6E-04 Yes ZNF22 Hs 108642 zinc finger protein 22 (KOX 15)
218154_at 9 8E-05 4 8E-03 4 1E-05 2 8E-03 Yes FLJ12150 Hs 118983 hypothetical protein FLJ 12150
218457_s_at 2 6E-03 7 5E-03 1 3E-03 6 5E-03 Yes DNMT3A Hs 241565 DNA (cytosιne-5-)-methyltransferase 3 alpha
218503_at 1 2E-03 8 9E-05 5 6E-03 6 2E-03 Yes KIAA1797 Hs 257696 KIAA1797
218618_s_at 3 5E-03 2 4E-03 6 4E-04 8 OE-05 Yes FAD 104 Hs 299883 FAD104
218676_s_at 1 5E-03 1 9E-04 2 5E-03 3 1E-04 Yes PCTP Hs 285218 phosphatidylcholine transfer protein
218689_at 5 6E-03 5 3E-03 3 1 E-03 8 7E-03 Yes FANCF Hs 65328 Fanconi anemia, complementation group F
218729_at 1 7E-04 6 6E-04 2 7E-04 34E-04 Yes LXN Hs 124491 latexin protein
219143 s at 2 8E-05 2 6E-05 1 2E-04 1 5E-04 Yes Rpp25 Hs 8562 RNase P protein subunit p25
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Gene Symbol UniGene ID Gene Title
219362_at 6 1E-03 7 8E-03 3 5E-03 1 3E-03 Yes Hs 325923 Homo sapiens transcribed sequence with strong similarity to protein ref NPJ378911 1
(H sapiens) hypothetical protein FLJ22643
[Homo sapiens]
219684 at 2 7E-05 4 9E-03 5 1 E-05 3 1E-03 Yes IFRG28 Hs 43388 28kD interferon responsive protein
219734_at 6 1 E-03 5 6E-03 1 3E-03 1 OE-03 Yes FLJ20174 Hs 272416 hypothetical protein FLJ20174
219953 s at 3 7E-04 1 5E-03 2 6E-03 3 OE-03 Yes C11orf17 Hs 131180 chromosome 11 open reading frame 17
220104_at 2 6E-03 9 OE-04 3 7E-03 5 7E-03 Yes ZC3HAV1 Hs 35254 zinc finger CCCH type, antiviral 1
220230 s_at 8 5E-03 7 4E-03 1 5E-03 1 3E-03 Yes CYB5R2 Hs 414362 cytochrome b5 reductase b5R 2
220235_s_at 1 3E-04 44E-03 5 OE-05 6 OE-03 Yes RIF1 Hs 25245 receptor-interacting factor 1
220784 s_at 4 OE-04 8 6E-04 7 9E-04 1 3E-03 Yes UTS2 Hs 162200 urotensin 2
221081 s at 2 2E-03 4 4E-03 2 7E-04 9 1 E-04 Yes FLJ22457 Hs 447624 hypothetical protein FLJ22457
221349_at 3 1E-03 1 7E-03 1 5E-04 3 OE-03 Yes VPREB1 Hs 247979 pre-B lymphocyte gene 1
221641_s_at 4 1E-03 2 1E-03 6 9E-03 7 6E-06 Yes ACATE2 Hs 298885 likely ortholog of mouse acyl-Coenzyme A thioesterase 2, mitochondrial
221666_s_at 9 7E-04 1 OE-04 2 5E-04 2 1 E-05 Yes ASC Hs 197875 apoptosis-associated speck-like protein containing a CARD
221690_s_at 3 2E-03 3 9E-03 1 9E-05 2 8E-06 Yes NALP2 Hs 369279 NACHT, leucine rich repeat and PYD containing 2
36030_at 3 3E-03 8 1 E-03 1 OE-02 8 4E-03 Yes HOM-TES-103 Hs 46659 HOM-TES-103 tumor antigen-like
51158_at 2 OE-03 7 1 E-03 5 OE-03 2 8E-03 Yes — Hs 27373 Homo sapiens, clone IMAGE 4816940, mRNA
207714_s_at 5 4E-04 2 8E-03 6 2E-04 3 2E-03 No SERPINH1 Hs 241579 serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1 ,
(collagen binding protein 1)
208816_x_at 7 8E-04 2 9E-04 3 8E-04 2 7E-04 No — Hs 437110 Human lipocortin (LIP) 2 pseudogene mRNA, complete cds-like region
211566_x_at 6 9E-03 6 7E-03 1 6E-03 5 5E-03 No
212235 at 4 1 E-03 2 2E-04 7 OE-04 7 9E-05 No PLXN D 1 Hs 301685 plexin D1
Table 4A: NFκB-Regulated Genes (See tables reference 1)
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
205481_at 5 59 6 35 5 96 5 42 5 21 5 36 5 63 6 59 6 09 5 66 5 40 5 42
216220 s at 5 39 5 61 5 43 5 33 5 38 5 22 5 31 5 82 5 51 5 34 5 33 5 21
202834_at 5 58 5 84 5 84 5 79 6 06 5 92 5 79 5 94 5 74 6 04 6 02 6 03
204151_x_at 6 84 6 88 7 03 6 63 6 91 6 98 6 88 6 99 6 92 6 90 7 04 6 74
216594_x_at 6 35 6 32 6 33 6 17 6 32 6 45 6 28 6 42 6 16 6 49 6 65 6 24
204445_s_at 7 06 6 70 6 75 6 37 6 41 6 19 7 05 6 65 6 46 6 54 6 72 6 55
204446_s_at 8 83 8 54 9 09 7 84 7 92 8 09 8 89 8 88 9 00 8 17 8 15 8 85
214366 s at 6 87 6 47 6 50 6 14 5 92 6 06 7 27 6 33 6 41 6 17 6 31 6 39
214953_s_at 4 78 5 06 5 02 4 53 5 03 5 06 4 63 5 05 4 79 4 81 5 35 5 10
211621 at 4 47 4 64 4 79 4 51 4 65 4 62 4 52 4 55 4 53 4 58 4 61 4 57
203174_s_at 7 70 7 86 7 69 7 88 7 93 7 79 7 74 7 78 1 11 8 15 7 84 7 80
215984_s_at 6 01 648 6 24 6 53 6 66 6 51 6 32 6 29 645 6 43 6 20 6 25
201891_s_at 12 00 12 00 12 13 12 01 12 13 11 98 11 99 12 32 12 04 12 14 11 85 11 88
216231_s_at 12 17 12 10 12 09 12 06 12 15 12 20 12 12 12 16 12 13 12 08 12 00 11 92 U\
OO
203685_at 4 75 4 61 4 79 4 33 4 46 4 42 4 62 4 65 4 68 4 48 4 58 4 41
207005 s at 6 62 6 60 6 62 6 35 6 12 5 92 7 06 6 73 6 62 6 53 6 85 6 23
205681_at 4 31 4 32 4 29 4 59 4 61 4 49 4 45 4 48 4 30 6 84 8 14 7 47
202076_at 8 63 8 09 8 59 8 79 8 32 8 73 8 67 8 13 8 76 7 56 7 54 8 28
210538_s_at 4 64 4 75 4 80 6 89 6 65 6 57 4 49 4 35 4 62 4 95 5 43 5 21
205114 s_at 4 61 4 61 4 69 4 63 5 15 4 59 461 4 81 4 46 4 99 6 04 4 94
204103 at 6 95 6 97 6 93 6 16 6 49 6 36 6 80 7 08 6 54 6 61 7 13 6 62
201700 at 9 37 9 74 9 72 10 56 10 72 10 78 9 35 9 64 9 48 8 39 8 57 8 77
204118_at 9 63 8 78 9 07 9 76 10 02 9 44 9 69 8 64 8 84 9 94 10 36 9 91
209795 at 4 56 4 42 4 80 4 00 4 14 4 03 4 36 4 48 4 27 4 07 4 06 4 06
209619_at 12 37 11 96 12 10 12 07 12 17 11 94 12 11 11 63 11 56 12 67 12 83 12 63
207176_s_at 6 11 6 33 6 32 6 31 6 25 6 39 6 13 6 37 6 25 6 58 6 49 6 50
204440_at 7 44 7 55 7 48 7 19 7 41 7 33 7 53 7 60 7 15 8 55 9 42 8 62
202246 s at 10 32 10 61 10 25 10 63 10 70 10 45 10 37 10 53 10 35 10 50 10 55 10 32
203198_at 7 63 7 79 7 90 8 06 7 91 7 96 768 7 75 7 82 7 36 7 11 7 11
202284_s_at 8 10 7 23 7 18 6 96 8 45 6 88 8 74 7 87 7 04 6 85 6 54 6 42
208485_x_at 5 64 5 22 5 33 5 39 5 51 5 40 5 30 5 36 5 30 5 31 5 25 4 96
209508_x_at 6 13 6 12 6 08 6 12 6 31 5 96 6 16 6 13 6 03 5 98 5 95 5 74
209939 x at 6 86 6 88 7 01 7 80 7 75 7 78 6 85 7 01 7 04 640 6 16 6 11
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly 1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
210563_x_at 661 684 671 762 736 739 674 673 685 659 634 651
211316_x_at 652 642 635 652 668 633 648 664 628 606 597 595
211317_s_at 450 460 470 466 465 471 451 460 459 442 451 447
211862_x_at 534 518 507 544 523 521 502 504 505 480 482 456
214618_at 441 469 477 470 455 485 468 469 473 481 498 474
209716_at 579 584 575 561 586 582 593 585 572 585 593 585
200838_at 536 536 527 518 500 504 541 550 537 535 515 518
200839_s_at 635 615 604 543 533 559 611 630 656 587 566 563
213274_s_at 490 491 500 466 502 502 486 512 495 484 501 483
204470_at 401 412 400 399 418 403 396 406 397 389 412 400
210163_at 384 375 375 379 386 378 373 378 381 376 381 382
214974_x_at 382 375 386 375 395 384 370 379 378 381 389 381
203700_s_at 540 539 532 545 526 544 530 550 537 555 557 535
201041_s_at 621 625 614 590 581 572 652 652 634 550 512 520
203692_s_at 719 693 666 729 706 697 705 691 707 715 702 717
203693_s_at 774 757 821 808 760 805 749 768 786 778 711 818
211551_at 594 590 589 571 615 596 576 582 580 598 604 578
201694_s_at 528 532 540 519 537 544 527 532 547 619 534 575
214766_s_at 528 551 555 606 557 587 538 538 559 476 460 505
201313_at 481 457 451 705 714 655 466 484 455 488 481 470
205767_at 377 379 377 377 375 374 385 379 378 378 377 376
202081_at 951 931 903 1039 1023 1027 952 916 915 1035 1075 1050
205756_s_at 546 528 532 506 529 522 525 525 534 513 530 527
214701_s_at 544 540 521 548 539 528 563 548 531 552 564 543
202275_at 707 709 680 702 711 667 711 711 689 727 749 732
207574_s_at 755 678 681 637 611 633 773 690 736 745 712 756
209304_x_at 793 732 699 693 671 664 780 738 766 792 770 783
209305_s_at 757 694 682 659 637 671 751 669 725 740 740 739
202269_x_at 445 513 503 396 399 397 466 502 511 398 395 387
202270_at 447 442 492 379 376 392 453 462 511 391 381 392
200651_at 1285 1293 1302 1261 1279 1273 1312 1303 1301 1285 1291 1285
222034_at 506 516 528 545 531 531 525 511 525 538 507 546
200824_at 1068 1043 1032 1131 1131 1117 1062 1037 1054 1094 1108 1094
208729_x_at 1262 1249 1218 961 963 955 1228 1226 1209 801 843 804
209140 x at 1305 1293 1301 1068 1095 1064 1305 1296 1289 824 859 846
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly 1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
211911_x_at 12 27 12 11 12 01 9 49 9 50 9 28 12 20 11 97 11 83 7 81 7 96 7 69
200943_at 11 40 11 49 11 48 11 74 11 63 11 66 11 26 11 62 11 44 11 65 11 60 11 63
200944_s_at 11 32 11 47 11 55 11 63 11 61 11 69 11 40 11 68 11 50 11 72 11 63 11 69
202638_s_at 8 64 7 77 7 46 7 18 7 29 6 90 7 99 7 52 7 28 7 32 7 87 7 25
215485_s_at 6 87 6 62 6 39 6 69 6 41 6 63 6 82 6 57 6 43 6 77 6 99 6 49
210354_at 4 51 4 61 4 52 4 46 4 57 4 57 443 4 67 443 4 67 4 73 4 57
202718_at 9 02 6 64 7 87 546 5 55 5 74 8 21 643 7 16 5 80 5 58 5 57
207901_at 4 00 4 00 3 99 3 97 4 10 3 96 3 90 3 97 3 92 4 01 3 94 3 99
208200_at 4 85 4 98 4 97 4 80 4 84 4 94 4 86 4 98 4 91 5 02 4 93 4 96
205207_at 4 73 4 82 4 86 4 76 4 90 4 82 4 92 4 79 4 74 4 91 4 84 4 75
202531_at 7 23 7 83 7 69 6 08 6 64 6 37 7 36 7 91 7 11 5 89 6 37 6 03
203275_at 6 41 6 61 6 81 6 03 6 11 6 08 6 61 6 52 6 60 4 37 5 36 4 62
204562_at 8 22 8 60 8 59 8 69 9 38 8 42 8 35 8 44 7 86 6 36 6 28 6 01
216986_s_at 6 51 6 37 6 35 6 45 6 80 6 42 6 55 6 43 6 23 6 43 6 42 6 01
208436_s_at 6 62 5 66 5 62 5 28 5 20 5 19 6 65 5 82 6 12 5 31 4 93 5 00
213281_at 4 36 4 50 448 4 33 4 39 4 32 441 447 4 41 440 443 4 37 §
201473_at 7 65 7 49 7 49 7 56 7 32 7 43 7 46 7 25 7 43 8 06 8 38 8 13
207029_at 4 03 4 08 4 03 3 88 4 14 4 00 4 05 4 06 3 93 4 00 4 06 4 02
216264_s_at 4 59 4 66 4 42 4 60 4 61 469 4 59 444 447 4 80 4 68 4 48
207339_s_at 6 04 5 63 5 88 6 78 6 47 6 58 5 99 5 80 5 68 6 82 7 57 6 95
213975_s_at 4 87 5 48 5 69 4 30 4 17 4 18 5 57 6 22 6 92 4 27 4 39 4 33
208037_s_at 6 64 646 649 640 649 6 61 6 54 647 6 43 6 72 666 6 55
206296_x_at 8 63 8 05 8 15 9 80 9 53 9 24 8 32 7 87 7 85 9 99 10 33 10 05
214219_x_at 8 30 7 85 7 89 9 41 9 21 8 89 8 23 7 62 7 57 9 52 10 01 9 75
214339_s_at 7 79 7 44 7 78 9 09 8 83 8 74 7 92 7 33 7 21 9 17 9 58 9 55
201126_s_at 7 87 7 81 7 67 7 65 7 70 7 28 7 65 7 90 7 56 7 26 7 14 7 03
203936_s_at 5 85 6 14 6 00 6 13 5 94 6 04 6 08 6 12 6 07 6 23 6 22 6 12
202086_at 5 28 5 17 5 31 5 47 5 32 5 27 5 42 5 37 5 29 5 49 5 29 5 26
204798_at 7 85 9 53 9 60 7 15 7 27 7 39 7 90 944 8 38 6 59 7 23 7 08
215152_at 3 85 4 08 3 91 3 91 3 91 3 86 3 98 3 94 3 90 3 90 3 90 3 86
202431_s_at 10 47 10 56 10 92 9 94 10 06 9 69 10 34 10 50 9 93 9 96 10 46 9 66
209239. .at 8 35 859 852 7 22 763 716 837 8 51 819 815 849 800
207535 _s_at 5 46 526 522 6 18 601 592 538 5 08 509 551 590 573
201502~ _s_at 9 28 898 875 9 09 914 867 901 8 78 868 909 969 961
201468 S at 6 10 624 614 6 15 599 605 600 6 26 621 683 657 661
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly 1 (A2) Ly 1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
210519_s_at 622 659 626 579 608 604 632 644 644 755 737 757
201866_s_at 588 584 606 695 702 682 572 583 592 619 647 630
211671_s_at 623 616 646 803 778 772 579 573 603 648 723 714
216321_s_at 582 576 616 765 757 758 529 544 578 698 738 757
204622_x_at 446 453 461 436 443 449 441 452 457 449 450 441
216248_s_at 430 422 423 410 405 408 424 418 446 413 412 405
210004_at 387 393 388 378 395 394 382 394 382 383 393 376
121_at 857 875 862 848 889 882 853 856 850 877 893 862
203557_s_at 738 733 719 560 583 566 756 750 737 652 671 657
201202_at 1096 1086 1078 1144 1145 1149 1087 1089 1098 1117 1060 1106
213791_at 472 499 502 462 499 495 473 475 476 478 490 484
200737_at 1076 1008 1046 946 945 954 1075 1013 1039 936 973 960
200738_s_at 1189 1148 1189 1119 1121 1105 1200 1168 1173 1133 1118 1125
217356_s_at 1183 1128 1178 1105 1093 1095 1200 1141 1161 1107 1100 1095
217383_at 641 580 653 553 555 593 583 582 632 580 566 607
209193_at 575 566 564 551 569 575 583 587 550 561 571 554 σ
Figure imgf000063_0001
\
210145_at 386 392 404 379 388 374 375 369 374 377 375 380
201979_s_at 780 788 765 774 781 780 768 762 111 739 765 753
214617_at 512 512 517 523 527 532 513 516 516 529 520 515
202545_at 669 649 636 795 792 761 705 664 657 705 733 717
204279_at 1003 1003 1006 883 906 896 1009 994 1006 549 588 575
211661_x_at 644 659 642 718 761 733 635 657 631 698 731 674
211892_s_at 487 475 478 469 All 482 484 482 483 504 484 482
206035_at 501 539 549 527 556 575 513 513 530 563 568 588
206036_s_at 583 545 571 654 647 601 588 548 539 628 765 667
205205_at 731 702 665 770 799 746 725 685 645 751 792 751
209544_at 432 430 429 430 415 433 431 425 423 429 438 441
209545_s_at 873 832 808 795 782 789 839 818 847 814 821 811
200872_at 854 754 817 639 593 611 798 703 720 646 621 615
203186_s_at 645 590 624 514 478 489 678 650 693 720 754 749
215223_s_at 753 757 764 726 709 761 781 741 780 654 654 698
216841_s_at 499 512 561 535 518 593 513 504 538 458 422 467
221477_s_at 726 705 729 709 685 705 735 704 731 636 620 649
201471_s_at 909 846 837 921 904 889 925 854 875 895 947 937
208048 at 455 460 436 464 451 440 458 463 436 458 472 463
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
202307_s_at 838 804 816 743 747 753 820 800 832 669 691 701 208829_at 972 927 930 945 904 909 956 923 901 900 923 919
207199_at 6 65511 6 64499 6 65566 7 75555 7 72200 7 71199 6 60066 6 61188 5 59966 5 59944 5 57722 5 53333
215775_at 5 50099 5 54433 5 53355 5 53344 5 53300 5 56688 5 52211 5 53300 5 52288 5 53344 5 53344 5 53377
216005_at 4 40066 4 41133 4 41122 4 41122 4 41122 4 42222 4 40055 4 41133 4 41122 4 42244 4 41166 4 41188
202643_s_at 5 55555 5 55588 5 54499 6 64455 6 64411 6 63377 5 54455 5 54433 5 51122 5 57700 5 57711 5 58855
202644_s_at 5 59977 6 62211 6 61100 7 70055 7 73322 7 71100 5 58888 6 60033 5 57700 6 63311 6 66633 6 63377
215346_at 664 615 616 682 686 641 644 649 592 697 690 683 35150_at 856 835 822 842 872 853 828 841 806 867 899 850 207536_s_at 511 546 506 516 517 531 518 522 517 517 531 520 202687_s_at 447 444 424 395 407 400 433 439 441 406 409 401 202688_at 495 486 495 428 436 431 509 480 522 424 425 437 214329_x_at 374 382 396 358 366 363 375 391 388 358 377 363 201746_at 996 988 1001 917 914 909 999 994 986 933 949 947 211300_s_at 965 910 944 824 839 836 959 917 928 845 869 862
205599_at 5 50000 5 55555 5 53300 5 54477 6 60033 5 56600 5 50077 5 54444 5 51166 5 55511 5 59900 5 55511 ^
213191_at 510 539 563 602 592 558 506 547 529 585 591 569 203109_at 975 971 942 997 993 987 982 975 965 989 988 984 208997_s_at 1061 1038 1034 965 989 937 1064 1036 1000 1014 1053 1007 208998_at 1118 1118 1118 1036 1057 1016 1129 1119 1086 1095 1101 1098 204881_s_at 773 702 711 821 778 801 767 706 762 770 830 850 221765_at 435 427 449 428 438 442 436 404 441 436 479 504 203868_s_at 431 432 439 431 451 447 424 452 424 424 443 434 209946_at 494 499 500 503 512 510 521 501 512 505 521 511 201426_s_at 1007 977 984 598 582 588 1004 978 963 588 601 526 210301_at 744 771 726 755 747 761 759 763 752 782 796 769 208544_at 590 578 557 580 602 582 558 585 566 600 602 577 210081_at 455 457 445 462 469 462 464 466 450 483 471 466
217046_s_at 5 51111 5 50044 4 47755 5 51166 5 50033 4 49955 4 49988 4 48833 4 49944 5 51144 4 49900 5 51122
207206_s_at 5 53377 5 54466 5 54422 5 54422 5 54433 5 53366 5 53300 5 53355 5 55511 5 55533 5 56644 5 53388
213952_s_at 5 52211 5 52200 5 51111 5 51188 5 51155 5 51166 5 52233 5 51199 5 51111 5 52266 5 54455 5 52233
206516_at 6 61155 5 58800 5 58822 6 61199 5 57788 6 60088 6 61177 5 57799 6 60011 6 62299 6 60077 6 67766
205820_s_at 4 47711 4 48866 4 46699 4 48877 4 46655 4 49966 4 49955 4 48822 4 49955 4 49999 5 50044 4 49944
200602_at 3 36633 3 37700 3 36699 3 36644 3 36644 3 36688 3 36644 3 37700 3 36677 3 37777 3 38888 3 38855
211277_x_at 5 50044 5 51100 5 50011 5 50099 5 52200 5 51133 5 50055 5 51122 5 51111 4 49999 5 50055 5 51100
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly 1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
211110_s_at 507 508 501 502 515 526 506 507 507 521 5 14 503 207367_at 571 582 569 560 589 580 587 578 563 613 5 87 564
217904_s_at 4 46655 4 47788 4 45522 4 46655 4 49977 4 47733 4 47799 4 46600 4 47722 4 46677 4 48 888 4 45588
203684_s_at 5 58833 5 58855 5 58800 5 56677 5 58800 5 57733 5 59900 5 59999 5 58833 5 58844 6 60 000 5 57700
207004_at 545 549 532 560 563 542 540 556 541 552 5 47 550
207510_at 5 51122 5 54466 5 51177 5 51166 5 53377 5 52200 5 51122 5 53300 5 51122 5 54411 5 53 388 5 52277
202357_s_at 4 45555 4 43399 4 44477 4 46655 4 45599 4 45577 4 46655 4 46644 4 45588 4 47744 4 46 611 4 46611
211920_at 580 588 533 576 579 549 572 573 542 590 5 52 565 201261_x_at 515 521 528 532 552 504 513 539 510 528 5 31 503 201262_s_at 469 459 448 467 459 455 459 462 451 459 4 78 458 205289_at 398 408 401 396 412 403 399 408 392 390 4 11 399 205290_s_at 494 488 490 510 490 509 497 502 505 552 5 32 505 204439_at 500 485 495 458 466 486 484 514 522 478 4 73 472 217767_at 601 589 572 615 595 601 617 608 596 634 6 05 598 220066_at 451 450 451 455 457 459 454 461 447 473 4 60 462
203065_s_at 5 53333 5 54466 5 53399 5 53388 5 54477 5 54422 5 55577 5 55577 5 52277 5 55522 5 57 700 5 53388 S
212097_at 510 515 517 502 520 510 499 515 507 507 5 19 513 210133_at 543 543 532 544 541 537 535 547 546 555 5 79 559 216598_s_at 503 514 510 514 520 510 496 498 508 512 5 25 515 205476_at 409 417 409 408 423 406 404 411 404 408 4 17 407 207861_at 729 731 711 712 715 701 713 717 689 713 7 34 712 1405_ι_at 435 439 442 448 436 448 444 437 456 452 4 61 469 204655_at 482 486 496 478 488 517 484 502 472 475 4 93 482 208711_s_at 490 480 489 493 500 497 495 498 494 493 5 06 488 208712_at 425 423 427 425 418 429 433 423 427 439 4 24 434 214019_at 461 460 469 455 447 458 464 458 459 469 4 74 467 206991_s_at 664 692 675 691 680 693 665 684 680 686 7 11 692 206337_at 434 466 427 441 444 443 456 452 440 463 4 54 445 207277 at 6 61188 6 63333 6 64466 6 62244 6 65533 6 65599 6 65500 6 65588 6 66611 6 67711 6 67 777 6 66655
207278 s at 528 521 507 522 509 521 520 521 527 566 5 35 525
206804_at 555588 558833 557766 556633 557722 557700 555577 557733 557733 660055 66 0011 557711
210564_x_at 556677 554477 554433 559944 556688 557733 556600 555555 556622 554400 55 5544 554488
214486_x_at 663399 665544 663388 664433 665588 663399 663300 664433 662288 662222 66 3344 660066
202403_s_at 559955 559900 558844 559977 559955 559955 558811 558888 559955 663377 55 9999 660055
202404_s_at 441100 440077 442299 442266 443322 442266 442288 441166 442200 441144 44 0055 442277
Log2 fluorescence intensity
Probesets Ly1 (A1 ) Ly1 (A2) Ly 1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
205753_at 513 522 515 503 524 526 498 515 511 506 522 487
37020_at 431 427 421 436 421 429 433 417 427 437 440 426
207082_at 621 631 653 617 635 622 638 636 602 624 629 618
210557_x_at 502 509 498 503 509 496 509 518 486 516 524 504
211839_s_at 549 551 531 553 538 558 548 544 546 599 551 552
210228_at 506 513 513 512 524 509 512 538 508 526 528 501
210229_s_at 588 598 568 585 597 588 586 595 568 606 611 593
207442_at 631 637 623 632 634 612 611 626 617 634 641 627
213275_x_at 487 483 486 451 463 451 484 506 500 467 470 466
202087_s_at 453 476 463 457 472 459 463 460 457 458 462 457
204533_at 506 535 529 491 520 509 495 531 498 507 520 489
211122_s_at 390 374 382 378 383 382 373 378 382 379 387 386
209774_x_at 405 411 413 419 416 422 411 429 412 412 429 407
207852_at 365 372 376 365 375 367 367 373 363 360 360 364
215101_s_at 405 405 411 408 406 407 402 410 404 407 400 407
203699_s_at 506 510 509 492 493 512 503 505 504 509 500 502 ON
210819_x_at 474 486 484 466 477 492 468 486 474 483 493 472
211215_x_at 720 724 688 707 724 732 709 711 708 740 725 714
201044_x_at 514 508 486 527 491 501 502 512 498 530 493 498
201983_s_at 530 524 512 542 514 530 527 508 519 558 544 528
201984_s_at 589 597 573 593 582 590 588 607 586 596 590 604
210984_x_at 714 701 706 707 728 722 702 702 705 751 731 707
211550_at 546 546 554 544 554 548 541 553 548 559 567 545
211607_x_at 646 635 627 621 642 637 631 634 626 681 668 631
201693_s_at 532 536 548 534 559 559 535 561 529 553 547 542
201808_s_at 574 584 574 555 562 591 574 585 586 590 571 562
201809_s_at 623 607 617 582 561 560 653 648 628 590 579 567
207257_at 452 456 440 478 452 450 458 442 459 470 460 446
204363_at 437 449 446 430 449 437 428 446 442 441 445 446
206759_at 475 458 459 506 488 478 463 451 449 509 488 468
206760_s_at 579 592 584 605 596 597 589 579 582 600 609 590
210495_x_at 542 531 543 516 555 534 516 539 508 519 547 518
211719_x_at 463 478 475 447 477 469 459 468 460 457 472 462
212464_s_at 464 471 469 469 485 469 459 487 448 466 483 474
214702 at 384 391 388 394 393 396 389 405 389 391 395 404
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly 1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
216442_x_at 4 89 5 00 4 92 4 69 5 19 4 75 4 71 4 89 4 70 4 88 4 84 4 77
205278_at 4 16 4 23 4 22 3 99 4 12 4 12 4 09 4 10 4 02 4 04 4 04 4 00
206669_at 5 07 4 97 4 95 5 09 4 85 5 00 4 92 4 95 5 05 5 10 4 94 4 95
206670_s_at 4 69 4 95 4 62 4 58 4 54 4 55 4 56 4 62 4 60 4 67 4 64 4 65
213560_at 5 74 5 81 5 58 5 53 5 79 5 52 5 60 5 68 5 57 5 63 5 63 5 58
220821_at 4 23 4 20 4 23 4 17 4 38 4 23 4 16 4 32 4 19 4 22 4 19 4 15
205914_s_at 5 27 518 485 544 509 520 532 506 518 563 534 514
205915_x_at 6 00 607 578 597 599 605 567 600 597 617 613 601
