CA2440703A1 - Methods of diagnosis of breast cancer, compositions and methods of screening for modulators of breast cancer - Google Patents

Abstract

Described herein are genes whose expression are up-regulated or down-regulated in breast cancer. Related methods and compositions that can be used for diagnosis and treatment of breast cancer are disclosed. Also described herein are methods that can be used to identify modulators of breast cancer.

Description

DEMANDE OU BREVET VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVET COMPREND
PLUS D'UN TOME.

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THIS SECTION OF THE APPLICATION/PATENT CONTAINS MORE THAN ONE
VOLUME

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NOTE POUR LE TOME / VOLUME NOTE:

METHODS OF DIAGNOSIS OF BREAST CANCER, COMPOSITIONS
AND METHODS OF SCREENING FOR MODULATORS OF BREAST
CANCER
CROSS-REFERENCES TO RELATED APPLICATIONS
This application claims priority to USSN 60/263,965, filed January 24, 2001;
USSN 60/265,928, filed February 2, 2001; USSN 09/829,472 filed April 9, 2001;
USSN
60/282,698, filed April 9, 2001; USSN 601288,590, filed May 4, 2001; and USSN
60/294,443, filed May 29, 2001, all of which are incorporated herein by reference in their entirety.
FIELD OF THE INVENTION
The invention relates to the identification of nucleic acid and protein expression profiles and nucleic acids, products, and antibodies thereto that are involved in breast cancer; and to the use of such expression profiles and compositions in the diagnosis, prognosis and therapy of breast cancer. The invention further relates to methods for identifying and using agents and/or targets that inhibit breast cancer.
BACKGROUND OF THE INVENTION
Breast cancer is one of the most frequently diagnosed cancers and the second leading cause of female cancer death in North America and northern Europe, with lung cancer being the leading cause. Lifetime incidence of the disease in the United States is one-in-eight, with a 1-in-29 lifetime risk of dying from breast cancer. Early detection of breast cancer, using mammography, clinical breast examination, and self breast examination, has dramatically improved the treatment of the disease, although sensitivity is still major concern, as mammographic sensitivity has been estimated at only 60%-90%. Treatment of breast cancer consists largely of surgical lumpectomy or mastectomy, radiation therapy, anti hormone therapy, and/or chemotherapy. Although many breast cancer patients are effectively treated, the current therapies can all induce serious side effects wluch diminish quality of life.
Deciding on a particular course of treatment is typically based on a variety of prognostic parameters and markers (Fitzgibbons et al., 2000, Arch. Pathol. Lab. Med.
124:966-978;
Hamilton and Piccart, 2000, Ann. Oncol. 11:647-663), including genetic predispostion markers BRCA-1 and BRCA-2 (Robson, 2000, J. Clin. Oncol. 18:113sup-118sup).
Imaging of breast cancer for diagnosis has been problematic and limited. In addition, dissemination of tumor cells (metastases) to locoregional lymph nodes is an important prognostic factor; five year survival rates drop from 80 percent in patients with no lymph node metastases to 45 to 50 percent in those patients who do have lymph node metastases. A recent report showed that micrometastases can be detected from lymph nodes using reverse transcriptase-PCR methods based on the presence of mRNA for carcinoembryonic antigen, which has previously been shown to be present in the vast majority of breast cancers but not in normal tissues. Liefers et aL, New England J. of Med.
339(4):223 (1998).
The identification of novel therapeutic targets and diagnostic markers is essential for improving the current treatment of breast cancer patients.
Recent advances in molecular medicine have increased the interest in tumor-specific cell surface antigens that could serve as targets for various immunotherapeutic or small molecule strategies. Antigens suitable for immunotherapeutic strategies should be highly expressed in cancer tissues and ideally not expressed in normal adult tissues. Expression in tissues that are dispensable for life, however, may be tolerated. Examples of such antigens include Her2/neu and the B-cell antigen CD20. Humanized monclonal antibodies directed to Her2/neu (Herceptin~/trastuzumab) are currently in use for the treatment of metastatic breast cancer (Ross and Fletcher, 1998, Stem Cells 16:413-428). Similarly, anti-CD20 monoclonal antibodies (Rituxin~/rituximab) are used to effectively treat non-Hodgekin's lymphoma (Maloney et al., 1997, Blood 90:2188-2195; Leget and Czuczman, 1998, Cunr.
Opin. Oncol.
10:548-551).
Other potential immunotherapeutic targets have been identified for breast cancer. One such target is polymorphic epithelial mucin (MUC1). MUC1 is a transmembrane protein, present at the apical surface of glandular epithelial cells. It is often overexpressed in breast cancer, and typically exhibits an altered glycosylation pattern, resulting in an antigenically distinct molecule, and is in early clinical trials as a vaccine target (Gilewski et al., 2000, Clin. Cancer Res. 6:1693-1701; Scholl et al., 2000, J. Immunother.
23:570-580).
The tumor-expressed protein is often cleaved into the circulation, where it is detectable as the tumor marker, CA 15-3 (Bon et al., 1997, Clin. Chem. 43:585-593). However, many patients have tumors that express neither HER2 nor MUC-1; therefore, it is clear that other targets need to be identified to manage localized and metastatic disease. Many other genes have been reported to be overexpressed in breast cancer, such as EGFR (Sainsbury et al., 1987, Lancet 1(8547):1398-1402), c-erbB3 (Naidu et al., 1988, Br. J. Cancer 78:1385-1390), (Penault-Llorca et al., 1991, Int. J. Cancer 61:170-176), PKW (Preiherr et al., 2000, Anticancer Res. 20:2255-2264), MTAl (Nawa et al., 2000, J. Cell Biochem.
79:202-212), breast cancer associated gene 1 (Kurt et al., 2000, Breast Cancer Res. Treat.
59:41-48).
Although monoclonal antibodies to the protein products of some of these overexpressed 1 S genes have been reported (for review, see Green et al., 2000, Cancer Treat. Rev. 26:269-286), none are currently approved .for breast cancer therapy in the US.
Disclosures of certain genes and ESTs described as being expressed in breast cancer are found in international patent applications WO-99/33869, WO-97/25426, WO-97/02280 and WO-00/55173, WO-98/45328 and WO-00/22130. Similarly, genes and ESTs described as being expressed in breast cancer are disclosed in US Patent Nos.
5,759,776 and 5,'693,522. The utility of such genes is described in each of these publications, and their disclosures are incorporated herein in their entirety.
While industry and academia have identified novel sequences, there has not been an equal effort exerted to identify the function of these novel sequences. The elucidation of a role for novel proteins and compounds in disease states for identification of therapeutic targets and diagnostic markers is essential for improving the current treatment of breast cancer patients. Accordingly, provided herein are molecular targets for therapeutic intervention in breast and other cancers. Additionally, provided herein are methods that can be used in diagnosis and prognosis of breast cancer. Further provided are methods that can be used to screen candidate bioactive agents for the ability to modulate breast cancer.

SUMMARY OF THE lIVVENTION
The present invention therefore provides nucleotide sequences of genes that are up- and down-regulated in breast cancer cells. Such genes are useful for diagnostic purposes, and also as targets fox screening for therapeutic compounds that modulate breast cancer, such as hormones or antibodies. Other aspects of the invention will become apparent to the skilled artisan by the following description of the invention.
In one aspect, the present invention provides a method of detecting a breast cancer-associated transcript in a cell from a patient, the method comprising contacting a biological sample from the patient with a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1-25.
In one embodiment, the present invention provides a method of determining the level of a breast cancer associated transcript in a cell from a patient.
In one embodiment, the present invention provides a method of detecting a breast cancer-associated transcript in a cell from a patient, the method comprising contacting a biological sample from the patient with a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1-25.
In one embodiment, the polynucleotide selectively hybridizes to a sequence at least 95% identical to a sequence as shown in Tables 1-25.
In one embodiment, the biological sample is a tissue sample. In another embodiment, the biological sample comprises isolated nucleic acids, e.g., mRNA.
In one embodiment, the polynucleotide is labeled, e.g., with a fluorescent label.
In one embodiment, the polynucleotide is immobilized on a solid surface.
In one embodiment, the patient is undergoing a therapeutic regimen to treat breast cancer. In another embodiment, the patient is suspected of having metastatic breast cancer.
In one embodiment, the patient is a human.
In one embodiment, the breast cancer associated transcript is mRNA.

In one embodiment, the method further comprises the step of amplifying nucleic acids before the step of contacting the biological sample with the polynucleotide.
In another aspect, the present invention provides a method of monitoring the efficacy of a therapeutic treatment of breast cancer, the method comprising the steps of (i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a breast cancer-associated transcript in the biological sample by contacting the biological sample with a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables ~1-25, thereby monitoring the efficacy of the therapy. In a further embodiment, the patient has metastatic breast cancer.
In a further embodiment, the patient has a drug resistant form of breast cancer.
In one embodiment, the method further comprises the step of: (iii) comparing the level of the breast cancer-associated transcript to a level of the breast cancer-associated transcript in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.
Additionally, provided herein is a method of evaluating the effect of a candidate breast cancer drug comprising administering the drug to a patient and removing a cell sample from the patient. The expression profile of the cell is then determined. This method may further comprise comparing the expression profile to an expression profile of a healthy individual. In a preferred embodiment, said expression profile includes a gene of Tables 1-25.
In one aspect, the present invention provides an isolated nucleic acid molecule consisting of a polynucleotide sequence as shown in Tables 1-25.
In one embodiment, an expression vector or cell comprises the isolated nucleic acid.
In one aspect, the present invention provides an isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1-25.
In another aspect, the present invention provides an antibody that specifically binds to an isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1-25.

In one embodiment, the antibody is conjugated to an effector component, e.g., a fluorescent label, a radioisotope or a cytotoxic chemical.
In one embodiment, the antibody is an antibody fragment. In another embodiment, the antibody is humanized.
In one aspect, the present invention provides a method of detecting a breast cancer cell in a biological sample from a patient, the method comprising contacting the biological sample with an antibody as described herein.
In another aspect, the present invention provides a method of detecting antibodies specific to breast cancer in a patient, the method comprising contacting a biological sample from the patient with a polypeptide encoded by a nucleic acid comprising a sequence from Tables 1-25.
In another aspect, the present invention provides a method for identifying a compound that modulates a breast cancer-associated polypeptide, the method comprising the steps of: (i) contacting the compound with a breast cancer-associated polypeptide, the polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least ~0% identical to a sequence as shown in Tables 1-25; and (ii) determining the functional effect of the compound upon the polypeptide.
In one embodiment, the functional effect is a physical effect, an enzymatic effect, or a chemical effect.
In one embodiment, the polypeptide is expressed in a eukaryotic host cell or cell membrane. In another embodiment, the polypeptide is recombinant.
In one embodiment, the functional effect is determined by measuring ligand binding to the polypeptide.
In another aspect, the present invention provides a method of inhibiting proliferation of a breast cancer-associated cell to treat breast cancer in a patient, the method comprising the step of administering to the subject a therapeutically effective amount of a compound identified as described herein.
In one embodiment, the compound is an antibody.
In another aspect, the present invention provides a drug screening assay comprising the steps of (i) administering a test compound to a mammal having breast cancer or to a cell sample isolated therefrom; (ii) comparing the level of gene expression of a polynucleotide that selectively hybridizes to a sequence at least 80%
identical to a sequence as shown in Tables 1-25 in a treated cell or mammal with the level of gene expression of the polynucleotide in a control cell sample or mammal, wherein a test compound that modulates the level of expression of the polynucleotide is a candidate for the treatment of breast cancer.
In one embodiment, the control is a mammal with breast cancer or a cell sample therefrom that has not been treated with the test compound. In another embodiment, the control is a normal cell or mammal.
In one embodiment, the test compound is administered in varying amounts or concentrations. In another embodiment, the test compound is administered for varying time periods. In another embodiment, the comparison can occur after addition or removal of the drug candidate.
In one embodiment, the levels of a plurality of polynucleotides that selectively hybridize to a sequence at least 80% identical to a sequence as shown in Tables 1-25 are individually compared to their respective levels in a control cell sample or mammal. In a preferred embodiment the plurality of polynucleotides is from three to ten.
In another aspect, the present invention provides a method for treating a mammal having breast cancer comprising administering a compound identified by the assay described herein.
In another aspect, the present invention provides a pharmaceutical composition for treating a mammal having breast cancer, the composition comprising a compound identified by the assay described herein and a physiologically acceptable excipient.
In one aspect, the present invention provides a method of screening drug candidates by providing a cell expressing a gene that is up- and down-regulated as in a breast cancer. In one embodiment, a gene is selected from Tables 1-25. The method further includes adding a drug candidate to the cell and determining the effect of the drug candidate on the expression of the expression profile gene.
In one embodiment, the method of screening drug candidates includes comparing the level of expression in the absence of the drug candidate to the level of expression in the presence of the drug candidate, wherein the concentration of the drug candidate can vary when present, and wherein the comparison can occur after addition or removal of the drug candidate. In a preferred embodiment, the cell expresses at least two expression profile genes. The profile genes may show an increase or decrease.
Also provided is a method of evaluating the effect of a candidate breast cancer drug comprising administering the drug to a transgenic animal expressing or over-expressing the breast cancer rnodulatory protein, or an animal lacking the breast cancer modulatory protein, for example as a result of a gene knockout.
Moreover, provided herein is a biochip comprising one or more nucleic acid segments of Tables 1-25, wherein the biochip comprises fewer than 1000 nucleic acid probes.
Preferably, at least two nucleic acid segments are included. More preferably, at least three nucleic acid segments are included.
Furthermore, a method of diagnosing a disorder associated with breast cancer is provided. The method comprises determining the expression of a gene of Tables 1-25, preferably a gene of Table 25, in a first tissue type of a first individual, and comparing the distribution to the expression of the gene from a second normal tissue type from the first individual or a second unaffected individual. A difference in the expression indicates that the first individual has a disorder associated with breast cancer.
In a further embodiment, the biochip also includes a polynucleotide sequence of a gene that is not up- and down-regulated in breast cancer.
In one embodiment a method for screening for a bioactive agent capable of interfering with the binding of a breast cancer modulating protein (breast cancer modulatory protein) or a fragment thereof and an antibody which binds to said breast cancer modulatory protein or fragment thereof. In a preferred embodiment, the method comprises combining a breast cancer modulatory protein or fragment thereof, a candidate bioactive agent and an antibody which binds to said breast cancer modulatory protein or fragment thereof. The method further includes determining the binding of said breast cancer modulatory protein or fragment thereof and said antibody. Wherein there is a change in binding, an agent is identified as an interfering agent. The interfering agent can be an agonist or an antagonist.
Preferably, the agent inhibits breast cancer.

Also provided herein are methods of eliciting an immune response in an individual. In one embodiment a method provided herein comprises administering to an individual a composition comprising a breast cancer modulating protein, or a fragment thereof. In another embodiment, the protein is encoded by a nucleic acid selected from those of Tables 1-25. _ Further provided herein are compositions capable of eliciting an immune response in an individual. In one embodiment, a composition provided herein comprises a breast cancer modulating protein, preferably encoded by a nucleic acid of Tables 1-25, more preferably of Table 25, or a fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, said composition comprises a nucleic acid comprising a sequence encoding a breast cancer modulating protein, preferably selected from the nucleic acids of Tables 1-25, and a pharmaceutically acceptable carrier.
Also provided are methods of neutralizing the effect of a breast cancer protein, or a fragment thereof, comprising contacting an agent specific for said protein with said protein in an amount sufficient to effect neutralization. In another embodiment, the protein is encoded by a nucleic acid selected from those. of Tables 1-25.
In another aspect of the invention, a method of treating an individual for breast cancer is provided. In one embodiment, the method comprises administering to said individual an inhibitor of a breast cancer modulating protein. In another embodiment, the method comprises administering to a patient having breast cancer an antibody to a breast cancer modulating protein conjugated to a therapeutic moiety. Such a therapeutic moiety can be a cytotoxic agent or a radioisotope.
DETAILED DESCRIPTION OF THE INVENTION
In accordance with the objects outlined above, the present invention provides novel methods for diagnosis and prognosis evaluation for breast cancer (PC), including metastatic breast cancer, as well as methods for screening for compositions which modulate breast cancer. Also provided are methods for treating breast cancer.
Tables 1-24B provide unigene cluster identification numbers for the nucleotide sequence of genes that exhibit increased or decreased expression in breast cancer samples. Tables 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, and 22 list those genes that are up-regulated in breast cancer cells. Table 14 lists those genes that are highly upregulated in breast cancer cells. Table 1, 2, 3, 15, and 23 list genes that are down-regulated in breast cancer cells and Table 16, lists genes that are highly down-regulated in breast cancer genes.
The Tables also provide an exemplar accession number that provides a nucleotide sequence that is part of the unigene cluster.
Definitions The term "breast cancer protein" or "breast cancer polynucleotide" or "breast cancer-associated transcript" refers to nucleic acid and polypeptide polyrnorphic variants, alleles, mutants, and interspecies homologues that: (1) have a nucleotide sequence that has greater than about 60% nucleotide sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater nucleotide sequence identity, preferably over a region of over a region of at least about 25, 50, 100, 200, 500, 1000, or more nucleotides, to a nucleotide sequence of or associated with a gene of Tables 1-25; (2) bind to antibodies, e.g., polyclonal antibodies, raised against an immunogen comprising an amino acid sequence encoded by a nucleotide sequence of or associated with a gene of Tables 1-25, and conservatively modified variants thereof; (3) specifically hybridize under stringent hybridization conditions to a nucleic acid sequence, or the complement thereof of Tables 1-25 and conservatively modified variants thereof or (4) have an amino acid sequence that has greater than about 60% amino acid sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater amino sequence identity, preferably over a region of over a region of at least about 25, 50, 100, 200, 500, 1000, or more amino acid, to an amino acid sequence encoded by a nucleotide sequence of or associated with a gene of Tables 1-25. A polynucleotide or polypeptide sequence is typically from a mammal including, but not limited to, primate, e.g., human;
rodent, e.g., rat, mouse, hamster; cow, pig, horse, sheep, or other mammal. A
"breast cancer polypeptide" and a "breast cancer polynucleotide," include both naturally occurring or recombinant forms.