210781_x_at 6 13 630 623 612 638 633 612 633 622 624 641 623
210782_x_at 5 80 585 524 555 582 537 592 561 541 587 549 548
211125_x_at 5 36 554 531 522 533 543 530 550 526 539 557 536
206534_at 5 54 556 544 543 566 557 540 554 554 568 565 551
221942_s_at 5 81 610 585 591 587 609 577 598 595 621 627 603
207316_at 4 84 491 481 486 499 498 491 487 490 501 497 487
205919_at 5 92 595 593 618 589 627 619 594 611 649 609 627
217683_at 5 72 576 556 567 573 578 568 559 569 584 573 563
203665_at 6 03 615 614 592 599 611 623 633 618 621 607 591
210439_at 4 62 471 472 482 480 477 471 482 474 471 475 470
201631_s_at 5 33 528 526 558 557 571 537 546 524 568 540 544
205302_at 3 75 384 380 365 380 380 363 379 372 374 373 369
207433_at 4 25 444 435 424 449 429 420 442 415 419 436 423
206924_at 4 30 442 430 418 422 432 428 427 424 432 448 424
206926_s_at 6 07 641 609 641 635 619 604 632 602 644 644 609
207844_at 5 13 530 482 529 526 516 509 523 514 569 518 499
205992_s_at 3 86 388 388 379 413 399 383 381 386 382 388 386
210118_s_at 4 46 452 444 435 441 448 434 446 445 463 451 445
205067_at 6 78 698 681 702 692 695 684 689 701 716 703 696
39402_at 5 03 528 506 507 515 507 503 505 495 519 534 511
212657_s_at 5 77 607 576 561 581 583 566 585 577 581 602 571
212659_s_at 5 39 540 478 521 536 526 545 533 516 581 542 535
216243_s_at 6 68 664 655 666 684 670 658 667 648 679 692 655
216244 at 4 55 446 435 472 456 457 466 447 460 468 456 461
216245_at 4 96 5 03 4 96 4 85 5 12 5 01 4 93 5 08 4 88 5 06 5 12 4 97
207849_at 3 81 3 82 3 88 3 82 3 86 3 85 3 84 3 86 3 86 3 83 3 96 3 83
206341_at 4 41 4 38 4 35 4 32 4 23 4 32 447 4 27 4 43 4 50 4 52 4 29
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly 1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
211269_s_at 599 592 607 593 613 599 601 615 598 584 590 596
202859_x_at 508 514 519 501 506 510 498 510 510 509 512 515
208193_at 439 445 437 437 447 440 440 438 426 441 441 438
216987_at 388 374 380 379 374 379 378 372 382 380 377 380
201464_x_at 507 475 509 470 488 490 509 499 494 502 487 498
201465_s_at 507 502 493 515 496 502 534 508 511 509 516 514
201466_s_at 420 421 423 416 412 423 430 413 428 422 423 429
211124_s_at 393 393 395 388 386 395 397 395 393 390 401 391
204582_s_at 438 424 420 426 427 423 439 437 429 451 441 431
204583_x_at 628 634 607 628 623 643 638 635 616 638 644 620
204734_at 453 448 450 469 451 455 452 464 449 484 443 456
208188_at 606 595 581 618 613 612 598 585 599 642 623 617
211652_s_at 668 670 680 673 663 688 664 658 662 706 717 673
214461_at 478 472 487 470 478 486 467 483 476 487 482 484
212531_at 568 567 538 585 530 547 533 539 555 604 553 564
208949_s_at 514 512 517 519 506 519 519 526 522 535 540 524
206975_at 518 531 523 518 525 513 549 545 512 538 609 530
204475_at 380 378 382 375 381 375 378 382 388 380 396 385
205828_at 405 413 405 395 419 416 402 415 405 408 427 413
205970_at 551 556 527 536 552 534 553 563 537 562 545 525
204673_at 627 612 594 626 626 628 632 630 616 655 622 625
209636_at 526 515 496 602 562 538 543 518 500 555 584 551
211524_at 438 448 455 430 455 448 431 447 437 440 444 443
203828_s_at 571 566 541 559 555 578 571 548 552 595 570 555
205440_s_at 400 405 420 388 406 410 402 408 410 392 406 402
201467_s_at 518 512 490 490 506 444 519 505 487 556 541 523
204621_s_at 472 467 443 452 442 448 479 462 468 465 457 454
205040_at 476 466 445 494 469 467 497 481 465 497 485 473
205041_s_at 420 407 404 424 402 427 430 419 419 432 420 421
214465_at 457 452 452 446 457 457 450 444 460 461 466 458
207921_x_at 481 491 509 502 497 488 485 491 500 514 511 486
207923_x_at 494 493 482 504 491 492 485 489 473 509 498 503
207924_x_at 472 469 475 487 484 484 490 507 479 501 498 501
209552_at 620 624 587 638 627 619 621 617 602 655 638 620
214528 s at 438 437 439 446 417 453 440 432 443 473 459 439
Log2 fluorescence intensity
Probesets Ly 1 (A1 ) Ly 1 (A2) Ly 1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
221990_at 568 586 572 587 589 575 590 576 570 587 614 578 204200_s_at 481 500 495 495 495 487 492 483 491 494 488 490
216055_at t 47i1l * 4t 9 ?U0 t 4 O8U0 H 4 C8u5 H 4 O89S H 4 O8S9 H 47I7I H 4 O8O6 H 4 »97 / O 51 I t4 t 4 y9O5 t 4 O8t4
216061_x_at 5 55533 5 57711 5 56611 5 57766 5 58877 5 58899 5 56677 5 56677 5 56677 5 57755 5 58822 5 57711
206803_at 5 50000 5 50011 4 49955 4 47799 5 50011 5 51199 4 48866 5 51133 4 49988 5 51111 5 52211 5 51100
204213_at 6 64400 6 66666 6 67744 6 66633 6 67733 6 66633 6 64455 6 66699 6 66633 6 68866 6 68877 6 65599
203649_s_at 5 52222 5 52222 5 51188 5 53300 5 53333 5 52233 5 51144 5 53388 5 52211 5 53300 5 53366 5 52233
205479_s_at 516 529 518 508 520 516 531 538 502 519 515 511
211668_s_at 534 552 546 557 544 549 552 559 555 576 540 562
205125_at 859 857 841 854 845 840 859 854 856 867 856 840
205720_at 519 532 511 528 542 514 549 540 521 539 544 524
215705_at 603 632 621 613 633 622 603 636 606 643 628 619
206278_at 481 473 429 472 537 452 462 456 417 465 499 448
211663_x_at 554 556 553 554 573 570 556 589 555 591 578 565
211748_x_at 687 690 674 700 708 691 687 710 673 711 705 683
212187_x_at 6 67733 6 68844 6 65588 6 69933 6 68877 6 68833 6 68822 6 69922 6 67744 7 72299 6 69944 6 67799 5
207388_s_at 654 671 628 678 658 652 649 664 650 696 683 664
210367_s_at 571 607 606 592 616 609 582 615 592 606 596 591
208131_s_at 477 478 463 476 474 490 474 471 466 506 486 474
210702_s_at 551 551 528 535 542 539 541 543 534 551 547 538
204748_at 408 417 411 411 406 415 419 412 416 439 421 425
204201_s_at 387 385 386 384 391 383 383 386 383 384 388 385
206157_at 360 372 377 373 372 371 363 375 372 369 385 367
216994_s_at 448 447 432 440 442 438 435 447 439 455 466 442
221282_x_at 565 574 576 552 581 566 547 601 549 569 572 572
221283_at 567 558 519 561 545 538 540 538 532 579 561 557
217728_at 472 463 463 479 451 470 468 458 466 502 479 476
208607_s_at 482 491 451 486 464 449 485 486 456 468 455 450
214456_x_at 5 58888 5 59999 5 55566 5 56666 5 59933 5 56666 5 56655 5 58833 5 56699 5 58822 5 58833 5 55544
202071_at 5 50077 5 51188 5 53311 4 49922 5 51155 5 52255 5 51188 5 53377 5 51155 5 52277 5 53366 5 51199
206211_at 3 38822 3 39911 3 39900 3 39922 3 39944 3 39911 3 38877 3 39933 3 38877 3 39933 3 39955 3 39922
206049_at 6 66644 6 66622 6 65577 6 64455 6 67700 6 68877 6 64422 6 68866 6 64400 6 65544 6 67722 6 65577
202627_s_at 5 50088 5 50088 4 49922 4 49933 5 50066 5 50066 5 50044 5 50033 4 47766 5 50055 4 47799 4 49911
202628_s_at 4 46666 4 46688 4 44466 4 46688 4 46688 4 46699 4 45555 4 48844 4 45522 4 46699 4 46655 4 46611
210073 at 3 38866 3 38833 3 37755 3 39911 3 38888 3 39922 3 38811 3 38888 3 38855 3 38844 3 37799 3
— 38800
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly 1 (A2) Ly 1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
215078_at 399 400 403 404 396 401 398 394 404 404 393 399 202935_s_at 410 416 412 414 415 414 404 415 419 419 428 420
454 461 458 442 456 453 450 452 453 458 451 447
213112_s_at 6 60088 6 60099 5 58811 5 59999 6 60000 5 59988 5 58877 6 61133 5 58800 6 60022 6 61144 6 61177
203010_at 7 71155 7 74444 7 72255 6 65533 6 67700 6 65588 7 72255 7 71188 7 71122 6 66688 6 67711 6 66622
208049_s_at 4 46699 4 45555 4 46688 4 48844 4 48833 4 47777 4 48800 4 47733 4 47766 4 47755 4 48811 4 47766
210637_at 5 52277 5 56611 5 52244 5 56655 5 53322 5 55511 5 54488 5 53344 5 54455 5 55588 5 55599 5 55555
210294_at 460 468 472 452 450 458 465 483 463 469 467 456
209277_at 375 357 355 361 371 364 366 365 356 360 381 362
209278_s_at 445 452 445 437 449 455 441 441 442 442 452 437
211003_x_at 533 535 513 536 534 544 534 525 542 546 542 544
211573_x_at 559 549 524 555 537 570 557 557 563 590 578 561
216183_at 600 612 599 589 607 595 599 605 576 608 614 590
201107_s_at 512 507 495 513 490 511 507 515 504 540 525 530
201108_s_at 546 559 552 544 570 565 568 575 562 574 562 573
201109_s_at 4 41144 4 43344 4 41166 4 40022 4 43399 4 41111 4 42211 4 42255 4 40066 4 40099 4 42244 4 41100 g$
201110_s_at 373 378 373 376 380 382 373 372 377 377 381 375
203083_at 533 547 532 519 523 523 523 552 528 526 544 519
201645_at 399 419 398 394 406 405 396 408 399 395 414 408
207113_s_at 542 540 517 528 549 528 534 543 525 606 622 575
202509_s_at 542 558 537 552 557 554 557 544 549 574 579 555
202510_s_at 640 666 651 658 658 660 655 655 644 659 672 641
203508_at 442 441 430 434 434 436 445 458 440 448 429 435
205153_s_at 594 542 524 604 624 603 575 547 533 625 650 610
222292_at 459 465 473 457 465 452 451 447 460 466 467 485
211786_at 461 453 449 464 453 464 452 465 462 471 476 467
207892_at 542 561 556 539 563 556 552 557 549 579 562 557
210865_at 513 525 492 508 506 481 502 499 464 523 519 497
211333_S_at 4 4 4 b66UU0 4 4 4 bb6i11 4 4 4333««8 4 4 46 66999 4 4 46 66bb5 4 4 4 b66555 4 4 44448«8 4 4 4 S55I11 4 4 4555333 4 4 4666111 4 4 47//111 4 4 4444666
204413 at 5 5 5666555 5 5 5999444 5 5 5555000 5 5 57 77888 5 5 59 99333 5 5 5555888 5 5 5444999 5 5 5888444 5 5 5444999 5 5 5444666 5 5 5777333 5 5 5222888
206067_s_at 44 4333666 44 4333111 44 4222777 44 4 333111 44 4 222333 44 4333333 44 4333222 44 4222555 44 4333222 44 4333444 44 4444111 44 4333111
216953 s_at 55 5666777 55 5666444 55 5666555 55 5 777888 55 5 666666 55 5999666 55 5888666 55 5888999 55 5888555 55 5888999 55 5999666 55 5999777
Table 4B: NFκB-Regulated Genes (See tables reference 1) t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
FDR Cutoff 1 OE-02 8 2E-03 1 2E-02 9 4E-03 AC v BD AC v BD
205481_at 9 OE-02 1 5E-01 1 0E-01 1 5E-01 Yes No ADORA1 Hs 77867 adenosine A1 receptor
216220_s_at 1 2E-01 94E-02 2 4E-01 2 2E-01 Yes No ADORA1 Hs 77867 adenosine A1 receptor
202834_at 2 1 E-01 8 4E-02 3 6E-01 7 2E-02 Yes No AGT Hs 19383 angiotensinogen
204151_x_at 5 8E-01 8 6E-01 5 1E-01 7 5E-01 Yes No AKR1C1 Hs 295131 aldo-keto reductase family 1, member C1
216594_x_at 8 4E-01 4 0E-01 8 3E-01 3 0E-01 Yes No AKR1C1 Hs 295131 aldo-keto reductase family 1 , member C1
204445_s_at 2 5E-02 1 7E-01 1 4E-01 5 8E-01 Yes No ALOX5 Hs 89499 arachidonate 5-lιpoxygenase
204446_s_at 1 9E-02 2 1E-01 1 1E-03 1 4E-01 Yes No ALOX5 Hs 89499 arachidonate 5-lιpoxygenase
214366_s_at 2 9E-02 1 1 E-01 1 7E-01 3 3E-01 Yes No ALOX5 Hs 89499 arachidonate 5-lιpoxygenase
214953_s_at 7 0E-01 5 2E-01 8 2E-01 2 6E-01 Yes No APP Hs 177486 amyloid beta (A4) precursor protein
211621_at 7 1 E-01 6 4E-01 2 7E-01 2 3E-02 Yes No AR Hs 99915 androgen receptor
203174_s_at 1 6E-01 2 5E-01 1 1 E-01 2 7E-01 Yes No ARFRP1 Hs 389277 ADP-πbosylation factor related protein 1
215984_s_at 1 2E-01 7 5E-01 3 7E-02 5 3E-01 Yes No ARFRP1 Hs 389277 ADP-nbosylation factor related protein 1
201891_s_at 9 5E-01 4 6E-01 5 4E-01 3 1 E-01 Yes No B2M Hs 48516 beta-2-mιcroglobulιn
216231_s_at 7 4E-01 9 9E-02 9 7E-01 8 1 E-02 Yes No B2M Hs 48516 beta-2-mιcroglobulιn
203685_at 1 2E-02 3 8E-02 1 3E-02 7 5E-02 Yes No BCL2 Hs 79241 B-cell CLL/lymphoma 2
207005_s_at 6 OE-02 7 0E-01 2 1 E-02 3 0E-01 Yes No BC L2 Hs 79241 B-cell CLL/lymphoma 2
205681_at 1 7E-02 1 4E-02 8 8E-02 1 3E-02 Yes No BCL2A1 Hs 227817 BCL2-related protein A1
202076_at 4 8E-01 1 1E-01 7 3E-01 84E-02 Yes No BIRC2 Hs 289107 baculoviral IAP repeat-containing 2
210538_s_at 4 3E-04 6 6E-02 7 OE-05 1 9E-02 Yes No BIRC3 Hs 127799 baculoviral IAP repeat-containing 3
205114_s_at 4 9E-01 2 0E-01 4 9E-01 1 9E-01 Yes No CCL3 Hs 73817 chemokine (C-C motif) ligand 3
204103_at 2 2E-02 4 3E-01 7 5E-02 9 2E-01 Yes No CCL4 Hs 75703 chemokine (C-C motif) ligand 4
201700_at 3 5E-03 3 1E-03 4 3E-04 3 2E-03 Yes No CCND3 Hs 83173 cyclin D3
204118_at 1 4E-01 4 8E-02 1 6E-01 7 OE-02 Yes No CD48 Hs 901 CD48 antigen
209795_at 2 8E-02 4 2E-02 1 9E-02 4 OE-02 Yes No CD69 Hs 82401 CD69 antigen
209619_at 5 7E-01 2 4E-02 2 3E-01 2 2E-02 Yes No CD74 Hs 446471 CD74 antigen
207176_s_at 5 0E-01 4 9E-02 4 5E-01 3 8E-02 Yes No CD80 Hs 838 CD80 antigen
204440_at 8 3E-02 3 7E-02 5 2E-01 2 OE-02 Yes No CD83 Hs 79197 CD83 antigen
202246_s_at 2 2E-01 6 6E-01 1 4E-01 6 7E-01 Yes No CDK4 Hs 95577 cyclin-dependent kinase 4
203198_at 1 0E-01 7 3E-03 1 9E-02 1 OE-02 Yes No CDK9 Hs 150423 cyclin-dependent kinase 9
202284 s at 9 1E-01 7 7E-02 5 6E-01 1 1E-01 Yes No CDKN1A Hs 370771 cyclin-dependent kinase inhibitor 1A (p21 ,
Cιp1)
208485 x at 8 3E-01 2 4E-01 9 3E-02 3 0E-01 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene lD Gene Title
Symbol
209508_x_at 8 8E-01 9 9E-02 8 5E-01 9 1 E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
209939_x_at 1 6E-03 5 6E-03 3 6E-03 3 5E-03 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
210563_x_at 2 5E-03 7 5E-02 5 7E-03 3 8E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
211316_x_at 5 4E-01 3 3E-03 7 8E-01 3 4E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
211317_s_at 3 5E-01 1 3E-01 4 3E-02 5 5E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
211862_x_at 4 3E-01 1 5E-02 7 OE-02 6 5E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
214618_at 6 0E-01 1 8E-01 9 9E-01 1 8E-01 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
209716_at 7 4E-01 8 3E-02 5 1 E-01 5 7E-01 Yes No CSF1 Hs 173894 colony stimulating factor 1 (macrophage)
200838_at 2 4E-02 2 3E-01 8 1 E-03 6 1 E-02 Yes No CTSB Hs 135226 cathepsin B
200839_s_at 3 7E-03 1 7E-02 8 6E-03 2 5E-02 Yes No CTSB Hs 135226 cathepsin B
213274_s_at 7 8E-01 5 5E-01 6 2E-01 4 3E-01 Yes No CTSB Hs 135226 cathepsin B
204470_at 7 6E-01 5 9E-01 3 6E-01 9 7E-01 Yes No CXCL1 Hs 789 chemokine (C-X-C motif) hgand 1
210163_at 4 9E-01 7 2E-01 3 1 E-01 4 9E-01 Yes No CXCL11 Hs 103982 chemokine (C-X-C motif) hgand 11
214974_x_at 5 9E-01 5 7E-01 2 4E-01 1 2E-01 Yes No CXCL5 Hs 89714 chemokine (C-X-C motif) hgand 5
203700_s_at 8 7E-01 2 2E-01 9 4E-01 3 2E-01 Yes No DIO2 Hs 436020 deiodmase, iodothyronine, type Il o
201041_s_at 4 7E-03 1 OE-02 1 3E-03 2 7E-03 Yes No DUSP1 Hs 171695 dual specificity phosphatase 1
203692_s_at 3 9E-01 3 5E-01 4 3E-01 2 1 E-01 Yes No E2F3 Hs 1189 E2F transcription factor 3
203693_s_at 7 7E-01 7 1 E-01 2 9E-01 9 8E-01 Yes No E2F3 Hs 1189 E2F transcription factor 3
211551_at 8 5E-01 8 2E-01 3 7E-01 2 1 E-01 Yes No EGFR Hs 77432 epidermal growth factor receptor
201694_s_at 9 8E-01 2 3E-01 8 7E-01 2 4E-01 Yes No EGR1 Hs 326035 early growth response 1
214766_s_at 9 4E-02 1 9E-02 9 6E-02 2 1 E-02 Yes No ELYS Hs 33363 ELYS transcription factor-like protein
TMBS62
201313_at 1 7E-03 2 1 E-01 2 2E-03 3 4E-01 Yes No ENO2 HS 511915 enolase 2, (gamma, neuronal)
205767_at 8 1 E-02 3 8E-01 1 5E-01 2 7E-01 Yes No EREG Hs 115263 epireguhn
202081_at 1 1 E-02 2 6E-03 7 1 E-03 1 8E-03 Yes No ETR101 Hs 737 immediate early protein
205756_s_at 1 3E-01 1 8E-01 3 1 E-01 5 0E-01 Yes No F8 Hs 413083 coagulation factor VIII
214701_s_at 7 2E-01 1 3E-01 4 7E-01 6 4E-01 Yes No FN1 Hs 418138 fibronectm 1
202275_at 7 7E-01 3 5E-02 5 3E-01 3 1 E-02 Yes No G6PD Hs 80206 glucose-6-phosphate dehydrogenase
207574_s_at 8 1 E-02 3 3E-01 3 6E-02 8 8E-01 Yes No GADD45B Hs 110571 growth arrest and DNA-damage-inducible, beta
209304_x_at 1 3E-01 2 8E-01 6 8E-03 2 4E-01 Yes No GADD45B Hs 110571 growth arrest and DNA-damage-inducible, beta 209305 s at 1 2E-01 3 4E-01 1 2E-01 4 1 E-01 Yes No GADD45B Hs 110571 growth arrest and DNA-damage-inducible, beta
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol 202269 x at 52E-02 4 5E-02 2 OE-02 1 5E-02 Yes No GBP1 Hs 62661 guanylate binding protein 1 , interferon- inducible, 67kDa
202270_at 2 9E-02 3 8E-02 2 9E-02 3 6E-02 Yes No GBP1 Hs 62661 guanylate binding protein 1 , interferon- inducible, 67kDa
200651_at 3 7E-02 3 3E-01 8 8E-03 1 5E-02 Yes No GNB2L1 Hs 5662 G protein, beta polypeptide 2-lιke 1
222034_at 8 6E-02 4 0E-01 8 OE-02 5 OE-01 Yes No GNB2L1 Hs 5662 G protein, beta polypeptide 2-lιke 1
200824_at 9 OE-03 2 6E-02 2 2E-03 8 8E-03 Yes No GSTP1 Hs 411509 glutathione S-transferase pi
208729_x_at 1 7E-03 2 2E-05 1 2E-04 1 8E-04 Yes Yes HLA-B Hs 77961 major histocompatibility complex, class I, B
209140_x_at 6 0E-04 1 4E-04 3 6E-04 6 9E-05 Yes Yes HLA-B Hs 77961 major histocompatibility complex, class I, B
211911_x_at 1 3E-05 2 4E-06 9 6E-05 1 3E-05 Yes Yes HLA-B Hs 77961 major histocompatibility complex, class I, B
200943 at 7 3E-03 1 2E-02 1 5E-01 2 2E-01 Yes No HMGN1 Hs 356285 high-mobility group nucleosome binding domain 1
200944 s at 8 2E-02 5 5E-02 2 8E-01 1 9E-01 Yes No HMGN1 Hs 356285 high-mobility group nucleosome binding domain 1
202638_s_at 1 3E-01 3 2E-01 1 4E-01 7 1E-01 Yes No ICAM 1 Hs 386467 intercellular adhesion molecule 1 (CD54) 215485_s_at 7 9E-01 5 7E-01 84E-01 4 9E-01 Yes No ICAM 1 Hs 386467 intercellular adhesion molecule 1 (CD54) 210354_at 74E-01 1 4E-01 8 1E-01 2 OE-01 Yes No IFNG Hs 856 interferon, gamma 202718_at 7 9E-02 84E-02 7 9E-02 8 5E-02 Yes No IGFBP2 Hs 433326 insulin-like growth factor binding protein 2,
36kDa
207901_at 7 8E-01 5 2E-01 2 3E-01 2 1E-01 Yes No IL12B Hs 674 interleukin 12B
208200_at 2 9E-01 4 9E-01 3 4E-01 3 0E-01 Yes No IL1A Hs 1722 interleukin 1 , alpha
205207_at 7 1E-01 6 5E-01 8 8E-01 8 OE-01 Yes No IL6 Hs 512234 interleukin 6 (interferon, beta 2)
202531_at 7 7E-03 3 6E-03 2 3E-02 1 2E-02 Yes No IRF1 Hs 80645 interferon regulatory factor 1
203275_at 3 7E-02 1 6E-02 2 7E-04 2 6E-02 Yes No IRF2 Hs 83795 interferon regulatory factor 2
204562_at 34E-01 2 1E-04 1 6E-01 1 7E-03 Yes No IRF4 Hs 127686 interferon regulatory factor 4
216986_s_at 3 5E-01 4 9E-01 3 8E-01 5 5E-01 Yes No IRF4 Hs 127686 interferon regulatory factor 4
208436_s_at 1 5E-01 1 0E-01 5 4E-02 2 7E-02 Yes No IRF7 Hs 166120 interferon regulatory factor 7
213281_at 1 3E-01 4 OE-01 4 OE-02 2 7E-01 Yes No JUN Hs 78465 v-jun sarcoma virus 17 oncogene homolog
(avian)
201473_at 3 2E-01 8 9E-03 56E-01 3 7E-03 Yes No JUNB Hs 400124 jun B proto-oncogene 207029_at 6 7E-01 4 8E-01 9 6E-01 7 9E-01 Yes No KITLG Hs 1048 KIT ligand 216264_s_at 4 1 E-01 4 6E-01 9 OE-02 2 4E-01 Yes No LAMB2 Hs 439726 laminin, beta 2 (laminin S) 207339_s_at 8 9E-03 1 7E-02 3 5E-03 2 OE-02 Yes No LTB Hs 376208 lymphotoxin beta 213975 S at 4 1E-02 5 2E-02 34E-02 3 8E-02 Yes No LYZ Hs 234734 lysozyme
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
208037_s_at 7 3E-01 2 1 E-01 8 1 E-01 6 9E-02 Yes No MADCAM1 Hs 102598 mucosal vascular addressin cell adhesion molecule 1
206296_x_at 6 8E-03 2 2E-03 2 5E-03 6 8E-04 Yes Yes MAP4K1 Hs 95424 mitogen-activated protein kinase kinase kinase kinase 1
214219_x_at 5 2E-03 1 OE-03 8 4E-03 2 7E-03 Yes Yes MAP4K1 Hs 95424 mitogen-activated protein kinase kinase kinase kinase 1
214339_s_at 1 5E-03 6 0E-04 1 2E-02 3 4E-03 Yes Yes MAP4K1 Hs 95424 mitogen-activated protein kinase kinase kinase kinase 1
201126_s_at 2 0E-01 1 9E-03 3 9E-01 1 4E-02 Yes No MGAT1 Hs 120870 mannosyl (alpha-1 ,3-)-glycoproteιn beta-
1 ,2-N-acetylglucosamιnyltransferase
203936_s_at 6 7E-01 1 3E-01 4 5E-01 8 5E-02 Yes No MMP9 Hs 151738 matrix metalloproteinase 9
202086_at 2 5E-01 3 4E-01 9 3E-01 8 7E-01 Yes No MX1 Hs 436836 myxovirus (influenza virus) resistance 1
204798_at 9 2E-02 5 9E-02 1 OE-01 5 5E-02 Yes No MYB Hs 407830 v-myb myeloblastosis viral oncogene homolog (avian)
215152_at 5 3E-01 4 8E-01 1 9E-01 1 4E-01 Yes No MYB Hs 407830 v-myb myeloblastosis viral oncogene homolog (avian) K)
202431_s_at 1 4E-02 1 0E-01 1 6E-01 4 7E-01 Yes No MYC Hs 202453 v-myc myelocytomatosis viral oncogene homolog (avian)
209239_at 6 6E-03 1 9E-01 6 8E-03 4 6E-01 Yes No NFKB1 Hs 160557 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105)
207535_s_at 2 4E-03 4 8E-02 3 2E-03 2 4E-02 Yes No NFKB2 Hs 73090 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)
201502_s_at 8 8E-01 1 3E-01 4 7E-01 5 5E-02 Yes No NFKBIA Hs 81328 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha
201468_s_at 2 1 E-01 1 1 E-02 3 7E-01 1 OE-02 Yes No NQO1 Hs 406515 NAD(P)H dehydrogenase, quinone 1
210519_s_at 6 2E-02 3 2E-03 2 7E-02 2 7E-04 Yes No NQO1 Hs 406515 NAD(P)H dehydrogenase, quinone 1
201866_s_at 4 5E-04 2 3E-02 1 6E-04 1 OE-02 Yes No NR3C1 Hs 512414 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
211671_s_at 2 8E-04 9 OE-02 1 1 E-04 3 OE-02 Yes No NR3C1 Hs 512414 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
216321_s_at 4 2E-03 3 9E-03 3 8E-03 1 5E-03 Yes Yes NR3C1 Hs 512414 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
204622 x at 1 6E-01 2 8E-01 3 3E-01 5 8E-01 Yes No NR4A2 Hs 82120 nuclear receptor subfamily 4, group A, member 2
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
216248_s_at 8 8E-03 1 3E-02 1 2E-01 1 4E-01 Yes No NR4A2 Hs 82120 nuclear receptor subfamily 4, group A, member 2
210004_at 9 3E-01 4 0E-01 6 9E-01 7 7E-01 Yes No OLR1 Hs 445299 oxidised low density lipoprotein (lectin-like) receptor 1
121_at 5 9E-01 2 9E-01 2 6E-01 1 1 E-01 Yes No PAX8 Hs 308061 paired box gene 8
203557 s at 6 9E-05 1 1 E-03 4 7E-05 4 2E-04 Yes Yes PCBD Hs 3192 dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1)
201202_at 4 6E-03 7 1 E-01 9 5E-04 8 9E-01 Yes No PCNA Hs 78996 proliferating cell nuclear antigen
213791_at 74E-01 5 4E-01 4 5E-01 9 5E-02 Yes No PENK Hs 339831 proenkephalin
200737_at 3 8E-02 2 8E-02 3 3E-02 2 3E-02 Yes No PGK1 Hs 78771 phosphoglycerate kinase 1
200738_s_at 3 6E-02 5 7E-02 9 5E-03 1 7E-02 Yes No PGK1 Hs 78771 phosphoglycerate kinase 1
217356_s_at 5 8E-02 6 6E-02 4 9E-02 5 6E-02 Yes No PGK1 Hs 78771 phosphoglycerate kinase 1
217383_at 1 1 E-01 2 1E-01 2 1E-01 5 1E-01 Yes No PGK1 Hs 78771 phosphoglycerate kinase 1
209193_at 7 0E-01 3 5E-01 5 7E-01 4 4E-01 Yes No PIM1 Hs 81170 pιm-1 oncogene
210145 at 1 2E-01 8 8E-02 2 0E-01 9 3E-02 Yes No PLA2G4A Hs 211587 phospholipase A2, group IVA (cytosolic, calcium-dependent)
201979_s_at 9 6E-01 6 8E-02 1 3E-01 1 6E-01 Yes No PPP5C Hs 431861 protein phosphatase 5, catalytic subunit
214617_at 1 9E-02 1 9E-01 3 7E-02 2 7E-01 Yes No PRF1 Hs 2200 perforin 1 (pore forming protein)
202545_at 9 1E-04 6 3E-03 5 7E-03 8 3E-02 Yes No PRKCD Hs 155342 protein kinase C, delta
204279 at 3 2E-03 6 5E-04 3 8E-04 1 5E-04 Yes Yes PSMB9 Hs 381081 proteasome (prosome, macropain) subunit, beta type, 9
211661_x_at 1 2E-02 7 6E-02 5 5E-03 4 9E-02 Yes No PTAFR Hs 46 platelet-activating factor receptor 211892_s_at 4 9E-01 2 8E-01 1 9E-01 4 1 E-01 Yes No PTGIS Hs 302085 prostaglandin I2 (prostacyclin) synthase 206035 at 32E-01 7 7E-02 1 2E-01 6 2E-03 Yes No REL Hs 44313 v-rel reticuloendotheliosis viral oncogene homolog (avian)
206036_s_at 34E-02 8 9E-02 2 8E-02 74E-02 Yes No REL Hs 44313 v-rel reticuloendotheliosis viral oncogene homolog (avian)
205205_at 4 6E-02 5 6E-02 4 3E-02 5 3E-02 Yes No RELB Hs 307905 v-rel reticuloendotheliosis viral oncogene homolog B
209544_at 5 3E-01 2 6E-01 9 8E-01 9 8E-02 Yes No RIPK2 Hs 103755 receptor-interacting serine-threonine kinase
9
209545_s_at 1 2E-01 3 6E-01 2 OE-02 1 4E-01 Yes No RIPK2 Hs 103755 receptor-interacting serine-threonine kinase
9
200872_at 1 1E-02 1 8E-02 3 3E-02 4 9E-02 Yes No S100A10 Hs 143873 S100 calcium binding protein A10
203186 s at 4 6E-03 5 1E-03 4 5E-04 1 6E-02 Yes No S100A4 Hs 81256 S100 calcium binding protein A4
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
215223_s_at 2 2E-01 2 2E-02 1 6E-01 8 OE-03 Yes No SOD2 Hs 384944 superoxide dismutase 2, mitochondrial
216841_s_at 4 5E-01 3 6E-02 3 2E-01 1 8E-02 Yes No SOD2 Hs 384944 superoxide dismutase 2, mitochondrial
221477_s_at 1 3E-01 1 9E-03 1 3E-01 2 6E-03 Yes No SOD2 Hs 384944 superoxide dismutase 2, mitochondrial
201471_s_at 2 1 E-01 9 6E-02 4 6E-01 1 9E-01 Yes No SQSTM 1 Hs 182248 sequestosome 1
208048_at 9 2E-01 2 0E-01 9 5E-01 2 8E-01 Yes No TACR1 Hs 469066 tachykinin receptor 1
202307_s_at 1 4E-02 64E-04 1 2E-02 5 9E-04 Yes No TAP1 Hs 352018 transporter 1 , ATP-binding cassette, subfamily B (MDR/TAP)
208829_at 2 9E-01 1 8E-01 7 3E-01 5 2E-01 Yes No TAPBP Hs 370937 TAP binding protein (tapasin) 207199_at 1 8E-02 3 9E-02 2 4E-03 1 4E-01 Yes No TERT Hs 439911 telomerase reverse transcriptase 215775_at 4 0E-01 6 1 E-01 2 9E-01 8 4E-02 Yes No THBS1 Hs 164226 thrombospondin 1 216005_at 2 6E-01 5 2E-02 2 7E-01 64E-02 Yes No TNC Hs 98998 tenascin C (hexabrachion) 202643_s_at 1 7E-05 3 5E-02 6 8E-03 3 9E-02 Yes No TNFAIP3 Hs 211600 tumor necrosis factor, alpha-induced protein 3
202644_s_at 7 OE-04 5 2E-02 5 8E-04 1 4E-02 Yes No TNFAIP3 Hs 211600 tumor necrosis factor, alpha-induced protein 3
215346_at 1 6E-01 6 1 E-02 1 5E-01 7 OE-02 Yes No TNFRSF5 Hs 504816 tumor necrosis factor receptor superfamily, member 5
35150_at 2 5E-01 1 3E-01 8 9E-02 6 3E-02 Yes No TNFRSF5 Hs 504816 tumor necrosis factor receptor superfamily, member 5
207536_s_at 9 7E-01 9 3E-01 64E-01 5 0E-01 Yes No TNFRSF9 Hs 193418 tumor necrosis factor receptor superfamily, member 9
202687_s_at 2 2E-02 3 8E-02 1 4E-03 6 6E-04 Yes No TNFSF10 Hs 387871 tumor necrosis factor (ligand) superfamily, member 10
202688_at 1 7E-04 36E-04 2 5E-02 1 8E-02 Yes No TNFSF10 Hs 387871 tumor necrosis factor (ligand) superfamily, member 10
214329_x_at 6 8E-02 1 1E-01 3 2E-02 76E-02 Yes No TNFSF10 Hs 387871 tumor necrosis factor (ligand) superfamily, member 10
201746_at 2 2E-04 1 6E-03 2 5E-04 1 8E-03 Yes Yes TP53 Hs 408312 tumor protein p53 (Li-Fraumeni syndrome) 211300_s_at 1 6E-02 2 3E-02 8 OE-03 1 2E-02 Yes No TP53 Hs 408312 tumor protein p53 (Li-Fraumeni syndrome) 205599_at 1 5E-01 1 6E-01 8 5E-02 7 2E-02 Yes No TRAF 1 Hs 438253 TNF receptor-associated factor 1 213191_at 8 6E-02 8 7E-02 3 6E-02 2 7E-02 Yes No TRIF Hs 29344 TIR domain containing adaptor inducing interferon-beta
203109 at 9 2E-02 1 3E-01 4 9E-02 1 1E-01 Yes No UBE2M Hs 406068 ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
208997_s_at 1 7E-02 3 2E-01 4 6E-02 7 4E-01 Yes No UCP2 Hs 80658 uncoupling protein 2 (mitochondrial, proton carrier)
208998_at 2 1 E-02 7 5E-03 1 3E-02 4 1 E-01 Yes No UCP2 Hs 80658 uncoupling protein 2 (mitochondrial, proton carrier)
204881_s_at 6 4E-02 5 4E-02 8 9E-02 8 3E-02 Yes No UGCG Hs 432605 UDP-glucose ceramide glucosyltransferase
221765_at 9 OE-01 2 1 E-01 5 2E-01 1 3E-01 Yes No UGCG Hs 432605 UDP-glucose ceramide glucosyltransferase
203868_s_at 2 7E-01 9 7E-01 4 5E-01 9 9E-01 Yes No VCAM 1 Hs 109225 vascular cell adhesion molecule 1
209946 at 3 5E-02 7 8E-02 7 OE-01 9 1 E-01 Yes No VEGFC Hs 79141 vascular endothelial growth factor C
201426_s_at 3 3E-05 1 OE-03 2 2E-04 5 5E-04 Yes Yes VIM Hs 435800 vimentin
210301_at 6 4E-01 9 7E-02 5 3E-01 7 OE-02 Yes No XDH Hs 250 xanthine dehydrogenase
208544_at 3 4E-01 2 2E-01 1 7E-01 1 1 E-01 No No ADRA2B Hs 247686 adrenergic, alpha-2B-, receptor
210081_at 6 1 E-02 3 OE-02 5 1 E-01 1 3E-01 No No AGER Hs 184 advanced glycosylation end product- specific receptor
217046_s_at 5 6E-01 5 6E-01 1 7E-01 2 2E-01 No No AGER Hs 184 advanced glycosylation end product- specific receptor -^J
207206_s_at 7 OE-01 3 3E-01 7 9E-01 2 6E-01 No No ALOX12 Hs 1200 arachidonate 12-lιpoxygenase ■
213952 s at 8 6E-01 1 8E-01 7 9E-01 1 9E-01 No No ALOX5 Hs 89499 arachidonate 5-lιpoxygenase
206516_at 6 1 E-01 1 4E-01 8 8E-01 1 9E-01 No No AMH Hs 112432 anti-Mullenan hormone
205820 s at 5 3E-01 2 8E-02 5 OE-01 2 1 E-01 No No APOC3 Hs 73849 apolipoprotein C-III
200602_at 4 8E-01 2 1 E-02 4 5E-01 2 2E-02 No No APP Hs 177486 amyloid beta (A4) precursor protein
211277 x at 1 1 E-01 8 3E-01 3 1 E-01 2 7E-01 No No APP Hs 177486 amyloid beta (A4) precursor protein
211110_s_at 3 2E-01 2 9E-01 3 8E-01 3 6E-01 No No AR Hs 99915 androgen receptor
207367_at 8 2E-01 4 4E-01 9 5E-01 5 1 E-01 No No ATP 12A Hs 147111 ATPase, H+/K+ transporting, nongastric, alpha polypeptide
217904 s at 3 3E-01 6 1 E-01 5 1 E-01 9 4E-01 No No BACE Hs 49349 beta-site APP-cleaving enzyme
203684 s at 1 2E-01 8 2E-01 4 8E-02 6 OE-01 No No BCL2 Hs 79241 B-cell CLL/lymphoma 2
207004 at 1 9E-01 2 6E-01 3 3E-01 5 3E-01 No No BC L2 Hs 79241 B-cell CLL/lymphoma 2
207510 at 9 6E-01 4 3E-01 5 3E-01 9 2E-02 No No BDKRB1 Hs 46348 bradykinin receptor B1
202357_s_at 8 6E-02 4 7E-02 5 8E-01 5 9E-01 No No BF Hs 69771 B-factor, properdin
211920 at 9 6E-01 9 2E-01 7 OE-01 6 7E-01 No No BF Hs 69771 B-factor, properdin
201261_x_at 6 7E-01 9 1 E-01 6 5E-01 1 OE+00 No No BGN Hs 821 biglycan
201262_s_at 7 9E-01 5 1 E-01 5 5E-01 3 8E-01 No No BGN Hs 821 biglycan
205289 at 8 1 E-01 8 OE-01 6 OE-01 9 5E-01 No No BMP2 Hs 73853 bone morphogenetic protein 2
205290 s at 1 9E-01 1 OE-01 8 3E-01 1 7E-01 No No BMP2 Hs 73853 bone morphogenetic protein 2
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
204439_at 9 1 E-02 3 7E-02 6 7E-02 1 0E-01 No No C1orf29 Hs 389724 chromosome 1 open reading frame 29 217767_at 2 1 E-01 1 6E-01 6 9E-01 7 0E-01 No No C3 Hs 284394 complement component 3 220066_at 1 3E-02 6 4E-02 5 2 E-01 1 1 E-01 No No CARD15 Hs 135201 caspase recruitment domain family, member 15
203065_s_at 5 4E-01 2 7E-01 6 8E-01 6 9E-01 No No CAV1 Hs 74034 caveolm 1 , caveolae protein, 22kDa
212097_at 5 8E-01 7 8E-01 6 5E-01 3 7E-01 No No CAV1 Hs 74034 caveolin 1 , caveolae protein, 22kDa
210133_at 7 6E-01 5 6E-02 7 1 E-01 7 7E-02 No No CCL11 Hs 54460 chemokine (C-C motif) ligand 11
216598_s_at 2 6E-01 1 7E-01 4 1 E-02 3 3E-02 No No CCL2 Hs 303649 chemokine (C-C motif) ligand 2
205476_at 9 2E-01 8 2E-01 3 8E-01 3 3E-01 No No CCL20 Hs 75498 chemokine (C-C motif) ligand 20
207861_at 1 4E-01 7 1 E-01 7 8E-01 2 9E-01 No No CCL22 Hs 97203 chemokine (C-C motif) ligand 22
1405_ι_at 3 4E-01 3 1 E-02 8 1 E-01 1 0E-01 No No CCL5 Hs 489044 chemokine (C-C motif) ligand 5
204655_at 6 4E-01 5 7E-01 6 1 E-01 8 2E-01 No No CCL5 Hs 489044 chemokine (C-C motif) ligand 5
208711_s_at 6 7E-02 2 4E-01 7 6E-01 9 9E-01 No No CCND1 Hs 371468 cyclin D1
208712_at 7 6E-01 2 5E-01 4 5E-01 4 5E-01 No No CCND1 Hs 371468 cyclin D1
214019_at 9 4E-02 1 2E-01 1 7E-01 2 6E-02 No No CCND1 Hs 371468 cyclin D1
206991_s_at 3 2E-01 1 6E-01 1 9E-01 1 1 E-01 No No CCR5 Hs 511796 chemokine (C-C motif) receptor 5
206337_at 9 8E-01 4 6E-01 3 0E-01 5 5E-01 No No CC R7 Hs 1652 chemokine (C-C motif) receptor 7
207277_at 3 9E-01 2 6E-02 4 3E-01 3 5E-02 No No CD209 Hs 278694 CD209 antigen
207278_s_at 8 8E-01 1 9E-01 3 0E-01 2 6E-01 No No CD209 Hs 278694 CD209 antigen
206804_at 6 5E-01 2 0E-01 9 7E-01 1 3E-01 No No CD3G Hs 2259 CD3G antigen, gamma polypeptide (TιT3 complex)
210564_x_at 7 5E-02 5 9E-01 1 2E-01 7 3E-02 No No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
214486_x_at 7 2E-01 8 1E-02 1 4E-01 2 5E-01 No No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
202403_s_at 1 9E-01 1 7E-01 2 1 E-01 1 5E-01 No No COL 1A2 Hs 232115 collagen, type I, alpha 2
202404_s_at 1 9E-01 9 8E-01 2 1E-01 4 6E-01 No No COL1A2 Hs 232115 collagen, type I, alpha 2
205753_at 8 9E-01 3 6E-01 3 5E-01 8 0E-01 No No CRP Hs 76452 C-reactive protein, pentraxin-related
37020_at 6 5E-01 1 9E-01 6 5E-01 2 4E-01 No No CRP Hs 76452 C-reactive protein, pentraxin-related
207082_at 4 0E-01 3 5E-01 9 6E-01 9 1 E-01 No No CSF1 Hs 173894 colony stimulating factor 1 (macrophage)
210557_x_at 9 4E-01 1 7E-01 8 6E-01 4 3E-01 No No CSF1 Hs 173894 colony stimulating factor 1 (macrophage)
211839_s_at 5 4E-01 2 7E-01 5 9E-01 3 0E-01 No No CSF1 Hs 173894 colony stimulating factor 1 (macrophage)
210228 at 4 9E-01 4 9E-01 6 8E-01 9 2E-01 No No CSF2 Hs 1349 colony stimulating factor 2 (granulocyte- macrophage)
210229 s at 6 2E-01 1 7E-01 4 7E-01 1 1 E-01 No No CSF2 Hs 1349 colony stimulating factor 2 (granulocyte- macrophage)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
207442 .at 6 OE-01 5 5E-01 3 9E-01 4 7E-02 No No CSF3 Hs 2233 colony stimulating factor 3 (granulocyte)
213275 _x_at 1 2E-02 9 2E-04 9 8E-03 4 3E-02 No No CTSB Hs 135226 cathepsin B
202087. s_at 8 9E-01 5 5E-01 6 5E-01 7 OE-01 No No CTSL Hs 418123 cathepsin L
204533 "at 2 5E-01 2 3E-01 9 3E-01 8 6E-01 No No CXCL10 Hs 413924 chemokine (C-X-C motif) ligand 10
211122. _s_at 8 5E-01 7 3E-01 3 6E-01 1 5E-01 No No CXCL11 Hs 103982 chemokine (C-X-C motif) ligand 11
209774 _x_at 32E-02 44E-01 7 8E-01 9 1E-01 No No CXCL2 Hs 75765 chemokine (C-X-C motif) ligand 2
207852. "at 6 8E-01 8 4E-02 7 1E-01 1 7E-01 No No CXCL5 Hs 89714 chemokine (C-X-C motif) ligand 5
215101 _s_at 94E-01 46E-01 5 5E-01 8 OE-01 No No CXCL5 Hs 89714 chemokine (C-X-C motif) ligand 5
203699. s_at 2 9E-01 2 3E-01 5 4E-01 9 7E-01 No No DIO2 Hs 436020 deiodinase, iodothyronine, type Il
210819 .x_at 7 6E-01 8 3E-01 8 3E-01 4 6E-01 No No DIO2 Hs 436020 deiodinase, iodothyronine, type Il
211215 x_at 4 8E-01 3 1E-01 2 6E-01 1 5E-01 No No DIO2 Hs 436020 deiodinase, iodothyronine, type Il
201044 "x_at 8 2E-01 7 9E-01 8 8E-01 8 5E-01 No No DUSP1 Hs 171695 dual specificity phosphatase 1
201983^ _s_at 5 3E-01 1 1E-01 3 4E-01 7 5E-02 No No EGFR Hs 77432 epidermal growth factor receptor
201984 _s_at 8 1E-01 3 OE-01 5 OE-01 7 6E-01 No No EGFR Hs 77432 epidermal growth factor receptor
210984^ x_at 2 0E-01 2 1E-01 1 3E-01 1 7E-01 No No EGFR Hs 77432 epidermal growth factor receptor
211550 .at 9 8E-01 3 4E-01 8 3E-01 3 OE-01 No No EGFR Hs 77432 epidermal growth factor receptor
211607 "x_at 7 9E-01 24E-01 6 9E-01 1 8E-01 No No EGFR Hs 77432 epidermal growth factor receptor
201693 s_at 3 1E-01 2 2E-01 5 4E-01 6 3E-01 No No EGR1 Hs 326035 early growth response 1
201808 _s_at 5 5E-01 7 6E-01 3 8E-01 4 8E-01 No No ENG Hs 76753 endoglm (Osler-Rendu-Weber syndrome 1)
201809. s_at 7 4E-03 1 3E-02 2 1E-03 3 5E-03 No No ENG Hs 76753 endoglm (Osler-Rendu-Weber syndrome 1)
207257. "at 3 8E-01 3 4E-01 5 4E-01 5 4E-01 No No EPO Hs 2303 erythropoietin
204363 at 4 4E-01 9 9E-01 9 9E-01 4 1 E-01 No No F3 Hs 62192 coagulation factor III (thromboplastin, tissue factor)
206759_at 5 8E-02 1 6E-01 2 7E-02 8 7E-02 No No FCER2 Hs 1416 Fc fragment of IgE, low affinity II, receptor for (CD23A) 206760_s_at 3 8E-02 9 5E-02 2 OE-02 7 OE-02 No No FCER2 Hs 1416 Fc fragment of IgE, low affinity II, receptor for (CD23A)
210495_x_at 7 8E-01 3 9E-01 3 8E-01 6 2E-01 No No FN1 Hs 418138 fibronectin 1
211719_x_at 4 7E-01 2 6E-01 8 8E-01 8 OE-01 No No FN1 Hs 418138 fibronectin 1
212464_s_at 3 9E-01 3 4E-01 5 1 E-01 5 1 E-01 No No FN1 Hs 418138 fibronectin 1
214702_at 6 2E-02 1 4E-01 9 8E-01 7 3E-01 No No FN1 Hs 418138 fibronectin 1
216442_x_at 7 5E-01 8 2E-02 5 6E-01 4 2E-01 No No FN 1 Hs 418138 fibronectin 1
205278_at 8 7E-02 3 8E-03 9 OE-01 2 6E-01 No No GAD1 Hs 420036 glutamate decarboxylase 1 (brain, 67kDa)
206669 at 8 4E-01 9 4E-01 9 3E-01 7 7E-01 No No GAD1 Hs 420036 glutamate decarboxylase 1 (brain, 67kDa)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
206670_s_at 1 8E-01 4 1 E-01 1 6E-01 5 8E-02 No No GAD1 Hs 420036 glutamate decarboxylase 1 (brain, 67kDa)
213560_at 4 5E-01 3 1 E-01 9 9E-01 9 7E-01 No No GADD45B Hs 110571 growth arrest and DNA-damage-inducible, beta
220821 at 5 8E-01 3 1 E-01 6 3E-01 6 2E-01 No No GALR1 Hs 272191 galanin receptor 1
205914_s_at 4 4E-01 2 3E-01 6 8E-01 3 3E-01 No No GRIN1 Hs 105 glutamate receptor, ionotropic, N-methyl D- aspartate 1
205915_x_at 6 0E-01 2 2E-01 3 5E-01 1 5E-01 No No GRIN1 Hs 105 glutamate receptor, ionotropic, N-methyl D- aspartate 1
210781_x_at 5 7E-01 3 9E-01 6 2E-01 4 6E-01 No No GRIN1 Hs 105 glutamate receptor, ionotropic, N-methyl D- aspartate 1
210782_x_at 8 5E-01 9 3E-01 76E-01 8 6E-01 No No GRIN1 Hs 105 glutamate receptor, ionotropic, N-methyl D- aspartate 1
211125_x_at 4 6E-01 7 3E-01 7 9E-01 4 3E-01 No No GRIN1 Hs 105 glutamate receptor, ionotropic, N-methyl D- aspartate 1
206534_at 6 1 E-01 1 9E-01 4 8E-01 1 5E-01 No No GRIN2A Hs 125338 glutamate receptor, ionotropic, N-methyl D- ^o aspartate 2A ∞
221942 s_at 7 7E-01 1 0E-01 5 7E-01 5 1 E-02 No No GUCY1A3 Hs 433488 guanylate cyclase 1, soluble, alpha 3
207316_at 1 7E-01 1 4E-01 3 4E-01 2 9E-01 No No HAS1 Hs 57697 hyaluronan synthase 1
205919 at 2 6E-01 9 6E-02 8 1E-01 2 3E-01 No No HBE1 Hs 117848 hemoglobin, epsilon 1
217683_at 5 8E-01 6 0E-01 1 9E-01 3 4E-01 No No HBE1 Hs 117848 hemoglobin, epsilon 1
203665_at 2 3E-01 7 0E-01 2 8E-02 1 5E-01 No No HMOX1 Hs 202833 heme oxygenase (decycling) 1
210439_at 4 6E-02 3 1 E-01 3 7E-01 4 2E-01 No No ICOS Hs 56247 inducible T-cell co-stimulator
201631 s_at 7 6E-03 1 2E-01 3 3E-02 2 4E-01 No No IER3 Hs 76095 immediate early response 3
205302_at 4 8E-01 7 3E-02 6 6E-01 9 5E-01 No No IGFBP1 Hs 401316 insulin-like growth factor binding protein 1
207433 at 9 3E-01 3 1 E-01 5 1 E-01 9 9E-01 No No IL10 Hs 193717 interleukin 10
206924_at 1 5E-01 9 5E-01 5 8E-01 3 8E-01 No No IL11 Hs 1721 interleukin 11
206926 s at 4 1E-01 4 6E-01 2 OE-01 2 7E-01 No No IL11 Hs 1721 interleukin 11
207844 at 3 9E-01 4 7E-01 2 1 E-01 5 9E-01 No No IL13 Hs 845 interleukin 13
205992_s_at 4 3E-01 4 5E-01 3 OE-01 3 5E-01 No No IL15 Hs 168132 interleukin 15
210118 s at 2 8E-01 3 9E-01 9 6E-01 1 6E-01 No No IL1A Hs 1722 interleukin 1 , alpha
205067_at 2 2E-01 9 OE-02 4 3E-01 1 6E-01 No No IL1 B Hs 126256 interleukin 1 , beta
39402 at 7 7E-01 4 6E-01 1 OE-01 7 7E-02 No No IL1B Hs 126256 interleukin 1 , beta
212657_s_at 3 9E-01 8 7E-01 94E-01 4 6E-01 No No IL1 RN Hs 81134 interleukin 1 receptor antagonist
212659 s at 7 3E-01 2 6E-01 7 2E-01 2 8E-01 No No IL1 RN Hs 81134 interleukin 1 receptor antagonist
216243_s_at 2 0E-01 3 6E-01 1 2E-01 2 5E-01 No No IL1RN Hs 81134 interleukin 1 receptor antagonist
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
216244_at 1 0E-01 9 4E-02 6 2E-01 6 1 E-01 No No IL1 RN Hs 81134 interleukin 1 receptor antagonist
216245_at 9 3E-01 2 6E-01 7 9E-01 3 0E-01 No No IL1RN Hs 81134 interleukin 1 receptor antagonist
207849_at 7 5E-01 4 9E-01 6 1 E-01 6 8E-01 No No IL2 Hs 89679 interleukin 2
206341_at 6 7E-02 54E-01 2 5E-01 6 7E-01 No No IL2RA Hs 130058 interleukin 2 receptor, alpha
211269_s_at 7 6E-01 1 7E-01 7 4E-01 8 7E-02 No No IL2RA Hs 130058 interleukin 2 receptor, alpha
202859_x_at 1 1 E-01 6 5E-01 9 1 E-01 2 6E-01 No No IL8 Hs 624 interleukin 8
208193_at 7 9E-01 9 8E-01 2 9E-01 3 3E-01 No No IL9 Hs 960 interleukin 9
216987_at 5 6E-01 7 4E-01 9 1 E-01 6 0E-01 No No IRF4 Hs 127686 interferon regulatory factor 4
201464_x_at 34E-01 94E-01 84E-02 5 0E-01 No No JUN Hs 78465 v-jun sarcoma virus 17 oncogene homolog
(avian)
201465_s_at 6 0E-01 7 9E-02 2 6E-01 6 3E-01 No No JUN Hs 78465 v-jun sarcoma virus 17 oncogene homolog
(avian) 201466_s_at 2 8E-01 2 9E-01 3 5E-01 8 9E-01 No No JUN Hs 78465 v-jun sarcoma virus 17 oncogene homolog
(avian)
211124_s_at 2 3E-01 9 1 E-01 1 6E-01 8 7E-01 No No KITLG Hs 1048 KIT ligand
204582_s_at 7 6E-01 1 5E-01 6 3E-02 4 2E-01 No No KLK3 Hs 171995 kallikrein 3, (prostate specific antigen)
204583_x_at 4 7E-01 3 6E-01 8 9E-01 6 9E-01 No No KLK3 Hs 171995 kallikrein 3, (prostate specific antigen)
204734_at 2 8E-01 4 5E-01 6 8E-01 6 7E-01 No No KRT15 Hs 80342 keratin 15
208188_at 9 6E-02 3 4E-02 3 OE-02 3 OE-02 No No KRT9 Hs 2783 keratin 9 (epidermolytic palmopla ar keratoderma)
211652_s_at 7 9E-01 1 8E-01 2 0E-01 1 1E-01 No No LBP Hs 154078 lipopolysaccharide binding protein 214461_at 8 8E-01 3 5E-01 6 7E-01 1 7E-01 No No LBP Hs 154078 lipopolysaccharide binding protein 212531_at 8 7E-01 44E-01 5 6E-01 1 7E-01 No No LCN2 Hs 204238 lipocalin 2 (oncogene 24p3) 208949_s_at 9 1 E-01 4 9E-02 2 2E-01 1 4E-01 No No LGALS3 Hs 411701 lectin, galactoside-binding, soluble, 3
(galectin 3)
206975_at 3 5E-01 2 9E-01 2 8E-01 4 6E-01 No No LTA Hs 36 lymphotoxin alpha (TNF superfamily, member 1) 204475_at 2 5E-01 2 9E-01 1 9E-01 4 7E-01 No No MMP1 Hs 83169 matrix metalloproteinase 1 (interstitial collagenase) 205828_at 8 0E-01 2 9E-01 7 5E-01 2 8E-01 No No MMP3 Hs 375129 matrix metalloproteinase 3 (stromelysin 1 , progelatmase) 205970_at 6 9E-01 9 5E-01 3 4E-01 6 4E-01 No No MT3 Hs 73133 metallothionein 3 (growth inhibitory factor
(neurotrophic)) 204673 at 2 4E-01 1 8E-01 9 3E-01 5 5E-01 No No MUC2 Hs 315 mucin 2, intestinal/tracheal
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
209636_at 8 2E-02 2 1E-02 1 2E-01 5 8E-02 No No NFKB2 Hs 73090 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)
211524_at 7 8E-01 4 7E-01 5 5E-01 5 OE-01 No No NFKB2 Hs 73090 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)
203828_s_at 7 1E-01 4 1E-01 5 OE-01 3 OE-01 No No NK4 Hs 943 natural killer cell transcript 4
205440_s_at 5 OE-01 3 3E-01 5 3E-01 2 5E-01 No No NPY1 R Hs 169266 neuropeptide Y receptor Y1
201467_s_at 2 9E-01 5 9E-02 3 4E-01 5 OE-02 No No NQO1 Hs 406515 NAD(P)H dehydrogenase, quinone 1
204621_s_at 2 7E-01 8 3E-01 2 4E-02 1 3E-01 No No NR4A2 Hs 82120 nuclear receptor subfamily 4, group A, member 2
205040_at 3 2E-01 1 3E-01 7 4E-01 7 6E-01 No No ORM1 Hs 278388 orosomucoid 1
205041_s_at 4 5E-01 1 OE-01 6 2E-01 8 OE-01 No No ORM1 Hs 278388 orosomucoid 1
214465_at 9 5E-01 6 6E-02 7 4E-01 1 5E-01 No No ORM1 Hs 278388 orosomucoid 1
207921 x at 8 1 E-01 4 4E-01 5 5E-01 3 2E-01 No No PAX8 Hs 308061 paired box gene 8
207923_x_at 3 6E-01 5 6E-02 1 2E-01 3 OE-02 No No PAX8 Hs 308061 paired box gene 8
207924 x at 4 5E-03 1 9E-04 4 9E-01 4 4E-01 No No PAX8 Hs 308061 paired box gene 8 OO
(•"• \
209552_at 2 6E-01 1 5E-01 1 4E-01 1 2E-01 No No PAX8 Hs 308061 paired box gene 8
214528_s at 9 7E-01 2 OE-01 9 6E-01 1 9E-01 No No PAX8 Hs 308061 paired box gene 8
221990_at 3 OE-01 2 5E-01 5 4E-01 3 3E-01 No No PAX8 Hs 308061 paired box gene 8
204200_s_at 1 OE+00 8 1 E-01 4 3E-01 6 OE-01 No No PDGFB Hs 1976 platelet-derived growth factor beta polypeptide
216055_at 3 1 E-01 1 8E-01 8 6E-01 3 6E-01 No No PDGFB Hs 1976 platelet-derived growth factor beta polypeptide
216061_x_at 2 9E-02 8 9E-02 5 5E-02 1 1E-01 No No PDGFB Hs 1976 platelet-derived growth factor beta polypeptide
206803_at 9 3E-01 3 1 E-02 9 8E-01 1 9E-01 No No PDYN Hs 22584 prodynorphin
204213_at 6 OE-01 2 7E-01 4 OE-01 1 8E-01 No No PIGR Hs 205126 polymeric immunoglobulin receptor
203649_s_at 1 1 E-01 1 1E-01 6 2E-01 5 3E-01 No No PLA2G2A Hs 76422 phospholipase A2, group HA