A "full length" breast cancer protein or nucleic acid refers to a breast cancer polypeptide or polynucleotide sequence, or a variant thereof, that contains all of the elements normally contained in one or more naturally occurring, wild type breast cancer polynucleotide or polypeptide sequences. The "full length" may be prior to, or after, various stages of post-translation processing or splicing, including alternative splicing.
"Biological sample" as used herein is a sample of biological tissue or fluid that contains nucleic acids or polypeptides, e.g., of a breast cancer protein, polynucleotide or transcript. Such samples include, but are not limited to, tissue isolated from primates, e.g., humans, or rodents, e.g., mice, and rats. Biological samples may also include sections of tissues such as biopsy and autopsy samples, frozen sections taken for histologic purposes, blood, plasma, serum, sputum, stool, tears, mucus, hair, skin, etc. Biological samples also include explants and primary and/or transformed cell cultures derived from patient tissues. A
biological sample is typically obtained from a eukaryotic organism, most preferably a mammal such as a primate e.g., chimpanzee or human; cow; dog; cat; a rodent, e.g., guinea pig, rat, mouse; rabbit; or a bird; reptile; or fish.
"Providing a biological sample" means to obtain a biological sample for use in methods described in this invention. Most often, this will be done by removing a sample of cells from an animal, but can also be accomplished by using previously isolated cells (e.g., isolated by another person, at another time, and/or for another purpose), or by performing the methods of the invention in vivo. Archival tissues, having treatment or outcome history, will be particularly useful.
The terms "identical" or percent "identity," in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, preferably 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI
web site http://www.ncbi.nlm.nih.govBLAST/ or the like). Such sequences are then said to be "substantially identical." This definition also refers to, or may be applied to, the compliment of a test sequence. The definition also includes sequences that have'deletions and/or additions, as well as those that have substitutions, as well as naturally occurnng, e.g., polymorphic or allelic variants, and man-made variants. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids. or nucleotides in length.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
Preferably, default program parameters can be used, or alternative parameters can be designated.
The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
A "comparison window", as used herein, includes reference to a segment of one of the number of contiguous positions selected from the group consisting typically of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl.
Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol.
Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l.
Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by manual alignment and visual inspection (see, e.g., Curre~zt Protocols ih Molecular Biology (Ausubel et al., eds.
1995 supplement)).
Preferred examples of algorithms that are suitable for determining percent sequence identity and sequence similarity include the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990). BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlin.nih.govn.
This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supYa).
These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, e.g., for nucleotide sequences, the parameters M (reward score for a pair of matching residues;
always > 0) and N (penalty score for mismatching residues; always < 0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score.
Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X
determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=-4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSLTM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=-4, and a comparison of both strands.
The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Marlin & Altschul, Proc. Nat'l. Acad. Sci.
USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.
Log values may be large negative numbers, e.g., 5, 10, 20, 30, 40, 40, 70, 90, 110, 150, 170, etc.
An indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, e.g., where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below.
Yet another indication that two nucleic acid sequences are substantially identical is that the same primers can be used to amplify the sequences.
A "host cell" is a naturally occurring cell or a transformed cell that contains an 1 S expression vector and supports the replication or expression of the expression vector. Host cells may be cultured cells, explants, cells ifa vivo, and the like. Host cells may be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, insect, amphibian, or mammalian cells such as CHO, HeLa, and the like (see, e.g., the American Type Culture Collection catalog or web site, www.atcc.org).
The terms "isolated," "purified," or "biologically pure" refer to material that is substantially or essentially free from components that normally accompany it as found in its native state. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein or nucleic acid that is the predominant species present in a preparation is substantially purified. In particular, an isolated nucleic acid is separated from some open reading frames that naturally flank the gene and encode proteins other than protein encoded by the gene. The term "purified" in some embodiments denotes that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel.
Preferably, it means that the nucleic acid or protein is at least 85% pure, more preferably at least 95% pure, and most preferably at least 99% pure. "Purify" or "purification" in other embodiments means removing at least one contaminant from the composition to be purified. In this sense, purification does not require that the purified compound be homogenous, e.g., 100% pure.
The terms "polypeptide," "peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers, those containing modified residues, and non-naturally occurring amino acid polymer.
The term "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function similarly to the naturally occurring amino acids. Naturally occurnng amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, y-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, e.g., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs may have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions similarly to a naturally occurring amino acid.
Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB
Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
"Conservatively modified variants" applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical or associated, e.g., naturally contiguous, sequences.
Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode most proteins. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to another of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes silent variations of the nucleic acid. One of skill will recognize that in certain contexts each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, often silent variations of a nucleic acid which encodes a polypeptide is implicit in a described sequence with respect to the expression product, but not with respect to actual probe sequences.
As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid.
Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.typically conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); S) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins (1984)).
Macromolecular structures such as polypeptide structures can be described in terms of various levels of organization. For a general discussion of this organization, see, e.g., Alberts et al., Molecular Biology of the Cell (3ra ed., 1994) and Cantor & Schimmel, Biophysical Chemistry Part L~ The Conformation of Biological Macromolecules (1980).
"Primary structure" refers to the amino acid sequence of a particular peptide.
"Secondary structure" refers to locally ordered, three dimensional structures within a polypeptide. These structures are commonly known as domains. Domains are portions of a polypeptide that often form a compact unit of the polypeptide and are typically 25 to approximately 500 amino acids long. Typical domains are made up of sections of lesser organization such as stretches of (3-sheet and a-helices. "Tertiary structure" refers to the complete three dimensional structure of a polypeptide monomer. "Quaternary structure" refers to the three dimensional structure formed, usually by the noncovalent association of independent tertiary units. Anisotropic terms are also known as energy terms.
"Nucleic acid" or "oligonucleotide" or "polynucleotide" or grammatical equivalents used herein means at least two nucleotides covalently linked together.
Oligonucleotides are typically from about 5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in length, up to about 100 nucleotides in length. Nucleic acids and polynucleotides are a polymers of any length, including longer lengths, e.g., 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000, etc. A nucleic acid of the present invention will generally contain phosphodiester bonds, although in some cases, nucleic acid analogs are included that may have alternate backbones, comprising, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press); and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U.S. Patent Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC
Symposium Series 580, Carbohydrate Modifications ira Antisense Research, Sanghui &
Cook, eds.. Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g. to increase the stability and half life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made.
A variety of references disclose such nucleic acid analogs, including, for example, phosphoramidate (Beaucage et al., Tetrahedron 49(10):1925 (1993) and references therein; Letsinger, J. Org. Chem. 35:3800 (1970); Sprinzl et al., Eur. J.
Biochem. 81:579 (1977); Letsinger et al., Nucl. Acids Res. 14:3487 (1986); Sawai et al, Chem.
Lett. 805 (1984), Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); and Pauwels et al., Chemica Scripts 26:141 91986)), phosphorothioate (Mag et al., Nucleic Acids Res.
19:1437 (1991);
and U.S. Patent No. 5,644,048), phosphorodithioate (Briu et al., J. Am. Chem.
Soc. 111:2321 (1989), O-methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues:
A Practical Approach, Oxford University Press), and peptide nucleic acid backbones and linkages (see Egholm, J. Am. Chem. Soc. 114:1895 (1992); Meier et al., Chem.
Int. Ed. Engl.
31:1008 (1992); Nielsen, Nature, 365:566 (1993); Carlsson et al., Nature 380:207 (1996), all of which are incorporated by reference). Other analog nucleic acids include those with positive backbones (Denpcy et al., Proc. Natl. Acad. Sci. USA 92:6097 (1995);
non-ionic backbones (U.S. Patent Nos. 5,386,023, 5,637,684, 5,602,240, 5,216,141 and 4,469,863;
Kiedrowshi et al., Angew. Chem. Intl. Ed. English 30:423 (1991); Letsinger et al., J. Am.
Chem. Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide 13:1597 (1994);
Chapters 2 and 3, ASC Symposium Series 580, "Carbohydrate Modifications in Antisense Research", Ed. Y.S. Sanghui and P. Dan Cook; Mesmaeker et al., Bioorganic &
Medicinal Chem. Lett. 4:395 (1994); Jeffs et al., J. Biomolecular NMR 34:17 (1994);
Tetrahedron Lett.
37:743 (1996)) and non-ribose backbones, including those described in U.S.
Patent Nos.
5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, "Carbohydrate Modifications in Antisense Research", Ed. Y.S. Sanghui and P. Dan Cook.
Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids (see Jerkins et al., Chem. Soc. Rev. (1995) pp 169-176). Several nucleic acid analogs are described in Ravels, C & E News June 2, 1997 page 35. All of these references are hereby expressly incorporated by reference.
Particularly preferred are peptide nucleic acids (PNA) which includes peptide nucleic acid analogs. These backbones are substantially non-ionic under neutral conditions, in contrast to the highly charged phosphodiester backbone of naturally occurring nucleic acids.
This results in two advantages. First, the PNA backbone exhibits improved hybridization kinetics. PNAs have larger changes in the melting temperature (Tm) for mismatched versus perfectly matched basepairs. DNA and RNA typically exhibit a 2-4°C drop in Tm for an internal mismatch. With the non-ionic PNA backbone, the drop is closer to 7-9°C. Similarly, due to their non-ionic nature, hybridization of the bases attached to these backbones is relatively insensitive to salt concentration. In addition, PNAs are not degraded by cellular enzymes, and thus can be more stable.
The nucleic acids may be single stranded or double stranded, as specified, or contain portions of both double stranded or single stranded sequence. As will be appreciated by those in the art, the depiction of a single strand also defines the sequence of the complementary strand; thus the sequences described herein also provide the complement of the sequence. The nucleic acid may be DNA, both genomic and cDNA, RNA or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine, isoguanine, etc. "Transcript" typically refers to a naturally occurring RNA, e.g., a pre-mRNA, hnRNA, or mRNA. As used herein, the term "nucleoside" includes nucleotides and nucleoside and nucleotide analogs, and modified nucleosides such as amino modified nucleosides. In addition, "nucleoside"
includes non-naturally occurring analog structures. Thus, e.g. the individual units of a peptide nucleic acid, each containing a base, are referred to herein as a nucleoside.
A "label" or a "detectable moiety" is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include 32P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins or other entities which can be made detectable, e.g., by incorporating a radiolabel into the peptide or used to detect antibodies specifically reactive with the peptide.
The labels may be incorporated into the breast cancer nucleic acids, proteins and antibodies at any position.
Any method known in the art for conjugating the antibody to the label may be employed, including those methods described by Hunter et al., Nature, 144:945 (1962);
David et al., Biochemistry, 13:1014 (1974); Pain et al., J. Immunol. Meth., 40:219 (1981);
and Nygren, J.
Histochem. and C ochem., 30:407 (1982).
An "effector" or "effector moiety" or "effector component" is a molecule that is bound (or linked, or conjugated), either covalently, through a linker or a chemical bond, or noncovalently, through ionic, van der Waals, electrostatic, or hydrogen bonds, to an antibody.
The "effector" can be a variety of molecules including, e.g., detection moieties including radioactive compounds, fluorescent compounds, an enzyme or substrate, tags such as epitope tags, a toxin; activatable moieties, a chemotherapeutic agent; a lipase; an antibiotic; or a radioisotope emitting "hard" e.g., beta radiation.
A "labeled nucleic acid probe or oligonucleotide" is one that is bound, either covalently, through a linker or a chemical bond, or noncovalently, through ionic, van der Waals, electrostatic, or hydrogen bonds to a label such that the presence of the probe may be detected by detecting the presence of the label bound to the probe.
Alternatively, method using high affinity interactions may achieve the same results where one of a pair of binding partners binds to the other, e.g., biotin, streptavidin.
As used herein a "nucleic acid probe or oligonucleotide" is defined as a nucleic acid capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. As used herein, a probe may include natural (i.e., A, G, C, or T) or modified bases (7-deazaguanosine, inosine, etc.). In addition, the bases in a probe may be joined by a linkage other than a phosphodiester bond, so long as it does not functionally interfere with hybridization. Thus, e.g., probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages.
It will be understood by one of skill in the art that probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency of the hybridization conditions. The probes are preferably directly labeled as with isotopes, chromophores, lumiphores, chromogens, or indirectly labeled such as with biotin to which a streptavidin complex may later bind. By assaying for the presence or absence of the probe, one can detect the presence or absence of the select sequence or subsequence.
Diagnosis or prognosis may be based at the genomic level, or at the level of RNA or protein expression.
The term "recombinant" when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, e.g., recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all. By the term "recombinant nucleic acid" herein is meant nucleic acid, originally formed in vitro, in general, by the manipulation of nucleic acid, e.g., using polymerases and endonucleases, in a form not normally found in nature. In this manner, operably linkage of different sequences is achieved. Thus an isolated nucleic acid, in a linear form, or an expression vector formed ih vitro by ligating DNA molecules that are not normally joined, are both considered recombinant for the purposes of this invention. It is understood that once a recombinant nucleic acid is made and reintroduced into a host cell or organism, it will replicate non-recombinantly, i.e., using the ih vivo cellular machinery of the host cell rather than in vitro manipulations; however, such nucleic acids, once produced recombinantly, although subsequently replicated non-recombinantly, are still considered recombinant for the purposes of the invention. Similarly, a "recombinant protein" is a protein made using recombinant techniques, i.e., through the expression of a recombinant nucleic acid as depicted above.
The term "heterologous" when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not normally found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences, e.g., from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein will often refer to two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).
A "promoter" is defined as an array of nucleic acid control sequences that direct transcription of a nucleic acid. As used herein, a promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element. A promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. A "constitutive" promoter is a promoter that is active under most environmental and developmental conditions. An "inducible" promoter~is a promoter that is active under environmental or developmental regulation. The term "operably linked" refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.
An "expression vector" is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell. The expression vector can be part of a plasmid, virus, or nucleic acid fragment. Typically, the expression vector includes a nucleic acid to be transcribed operably linl~ed to a promoter.
The phrase "selectively (or specifically) hybridizes to" refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).
The phrase "stringent hybridization conditions" refers to conditions under which a probe will hybridize to its taxget subsequence, typically in a complex mixture of nucleic acids, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tij ssen, Techniques in Biochemistry atad Molecular Biology--Hybridization with Nucleic Probes, "Overview of principles of hybridization and the strategy of nucleic acid assays"
(1993). Generally, stringent conditions are selected to be about 5-10°C
lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50%
of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to S.3 and the temperature is at least about 30°C for short probes (e.g., 10 to 50 nucleotides) and at least about 60°C for long probes (e.g., greater than 50 nucleotides).
Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, preferably 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50% formamide, Sx SSC, and 1%
SDS, incubating at 42°C, or, Sx SSC, 1% SDS, incubating at 65°C, with wash in 0.2x SSC, and 0.1 % SDS at 65°C. For PCR, a temperature of about 36°C is typical for low stringency amplification, although annealing temperatures may vary between about 32°C and 4~°C
depending on primer length. For high stringency PCR amplification, a temperature of about 62°C is typical, although high stringency annealing temperatures can range from about 50°C
to about 65°C, depending on the primer length and specificity. Typical cycle conditions for both high and low stringency amplifications include a denaturation phase of 90°C - 95°C for 30 sec - 2 min., an annealing phase lasting 30 sec. - 2 min., and an extension phase of about 72°C for I - 2 min. Protocols and guidelines for low and high stringency amplification reactions are provided, e.g., in Innis et al. (1990) PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc. N.Y.).
Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical.
This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary "moderately stringent hybridization conditions" include a hybridization in a buffer of 40%
forxnamide, 1 M NaCI, 1% SDS at 37°C, and a wash in 1X SSC at 45°C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.
Additional guidelines for determining hybridization parameters are provided in numerous reference, e.g., and Current Protocols in Molecular Biology, ed. Ausubel, et al.
~ The phrase "functional effects" in the context of assays for testing compounds that modulate activity of a breast cancer protein includes the determination of a parameter that is indirectly or directly under the influence of the breast cancer protein or nucleic acid, e.g., a functional, physical, or chemical effect, such as the ability to decrease breast cancer. It includes ligand binding activity; cell growth on soft agar; anchorage dependence; contact inhibition and density limitation of growth; cellular proliferation; cellular transformation;
growth factor or serum dependence; tumor specific marker levels; invasiveness into Matrigel;
tumor growth and metastasis in vivo; mRNA and protein expression in cells undergoing metastasis, and other characteristics of breast cancer cells. "Functional effects" include in vitro, in vivo, and ex vivo activities.
By "determining the functional effect" is meant assaying for a compound that increases or decreases a parameter that is indirectly or directly under the influence of a breast cancer protein sequence, e.g., functional, enzymatic, physical and chemical effects. Such functional effects can be measured by any means known to those skilled in the art, e.g., changes in spectroscopic characteristics (e.g., fluorescence, absorbance, refractive index), hydrodynamic (e.g., shape), chromatographic, or solubility properties for the protein, measuring inducible markers or transcriptional activation of the breast cancer protein;
measuring binding activity or binding assays, e.g. binding to antibodies or other ligands, and measuring cellular proliferation. Determination of the functional effect of a compound on breast cancer can also be performed using breast cancer assays known to those of skill in the art such as an ih vitYO assays, e.g., cell growth on soft agar; anchorage dependence; contact inhibition and density limitation of growth; cellular proliferation; cellular transformation;
growth factor or serum dependence; tumor specific marker levels; invasiveness into Matrigel;
tumor growth and metastasis ih vivo; mRNA and protein expression in cells undergoing metastasis, and other characteristics of breast cancer cells. The functional effects can be evaluated by many means known to those skilled in the art, e.g., microscopy for quantitative or qualitative measures of alterations in morphological features, measurement of changes in RNA or protein levels for breast cancer-associated sequences, measurement of RNA stability, identification of downstream or reporter gene expression (CAT, luciferase, (3-gal, GFP and the like), e.g., via chemiluminescence, fluorescence, colorimetric reactions, antibody binding, inducible markers, and ligand binding assays.
"Inhibitors", "activators", and "modulators" of breast cancer polynucleotide and polypeptide sequences are used to refer to activating, inhibitory, or modulating molecules or compounds identified using ira vitro and iya vivo assays of breast cancer polynucleotide and polypeptide sequences. Inhibitors are compounds that, e.g., bind to, partially or totally block activity, decrease, prevent, delay activation, inactivate, desensitize, or down regulate the activity or expression of breast cancer proteins, e.g., antagonists. Antisense nucleic acids may seem to inhibit expression and subsequent function of the protein.
"Activators" are compounds that increase, open, activate, facilitate, enhance activation, sensitize, agonize, or up regulate breast cancer protein activity. Inhibitors, activators, or modulators also include genetically modified versions of breast cancer proteins, e.g., versions with altered activity, as well as naturally occurring and synthetic ligands, antagonists, agonists, antibodies, small chemical molecules and the like. Such assays for inhibitors and activators include, e.g., expressing the breast cancer protein in vitro, in cells, or cell membranes, applying putative modulator compounds, and then determining the functional effects on activity, as described above. Activators and inhibitors of breast cancer can also be identified by incubating breast cancer cells with the test compound and determining increases or decreases in the expression of 1 or more breast cancer proteins, e.g., 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50 or more breast cancer proteins, such as breast cancer proteins encoded by the sequences set out in Tables 1-25.
Samples or assays comprising breast cancer proteins that are treated with a potential activator, inhibitor, or modulator are compared to control samples without the inhibitor, activator, or modulator to examine the extent of inhibition.
Control samples (untreated with inhibitors) are assigned a relative protein activity value of 100%. Inhibition of a polypeptide is achieved when the activity value relative to the control is about 80%, preferably 50%, more preferably 25-0%. Activation of a breast cancer polypeptide is achieved when the activity value relative to the control (untreated with activators) is 110%, more preferably 150%, more preferably 200-500% (i.e., two to five fold higher relative to the control), more preferably 1000-3000% higher.
The phrase "changes in cell growth" refers to any change in cell growth and proliferation characteristics in vitro or in vivo, such as formation of foci, anchorage independence, semi-solid or soft agar growth, changes in contact inhibition and density limitation of growth, loss of growth factor or serum requirements, changes in cell morphology, gaining or losing immortalization, gaining or losing tumor specific markers, ability to form or suppress tumors when injected into suitable animal hosts, and/or immortalization of the cell. See, e.g., Freshney, Culture of Animal Cells a Manual of Basic Technique pp. 231-241 (3rd ed. 1994).
"Tumor cell" refers to precancerous, cancerous, and normal cells in a tumor.
"Cancer cells," "transformed" cells or "transformation" in tissue culture, refers to spontaneous or induced phenotypic changes that do not necessarily involve the uptake of new genetic material. Although transformation can arise from infection with a transforming virus and incorporation of new genomic DNA, or uptake of exogenous DNA, it can also arise spontaneously or following exposure to a carcinogen, thereby mutating an endogenous gene.
Transformation is associated with phenotypic changes, such as immortalization of cells, aberrant growth control, nonmorphological changes, and/or malignancy (see, Freshney, Culture of Animal Cells a Manual of Basic Technique (3rd ed. 1994)).
"Antibody" refers to a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen.
The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively. Typically, the antigen-binding~region of an antibody or its functional equivalent will be most critical in specificity and affinity of binding. See Paul, Fundamentallmmuraology.
An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light" (about 25 kD) and one "heavy" chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chains respectively.
Antibodies exist, e.g., as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases. Thus, e.g., pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)'Z, a dimer of Fab which itself is a light chain joined to VH-CHl by a disulfide bond. The F(ab)'2 may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab)'a dimer into an Fab' monomer. The Fab' monomer is essentially Fab with part of the hinge region (see Furadamental Immunology (Paul ed., 3d ed.
1993). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty et al., Nature 348:552-554 (1990)) For preparation of antibodies, e.g., recombinant, monoclonal, or polyclonal antibodies, many technique known in the art can be used (see, e.g., Kohler &
Milstein, Nature 256:495-497 (1975); Kozbor et al., Imnaunology Today 4:72 (1983); Cole et al., pp.
77-96 in Monocloraal Antibodies arad Cancer Therapy (1985); Coligan, Current Protocols in Immunology (1991); Harlow & Lane, Antibodies, A Laboratory Manual (1988); and Goding, Monoelonal Antibodies: Principles and Practice (2d ed. 1986)). Techniques for the production of single chain antibodies (U.S. Patent 4,946,778) can be adapted to produce antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms such as other mammals, may be used to express humanized antibodies. Alternatively, phage display technology can be used to identify antibodies and heteromeric Fab fragments that specifically bind to selected antigens (see, e.g., McCafferty et al., Nature 348:552-554 (1990); Marks et al., Biotechnology 10:779-783 (1992)).
A "chimeric antibody" is an antibody molecule in which (a) the constant region, or a portion thereof, is altered, replaced or exchanged so that the antigen binding site (variable region) is linked to a constant region of a different or altered class, effector function and/or species, or an entirely different molecule which confers new properties to the chimeric antibody, e.g., an enzyme, toxin, hormone, growth factor, drug, etc.; or (b) the variable region, or a portion thereof, is altered, replaced or exchanged with a variable region having a different or altered antigen specificity.

Identification of breast cancer-associated sequences In one aspect, the expression levels of genes are determined in different patient samples for which diagnosis information is desired, to provide expression profiles.
An expression profile of a particular sample is essentially a "fingerprint" of the state of the sample; while two states may have any particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is characteristic of the state of the cell. That is, normal tissue (e.g., normal breast or other tissue) may be distinguished from cancerous or metastatic cancerous tissue of the breast, or breast cancer tissue or metastatic breast cancerous tissue can be compared with tissue samples of breast and other tissues from surviving cancer patients. By comparing expression profiles of tissue in known different breast cancer states, information regarding which genes are important (including both up- and down-regulation of genes) in each of these states is obtained.
The identification of sequences that are differentially expressed in breast cancer versus non-breast cancer tissue allows the use of this information in a number of ways.
For example, a particular treatment regime may be evaluated: does a chemotherapeutic drug act to down-regulate breast cancer, and thus tumor growth or recurrence, in a particular patient. Similarly, diagnosis and treatment outcomes may be done or confirmed by comparing patient samples with the known expression profiles. Metastatic tissue can also be analyzed to determine the stage of breast cancer in the tissue. Furthermore, these gene expression profiles (or individual genes) allow screening of drug candidates with an eye to mimicking or altering a particular expression profile; e.g., screening can be done for drugs that suppress the breast cancer expression profile. This may be done by making biochips comprising sets of the important breast cancer genes, which can then be used in these screens.
These methods can also be done on the protein basis; that is, protein expression levels of the breast cancer proteins can be evaluated for diagnostic purposes or to screen candidate agents.
In addition, the breast cancer nucleic acid sequences can be administered for gene therapy purposes, including the administration of antisense nucleic acids, or the breast cancer proteins (including antibodies and other modulators thereof) achninistered as therapeutic drugs.
2~

Thus the present invention provides nucleic acid and protein sequences that are differentially expressed in breast cancer, herein termed "breast cancer sequences." As outlined below, breast cancer sequences include those that are up-regulated (i.e., expressed at a higher level) in breast cancer, as well as those that are down-regulated (i.e., expressed at a lower level). In a preferred embodiment, the breast cancer sequences are from humans;
however, as will be appreciated by those in the art, breast cancer sequences from other organisms may be useful in animal models of disease and drug evaluation; thus, other breast cancer sequences are provided, from vertebrates, including mammals, including rodents (rats, mice, hamsters, guinea pigs, etc.), primates, farm animals (including sheep, goats, pigs, cows, horses, etc.) and pets, e.g., (dogs, cats, etc.). Breast cancer sequences from other organisms may be obtained using the techniques outlined below.
Breast cancer sequences can include both nucleic acid and amino acid sequences. As will be appreciated by those in the art and is more fully outlined below, breast cancer nucleic acid sequences are useful in a variety of applications, including diagnostic applications, which will detect naturally occurring nucleic acids, as well as screening applications; e.g., biochips comprising nucleic acid probes or PCR microtiter plates with selected probes to the breast cancer sequences can be generated.
A breast cancer sequence can be initially identified by substantial nucleic acid and/or amino acid sequence homology to the breast cancer sequences outlined herein. Such homology can be based upon the overall nucleic acid or amino acid sequence, and is generally determined as outlined below, using either homology programs or hybridization conditions.
For identifying breast cancer-associated sequences, the breast cancer screen typically includes comparing genes identified in different tissues, e.g., normal and cancerous tissues, or tumor tissue samples from patients who have metastatic disease vs.
non metastatic tissue. Other suitable tissue comparisons include comparing breast cancer samples with metastatic cancer samples from other cancers, such as lung, breast, gastrointestinal cancers, ovarian, etc. Samples of different stages of breast cancer, e.g., survivor tissue, drug resistant states, and tissue undergoing metastasis, are applied to biochips comprising nucleic acid probes. The samples are first microdissected, if applicable, and treated as is known in the art for the preparation of mRNA. Suitable biochips are commercially available, e.g. from Affymetrix. Gene expression profiles as described herein are generated and the data analyzed.
In one embodiment, the genes showing changes in expression as between normal and disease states are compared to genes expressed in other normal tissues, preferably normal breast, but also including, and not limited to lung, heart, brain, liver, breast, kidney, muscle, colon, small intestine, large intestine, spleen, bone and placenta. In a preferred embodiment, those genes identified during the breast cancer screen that are expressed in any significant amount in other tissues are removed from the profile, although in some embodiments, this is not necessary. That is, when screening for drugs, it is usually preferable that the target be disease specific, to minimize possible side effects.
In a preferred embodiment, breast cancer sequences are those that are up-regulated in breast cancer; that is, the expression of these genes is higher in the breast cancer tissue as compared to non-cancerous tissue. "Up-regulation" as used herein often means at least about a two-fold change, preferably at least about a three fold change, with at least about five-fold or higher being preferred. All unigene cluster identification numbers and accession numbers herein are for the GenBank sequence database and the sequences of the accession numbers are hereby expressly incorporated by reference. GenBank is known in the art, see, e.g., Benson, DA, et al., Nucleic Acids Research 26:1-7 (1998) and http://www.ncbi.nlm.nih.gov/. Sequences are also available in other databases, e.g., European Molecular Biology Laboratory (EMBL) and DNA Database of Japan (DDBJ).
U.S. Patent Application N. 09/687,576, with the same assignee as the present application, further discloses related sequences, compositions, and methods of diagnosis and treatment of breast cancer is hereby expressly incorporated by reference.
In another preferred embodiment, breast cancer sequences are those that are down-regulated in the breast cancer; that is, the expression of these genes is lower in breast cancer tissue as compared to non-cancerous tissue (see, e.g., Tables 1,2, 3, 15, 16 etc...).
"Down-regulation" as used herein often means at least about a two-fold change, preferably at least about a three fold change, with at least about five-fold or higher being preferred.

Informatics The ability to identify genes that are over or under expressed in breast cancer can additionally provide high-resolution, high-sensitivity datasets which can be used in the areas of diagnostics, therapeutics, drug development, pharmacogenetics, protein structure, biosensor development, and other related areas. For example, the expression profiles can be used in diagnostic or prognostic evaluation of patients with breast cancer. Or as another example, subcellular toxicological information can be generated to better direct drug structure and activity correlation (see Anderson, PhaYmaceutical Proteomics: Targets, Mechanism, and Function, paper presented at the IBC Proteomics conference, Coronado, CA
(June 11-12, 1998)). Subcellular toxicological information can also be utilized in a biological sensor device to predict the likely toxicological effect of chemical exposures and likely tolerable exposure thresholds (see U.S. Patent No. 5,811,231). Similar advantages accrue from datasets relevant to other biomolecules and bioactive agents (e.g., nucleic acids, saccharides, lipids, drugs, and the like).
Thus, in another embodiment, the present invention provides a database that includes at least one set of assay data. The data contained in the database is acquired, e.g., using array analysis either singly or in a library format. The database can be in substantially any form in which data can be maintained and transmitted, but is preferably an electronic database. The electronic database of the invention can be maintained on any electronic device allowing for the storage of and access to the database, such as a personal computer, but is preferably distributed on a wide area network, such as the World Wide Web.
The focus of the present section on databases that include peptide sequence data is for clarity of illustration only. It will be apparent to those of skill in the art that similar databases can be assembled for any assay data acquired using an assay of the invention.
The compositions and methods for identifying and/or quantitating the relative and/or absolute abundance of a variety of molecular and macromolecular species from a biological sample undergoing breast cancer, i.e., the identification of breast cancer-associated sequences described herein, provide an abundance of information, which can be correlated with pathological conditions, predisposition to disease, drug testing, therapeutic monitoring, gene-disease causal linkages, identification of correlates of immunity and physiological status, among others. Although the data generated from the assays of the invention is suited for manual review and analysis, in a preferred embodiment, prior data processing using high-speed computers is utilized.
An array of methods for indexing and retrieving biomolecular information is known in the art. For example, U.S. Patents 6,023,659 and 5,966,712 disclose a relational database system for storing biomolecular sequence information in a manner that allows sequences to be catalogued and searched according to one or more protein function hierarchies. U.S. Patent 5,953,727 discloses a relational database having sequence records containing information in a format that allows a collection of partial-length DNA sequences to be catalogued and searched according to association with one or more sequencing projects for obtaining full-length sequences from the collection of partial length sequences. U.S.
Patent 5,706,498 discloses a gene database retrieval system for making a retrieval of a gene sequence similar to a sequence data item in a gene database based on the degree of similarity between a key sequence and a target sequence. U.S. Patent 5,538,897 discloses a method using mass spectroscopy fragmentation patterns of peptides to identify amino acid sequences in computer databases by comparison of predicted mass spectra with experimentally-derived mass spectra using a closeness-of fit measure. U.S. Patent 5,926,818 discloses a multi-dimensional database comprising a functionality for mufti-dimensional data analysis described as on-line analytical processing (OLAP), which entails the consolidation of projected and actual data according to more than one consolidation path or dimension. U.S.
Patent 5,295,261 reports a hybrid database structure in which the fields of each database record are divided into two classes, navigational and informational data, with navigational fields stored in a hierarchical topological map which can be viewed as a tree structure or as the merger of two or more such tree structures.
See also Mount et al., Bioinformatics (2001); Biologieal Sequence Analysis:
Probabilistic Models of Proteins and Nucleic Acids (Durbin et al., eds., 1999);
Bioirzformatics: A Practical Guide to the Analysis of Genes and Proteizzs (Baxevanis &
Oeullette eds., 1998)); Rashidi & Buehler, Bioinformatics: Basic Applications in Biological Science and Medicine (1999); Irztroduction to Computational Molecular Biology (Setubal et al., eds 1997); Bioinforrnatics: Methods arad Protocols (Misener & Krawetz, eds, 2000);
Bioinformatics: Sequence, Structure, and Databanks: A Practical Approach (Higgins &
Taylor, eds., 2000); Brown, Bioinformatics: A Biologist's Guide to Biocornputing and the Iraterraet (2001); Han ~z Kamber, Data Mining: Concepts and Techniques (2000);
and Waterman, Introduction to Computatioraal Biology: Maps, Sequences, and Genomes (1995).
The present invention provides a computer database comprising a computer and software for storing in computer-retrievable form assay data records cross-tabulated, e.g., with data specifying the source of the target-containing sample from which each sequence specificity record was obtained.
In an exemplary embodiment, at least one of the sources of target-containing sample is from a control tissue sample known to be free of pathological disorders. In a variation, at least one of the sources is a known pathological tissue specimen, e.g., a neoplastic lesion or another tissue specimen to be analyzed for breast cancer.
In another variation, the assay records cross-tabulate one or more of the following parameters for each target species in a sample: (1) a unique identification code, which can include, e.g., a target molecular structure and/or characteristic separation coordinate (e.g., electrophoretic coordinates); (2) sample source; and (3) absolute and/or relative quantity of the target species present in the sample.
The invention also provides for the storage and retrieval of a collection of target data in a computer data storage apparatus, which can include magnetic disks, optical disks, magneto-optical disks, DRAM, SRAM, SGRAM, SDRAM, RDRAM, DDR RAM, magnetic bubble memory devices, and other data storage devices, including CPU
registers and on-CPU data storage arrays. Typically, the target data records are stored as a bit pattern in an array of magnetic domains on a magnetizable medium or as an array of charge states or transistor gate states, such as an array of cells in a DRAM device (e.g., each cell comprised of a transistor and a charge storage area, which may be on the transistor). In one embodiment, the invention provides such storage devices, and computer systems built therewith, comprising a bit pattern encoding a protein expression fingerprint record comprising unique identifiers for at least 10 target data records cross-tabulated with target source.

When the target is a peptide or nucleic acid, the invention preferably provides a method for identifying related peptide or nucleic acid sequences, comprising performing a computerized comparison between a peptide or nucleic acid sequence assay record stored in or retrieved from a computer storage device or database and at least one other sequence. The comparison can include a sequence analysis or comparison algorithm or computer program embodiment thereof (e.g., FASTA, TFASTA, GAP, BESTFIT) and/or the comparison may be of the relative amount of a peptide or nucleic acid sequence in a pool of sequences determined from a polypeptide or nucleic acid sample of a specimen.
The invention also preferably provides a magnetic disk, such as an IBM-compatible (DOS, Windows, Windows95/98/2000, Windows NT, OS/2) or other format (e.g., Linux, SunOS, Solaris, AIX, SCO Unix, VMS, MV, Macintosh, etc.) floppy diskette or hard (fixed, Winchester) disk drive, comprising a bit pattern encoding data from an assay of the invention in a file format suitable for retrieval and processing in a computerized sequence analysis, comparison, or relative quantitation method.
The invention also provides a network, comprising a plurality of computing devices linked via a data link, such as an Ethernet cable (coax or l OBaseT), telephone line, ISDN line, wireless network, optical fiber, or other suitable signal transmission medium, whereby at least one network device (e.g., computer, disk array, etc.) comprises a pattern of magnetic domains (e.g., magnetic disk) and/or charge domains (e.g., an array of DRAM
cells) composing a bit pattern encoding data acquired from an assay of the invention.
The invention also provides a method for transmitting assay data that includes generating an electronic signal on an electronic communications device, such as a modem, ISDN terminal adapter, DSL, cable modem, ATM switch, or the like, wherein the signal includes (in native or encrypted format) a bit pattern encoding data from an assay or a database comprising a plurality of assay results obtained by the method of the invention.
In a preferred embodiment, the invention provides a computer system for comparing a query target to a database containing an array of data structures, such as an assay result obtained by the method of the invention, and ranking database targets based on the ' degree of identity and gap weight to the target data. A central processor is preferably initialized to load and execute the computer program for alignment and/or comparison of the assay results. Data for a query target is entered into the central processor via an I/O device.
Execution of the computer program results in the central processor retrieving the assay data from the data file, which comprises a binary description of an assay result.
The target data or record and the computer program can be transferred to secondary memory, which is typically random access memory (e.g., DRAM, SRAM, SGRAM, or SDRAM). Targets are ranked according to the degree of correspondence between a selected assay characteristic (e.g., binding to a selected affinity moiety) and the same characteristic of the query target and results are output via an I/O
device. For example, a central processor can be a conventional computer (e.g., Intel Pentium, PowerPC, Alpha, PA-8000, SPARC, MIPS 4400, MIPS 10000, VAX, etc.); a program can be a commercial or public domain molecular biology software package (e.g., UWGCG Sequence Analysis Software, Darwin); a data file can be an optical or magnetic disk, a data server, a memory device (e.g., DR.AM, SRAM, SGRAM, SDRAM, EPROM, bubble memory, flash memory, etc.); an I/O device can be a terminal comprising a video display and a keyboard, a modem, an ISDN terminal adapter, an Ethernet port, a punched card reader, a magnetic strip reader, or other suitable I/O device.
The invention also preferably provides the use of a computer system, such as that described above, which comprises: (1) a computer; (2) a stored bit pattern encoding a collection of peptide sequence specificity records obtained by the methods of the invention, which may be stored in the computer; (3) a comparison target, such as a query target; and (4) a program for alignment and comparison, typically with rank-ordering of comparison results on the basis of computed similarity values.
Characteristics of breast cancer-associated proteins Breast cancer proteins of the present invention may be classified as secreted proteins, transmembrane proteins or intracellular proteins. In one embodiment, the breast cancer protein is an intracellular protein. Intracellular proteins may be found in the cytoplasm and/or in the nucleus. Intracellular proteins are involved in all aspects of cellular function and replication (including, e.g., signaling pathways); aberrant expression of such proteins often results in unregulated or disregulated cellular processes (see, e.g., Molecular Biology of the Cell (Alberts, ed., 3rd ed., 1994). For example, many intracellular proteins have enzymatic activity such as protein kinase activity, protein phosphatase activity, protease activity, nucleotide cyclase activity, polymerase activity and the like.
Intracellular proteins also serve as docking proteins that are involved in organizing complexes of proteins, or targeting proteins to various subcellular localizations, and are involved in maintaining the structural integrity of organelles.
An increasingly appreciated concept in characterizing proteins is the presence in the proteins of one or more motifs for which defined functions have been attributed. In addition to the highly conserved sequences found in the enzymatic domain of proteins, highly conserved sequences have been identified in proteins that are involved in protein-protein interaction. For example, Src-homology-2 (SH2) domains bind tyrosine-phosphorylated targets in a sequence dependent manner. PTB domains, which are distinct from domains, also bind tyrosine phosphorylated targets. SH3 domains bind to proline-rich targets. In addition, PH domains, tetratricopeptide repeats and WD domains to name only a few, have been shown to mediate protein-protein interactions. Some of these may also be involved in binding to phospholipids or other second messengers. As will be appreciated by one of ordinary skill in the art, these motifs can be identified on the basis of primary sequence; thus, an analysis of the sequence of proteins may provide insight into both the enzymatic potential of the molecule and/or molecules with which the protein may associate.
One useful database is Pfam (protein families), which is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
Versions are available via the Internet from Washington University in St.
Louis, the Sanger Center in England, and the I~arolinska Institute in Sweden (see, e.g., Bateman et al., Nuc.
Acids Res. 28:263-266 (2000); Sonnhammer et al., Proteins 28:405-420 (1997);
Bateman et al., Nuc. Acids Res. 27:260-262 (1999); and Sonnhammer et al., Nue. Acids Res.
26:320-322-(1998)).
In another embodiment, the breast cancer sequences are transmembrane proteins. Transmembrane proteins are molecules that span a phospholipid bilayer of a cell.
They may have an intracellular domain, an extracellular domain, or both. The intracellular domains of such proteins may have a number of functions including those already described for intracellular proteins. For example, the intracellular domain may have enzymatic activity and/or may serve as a binding site for additional proteins. Frequently the intracellular domain of transmembrane proteins serves both roles. For example certain receptor tyrosine kinases have both protein kinase activity and SH2 domains. In addition, autophosphorylation , of tyrosines on the receptor molebule itself, creates binding sites for additional SH2 domain containing proteins.
Transmembrane proteins may contain from one to many transmembrane domains. For example, receptor tyrosine kinases, certain cytokine receptors, receptor guanylyl cyclases and receptor serine/threonine protein kinases contain a single transmembrane domain. However, various other proteins including channels and adenylyl cyclases contain numerous transmembrane domains. Many important cell surface receptors such as G protein coupled receptors (GPCRs) are classified as "seven transmembrane domain" proteins, as they contain 7 membrane spanning regions. Characteristics of transmembrane domains include approximately 20 consecutive hydrophobic amino acids that may be followed by charged amino acids. Therefore, upon analysis of the amino acid sequence of a particular protein, the localization and number of transmembrane domains within the protein may be predicted (see, e.g. PSORT web site http://psort.nibb.ac.jp~.
Important transmembrane protein receptors include, but are not limited to the insulin receptor, insulin-like growth factor receptor, human growth hormone receptor, glucose transporters, transferrin receptor, epidermal growth factor receptor, low density lipoprotein receptor, epidermal growth factor receptor, leptin receptor, interleukin receptors, e.g. IL-1 receptor, IL-2 receptor, The extracellulax domains of transmembrane proteins are diverse; however, conserved motifs are found repeatedly among vaxious extracellular domains.
Conserved structure and/or functions have been ascribed to different extracellular motifs. Many extracellular domains are involved in binding to other molecules. In one aspect, extracellular domains are found on receptors. Factors that bind the receptor domain include circulating ligands, which may be peptides, proteins, or small molecules such as adenosine and the like.
For example, growth factors such as EGF, FGF and PDGF are circulating growth factors that bind to their cognate receptors to initiate a variety of cellular responses.
Other factors include cytokines, mitogenic factors, neurotrophic factors and the like. Extracellular domains also bind to cell-associated molecules. In this respect, they mediate cell-cell interactions. Cell-associated ligands can be tethered to the cell, e.g., via a glycosylphosphatidylinositol (GPI) anchor, or may themselves be transmembrane proteins. Extracellular domains also associate with the extracellular matrix and contribute to the maintenance of the cell structure.
Breast cancer proteins that are transmembrane are particularly preferred in the present invention as they are readily accessible targets for immunotherapeutics, as are described herein. In addition, as outlined below, transmembrane proteins can be also useful in imaging modalities. Antibodies may be used to label such readily accessible proteins iya situ. Alternatively, antibodies can also label intracellular proteins, in which case samples are typically permeablized to provide access to intracellular proteins.
It will also be appreciated by those in the art that a transmembrane protein can be made soluble by removing transmembrane sequences, e.g., through recombinant methods.
Furthermore, transmembrane proteins that have been made soluble can be made to be secreted through recombinant means by adding an appropriate signal sequence.
In another embodiment, the breast cancer proteins are secreted proteins; the secretion of which can be either constitutive or regulated. These proteins have a signal peptide or signal sequence that targets the molecule to the secretory pathway.
Secreted proteins are involved in numerous physiological events; by virtue of their circulating nature, they serve to transmit signals to various other cell types. The secreted protein may function in an autocrine manner (acting on the cell that secreted the factor), a paracrine manner (acting on cells in close proximity to the cell that secreted the factor) or an endocrine manner (acting on cells at a distance). Thus secreted molecules find use in modulating or altering numerous aspects of physiology. Breast cancer proteins that are secreted proteins are particularly preferred in the present invention as they serve as good targets for diagnostic markers, e.g., for blood, plasma, serum, or stool tests.
Use of breast cancer nucleic acids As described above, breast cancer sequence is initially identified by substantial nucleic acid and/or amino acid sequence homology or linkage to the breast cancer 3~