205479 s at 2 8E-01 2 7E-01 5 1 E-01 5 3E-01 No No PLAU Hs 77274 plasminogen activator, urokinase
211668_s_at 4 3E-01 2 8E-01 2 9E-01 7 3E-01 No No PLAU Hs 77274 plasminogen activator, urokinase
205125_at 4 7E-01 84E-01 1 2E-01 8 2E-01 No No PLCD1 Hs 80776 phospholipase C, delta 1
205720 at 5 2E-01 1 6E-01 4 9E-01 9 2E-01 No No POMC Hs 1897 proopiomelanocortin (beta-endorphin)
215705_at 7 6E-01 3 9E-01 5 9E-01 3 2E-01 No No PPP5C Hs 431861 protein phosphatase 5, catalytic subunit
206278_at 4 5E-01 6 8E-01 2 5E-01 2 8E-01 No No PTAFR Hs 46 platelet-activating factor receptor
211663 x at 2 1 E-01 8 9E-02 9 4E-01 4 6E-01 No No PTGDS Hs 446429 prostaglandin D2 synthase 2 IkDa (brain)
211748 x at 8 3E-02 2 OE-01 4 7E-01 5 2E-01 No No PTGDS Hs 446429 prostaglandin D2 synthase 2 IkDa (brain)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
212187_x_at 1 5E-01 1 8E-01 4 5E-01 3 6E-01 No No PTGDS Hs 446429 prostaglandin D2 synthase 21kDa (brain)
207388_s_at 4 8E-01 1 3E-01 4 1 E-01 8 3E-02 No No PTGES Hs 146688 prostaglandin E synthase
210367_s_at 4 9E-01 8 4E-01 5 1 E-01 9 3E-01 No No PTGES Hs 146688 prostaglandin E synthase
208131_s_at 3 5E-01 2 2E-01 1 8E-01 1 8E-01 No No PTGIS Hs 302085 prostaglandin I2 (prostacyclin) synthase
210702_s_at 6 0E-01 8 2E-01 8 2E-01 2 7E-01 No No PTGIS Hs 302085 prostaglandin I2 (prostacyclin) synthase
204748_at 7 7E-01 8 1E-02 2 2E-01 1 5E-01 No No PTGS2 Hs 196384 prostaglandin-endoperoxide synthase 2
204201_s_at 9 7E-01 7 3E-01 5 4E-01 4 7E-01 No No PTPN13 Hs 387553 APO-1/CD95 (Fas)-assocιated phosphatase
206157_at 7 1 E-01 6 6E-01 5 9E-01 6 3E-01 No No PTX3 Hs 2050 pentaxin-related gene, rapidly induced by
IL-1 beta
216994_s_at 7 3E-01 2 4E-01 9 9E-01 1 6E-01 No No RUNX2 Hs 122116 runt-related transcription factor 2
221282_x_at 6 1 E-01 9 1 E-01 9 7E-01 7 8E-01 No No RUNX2 Hs 122116 runt-related transcription factor 2
221283_at 9 9E-01 3 6E-01 2 4E-01 3 9E-02 No No RUNX2 Hs 122116 runt-related transcription factor 2
217728_at 9 2E-01 1 3E-01 7 9E-01 1 1 E-01 No No S100A6 Hs 275243 S100 calcium binding protein A6 (calcyclin)
208607_s_at 6 3E-01 2 9E-01 5 5E-01 2 0E-01 No No SAA2 Hs 1955 serum amyloid A2 ∞
214456_x_at 7 2E-01 6 4E-01 8 1 E-01 9 6E-01 No No SAA2 Hs 1955 serum amyloid A2 '
202071_at 54E-01 3 8E-01 36E-01 6 7E-01 No No SDC4 Hs 252189 syndecan 4
206211_at 2 1 E-01 1 6E-01 2 2E-01 1 5E-01 No No SELE Hs 89546 selectin E
206049_at 6 5E-01 9 9E-01 5 9E-01 7 8E-01 No No SELP Hs 73800 selectin P
202627 s at 9 2E-01 3 1 E-01 5 2E-01 8 4E-01 No No SERPINE1 Hs 414795 serine (or cysteine) proteinase inhibitor, clade E, member 1
202628 s at 3 5E-01 5 6E-01 6 8E-01 9 0E-01 No No SERPINE1 Hs 414795 serine (or cysteine) proteinase inhibitor, clade E, member 1
210073_at 1 1 E-01 9 6E-01 8 8E-02 2 5E-01 No No SIAT8A Hs 408614 sialyltransferase 8A
215078_at 7 8E-01 5 6E-01 7 0E-01 9 6E-01 No No SOD2 Hs 384944 superoxide dismutase 2, mitochondrial
202935_s_at 5 1E-01 5 8E-02 7 7E-01 1 5E-01 No No SOX9 Hs 2316 SRY (sex determining region Y)-box 9
202936_s_at 2 1 E-01 2 3E-01 7 6E-01 9 2E-01 No No SOX9 Hs 2316 SRY (sex determining region Y)-box 9
213112_s_at 9 7E-01 34E-01 6 6E-01 2 2E-01 No No SQSTM 1 Hs 182248 sequestosome 1
203010 at 4 9E-03 1 2E-02 1 OE-03 6 7E-04 No No STAT5A Hs 437058 signal transducer and activator of transcription 5A
208049_s_at 5 2E-02 9 1 E-02 1 6E-01 7 6E-01 No No TACR1 Hs 469066 tachykinin receptor 1
210637_at 4 8E-01 2 2E-01 5 8E-01 6 OE-02 No No TACR1 Hs 469066 tachykinin receptor 1
210294_at 4 1E-02 6 3E-01 1 1E-01 4 5E-01 No No TAPBP Hs 370937 TAP binding protein (tapasin)
209277 at 6 9E-01 5 9E-01 5 5E-01 5 4E-01 No No TFPI2 Hs 438231 tissue factor pathway inhibitor 2
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
209278_s_at 9 7E-01 5 1E-01 3 9E-01 6 7E-01 No No TFPI2 Hs 438231 tissue factor pathway inhibitor 2
211003_x_at 2 5E-01 1 3E-01 5 1 E-01 1 6E-01 No No TGM2 Hs 512708 transglutaminase 2
211573_x_at 5 1E-01 7 7E-02 6 7E-01 1 6E-01 No No TGM2 Hs 512708 transglutaminase 2
216183_at 3 7E-01 9 8E-01 72E-01 3 9E-01 No No TGM2 Hs 512708 transglutaminase 2
201107_s_at 9 8E-01 1 6E-02 6 2E-01 1 8E-02 No No THBS1 Hs 164226 thrombospondin 1
201108_s_at 4 8E-01 3 5E-02 4 1 E-01 8 2E-01 No No THBS1 Hs 164226 thrombospondin 1
201109_s_at 7 6E-01 4 5E-01 9 8E-01 7 3E-01 No No THBS1 Hs 164226 thrombospondin 1
201110_s_at 1 5E-01 O 3O 6E-01 9 9E-02 2 5E-01 No No THBS1 Hs 164226 thrombospondin 1
203083_at 7 6E-02 4 5E-01 3 0E-01 7 1 E-01 No No THBS2 Hs 458354 thrombospondin 2
201645_at 6 8E-01 9 6E-01 9 0E-01 5 2E-01 No No TNC Hs 98998 tenascin C (hexabrachion)
207113_s_at 8 6E-01 2 OE-02 9 0E-01 2 7E-02 No No TNF Hs 241570 tumor necrosis factor (TNF superfamily, member 2)
202509_s_at 3 2E-01 7 4E-02 3 7E-01 1 OE-01 No No TNFAIP2 Hs 101382 tumor necrosis factor, alpha-induced protein 2
202510_s_at 4 8E-01 6 8E-01 1 7E-01 5 7E-01 No No TNFAIP2 Hs 101382 tumor necrosis factor, alpha-induced OO protein 2
203508_at 5 2E-01 9 9E-01 1 4E-01 2 7E-01 No No TNFRSF1 B Hs 256278 tumor necrosis factor receptor superfamily member 1B
205153_s_at 1 0E-01 4 9E-02 2 3E-02 1 1 E-02 No No TNFRSF5 Hs 504816 tumor necrosis factor receptor superfamily member 5
222292_at 2 1E-01 4 4E-01 4 1E-01 6 6E-02 No No TNFRSF5 Hs 504816 tumor necrosis factor receptor superfamily member 5
211786_at 2 9E-01 2 OE-02 9 3E-01 8 OE-02 No No TNFRSF9 Hs 193418 tumor necrosis factor receptor superfamily member 9
207892_at 9 8E-01 2 2E-01 9 7E-01 1 8E-01 No No TNFSF5 Hs 652 tumor necrosis factor (ligand) superfamily, member 5
210865_at 4 0E-01 3E-01 5 6E-01 1 8E-01 No No TNFSF6 Hs 2007 tumor necrosis factor (ligand) superfamily, member 6
211333_s_at 2 2E-01 5 8E-01 1 7E-03 3 2E-01 No No TNFSF6 Hs 2007 tumor necrosis factor (ligand) superfamily, member 6
204413_at 7 0E-01 3 3E-01 3 7E-01 5 3E-01 No No TRAF2 Hs 437575 TNF receptor-associated factor 2 206067_s_at 4 8E-01 4 1E-01 8 3E-01 2 1 E-01 No No WT1 Hs 1145 Wilms tumor 1 216953 s at 2 4E-01 5 2E-03 5 0E-01 9 6E-02 No No WT1 Hs 1145 Wilms tumor 1
Table 5A: Apoptosis Genes (See tables reference 2)
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly 1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
FDR Cutoff
201715_s_at 749 734 738 781 743 720 758 731 742 752 726 731
205013_s_at 680 661 716 805 854 791 683 696 609 808 897 850
204833_at 713 679 697 646 626 645 708 686 726 687 670 701
213026_at 790 723 761 716 645 679 793 741 772 715 691 743
213930_at 496 473 468 451 447 451 497 454 472 464 452 468
221666_s_at 811 825 815 595 554 561 825 798 813 549 541 520
1861_at 538 557 556 528 568 561 546 550 571 531 575 586
209406_at 702 741 in 740 725 740 673 735 741 752 754 765
217911_s_at 704 717 741 554 484 501 802 790 753 487 490 480
202984_s_at 559 540 634 566 560 570 603 616 677 535 541 570
202985_s_at 947 941 960 916 896 919 985 978 977 803 859 847
203728_at 734 740 741 730 736 743 731 743 733 711 704 736
208478_s_at 611 537 576 584 627 623 576 561 571 488 572 659 OO UJ
211833_s_at 677 622 694 658 669 692 643 632 674 576 611 750
205263_at 740 711 748 715 715 730 721 726 775 652 652 701
208536_s_at 489 482 466 500 435 482 494 481 500 497 522 493
222343_at 534 563 516 501 499 484 536 550 535 519 588 532
205780_at 940 919 901 1002 947 965 934 902 914 850 884 907
220451_s_at 505 497 489 515 511 503 492 526 492 541 518 520
221478_at 713 529 673 619 658 654 714 577 678 613 607 641
221479_s_at 797 669 753 713 746 751 820 714 763 707 732 738
204950_at 657 649 683 605 619 628 623 637 649 603 601 588
220162_s_at 513 496 495 488 487 492 503 491 491 492 492 488
209970_x_at 775 808 753 551 556 528 744 798 785 544 542 520
211366_x_at 801 827 809 591 604 589 806 805 833 583 613 567
211367_s_at 599 623 616 432 402 413 612 625 663 438 441 414
211368_s_at 723 748 716 488 489 478 707 748 778 484 475 456
202763_at 685 655 650 721 689 688 697 671 680 687 651 704
209310_s_at 706 666 729 521 480 495 661 644 684 508 493 497
213596_at 450 430 447 434 421 433 434 433 438 438 440 425
209790_s_at 667 685 671 530 523 519 699 704 733 629 619 640
211464_x_at 488 496 517 433 456 444 497 527 539 468 476 483
222201 s at 669 656 688 672 661 688 670 656 701 656 620 669
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly 1 (A2) Ly1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
221188_s_at 736 750 739 691 714 676 730 763 728 712 715 709
209833_at 699 704 686 648 652 673 698 678 698 725 726 729
201111_at 818 884 916 971 966 989 835 876 892 857 854 909
201112_s_at 1007 1029 1014 1054 1037 1061 1004 1031 1040 1012 988 1012
210766_s_at 910 959 933 977 960 970 921 953 958 906 899 927
202468_s_at 792 828 813 732 729 753 825 848 864 802 787 847
208905_at 1204 1219 1214 1195 1177 1192 1205 1217 1217 1230 1214 1228
201095_at 880 875 851 892 884 866 857 836 837 829 850 847
208822_s_at 968 955 962 978 966 979 978 947 969 953 943 957
203890_s_at 639 633 645 665 641 662 669 637 670 624 665 641
203891_s_at 549 510 525 576 523 539 554 541 539 572 514 537
217840_at 940 897 891 908 905 871 940 891 884 880 883 881
202480_s_at 582 586 576 644 646 639 582 591 573 599 605 596
211255_x_at 535 538 542 576 623 615 524 522 506 560 569 568
215158_s_at 759 763 764 825 840 816 764 746 750 796 806 798
203277_at 842 850 815 890 884 848 854 851 830 843 864 818 OO
219350_s_at 944 931 926 937 940 941 941 926 936 907 911 918
205554_s_at 534 535 526 552 525 543 565 539 560 554 544 547
209831_x_at 853 839 795 803 851 817 844 825 804 780 784 776
214992_s_at 695 624 585 630 684 629 662 612 625 551 556 530
208289_s_at 721 713 721 742 720 749 715 723 731 726 689 731
216396_s_at 860 855 870 869 903 903 861 870 854 855 896 880
202535_at 837 843 845 853 837 838 839 822 828 787 820 809
218080_x_at 863 878 839 931 952 952 865 856 887 913 917 924
202723_s_at 781 803 797 662 675 677 766 826 759 691 766 716
202724_s_at 853 870 902 733 744 724 863 885 829 829 870 815
204132_s_at 611 580 585 593 530 576 651 584 621 606 605 616
201635_s_at 905 888 903 894 889 914 912 885 926 891 910 934
201636_at 626 613 667 625 594 610 602 639 654 618 596 671
201637_s_at 955 926 958 954 945 972 968 940 971 950 955 996
203725_at 909 862 919 820 811 837 959 895 920 799 732 824
207574_s_at 755 678 681 637 611 633 773 690 736 745 712 756
209304_x_at 793 732 699 693 671 664 780 738 766 792 770 783
209305_s_at 757 694 682 659 637 671 751 669 725 740 740 739
214467 at 683 646 661 638 617 615 621 642 651 644 653 657
Log2 fluorescence intensity
Probesets Ly1 (A1 ) Ly1 (A2) Ly 1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
220864_s_at 1048 1034 1040 1040 1041 1016 1051 1015 1037 1090 1111 1103
206864_s_at 575 574 660 493 499 490 634 597 598 447 458 449
206865_at 688 692 733 602 627 614 720 719 648 610 603 602
207180_s_at 789 783 760 613 554 622 798 764 801 750 750 757
209448_at 729 726 743 467 494 474 746 746 785 741 682 746
210253_at 584 614 594 506 507 511 589 597 630 583 564 588
209929_s_at 693 693 700 699 700 690 688 685 674 685 683 692
36004_at 859 864 838 844 866 844 853 856 833 860 866 842
203836_s_at 475 526 539 540 605 584 505 534 509 484 510 507
203837_at 491 495 512 520 551 526 469 502 477 482 489 486
202086_at 528 517 531 547 532 527 542 537 529 549 529 526
207738_s_at 451 458 463 420 444 420 471 474 458 459 548 516
217465_at 424 429 434 427 424 439 420 435 439 430 445 437
201502_s_at 928 898 875 909 914 867 901 878 868 909 969 961
204862_s_at 759 726 736 659 648 659 769 740 743 666 618 654
205851_at 587 641 630 574 571 579 599 613 595 560 561 554 OO
204004_at 869 902 897 819 792 796 850 906 858 897 912 898
204005_s_at 537 563 598 503 480 512 524 526 564 580 560 589
204025_s_at 656 631 659 670 658 663 657 638 654 654 648 679
213581_at 825 861 856 788 779 768 832 865 859 805 783 806
202730_s_at 712 685 710 678 684 693 701 686 691 647 694 699
202731_at 740 715 783 714 706 728 744 718 755 696 720 738
212593_s_at 963 946 983 942 942 950 957 959 950 929 944 953
212594_at 565 516 588 513 493 484 559 538 546 555 532 608
219275_at 757 774 111 770 770 783 755 763 808 738 750 795
203415_at 896 879 898 900 885 899 870 853 872 884 885 902
217746_s_at 970 961 988 975 967 979 1013 974 1003 948 925 964
205512_s_at 895 924 921 881 881 887 920 917 946 895 931 937
207002_s_at 375 382 374 365 373 366 368 371 369 363 370 370
209318_x_at 393 392 394 383 392 396 382 398 397 389 390 393
216347_s_at 607 566 570 595 557 569 609 579 594 620 564 591
203089_s_at 778 772 744 821 802 808 779 750 761 797 807 811
211152_s_at 693 692 673 715 715 707 678 682 667 714 711 709
209941_at 682 604 628 648 624 640 670 641 652 703 710 713
209544 at 432 430 429 430 415 433 431 425 423 429 438 441
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly 1 (A2) Ly 1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
209545_s_at 873 832 808 795 782 789 839 818 847 814 821 811 218286_s_at 823 795 838 806 778 802 822 801 810 814 820 843
203489_at 9 92288 9 91155 9 90055 8 86688 8 86611 8 85577 9 95588 9 95522 9 97744 8 86633 8 89955 8 88811
210792_x_at 9 97722 9 98833 9 94466 9 92222 9 91188 9 91133 9 99988 1 1000022 1 1000055 9 90088 9 95588 9 93377
222030_at 5 59944 6 60066 6 60033 5 59988 6 61155 5 59966 6 60011 6 61155 6 60022 5 58800 5 59955 5 58866
202693_s_at 8 83344 7 73388 7 76699 7 72266 6 63344 6 68833 8 84488 7 17171 7 78877 9 97788 9 95511 9 94422
202695_s_at 5 57700 5 55566 5 57722 5 57700 5 55511 5 57744 5 58866 5 55588 5 57711 7 72200 7 74488 7 73399
205214_at 514 518 577 619 635 638 529 551 550 635 694 659 200976_s_at 889 851 865 822 805 818 908 877 901 845 863 876 200977_s_at 906 877 890 836 820 844 910 882 947 887 855 919 213786_at 427 416 442 414 426 421 423 432 439 420 428 462 201446_s_at 775 762 784 768 750 774 778 749 789 745 725 742 201447_at 671 633 653 612 628 638 635 612 628 609 586 634 201448_at 694 675 743 677 648 680 659 652 699 657 615 692 201449_at 561 551 590 566 552 560 526 556 575 505 498 541
201450_s_at 5 54422 5 54400 5 58833 5 54433 5 54422 5 54411 5 54422 5 54433 5 55544 5 52299 4 49933 5 53388 ∞
217052_x_at 583 569 588 592 592 581 579 580 575 598 586 587 217164_at 444 424 417 417 408 409 437 413 421 418 408 418 202406_s_at 980 975 965 981 967 980 981 973 992 925 926 967 217500_at 526 519 495 534 506 524 518 504 519 521 517 524 207643_s_at 610 591 576 619 629 586 593 593 572 509 522 532 215346_at 664 615 616 682 686 641 644 649 592 697 690 683 35150_at 856 835 822 842 872 853 828 841 806 867 899 850 204780_s_at 490 478 486 490 493 500 459 462 482 471 465 478 215719_x_at 438 420 435 443 435 440 400 426 428 407 427 415 216252_x_at 483 465 467 491 491 479 455 461 466 453 465 447 206150_at 936 887 924 795 797 790 942 900 886 966 962 970 207536_s_at 511 546 506 516 517 531 518 522 517 517 531 520
202687_s_at 4 44477 4 44444 4 42244 3 39955 4 40077 4 40000 4 43333 4 43399 4 44411 4 40066 4 40099 4 40011
202688_at 4 49955 4 48866 4 49955 4 42288 4 43366 4 43311 5 50099 4 48800 5 52222 4 42244 4 42255 4 43377
214329_x_at 3 37744 3 38822 3 39966 3 35588 3 36666 3 36633 3 37755 3 39911 3 38888 3 35588 3 37777 3 36633
206508_at 5 55599 5 56655 5 56600 7 78855 8 88899 7 79933 5 55599 5 58811 5 54455 5 56699 5 59966 5 58811
207216_at 6 61144 6 61111 6 60055 6 66688 6 69955 6 68866 6 62211 6 62288 5 59955 6 62277 6 63322 6 60033
206907_at 5 51155 5 50099 5 51100 5 57766 6 67733 6 61155 5 50088 5 51155 4 49944 5 54499 6 61144 5 58811
203120 at 6 60099 6 62277 6 62233 5 56600 5 55577 5 56666 5 59933 6 62211 6 61144 5 52288 5 53322 5 50099
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly 1 (A2) Ly1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
209863_s_at 489 489 504 514 561 549 474 500 492 4 93 506 499 211193_at 437 460 438 435 452 450 433 443 442 4 50 445 447
1729_at 6 6 63 33777 6 6 6333222 6 6 63 33999 6 6 6222666 6 6 6222555 6 6 6333333 6 6 6333222 6 6 6333999 6 6 6333333 6 6 622 2888 6 6 63 33666 6 6 6333000
205599 at 5 5 50 00000 5 5 5555555 5 5 53 33000 5 5 5444777 6 6 6000333 5 5 5666000 5 5 5000777 5 5 5444444 5 5 5111666 5 5 555 5111 5 5 59 99000 5 5 5555111
208315_x_at 55 5 555555 55 5666555 55 5 555666 55 5333333 55 5333111 44 4999333 55 5777444 55 5555777 55 5555111 55 577 7555 55 5 888111 55 5888000
221571_at 77 7 000999 66 6999444 77 7 333555 55 5888333 55 5444666 55 5888555 66 6777777 66 6777333 66 6999333 77 722 2666 77 7 444111 77 7666000
202871 at 7 7 n0c6 ° 68 QC6 c 68 or0> v 74 Λ r0> 7 74 ^20 τ 7 o28t> 7 72 o3-3 7 7 n0<65 " 6 R68Q i 7 Λ 14A I 7 R6C5 ~ 7? 3 "ΪQ9
211899ls_at 763 752 746 786 818 814 756 739 710 7 55 836 784
204352_at 572 567 602 604 616 588 554 554 540 5 16 587 535
207953_at 494 525 511 509 512 498 505 530 488 5 01 492 502
208014_x_at 509 522 526 484 572 546 520 535 509 5 60 538 521
209364_at 632 616 606 606 605 611 635 616 640 6 32 661 660
221454_at 531 526 513 534 523 515 532 531 529 5 56 538 519
210025_s_at 603 603 571 603 583 587 588 590 594 6 24 590 590
210026_s_at 508 517 507 497 523 510 501 507 503 5 02 503 502
479 474 OO
214207_s_at 485 486 483 479 496 490 471 4 94 499 489
220598_at 589 575 550 584 579 573 583 568 571 6 01 579 570
220599_s_at 541 536 547 554 544 540 530 552 540 5 37 557 558
220066_at 451 450 451 455 457 459 454 461 447 4 73 460 462
221073_s_at 760 763 740 724 741 730 753 747 747 7 45 724 707
206011_at 571 571 564 495 489 507 544 583 576 5 12 510 517
207500_at 476 479 481 472 479 463 481 481 479 4 78 497 473
208791_at 489 494 495 493 507 505 479 485 488 5 14 494 490
208792_s_at 508 498 494 513 487 505 500 505 505 5 26 505 500
222043_at 435 437 438 429 450 437 426 433 423 4 41 443 434
210765_at 549 546 550 564 555 580 540 556 540 5 55 551 554
213712_at 421 407 399 409 415 399 409 395 410 4 23 406 415
203139_at 474 500 517 468 499 493 477 496 467 4 95 498 485
218325_s_at 6 61133 6 67755 6 67700 6 63355 6 67755 6 66666 6 60066 6 67799 6 64499 5 57 799 6 64455 5 58833
206939_at 4 43399 4 44499 4 46677 4 44488 4 46655 4 45555 4 44477 4 47744 4 44477 4 46 677 4 47744 4 46600
210165_at 5 54444 5 54455 5 53333 5 54444 5 56622 5 53355 5 53399 5 54411 5 50055 5 55 588 5 57733 5 54433
210655_s_at 6 68866 6 64411 6 60066 6 61122 5 59922 6 60055 6 66666 6 64411 6 64488 6 63 366 6 65577 6 63399
213560_at 5 57744 5 58811 5 55588 5 55533 5 57799 5 55522 5 56600 5 56688 5 55577 5 56 633 5 56633 5 55588
204121_at 4 44466 4 46633 4 44422 4 46677 4 46611 4 46677 4 46677 4 46688 4 46644 4 47 799 4 48899 4 47700
205848 at 3 38888 4 40022 3 39900 3 38866 3 38888 3 39900 3 38844 3 39933 3 38899 3 38 822 4 40022 3 38888
—
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
208000_at 5 69 5 89 5 89 5 78 5 72 6 05 5 71 5 78 5 92 6 06 6 05 5 88
205488 at 4 57 445 444 4 51 440 449 4 51 449 446 4 70 4 57 4 53
210164_at 4 43 4 47 4 35 4 39 4 33 4 37 4 40 4 27 4 27 4 49 4 41 4 37
210321 at 4 93 5 23 4 77 5 03 5 03 4 95 5 12 5 04 5 00 5 13 5 21 5 07
206863_x_at 4 78 4 58 4 46 4 74 4 76 4 46 4 61 4 60 4 50 4 66 4 68 4 50
207062_at 4 27 4 35 4 43 4 28 4 49 4 53 4 10 4 41 4 27 4 32 4 38 4 36
206975_at 5 18 5 31 5 23 5 18 5 25 5 13 5 49 545 5 12 5 38 6 09 5 30
203005 at 5 39 5 35 5 25 5 47 5 27 5 12 5 62 5 42 5 10 5 66 5 38 5 30
205858_at 4 54 4 55 446 4 63 4 43 461 4 57 4 64 4 36 4 62 4 50 4 53
220402 at 4 06 4 01 4 15 4 01 4 21 4 05 3 98 4 09 4 08 4 06 4 09 4 08
220403_s_at 4 71 4 63 4 63 4 73 4 70 4 64 4 86 4 69 4 68 4 86 4 74 4 71
214090 at 3 92 4 10 4 18 4 02 4 13 4 08 3 95 3 96 4 02 4 02 4 25 4 17
214237_x_at 5 58 5 52 5 46 5 71 5 41 5 50 5 50 5 64 5 57 5 83 5 75 5 59
207634 at 5 73 5 79 541 5 66 5 80 5 69 5 59 6 06 5 52 5 86 5 68 5 60
213585_s_at 6 04 6 08 6 08 6 01 6 08 6 14 5 89 6 12 5 93 6 03 6 17 5 97
222152_at 5 25 5 20 5 19 5 17 5 29 5 21 5 15 5 21 5 13 5 52 5 16 5 30 OO OO
207943_x_at 3 89 4 05 3 99 3 87 4 00 4 01 3 92 3 96 4 01 3 93 3 94 3 95
218849_s_at 5 97 5 82 5 83 5 89 5 97 6 07 5 74 5 93 5 91 5 91 6 02 5 97
207468_s_at 4 50 4 48 4 34 4 62 4 50 4 52 4 57 4 52 4 40 4 57 4 55 4 48
202694 at 4 38 4 55 4 63 4 23 4 52 4 41 4 41 4 47 4 43 4 45 4 60 463
206222_at 4 61 4 55 4 45 4 59 4 42 4 54 4 51 4 54 4 62 4 78 4 55 4 54
211163 s at 4 67 4 57 4 53 4 71 4 47 4 65 4 65 4 54 4 66 4 85 4 68 4 68
210654_at 5 17 4 86 4 83 4 94 4 89 4 96 5 28 4 89 4 93 5 01 5 03 5 07
210847 x at 4 91 5 00 4 85 5 02 5 04 4 82 5 03 5 11 4 92 5 23 5 23 4 89
211282_x_at 5 86 6 00 5 84 5 97 5 96 5 93 5 90 6 08 5 88 6 36 6 28 5 89
211841 s at 5 74 5 87 5 59 5 80 5 82 5 81 5 88 5 81 5 80 6 08 5 85 5 76
216042_at 6 20 6 41 6 49 645 6 50 6 47 643 648 6 39 6 54 6 51 6 40
219422 at 4 87 4 97 4 78 5 02 5 07 4 91 5 02 5 00 4 89 5 22 4 93 4 85
219423_x_at 5 37 5 36 5 32 5 35 5 20 5 38 5 27 5 35 5 26 5 45 5 37 5 30
205153_s_at 5 94 5 42 5 24 6 04 6 24 6 03 5 75 5 47 5 33 6 25 6 50 6 10
222292 at 4 59 4 65 4 73 4 57 4 65 4 52 4 51 4 47 4 60 4 66 4 67 4 85
204781_s_at 5 53 5 72 5 57 5 90 5 74 5 89 5 33 5 36 5 67 5 53 5 76 5 52
211786 at 4 61 4 53 4 49 4 64 4 53 4 64 4 52 4 65 4 62 4 71 4 76 4 67
207907_at 4 98 4 62 4 72 5 11 4 72 4 74 5 00 4 87 4 78 5 11 5 00 4 92
207892 at 5 42 5 61 5 56 5 39 5 63 5 56 5 52 5 57 5 49 5 79 5 62 5 57
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
210865 at 5 13 5 25 4 92 5 08 5 06 4 81 5 02 4 99 4 64 5 23 5 19 4 97
211333_s_at 4 60 4 61 4 38 4 69 4 65 4 65 4 48 4 51 4 53 4 61 4 71 4 46
220804 s at 4 87 4 91 4 80 5 16 4 87 5 00 4 99 4 91 5 03 5 34 5 06 5 12
207382_at 547 547 5 56 5 45 5 39 5 49 5 01 5 50 5 43 5 52 5 44 5 54
211194 s at 4 44 4 51 4 48 4 46 4 65 4 65 4 41 4 42 4 35 4 42 4 67 4 49
211195_s_at 5 10 5 42 5 38 4 98 5 35 5 36 5 08 5 46 5 19 5 27 5 34 5 40
211834_s_at 4 82 4 91 4 73 4 96 4 84 4 82 4 95 4 97 4 79 5 01 4 88 4 63
205641_s_at 6 94 6 99 6 88 6 96 6 83 6 62 7 00 7 03 6 98 7 00 7 02 6 90
213443 at 5 19 5 29 5 31 5 18 5 28 5 19 5 33 5 23 5 26 5 43 5 33 5 21
Table 5B Apoptosis Genes (See tables reference 2) t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene IC
FDR Cutoff 1 OE-02 8 2E-03 1 2E-02 94E-03 AC v BD AC v BD Co
201715_s_at 7 2E-01 6 7E-01 8 4E-01 5 4E-01 Yes No ACINUS Hs 227133 apoptotic chromatin condensation inducer in the nucleus
205013 s at 66E-03 9 OE-03 1 2E-02 7 2E-03 Yes No ADORA2A Hs 197029 adenosine A2a receptor
204833 at 1 1 E-02 5 0E-01 1 3E-02 2 4E-01 Yes No APG12L Hs 264482 APG 12 autophagy 12-lιke (S cerevisiae)
213026 at 5 1 E-02 1 7E-01 2 9E-02 6 9E-02 Yes No APG12L Hs 264482 APG12 autophagy 12-lιke (S cerevisiae)
213930_at 74E-02 1 7E-01 1 8E-01 4 1E-01 Yes No APG12L Hs 264482 APG 12 autophagy 12-lιke (S cerevisiae)
221666_s_at 9 7E-04 1 OE-04 2 5E-04 2 1 E-05 Yes Yes ASC Hs 197875 apoptosis-associated speck-like protein containing a CARD
1861_at 9 1E-01 5 2E-01 84E-01 6 8E-01 Yes No BAD Hs 76366 BCL2-antagonιst of cell death
209406 at 8 6E-01 5 1E-01 4 8E-01 2 0E-01 Yes No BAG2 Hs 55220 BCL2-assocιated athanogene 2
217911_s_at 3 2E-03 1 1 E-03 8 4E-04 1 7E-03 Yes Yes BAG3 Hs 15259 BCL2-assocιated athanogene 3
202984 s at 7 3E-01 4 3E-01 9 9E-02 4 9E-02 Yes No BAG5 Hs 5443 BCL2-assocιated athanogene 5
202985_s_at 1 5E-02 1 5E-02 5 9E-03 1 2E-02 Yes No BAG5 Hs 5443 BCL2-assocιated athanogene 5
203728 at 6 6E-01 1 5E-01 8 7E-01 1 9E-01 Yes No BAK1 Hs 93213 BCL2-antagonιst/kιller 1
208478_s_at 2 4E-01 9 8E-01 8 1 E-02 9 5E-01 Yes No BAX Hs 159428 BCL2-assocιated X protein
211833 s at 7 5E-01 7 7E-01 2 2E-01 9 5E-01 Yes No BAX Hs 159428 BCL2-assocιated X protein
205263_at 3 9E-01 3 7E-02 3 6E-01 3 9E-02 Yes No BCL10 Hs 193516 B-cell CLL/lymphoma 10
208536_s_at 7 7E-01 9 9E-02 4 2E-01 3 4E-01 Yes No BCL2L1 1 Hs 84063 BCL2-lιke 11 (apoptosis facilitator)
222343 at 7 3E-02 7 5E-01 3 1 E-03 8 1 E-01 Yes No BCL2L11 Hs 84063 BCL2-lιke 11 (apoptosis facilitator)
205780 at 6 5E-02 1 3E-01 54E-02 1 5E-01 Yes No BIK Hs 155419 BCL2-ιnteractιng killer (apoptosis-inducing)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title
220451_s_at 9 6E-02 3 6E-02 6 6E-01 1 8E-01 Yes No BIRC7 Hs 256126 baculoviral IAP repeat-containing 7 (livin)
221478_at 9 4E-01 7 8E-01 7 8E-01 4 7E-01 Yes No BNIP3L Hs 132955 BCL2/adenovιrus E1 B 19kDa interacting protein 3-lιke
221479_s_at 9 4E-01 7 4E-01 4 5E-01 3 2E-01 Yes No BNIP3L Hs 132955 BCL2/adenovιrus E1 B 19kDa interacting protein 3-lιke
204950_at 2 7E-02 1 3E-02 1 4E-01 1 8E-02 Yes No CARD8 Hs 446146 caspase recruitment domain family, member 8
220162_s_at 1 7E-01 2 2E-01 2 8E-01 3 9E-01 Yes No CARD9 Hs 271815 caspase recruitment domain family, member 9
209970 x at 8 9E-04 1 OE-03 1 OE-03 1 2E-03 Yes Yes CASP1 Hs 2490 caspase 1
211366_x_at 8 1E-05 54E-04 2 4E-04 3 5E-04 Yes Yes CASP1 Hs 2490 caspase 1
211367 s at 8 7E-05 1 1E-04 8 7E-04 1 1E-03 Yes Yes CAS P 1 Hs 2490 caspase 1
211368 s at 4 8E-04 3 8E-05 5 3E-03 2 2E-03 Yes Yes CAS P 1 Hs 2490 caspase 1
202763_at 8 2E-02 4 2E-01 2 9E-01 9 1 E-01 Yes No CAS P3 Hs 141125 caspase 3
209310 s at 1 5E-03 6 OE-03 6 1 E-04 2 OE-03 Yes Yes CAS P4 Hs 74122 caspase 4
213596_at 1 7E-01 3 7E-01 3 1E-01 9 1 E-01 Yes No CASP4 Hs 74122 caspase 4
209790_s_at 1 1 E-04 5 7E-03 1 7E-03 5 6E-03 Yes Yes CASP6 Hs 3280 caspase 6
211464_x_at 7 9E-03 8 8E-02 1 2E-02 5 8E-02 Yes No CASP6 Hs 3280 caspase 6
222201_s_at 8 5E-01 2 8E-01 8 9E-01 2 4E-01 Yes No CASP8AP2 Hs 122843 CASP8 associated protein 2
221188_s_at 3 6E-02 9 OE-03 4 3E-02 1 3E-01 Yes No CIDEB Hs 448590 cell death-inducing DFFA-like effector b
209833_at 2 OE-02 2 6E-02 3 2E-02 2 9E-02 Yes No CRADD Hs 155566 CASP2 and RIPK1 domain containing adaptor with death domain
201111_at 6 3E-02 9 8E-01 1 4E-02 8 2E-01 Yes No CSE1L Hs 90073 CSE1 chromosome segregation 1-lιke
(yeast)
201112_s_at 2 5E-02 2 8E-01 1 3E-01 2 0E-01 Yes No CSE1L Hs 90073 CSE1 chromosome segregation 1-lιke
(yeast)
210766_s_at 1 2E-01 2 5E-01 1 5E-01 8 4E-02 Yes No CSE1L Hs 90073 CSE1 chromosome segregation 1-lιke
(yeast)
202468_s_at 6 5E-03 9 5E-01 2 4E-03 2 1 E-01 Yes No CTN NAL 1 Hs 58488 catenin (cadherin-associated protein), alpha-like 1
208905_at 3 2E-02 1 6E-01 2 7E-02 1 6E-01 Yes No CYCS Hs 437060 cytochrome c, somatic
201095_at 3 7E-01 8 5E-02 2 3E-02 8 9E-01 Yes No DAP Hs 75189 death-associated protein
208822 s at 9 5E-02 1 4E-01 4 2E-01 2 8E-01 Yes No DAP3 Hs 270920 death associated protein 3
203890_s_at 1 5E-01 76E-01 84E-01 3 9E-01 Yes No DAPK3 Hs 153908 death-associated protein kinase 3
203891 s at 4 3E-01 5 7E-01 9 5E-01 8 6E-01 Yes No DAPK3 Hs 153908 death-associated protein kinase 3
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title 217840_at 5 OE-01 2 2E-01 6 6E-01 3 1 E-01 Yes No DDX41 Hs 274317 DEAD (Asp-Glu-Ala-Asp) box polypeptide
41
202480 s_at 1 OE-04 8 OE-03 2 7E-03 5 3E-02 Yes No DEDD Hs 169681 death effector domain containing 211255_x_at 4 3E-02 2 5E-03 1 7E-02 44E-03 Yes No DEDD Hs 169681 death effector domain containing 215158_s_at 8 7E-03 1 8E-03 1 3E-03 4 2E-03 Yes Yes DEDD Hs 169681 death effector domain containing 203277_at 8 8E-02 7 4E-01 1 4E-01 8 5E-01 Yes No DFFA Hs 484782 DNA fragmentation factor, 45kDa, alpha polypeptide
219350_s_at 4 2E-01 3 8E-02 3 8E-01 1 9E-02 Yes No DIABLO Hs 169611 diablo homolog (Drosophila) 205554 s at 4 OE-01 1 5E-02 2 7E-01 5 2E-01 Yes No DNASE1L3 Hs 88646 deoxyribonuclease l-like 3 209831_x_at 8 3E-01 1 1E-01 9 7E-01 5 6E-02 Yes No DNASE2 Hs 118243 deoxyπbonuclease II, lysosomal 214992 s at 7 4E-01 1 OE-01 5 6E-01 1 3E-02 Yes No DNASE2 Hs 118243 deoxyribonuclease II, lysosomal 208289_s_at 1 6E-01 8 6E-01 2 5E-01 6 5E-01 Yes No EI24 Hs 343911 etoposide induced 2 4 mRNA 216396_s_at 1 OE-01 3 3E-01 1 OE-01 3 3E-01 Yes No EI24 Hs 343911 etoposide induced 2 4 mRNA 202535_at 8 6E-01 5 8E-02 1 4E-01 1 1E-01 Yes No FADD Hs 86131 Fas (TNFRSF6)-assocιated via death domain
218080 x at 5 5E-03 2 7E-02 3 3E-03 2 2E-02 Yes No FAF 1 Hs 12899 Fas (TNFRSF6) associated factor 1 VO 202723_s_at 1 8E-04 7 7E-02 2 8E-02 1 2E-01 Yes No FOXO 1 A Hs 170133 forkhead box 01 A (rhabdomyosarcoma) 202724 s at 4 8E-03 1 7E-01 1 OE-02 4 2E-01 Yes No FOXO 1 A Hs 170133 forkhead box O1 A (rhabdomyosarcoma) 204132_s_at 32E-01 2 OE-01 1 3E-01 6 7E-01 Yes No FOXO3A Hs 14845 forkhead box O3A 201635_s_at 96E-01 4 2E-01 5 9E-01 8 3E-01 Yes No FXR 1 Hs 408096 fragile X mental retardation, autosomal homolog 1
201636_at 2 6E-01 8 2E-01 3 1 E-01 9 1 E-01 Yes No FXR 1 Hs 408096 fragile X mental retardation, autosomal homolog 1
201637_s_at 44E-01 3 OE-01 8 6E-01 6 9E-01 Yes No FXR 1 Hs 408096 fragile X mental retardation, autosomal homolog 1
203725_at 3 6E-02 3 5E-02 2 OE-02 1 8E-02 Yes No GADD45A Hs 80409 growth arrest and DNA-damage-inducible, alpha
207574_s_at 8 1 E-02 3 3E-01 3 6E-02 8 8E-01 Yes No GADD45B Hs 110571 growth arrest and DNA-damage-inducible, beta
209304_x_at 1 3E-01 2 8E-01 6 8E-03 2 4E-01 Yes No GADD45B Hs 110571 growth arrest and DNA-damage-inducible, beta
209305_s_at 1 2E-01 3 4E-01 1 2E-01 4 1 E-01 Yes No GADD45B Hs 110571 growth arrest and DNA-damage-inducible, beta
214467_at 4 4E-02 3 9E-01 2 8E-01 2 8E-01 Yes No GPR65 Hs 131924 G protein-coupled receptor 65 220864 s at 44E-01 1 8E-03 9 OE-01 1 OE-02 Yes No GRIM19 Hs 279574 cell death-regulatory protein GRIM19
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title 206864_s_at 6 1 E-02 3 2E-02 8 5E-03 3 5E-03 Yes No HRK Hs 87247 harakiπ, BCL2 interacting protein (contains only BH3 domain)
206865_at 1 1 E-02 1 8E-02 6 5E-02 6 1 E-02 Yes No HRK Hs 87247 harakiπ, BCL2 interacting protein (contains only BH3 domain)
207180_s_at 6 7E-03 9 8E-02 3 9E-03 9 OE-02 Yes No HTATIP2 Hs 90753 HIV-1 Tat interactive protein 2, 3OkDa 209448_at 5 1 E-05 6 9E-01 1 9E-04 2 3E-01 Yes No HTATI P2 Hs 90753 HIV-1 Tat interactive protein 2, 3OkDa 210253_at 7 9E-03 1 7E-01 1 5E-02 1 6E-01 Yes No HTATI P2 Hs 90753 HIV-1 Tat interactive protein 2, 3OkDa 209929_s_at 7 6E-01 7 5E-02 5 9E-02 4 6E-01 Yes No IKBKG Hs 43505 inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma
36004_at 8 4E-01 8 5E-01 7 1 E-01 4 5E-01 Yes No IKBKG Hs 43505 inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma
203836_s_at 8 2E-02 5 9E-01 6 9E-02 2 7E-01 Yes No MAP3K5 Hs 151988 mitogen-activated protein kinase kinase kinase 5
203837_at 5 5E-02 1 6E-01 2 3E-02 8 1E-01 Yes No MAP3K5 Hs 151988 mitogen-activated protein kinase kinase kinase 5
202086_at 2 5E-01 3 4E-01 9 3E-01 8 7E-01 Yes No MX1 Hs 436836 myxovirus (influenza virus) resistance 1 to 207738_s_at 5 3E-02 1 9E-01 2 1 E-02 2 7E-01 Yes No NCKAP1 Hs 278411 NCK-associated protein 1 217465_at 9 1 E-01 2 OE-01 8 5E-01 4 4E-01 Yes No NCKAP1 Hs 278411 NCK-associated protein 1 201502_s_at 8 8E-01 1 3E-01 4 7E-01 5 5E-02 Yes No NFKBIA Hs 81328 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha
204862_s_at 7 1 E-03 8 4E-03 4 2E-03 6 2E-03 Yes No NME3 Hs 81687 non-metastatic cells 3, protein expressed in 205851_at 1 1 E-01 6 4E-02 2 4E-02 8 1 E-03 Yes No NME6 Hs 465558 non-metastatic cells 6, protein expressed in
(nucleoside-diphosphate kinase)
204004_at 3 4E-03 3 4E-01 4 2E-02 2 1 E-01 Yes No PAWR Hs 406074 PRKC, apoptosis, WT1 , regulator 204005 s at 4 2E-02 6 1E-01 7 6E-02 8 OE-02 Yes No PAWR Hs 406074 PRKC, apoptosis, WT1 , regulator 204025_s_at 2 3E-01 4 3E-01 1 2E-01 4 1 E-01 Yes No PDCD2 Hs 367900 programmed cell death 2 213581 at 1 1E-02 2 7E-02 6 1 E-03 1 5E-02 Yes No PDCD2 Hs 367900 programmed cell death 2 202730_s_at 1 8E-01 3 2E-01 3 OE-01 5 3E-01 Yes No PDCD4 Hs 257697 programmed cell death 4 (neoplastic transformation inhibitor)
202731_at 2 7E-01 3 1 E-01 1 6E-01 2 7E-01 Yes No PDCD4 Hs 257697 programmed cell death 4 (neoplastic transformation inhibitor)
212593_s_at 2 1 E-01 1 7E-01 5 5E-02 2 OE-01 Yes No PDCD4 Hs 257697 programmed cell death 4 (neoplastic transformation inhibitor)
212594_at 9 OE-02 8 OE-01 1 OE-02 5 3E-01 Yes No PDCD4 Hs 257697 programmed cell death 4 (neoplastic transformation inhibitor)
219275 at 5 6E-01 6 9E-01 9 5E-01 5 8E-01 Yes No PDCD5 Hs 443831 programmed cell death 5
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title 203415_at 6 7E-01 9 4E-01 2 2E-02 4 3E-02 Yes No PDCD6 Hs 24087 programmed cell death 6 217746_s_at 9 2E-01 1 3E-01 1 8E-01 3 4E-02 Yes No PDCD6IP Hs 9663 programmed cell death 6 interacting protein 205512_s_at 7 9E-02 6 7E-01 3 7E-02 7 0E-01 Yes No PDCD8 Hs 18720 programmed cell death 8 (apoptosis- inducing factor)
207002_s_at 6 9E-02 5 4E-02 6 4E-01 5 8E-01 Yes No PLAGL1 Hs 132911 pleomorphic adenoma gene-like 1 209318 x_at 5 6E-01 1 8E-01 7 6E-01 7 9E-01 Yes No PLAGL1 Hs 132911 pleomorphic adenoma gene-like 1 216347_s_at 6 8E-01 6 5E-01 2 3E-01 8 9E-01 Yes No PPP1R13B Hs 371546 protein phosphatase 1 , regulatory (inhibitor) subunit 13B
203089 s_at 3 OE-02 4 5E-02 1 3E-02 2 1E-02 Yes No PRSS25 Hs 115721 protease, serine, 25 211152_s_at 4 OE-02 54E-02 5 6E-03 1 2E-02 Yes No PRSS25 Hs 115721 protease, serine, 25 209941_at 9 7E-01 9 OE-02 2 0E-01 1 6E-02 Yes No RIPK1 Hs 390758 receptor (TNFRSF)-ιnteractιng serine- threonine kinase 1
209544_at 5 3E-01 2 6E-01 9 8E-01 9 8E-02 Yes No RIPK2 Hs 103755 receptor-interacting serine-threonine kinase 2
209545_s_at 1 2E-01 3 6E-01 2 OE-02 1 4E-01 Yes No RIPK2 Hs 103755 receptor-interacting serine-threonine kinase 2
218286 s at 2 1E-01 6 7E-01 2 2E-01 2 4E-01 Yes No RNF7 Hs 512849 ring finger protein 7 203489_at 5 8E-03 4 1 E-02 9 7E-04 3 2E-03 Yes No SIVA Hs 112058 CD27-bιndιng (Siva) protein 210792 x at 3 7E-02 1 5E-01 2 4E-05 4 OE-02 Yes No SIVA Hs 112058 CD27-bιndιng (Siva) protein 222030_at 8 1 E-01 6 7E-02 7 1 E-01 3 7E-02 Yes No SIVA Hs 112058 CD27-bιndιng (Siva) protein 202693_s_at 6 2E-02 1 5E-02 2 5E-02 9 4E-03 Yes No STK17A Hs 9075 serine/threonine kinase 17a (apoptosis- induαng)
202695_s_at 9 0E-01 2 1E-04 5 6E-01 1 5E-04 Yes No STK17A Hs 9075 serine/threonine kinase 17a (apoptosis- mducing)
205214_at 3 5E-02 9 7E-03 9 1E-04 1 1E-02 Yes No STK17B Hs 88297 serine/threonine kinase 17b (apoptosis- inducing)
200976_s_at 2 7E-02 64E-01 4 8E-03 5 9E-02 Yes No TAX1BP1 Hs 5437 Taxi (human T-cell leukemia virus type I) binding protein 1
200977_s_at 6 7E-03 8 6E-01 3 8E-02 3 8E-01 Yes No TAX1 BP1 Hs 5437 Taxi (human T-cell leukemia virus type I) binding protein 1
213786_at 4 0E-01 6 1 E-01 1 3E-01 7 4E-01 Yes No TAX1 BP1 Hs 5437 Taxi (human T-cell leukemia virus type I) binding protein 1
201446_s_at 3 7E-01 1 5E-02 6 1E-01 8 OE-02 Yes No TIA1 Hs 391858 TIA1 cytotoxic granule-associated RNA binding protein
201447 at 1 2E-01 7 7E-02 92E-01 4 0E-01 Yes No TIA1 Hs 391858 TIA1 cytotoxic granule-associated RNA binding protein
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title 201448_at 2 2E-01 1 8E-01 9 4E-01 6 OE-01 Yes No TIA1 Hs 391858 TIA1 cytotoxic granule-associated RNA binding protein
201449_at 5 9E-01 4 3E-02 6 7E-01 1 3E-01 Yes No TIA1 Hs 391858 TIA1 cytotoxic granule-associated RNA binding protein
201450_s_at 4 5E-01 1 5E-01 3 5E-01 1 8E-01 Yes No TIA1 Hs 391858 TIA1 cytotoxic granule-associated RNA binding protein
217052_x_at 3 OE-01 2 1 E-01 9 7E-02 7 7E-02 Yes No TIA1 Hs 391858 TIA1 cytotoxic granule-associated RNA binding protein
217164_at 1 6E-01 2 3E-01 2 1 E-01 3 3E-01 Yes No TIA1 Hs 391858 TIA1 cytotoxic granule-associated RNA binding protein
202406_s_at 6 7E-01 1 2E-01 4 8E-01 7 8E-02 Yes No TIAL1 Hs 335786 TIA1 cytotoxic granule-associated RNA binding protein-like 1
217500_at 5 6E-01 5 1E-01 4 9E-01 3 OE-01 Yes No TIAL1 Hs 335786 TIA1 cytotoxic granule-associated RNA binding protein-like 1
207643_s_at 3 2E-01 5 6E-03 1 8E-01 2 6E-03 Yes No TNFRSF1A Hs 159 tumor necrosis factor receptor superfamily, member 1A vθ
215346_at 1 6E-01 6 1 E-02 1 5E-01 7 OE-02 Yes No TNFRSF5 Hs 504816 tumor necrosis factor receptor superfamily, member 5
35150_at 2 5E-01 1 3E-01 8 9E-02 6 3E-02 Yes No TNFRSF5 Hs 504816 tumor necrosis factor receptor superfamily, member 5
204780_s_at 1 OE-01 5 7E-02 5 1 E-02 6 6E-01 Yes No TNFRSF6 Hs 82359 tumor necrosis factor receptor superfamily, member 6
215719_x_at 2 9E-01 1 4E-01 1 3E-01 8 9E-01 Yes No TNFRSF6 Hs 82359 tumor necrosis factor receptor superfamily, member 6
216252_x_at 1 1 E-01 1 OE-01 8 6E-03 4 OE-01 Yes No TNFRSF6 Hs 82359 tumor necrosis factor receptor superfamily, member 6
206150_at 1 3E-02 74E-02 1 9E-02 7 5E-02 Yes No TNFRSF7 Hs 355307 tumor necrosis factor receptor superfamily, member 7
207536_s_at 9 7E-01 9 3E-01 6 4E-01 5 OE-01 Yes No TNFRSF9 Hs 193418 tumor necrosis factor receptor superfamily, member 9
202687_s_at 2 2E-02 3 8E-02 1 4E-03 6 6E-04 Yes No TNFSF10 Hs 387871 tumor necrosis factor (ligand) superfamily, member 10
202688_at 1 7E-04 3 6E-04 2 5E-02 1 8E-02 Yes No TNFSF10 Hs 387871 tumor necrosis factor (ligand) superfamily, member 10
214329 x at 6 8E-02 1 1E-01 3 2E-02 7 6E-02 Yes No TNFSF10 Hs 387871 tumor necrosis factor (ligand) superfamily, member 10
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title
206508_at 1 6E-02 1 2E-01 1 OE-02 2 1 E-01 Yes No TNFSF7 Hs 99899 tumor necrosis factor (ligand) superfamily, member 7
207216_at 7 1 E-03 3 6E-01 6 7E-03 6 7E-01 Yes No TNFSF8 Hs 177136 tumor necrosis factor (ligand) superfamily, member 8
206907_at 5 9E-02 6 2E-02 4 9E-02 44E-02 Yes No TNFSF9 Hs 1524 tumor necrosis factor (ligand) superfamily, member 9
203120 at 2 8E-03 6 3E-04 2 1 E-02 1 5E-03 Yes No TP53BP2 Hs 44585 tumor protein p53 binding protein, 2
209863_s_at 6 4E-02 4 2E-01 4 3E-02 2 9E-01 Yes No TP73L Hs 137569 tumor protein p73-lιke
211193 at 9 3E-01 7 6E-01 3 8E-01 1 0E-01 Yes No TP73L Hs 137569 tumor protein p73-lιke
1729_at 8 2E-02 2 1 E-01 1 3E-01 3 6E-01 Yes No TRADD Hs 89862 TNFRSFIA-associated via death domain
205599_at 1 5E-01 1 6E-01 8 5E-02 7 2E-02 Yes No TRAF 1 Hs 438253 TNF receptor-associated factor 1
208315 x at 8 4E-02 1 4E-02 6 4E-02 1 2E-01 Yes No TRAF3 Hs 297660 TNF receptor-associated factor 3
221571_at 1 3E-03 1 3E-01 5 2E-03 9 5E-03 Yes No TRAF3 Hs 297660 TNF receptor-associated factor 3
202871_at 1 2E-02 6 OE-02 1 3E-01 1 4E-01 Yes No TRAF4 Hs 8375 TNF receptor-associated factor 4
211899_s_at 2 OE-02 2 5E-01 1 6E-02 1 2E-01 Yes No TRAF4 Hs 8375 TNF receptor-associated factor 4
204352_at 1 8E-01 2 5E-01 9 OE-03 8 9E-01 Yes No TRAF5 Hs 385685 TNF receptor-associated factor 5
207953_at 7 8E-01 34E-01 9 5E-01 54E-01 No No AD7C-NTP Hs 129735 neuronal thread protein
208014 x at 6 3E-01 2 0E-01 6 8E-01 2 6E-01 No No AD7C-NTP Hs 129735 neuronal thread protein
209364_at 2 9E-01 5 6E-02 8 OE-02 1 6E-01 No No BAD Hs 76366 BCL2-antagonιst of cell death
221454_at 9 5E-01 3 2E-01 3 3E-01 5 7E-01 No No BOK Hs 293753 /// BCL2-related ovarian killer /// BCL2-related
Hs 293753 ovarian killer
210025_s_at 9 1 E-01 5 9E-01 9 9E-01 4 5E-01 No No CARD10 Hs 57973 caspase recruitment domain family, member 10
210026_s_at 9 4E-01 1 1 E-01 5 OE-01 4 1 E-01 No No CARD10 Hs 57973 caspase recruitment domain family, member 10
214207_s_at 4 1 E-01 2 5E-02 7 8E-01 3 8E-01 No No CARD10 Hs 57973 caspase recruitment domain family, member 10
220598_at 6 1E-01 4 6E-01 4 7E-01 4 2E-01 No No CARD14 Hs 306227 caspase recruitment domain family, member 14
220599_s_at 4 5E-01 3 3E-01 5 4E-01 3 6E-01 No No CARD14 Hs 306227 caspase recruitment domain family, member 14
220066_at 1 3E-02 6 4E-02 5 2E-01 1 1 E-01 No No CARD15 Hs 135201 caspase recruitment domain family, member 15
221073_s_at 7 3E-02 1 1E-01 6 1E-02 1 7E-01 No No CARD4 Hs 19405 caspase recruitment domain family, member 4
206011 at 2 OE-03 5 4E-05 1 4E-02 4 OE-02 No No CASP1 Hs 2490 caspase 1
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title
207500_at 2 6E-01 6 3E-01 1 9E-01 7 7E-01 No No CAS P5 Hs 213327 caspase 5, apoptosis-related cysteine protease
208791_at 1 7E-01 4 6E-01 3 9E-02 1 7E-01 No No CLU Hs 436657 clusterin
208792 s at 8 5E-01 34E-01 8 5E-01 4 9E-01 No No CLU Hs 436657 clusterin
222043 at 7 9E-01 4 7E-01 1 9E-01 4 2E-02 No No CLU Hs 436657 clusterin
210765_at 1 4E-01 3 4E-02 9 5E-02 2 8E-01 No No CSE1 L Hs 90073 CSE1 chromosome segregation 1 -like
(yeast)
213712_at 8 7E-01 5 2E-01 6 5E-01 2 OE-01 No No CTNNAL1 Hs 58488 catenin (cadheππ-associated protein), alpha-like 1
203139 at 5 5E-01 7 5E-01 6 3E-01 2 9E-01 No No DAPK1 Hs 244318 death-associated protein kinase 1
218325_s_at 8 OE-01 1 6E-01 6 OE-01 2 3E-01 No No DATF 1 Hs 438300 death associated transcription factor 1
206939 at 6 7E-01 1 8E-01 9 9E-01 3 4E-01 No No DCC Hs 172562 deleted in colorectal carcinoma
210165_at 5 3E-01 1 7E-01 2 7E-01 1 2E-01 No No DNASE1 Hs 436928 deoxyribonuclease I
210655_s_at 2 1E-01 9 8E-01 7 2E-03 4 5E-01 No No FOXO3A Hs 14845 forkhead box O3A
213560_at 4 5E-01 3 1E-01 9 9E-01 9 7E-01 No No GADD45B Hs 110571 growth arrest and DNA-damage-inducible, beta jo
204121_at 1 4E-01 2 8E-02 5 7E-01 1 4E-01 No No GADD45G Hs 9701 growth arrest and DNA-damage-inducible, ' gamma
205848 at 34E-01 7 6E-01 8 OE-01 7 6E-01 No No GAS2 Hs 135665 growth arrest-specific 2
208000_at 8 4E-01 1 3E-01 6 9E-01 8 2E-02 No No GML Hs 86161 GPI anchored molecule like protein
205488 at 7 6E-01 1 6E-01 6 1E-01 1 5E-01 No No GZMA Hs 90708 granzyme A
210164_at 2 8E-01 8 9E-01 3 5E-01 1 1E-01 No No GZMB Hs 1051 granzyme B
210321_at 8 6E-01 3 6E-01 3 2E-01 2 2E-01 No No GZMH Hs 348264 granzyme H
206863 x_at 7 6E-01 9 5E-01 4 9E-01 54E-01 No No HRK Hs 87247 harakiπ
207062_at 4 2E-01 9 6E-01 2 2E-01 4 OE-01 No No IAPP Hs 142255 islet amyloid polypeptide
206975_at 3 5E-01 2 9E-01 2 8E-01 4 6E-01 No No LTA Hs 36 lymphotoxin alpha (TNF superfamily, member 1)
203005_at 7 3E-01 4 OE-01 6 4E-01 7 5E-01 No No LTBR Hs 1116 lymphotoxin beta receptor (TNFR superfamily, member 3)
205858_at 6 3E-01 5 5E-01 7 7E-01 7 9E-01 No No NGFR Hs 415768 nerve growth factor receptor (TNFR superfamily, member 16)
220402_at 8 4E-01 9 2E-01 6 3E-01 5 4E-01 No No P53AIP1 Hs 160953 p53-regulated apoptosis-inducing protein 1
220403 s at 4 4E-01 1 3E-01 4 7E-01 7 7E-01 No No P53AIP1 Hs 160953 p53-regulated apoptosis-inducing protein 1
214090_at 9 1E-01 4 7E-01 7 2E-02 1 OE-01 No No PAWR Hs 406074 PRKC, apoptosis, WT1, regulator