sequences outlined herein. Such homology can be based upon the overall nucleic acid or amino acid sequence, and is generally determined as outlined below, using either homology programs or hybridization conditions. Typically, linked sequences on a mRNA
are found on the same molecule.
The breast cancer nucleic acid sequences of the invention, e.g., the sequences in Tables 1-25, can be fragments of larger genes, i.e., they are nucleic acid segments.
"Genes" in this context includes coding regions, non-coding regions, and mixtures of coding and non-coding regions. Accordingly, as will be appreciated by those in the art, using the sequences provided herein, extended sequences, in either direction, of the breast cancer genes can be obtained, using techniques well known in the art for cloning either longer sequences or the full length sequences; see Ausubel, et al., supf~a. Much can be done by informatics and many sequences can be clustered to include multiple sequences corresponding to a single gene, e.g., systems such as UniGene (see, http://www.ncbi.nlm.nih.gov/UniGene~.
Once the breast cancer nucleic acid is identified, it can be cloned and, if necessary, its constituent parts recombined to form the entire breast cancer nucleic acid coding regions or the entire mRNA sequence. Once isolated from its natural source, e.g., contained within a plasmid or other vector or excised therefrom as a linear nucleic acid segment, the recombinant breast cancer nucleic acid can be further-used as a probe to identify and isolate other breast cancer nucleic acids, e.g., extended coding regions.
It can also be used as a "precursor" nucleic acid to make modified or variant breast cancer nucleic acids and proteins.
The breast cancer nucleic acids of the present invention are used in several ways. In a first embodiment, nucleic acid probes to the breast cancer nucleic acids are made and attached to biochips to be used in screening and diagnostic methods, as outlined below, or for administration, e.g., for gene therapy, vaccine, and/or antisense applications.
Alternatively, the breast cancer nucleic acids that include coding regions of breast cancer proteins can be put into expression vectors for the expression of breast cancer proteins, again for screening purposes or for administration to a patient.
In a preferred embodiment, nucleic acid probes to breast cancer nucleic acids (both the nucleic acid sequences outlined in the figures and/or the complements thereof) are made. The nucleic acid probes attached to the biochip are designed to be substantially complementary to the breast cancer nucleic acids, i.e. the target sequence (either the target sequence of the sample or to other probe sequences, e.g., in sandwich assays), such that hybridization of the target sequence and the probes of the present invention occurs. As outlined below, this complementarity need not be perfect; there may be any number of base pair mismatches which will interfere with hybridization between the target sequence and the single stranded nucleic acids of the present invention. However, if the number of mutations is so great that no hybridization can occur under even the least stringent of hybridization conditions, the sequence is not a complementary target sequence. Thus, by "substantially complementary" herein is meant that the probes are sufficiently complementary to the target sequences to hybridize under normal reaction conditions, particularly high stringency conditions, as outlined herein.
A nucleic acid probe is generally single stranded but can be partially single and partially double stranded. The strandedness of the probe is dictated by the structure, composition, and properties of the target sequence. In general, the nucleic acid probes range from about 8 to about 100 bases long, with from about 10 to about 80 bases being preferred, and from about 30 to about 50 bases being particularly preferred. That is, generally whole genes are not used. In some embodiments, much longer nucleic acids can be used, up to hundreds of bases.
In a preferred embodiment, more than one probe per sequence is used, with either overlapping probes or probes to different sections of the target being used. That is, two, three, four or more probes, with three being preferred, are used to build in a redundancy for a particular target. The probes can be overlapping (i.e., have some sequence in common), or separate. In some cases, PCR primers may be used to amplify signal for higher sensitivity.
As will be appreciated by those in the art, nucleic acids can be attached or immobilized to a solid support in a wide variety of ways. By "immobilized" and grammatical equivalents herein is meant the association or binding between the nucleic acid probe and the solid support is sufficient to be stable under the conditions of binding, waslung, analysis, and removal as outlined below. The binding can typically be covalent or non-covalent. By "non-covalent binding" and grammatical equivalents herein is meant one or more of electrostatic, hydrophilic, and hydrophobic interactions. Included in non-covalent binding is the covalent attachment of a molecule, such as, streptavidin to the support and the non-covalent binding of the biotinylated probe to the streptavidin. By "covalent binding" and grammatical equivalents herein is meant that the two moieties, the solid support and the probe, are attached by at least one bond, including sigma bonds, pi bonds and coordination bonds.
Covalent bonds can be formed directly between the probe and the solid support or can be formed by a cross linker or by inclusion of a specific reactive group on either the solid support or the probe or both molecules. Immobilization may also involve a combination of covalent and non-covalent interactions.
In general, the probes are attached to the biochip in a wide variety of ways, as will be appreciated by those in the art. As described herein, the nucleic acids can either be synthesized first, with subsequent attachment to the biochip, or can be directly synthesized on the biochip.
The biochip comprises a suitable solid substrate. By "substrate" or "solid support" or other grammatical equivalents herein is meant a material that can be modified to contain discrete individual sites appropriate for the attachment or association of the nucleic acid probes and is amenable to at least one detection method. As will be appreciated by those in the art, the number of possible substrates are very large, and include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, TeflonJ, etc.), polysaccharides, nylon or nitrocellulose, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses, plastics, etc. In general, the substrates allow optical detection and do not appreciably fluoresce. A preferred substrate is described in copending application entitled Reusable Low Fluorescent Plastic Biochip, U.S. Application Serial No. 09/270,214, filed March 15, 1999, herein incorporated by reference in its entirety.
Generally the substrate is planar, although as will be appreciated by those in the art, other configurations of substrates may be used as well. For example, the probes may be placed on the inside surface of a tube, for flow-through sample analysis to minimize sample volume. Similarly, the substrate may be flexible, such as a flexible foam, including closed cell foams made of particular plastics.
In a preferred embodiment, the surface of the biochip and the probe may be derivatized with chemical functional groups for subsequent attachment of the two. Thus, e.g., the biochip is derivatized with a chemical functional group including, but not limited to,' amino groups, carboxy groups, oxo groups and thiol groups, with amino groups being particularly preferred. Using these functional groups, the probes can be attached using functional groups on the probes. For example, nucleic acids containing amino groups can be attached to surfaces comprising amino groups, e.g. using linkers as are known in the art; e.g., homo-or hetero-bifunctional linkers as axe well known (see 1994 Pierce Chemical Company catalog, technical section on cross-linkers, pages 155-200). In addition, in some cases, additional linkers, such as alkyl groups (including substituted and heteroalkyl groups) may be used.
In this embodiment, oligonucleotides are synthesized as is known in the art, and then attached to the surface of the solid support. As will be appreciated by those skilled in the art, either the 5' or 3' terminus may be attached to the solid support, or attachment may be via an internal nucleoside.
In another embodiment, the immobilization to the solid support may be very strong, yet non-covalent. For example, biotinylated oligonucleotides can be made, which bind to surfaces covalently coated with streptavidin, resulting in attachment.
Alternatively, the oligonucleotides may be synthesized on the surface, as is known in the art. For example, photoactivation techniques utilizing photopolymerization compounds and techniques are used. In a preferred embodiment, the nucleic acids can be synthesized in situ, using well known photolithographic techniques, such as those described in WO 95/25116; WO 95/35505; U.S. Patent Nos. 5,700,637 and 5,445,934; and references cited within, all of which are expressly incorporated by reference; these methods of attachment form the basis of the Affimetrix GeneChipTM technology.
Often, amplification-based assays are performed to measure the expression level of breast cancer-associated sequences. These assays are typically performed in conjunction with reverse transcription. In such assays, a breast cancer-associated nucleic acid sequence acts as a template in an amplification reaction (e.g., Polymerase Chain Reaction, or PCR). In a quantitative amplification, the amount of amplification product will be proportional to the amount of template in the original sample. Comparison to appropriate controls provides a measure of the amount of breast cancer-associated RNA.
Methods of quantitative amplification are well known to those of skill in the art.
Detailed protocols for quantitative PCR are provided, e.g., in Innis et al., PCR Protocols, A Guide to Methods and Applications (1990).
In some embodiments, a TaqMan based assay is used to measure expression.
TaqMan based assays use a fluorogenic oligonucleotide probe that contains a 5' fluorescent dye and a 3' quenching agent. The probe hybridizes to a PCR product, but cannot itself be extended due to a blocking agent at the 3' end. When the PCR product is amplified in subsequent cycles, the 5' nuclease activity of the polymerase, e.g., AmpliTaq, results in the cleavage of the TaqMan probe. This cleavage separates the 5' fluorescent dye and the 3' quenching agent, thereby resulting in an increase in fluorescence as a function of amplification (see, e.g., literature provided by Perkin-Eliner, e.g., www2.perkin-elmer.com) Other suitable amplification methods include, but are not limited to, ligase chain reaction (LCR) (see Wu & Wallace, Genomics 4:560 (1989), Landegren et al., Science 241:1077 (1988), and Barringer et al., Gene 89:117 (1990)), transcription amplification (Kwon et al., Proe. Natl. Acad. Sci. USA 86:1173 (1989)), self sustained sequence replication (Guatelli et al., Proc. Nat. Acad. Sci. USA 87:1874 (1990)), dot PCR, and linker adapter PCR, etc.
Expression of breast cancer proteins from nucleic acids In a preferred embodiment, breast cancer nucleic acids, e.g., encoding breast cancer proteins are used to make a variety of expression vectors to express breast cancer proteins which can then be used in screening assays, as described below.
Expression vectors and recombinant DNA technology are well known to those of skill in,the art (see, e.g., Ausubel, supra, and Gene Expression Systems (Fernandez & Hoeffler, eds, 1999)) and are used to express proteins. The expression vectors may be either self replicating extrachromosomal vectors or vectors which integrate into a host genome.
Generally, these expression vectors include transcriptional and translational regulatory nucleic acid operably linked to the nucleic acid encoding the breast cancer protein. The term "control sequences"
refers to DNA sequences used for the expression of an operably linked coding sequence in a particular host organism. Control sequences that are suitable for prokaryotes, e.g., include a promoter, optionally an operator sequence, and a ribosome binding site.
Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
Generally, "operably linked" means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase.
However, enhancers do not have to be contiguous. Linking is typically accomplished by ligation at convenient restriction sites. If such sites do not exist, synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice. Transcriptional and translational regulatory nucleic acid will generally be appropriate to the host cell used to express the breast cancer protein. Numerous types of appropriate expression vectors, and suitable regulatory sequences are known in the art for a variety of host cells.
In general, transcriptional and translational regulatory sequences may include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences.
In a preferred embodiment, the regulatory sequences include a promoter and transcriptional start and stop sequences.
Promoter sequences encode either constitutive or inducible promoters. The promoters may be either naturally occurring promoters or hybrid promoters.
Hybrid promoters, which combine elements of more than one promoter, are also known in the art, and are useful in the present invention.

In addition, an expression vector may comprise additional elements. For example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, e.g. in mammalian or insect cells for expression and in a procaryotic host for cloning and amplification. Furthermore, for integrating expression vectors, the expression vector contains at least one sequence homologous to the host cell genome, and preferably two homologous sequences which flank the expression construct.
The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art (e.g., Fernandez & Hoeffler, supYa).
In addition, in a preferred embodiment, the expression vector contains a selectable marker gene to allow the selection of transformed host cells.
Selection genes are well known in the art and will vary with the host cell used.
The breast cancer proteins of the present invention are produced by culturing a host cell transformed with an expression vector containing nucleic acid encoding a breast cancer protein, under the appropriate conditions to induce or cause expression of the breast cancer protein. Conditions appropriate for breast cancer protein expression will vary with the choice of the expression vector and the host cell, and will be easily ascertained by one skilled in the art through routine experimentation or optimization. For example, the use of constitutive promoters in the expression vector will require optimizing the growth and proliferation of the host cell, while the use of an inducible promoter requires the appropriate growth conditions for induction. In addition, in some embodiments, the timing of the harvest is important. For example, the baculoviral systems used in insect cell expression are lytic viruses, and thus harvest time selection can be crucial for product yield.
Appropriate host cells include yeast, bacteria, archaebacteria, fungi, and insect and animal cells, including mammalian cells. Of particular interest are Saccharomyces ceYevisiae and other yeasts, E. coli, Bacillus subtilis, Sf~ cells, C129 cells, 293 cells, Neurospora, BHK, CHO, COS, HeLa cells, HUVEC (human umbilical vein endothelial cells), THP1 cells (a macrophage cell line) and various other human cells and cell lines.
In a preferred embodiment, the breast cancer proteins are expressed in mammalian cells. Mammalian expression systems are also known in the art, and include retroviral and adenoviral systems. One expression vector system is a retroviral vector system such as is generally described in PCTlLTS97/01019 and PCTlLTS97/01048, both of which are hereby expressly incorporated by reference. Of particular use as mammalian promoters are the promoters from mammalian viral genes, since the viral genes are often highly expressed and have a broad host range. Examples include the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late promoter, herpes simplex virus promoter, and the CMV promoter (see, e.g., Fernandez & Hoeffler, supra). Typically, transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3' to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. Examples of transcription terminator and polyadenlyation signals include those derived form SV40.
The methods of introducing exogenous nucleic acid into mammalian hosts, as well as other hosts, is well known in the art, and will vary with the host cell used.
Techniques include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, viral infection, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA
into nuclei.
In a preferred embodiment, breast cancer proteins are expressed in bacterial systems. Bacterial expression systems are well known in the art. Promoters from bacteriophage may also be used and are known in the art. In addition, synthetic promoters and hybrid promoters are also useful; e.g., the tac promoter is a hybrid of the trp and lac promoter sequences. Furthermore, a bacterial promoter can include naturally occurnng promoters of non-bacterial origin that have the ability to bind bacterial RNA
polymerase and initiate transcription. In addition to a functioning promoter sequence, an efficient ribosome binding site is desirable. The expression vector may also include a signal peptide sequence that provides for secretion of the breast cancer protein in bacteria. The protein is either secreted into the growth media (gram-positive bacteria) or into the periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). The bacterial expression vector may also include a selectable marker gene to allow for the selection of bacterial strains that have been transformed. Suitable selection genes include genes which render the bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracycline. Selectable markers also include biosynthetic genes, such as those in the histidine, tryptophan and leucine biosynthetic pathways.
These components are assembled into expression vectors. Expression vectors for bacteria are well known in the art, and include vectors for Bacillus subtilis, E. coli, Streptococcus cremoris, and Streptococcus lividaras, among others (e.g., Fernandez & Hoeffler, supYa).
The bacterial expression vectors are transformed into bacterial host cells using techniques well known in the art, such as calcium chloride treatment, electroporation, and others.
In one embodiment, breast cancer proteins are produced in insect cells.
Expression vectors for the transformation of insect cells, and in particular, baculovirus-based expression vectors, are well known in the art.
In a preferred embodiment, breast cancer protein is produced in yeast cells.
Yeast expression systems are well known in the art, and include expression vectors for Saccharomyces ce~evisiae, Candida albicaf2s and C. maltosa, Hansenula polymorpha, Kluyveromyces fi~agilis and K. lactis, Pichia guillerimondii and P. pastoris, SchizosacclzaYOmyces pombe, and Yarrowia lipolytica.
The breast cancer protein may also be made as a fusion protein, using techniques well known in the art. Thus, e.g., for the creation of monoclonal antibodies, if the desired epitope is small, the breast cancer protein may be fused to a Garner protein to form an immunogen. Alternatively, the breast cancer protein may be made as a fusion protein to increase expression, or for other reasons. For example, when the breast cancer protein is a breast cancer peptide, the nucleic acid encoding the peptide may be linked to other nucleic acid for expression purposes.
In a preferred embodiment, the breast cancer protein is purified or isolated after expression. Breast cancer proteins may be isolated or purified in a variety of ways known to those skilled in the art depending on what other components are present in the sample. Standard purification methods include electrophoretic, molecular, immunological and chromatographic techniques, including ion exchange, hydrophobic, affinity, and reverse-phase HPLC chromatography, and chromatofocusing. For example, the breast cancer protein may be purified using a standard anti-breast cancer protein antibody column.
LJltrafiltration and diafiltration techniques, in conjunction with protein concentration, are also useful. For general guidance in suitable purification techniques, see Scopes, Protein PurificatiofZ (1982).
The degree of purification necessary will vary depending on the use of the breast cancer protein. In some instances no purification will be necessary.
Once expressed and purified if necessary, the breast cancer proteins and nucleic acids are useful in a number of applications. They may be used as immunoselection reagents, as vaccine reagents, as screening agents, etc.
Variants of breast cancer proteins In one embodiment, the breast cancer proteins are derivative or variant breast cancer proteins as compared to the wild-type sequence. That is, as outlined more fully below, the derivative breast cancer peptide will often contain at least one amino acid substitution, deletion or insertion, with amino acid substitutions being particularly preferred. The amino acid substitution, insertion or deletion may occur at any residue within the breast cancer peptide.
Also included within one embodiment of breast cancer proteins of the present invention are amino acid sequence variants. These variants typically fall into one or more of three classes: substitutional, insertional or deletional variants. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DNA encoding the breast cancer protein, using cassette or PCR mutagenesis or other techniques well known in the art, to produce DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture as outlined above. However, variant breast cancer protein fragments having up to about 100-150 residues may be prepared by in vitro synthesis using established techniques.
Amino acid sequence variants are characterized by the predetermined nature of the variation, a feature that sets them apart from naturally occurring allelic or interspecies variation of the breast cancer protein amino acid sequence. The variants typically exhibit the same qualitative biological activity as the naturally occurring analogue, although variants can also be selected which have modified characteristics as will be more fully outlined below.
While the site or region for introducing an.amino acid sequence variation is predetermined, the mutation per se need not be predetermined. For example, in order to optimize the performance of a mutation at a given site, random mutagenesis may be conducted at the target codon or region and the expressed breast cancer variants screened for the optimal combination of desired activity. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, e.g., M13 primer mutagenesis and PCR mutagenesis. Screening of the mutants is done using assays of breast cancer protein activities.
Amino acid substitutions are typically of single residues; insertions usually will be on the order of from about 1 to 20 amino acids, although considerably larger insertions may be tolerated. Deletions range from about 1 to about 20 residues, although in some cases deletions may be much larger.
Substitutions, deletions, insertions or any combination thereof may be used to arnve at a final derivative. Generally these changes are done on a few amino acids to minimize the alteration of the molecule. However, larger changes may be tolerated in certain circumstances. When small alterations in the characteristics of the breast cancer protein are desired, substitutions are generally made in accordance with the amino acid substitution relationships provided in the definition section.
The variants typically exhibit the same qualitative biological activity and will elicit the same immune response as the naturally-occurring analog, although variants also are selected to modify the characteristics of the breast cancer proteins as needed. Alternatively, the variant may be designed such that the biological activity of the breast cancer protein is altered. For example, glycosylation sites may be altered or removed.
Substantial changes in function or immunological identity are made by selecting substitutions that are less conservative than those described above.
For example, substitutions may be made which more significantly affect: the structure of the polypeptide backbone in the area of the alteration, for example the alpha-helical or beta-sheet structure;
the charge or hydrophobicity of the molecule at the target site; or the bulk of the side chain.
The substitutions which in general are expected to produce the greatest changes in the polypeptide's properties are those in which (a) a hydrophilic residue, e.g.
seryl or threonyl is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g. lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g. glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g. phenylalanine, is substituted for (or by) one not having a side chain, e.g. glycine.
Covalent modifications of breast cancer polypeptides are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a breast cancer polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N-or C-terminal residues of a breast cancer polypeptide. Derivatization with bifunctional agents is useful, for instance, for crosslinking breast cancer polypeptides to a water-insoluble support matrix or surface for use in the method for purifying anti-breast cancer polypeptide antibodies or screening assays, as is more fully described below. Commonly used crosslinking agents include, e.g., l,l-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, e.g., esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3'-dithiobis(succinimidylpropionate), bifunctional maleimides such as bis-N-maleimido-1,8-octane and agents such as methyl-3-((p-azidophenyl)dithio)propioimidate. , Other modifications include deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues, respectively, hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl, threonyl or tyrosyl residues, methylation of the amino groups of the lysine, arginine, and histidine side chains (Creighton, Proteins: St~uctu~e and Molecular Properties, pp. 79-86 (1983)), acetylation of the N-terminal amine, and amidation of any C-terminal carboxyl group.
Another type of covalent modification of the breast cancer polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of the polypeptide. "Altering the native glycosylation pattern" is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence breast cancer polypeptide, and/or adding one or more glycosylation sites that are not present in the native sequence breast cancer polypeptide. Glycosylation patterns can be altered in many ways. For example the use of different cell types to express breast cancer-associated sequences can result in different glycosylation patterns.