214237_x_at 8 2E-01 7 7E-02 7 8E-01 1 5E-01 No No PAWR Hs 406074 PRKC, apoptosis, WT1 , regulator
207634_at 6 2E-01 6 6E-01 9 7E-01 9 6E-01 No No PDCD1 Hs 158297 programmed cell death 1
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title 213585 s at 8 5E-01 8 7E-01 3 0E-01 4 3E-01 No No PDCD2 Hs 367900 programmed cell death 2 222152_at 8 3E-01 4 0E-01 2 2E-01 2 5E-01 No No PDCD6 Hs 24087 programmed cell death 6 207943_x_at 7 6E-01 5 0E-01 9 0E-01 4 5E-01 No No PLAGL1 Hs 132911 pleomorphic adenoma gene-like 1 218849_s_at 2 3E-01 1 9E-01 2 1 E-01 1 9E-01 No No RAI Hs 324051 RelA-associated inhibitor 207468 s at 1 6E-01 1 9E-01 4 8E-01 5 7E-01 No No SFRP5 Hs 279565 secreted fπzzled-related protein 5 202694_at 2 9E-01 6 7E-01 6 1E-01 1 5E-01 No No STK17A Hs 9075 serine/threonine kinase 17a (apoptosis- inducmg)
206222_at 7 5E-01 4 2E-01 5 5E-01 5 OE-01 No No TNFRSF10C Hs 119684 tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain
211163_s_at 8 2E-01 1 1 E-01 9 2E-01 1 7E-01 No No TNFRSF10C Hs 119684 tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain
210654_at 8 5E-01 5 2E-01 4 9E-01 9 8E-01 No No TNFRSF10D Hs 129844 tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain ^,
210847_x_at 6 5E-01 2 2E-01 5 3E-01 5 1 E-01 No No TNFRSF25 Hs 299558 ~-J tumor necrosis factor receptor superfamily, member 25
211282_x_at 4 2E-01 1 9E-01 9 9E-01 2 6E-01 No No TNFRSF25 Hs 299558 tumor necrosis factor receptor superfamily, member 25
211841_s_at 4 3E-01 2 5E-01 4 7E-01 5 6E-01 No No TNFRSF25 Hs 299558 tumor necrosis factor receptor superfamily, member 25
216042_at 3 3E-01 3 1E-01 2 5E-01 3 9E-01 No No TNFRSF25 Hs 299558 tumor necrosis factor receptor superfamily, member 25
219422_at 1 5E-01 3 7E-01 6 1E-01 8 OE-01 No No TNFRSF25 Hs 299558 tumor necrosis factor receptor superfamily, member 25
219423_x_at 5 8E-01 6 7E-01 7 7E-01 2 0E-01 No No TNFRSF25 Hs 299558 tumor necrosis factor receptor superfamily, member 25
205153_s_at 1 0E-01 4 9E-02 2 3E-02 1 1E-02 No No TNFRSF5 Hs 504816 tumor necrosis factor receptor superfamily, member 5
222292_at 2 1E-01 4 4E-01 4 1E-01 6 6E-02 No No TNFRSF5 Hs 504816 tumor necrosis factor receptor superfamily, member 5
204781_s_at 4 1E-02 9 5E-01 5 2E-02 3 3E-01 No No TNFRSF6 Hs 82359 tumor necrosis factor receptor superfamily, member 6
211786_at 2 9E-01 2 OE-02 9 3E-01 8 OE-02 No No TNFRSF9 Hs 193418 /// tumor necrosis factor receptor superfamily, Hs 193418 member 9
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene Symbol UniGene ID Gene Title
207907_at 6 4E-01 1 4E-01 8 7E-01 2 1 E-01 No No TNFSF14 Hs 129708 tumor necrosis factor (ligand) superfamily, member 14
207892_at 9 8E-01 2 2E-01 9 7E-01 1 8E-01 No No TNFSF5 Hs 652 tumor necrosis factor (ligand) superfamily, member 5 (hyper-lgM syndrome)
210865_at 4 0E-01 8 3E-01 5 6E-01 1 8E-01 No No TNFSF6 Hs 2007 tumor necrosis factor (ligand) superfamily, member 6
211333_s_at 2 2E-01 5 8E-01 1 7E-03 3 2E-01 No No TNFSF6 Hs 2007 tumor necrosis factor (ligand) superfamily, member 6
220804 s at 2 1 E-01 5 2E-02 7 5E-01 1 4E-01 No No TP73 Hs 192132 tumor protein p73
207382_at 2 6E-01 9 7E-01 4 9E-01 3 5E-01 No No TP73L Hs 137569 tumor protein p73-lιke
211194 s at 2 1E-01 6 2E-01 7 4E-02 2 2E-01 No No TP73L Hs 137569 tumor protein p73-lιke
211195_s_at 6 7E-01 7 9E-01 9 3E-01 5 3E-01 No No TP73L Hs 137569 tumor protein p73-lιke
211834 s at 4 7E-01 8 6E-01 6 9E-01 6 5E-01 No No TP73L Hs 137569 tumor protein p73-lιke
205641_s_at 3 3E-01 44E-01 1 8E-01 5 2E-01 No No TRADD Hs 89862 TNFRSFIA-associated via death domain
213443_at 4 0E-01 4 3E-01 2 5E-01 4 9E-01 No No TRADD Hs 89862 TNFRSFIA-associated via death domain
^o
Table 6A: Anti-apoptosis Genes (See tables reference 2)
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly 1 (A2) Ly1 (A3) Ly7(B1) Ly7 (B2) Ly7 (B3) Ly8(C1) Ly8 (C2) Ly8 (C3) D4(D1) D4 (D2) D4 (D3)
209165_at 862 8 82 867 902 904 905 863 875 887 879 883 888
207163_s_at 8 37 8 44 822 802 799 773 891 888 902 782 807 805
219366_at 6 89 7 05 718 720 726 711 672 691 716 739 724 757
202387_at 8 52 8 61 878 820 816 825 852 855 867 888 919 928
211475_s_at 8 87 9 19 917 866 862 874 886 900 914 948 971 988
219624_at 4 35 4 34 442 454 447 464 435 441 463 453 444 465
203685_at 4 75 4 61 479 433 446 442 462 465 468 448 458 441
207005_s_at 6 62 6 60 662 635 612 592 706 673 662 653 685 623
205681_at 4 31 4 32 429 459 461 449 445 448 430 684 814 747
206665_s_at 449 459 455 482 499 484 470 449 454 463 457 451
212312_at 594 629 648 661 693 642 613 605 630 607 630 633
215037_s_at 626 614 606 632 632 615 621 600 584 572 604 580
209311_at 534 542 537 536 530 548 526 552 531 513 513 511
208945_s_at 770 753 775 737 722 731 778 750 793 741 717 754
208946_s_at 810 784 804 739 720 716 803 806 809 774 743 793
202076_at 863 809 859 879 832 873 867 813 876 756 754 828
210538_s_at 464 475 480 689 665 657 449 435 462 495 543 521
206536_s_at 428 441 482 426 440 442 442 448 462 425 444 433
202094_at 805 801 773 869 838 837 794 810 808 854 831 845
202095_s_at 908 907 869 895 859 879 892 879 901 952 938 959
210334_x_at 824 819 787 834 821 827 813 797 829 875 854 849
220451_s_at 505 497 489 515 511 503 492 526 492 541 518 520
204930_s_at 645 622 630 633 624 640 646 644 650 661 640 644
207829_s_at 653 620 604 606 597 591 629 582 614 609 625 611
37226_at 607 586 575 562 575 571 590 581 590 582 576 583
209308_s_at 778 794 801 821 848 842 782 798 809 773 751 799
201848_s_at 863 693 789 757 762 752 902 771 866 681 687 716
201849_at 901 737 880 863 871 880 958 866 943 794 751 825
206044_s_at 545 587 568 576 594 590 559 579 566 582 586 571
208485_x_at 564 522 533 539 551 540 530 536 530 531 525 496
209508_x_at 613 612 608 612 631 596 616 613 603 598 595 574
209939_x_at 686 688 701 780 775 778 685 701 704 640 616 611
210563_x_at 661 684 671 762 736 739 674 673 685 659 634 651
211316 x at 652 642 635 652 668 633 648 664 628 606 597 595
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7(B1) Ly7 (B2) Ly7 (B3) Ly8(C1) Ly8 (C2) Ly8 (C3) D4(D1) D4 (D2) D4 (D3)
211317_s_at 450 460 470 466 465 471 451 460 459 442 451 447
211862_x_at 534 518 507 544 523 521 502 504 505 480 482 456
214618_at 441 469 477 470 455 485 468 469 473 481 498 474
200046_at 967 939 948 981 969 987 964 929 963 1002 1012 1022
208309_s_at 642 654 655 669 671 679 649 649 656 710 729 723
210017_at 477 461 496 515 509 535 457 464 490 535 534 591
210018_x_at 659 648 663 663 676 677 625 620 668 695 711 728
209239_at 835 859 852 722 763 716 837 851 819 815 849 800
201739_at 551 560 545 704 657 694 546 543 543 623 692 669
218878_s_at 786 741 782 801 775 814 774 738 789 759 724 767
207827_x_at 496 509 507 542 536 517 494 548 504 537 508 518
211546_x_at 485 505 498 520 508 495 509 524 498 535 511 512
201085_s_at 733 739 810 728 732 753 750 744 787 648 717 728
201086_x_at 982 989 988 981 967 954 987 988 969 929 929 940
213538_at 715 726 753 758 773 769 704 729 730 694 714 732
214988_s_at 949 956 984 965 946 944 960 967 960 902 909 932 O
200803_s_at 979 957 921 970 O
980 980 959 950 951 1010 1030 1017
200804_at 984 929 926 940 938 924 962 939 929 975 1002 1000
202643_s_at 555 558 549 645 641 637 545 543 512 570 571 585
202644_s_at 597 621 610 705 732 710 588 603 570 631 663 637
206092_x_at 640 662 647 678 677 653 647 653 628 644 653 629
206467_x_at 520 529 520 560 561 543 497 554 521 531 545 540
213829_x_at 699 706 706 675 716 699 716 721 691 700 719 673
203684_s_at 583 585 580 567 580 573 590 599 583 584 600 570
207004_at 545 549 532 560 563 542 540 556 541 552 547 550
221320_at 508 513 493 510 514 507 507 534 500 529 513 509
204861_s_at 472 463 466 441 456 438 438 434 436 444 432 427
206537_at 452 459 474 453 472 461 463 456 461 470 465 459
210564_x_at 567 547 543 594 568 573 560 555 562 540 554 548
214486_x_at 639 654 638 643 658 639 630 643 628 622 634 606
201631_s_at 533 528 526 558 557 571 537 546 524 568 540 544
221566_s_at 507 497 476 518 475 503 516 501 519 537 510 506
221567_at 533 541 525 518 511 518 546 547 535 541 546 528
206248_at 594 588 569 578 587 591 580 583 583 609 593 570
204466 s at 534 561 550 534 568 551 533 550 537 546 568 539
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7(B1) Ly7 (B2) Ly7 (B3) Ly8(C1) Ly8 (C2) Ly8 (C3) D4(D1) D4 (D2) D4 (D3) 204467_s_at 523 524 543 527 516 536 523 512 535 542 527 529 221371_at 535 552 546 520 525 547 523 545 534 536 558 553 221601_s_at 663 671 650 584 582 609 648 645 636 618 628 585 221602 s at 702 691 692 678 673 661 712 715 683 725 688 678
Table 6B- Anti-apoptosis Genes (See tables reference 2) t-test (two-tailed) Probesets pAB pAD pBC pCD Measured Changed Gene UniGene lD Gene Title
Symbol
209165 at 2 6E-02 1 4E-01 5 OE-02 3 4E-01 Yes No AATF Hs 311079 apoptosis antagonizing transcription factor
207163 s at 2 3E-02 2 5E-02 2 6E-03 1 5E-03 Yes No AKT1 Hs 368861 v-akt murine thymoma viral oncogene homolog 1
219366_at 2 2E-01 4 9E-02 1 7E-01 4 7E-02 Yes No AVEN Hs 63168 apoptosis, caspase activation inhibitor
202387_at 2 2E-02 3 8E-02 4 9E-03 3 6E-02 Yes No BAG1 Hs 377484 BCL2-assocιated athanogene
211475_s_at 4 7E-02 1 7E-02 3 9E-02 1 1E-02 Yes No BAG1 Hs 377484 BCL2-assocιated athanogene
219624_at 4 6E-02 9 1 E-02 4 4E-01 5 0E-01 Yes No BAG4 Hs 194726 BCL2-assocιated athanogene 4
203685_at 1 2E-02 3 8E-02 1 3E-02 7 5E-02 Yes No BCL2 Hs 79241 B-cell CLL/lymphoma 2
207005_s_at 6 OE-02 7 0E-01 2 1 E-02 3 0E-01 Yes No BCL2 Hs 79241 B-cell CLL/lymphoma 2
205681_at 1 7E-02 1 4E-02 8 8E-02 1 3E-02 Yes No BCL2A1 Hs 227817 BCL2-related protein A1
206665_s_at 1 2E-02 5 8E-01 2 2E-02 9 5E-01 Yes No BCL2L1 Hs 305890 BCL2-lιke 1
212312_at 1 3E-01 9 8E-01 6 1E-02 5 7E-01 Yes No BCL2L1 Hs 305890 BCL2-lιke 1
215037_s_at 24E-01 6 7E-02 1 3E-01 3 3E-01 Yes No BCL2L1 Hs 305890 BCL2-hke 1
209311_at 9 4E-01 4 8E-03 8 8E-01 9 5E-02 Yes No BCL2L2 Hs 410026 BCL2-lιke 2
208945 s at 1 5E-02 1 1E-01 6 2E-02 9 8E-02 Yes No BECN1 Hs 12272 beclin 1 (coiled-coil, myosin-like BCL2 interacting protein)
208946 s at 2 4E-03 1 7E-01 5 6E-03 1 3E-01 Yes No BECN1 Hs 12272 beclin 1 (coiled-coil, myosin-like BCL2 interacting protein)
202076_at 4 8E-01 1 1 E-01 7 3E-01 8 4E-02 Yes No BIRC2 Hs 289107 baculoviral IAP repeat-containing 2 210538_s_at 4 3E-04 6 6E-02 7 OE-05 1 9E-02 Yes No BIRC3 Hs 127799 /// baculoviral IAP repeat-containing 3 Hs 127799
206536_s_at 5 OE-01 4 3E-01 1 5E-01 1 1E-01 Yes No BIRC4 Hs 356076 baculoviral IAP repeat-containing 4 202094 at 1 9E-02 1 9E-02 3 6E-02 1 1 E-02 Yes No BIRC5 Hs 1578 baculoviral IAP repeat-containing 5
(survivin)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol
202095_s_at 3 6E-01 3 2E-02 3 6E-01 2 7E-03 Yes No BIRC5 Hs 1578 baculoviral IAP repeat-containing 5
(survivin)
210334_x_at 2 6E-01 3 OE-02 2 5E-01 2 1 E-02 Yes No BIRC5 Hs 1578 baculoviral IAP repeat-containing 5
(survivin)
220451_s_at 9 6E-02 3 6E-02 6 6E-01 1 8E-01 Yes No BIRC7 Hs 256126 baculoviral IAP repeat-containing 7 (livin)
204930_s_at 96E-01 1 6E-01 7 1E-02 8 6E-01 Yes No BNIP1 Hs 145726 BCL2/adenovιrus E1 B 19kDa interacting protein 1
207829_s_at 1 9E-01 5 5E-01 5 3E-01 6 9E-01 Yes No BNIP1 Hs 145726 BCL2/adenovιrus E1 B 19kDa interacting protein 1
37226_at 1 6E-01 4 4E-01 2 5E-02 1 6E-01 Yes No BNIP1 Hs 145726 BCL2/adenovιrus E1B 19kDa interacting protein 1
209308_s_at 1 3E-02 3 7E-01 2 3E-02 2 6E-01 Yes No BNIP2 Hs 204539 BCL2/adenovιrus E1 B 19kDa interacting protein 2
201848_s_at 6 7E-01 2 2E-01 1 5E-01 5 1 E-02 Yes No BNIP3 Hs 79428 BCL2/adenovιrus E1 B 19kDa interacting protein 3 O
201849_at 6 OE-01 4 5E-01 2 1 E-01 2 4E-02 Yes No BNIP3 Hs 79428 BCL2/adenovιrus E1 B 19kDa interacting protein 3
206044_s_at 2 2E-01 3 9E-01 7 9E-02 2 0E-01 Yes No BRAF Hs 162967 v-raf murine sarcoma viral oncogene homolog B1
208485_x_at 8 3E-01 2 4E-01 9 3E-02 3 0E-01 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
209508_x_at 8 8E-01 9 9E-02 8 5E-01 9 1E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
209939_x_at 1 6E-03 5 6E-03 3 6E-03 3 5E-03 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
210563_x_at 2 5E-03 7 5E-02 5 7E-03 3 8E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
211316_x_at 54E-01 3 3E-03 7 8E-01 3 4E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
211317_s_at 3 5E-01 1 3E-01 4 3E-02 5 5E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
211862_x_at 4 3E-01 1 5E-02 7 OE-02 6 5E-02 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
214618_at 6 0E-01 1 8E-01 9 9E-01 1 8E-01 Yes No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator
200046_at 5 5E-02 5 4E-03 1 3E-01 2 OE-02 Yes No DAD1 Hs 82890 defender against cell death 1
208309_s_at 1 5E-02 7 2E-04 5 9E-03 2 4E-03 Yes No MALT1 Hs 180566 mucosa associated lymphoid tissue lymphoma translocation gene 1
210017_at 3 6E-02 3 7E-02 2 OE-02 2 9E-02 Yes No MALT1 Hs 180566 mucosa associated lymphoid tissue lymphoma translocation gene 1
210018 x at 7 4E-02 1 6E-02 1 4E-01 2 OE-02 Yes No MALT1 Hs 180566 mucosa associated lymphoid tissue lymphoma translocation gene 1
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title
Symbol 209239_at 6 6E-03 1 9E-01 6 8E-03 4 6E-01 Yes No NFKB1 Hs 160557 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105)
201739_at 7 2E-03 2 8E-02 9 8E-03 2 9E-02 Yes No SGK Hs 296323 serum/glucocorticoid regulated kinase 218878_s_at 2 1 E-01 3 7E-01 2 0E-01 4 4E-01 Yes No SIRT1 Hs 31176 sirtuin (silent mating type information regulation 2 homolog) 1 (S cerevisiae)
207827_x_at 4 4E-02 1 8E-01 4 4E-01 7 9E-01 Yes No SNCA Hs 76930 synuclein, alpha (non A4 component of amyloid precursor) 211546_x_at 2 7E-01 8 2E-02 8 1E-01 4 5E-01 Yes No SNCA Hs 76930 synuclein, alpha (non A4 component of amyloid precursor)
201085_s_at 4 6E-01 1 5E-01 2 3E-01 1 1 E-01 Yes No SON Hs 430541 SON DNA binding protein
201086_x_at 1 3E-01 5 3E-04 2 3E-01 5 1 E-03 Yes No SON Hs 430541 SON DNA binding protein
213538_at 7 5E-02 3 1 E-01 1 7E-02 6 0E-01 Yes No SON Hs 430541 SON DNA binding protein
214988_s_at 4 3E-01 2 6E-02 2 6E-01 2 6E-02 Yes No SON Hs 430541 SON DNA binding protein
200803_s_at 2 8E-01 4 6E-02 6 2E-03 2 3E-03 Yes No TEGT Hs 35052 testis enhanced gene transcript (BAX inhibitor 1 ) o
200804_at 5 9E-01 1 2E-01 4 6E-01 2 OE-02 Yes No TEGT Hs 35052 testis enhanced gene transcript (BAX inhibitor 1)
202643_s_at 1 7E-05 3 5E-02 6 8E-03 3 9E-02 Yes No TNFAIP3 Hs 211600 tumor necrosis factor, alpha-induced protein 3
202644_s_at 7 0E-04 5 2E-02 5 8E-04 1 4E-02 Yes No TNFAIP3 Hs 211600 tumor necrosis factor, alpha-induced protein 3
206092_x_at 1 3E-01 4 6E-01 7 OE-02 9 4E-01 Yes No TNFRSF6B Hs 348183 tumor necrosis factor receptor superfamily, member 6b, decoy
206467_x_at 1 6E-02 3 7E-02 2 0E-01 4 6E-01 Yes No TNFRSF6B Hs 348183 tumor necrosis factor receptor superfamily, member 6b, decoy
213829_x_at 6 2E-01 6 9E-01 4 5E-01 5 1 E-01 Yes No TNFRSF6B Hs 348183 tumor necrosis factor receptor superfamily, member 6b, decoy
203684_s_at 1 2E-01 8 2E-01 4 8E-02 6 0E-01 No No BCL2 Hs 79241 B-cell CLL/lymphoma 2 207004_at 1 9E-01 2 6E-01 3 3E-01 5 3E-01 No No BCL2 Hs 79241 B-cell CLL/lymphoma 2 221320_at 4 3E-01 2 2E-01 7 9E-01 7 9E-01 No No BCL2L10 Hs 283672 BCL2-lιke 10 (apoptosis facilitator) 204861_s_at 4 6E-02 9 8E-03 2 7E-01 7 8E-01 No No BIRC1 Hs 79019 baculoviral IAP repeat-containing 1 206537_at 9 6E-01 6 9E-01 7 6E-01 3 0E-01 No No BIRC4 Hs 356076 baculoviral IAP repeat-containing 4 210564_x_at 7 5E-02 5 9E-01 1 2E-01 7 3E-02 No No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator 214486_x_at 7 2E-01 8 1 E-02 1 4E-01 2 5E-01 No No CFLAR Hs 355724 CASP8 and FADD-like apoptosis regulator 201631 s at 7 6E-03 1 2E-01 3 3E-02 2 4E-01 No No IER3 Hs 76095 immediate early response 3
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title Symbol
221566_s_at 7 3E-01 1 4E-01 4 1 E-01 6 4E-01 No No NOL3 Hs 462911 nucleolar protein 3 (apoptosis repressor with CARD domain)
221567_at 4 1E-02 5 OE-01 7 OE-03 5 5E-01 No No NOL3 Hs 462911 nucleolar protein 3 (apoptosis repressor with CARD domain)
206248_at 8 9E-01 6 5E-01 4 7E-01 5 1 E-01 No No PRKCE Hs 155281 protein kinase C, epsilon
204466_s_at 8 3E-01 8 2E-01 4 OE-01 3 6E-01 No No SNCA Hs 76930 synuclein, alpha (non A4 component of amyloid precursor)
204467_s_at 6 9E-01 7 3E-01 7 6E-01 3 2E-01 No No SNCA Hs 76930 synuclein, alpha (non A4 component of amyloid precursor)
221371_at 2 7E-01 5 9E-01 7 6E-01 1 9E-01 No No TNFSF18 Hs 248197 tumor necrosis factor (hgand) superfamily, member 18
221601_s_at 4 OE-03 4 2E-02 1 7E-02 1 2E-01 No No TOSO Hs 58831 regulator of Fas-induced apoptosis
221602 s at 2 1 E-02 9 1 E-01 6 5E-02 7 2E-01 No No TOSO Hs 58831 regulator of Fas-induced apoptosis
O
Table 7A: B-CeIl Maturation Specific Genes
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1 ) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
202094_at 8 05 8 01 7 73 8 69 8 38 8 37 7 94 8 10 8 08 8 54 8 31 845
202095_s_at 9 08 9 07 8 69 8 95 8 59 8 79 8 92 8 79 9 01 9 52 9 38 9 59
210334 x_at 8 24 8 19 7 87 8 34 8 21 8 27 8 13 7 97 8 29 8 75 8 54 8 49
204581_at 7 31 6 65 6 97 9 29 9 12 9 07 7 64 6 88 7 08 9 45 9 76 9 57
217422_s_at 648 6 12 6 21 8 47 8 56 8 33 6 65 5 98 5 96 8 61 9 38 8 76
38521_at 8 75 8 60 8 51 9 72 9 86 9 76 8 71 8 54 8 42 9 89 10 19 10 05
206545_at 4 02 3 98 4 01 6 13 6 64 5 89 3 90 3 92 3 96 4 05 3 99 3 95
211856_x_at 5 39 5 68 5 60 5 93 6 48 6 52 5 47 5 51 5 52 5 61 5 69 5 51
211861 x at 4 01 4 10 3 93 4 35 4 88 4 82 3 89 3 97 4 11 4 17 4 14 4 07
204192_at 10 20 8 83 9 62 9 58 9 67 9 21 9 74 8 62 8 54 9 85 9 94 9 72
205692_s_at 6 94 7 34 7 45 9 32 9 34 9 36 6 89 7 41 7 26 9 01 9 14 8 98
209835_x_at 4 51 441 4 43 4 50 4 51 4 58 4 52 4 56 4 51 4 57 4 59 4 57
209795 at 4 56 4 42 4 80 4 00 4 14 4 03 4 36 4 48 4 27 4 07 4 06 4 06
200675_at 11 42 11 58 11 30 10 93 10 69 10 90 11 18 11 33 11 20 11 17 11 01 11 17 o
202910 s_at 6 46 6 62 6 38 6 06 6 19 5 99 6 51 6 78 6 67 6 22 6 45 6 40
207691_x_at 5 60 5 66 5 54 5 00 5 03 4 97 5 40 5 14 5 33 4 95 4 99 4 73
209473_at 6 69 6 41 6 61 5 49 6 05 6 08 6 38 6 44 6 45 5 77 5 45 5 61
209474 s at 4 91 4 79 4 92 4 40 4 63 4 46 4 79 4 71 4 87 4 27 4 51 4 34
219731_at 664 7 01 6 91 6 84 6 91 6 64 6 59 6 86 6 69 6 28 6 68 6 18
211430_s_at 10 70 10 74 10 73 5 10 5 78 5 96 11 52 11 37 10 89 10 06 10 59 9 59
211641 x at 5 33 5 52 5 28 5 10 4 90 4 92 5 28 5 34 5 36 4 95 5 09 4 95
214973_x_at 6 67 6 76 6 76 6 37 6 65 6 31 6 67 7 06 6 47 6 48 6 50 6 49
217281 x at 5 93 5 68 5 35 5 19 4 81 5 11 5 87 5 69 5 41 5 41 5 27 5 05
203233_at 6 56 6 42 6 48 7 84 7 90 7 58 6 86 6 55 6 39 7 02 7 41 6 91
204864 s at 4 96 4 97 4 82 4 84 4 96 5 03 5 02 5 02 4 99 5 10 4 94 4 98
212195_at 4 36 4 05 4 17 4 19 4 22 4 08 5 14 449 4 80 3 83 3 92 3 88
204562_at 8 22 8 60 8 59 8 69 9 38 8 42 8 35 8 44 7 86 6 36 6 28 6 01
216986_s_at 6 51 6 37 6 35 6 45 6 80 6 42 6 55 6 43 6 23 6 43 6 42 6 01
201286_at 4 49 4 58 4 38 4 48 4 61 4 54 4 48 4 46 4 55 4 70 4 60 4 43
206641 at 4 61 4 74 444 7 47 8 13 740 4 55 4 51 4 66 6 82 7 58 7 39
206729_at 5 68 5 98 5 69 5 51 5 49 5 75 5 68 5 76 5 65 5 70 5 76 5 59
206508 at 5 59 5 65 5 60 7 85 8 89 7 93 5 59 5 81 5 45 5 69 5 96 5 81
220674_at 4 69 4 54 4 34 4 92 4 75 4 68 4 72 4 52 4 54 4 81 4 87 468
204489 s at 5 37 5 38 5 30 5 34 5 37 5 26 5 34 5 40 5 22 5 33 5 32 5 20
Log2 fluorescence intensity
Probesets Ly1 (A1 ) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
204490_s_at 432 447 455 472 451 447 4 44 435 438 472 451 444 210916_s_at 467 458 452 458 454 457 4 65 459 461 493 481 467
212014_x_at 4 4 4444555 4 4 4444555 4 4 4333222 4 4 4444222 4 4 4444888 4 4 4444555 4 4 444 4444 4 4 4444444 4 4 4444333 4 4 4555777 4 4 4555111 4 4 4444888
212063 at 3 3 3999444 4 4 4111555 4 4 4111111 4 4 4000222 4 4 4111777 4 4 4000666 3 3 399 9555 4 4 4000888 3 3 3999777 4 4 4000444 4 4 4000666 4 4 4111444
216056_at 44 4666999 44 4999222 55 5000000 44 4777777 55 5000333 55 5000444 44 477 7111 44 4777999 44 4777999 44 4888666 44 4888666 44 4777888
216062_at 55 5777888 55 5666555 55 5777333 55 5888111 55 5555777 55 5777666 55 577 7777 55 5777222 55 5777666 66 6111333 55 5777666 55 5888999 n ^ ycpo *af 3 o ~77C6 n 38 on0 n 3 o8n0 n 3 ~77n9 n 37708 O 3 Q8G6 O 3 " 77O9 O 377C6 O 3 Q8O2 O 3 Q84Λ Q 3 Q8-1I 3 *3 7777
205544j5_at 495 495 488 482 497 488 4 88 483 504 490 495 483
203716_sjat 497 502 503 520 475 508 5 16 495 507 569 514 522
203717_at 407 392 405 407 407 405 3 97 406 403 416 412 407
211478_s_at 398 398 395 398 409 402 4 10 403 385 403 409 402
206759_at 475 458 459 506 488 478 4 63 451 449 509 488 468
206760_s_at 579 592 584 605 596 597 5 89 579 582 600 609 590
211636_at 417 418 393 413 409 416 4 32 418 414 420 424 409
211642_at 435 444 433 441 410 436 4 57 424 437 455 423 429
211878_at 4 40066 3 39900 3 38822 4 40000 3 39922 4 40011 3 39 999 3 39944 3 38899 3 39966 3 39999 3 39988 o
215721_at 5 " 2"1' 5 " 0"4 5 " 0 "2" 4 ' 8"4 4 ' 6"4' 4 ' 8"1' 5 " 1 '5" 506 500 487 486 469