Addition of glycosylation sites to breast cancer polypeptides may also be accomplished by altering the amino acid sequence thereof. The alteration may be made, e.g., by the addition of, or substitution by, one or more serine or threonine residues to the native sequence breast cancer polypeptide (for O-linked glycosylation sites). The breast cancer amino acid sequence may optionally be altered through changes at the DNA
level, particularly by mutating the DNA encoding the breast cancer polypeptide at preselected bases such that codons axe generated that will translate into the desired amino acids.
Another means of increasing the number of carbohydrate moieties on the breast cancer polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g., in WO 87/05330, and in Aplin &
Wriston, CRC Crit. Rev. Biochem., pp. 259-306 (1981).
Removal of carbohydrate moieties present on the breast cancer polypeptide may be accomplished chemically or enzymatically or by mutational substitution of codons encoding for amino acid residues that serve as targets for glycosylation.
Chemical deglycosylation techniques are known in the art and described, for instance, by Hakimuddin, et al., Arch. Biochem. Biophys., 259:52 (1987) and by Edge et al., Ahal.
Biochem., 118:131 (1981). Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo-and exo-glycosidases as described by Thotakura et al., Meth.
Eyazymol., 138:350 (1987).
Another type of covalent modification of breast cancer comprises linking the breast cancer polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Patent Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.
Breast cancer polypeptides of the present invention may also be modified in a way to form chimeric molecules comprising a breast cancer polypeptide fused to another, heterologous polypeptide or amino acid sequence. In one embodiment, such a chimeric molecule comprises a fusion of a breast cancer polypeptide with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind. The epitope tag is generally placed at the amino-or carboxyl-terminus of the breast cancer polypeptide. The presence of such epitope-tagged forms of a breast cancer polypeptide can be detected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the breast cancer polypeptide to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag. In an alternative embodiment, the chimeric molecule may comprise a fusion of a breast cancer polypeptide with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule, such a fusion could be to the Fc region of an IgG molecule.
Various tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags;
HIS6 and metal chelation tags, the flu HA tag polypeptide and its antibody 12CA5 (Field et al., Mol. Cell. Biol. 8:2159-2165 (1988)); the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto (Evan et al., Molecular and Cellular Biology 5:3610-3616 (1985));
and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody (Paborsky et al., Protein Engineering 3(6):547-553 (1990)). Other tag polypeptides include the Flag-peptide (Hopp et al., BioTechraology 6:1204-1210 (1988)); the KT3 epitope peptide (Martin et al., Science 255:192-194 (1992)); tubulin epitope peptide (Skinner et al., J. Biol.
Chem.
266:15163-15166 (1991)); and the T7 gene 10 protein peptide tag (Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. TISA 87:6393-6397 (1990)).
Also included are other breast cancer proteins of the breast cancer family, and breast cancer proteins from other organisms, which are cloned and expressed as outlined below. Thus, probe or degenerate polymerase chain reaction (PCR) primer sequences may be used to find other related breast cancer proteins from humans or other organisms. As will be appreciated by those in the art, particularly useful probe and/or PCR primer sequences include the unique areas of the breast cancer nucleic acid sequence. As is generally known in the art, preferred PCR primers are from about 15 to about 35 nucleotides in length, with from about 20 to about 30 being preferred, and may contain inosine as needed. The conditions for the PCR reaction are well known in the art (e.g., Innis, PCR Protocols, supra).
Antibodies to breast cancer proteins In a preferred embodiment, when the breast cancer protein is to be used to generate antibodies, e.g., for immunotherapy or immunodiagnosis, the breast cancer protein should share at least one epitope or determinant with the full length protein.
By "epitope" or "determinant" herein is typically meant a portion of a protein which will generate and/or bind an antibody or T-cell receptor in the context of MHC. Thus, in most instances, antibodies made to a smaller breast cancer protein will be able to bind to the full-length protein, particularly linear epitopes. In a preferred embodiment, the epitope is unique; that is, antibodies generated to a unique epitope show little or no cross-reactivity.
Methods of preparing polyclonal antibodies are known to the skilled artisan (e.g., Coligan, supra; and Harlow & Lane, supra). Polyclonal antibodies can be raised in a mammal, e.g., by one or more injections of an immunizing agent and, if desired, an adjuvant.
Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. The immunizing agent may include a protein encoded by a nucleic acid of the figures or fragment thereof or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants which may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The innnunization protocol may be selected by one skilled in the art without undue experimentation.
The antibodies may, alternatively, be monoclonal antibodies. Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler &
Milstein, Nature 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro. The immunizing agent will typically include a polypeptide encoded by a nucleic acid of Tables 1-25 or fragment thereof, or a fusion protein thereof. Generally, either peripheral blood lymphocytes ("PBLs") are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (coding, Monoclonal Antibodies: Principles arid Practice, pp. 59-103 (1986)). Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ("HAT
medium"), which substances prevent the growth of HGPRT-deficient cells.
In one embodiment, the antibodies are bispecific antibodies. Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens or that have binding specificities for two epitopes on the same antigen. In one embodiment, one of the binding specificities is for a protein encoded by a nucleic acid Tables 1-25 or a fragment thereof, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit, preferably one that is tumor specific. Alternatively, tetramer-type technology may create multivalent reagents.
In a preferred embodiment, the antibodies to breast cancer protein are capable of reducing or eliminating a biological function of a breast cancer protein, as is described below. That is, the addition of anti-breast cancer protein antibodies (either polyclonal or preferably monoclonal) to breast cancer tissue (or cells containing breast cancer) may reduce or eliminate the breast cancer. Generally, at least a 25% decrease in activity, growth, size or the like is preferred, with at least about 50% being particularly preferred and about a 95-100% decrease being especially preferred.
In a preferred embodiment the antibodies to the breast cancer proteins are humanized antibodies (e.g., Xenerex Biosciences, Mederex, Inc., Abgenix, Inc., Protein Design Labs,Inc.) Humanized forms of non-human (e.g., marine) antibodies are chimeric molecules of immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR
of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework (FR) regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., Nature 321:522-525 (1986); Riechmann et al., Natune 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992)).
Humanization can be essentially performed following the method of Winter and co-workers (Jones et al., NatuYe 321:522-525 (1986); Riechmann et al., Nature 332:323-327 (1988);
Verhoeyen et al., Science 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such humanized antibodies are chimeric antibodies (U.S. Patent No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species.
Human antibodies can also be produced using various techniques known in the art, including phage display libraries (Hoogenboom & Winter, J. Mol. Biol.
227:381 (1991);
Marks et al., J. Mol. Biol. 222:581 (1991)). The techniques of Cole et al. and Boerner et al.
are also available for the preparation of human monoclonal antibodies (Cole et al., Monoclonal Antibodies arad Cancer They~apy, p. 77 (1985) and Boerner et al., J. Immunol.
147(1):86-95 (1991)). Similarly, human antibodies can be made by introducing of human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire.
This approach is described, e.g., in U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825;
5,625,126; 5,633,425;
5,661,016, and in the following scientific publications: Marks et al., BiolTechnology 10:779-783 (1992); Lonberg et al., Nature 368:856-859 (1994); Morrison, Nature 368:812-13 (1994); Fishwild et al., Nature Biotechnology 14:845-51 (1996); Neuberger, Nature Biotechnology 14:826 (1996); Lonberg & Huszar, Intern. Rev. Immunol. 13:65-93 (1995).
By immunotherapy is meant treatment of breast cancer with an antibody raised against breast cancer proteins. As used herein, immunotherapy can be passive or active.
Passive immunotherapy as defined herein is the passive transfer of antibody to a recipient (patient). Active immunization is the induction of antibody and/or T-cell responses in a recipient (patient). Induction of an immune response is the result of providing the recipient with an antigen to which antibodies are raised. As appreciated by one of ordinary skill in the art, the antigen may be provided by injecting a polypeptide against which antibodies are desired to be raised into a recipient, or contacting the recipient with a nucleic acid capable of 1 S expressing the antigen and under conditions for expression of the antigen, leading to an immune response.
In a preferred embodiment the breast cancer proteins against which antibodies are raised are secreted proteins as described above. Without being bound by theory, antibodies used for treatment, bind and prevent the secreted protein from binding to its receptor, thereby inactivating the secreted breast cancer protein.
In another preferred embodiment, the breast cancer protein to which antibodies are raised is a transmembrane protein. Without being bound by theory, antibodies used for treatment, bind the extracellular domain of the breast cancer protein and prevent it from binding to other proteins, such as circulating ligands or cell-associated molecules. The antibody may cause down-regulation of the transmembrane breast cancer protein.
As will be appreciated by one of ordinary skill in the art, the antibody may be a competitive, non-competitive or uncompetitive inhibitor of protein binding to the extracellular domain of the breast cancer protein. The antibody is also an antagonist of the breast cancer protein.
Further, the antibody prevents activation of the transmembrane breast cancer protein. In one aspect, when the antibody prevents the binding of other molecules to the breast cancer protein, the antibody prevents growth of the cell. The antibody may also be used to target or sensitize the cell to cytotoxic agents, including, but not limited to TNF-a, TNF-Vii, IL-1, INF-y and IL-2, or chemotherapeutic agents including SFU, vinblastine, actinomycin D, cisplatin, methotrexate, and the like. In some instances the antibody belongs to a sub-type that activates serum complement when complexed with the transmembrane protein thereby mediating cytotoxicity or antigen-dependent cytotoxicity (ADCC). Thus, breast cancer is treated by administering to a patient antibodies directed against the transmembrane breast cancer protein. Antibody-labeling may activate a co-toxin, localize a toxin payload, or otherwise provide means to locally ablate cells.
In another preferred embodiment, the antibody is conjugated to an effector moiety. The effector moiety can be any number of molecules, including labelling moieties such as radioactive labels or fluorescent labels, or can be a therapeutic moiety. In one aspect the therapeutic moiety is a small molecule that modulates the activity of the breast cancer protein. In another aspect the therapeutic moiety modulates the activity of molecules associated with or in close proximity to the breast cancer protein. The therapeutic moiety may inhibit enzymatic activity such as protease or collagenase or protein kinase activity associated with breast cancer.
In a preferred embodiment, the therapeutic moiety can also be a cytotoxic agent. In this method, targeting the cytotoxic agent to breast cancer tissue or cells, results in a reduction in the number of afflicted cells, thereby reducing symptoms associated with breast cancer. Cytotoxic agents are numerous and varied and include, but are not limited to, cytotoxic drugs or toxins or active fragments of such toxins. Suitable toxins and their corresponding fragments include diphtheria A chain, exotoxin A chain, ricin A
chain, abrin A
chain, curcin, crotin, phenomycin, enomycin and the like. Cytotoxic agents also include radiochemicals made by conjugating radioisotopes to antibodies raised against breast cancer proteins, or binding of a radionuclide to a chelating agent that has been covalently attached to the antibody. Targeting the therapeutic moiety to transmembrane breast cancer proteins not only serves to increase the local concentration of therapeutic moiety in the breast cancer afflicted area, but also serves to reduce deleterious side effects that may be associated with the therapeutic moiety.

In another preferred embodiment, the breast cancer protein against which the antibodies are raised is an intracellular protein. In this case, the antibody may be conjugated to a protein which facilitates entry into the cell. In one case, the antibody enters the cell by endocytosis. In another embodiment, a nucleic acid encoding the antibody is administered to the individual or cell. Moreover, wherein the breast cancer protein can be targeted within a cell, i.e., the nucleus, an antibody thereto contains a signal for that target localization, i.e., a nuclear localization signal.
The breast cancer antibodies of the invention specifically bind to breast cancer proteins. By "specifically bind" herein is meant that the antibodies bind to the protein with a Kd of at least about 0.1 mM, more usually at least about 1 wM, preferably at least about 0.1 p,M or better, and most preferably, 0.01 p.M or better. Selectivity of binding is also important.
Detection of breast cancer sequence for diagnostic and therapeutic applications In one aspect, the RNA expression levels of genes are determined for different cellular states in the breast cancer phenotype. Expression levels of genes in normal tissue (i.e., not undergoing breast cancer) and in breast cancer tissue (and in some cases, for varying severities of breast cancer that relate to prognosis, as outlined below) are evaluated to provide expression profiles. An expression profile of a particular cell state or point of development is essentially a "fingerprint" of the state. While two states may have any particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is reflective of the state of the cell. By comparing expression profiles of cells in different states, information regarding which genes are important (including both up- and down-regulation of genes) in each of these states is obtained. Then, diagnosis may be performed or confirmed to determine whether a tissue sample has the gene expression profile of normal or cancerous tissue. This will provide for molecular diagnosis of related conditions.
"Differential expression," or grammatical equivalents as used herein, refers to qualitative or quantitative differences in the temporal and/or cellular gene expression patterns within and among cells and tissue. Thus, a differentially expressed gene can qualitatively have its expression altered, including an activation or inactivation, in, e.g., normal versus breast cancer tissue. Genes may be turned on or turned off in a particular state, relative to another state thus permitting comparison of two or more states. A
qualitatively regulated gene will exhibit an expression pattern within a state or cell type which is detectable by standard techniques. Some genes will be expressed in one state or cell type, but not in both. Alternatively, the difference in expression may be quantitative, e.g., in that expression is increased or decreased; i.e., gene expression is either upregulated, resulting in an increased amount of transcript, or downregulated, resulting in a decreased amount of transcript. The degree to which expression differs need only be large enough to quantify via standard characterization techniques as outlined below, such as by use of Affymetrix GeneChipTM expression arrays, Lockhart, Nature Biotechrzology 14:1675-1680 (1996), hereby expressly incorporated by reference. Other techniques include, but are not limited to, quantitative reverse transcriptase PCR, northern analysis and RNase protection. As outlined above, preferably the change in expression (i.e., upregulation or downregulation) is at least about 50%, more preferably at least about 100%, more preferably at least about 150%, more preferably at least about 200%, with from 300 to at least 1000% being especially preferred.
Evaluation may be at the gene transcript, or the protein level. The amount of gene expression may be monitored using nucleic acid probes to the DNA or RNA
equivalent of the gene transcript, and the quantification of gene expression levels, or, alternatively, the final gene product itself (protein) can be monitored, e.g., with antibodies to the breast cancer protein and standard immunoassays (ELISAs, etc.) or other techniques, including mass spectroscopy assays, 2D gel electrophoresis assays, etc. Proteins corresponding to breast cancer genes, i.e., those identified as being important in a breast cancer phenotype, can be evaluated in a breast cancer diagnostic test.
In a preferred embodiment, gene expression monitoring is performed simultaneously on a number of genes. Multiple protein expression monitoring can be performed as well. Similarly, these assays may be performed on an individual basis as well.
In this embodiment, the breast cancer nucleic acid probes are attached to biochips as outlined herein for the detection and quantification of breast cancer sequences in WO 02/059377 'CT/US02/02242 a particular cell. The assays are further described below in the example. PCR
techniques can be used to provide greater sensitivity.
In a preferred embodiment nucleic acids encoding the breast cancer protein are detected. Although DNA or RNA encoding the breast cancer protein may be detected, of particular interest are methods wherein an mRNA encoding a breast cancer protein is detected. Probes to detect mRNA can be a nucleotide/deoxynucleotide probe that is complementary to and hybridizes with the mRNA and includes, but is not limited to, oligonucleotides, cDNA or RNA. Probes also should contain a detectable label, as defined herein. In one method the mRNA is detected after immobilizing the nucleic acid to be examined on a solid support such as nylon membranes and hybridizing the probe with the sample. Following washing to remove the non-specifically bound probe, the label is detected. In another method detection of the mRNA is performed in situ. In this method permeabilized cells or tissue samples are contacted with a detectably labeled nucleic acid probe for sufficient time to allow the probe to hybridize with the target mRNA. Following washing to remove the non-specifically bound probe, the label is detected. For example a digoxygenin labeled riboprobe (RNA probe) that is complementary to the mRNA
encoding a breast cancer protein is detected by binding the digoxygenin with an anti-digoxygenin secondary antibody and developed with nitro blue tetrazolium and 5-bromo-4-chloro-3-indoyl phosphate.
In a preferred embodiment, various proteins from the three classes of proteins as described herein (secreted, transmembrane or intracellular proteins) are used in diagnostic assays. The breast cancer proteins, antibodies, nucleic acids, modified proteins and cells containing breast cancer sequences are used in diagnostic assays. This can be performed on an individual gene or corresponding polypeptide level. In a preferred embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes and/or corresponding polypeptides.
As described and defined herein, breast cancer proteins, including intracellular, transmembrane or secreted proteins, find use as marleers of breast cancer.
Detection of these proteins in putative breast cancer tissue allows for detection or diagnosis of breast cancer. In one embodiment, antibodies are used to detect breast cancer proteins. A
preferred method separates proteins from a sample by electrophoresis on a gel (typically a denaturing and reducing protein gel, but may be another type of gel, including isoelectric focusing gels and the like). Following separation of proteins, the breast cancer protein is detected, e.g., by immunoblotting with antibodies raised against the breast cancer protein.
Methods of immunoblotting are well known to those of ordinary skill in the art.
In another preferred method, antibodies to the breast cancer protein find use in iu situ imaging techniques, e.g., in histology (e.g., Methods in Cell Biology:
Antibodies ira Cell Biology, volume 37 (Asai, ed. 1993)). In this method cells are contacted with from one to many antibodies to the breast cancer protein(s). Following washing to remove non-specific antibody binding, the presence of the antibody or antibodies is detected. In one embodiment the antibody is detected by incubating with a secondary antibody that contains a detectable label. In another method the primary antibody to the breast cancer proteins) contains a detectable label, e.g. an enzyme marker that can act on a substrate. In another preferred embodiment each one of multiple primary antibodies contains a distinct and detectable label. This method finds particular use in simultaneous screening for a plurality of breast cancer proteins. As will be appreciated by one of ordinary skill in the art, many other histological imaging techniques are also provided by the invention.
In a preferred embodiment the label is detected in a fluorometer which has the ability to detect and distinguish emissions of different wavelengths. In addition, a fluorescence activated cell sorter (FACS) can be used in the method.
In another preferred embodiment, antibodies find use in diagnosing breast cancer from blood, serum, plasma, stool, and other samples. Such samples, therefore, are useful as samples to be probed or tested for the presence of breast cancer proteins.
Antibodies can be used to detect a breast cancer protein by previously described immunoassay techniques including ELISA, immunoblotting (western blotting), immunoprecipitation, BIACORE technology and the like. Conversely, the presence of antibodies may indicate an immune response against an endogenous breast cancer protein.
In a preferred embodiment, in situ hybridization of labeled breast cancer nucleic acid probes to tissue arrays is done. For example, arrays of tissue samples, including breast cancer tissue and/or normal tissue, are made. Ifz situ hybridization (see, e.g., Ausubel, supf°a) is then performed. When comparing the fingerprints between an individual and a standard, the skilled artisan can make a diagnosis, a prognosis, or a prediction based on the findings. It is further understood that the genes which indicate the diagnosis may differ from those which indicate the prognosis and molecular profiling of the condition of the cells may lead to distinctions between responsive or refractory conditions or may be predictive of -outcomes.
In a preferred embodiment, the breast cancer proteins, antibodies, nucleic acids, modified proteins and cells containing breast cancer sequences are used in prognosis assays. As above, gene expression profiles can be generated that correlate to breast cancer, in terms of long term prognosis. Again, this may be done on either a protein or gene level, with the use of genes being preferred. As above, breast cancer probes may be attached to biochips for the detection and quantification of breast cancer sequences in a tissue or patient.
The assays proceed as outlined above for diagnosis. PCR method may provide more sensitive and accurate quantification.
Assays for therapeutic compounds In a preferred embodiment members of the proteins, nucleic acids, and antibodies as described herein are used in drug screening assays. The breast cancer proteins, antibodies, nucleic acids, modified proteins and cells containing breast cancer sequences are used in drug screening assays or by evaluating the effect of drug candidates on a "gene expression profile" or expression profile of polypeptides. In a preferred embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after treatment with a candidate agent (e.g., Zlokarnik, et al., Science 279:84-8 (1998); Heid, Genofrae Res 6:986-94, 1996).
In a preferred embodiment, the breast cancer proteins, antibodies, nucleic acids, modified proteins and cells containing the native or modified breast cancer proteins are used in screening assays. That is, the present invention provides novel methods for screening for compositions which modulate the breast cancer phenotype or an identified physiological function of a breast cancer protein. As above, this can be done on an individual gene level or by evaluating the effect of drug candidates on a "gene expression profile". In a preferred embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after treatment with a candidate agent, see Zlokarnik, supra.
Having identified the differentially expressed genes herein, a variety of assays may be executed. In a preferred embodiment, assays may be run on an individual gene or protein level. That is, having identified a particular gene as up regulated in breast cancer, test compounds can be screened for the ability to modulate gene expression or for binding to the breast cancer protein. "Modulation" thus includes both an increase and a decrease in gene expression. The preferred amount of modulation will depend on the original change of the gene expression in normal versus tissue undergoing breast cancer, with changes of at least 10%, preferably 50%, more preferably 100-300%, and in some embodiments 300-1000% or greater. Thus, if a gene exhibits a 4-fold increase in breast cancer tissue compared to normal tissue, a decrease of about four-fold is often desired; similarly, a 10-fold decrease in breast cancer tissue compared to normal tissue often provides a target value of a 10-fold increase in expression to be induced by the test compound.
The amount of gene expression may be monitored using nucleic acid probes and the quantification of gene expression levels, or, alternatively, the gene product itself can be monitored, e.g., through the use of antibodies to the breast cancer protein and standard immunoassays. Proteomics and separation techniques may also allow quantification of expression.
In a preferred embodiment, gene expression or protein monitoring of a number of entities, i.e., an expression profile, is monitored simultaneously. Such profiles will typically involve a plurality of those entities described herein..
In this embodiment, the breast cancer nucleic acid probes are attached to biochips as outlined herein for the detection and quantification of breast cancer sequences in a particular cell. Alternatively, PCR may be used. Thus, a series, e.g., of microtiter plate, may be used with dispensed primers in desired wells. A PCR reaction can then be performed and analyzed for each well.

Expression monitoring can be performed to identify compounds that modify the expression of one or more breast cancer-associated sequences, e.g., a polynucleotide sequence set out inTable 17. Generally, in a preferred embodiment, a test modulator is added to the cells prior to analysis. Moreover, screens are also provided to identify agents that modulate breast cancer, modulate breast cancer proteins, bind to a breast cancer protein, or interfere with the binding of a breast cancer protein and an antibody or other binding partner.
The term "test compound" or "drug candidate" or "modulator" or grammatical equivalents as used herein describes any molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., to be tested for the capacity to directly or indirectly alter the breast cancer phenotype or the expression of a breast cancer sequence, e.g., a nucleic acid or protein sequence. In preferred embodiments, modulators alter expression profiles, or expression profile nucleic acids or proteins provided herein. In one embodiment, the modulator suppresses a breast cancer phenotype, e.g. to a normal tissue fingerprint. In another embodiment, a modulator induced a breast cancer phenotype.
Generally, a plurality of assay mixtures axe run in parallel with different agent concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection.
Drug candidates encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 100 and less than about 2,500 daltons. Preferred small molecules are less than 2000, or less than 1500 or less than 1000 or less than S00 D. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups.
Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.
Particularly preferred are peptides.