217260_x_at 540 536 529 482 515 513 4 98 547 521 515 521 482
206341_at 441 438 435 432 423 432 4 47 427 443 450 452 429
211269_s_at 599 592 607 593 613 599 6 01 615 598 584 590 596
205945_at 407 413 408 402 416 417 3 99 408 405 406 425 406
217489_s_at 453 454 444 451 447 454 4 59 444 451 456 489 461
204863_s_at 410 416 408 411 419 416 4 12 410 418 419 412 414
211000_s_at 505 501 488 498 495 502 5 03 517 505 514 509 490
212196_at 413 406 404 404 407 413 4 26 425 422 402 415 409
216987_at 388 374 380 379 374 379 3 78 372 382 380 377 380
201287_s_at 637 641 638 627 636 624 6 32 644 629 643 624 628
Table 7B: B-CeIl Maturation Specific Genes t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title Ref
Symbol
FDR Cutoff 1 OE-02 8 2E-03 1 2E-02 9 4E-03 AC v BD AC v BD
202094_at 1 9E-02 1 9E-02 3 6E-02 1 1 E-02 Yes No BIRC5 Hs 1578 baculoviral IAP repeat-containing 5 3
(survivin)
202095_s_at 3 6E-01 3 2E-02 3 6E-01 2 7E-03 Yes No BIRC5 Hs 1578 baculoviral IAP repeat-containing 5 3
(survivin)
210334_x_at 2 6E-01 3 OE-02 2 5E-01 2 1 E-02 Yes No BIRC5 Hs 1578 baculoviral IAP repeat-containing 5 3
(survivin)
204581 at 3 8E-03 1 4E-03 8 7E-03 3 9E-03 Yes Yes CD22 Hs 262150 CD22 antigen 4
217422_s_at 2 4E-04 2 7E-03 6 2E-03 1 2E-03 Yes Yes CD22 Hs 262150 CD22 antigen 4
38521_at 4 5E-04 3 0E-04 1 3E-03 2 6E-04 Yes Yes CD22 Hs 262150 CD22 antigen 4
206545_at 9 6E-03 8 7E-01 8 8E-03 1 3E-01 Yes No CD28 Hs 1987 CD28 antigen (Tp44) 4
211856_x_at 4 2E-02 6 6E-01 5 OE-02 1 7E-01 Yes No CD28 Hs 1987 CD28 antigen (Tp44) 4
211861 x at 4 7E-02 1 2E-01 3 9E-02 1 6E-01 Yes No CD28 Hs 1987 CD28 antigen (Tp44) 4
O
204192_at 8 9E-01 5 5E-01 3 1 E-01 1 5E-01 Yes No CD37 Hs 153053 CD37 antigen 4
205692 s at 5 2E-03 4 2E-03 4 9E-03 3 9E-03 Yes Yes CD38 Hs 174944 CD38 antigen (p45) 4
209835_x_at 1 1E-01 4 6E-02 9 6E-01 8 9E-02 Yes No CD44 Hs 306278 CD44 antigen 5
209795_at 2 8E-02 4 2E-02 1 9E-02 4 OE-02 Yes No CD69 Hs 82401 CD69 antigen (p60, early T-cell 4 activation antigen)
200675_at 5 9E-03 3 7E-02 1 7E-02 1 7E-01 Yes No CD81 Hs 54457 CD81 antigen (target of 4 antiproliferative antibody 1)
202910 s at 1 2E-02 2 5E-01 5 7E-03 4 9E-02 Yes No CD97 Hs 3107 CD97 antigen 4
207691_x_at 1 OE-03 5 2E-03 6 OE-02 2 3E-02 Yes No ENTPD1 Hs 444105 CD39 antigen 4
209473 at 5 1E-02 1 6E-03 1 0E-01 9 3E-03 Yes No ENTPD1 Hs 444105 CD39 antigen 4
209474_s_at 1 5E-02 6 4E-03 3 OE-02 1 1E-02 Yes No ENTPD1 Hs 444105 CD39 antigen 4
219731_at 7 1 E-01 7 4E-02 5 0E-01 1 5E-01 Yes No ENTPD1 Hs 444105 CD39 antigen 4
211430_s_at 2 6E-03 1 6E-01 1 2E-04 3 4E-02 Yes No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
211641_x_at 1 5E-02 1 7E-02 1 9E-02 8 8E-03 Yes No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
214973_x_at 1 0E-01 1 2E-02 2 3E-01 2 9E-01 Yes No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
217281_x_at 4 6E-02 1 2E-01 2 7E-02 7 7E-02 Yes No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title Ref
Symbol
203233_at 2 2E-03 4 6E-02 3 2E-03 6 6E-02 Yes No IL4R Hs 75545 CD124 antigen 4
204864 s at 7 5E-01 2 4E-01 3 4E-01 9 8E-01 Yes No IL6ST Hs 71968 gp130 4
212195_at 8 0E-01 6 6E-02 6 8E-02 3 6E-02 Yes No IL6ST Hs 71968 gp130 4
204562 at 34E-01 2 1E-04 1 6E-01 1 7E-03 Yes No IRF4 Hs 127686 interferon regulatory factor 4 6
216986_s_at 3 5E-01 4 9E-01 3 8E-01 5 5E-01 Yes No IRF4 Hs 127686 interferon regulatory factor 4 6
201286 at 4 8E-01 4 OE-01 4 OE-01 4 2E-01 Yes No SDC1 Hs 82109 CD138 antigen 4
206641_at 24E-03 3 1E-03 4 3E-03 5 5E-03 Yes Yes TNFRSF17 Hs 2556 B-cell maturation factor 7
206729_at 2 OE-01 44E-01 3 2E-01 86E-01 Yes No TNFRSF8 Hs 1314 CD30 antigen 4
206508_at 1 6E-02 1 2E-01 1 OE-02 2 1E-01 Yes No TNFSF7 Hs 99899 CD70 antigen 4
220674_at 1 1 E-01 1 1E-01 1 1E-01 8 5E-02 No No CD22 Hs 262150 CD22 antigen 4
204489_s_at 5 3E-01 2 4E-01 9 7E-01 6 OE-01 No No CD44 Hs 306278 CD44 antigen 5
204490 s at 3 1E-01 3 6E-01 1 5E-01 1 8E-01 No No CD44 Hs 306278 CD44 antigen 5
210916_s_at 6 4E-01 8 4E-02 8 2E-02 1 2E-01 No No CD44 Hs 306278 CD44 antigen 5
212014 x at 4 2E-01 1 1 E-01 4 5E-01 9 OE-02 No No CD44 Hs 306278 CD44 antigen 5
212063 at 8 0E-01 8 1E-01 2 2E-01 1 8E-01 No No CD44 Hs 306278 CD44 antigen 5 O
OO
216056_at 5 8E-01 7 4E-01 1 6E-01 1 3E-01 No No CD44 Hs 306278 CD44 antigen 5
216062_at 9 5E-01 1 9E-01 6 7E-01 24E-01 No No CD44 Hs 306278 CD44 antigen 5
217523_at 4 2E-01 4 OE-01 4 5E-01 4 5E-01 No No CD44 Hs 306278 CD44 antigen 5
205544_s_at 5 5E-01 5 1E-01 8 1E-01 8 3E-01 No No CR2 Hs 73792 CD21 antigen 4
203716_s_at 9 9E-01 1 8E-01 7 5E-01 2 2E-01 No No DPP4 Hs 44926 CD26 antigen 4
203717_at 3 7E-01 1 4E-01 2 4E-01 6 3E-02 No No DPP4 Hs 44926 CD26 antigen 4
211478 s at 2 0E-01 4 2E-02 7 3E-01 5 7E-01 No No DPP4 Hs 44926 CD26 antigen 4
206759_at 5 8E-02 1 6E-01 2 7E-02 8 7E-02 No No FCER2 Hs 1416 CD23 antigen 4
206760 s at 3 8E-02 9 5E-02 2 OE-02 7 OE-02 No No FCER2 Hs 1416 CD23 antigen 4
211636_at 7 2E-01 4 3E-01 2 3E-01 6 1E-01 No No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
211642_at 5 0E-01 9 0E-01 4 8E-01 7 9E-01 No No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
211878_at 5 5E-01 5 7E-01 3 8E-01 3 3E-01 No No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
215721_at 1 9E-02 2 7E-02 2 OE-02 2 5E-02 No No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
217260_x_at 8 6E-02 1 3E-01 3 6E-01 4 4E-01 No No IGHG3 Hs 413826 immunoglobulin heavy constant 4 gamma 3 (G3m marker)
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title Ref
Symbol
206341_at 6 7E-02 5 4E-01 2 5E-01 6 7E-01 No No IL2RA Hs 130058 CD25 antigen 4
211269_s at 7 6E-01 1 7E-01 7 4E-01 8 7E-02 No No IL2RA Hs 130058 CD25 antigen 4
205945_at 7 1 E-01 7 1 E-01 2 5E-01 3 1 E-01 No No IL6R Hs 193400 CD126 antigen 4
217489_s_at 8 6E-01 2 1E-01 96E-01 2 3E-01 No No IL6R Hs 193400 CD126 antigen 4
204863_s_at 2 5E-01 2 9E-01 5 7E-01 6 4E-01 No No IL6ST Hs 71968 CD126 antigen 4
211000 s at 9 8E-01 5 4E-01 1 2E-01 64E-01 No No IL6ST Hs 71968 CD126 antigen 4
212196_at 96E-01 8 8E-01 1 3E-02 4 1E-02 No No IL6ST Hs 71968 CD126 antigen 4
216987_at 56E-01 74E-01 9 1E-01 6 0E-01 No No IRF4 Hs 127686 interferon regulatory factor 4 6
201287 s at 1 1 E-01 3 6E-01 3 6E-01 6 6E-01 No No SDC1 Hs 82109 CD138 antigen 4
o
Table 8A: Pan-B-Cell Genes
Log2 fluorescence intensity
Probesets Ly1 (At ) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
206398 s at 10 29 10 05 10 02 9 37 943 9 01 10 05 9 89 9 62 8 35 8 93 8 50
215925_s_at 7 46 6 84 7 74 6 66 7 11 6 71 7 15 6 81 6 93 7 20 7 36 7 17
209619_at 12 37 11 96 12 10 12 07 12 17 11 94 12 1 1 11 63 11 56 12 67 12 83 12 63
205049_s_at 10 15 9 84 9 81 10 50 1049 10 12 9 82 9 54 9 51 10 19 10 41 10 05
205297 s at 10 93 10 97 10 91 9 82 9 84 9 68 10 91 10 80 10 64 9 51 9 79 9 71
207176 s at 6 11 6 33 6 32 6 31 6 25 6 39 6 13 6 37 6 25 6 58 6 49 6 50
210356_x_at 10 06 9 78 10 31 10 94 11 02 10 94 9 54 9 82 9 63 11 02 11 32 10 99
217418 x at 10 10 9 76 10 14 10 89 10 94 10 87 9 45 9 75 9 59 10 96 11 22 10 85
221969_at 841 8 70 8 84 7 69 7 68 7 55 846 8 75 841 8 01 8 06 7 96
215346 at 6 64 6 15 6 16 6 82 6 86 6 41 6 44 6 49 5 92 6 97 6 90 6 83
35150 at 8 56 8 35 8 22 8 42 8 72 8 53 8 28 8 41 8 06 8 67 8 99 8 50
220068_at 10 38 10 38 10 30 10 12 10 15 10 03 9 95 10 02 10 07 9 85 10 05 10 03
206802_at 6 05 6 11 5 94 6 12 6 03 5 87 6 18 6 05 5 78 6 25 6 05 5 91
205153_s_at 5 94 5 42 5 24 6 04 6 24 6 03 5 75 5 47 5 33 6 25 6 50 6 10
222292 at 4 59 4 65 4 73 4 57 4 65 4 52 4 51 4 47 4 60 4 66 4 67 4 85
Table 8B: Pan-B-Cell Genes t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title Re
Symbol
TABLE 8B
206398_s_at 8 4E-03 4 9E-03 3 3E-02 5 8E-03 Yes No CD19 Hs 96023 CD19 antigen 4
215925 s at 1 8E-01 7 4E-01 4 8E-01 8 8E-02 Yes No CD72 Hs 116481 CD72 antigen 4
209619_at 5 7E-01 2 4E-02 2 3E-01 2 2E-02 Yes No CD74 Hs 446471 CD74 antigen 4
205049_s_at 5 9E-02 1 4E-01 1 OE-02 1 5E-02 Yes No CD79A Hs 79630 CD79A antigen (immunoglobuhn- 4 associated alpha)
205297_s_at 7 OE-04 3 1 E-03 1 1 E-03 6 3E-04 Yes Yes CD79B Hs 89575 CD79B antigen (immunoglobulm- 4 associated beta)
207176_s_at 5 0E-01 4 9E-02 4 5E-01 3 8E-02 Yes No CD80 Hs 838 CD80 antigen (CD28 antigen hgand 4
1 , B7-1 antigen)
210356_x_at 2 4E-02 6 6E-03 1 9E-03 5 9E-04 Yes No MS4A1 Hs 438040 CD20 antigen 4
217418_x_at 1 5E-02 3 5E-03 3 OE-03 7 2E-04 Yes No MS4A1 Hs 438040 CD20 antigen 4
221969_at 8 5E-03 3 2E-02 6 1 E-03 3 1 E-02 Yes No PAX5 Hs 22030 paired box gene 5 (B-cell lineage 7 specific activator protein)
215346_at 1 6E-01 6 1 E-02 1 5E-01 7 OE-02 Yes No TNFRSF5 Hs 504816 CD40 antigen 4
35150 at 2 5E-01 1 3E-01 8 9E-02 6 3E-02 Yes No TNFRSF5 Hs 504816 CD40 antigen 4
220068_at 6 7E-03 1 5E-02 1 7E-01 6 4E-01 Yes No VPREB3 Hs 136713 pre-B lymphocyte gene 3 8
206802_at 8 0E-01 7 5E-01 9 8E-01 6 8E-01 No No PAX5 Hs 22030 paired box gene 5 (B-cell lineage 7 specific activator protein)
205153_s_at 1 0E-01 4 9E-02 2 3E-02 1 1 E-02 No No TNFRSF5 Hs 504816 CD40 antigen 4
222292 at 2 1 E-01 4 4E-01 4 1 E-01 6 6E-02 No No TNFRSF5 Hs 504816 CD40 antigen 4
Table 9A: Pre-B/GC Marker Genes
Log2 fluorescence intensity
Probesets Ly 1 (A1) Ly1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1) D4 (D2) D4 (D3)
219488_at 5 20 5 39 5 13 5 80 5 94 5 60 5 40 5 34 5 33 5 84 5 77 5 52
204639 at 8 75 8 80 8 72 9 11 9 15 8 83 8 78 8 89 8 83 5 93 6 35 5 98
203140_at 8 23 7 80 9 55 9 61 9 72 9 33 8 39 8 31 7 70 9 82 1045 9 94
215990_s_at 7 37 6 79 7 81 8 18 8 00 7 78 7 47 7 01 6 83 8 45 8 89 8 25
208650_s_at 8 87 8 94 9 42 8 48 8 33 8 51 9 08 9 14 9 02 3 88 3 93 4 12
208651_x_at 9 18 9 18 9 57 8 92 8 82 8 87 9 26 9 36 9 01 6 22 6 34 6 23
209771_x_at 11 06 11 00 11 43 10 63 10 45 10 50 11 13 11 13 10 86 6 02 6 69 6 70
209772_s_at 9 04 8 92 9 10 8 21 8 10 8 25 9 20 8 71 8 61 7 01 6 93 6 84
266_s_at 8 55 8 65 9 22 8 30 8 13 8 35 8 60 8 66 8 61 5 50 4 92 5 35
201005 at 10 54 10 55 10 64 4 88 4 53 4 83 10 91 10 82 10 60 5 25 4 95 4 80
203066_at 8 28 9 29 9 15 5 61 6 06 5 98 8 64 9 25 8 62 6 19 6 26 6 02
209374 s at 12 45 12 38 12 47 12 36 12 36 12 26 1249 12 46 1241 6 35 5 73 5 78
212827_at 12 25 12 13 12 18 11 99 12 17 11 86 12 24 12 01 11 91 6 42 6 55 6 25
213674 x at 9 33 7 92 9 07 7 08 7 36 7 05 9 34 8 15 8 32 6 30 6 00 5 70
222285_at 6 09 5 74 6 62 5 59 5 99 548 5 90 5 86 5 69 5 61 5 54 5 43 K)
206660_at 10 68 11 35 10 55 5 41 4 82 4 94 9 07 10 28 10 32 5 10 4 93 5 30
203434_s_at 7 60 7 86 8 01 7 56 7 39 7 64 8 20 8 29 8 55 8 97 8 79 9 05
203435_s_at 8 64 8 83 8 81 8 37 7 97 843 8 75 8 99 9 11 8 96 8 86 8 97
206591_at 7 55 8 15 8 76 4 39 4 15 4 25 8 34 8 84 8 68 4 23 4 00 4 32
215117 at 4 08 4 38 4 81 3 72 3 60 3 69 4 16 4 87 4 38 3 78 3 78 3 72
213435_at 6 68 6 84 7 27 5 62 5 52 5 94 7 01 7 31 7 28 5 24 4 63 5 11
215591_at 3 86 3 90 3 70 3 83 3 66 3 76 3 85 3 77 3 84 3 85 3 75 3 77
209995_s_at 11 95 12 19 12 19 10 79 11 03 10 72 12 13 12 27 12 15 8 59 8 80 8 85
39318 at 12 14 12 32 12 26 11 06 11 18 10 93 12 27 12 49 12 25 8 75 8 94 848
221349_at 7 42 7 98 8 39 3 97 4 10 3 83 7 19 7 15 7 10 4 75 4 85 4 35
210487 at 4 94 4 60 4 78 5 05 4 70 4 78 4 91 4 79 4 89 5 12 5 05 4 87
203939 at 4 68 4 72 4 66 4 71 4 61 4 67 4 68 4 62 4 78 4 66 4 73 4 73
Table 9B: Pre-B/GC Marker Genes t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene ID Gene Title Ref
Symbol
219488_at 1 4E-02 2 2E-02 4 3E-02 6 3E-02 Yes No A4GALT Hs 105956 alpha 1 ,4-galactosyltransferase 9
204639 at 1 0E-01 1 8E-03 1 8E-01 1 4E-03 Yes No ADA Hs 407135 adenosine deaminase 10
203140_at 1 9E-01 8 5E-02 9 9E-03 2 8E-03 Yes No BCL6 Hs 155024 B-cell CLL/lymphoma 6 (zinc finger 6 protein 51)
215990_s_at 1 4E-01 3 4E-02 2 5E-02 6 1E-03 Yes No BCL6 Hs 155024 B-cell CLL/lymphoma 6 (zinc finger protein 51)
208650_s_at 54E-02 2 1E-04 1 3E-03 1 2E-05 Yes No CD24 Hs 375108 CD24 antigen 4
208651 x at 7 OE-02 8 9E-04 7 2E-02 3 9E-04 Yes No CD24 Hs 375108 CD24 antigen 4
209771 x at 2 8E-02 2 2E-04 1 2E-02 7 2E-04 Yes No CD24 Hs 375108 CD24 antigen 4
209772_s_at 3 4E-04 9 5E-06 6 2E-02 6 OE-03 Yes No CD24 Hs 375108 CD24 antigen 4
266_s_at 1 1 E-01 2 5E-04 2 5E-02 2 4E-03 Yes No CD24 Hs 375108 CD24 antigen 4
201005_at 1 1E-04 2 7E-04 2 4E-06 1 OE-05 Yes Yes CD9 Hs 387579 CD9 antigen (p24) 4
203066_at 4 3E-03 9 8E-03 5 9E-04 2 7E-03 Yes No GALNAC4S- Hs 523379 B cell RAG associated protein 4
R DOCT I UJ
209374_s_at 8 OE-02 7 5E-04 5 OE-02 7 6E-04 Yes No IGHM Hs 439852 immunoglobulin heavy constant mu 4
212827 at 1 7E-01 3 8E-05 74E-01 2 OE-06 Yes No IGHM Hs 439852 immunoglobulin heavy constant mu 4
213674_x_at 5 9E-02 1 4E-02 5 3E-02 9 4E-03 Yes No IGHM Hs 439852 immunoglobulin heavy constant mu 4
222285 at 2 1E-01 1 3E-01 5 1E-01 3 OE-02 Yes No IGHM Hs 439852 immunoglobulin heavy constant mu 4
206660_at 8 7E-05 4 3E-04 2 5E-03 4 9E-03 Yes Yes IGLL1 Hs 348935 immunoglobulin lambda-like 11 polypeptide 1
203434_s_at 1 2E-01 2 8E-03 4 7E-03 1 4E-02 Yes No MME Hs 307734 CALLA (CDIO) 4
203435_s at 5 9E-02 8 OE-02 2 2E-02 8 8E-01 Yes No MME Hs 307734 CALLA (CDIO) 4
206591_at 6 2E-03 4 9E-03 1 5E-04 5 3E-05 Yes Yes RAG1 Hs 73958 recombination activating gene 1 4
215117_at 6 6E-02 8 5E-02 5 8E-02 74E-02 Yes No RAG2 Hs 159376 recombination activating gene 2 4
213435_at 6 2E-03 1 6E-03 1 OE-03 1 8E-03 Yes Yes SATB2 Hs 412327 SATB family member 2 12
215591_at 4 OE-01 6 7E-01 2 9E-01 5 1E-01 Yes No SATB2 Hs 412327 SATB family member 2 12
209995 s at 6 OE-04 7 8E-06 1 4E-03 2 9E-05 Yes Yes TCL1A Hs 2484 T-cell leukemia/lymphoma 1A 13
39318_at 3 2E-04 3 8E-04 2 7E-04 1 2E-04 Yes Yes TCL1A Hs 2484 T-cell leukemia/lymphoma 1A 13
221349_at 3 1 E-03 1 7E-03 1 5E-04 3 OE-03 Yes Yes VPREB1 Hs 247979 pre-B lymphocyte gene 1 4
210487_at 6 5E-01 1 3E-01 8 6E-01 1 7E-01 No No DNTT Hs 397294 deoxynucleotidyitransferase, 4 terminal
203939 at 5 7E-01 5 2E-01 6 4E-01 8 1E-01 No No NT5E Hs 153952 5'-nucleotιdase, ecto (CD73)
Table 1OA: CD40/BCR Signaling Genes
Log2 fluorescence intensity
Probesets Ly 1 (A1 ) Ly 1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
207163_s_at 8 37 8 44 8 22 8 02 7 99 7 73 8 91 8 88 9 02 7 82 8 07 8 05
205367_at 7 63 7 61 7 50 10 59 10 54 10 27 7 14 7 60 742 10 20 10 20 10 16
205263_at 7 40 7 11 7 48 7 15 7 15 7 30 7 21 7 26 7 75 6 52 6 52 7 01
207655_s_at 8 48 8 44 9 00 9 52 9 42 9 15 8 32 8 53 8 60 7 89 7 90 8 20
220059_at 8 32 8 08 8 17 10 14 10 19 10 19 8 09 7 95 7 95 9 89 9 72 9 93
205504_at 5 84 5 90 6 11 8 32 8 16 7 96 6 01 5 67 5 89 8 53 8 41 8 56
202987_at 3 92 4 01 3 98 3 91 3 98 3 98 3 98 3 98 3 91 4 05 4 00 3 99
215411_s_at 8 69 8 39 8 38 7 63 7 89 7 72 8 67 8 42 8 46 7 63 8 29 7 97
202514_at 5 84 5 68 6 02 6 28 5 89 6 29 5 72 5 37 5 83 7 48 7 16 7 52
202515_at 7 80 7 90 8 22 8 34 8 38 8 41 7 32 7 66 7 95 9 27 9 16 9 57
202516_s_at 4 11 4 09 4 21 4 25 4 27 4 29 4 08 4 01 4 00 4 35 4 38 4 65
210105_s_at 7 34 6 89 7 31 9 23 9 39 9 09 8 35 7 31 7 86 6 33 6 57 6 74
212486_s_at 4 25 4 27 4 29 4 44 4 47 4 50 4 50 4 35 4 41 4 34 4 45 4 27
216033_s_at 5 83 5 47 5 45 7 46 7 51 7 15 6 70 5 65 5 99 5 34 5 24 5 18 ~
215075_s_at 8 22 8 28 8 29 9 36 8 96 9 22 8 40 8 16 8 52 8 88 8 84 8 95 f-
209341_s_at 6 54 6 37 6 60 6 94 6 59 6 67 6 40 6 25 6 63 6 68 6 61 7 33
209342_s_at 5 13 5 16 5 24 5 28 5 44 5 22 5 11 4 98 5 01 5 21 5 56 5 47
204890_s_at 6 02 5 83 5 85 8 82 8 88 8 99 6 16 6 07 5 98 8 20 8 66 8 47
204891_s_at 6 82 6 23 6 68 10 30 10 26 10 18 6 71 6 30 6 10 9 51 9 88 9 69
202625_at 7 52 7 05 6 96 8 05 8 27 7 82 7 75 7 24 7 63 8 01 8 07 8 29
202626_s_at 8 72 8 09 8 04 9 19 9 51 8 74 9 08 8 55 8 65 9 02 9 22 9 30
210754_s_at 8 53 7 97 8 02 9 13 9 22 8 82 8 96 8 19 8 62 9 01 9 00 9 13
202670_at 8 89 8 59 8 73 9 68 9 64 9 73 8 99 8 45 8 93 9 89 9 95 10 12
202424_at 9 87 9 65 9 69 9 89 9 91 9 76 9 95 9 69 9 59 10 40 10 75 10 68
213490_s_at 7 94 7 58 7 44 7 80 7 95 7 56 7 97 7 51 7 38 8 42 8 90 8 51
205192_at 5 77 5 64 5 85 6 24 6 35 6 41 5 69 6 02 5 69 5 95 5 90 5 78
204725_s_at 7 15 6 75 7 14 7 83 7 71 7 78 7 05 6 66 6 99 7 45 7 60 7 70
211063_s_at 6 89 6 73 7 12 7 76 7 33 7 66 6 79 6 67 6 99 7 56 7 21 7 74
209239_at 8 35 8 59 8 52 7 22 7 63 7 16 8 37 8 51 8 19 8 15 8 49 8 00
207535_s_at 5 46 5 26 5 22 6 18 6 01 5 92 5 38 5 08 5 09 5 51 5 90 5 73
201502_s_at 9 28 8 98 8 75 9 09 9 14 8 67 9 01 8 78 8 68 9 09 9 69 9 61
203879_at 8 35 8 58 8 42 7 09 6 98 6 98 7 93 8 47 8 19 7 56 7 75 7 61
211230_s_at 6 07 5 96 5 42 5 58 5 82 5 30 5 95 5 81 5 37 5 58 5 98 5 40
204613 at 9 30 9 43 9 38 9 25 9 63 9 25 9 37 9 37 9 34 9 19 9 44 9 34
Log2 fluorescence intensity
Probesets Ly1 (A1) Ly 1 (A2) Ly1 (A3) Ly7 (B1) Ly7 (B2) Ly7 (B3) Ly8 (C1 ) Ly8 (C2) Ly8 (C3) D4 (D1 ) D4 (D2) D4 (D3)
207957_s_at 570 509 570 541 587 558 816 7 82 767 439 459 442 209685_s_at 737 644 692 733 747 724 965 9 18 897 598 598 571
201244_s_at 8 82299 8 83300 8 81199 8 86622 8 82299 8 84433 8 86633 8 84 444 8 84499 8 80066 8 82288 8 83388
201783_s_at 8 89922 8 87755 8 87733 9 90022 8 87788 8 87744 8 89900 8 87 788 8 86677 8 85522 8 83399 8 84455
209878_s_at 8 80044 7 77744 7 76644 7 79977 8 80000 7 78877 8 80099 7 76 677 7 77733 7 73333 7 78822 7 74422
205205_at 7 73311 7 70022 6 66655 7 77700 7 79999 7 74466 7 72255 6 68 855 6 64455 7 75511 7 79922 7 75511
212777_at 5 57766 5 57733 5 56677 5 59922 6 60099 6 60000 5 57788 5 56 688 5 57722 6 60033 5 57788 5 58822
212780_at 636 594 597 628 581 613 625 5 69 641 582 579 627 208991_at 805 795 788 714 751 743 824 8 17 794 672 686 739 207540_s_at 918 926 923 825 811 830 916 9 14 944 820 838 856 209269_s_at 675 681 710 633 652 635 694 6 74 714 622 622 625 207616_s_at 831 768 748 812 806 805 829 7 58 820 865 861 853 209451_at 519 451 520 532 525 566 518 4 88 539 559 565 570 210458_s_at 397 383 398 391 391 399 393 3 84 398 414 412 411 205599_at 500 555 530 547 603 560 507 5 44 516 551 590 551 208315_x_at 555 565 556 533 531 493 574 5 57 551 575 581 580 221571_at 709 694 735 583 546 585 677 6 73 693 726 741 760 204352_at 572 567 602 604 616 588 554 5 54 540 516 587 535 206219_s_at 609 619 590 823 818 801 640 6 15 604 844 886 903 215988_s_at 445 432 429 434 432 423 434 4 39 426 433 415 436 211027_s_at 496 464 482 493 498 492 482 4 63 492 493 495 499 207187_at 717 741 719 719 737 731 741 7 34 708 713 730 698 211108_s_at 489 486 480 487 490 475 510 4 77 481 491 475 465 211109_at 461 470 463 477 465 464 470 4 67 462 461 474 463 213487_at 608 609 575 604 597 603 579 5 95 600 617 623 599 209636_at 526 515 496 602 562 538 543 5 18 500 555 584 551 211524_at 438 448 455 430 455 448 431 4 47 437 440 444 443 216995_x_at 536 554 537 545 558 539 535 5 51 541 541 542 527
208992_s_at 7 78888 7 79900 7 77711 7 74455 7 75522 7 75511 7 79955 7 77 755 7 79988 7 76611 7 73333 7 75522
204413_at 5 56655 5 59944 5 55500 5 57788 5 59933 5 55588 5 54499 5 58 844 5 54499 5 54466 5 57733 5 52288
205558_at 6 64499 6 63366 6 67722 6 63311 6 64411 6 64411 6 63300 6 65 500 6 64444 6 60000 6 64455 6 62200
Table 1OB: CD40/BCR Signaling Genes t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene l[ Ref
Symbol
207163_s_at 2 3E-02 2 5E-02 2 6E-03 1 5E-03 Yes No AKT1 Hs 368861 v-akt murine thymoma viral oncogene 14 homolog 1
205367_at 2 9E-04 7 2E-05 8 6E-05 2 1E-03 Yes Yes APS Hs 371366 adaptor protein with pleckstrin homology and 15 src homology 2 domains
205263_at 3 9E-01 3 7E-02 3 6E-01 3 9E-02 Yes No BCL10 Hs 193516 B-cell CLL/lymphoma 10 16
207655_s_at 3 6E-02 5 OE-02 3 8E-03 2 2E-02 Yes No BLNK Hs 167746 B-cell linker 17
220059_at 7 OE-04 6 3E-05 1 2E-04 3 9E-05 Yes Yes BRDG1 Hs 121128 BCR downstream signaling 1 18
205504_at 1 2E-04 7 OE-05 9 4E-05 2 2E-04 Yes Yes BTK Hs 159494 Bruton agammaglobulinemia tyrosine kinase 19
202987_at 7 1 E-01 2 8E-01 9 9E-01 1 3E-01 Yes No ACT1 Hs 437508 Nuclear factor kappa B activator 1 20
215411_s_at 5 2E-03 9 2E-02 2 2E-03 8 5E-02 Yes No ACT1 Hs 437508 Nuclear factor kappa B activator 1 20
202514 at 1 4E-01 5 5E-04 5 5E-02 7 3E-04 Yes No DLG1 Hs 389893 discs, large homolog 1 (Drosophila) 21
202515_at 8 1 E-02 1 5E-03 5 6E-02 2 7E-03 Yes No DLG1 Hs 389893 discs, large homolog 1 (Drosophila) 21
202516 s at 5 6E-02 6 4E-02 2 6E-03 4 OE-02 Yes No DLG1 Hs 389893 discs, large homolog 1 (Drosophila) 22
210105_s_at 8 1 E-04 3 1 E-02 3 5E-02 3 6E-02 Yes No FYN Hs 390567 FYN oncogene related to SRC, FGR, YES 22 ON
212486_s_at 1 OE-03 2 6E-01 3 8E-01 3 7E-01 Yes No FYN Hs 390567 FYN oncogene related to SRC, FGR, YES 22
216033_s_at 44E-04 9 9E-02 4 3E-02 1 0E-01 Yes No FYN Hs 390567 FYN oncogene related to SRC, FGR, YES 22
215075_s_at 1 4E-02 1 9E-04 6 8E-03 2 9E-02 Yes No GRB2 Hs 411366 growth factor receptor-bound protein 2 23
209341_s_at 1 6E-01 2 5E-01 1 2E-01 1 8E-01 Yes No IKBKB Hs 413513 inhibitor of kappa light polypeptide gene 24 enhancer in B-cells, kinase beta
209342_s_at 1 5E-01 1 4E-01 2 8E-02 5 5E-02 Yes No IKBKB Hs 413513 inhibitor of kappa light polypeptide gene 24 enhancer in B-cells, kinase beta
204890_s_at 4 OE-06 6 5E-04 2 6E-06 1 OE-03 Yes Yes LCK Hs 1765 lymphocyte-specific protein tyrosine kinase 25
204891 s at 1 6E-03 3 6E-04 1 5E-03 3 3E-04 Yes Yes LCK Hs 1765 lymphocyte-specific protein tyrosine kinase 25
202625_at 1 9E-02 1 8E-02 6 7E-02 4 2E-02 Yes No LYN Hs 80887 v-yes-1 Yamaguchi sarcoma viral related 26 oncogene homolog
202626_s_at 5 1 E-02 4 1 E-02 2 4E-01 1 1 E-01 Yes No LYN Hs 80887 v-yes-1 Yamaguchi sarcoma viral related 26 oncogene homolog
210754_s_at 2 OE-02 3 4E-02 1 6E-01 1 7E-01 Yes No LYN Hs 80887 v-yes-1 Yamaguchi sarcoma viral related 26 oncogene homolog
202670_at 4 6E-03 4 5E-04 3 2E-02 1 1 E-02 Yes No MAP2K1 Hs 132311 mitogen-activated protein kinase kinase 1 27
202424_at 2 4E-01 4 2E-03 4 2E-01 4 6E-03 Yes No MAP2K2 Hs 366546 mitogen-activated protein kinase kinase 2 27
213490_s_at 5 6E-01 1 OE-02 5 1E-01 1 4E-02 Yes No MAP2K2 Hs 366546 mitogen-activated protein kinase kinase 2 27
205192 at 2 2E-03 1 9E-01 2 5E-02 5 8E-01 Yes No MAP3K14 Hs 440315 NIK 28
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene IC Ref Symbol
204725 s at 2 2E-02 2 9E-02 1 3E-02 1 4E-02 Yes No NCK1 Hs 54589 NCK adaptor protein 1 29 211063_s_at 1 8E-02 4 3E-02 1 1E-02 2 8E-02 Yes No NCK1 Hs 54589 NCK adaptor protein 1 29 209239_at 6 6E-03 1 9E-01 6 8E-03 4 6E-01 Yes No NFKB1 Hs 160557 nuclear factor of kappa light polypeptide 30 gene enhancer in B-cells 1 (p105)
207535_s_at 2 4E-03 4 8E-02 32E-03 2 4E-02 Yes No NFKB2 Hs 73090 nuclear factor of kappa light polypeptide 31 gene enhancer in B-cells 2 (p49/p100)
201502_s_at 8 8E-01 1 3E-01 4 7E-01 5 5E-02 Yes No NFKBIA Hs 81328 nuclear factor of kappa light polypeptide 30 gene enhancer in B-cells inhibitor, alpha
203879_at 2 5E-04 8 6E-04 1 3E-02 5 7E-02 Yes No PIK3CD Hs 426967 phosphoιnosιtιde-3-kιnase, catalytic, delta 26 polypeptide
211230_s_at 3 8E-01 5 7E-01 5 7E-01 8 2E-01 Yes No PIK3CD Hs 426967 phosphoιnosιtιde-3-kιnase, catalytic, delta 26 polypeptide
204613_at 9 7E-01 5 9E-01 9 1 E-01 6 5E-01 Yes No PLCG2 Hs 512298 phospholipase C, gamma 2 26
(phosphatidylinositol-specific)
207957_s_at 64E-01 2 8E-02 3 5E-04 42E-04 Yes No PRKCB1 Hs 349845 protein kinase C, beta 1 32 209685 s at 24E-01 52E-02 6 1E-03 9 2E-04 Yes No PRKCB1 Hs 349845 protein kinase C, beta 1 32 201244_s_at 1 8E-01 8 7E-01 5 7E-01 8 4E-02 Yes No RAF 1 Hs 257266 v-raf-1 murine leukemia viral oncogene 26 homolog 1
201783_s_at 7 2E-01 1 4E-02 6 1E-01 1 9E-02 Yes No RELA Hs 132594 v-rel reticuloendotheliosis viral oncogene 30 homolog A
209878_s_at 3 8E-01 22E-01 4 8E-01 2 0E-01 Yes No RELA Hs 132594 v-rel reticuloendotheliosis viral oncogene 30 homolog A
205205_at 4 6E-02 5 6E-02 4 3E-02 5 3E-02 Yes No RELB Hs 307905 v-rel reticuloendotheliosis viral oncogene 31 homolog B
212777 at 1 4E-02 1 7E-01 1 4E-02 1 9E-01 Yes No SOS1 Hs 326392 son of sevenless homolog 1 (Drosophila) 23 212780 at 94E-01 5 6E-01 8 8E-01 6 OE-01 Yes No SOS1 Hs 326392 son of sevenless homolog 1 (Drosophila) 23 208991_at 1 9E-02 3 5E-02 6 8E-03 1 9E-02 Yes No STAT3 Hs 421342 signal transducer and activator of 26 transcription 3
207540_s_at 7 9E-04 1 1 E-02 2 OE-03 3 7E-03 Yes No SYK Hs 192182 spleen tyrosine kinase 26 209269 s at 2 7E-02 2 6E-02 2 6E-02 2 6E-02 Yes No SYK Hs 192182 spleen tyrosine kinase 26 207616_s_at 4 2E-01 8 7E-02 8 2E-01 1 2E-01 Yes No TANK Hs 146847 TRAF family member-associated NFKB 33 activator
209451 at 1 9E-01 9 5E-02 2 6E-01 7 4E-02 Yes No TANK Hs 146847 TRAF family member-associated NFKB 33 activator
t-test (two-tailed)
Probesets pAB pAD pBC pCD Measured Changed Gene UniGene If Gene Title Ref Symbol 210458_s_at 9 1 E-01 4 8E-02 7 3E-01 3 3E-02 Yes No TANK Hs 146847 TRAF family member-associated NFKB 33 activator
205599_at 1 5E-01 1 6E-01 8 5E-02 7 2E-02 Yes No TRAF 1 Hs 438253 TNF receptor-associated factor 1 26 208315_x_at 8 4E-02 1 4E-02 6 4E-02 1 2E-01 Yes No TRAF3 Hs 297660 TNF receptor-associated factor 3 26 221571 at 1 3E-03 1 3E-01 5 2E-03 9 5E-03 Yes No TRAF3 Hs 297660 TNF receptor-associated factor 3 26 204352_at 1 8E-01 2 5E-01 9 OE-03 8 9E-01 Yes No TRAF5 Hs 385685 TNF receptor-associated factor 5 26 206219 s at 6 2E-05 9 8E-04 2 9E-04 6 7E-04 Yes Yes VAV1 Hs 116237 vav 1 oncogene 23 215988_s_at 4 0E-01 4 3E-01 5 7E-01 5 8E-01 No No DLG1 Hs 389893 discs, large homolog 1 (Drosophila) 21 211027_s_at 2 8E-01 2 4E-01 2 2E-01 1 8E-01 No No IKBKB Hs 413513 inhibitor of kappa light polypeptide gene 24 enhancer in B-cells, kinase beta
207187_at 7 5E-01 3 8E-01 9 1 E-01 3 7E-01 No No JAK3 Hs 210387 Janus kinase 3 (a protein tyrosine kinase, 26 leukocyte)
211108_s_at 9 1 E-01 4 3E-01 6 7E-01 4 OE-01 No No JAK3 Hs 210387 Janus kinase 3 (a protein tyrosine kinase, 26 leukocyte)
211109_at 4 6E-01 8 1 E-01 6 2E-01 9 5E-01 No No JAK3 Hs 210387 Janus kinase 3 (a protein tyrosine kinase, 26 leukocyte) OO
213487 at 7 4E-01 3 1 E-01 2 4E-01 8 2E-02 No No MAP2K2 Hs 366546 mitogen-activated protein kinase kinase 2 27 209636_at 8 2E-02 2 1 E-02 1 2E-01 5 8E-02 No No NFKB2 Hs 73090 nuclear factor of kappa light polypeptide 14 gene enhancer in B-cells 2 (p49/p100)
211524_at 7 8E-01 4 7E-01 5 5E-01 5 OE-01 No No NFKB2 Hs 73090 nuclear factor of kappa light polypeptide 14 gene enhancer in B-cells 2 (p49/p100)
216995_x_at 5 8E-01 4 8E-01 5 4E-01 4 4E-01 No No RAF 1 Hs 257266 v-raf-1 murine leukemia viral oncogene 26 homolog 1
208992_s_at 2 OE-02 3 1E-02 24E-02 2 1E-02 No No STAT3 Hs 421342 signal transducer and activator of 26 transcription 3
204413_at 7 0E-01 3 3E-01 3 7E-01 5 3E-01 No No TRAF2 Hs 437575 TNF receptor-associated factor 2 26 205558 at 3 0E-01 1 4E-01 6 5E-01 2 7E-01 No No TRAF6 Hs 444172 TNF receptor-associated factor 6 26
FDR (false discovery rate) cutoffs are the same for Tables 5B and 6B. FDR cutoffs are the same for Tables 7B, 8B, 9B and 1OB.
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3. Granziero L, Ghia P, Circosta P, Gottardi D, Strola G, Geuna M, Montagna L, Piccoli P, Chilosi M, Caligaris-Cappio F. Survivin is expressed on CD40 stimulation and interfaces proliferation and apoptosis in B-cell chronic lymphocytic leukemia. Blood. 2001 ;97:2777-2783.
4. Janeway CA, Travers P, Walport M, Shlomchik M. Immunobiology (ed 5th): Garland Publishing; 2001.
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7. Hamada T, Yonetani N, Ueda C, Maesako Y, Akasaka H, Akasaka T, Ohno H, Kawakami K, Amakawa R, Okuma M. Expression of the PAX5/BSAP transcription factor in haematological tumour cells and further molecular characterization of the t(9;14)(pl3;q32) translocation in B-cell non-Hodgkin's lymphoma. Br J Haematol. 1998;102:691-700.
8. Rosnet O, Mattei MG, Delattre O, Schiff C. VPREB3: cDNA characterization and expression in human and chromosome mapping in human and mouse. Cytogenet Cell Genet. 1999;87:205-208.
9. Taga S, Tetaud C, Mangeney M, Tursz T, Wiels J. Sequential changes in glycolipid expression during human B cell differentiation: enzymatic bases. Biochim Biophys
Acta. 1995;1254:56-65.
10. Pieters R, Huismans DR, Loonen AH, Peters GJ, Hahlen K, van der Does-van den Berg A, van Wering ER, Veerman AJ. Adenosine deaminase and purine nucleoside phosphorylase in childhood lymphoblastic leukemia: relation with differentiation stage, in vitro drug resistance and clinical prognosis. Leukemia. 1992;6:375-380.
11. Wang YH, Nomura J, Faye-Petersen OM, Cooper MD. Surrogate light chain production during B cell differentiation: differential intracellular versus cell surface expression. J Immunol. 1998;161 :1132-1139.
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13. Narducci MG, Pescarmona E, Lazzeri C, Signoretti S, Lavinia AM, Remotti D, Scala E, Baroni CD, Stoppacciaro A, Croce CM, Russo G. Regulation of TCLl expression in B- and T-cell lymphomas and reactive lymphoid tissues. Cancer Res. 2000;60:2095-2100.
14. Andjelic S, Hsia C, Suzuki H, Kadowaki T, Koyasu S, Liou HC. Phosphatidylinositol 3-kinase and NF-kappa B/Rel are at the divergence of CD40- mediated proliferation and survival pathways. J Immunol. 2000;165:3860-3867.
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Example 3
Signaling in the LCK-VAV-MAPK pathway differs in CD40-sensitive and CD40-resistant cell lines In lymphoma cells, CD40 signaling is mediated by three interacting pathways.
Current evidence suggests that the NFKB pathway is the most important of these pathways for controlling cell survival. Microarray studies showed that CD40 sensitivity was not associated with differences in expression of transcripts encoding members of this pathway, but rather with changes in the expression level of LCK and VAVl, which activate the RAS-RAF-ERK pathway. To further characterize the association between the MAPK pathway and CD40 sensitivity, we investigated activation of LCK (which activates VAVl) and MAP kinases (which are activated by VAVl). LCK is a member of the src protein family of kinases, which can be phosphorylated at two sites, one of which activates the kinase, whereas the other is inhibitory. Western blots showed that activated LCK was present in all four cell lines in the absence of CD40 stimulation (Figure 7A). This is consistent with previous results that have identified constitutively active LCK in the majority of B-cell malignancies (27). In contrast, only CD40-sensitive OCI-Ly7 and Su- DHL4 (but not CD40-resistant OCI-LyI or OCI-Ly8) contained constitutively phosphorylated ERK p42/p44 (Figure 7B). As p38 and jnk have also been shown to be activated by CD40 (28), and are known to be downstream targets of VAV (29, 30), we investigated the phosphorylation state of these MAPK family proteins. p38 was constitutively phosphorylated in all cell lines and JNK was present but not phosphorylated in any of the cell lines.
LCK transgenic mice have been shown to develop thymic lymphomas containing constitutively activated VAV and ERK, and cell lines derived from such tumors were dependent on tyrosine phosphorylation and raf-dependent ERK activation for survival (31). CD40-sensitive but not CD40-resistant cell lines express VAV, a central part of the LCK- ERK signal transduction pathway; therefore, we would expect growth of CD40-sensitive but not CD40-resistant cells would be expected to be inhibited by blocking LCK or ERK activity. Cells were exposed to a range of concentrations of the src family kinase inhibitor PP 1(32). As predicted, growth of CD40-sensitive OCI-Ly7 and Su-DHL4 cells was inhibited by PPl more efficiently than growth of CD40-resistant OCI-LyI and OCI-Ly8 cells (Figure 8A). In contrast, similar experiments with the MEK 1/2 inhibitor UO 126, which prevents phosphorylation of ERK (33), did not show differential effects on growth of CD40-sensitive and CD40-resistant DLCBL lines (Figure 8B). These observations suggest that LCK but not ERK is involved in maintaining growth of CD40-sensitive DLCBL cell lines.
Example 4
Phosphorylated ERK is required for CD40-mediated cell death.
CD40 stimulation has been shown to activate both ERK and p38; however, inhibition of ERK, but not p38 phosphorylation, has been reported to enhance CD40- mediated apoptosis in a carcinoma cell line (34). We therefore determined the effect of CD40 stimulation on ERK activation by Western blotting for phosphorylated and total ERK. ERK was constitutively phosphorylated in OCI-Ly7 and Su-DHL4 cells, and not phosphorylated before or after CD40 ligation in OCI-I and OCI-Ly8 cells (Figure 9). This suggests that unlike carcinoma cell lines, DLCBL cell lines do not upregulate ERK activity upon CD40 signaling; however, constitutively active ERK may influence the outcome of CD40 signaling. For example, if ERK protects DLCBL against CD40-mediated apoptosis, inhibition of ERK prior to CD40 stimulation should enhance cell death in OCI-Ly7 and Su-DHL4 cells by reducing constitutive ERK activity, whereas OCI-LyI and OCI-Ly8 cells which lack active ERK should be unaffected by an ERK inhibitor. This hypothesis was tested using pharmacologic inhibitors of MEK. Su-DHL4 cells were incubated in the presence of 10 μM UO 126 for 48 hours, permeabilized and stained with an anti-phospho- ERK antibody. Phosphorylation of ERK was reduced after addition of the MEK inhibitor U0126 as shown by flow cytometry. See Materials and Methods section of Examples. To determine if ERK is involved in CD40-mediated cell death, cells were treated with the MEK1/2 inhibitors U0126 or PD98058 prior to CD40 stimulation. The p38 inhibitor
SB230580, which has been shown previously to have no effect on activation-induced cell death (11) was used as a negative control. Viable cell counts were measured 96 hours after CD40 ligation. The MEK 1/2 inhibitors UO 126 and PD98058, but not the p38 inhibitor SB230580, reduced CD40-mediated cell death in OCI-Ly7 and Su-DHL4 cells (Figure 10), suggesting that ERK promotes rather than opposes activation-induced cell death in DLCBL cell lines.
Example 5
Expression of p-SRC, VAV, and p-ERK in DLCBL tumor samples.
To determine if variations in ERK signaling exist in human tumors, immunohistochemical staining for phosphorylated SRC family kinases (p-SRC), VAV, and p-ERK was performed. An initial set of 25 blocks was pre-screened for expression of the B-cell markers CD20 and CD79a. Twenty samples were found to be positive and stained with antibodies to p-SRC, VAV, and p-ERK. Staining intensity was scored using the H- score system, which combines the percentage of positive cells with an intensity grade to yield a final range of 0 (negative staining) to 300 (all cells strongly positive).
Table 11
Intensity p-SRC VAV p-ERK
~0 Ϊ0 0 6
1-99 7 5 5
100-199 1 3 3
200-300 2 12 6
The following correlations were observed. All six samples lacking phosphorylated
ERK were also p-SRC negative. The four p-ERK positive samples lacking p-SRC had very high levels of VAV expression, suggesting that constitutive activation of VAV may abrogate the need for active SRC family kinases. Where VAV expression was moderate, staining intensity of p-ERK correlated with intensity of p-SRC. The tumor samples were from biopsies performed at the Montreal General and
Royal Victoria Hospitals in Montreal between 1991 and 1993. All samples had been classified as diffuse large B-cell lymphoma at diagnosis. This was confirmed by staining for expression of CD20 with an antibody from DAKO. CD20 is the standard marker for B-cells. Dr. Rene Michel of McGiIl University is kindly thanked for his assistance in these immunohistochemical studies on tumor samples. Antibodies for staining of VAV, phospho-ERK, and phospho-SRC family were from Cell Signaling Technology, Danvers, MA, USA (www.cellsignal.com). The VAV antibody was #2502. The presence of VAV has been associated with increased NFKB activity. The phospho-ERK antibody #4376 detects specifically the active form of ERK, the form that is required for CD40-mediated cell death. The phospho-SRC family #2101 detects SRC as well as the related kinases Lyn, Fyn, Lck, Yes and Hck in the active form. These kinases are part of a signaling pathway that can activate ERK.
While this invention has been particularly shown and described with references to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims.

Claims

CLAIMSWhat is claimed is:
1. A method of determining whether first cells respond to CD40 stimulation by undergoing apoptosis, said method comprising testing said first cells for their profile of gene expression, and comparing said profile with a second profile of gene expression of second cells known to respond to CD40 stimulation by undergoing apoptosis; wherein, if said profile of gene expression shows expression levels of genes characteristic of the second profile, said cells respond to CD40 stimulation by undergoing apoptosis.
2. The method of Claim 1 wherein testing is by analysis of RNA from said first cells and said second cells on one or more arrays.
3. A method of determining whether first cells respond to CD40 stimulation by undergoing apoptosis, said method comprising testing said first cells for levels of expression of one or more genes, and comparing a first set of levels of expression of said one or more genes to a second set of levels of expression of said one or more genes in second cells known to respond to CD40 stimulation by undergoing apoptosis; wherein, if the first set of levels of expression of said one or more genes in said first cells is characteristic of said second set of levels of the second cells, said first cells respond to CD40 stimulation by undergoing apoptosis.
4. The method of Claim 3 wherein testing is by analysis of RNA from said first cells and said second cells on one or more arrays.
5. A method for determining whether a population of cells is CD40-sensitive, said method comprising quantitating expression of one or more genes in a sample of cells from the population, wherein said one or more genes in diffuse large-cell B- lymphoma (DLCBL) cell lines are differentially regulated between CD40-sensitive
DLCBL cell lines and CD40-resistant DLCBL cell lines, and comparing quantities of expression of said one or more genes in said sample to quantities of expression of said one or more genes in CD40-resistant DLCBL cell lines, wherein if said one or more genes are differentially regulated between the cells in the sample and the CD40-resistant DLCBL cell lines, then the population of cells is CD40-sensitive.
6. The method of Claim 5 wherein the one or more genes are selected from B-cell maturation specific genes.
7. The method of Claim 5 wherein the one or more genes are selected from members of the CD40 signaling pathway.
8. The method of Claim 5 wherein the one or more genes are selected from the group consisting of: RAGl, RAG2, IGLLl, CD9, VPREBl, CD22, CD38, Bruton's tyrosine kinase, VAVl, LYN, LCK and MEK1/MAP2K1.
9. The method of Claim 5 wherein the gene is RAGl .
10. The method of Claim 5 wherein the gene is VAV 1.
1 1. The method of Claim 5 wherein quantitating expression is by reverse transcription polymerase chain reaction (RT-PCR).
12. The method of Claim 5 wherein quantitating expression and comparing quantities is by analysis on arrays.
13. The method of Claim 5 wherein quantitating expression and comparing quantities is by immunohistochemistry.
14. A method for determining whether a population of cells is CD40-sensitive or CD40-resistant, said method comprising testing a sample of cells from said population for the presence or absence of phosphorylated ERK, whereby, if phosphorylated ERK is present, the population of cells is CD40-sensitive, and if phosphorylated ERK is absent, the population of cells is CD40-resistant.
15. The method of Claim 14 wherein the sample of cells is tested by immunoblot of non-denatured lysates from the sample of cells using anti-phospho-ERK antibodies.
16. The method of Claim 14 wherein the sample of cells is tested by immunostaining.
17. The method of Claim 14 wherein the immunostaining is by immunofluorescent labeled anti-phospho-ERK antibodies
18. The method of Claim 14 wherein the immunostaining is by immunohistochemistry using anti-phospho-ERK antibodies conjugated to a reactive label.
19. The method of Claim 14 wherein the sample of cells is a tissue biopsy or a fluid sample from a human or animal.
20. The method of Claim 14 wherein the population of cells is a primary culture of cells from a human or animal.
21. The method of Claim 14 wherein the population of cells is a cell line.
22. The method of Claim 14 wherein the population of cells comprises B-cell lymphoma cells.
23. The method of Claim 14 wherein the population of cells comprises diffuse large- cell B-lymphoma cells.
24. The method of Claim 14 wherein the population of cells comprises cancer cells.
25. The method of Claim 14 wherein the cancer cells are derived from endothelial cells.
26. The method of Claim 14 wherein the cancer cells are derived from epithelial cells.
27. The method of Claim 14 wherein the cancer cells are derived from fibroblasts.
28. The method of Claim 14 wherein the cancer cells are breast cancer cells.
29. The method of Claim 14 wherein the cancer cells are prostate cancer cells.
30. The method of Claim 14 wherein the cancer cells are lung cancer cells.
31. The method of Claim 14 wherein the cancer cells are colon cancer cells.
32. A method for determining whether a population of cells is CD40-sensitive or CD40-resistant, said method comprising testing a sample of cells from said population for the presence or absence of p-SRC, whereby, if p-SRC is absent, the population of cells is CD40-resistant.
33. A kit for determining whether a population of cells is CD40-sensitive or CD40- resistant, comprising anti-phospho-ERK antibody, anti-VAV antibody, and anti- RAGl antibody.
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