In one aspect, a modulator will neutralize the effect of a breast cancer protein.
By "neutralize" is meant that activity of a protein is inhibited or blocked and the consequent effect on the cell.
In certain embodiments, combinatorial libraries of potential modulators will be screened for an ability to bind to a breast cancer polypeptide or to modulate activity.
Conventionally, new chemical entities with useful properties are generated by identifying a chemical compound (called a "lead compound") with some desirable property or activity, e.g., inhibiting activity, creating variants of the lead compound, and evaluating.the property and activity of those variant compounds. Often, high throughput screening (HTS) methods are employed for such an analysis.
In one preferred embodiment, high throughput screening methods involve providing a library containing a large number of potential therapeutic compounds (candidate compounds). Such "combinatorial chemical libraries" are then screened in one or more assays to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional "lead compounds" or can themselves be used as potential or actual therapeutics.
A combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical "building blocks" such as reagents. For example, a linear combinatorial chemical library, such as a polypeptide (e.g., mutein) library, is formed by combining a set of chemical building blocks called amino acids in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Millions of chemical compounds can be synthesized through such combinatorial mixing of chemical building blocks (Gallop et al., J. Med. Chem. 37(9):1233-1251 (1994)).
Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Patent No. 5,010,175, Furka, Pept. Prot.
Res. 37:487-493 (1991), Houghton et al., Natuf~e, 354:84-88 (1991)), peptoids (PCT Publication No WO
91/19735), encoded peptides (PCT Publication WO 93/20242), random bio-oligomers (PCT
Publication WO 92/00091), benzodiazepines (U.S. Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., Pf°oc. Nat.
Acad. Sci. USA
90:6909-6913 (1993)), vinylogous polypeptides (Hagihara et al., J. Amer. Chem.
Soc.
114:6568 (1992)), nonpeptidal peptidomimetics with a Beta-D-Glucose scaffolding (Hirschmann et al., J. Amer. Chena. Soc. 114:9217-9218 (1992)), analogous organic syntheses of small compound libraries (Chen et al., J. Amer. Clzern. Soc. 116:2661 (1994)), oligocarbamates (Cho, et al., Science 261:1303 (1993)), and/or peptidyl phosphonates (Campbell et al., J. Ong. Chem. 59:658 (1994)). See, genet~ally, Gordon et al., J. Med. Chem.
37:1385 (1994), nucleic acid libraries (see, e.g., Strategene, Corp.), peptide nucleic acid libraries (see, e.g., U.S. Patent 5,539,083), antibody libraries (see, e.g., Vaughn et al., Nature Biotechnology 14(3):309-314 (1996), and PCT/LTS96l10287), carbohydrate libraries (see, e.g., Liang et al., Science 274:1520-1522 (1996), and U.S. Patent No.
5,593,853), and small organic molecule libraries (see, e.g., benzodiazepines, Baum, C&EN, Jan 18, page 33 (1993);
isoprenoids, U.S. Patent No. 5,569,588; thiazolidinones and metathiazanones, U.S. Patent No.
5,549,974; pyrrolidines, U.S. Patent Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Patent No. 5,506,337; benzodiazepines, U.S. Patent No. 5,288,514; and the like).
Devices for the preparation of combinatorial libraries are commercially available (see, e.g., 357 MPS, 390 MPS, Advanced Chem Tech, Louisville KY, Symphony, Rainin, Woburn, MA, 433A Applied Biosystems, Foster City, CA, 9050 Plus, Millipore, Bedford, MA).
. A number of well known robotic systems have also been developed for solution phase chemistries. These systems include automated workstations like the automated synthesis apparatus developed by Takeda Chemical Industries, LTD.
(Osaka, Japan) and many robotic systems utilizing robotic arms (Zymate II, Zymark Corporation, Hopkinton, Mass.; Orca, Hewlett-Packard, Palo Alto, Calif.), which mimic the manual synthetic operations performed by a chemist. Any of the above devices are suitable for use with the present invention. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein will be apparent to persons skilled in the relevant art. In addition, numerous combinatorial libraries are themselves commercially available (see, e.g., ComGenex, Princeton, N.J., Asinex, Moscow, Ru, Tripos, Inc., St. Louis, MO, ChemStar, Ltd, Moscow, RU, 3D Pharmaceuticals, Exton, PA, Martek Biosciences, Columbia, MD, etc.).
The assays to identify modulators are amenable to high throughput screening.
Preferred assays thus detect enhancement or inhibition of breast cancer gene transcription, inhibition or enhancement of polypeptide expression, and inhibition or enhancement of polypeptide activity.
High throughput assays for the presence, absence, quantification, or other properties of particular nucleic acids or protein products are,well known to those of skill in the art. Similarly, binding assays and reporter gene assays are similarly well known. Thus, e.g., U.S. Patent No. 5,559,410 discloses high throughput screening methods for proteins, U.S. Patent No. 5,585,639 discloses high throughput screening methods for nucleic acid binding (i.e., in arrays), while U.S. Patent Nos. 5,576,220 and 5,541,061 disclose high throughput methods of screening for ligandlantibody binding.
In addition, high throughput screening systems are commercially available (see, e.g., Zymark Corp., Hopkinton, MA; Air Technical Industries, Mentor, OH;
Beckman Instruments, Inc. Fullerton, CA; Precision Systems, Inc., Natick, MA, etc.).
These systems typically automate entire procedures, including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detectors) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. The manufacturers of such systems provide detailed protocols for various high throughput systems. Thus, e.g., Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like.
In one embodiment, modulators are proteins, often naturally occurnng proteins or fragments of naturally occurring proteins. Thus, e.g., cellular extracts containing proteins, or random or directed digests of proteinaceous cellular extracts, may be used. In this way libraries of proteins may be made for screening in the methods of the invention.
Particularly preferred in this embodiment are libraries of bacterial, fungal, viral, and mammalian proteins, with the latter being preferred, and human proteins being especially preferred. Particularly useful test compound will be directed to the class of proteins to which the target belongs, e.g., substrates for enzymes or ligands and receptors.
In a preferred embodiment, modulators are peptides of from about 5 to about 30 amino acids, with from about 5 to about 20 amino acids being preferred, and from about 7 to about 15 being particularly preferred. The peptides may be digests of naturally occurring proteins as is outlined above, random peptides, or "biased" random peptides.
By "randomized" or grammatical equivalents herein is meant that each nucleic acid and peptide consists of essentially random nucleotides and amino acids, respectively.
Since generally these random peptides (or nucleic acids, discussed below) are chemically synthesized, they may incorporate any nucleotide or amino acid at any position. The synthetic process can be designed to generate randomized proteins or nucleic acids, to allow the formation of all or most of the possible combinations over the length of the sequence, thus forming 'a library of randomized candidate bioactive proteinaceous agents.
In one embodiment, the library is fully randomized, with no sequence preferences or constants at any position. In a preferred embodiment, the library is biased.
That is, some positions within the sequence are either held constant, or are selected from a limited number of possibilities. For example, in a preferred embodiment, the nucleotides or amino acid residues are randomized within a defined class, e.g., of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of nucleic acid binding domains, the creation of cysteines, for cross-linking, prolines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, etc., or to purines, etc.
Modulators of breast cancer can also be nucleic acids, as defined above.
As described above generally for proteins, nucleic acid modulating agents may be naturally occurnng nucleic acids, random nucleic acids, or "biased" random nucleic acids.
For example, digests of procaryotic or eucaryotic genomes may be used as is outlined above for proteins.
In a preferred embodiment, the candidate compounds are organic chemical moieties, a wide variety of which are available in the literature.

After the candidate agent has been added and the cells allowed to incubate for some period of time, the sample containing a target sequence to be analyzed is added to the biochip. If required, the target sequence is prepared using known techniques.
For example, the sample may be treated to lyse the cells, using known lysis buffers, electroporation, etc., with purification and/or amplification such as PCR performed as appropriate.
For example, an in vitro transcription with labels covalently attached to the nucleotides is performed.
Generally, the nucleic acids are labeled with biotin-FITC or PE, or with cy3 or cy5.
In a preferred embodiment, the target sequence is labeled with, e.g., a fluorescent, a chemilumine~cent, a chemical, or a radioactive signal, to provide a means of detecting the target sequence's specific binding to a probe. The label also can be an enzyme, such as, alkaline phosphatase or horseradish peroxidase, which when provided with an appropriate substrate produces a product that can be detected. Alternatively, the label can be a labeled compound or small molecule, such as an enzyme inhibitor, that binds but is not catalyzed or altered by the enzyme. The label also can be a moiety or compound, such as, an epitope tag or biotin which specifically binds to streptavidin. For the example of biotin, the streptavidin is labeled as described above, thereby, providing a detectable signal for the bound target sequence. Unbound labeled streptavidin is typically removed prior to analysis.
As will be appreciated by those in the art, these assays can be direct hybridization assays or can comprise "sandwich assays", which include the use of multiple probes, as is generally outlined in U.S. Patent Nos. 5,681,702, 5,597,909, 5,545,730, 5,594,117, 5,591,584, 5,571,670, 5,580,731, 5,571,670, 5,591,584, 5,624,802, 5,635,352, 5,594,118, 5,359,100, 5,124,246 and 5,681,697, all of which are hereby incorporated by reference. In this embodiment, in general, the target nucleic acid is prepared as outlined above, and then added to the biochip comprising a plurality of nucleic acid probes, under conditions that allow the formation of a hybridization complex.
A variety of hybridization conditions may be used in the present invention, including high, moderate and low stringency conditions as outlined above. The assays are generally run under stringency conditions which allows formation of the label probe hybridization complex only in the presence of target. Stringency can be controlled by altering a step parameter that is a thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt concentration, chaotropic salt concentration pH, organic solvent concentration, etc.
These parameters may also be used to control non-specific binding, as is generally outlined in U.S. Patent No. 5,681,697. Thus it may be desirable to perform certain steps at higher stringency conditions to reduce non-specific binding.
The reactions outlined herein may be accomplished in a variety of ways.
Components of the reaction may be added simultaneously, or sequentially, in different orders, with preferred embodiments outlined below. In addition, the reaction may include a variety of other reagents. These include salts, buffers, neutral proteins, e.g.
albumin, detergents, etc.
which may be used to facilitate optimal hybridization and detection, and/or reduce non-specific or background interactions. Reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may also be used as appropriate, depending on the sample preparation methods and purity of the target.
The assay data are analyzed to determine the expression levels, and changes in expression levels as between states, of individual genes, forming a gene expression profile.
Screens are performed to identify modulators of the breast cancer phenotype.
In one embodiment, screening is performed to identify modulators that can induce or suppress a particular expression profile, thus preferably generating the associated phenotype.
In another embodiment, e.g., for diagnostic applications, having identified differentially expressed genes important in a particular state, screens can be performed to identify modulators that alter expression of individual genes. In an another embodiment, screening is performed to identify modulators that alter a biological function of the expression product of a differentially expressed gene. Again, having identified the importance of a gene in a particular state, screens are performed to identify agents that bind and/or modulate the biological activity of the gene product.
In addition screens can be done for genes that are induced in response to a candidate agent. After identifying a modulator based upon its ability to suppress a breast cancer expression pattern leading to a normal expression pattern, or to modulate a single breast cancer gene expression profile so as to mimic the expression of the gene from normal tissue, a screen as described above can be performed to identify genes that are specifically modulated in response to the agent. Comparing expression profiles between normal tissue and agent treated breast cancer tissue reveals genes that are not expressed in normal tissue or breast cancer tissue, but are expressed in agent treated tissue. These agent-specific sequences can be identified and used by methods described herein for breast cancer genes or proteins.
In particular these sequences and the proteins they encode find use in marking or identifying agent treated cells. In addition, antibodies can be raised against the agent induced proteins and used to target novel therapeutics to the treated breast cancer tissue sample.
Thus, in one embodiment, a test compound is administered to a population of breast cancer cells, that have an associated breast cancer expression profile.
By "administration" or "contacting" herein is meant that the candidate agent is added to the cells in such a manner as to allow the agent to act upon the cell, whether by uptake and intracellular action, or by action at the cell surface. In some embodiments, nucleic acid encoding a proteinaceous candidate agent (i.e., a peptide) may be put into a viral construct such as an adenoviral or retroviral construct, and added to the cell, such that expression of the peptide agent is accomplished, e.g., PCT US97/01019. Regulatable gene therapy systems can also be used.
Once the test compound has been administered to the cells, the cells can be washed if desired and are allowed to incubate under preferably physiological conditions for some period of time. The cells are then harvested and a new gene expression profile is generated, as outlined herein.
Thus, e.g., breast cancer tissue may be screened for agents that modulate, e.g., induce or suppress the breast cancer phenotype. A change in at least one gene, preferably many, of the expression profile indicates that the agent has an effect on breast cancer activity.
By defining such a signature for the breast cancer phenotype, screens for new drugs that alter the phenotype can be devised. With this approach, the drug target need not be known and need not be represented in the original expression screening platform, nor does the level of transcript for the target protein need to change.
In a preferred embodiment, as outlined above, screens may be done on individual genes and gene products (proteins). That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of either the expression of the gene or the gene product itself can be done. The gene products of differentially expressed genes are sometimes referred to herein as "breast cancer proteins" or a "breast cancer modulatory protein". The breast cancer modulatory protein may be a fragment, or alternatively, be the full length protein to the fragment encoded by the nucleic acids of the Tables. Preferably, the breast cancer modulatory protein is a fragment. In a preferred embodiment, the breast cancer amino acid sequence which is used to determine sequence identity or similarity is encoded by a nucleic acid of Table 25. In another embodiment, the sequences are naturally occurnng allelic variants of a protein encoded by a nucleic acid of Table 25. In another embodiment, the sequences are sequence variants as further described herein.
Preferably, the breast cancer modulatory protein is a fragment of approximately 14 to 24 amino acids long. More preferably the fragment is a soluble fragment. Preferably, the fragment includes a non-transmembrane region. In a preferred embodiment, the fragment has an N-terminal Cys to aid in solubility. In one embodiment, the C-terminus of the fragment is kept as a free acid and the N-terminus is a free amine to aid in coupling, i.e., to cysteine.
In one embodiment the breast cancer proteins are conjugated to an immunogenic agent as discussed herein. In one embodiment the breast cancer protein is conjugated to BSA.
Measurements of breast cancer polypeptide activity, or of breast cancer or the breast cancer phenotype can be performed using a variety of assays. For example, the effects of the test compounds upon the function of the breast cancer polypeptides can be measured by examining parameters described above. A suitable physiological change that affects activity can be used to assess the influence of a test compound on the polypeptides of this invention. When the functional consequences are determined using intact cells or animals, one can also measure a variety of effects such as, in the case of breast cancer associated with tumors, tumor growth, tumor metastasis, neovascularization, hormone release, transcriptional changes to both known and uncharacterized genetic markers (e.g., northern blots), changes in cell metabolism such as cell growth or pH changes, and changes in intracellular second messengers such as cGMP. In the assays of the invention, mammalian breast cancer polypeptide is typically used, e.g., mouse, preferably human.
Assays to identify compounds with modulating activity can be performed in vitro. For example, a breast cancer polypeptide is first contacted with a potential modulator and incubated for a suitable amount of time, e.g., from 0.5 to 48 hours. In one embodiment, the breast cancer polypeptide levels are determined ih vitro by measuring the level of protein or mRNA. The level of protein is measured using immunoassays such as western blotting, ELISA and the like with an antibody that selectively binds to the breast cancer polypeptide or a fragment thereof. For measurement of mRNA, amplification, e.g., using PCR, LCR, or hybridization assays, e.g., northern hybridization, RNAse protection, dot blotting, are preferred. The level of protein or mRNA is detected using directly or indirectly labeled detection agents, e.g., fluorescently or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein.
Alternatively, a reporter gene system can be devised using the breast cancer protein promoter operably linked to a reporter gene such as luciferase, green fluorescent protein, CAT, or (3-gal. The reporter construct is typically transfected into a cell. After treatment with a potential modulator, the amount of reporter gene transcription, translation, or activity is measured according to standard techniques known to those of skill in the art.
In a preferred embodiment, as outlined above, screens may be done on individual genes and gene products (proteins). That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of the expression of the gene or the gene product itself can be done. The gene products of differentially expressed genes are sometimes referred to herein as "breast cancer proteins."
The breast cancer protein may be a fragment, or alternatively, be the full length protein to a fragment shown herein.
In one embodiment, screening for modulators of expression of specific genes is performed. Typically, the expression of only one or a few genes are evaluated. In another embodiment, screens are designed to first find compounds that bind to differentially expressed proteins. These compounds are then evaluated for the ability to modulate differentially expressed activity. Moreover, once initial candidate compounds are identified, variants can be further screened to better evaluate structure activity relationships.
In a preferred embodiment, binding assays are done. In general, purified or isolated gene product is used; that is, the gene products of one or more differentially expressed nucleic acids are made. For example, antibodies are generated to the protein gene products, and standard immunoassays are run to determine the amount of protein present.
Alternatively, cells comprising the breast cancer proteins can be used in the assays.
Thus, in a preferred embodiment, the methods comprise combining a breast cancer protein and a candidate compound, and determining the binding of the compound to the breast cancer protein. Preferred embodiments utilize the human breast cancer protein, although other mammalian proteins may also be used, e.g. for the development of animal models of human disease. In some embodiments, as outlined herein, variant or derivative breast cancer proteins may be used.
Generally, in a preferred embodiment of the methods herein, the breast cancer protein or the candidate agent is non-diffusably bound to an insoluble support having isolated sample receiving areas (e.g. a microtiter plate, an array, etc.). The insoluble supports may be made of any composition to which the compositions can be bound, is readily separated from soluble material, and is otherwise compatible with the overall method of screening. The surface of such supports may be solid or porous and of any convenient shape.
Examples of suitable insoluble supports include microtiter plates, arrays, membranes and beads. These are typically made of glass, plastic (e.g., polystyrene), polysaccharides, nylon or nitrocellulose, teflonTM, etc. Microtiter plates and arrays are especially convenient because a large number of assays can be carned out simultaneously, using small amounts of reagents and samples.
The particular manner of binding of the composition is not crucial so long as it is compatible with the reagents and overall methods of the invention, maintains the activity of the composition and is nondiffusable. Preferred methods of binding include the use of antibodies (which do not sterically block either the ligand binding site or activation sequence when the protein is bound to the support), direct binding to "sticky" or ionic supports, chemical crosslinking, the synthesis of the protein or agent on the surface, etc.
Following binding of the protein or agent, excess unbound material is removed by washing. The sample receiving areas may then be blocked through incubation with bovine serum albumin (BSA), casein or other innocuous protein or other moiety.
In a preferred embodiment, the breast cancer protein is bound to the support, and a test compound is added to the assay. Alternatively, the candidate agent is bound to the support and the breast cancer protein is added. Novel binding agents include specific antibodies, non-natural binding agents identified in screens of chemical libraries, peptide analogs, etc. Of particular interest are screening assays for agents that have a low toxicity for human cells. A wide variety of assays may be used for this purpose, including labeled in vitro protein-protein binding assays, electrophoretic mobility shift assays, immunoassays for protein binding, functional assays (phosphorylation assays, etc.) and the like.
The determination of the binding of the test modulating compound to the breast cancer protein may be done in a number of ways. In a preferred embodiment, the compound is labeled, and binding determined directly, e.g., by attaching all or a portion of the breast cancer protein to a solid support, adding a labeled candidate agent (e.g., a fluorescent label), washing off excess reagent, and determining whether the label is present on the solid support. Various blocking and washing steps may be utilized as appropriate.
In some embodiments, only one of the components is labeled, e.g., the proteins (or proteinaceous candidate compounds) can be labeled. Alternatively, more than one component can be labeled with different labels, e.g., lasl for the proteins and a fluorophor for the compound. Proximity reagents, e.g., quenching or energy transfer reagents are also useful.
In one embodiment, the binding of the test compound is determined by competitive binding assay. The competitor is a binding moiety known to bind to the target molecule (i.e., a breast cancer protein), such as an antibody, peptide, binding partner, ligand, etc. Under certain circumstances, there may be competitive binding between the compound and the binding moiety, with the binding moiety displacing the compound. In one embodiment, the test compound is labeled. Either the compound, or the competitor, or both, is added first to the protein for a time sufficient to allow binding, if present. Incubations may be performed at a temperature which facilitates optimal activity, typically between 4 and 40°C. Incubation periods are typically optimized, e.g., to facilitate rapid high throughput screening. Typically between 0.1 and 1 hour will be sufficient. Excess reagent is generally removed or washed away. The second component is then added, and the presence or absence of the labeled component is followed, to indicate binding.
In a preferred embodiment, the competitor is added first, followed by the test compound. Displacement of the competitor is an indication that the test compound is binding to the breast cancer protein and thus is capable of binding to, and potentially modulating, the activity of the breast cancer protein. In this embodiment, either component can be labeled.
Thus, e.g., if the competitor is labeled, the presence of label in the wash solution indicates displacement by the agent. Alternatively, if the test compound is labeled, the presence of the label on the support indicates displacement.
In an alternative embodiment, the test compound is added first, with incubation and washing, followed by the competitor. The absence of binding by the competitor may indicate that the test compound is bound to the breast cancer protein with a higher affinity. Thus, if the test compound is labeled, the presence of the label on the support, coupled with a lack of competitor binding, may indicate that the test compound is capable of binding to the breast cancer protein.
In a preferred embodiment, the methods comprise differential screening to identity agents that are capable of modulating the activity of the breast cancer proteins. In this embodiment, the methods comprise combining a breast cancer protein and a competitor in a first sample. A second sample comprises a test compound, a breast cancer protein, and a competitor. The binding of the competitor is determined for both samples, and a change, or difference in binding between the two samples indicates the presence of an agent capable of binding to the breast cancer protein and potentially modulating its activity.
That is, if the binding of the competitor is different in the second sample relative to the first sample, the agent is capable of binding to the breast cancer protein.
Alternatively, differential screening is used to identify drug candidates that bind to the native breast cancer protein, but cannot bind to modiFed breast cancer proteins.
The structure of the breast cancer protein may be modeled, and used in rational drug design to synthesize agents that interact with that site. Drug candidates that affect the activity of a breast cancer protein are also identified by screening drugs for the ability to either enhance or reduce the activity of the protein.
Positive controls and negative controls may be used in the assays. Preferably control and test samples are performed in at least triplicate to obtain statistically significant results. Incubation of all samples is for a time sufficient for the binding of the agent to the protein. Following incubation, samples are washed free of non-specifically bound material and the amount of bound, generally labeled agent determined. For example, where a radiolabel is employed, the samples may be counted in a scintillation counter to determine the amount of bound compound.
A variety of other reagents may be included in the screening assays. These include reagents like salts, neutral proteins, e.g. albumin, detergents, etc.
which may be used to facilitate optimal protein-protein binding and/or reduce non-specific or background interactions. Also reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may be used. The mixture of components may be added in an order that provides for the requisite binding.
In a preferred embodiment, the invention provides methods for screening for a compound capable of modulating the activity of a breast cancer protein. The methods comprise adding a test compound, as defined above, to a cell comprising breast cancer proteins. Preferred cell types include almost any cell. The cells contain a recombinant nucleic acid that encodes a breast cancer protein. In a preferred embodiment, a library of candidate agents are tested on a plurality of cells.
In one aspect, the assays are evaluated in the presence or absence or previous or subsequent exposure of physiological signals, e.g. hormones, antibodies, peptides, antigens, cytokines, growth factors, action potentials, pharmacological agents including chemotherapeutics, radiation, carcinogenics, or other cells (i.e. cell-cell contacts). In another example, the determinations are determined at different stages of the cell cycle process.
In this way, compounds that modulate breast cancer agents are identified.
Compounds with pharmacological activity are able to enhance or interfere with the activity of the breast cancer protein. Once identified, similar structures are evaluated to identify critical structural feature of the compound.

In one embodiment, a method of inhibiting breast cancer cell division is provided. The method comprises administration of a breast cancer inhibitor. In another embodiment, a method of inhibiting breast cancer is provided. The method comprises administration of a breast cancer inhibitor. In a further embodiment, methods of treating cells or individuals with breast cancer are provided. The method comprises administration of a breast cancer inhibitor.
In one embodiment, a breast cancer inhibitor is an antibody as discussed above. In another embodiment, the breast cancer inhibitor is an antisense molecule.
A variety of cell growth, proliferation, and metastasis assays are known to those of skill in the art, as described below.
Soft agar growth or colony formation in suspehsi~h Normal cells require a solid substrate to attach and grow. When the cells are transformed, they lose this phenotype and grow detached from the substrate.
For example, transformed cells can grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft agar. The transformed cells, when transfected with tumor suppressor genes, regenerate normal phenotype and require a solid substrate to attach and grow. Soft agar growth or colony formation in suspension assays can be used to identify modulators of breast cancer sequences, which when expressed in host cells, inhibit abnormal cellular proliferation and transformation. A therapeutic compound would reduce or eliminate the host cells' ability to grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft.
Techniques for soft agar growth or colony formation in suspension assays are described in Freshney, Culture ofAhimal Cells a Manual ofBasic Techfzique (3ra ed., 1994), herein incorporated by reference. See also, the methods section of Garkavtsev et al. (1996), supra, herein incorporated by reference.
Contact iyalaibitioh and density limitation ~f growth Normal cells typically grow in a flat and organized pattern in a petri dish until they touch other cells. When the cells touch one another, they are contact inhibited and stop growing. When cells are transformed, however, the cells are not contact inhibited and continue to grow to high densities in disorganized foci. Thus, the transformed cells grow to a higher saturation density than normal cells. This can be detected morphologically by the formation of a disoriented monolayer of cells or rounded cells in foci within the regular pattern of normal surrounding cells. Alternatively, labeling index with (3H)-thymidine at saturation density can be used to measure density limitation of growth. See Freshney (1994), S supra. The transformed cells, when transfected with tumor suppressor genes, regenerate a normal phenotype and become contact inhibited and would grow to a lower density.
In this assay, labeling index with (3H)-thymidine at saturation density is a preferred method of measuring density limitation of growth. Transformed host cells are transfected with a breast cancer-associated sequence and are grown for 24 hours at saturation density in non-limiting medium conditions. The percentage of cells labeling with (3H)-thymidine is determined autoradiographically. See, Freshney (1994), supra.
Growth factor or' serum dependence Transformed cells have a lower serum dependence than their normal counterparts (see, e.g., Temin, J. Natl. Cancer Insti. 37:167-175 (1966);
Eagle et al., J. Exp.
Med. 131:836-879 (1970)); Freshney, supy~a. This is in part due to release of various growth factors by the transformed cells. Growth factor or serum dependence of transformed host cells can be compared with that of control.
Tumor specific markers levels Tumor cells release an increased amount of certain factors (hereinafter "tumor specific markers") than their normal counterparts. For example, plasminogen activator (PA) is released from human glioma at a higher level than from normal brain cells (see, e.g., Gullino, Angiogenesis, tumoy~ vasculay~izatiora, and potential inteYference witla tumor growth.
in Biological Responses in Cancef~, pp. 178-184 (Mihich (ed.) 1985)).
Similarly, Tumor angiogenesis factor (TAF) is released at a higher level in tumor cells than their normal counterparts. See, e.g., Folkman, Angiogenesis and Cancer, Sem Cancer Biol.
(1992)).
Various techniques which measure the release of these factors are described in Freshney (1994), supra. Also, see, Unkless et al. , J. Biol. Chem. 249:4295-4305 (1974);
Strickland & Beers, J. Biol. Claem. 251:5694-5702 (1976); Whur et al., Br. J.
Cancef~ 42:305-312 (1980); Gullino, ArZgiogerr.esis, tumor vascularization, and potential irrterfereh.ce with turraor growth. in Biological Responses i>z Cancer, pp. 178-184 (Mihich (ed.) 1985);
Freshney Anticancer Res. 5:111-130 (1985).
Invasiveness into Matrigel The degree of invasiveness into Matrigel or some other extracellular matrix constituent can be used as an assay to identify compounds that modulate breast cancer-associated sequences. Tumor cells exhibit a good correlation between malignancy and invasiveness of cells into Matrigel or some other extracellular matrix constituent. In this assay, tumorigenic cells are typically used as host cells. Expression of a tumor suppressor gene in these host cells would decrease invasiveness of the host cells.
Techniques described in Freshney (1994), supra, can be used. Briefly, the level of invasion of host cells can be measured by using filters coated with Matrigel or some other extracellular matrix constituent. Penetration into the gel, or through to the distal side of the filter, is rated as invasiveness, and rated histologically by number of cells and distance moved, or by prelabeling the cells with lzsl and counting the radioactivity on the distal side of the filter or bottom of the dish. See, e.g., Freshney (1984), supra.
Tumor growth i>z vivo Effects of breast cancer-associated sequences on cell growth can be tested in transgenic or immune-suppressed mice. Knock-out transgenic mice can be made, in which the breast cancer gene is disrupted or in which a breast cancer gene is inserted. Knock-out transgenic mice can be made by insertion of a marker gene or other heterologous gene into the endogenous breast cancer gene site in the mouse genome via homologous recombination.
Such mice can also be made by substituting the endogenous breast cancer gene with a mutated version of the breast cancer gene, or by mutating the endogenous breast cancer gene, e.g., by exposure to carcinogens.
A DNA construct is introduced into the nuclei of embryonic stem cells. Cells containing the newly engineered genetic lesion are injected into a host mouse embryo, which is re-implanted into a recipient female. Some of these embryos develop into chimeric mice that possess germ cells partially derived from the mutant cell line.
Therefore, by breeding the chimeric mice it is possible to obtain a new line of mice containing the introduced genetic lesion (see, e.g., Capecchi et al., Science 244:1288 (1989)). Chimeric targeted mice can be derived according to Hogan et al., Marzipulatizzg tlae Mouse Embryo: A
Laboratory Muzzual, Cold Spring Harbor Laboratory (1988) and Teratocarciyzomas and Embryonic Stem Cells: A .
Practical AppYOach, Robertson, ed., IRL Press, Washington, D.C., (1987).
Alternatively, various immune-suppressed or immune-deficient host animals can be used. For example, genetically athymic "nude" mouse (see, e.g., Giovanella et al., J.
Natl. Cancer Izzst. 52:921 (1974)), a SLID mouse, a thymectomized mouse, or an irradiated mouse (see, e.g., Bradley et al., Br. J. Cancer 38:263 (1978); Selby et al., Br. J. Cancer 41:52 (1980)) can be used as a host. Transplantable tumor cells (typically about 106 cells) injected into isogenic hosts will produce invasive tumors in a high proportions of cases, while normal cells of similar origin will not. In hosts which developed invasive tumors, cells expressing a breast cancer-associated sequences are injected subcutaneously.
After a suitable length of time, preferably 4-8 weeks, tumor growth is measured (e.g., by volume or by its two largest dimensions) and compared to the control. Tumors that have statistically significant reduction (using, e.g., Student's T test) are said to have inhibited growth.
Polynucleotide modulators of breast cancer Azztisezzse Polyzzucleotides In certain embodiments, the activity of a breast cancer-associated protein is down-regulated, or entirely inhibited, by the use of antisense polynucleotide, i.e., a nucleic acid complementary to, and which can preferably hybridize specifically to, a coding mRNA
nucleic acid sequence, e.g., a breast cancer protein mRNA, or a subsequence thereof.
Binding of the antisense polynucleotide to the mRNA reduces the translation andlor stability of the mRNA.
In the context of this invention, antisense polynucleotides can comprise naturally-occurnng nucleotides, or synthetic species formed from naturally-occurnng subunits or their close homologs. Antisense polynucleotides may also have altered sugar moieties or inter-sugar linkages. Exemplary among these are the phosphorothioate and other sulfur containing species which are known for use in the art. Analogs are comprehended by this invention so long as they function effectively to hybridize with the breast cancer protein mRNA. See, e.g., Isis Pharmaceuticals, Carlsbad, CA; Sequitor, Inc., Natick, MA.
Such antisense polynucleotides can readily be synthesized using recombinant S means, or can be synthesized in vitro. Equipment for such synthesis is sold by several vendors, including Applied Biosystems. The preparation of other oligonucleotides such as phosphorothioates and alkylated derivatives is also well known to those of skill in the art.
Antisense molecules as used herein include antisense or sense oligonucleotides. Sense oligonucleotides can, e.g., be employed to block transcription by binding to the anti-sense strand. The antisense and sense oligonucleotide comprise a single-stranded nucleic acid sequence (either RNA or DNA) capable of binding to target mRNA
(sense) or DNA (antisense) sequences for breast cancer molecules. A preferred antisense molecule is for a breast cancer sequences in Tables 1-25, or for a ligand or activator thereof.
Antisense or sense oligonucleotides, according to the present invention, comprise a fragment 1S generally at least about 14 nucleotides, preferably from about 14 to 30 nucleotides. The ability to derive an antisense or a sense oligonucleotide, based upon a cDNA
sequence encoding a given protein is described in, e.g., Stein & Cohen (Cancer Res.
48:2659 (1988 and van der Krol et al. (BioTechniques 6:958 (1988)).
Ribozymes In addition to antisense polynucleotides, ribozymes can be used to target and inhibit transcription of breast cancer-associated nucleotide sequences. A
ribozyme is an RNA molecule that catalytically cleaves other RNA molecules. Different kinds of ribozymes have been described, including group I ribozymes, hammerhead ribozymes, hairpin 2S ribozymes, RNase P, and axhead ribozymes (see, e.g., Castanotto et al., Adv. in Pharmacology 2S: 289-317 (1994) for a general review of the properties of different ribozymes).
The general features of hairpin ribozymes are described, e.g., in Hampel et al., Nucl. Acids Res. 18:299-304 (1990); European Patent Publication No. 0 360 257;
U.S. Patent No. 5,254,678. Methods of preparing are well known to those of skill in the art (see, e.g., WO 94/26877; Ojwang et al., Proc. Natl. Acad. Sci. IJSA 90:6340-6344 (1993);
Yamada et al., Human Geue Tlaerapy 1:39-45 (1994); Leavitt et al., Proc. Natl. Acad.
Sci. USA 92:699-703 (1995); Leavitt et al., Hufyaafz Gene Therapy 5:1151-120 (1994); and Yamada et al., Virology 205: 121-126 (1994)).
Polynucleotide modulators of breast cancer may be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand binding molecule, as described in WO 91/04753. Suitable ligand binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors. Preferably, conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell. Alternatively, a polynucleotide modulator of breast cancer may be introduced into a cell containing the target nucleic acid sequence, e.g., by formation of an polynucleotide-lipid complex, as described in WO 90110448. It is understood that the use of antisense molecules or knock out and knock in models may also be used in screening assays as discussed above, in addition to methods of treatment.
Thus, in one embodiment, methods of modulating breast cancer in cells or organisms are provided. In one embodiment, the methods comprise administering to a cell an anti-breast cancer antibody that reduces or eliminates the biological activity of an endogenous breast cancer protein. Alternatively, the methods comprise administering to a cell or ' organism a recombinant nucleic acid encoding a breast cancer protein. This may be accomplished in any number of ways. In a preferred embodiment, e.g. when the breast cancer sequence is down-regulated in breast cancer, such state may be reversed by increasing the amount of breast cancer gene product in the cell. This can be accomplished, e.g., by overexpressing the endogenous breast cancer gene or administering a gene encoding the breast cancer sequence, using known gene-therapy techniques, e.g.. In a preferred embodiment, the gene therapy techniques include the incorporation of the exogenous gene using enhanced homologous recombination (EHR), e.g. as described in PCT/LTS93/03868, hereby incorporated by reference in its entirety. Alternatively, e.g. when the breast cancer sequence is up-regulated in breast cancer, the activity of the endogenous breast cancer gene is decreased, e.g. by the administration of a breast cancer antisense nucleic acid.
In one embodiment, the breast cancer proteins of the present invention may be used to generate polyclonal and monoclonal antibodies to breast cancer proteins. Similarly, the breast cancer proteins can be coupled, using standard technology, to affinity chromatography columns. These columns may then be used to purify breast cancer antibodies useful for production, diagnostic, or therapeutic purposes. In a preferred embodiment, the antibodies are generated to epitopes unique to a breast cancer protein; that is, the antibodies show little or no cross-reactivity to other proteins. The breast cancer antibodies may be coupled to standard affinity chromatography columns and used to purify breast cancer proteins. The antibodies may also be used as blocking polypeptides, as outlined above, since they will specifically bind to the breast cancer protein.
Methods of identifying variant breast cancer-associated sequences Without being bound by theory, expression of various breast cancer sequences is correlated with breast cancer. Accordingly, disorders based on mutant or variant breast cancer genes may be determined. In one embodiment, the invention provides methods for identifying cells containing variant breast cancer genes, e.g., determining all or part of the sequence of at least one endogenous breast cancer genes in a cell. This may be accomplished using any number of sequencing techniques. In a preferred embodiment, the invention provides methods of identifying the breast cancer genotype of an individual, e.g., determining all or part of the sequence of at least one breast cancer gene of the individual. This is generally done in at least one tissue of the individual, and may include the evaluation of a number of tissues or different samples of the same tissue. The method may include comparing the sequence of the sequenced breast cancer gene to a known breast cancer gene, i.e., a wild-type gene.
The sequence of all or part of the breast cancer gene can then be compared to the sequence of a known breast cancer gene to determine if any differences exist. This can be done using any number of known homology programs, such as Bestfit, etc. In a preferred embodiment, the presence of a difference in the sequence between the breast cancer gene of the patient and the known breast cancer gene correlates with a disease state or a propensity for a disease state, as outlined herein.
In a preferred embodiment, the breast cancer genes are used as probes to determine the number of copies of the breast cancer gene in the genome.
In another preferred embodiment, the breast cancer genes are used as probes to determine the chromosomal localization of the breast cancer genes. Information such as chromosomal localization finds use in providing a diagnosis or prognosis in particular when chromosomal abnormalities such as translocations, and the like are identified in the breast cancer gene locus.
Administration of pharmaceutical and vaccine compositions In one embodiment, a therapeutically effective dose of a breast cancer protein or modulator thereof, is administered to a patient. By "therapeutically effective dose" herein is meant a dose that produces effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (e.g., Ansel et al., Pharmaceutical Dosage Forms and Drug Delivery;
Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992), Dekker, ISBN
0824770846, 082476918X, 0824712692, 0824716981; Lloyd, The Art, Science and Technology of Plaarnaaceutical Compourading (1999); and Pickar, Dosage Calculations (1999)).
As is known in the art, adjustments for breast cancer degradation, systemic versus localized delivery, and rate of new protease synthesis, as well as the age, body weight, general health, sex, diet, time of administration, drug interaction and the severity of the condition may be necessary, and will be ascertainable with routine experimentation by those skilled in the art.
U.S. Patent Application N. 09/687,576, further discloses the use of compositions and methods of diagnosis and treatment in breast cancer is hereby expressly incorporated by reference.
A "patient" for the purposes of the present invention includes both humans and other animals, particularly mammals. Thus the methods are applicable to both human therapy and veterinary applications. In the preferred embodiment the patient is a mammal, preferably a primate, and in the most preferred embodiment the patient is human.

The administration of the breast cancer proteins and modulators thereof of the present invention can be done in a variety of ways as discussed above, including, but not limited to, orally, subcutaneously, intravenously, intranasally, transdermally, intraperitoneally, intramuscularly, intrapulmonary, vaginally, rectally, or intraocularly. In some instances, e.g., in the treatment of wounds and inflammation, the breast cancer proteins and modulators may be directly applied as a solution or spray.
The pharmaceutical compositions of the present invention comprise a breast cancer protein in a form suitable for administration to a patient. In the preferred embodiment, the pharmaceutical compositions are in a water soluble form, such as being present as pharmaceutically acceptable salts, which is meant to include both acid and base addition salts. "Pharmaceutically acceptable acid addition salt" refers to those salts that retain the biological effectiveness of the free bases and that are not biologically or otherwise undesirable, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, malefic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and the like.
"Pharmaceutically acceptable base addition salts" include those derived from inorganic bases such as sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Particularly preferred are the ammonium, potassium, sodium, calcium, and magnesium salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine.
The pharmaceutical compositions may also include one or more of the following: carrier proteins such as serum albumin; buffers; fillers such as microcrystalline cellulose, lactose, corn and other starches; binding agents; sweeteners and other flavoring agents; coloring agents; and polyethylene glycol.

The pharmaceutical compositions can be administered in a variety of unit dosage forms depending upon the method of administration. For example, unit dosage forms suitable for oral administration include, but are not limited to, powder, tablets, pills, capsules and lozenges. It is recognized that breast cancer protein modulators (e.g., antibodies, antisense constructs, ribozymes, small organic molecules, etc.) when administered orally, should be protected from digestion. This is typically accomplished either by complexing the molecules) with a composition to render it resistant to acidic and enzymatic hydrolysis, or by packaging the molecules) in an appropriately resistant carrier, such as a liposome or a, protection barner. Means of protecting agents from digestion are well known in the art.
The compositions for administration will commonly comprise a breast cancer protein modulator dissolved in a pharmaceutically acceptable earner, preferably an aqueous carrier. A variety of aqueous carriers can be used, e.g., buffered saline and the like. These solutions are sterile and generally free of undesirable matter. These compositions may be sterilized by conventional, well known sterilization techniques. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, e.g., sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like. The concentration of active agent in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the patient's needs (e.g., Remington's Pharmaceutical Science (15th ed., 1980) and Goodman ~
Gillman, Tlae Pharmacologial Basis of Therapeutics (Hardman et al.,eds., 1996)).
Thus, a typical pharmaceutical composition for intravenous administration would be about 0.1 to 10 mg per patient per day. Dosages from 0.1 up to about 100 mg per patient per day may be used, particularly when the drug is administered to a secluded site and not into the blood stream, such as into a body cavity or into a lumen of an organ.
Substantially higher dosages are possible in topical administration. Actual methods for preparing parenterally administrable compositions will be known or apparent to those skilled in the art, e.g., Remington's Pharmaceutical Science and Goodman and Gillman, The Pharmacologial Basis of Therapeutics, supra.

The compositions containing modulators of breast cancer proteins can be administered for therapeutic or prophylactic treatments. In therapeutic applications, compositions are administered to a patient suffering from a disease (e.g., a cancer) in an amount sufficient to cure or at least partially arrest the disease and its complications. An amount adequate to accomplish this is defined as a "therapeutically effective dose." Amounts effective for this use will depend upon the severity of the disease and the general state of the patient's health. Single or multiple administrations of the compositions may be administered depending on the dosage and frequency as required and tolerated by the patient. In any event, the composition should provide a sufficient quantity of the agents of this invention to effectively treat the patient. An amount of modulator that is capable of preventing or slowing the development of cancer in a mammal is referred to as a "prophylactically effective dose."
The particular dose required for a prophylactic treatment will depend upon the medical condition and history of the mammal, the particular cancer being prevented, as well as other factors such as age, weight, gender, administration route, efficiency, etc.
Such prophylactic treatments may be used, e.g., in a mammal who has previously had cancer to prevent a recurrence of the cancer, or in a mammal who is suspected of having a significant likelihood of developing cancer.
It will be appreciated that the present breast cancer protein-modulating compounds can be administered alone or in combination with additional breast cancer modulating compounds or with other therapeutic agent, e.g., other anti-cancer agents or treatments.
In numerous embodiments, one or more nucleic acids, e.g., polynucleotides comprising nucleic acid sequences set forth in Tables I-25, such as antisense polynucleotides or ribozymes, will be introduced into cells, in vitro or ih vivo. The present invention provides methods, reagents, vectors, and cells useful for expression of breast cancer-associated polypeptides and nucleic acids using ih vitro (cell-free), ex vivo or in vivo (cell or organism-based) recombinant expression systems.
The particular procedure used to introduce the nucleic acids into a host cell for expression of a protein or nucleic acid is application specific. Many procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, spheroplasts, electroporation, liposomes, microinjection, plasma vectors, viral vectors and any of the other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Berger & Kimmel, Guide to Molecular Cloning Techniques, Methods in EyazynZOlogy volume 152 (Berger), Ausubel et al., eds., Current Protocols (supplemented through 1999), and Sambrook et al., Molecular Cloning - A Laboratory Manual (2nd ed., Vol. 1-3, 1989.
In a preferred embodiment, breast cancer proteins and modulators are administered as therapeutic agents, and can be formulated as outlined above.
Similarly, breast cancer genes (including both the full-length sequence, partial sequences, or regulatory sequences of the breast cancer coding regions) can be administered in a gene therapy application. These breast cancer genes can include antisense applications, either as gene therapy (i.e. for incorporation into the genome) or as antisense compositions, as will be appreciated by those in the art.
Breast cancer polypeptides and polynucleotides can also be administered as vaccine compositions to stimulate HTL, CTL and antibody responses.. Such vaccine compositions can include, e.g., lipidated peptides (see, e.g.,Vitiello, A. et al., J. Clin. Invest.
95:341 (1995)), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) ("PLG") microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, (1991);
Alonso et al., ~accirze 12:299-306 (1994); Jones et al., Vaccine .13:675-681 (1995)), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875 (1990); Hu et al., Clin Exp Immunol. 113:235-243 (1998)), multiple antigen peptide systems (MAPS) (see, e.g., Tam, Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413 (1988);
Tam, J. Immunol. Metlaods 196:17-32 (1996)), peptides formulated as multivalent peptides;
peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, et al., In: Concepts in vaccine development (Kaufinann, ed., p. 379, 1996);
Chakrabarti, et al., Nature 320:535 (1986); Hu et al., Nature 320:537 (1986);
Kieny, et al., AIDS BiolTechnology 4:790 (1986); Top et al., J. Infect. Dis. 124:148 (1971);
Chanda et al., Virology 175:535 (1990)), particles of viral or synthetic origin (see, e.g., Kofler et al., J.
Immunol. Methods. 192:25 (1996); Eldridge et al., Senz. Henaatol. 30:16 (1993); Falo et al., Nature Med. 7:649 (1995)), adjuvants (Warren et al., Anrau. Rev. Immunol.
4:369 (1986);

Gupta et al., Vaccine 11:293 (1993)), liposomes (Reddy et al., J. Irnrnunol.
148:1585 (1992);
Rock, Imrraunol. Today 17:131 (1996)), or, naked or particle absorbed cDNA
(Ulmer, et al., Science 259:1745 (1993); Robinson et al., Yaccirae 11:957 (1993); Shiver et al., In: Concepts ira vaccine development (Kaufinann, ed., p. 423, 1996); Cease & Berzofsky, Annu. Rev.
InanZUrzol. 12:923 (1994) and Eldridge et al., Sern. Hematol. 30:16 (1993)).
Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Massachusetts) may also be used.
Vaccine compositions often include adjuvants. Many adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins. Certain adjuvants are commercially available as, e.g., Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, MI); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, NJ); AS-2 (SmithKline Beecham, Philadelphia, PA); aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides;
polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quit A.
Cytokines, such as GM-CSF, interleukin-2, -7, -12, and other like growth factors, may also be used as adjuvants.
Vaccines can be administered as nucleic acid compositions wherein DNA or RNA encoding one or more of the polypeptides, or a fragment thereof, is administered to a patient. This approach is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Patent Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118;
5,736,524; 5,679,647;
W~ 98/04720; and in more detail below. Examples of DNA-based delivery technologies include "naked DNA", facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated ("gene gun") or pressure-mediated delivery (see, e.g., U.S. Patent No. 5,922,687).
For therapeutic or prophylactic immunization purposes, the peptides of the invention can be expressed by viral or bacterial vectors. Examples of expression vectors include attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus, e.g., as a vector to express nucleotide sequences that encode breast cancer polypeptides or polypeptide fragments. Upon introduction into a host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits an immune response.
Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S.
Patent No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG
vectors are described in Stover et al., Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein (see, e.g., Shata et al., Mol Med Today 6:66-71 (2000); Shedlock et al., JLeukoc Biol 68:793-806 (2000);
Hipp et al., he Vivo 14:571-85 (2000)).
Methods for the use of genes as DNA vaccines are well known, and include placing a breast cancer gene or portion of a breast cancer gene under the control of a regulatable promoter or a tissue-specific promoter for expression in a breast cancer patient.
The breast cancer gene used for DNA vaccines can encode full-length breast cancer proteins, but more preferably encodes portions of the breast cancer proteins including peptides derived from the breast cancer protein. In one embodiment, a patient is immunized with a DNA
vaccine comprising a plurality of nucleotide sequences derived from a breast cancer gene. For example, breast cancer-associated genes or sequence encoding subfragments of a breast cancer protein are introduced into expression vectors and tested for their immunogenicity in the context of Class I MHC and an ability to generate cytotoxic T cell responses. This procedure provides for production of cytotoxic T cell responses against cells which present antigen, including intracellular epitopes.
In a preferred embodiment, the DNA vaccines include a gene encoding an adjuvant molecule with the DNA vaccine. Such adjuvant molecules include cytokines that increase the immunogenic response to the breast cancer polypeptide encoded by the DNA
vaccine. Additional or alternative adjuvants are available.
In another preferred embodiment breast cancer genes find use in generating animal models of breast cancer. When the breast cancer gene identified is repressed or diminished in cancer tissue, gene therapy technology, e.g., wherein antisense RNA directed to the breast cancer gene will also diminish or repress expression of the gene. Animal models of breast cancer find use in screening for modulators of a breast cancer-associated sequence or modulators of breast cancer. Similarly, transgenic animal technology including gene knockout technology, e.g. as a result of homologous recombination with an appropriate gene S targeting vector, will result in the absence or increased expression of the breast cancer protein. When desired, tissue-specific expression or knockout of the breast cancer protein may be necessary.
It is also possible that the breast cancer protein is overexpressed in breast cancer. As such, transgenic animals can be generated that overexpress the breast cancer protein. Depending on the desired expression level, promoters of various strengths can be employed to express the transgene. Also, the number of copies of the integrated transgene can be determined and compared for a determination of the expression level of the transgene.
Animals generated by such methods find use as animal models of breast cancer and are additionally useful in screening for modulators to treat breast cancer.
Kits for Use in Diagnostic and/or Prognostic Applications For use in diagnostic, research, and therapeutic applications suggested above, kits are also provided by the invention. In the diagnostic and research applications such kits may include any or all of the following: assay reagents, buffers, breast cancer-specific nucleic acids or antibodies, hybridization probes and/or primers, antisense polynucleotides, ribozymes, dominant negative breast cancer polypeptides or polynucleotides, small molecules inhibitors of breast cancer-associated sequences etc. A therapeutic product may include sterile saline or another pharmaceutically acceptable emulsion and suspension base.
In addition, the kits may include instructional materials containing directions (i.e., protocols) for the practice of the methods of this invention. While the instructional materials typically comprise written or printed materials they are not limited to such. Any medium capable of storing such instructions and communicating them to an end user is contemplated by this invention. Such media include, but are not limited to electronic storage media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media may include addresses to Internet sites that provide such instructional materials.
The present invention also provides for kits for screening for modulators of breast cancer-associated sequences. Such kits can be prepared from readily available materials and reagents. For example, such kits can comprise one or more of the following materials: a breast cancer-associated polypeptide or polynucleotide, reaction tubes, and instructions for testing breast cancer-associated activity. Optionally, the kit contains biologically active breast cancer protein. A wide variety of kits and components can be prepared according to the present invention, depending upon the intended user of the kit and the particular needs of the user. Diagnosis would typically involve evaluation of a plurality of genes or products. The genes will be selected based on correlations with important parameters in disease which may be identified in historical or outcome data.
EXAMPLES
Example 1: Tissue Preparation, Labeling Chips, and Fingerprints Purifying_total RNA from tissue sample using TRIzoI Reagent The sample weight is first estimated. The tissue samples are homogenized in 1 ml of TRIzoI per 50 mg of tissue using a homogenizer (e.g., Polytron 3100).
The size of the generator/probe used depends upon the sample amount. A generator that is too large for the amount of tissue to be homogenized will cause a loss of sample and lower RNA yield. A
larger generator (e.g., 20 mm) is suitable for tissue samples weighing more than 0.6 g. Fill tubes should not be overfilled. If the working volume is greater than 2 ml and no greater than 10 ml, a 15 ml polypropylene tube (Falcon 2059) is suitable for homogenization.
Tissues should be kept frozen until homogenized. The TRIzoI is added directly to the frozen tissue before homogenization. Following homogenization, the insoluble material is removed from the homogenate by centrifugation at 7500 x g for 15 min. in a Sorvall superspeed or 12,000 x g for 10 min. in an Eppendorf centrifuge at 4oC. The cleared homogenate is then transferred to a new tube(s). Samples may be frozen and stored at -60 to -70oC for at least one month or else continue with the purification.
The next process is phase separation. The homogenized samples are incubated for 5 minutes at room temperature. Then, 0.2 ml of chloroform per lml of TRIzol reagent is added to the homogenization mixture. The tubes are securely capped and shaken vigorously by hand (do not vortex) for 15 seconds. The samples are then incubated at room temp. for 2-3 minutes and next centrifuged at 6500 rpm in a Sorvall superspeed for 30 min. at 4oC.
The next process is RNA Precipitation. The aqueous phase is transferred to a fresh tube. The organic phase can be saved if isolation of DNA or protein is desired. Then 0.5 ml of isopropyl alcohol is added per 1ml of TRIzoI reagent used in the original homogenization. Then, the tubes are securely capped and inverted to mix. The samples are then incubated at room temp. for 10 minutes an centrifuged at 6500 rpm in Sorvall for 20 min. at 4oC.
The RNA is then washed. The supernatant is poured off and the pellet washed with cold 75% ethanol. 1 ml of 75% ethanol is used per 1 ml of the TRIzoI
reagent used in the initial homogenization. The tubes are capped securely and inverted several times to loosen pellet without vortexing . They are next centrifuged at <8000 rpm (<7500 x g) for 5 minutes at 4°C.
The RNA wash is decanted. The pellet is carefully transferred to an Eppendorf tube (sliding down the tube into the new tube by use of a pipet tip to help guide it in if necessary). Tubes) sizes for precipitating the RNA depending on the working volumes.
Larger tubes may take too long to dry. Dry pellet. The RNA is then resuspended in an appropriate volume (e.g., 2 -5 ug/ul) of DEPC H20. The absorbance is then measured.
The poly A+ mRNA may next be purified from total RNA by other methods such as Qiagen' s RNeasy kit. The poly A + mRNA is purified from total RNA by adding the oligotex suspension which has been heated to 37oC and mixing prior to adding to RNA.
The Elution Buffer is incubated at 70oC. If there is precipitate in the buffer, warm up the 2 x Binding Buffer at 65oC. The the total RNA is mixed with DEPC-treated water, 2 x Binding Buffer, and Oligotex according to Table 2 on page 16 of the Oligotex Handbook and next incubated for 3 minutes at 65oC and 10 minutes at room temperature.
The preparation is centrifuged for 2 minutes at 14,000 to 18,000 g, preferably, at a "soft setting," The supernatant is removed without disturbing Oligotex pellet. A little bit of solution can be left behind to reduce the loss of Oligotex. The supernatant is saved until satisfactory binding and elution of poly A+ mRNA has been found.
Then, the preparation is gently resuspended in Wash Buffer OW2 and pipetted onto the spin column and centrifuged at full speed (soft setting if possible) for 1 minute.
Next, the spin column is transferred to a new collection tube and gently resuspended in Wash Buffer OW2 and centrifuged as described herein.
Then, the spin column is transferred to a new tube and eluted with 20 to 100 ul of preheated (70oC) Elution Buffer. The Oligotex resin is gently resuspended by pipetting up and down. The centrifugation is repeated as above and the elution repeated with fresh elution buffer or first eluate to keep the elution volume low.
The absorbance is next read to determine the yield, using diluted Elution Buffer as the blank.
Before proceeding with cDNA synthesis, the mRNA is precipitated before proceeding with cDNA synthesis, as components leftover or in the Elution Buffer from the Oligotex purification procedure will inhibit downstream enzymatic reactions of the mRNA.
0.4 vol. of 7.5 M NH40Ac + 2.5 vol. of cold 100% ethanol is added and the preparation precipitated at -20°C 1 hour to overnight (or 20-30 min. at -70°C), and centrifuged at 14,000-16,000 x g for 30 minutes at 4°C. Next, the pellet is washed with 0.5 ml of 80%
ethanol (-20°C) and then centrifuged at 14,000-16,000 x g for 5 minutes at room temperature.
The80% ethanol wash is then repeated. The last bit of ethanol from the pellet is then dried without use of a speed vacuum and the pellet is then resuspended in DEPC H20 at lug/ul concentration.
Alternatively the RNA may be purified using other methods (e.g.-Oiagen's RNeasy kitl.

No more than 100 ug is added to the RNeasy column. The sample volume is adjusted to 100 ul with RNase-free water. 350 ul Buffer RLT and then 250 ul ethanol (100%) are added to the sample. The preparation is then mixed by pipetting and applied to an RNeasy mini spin column for centrifugation (15 sec at >10,000 rpm). If yield is low, reapply the flowthrough to the column and centrifuge again.
Then, transfer column to a new 2 ml collection tube and add 500 ul Buffer RPE and centrifuge for 15 sec at >10,000 rpm. The flowthrough is discarded.
500 ul Buffer RPE and is then added and the preparation is centriuged for 15 sec at >10,000 rpm. The flowthrough is discarded. and the column membrane dried by centrifuging for 2 min at maximum speed. The column is transferred to a new 1.5-ml collection tube. 30-50 ul of RNase-free water is applied directly onto column membrane. The column is then centrifuged for 1 min at >10,000 rpm and the elution step repeated.
The absorbance is then read to determine yield. If necessary, the material may be ethanol precipitated with ammonium acetate and 2.SX volume 100% ethanol.
First Strand cDNA Synthesis The first strand can be make using using Gibco's "Superscript Choice System for cDNA Synthesis" kit. The starting material is 5 ug of total RNA or 1 ug of polyA+
mRNAI. For total RNA, 2 ul of Superscript RT is used; for polyA+ mRNA, 1 ul of Superscript RT is used. The final volume of first strand synthesis mix is 20 ul. The RNA
should be in a volume no greater than 10 ul. The RNA is incubated with 1 ul of 100 pmol T7-T24 oligo for 10 min at 70°C followed by addition on ice of 7 ul of:
4ul SX 1st Strand Buffer, 2 ul of O.1M DTT, and 1 ul of lOmM dNTP mix. The preparation is then incubated at 37°C for 2 min before addition of the Superscript RT followed by incubation at 37°C for 1 hour.
Second Strand Synthesis For the second strand synthesis, place 1 st strand reactions on ice and add:

ul DEPC H20; 30 ul 5X 2nd Strand Buffer; 3 ul lOmM dNTP mix; 1 ul 10 U/ul E.coli DNA
Ligase; 4 ul 10 U/ul E.coli DNA Polymerase; and 1 ul 2 U/ul RNase H. Mix and incubate 2 hours at 16°C. Add 2 ul T4 DNA Polymerase. Incubate 5 min at 16°C. Add 10 ul of O.SM
EDTA.
Cleaning up cDNA
The cDNA is purified using Phenol:Chloroform:Isoamyl Alcohol (25:24:1) and Phase-Lock gel tubes. The PLG tubes are centrifuged for 30 sec at maximum speed.
The cDNA mix is then transferred to PLG tube. An equal volume of phenol:chloroform:isamyl alcohol is then added, the preparation shaken vigorously (no vortexing), and centrifuged for 5 minutes at maximum speed. The top aqueous solution is transferred to a new tube and ethanol precipitated by adding 7.SX SM NH40Ac and 2.SX
volume of 100% ethanol. Next, it is centrifuged immediately at room temperature for 20 min, maximum speed. The supernatant is removed, and the pellet washed with 2X
with cold ~0% ethanol. As much ethanol wash as possible should be removed before air drying the pellet; and resuspending it in 3 ul RNase-free water.
In vitro Transcription~IVT) and labeli:n~ with biotin In vitro Transcription (IVT) and labeling with biotin is performed as follows:
Pipet 1.5 ul of cDNA into a thin-wall PCR tube. Make NTP labeling mix by combining 2 ul T7 lOxATP (75 mM) (Ambion); 2 ul T7 lOxGTP (75 mM) (Ambion); 1.5 ul T7 lOxCTP
(75 mM) (Ambion); 1.5 ul T7 lOxUTP (75 mM) (Ambion); 3.75 ul 10 mM Bio-11-UTP
(Boehringer-Mannheim/Roche or Enzo); 3.75 ul 10 mM Bio-16-CTP (Enzo); 2 ul lOx transcription buffer (Ambion); and 2 ul 10x T7 enzyme mix (Ambion). The final volume is 20 ul. Incubate 6 hours at 37°C in a PCR machine. The RNA can be furthered cleaned.
Clean-up follows the previous instructions for RNeasy columns or Qiagen's RNeasy protocol handbook. The cRNA often needs to be ethanol precipitated by resuspension in a volume compatible with the fragmentation step.
Fragmentation is performed as follows. 15 ug of labeled RNA is usually fragmented. Try to minimize the fragmentation reaction volume; a 10 ul volume is recommended but 20 ul is all right. Do not go higher than 20 ul because the magnesium in the fragmentation buffer contributes to precipitation in the hybridization buffer. Fragment RNA by incubation at 94 C for 35 minutes in 1 x Fragmentation buffer (5 x Fragmentation buffer is 200 mM Tris-acetate, pH 8.1; 500 mM I~OAc; 150 mM MgOAc). The labeled RNA transcript can be analyzed before and after fragmentation. Samples can be heated to 65°C for 15 minutes and electrophoresed on 1% agarose/TBE gels to get an approximate idea of the transcript size range .
For hybridization, 200 ul (10 ug cRNA) of a hybridization mix is put on the chip. If multiple hybridizations are to be done (such as cycling through a 5 chip set), then it is recommended that an initial hybridization mix of 300 ul or more be made.
The hybridization mix is: fragment labeled RNA (50 ng/ul final cone); 50 pM 948-b control oligo; 1.5 pM BioB; 5 pM BioC; 25 pM BioD; 100 pM CRE; 0.1 mg/ml hernng sperm DNA;
0.5 mg/ml acetylated BSA; and 300 ul with lxMES hyb buffer.
The hybridization reaction is conducted with non-biotinylated IVT (purified by RNeasy columns) (see example 1 for steps from tissue to IVT): The following mixture is prepared:
IVT antisense RNA; 4 ~,g: ~,1 Random Hexamers (1 ~,g/~,1): 4 ~,1 H20: -~,l 14 ~1 Incubate the above 14 ~l mixture at 70oC for 10 min.; then put on ice.
The Reverse transcription procedure uses the following mixture:
0.1 M DTT: 3 ~1 SOX dNTP mix: 0.6 ~.1 H20: 2.4 ~,l Cy3 or Cy5 dUTP (1mM): 3 ~1 SS RT II (BRL): 1 ~,1 16 ~l The above solution is added to the hybridization reaction and incubated for 30 min., 42oC.
Then, 1 ~.1 SSII is added and incubated for another hour before being placed on ice.

The SOX dNTP mix contains 2SmM of cold dATP, dCTP, and dGTP, lOmM
of dTTP and is made by adding 2S ~,1 each of 100mM dATP, dCTP, and dGTP; 10 ~,1 of lOOmM dTTP to 1S ~1 HZO. ]
RNA degradation is performed as follows. Add 86 ~.1 H2O, 1.S ~1 1M NaOH/
S 2 mM EDTA and incubate at 6S°C, 10 min.. For U-Con 30, S00 ~,1 TE/sample spin at 7000 g for 10 min, save flow through for purification. For Qiagen purification, suspend u-con recovered material in S00 p.l buffer PB and proceed using Qiagen protocol. For DNAse digestion, add 1 ul of 1/100 dilution of DNAse/30 ul Rx and incubate at 37°C for 1S min.
Incubate at S min 9S°C to denature the DNAse.
Sample preparation For sample preparation, add Cot-1 DNA, 10 p,l; SOX dNTPs, 1 ~1; 20X SSC, 2.3 ~.1; Na gyro phosphate, 7.S p.l; 10 mg/ml Herring sperm DNA; 1 ul of 1/10 dilution to 21.8 final vol. Dry in speed vac. Resuspend in 1S p,l HZO. Add 0.38 x,110% SDS. Heat 9S°C, 2 min and slow 1 S cool at room temp. for 20 min. Put on slide and hybridize overnight at 64°C. Washing after the hybridization: 3X SSC/0.03% SDS: 2 min., 37.5 ml 20X SSC+0.7Sm1 10% SDS in 2SOm1 H20; 1X SSC: S min., 12.5 ml 20X SSC in 2SOml H20; 0.2X SSC: S min., 2.S
ml 20X
SSC in 2SOm1 H20. Dry slides and scan at appropiate PMT's and channels.

TABLE 1: Figure 1 from BRCA 001 US
Table 1 shows genes, (incorporated in their entirety here and throughout the application where primekeys are provided), downregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: ExempIarAccession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title 1$ R1: Ratio of normal breast tissue to tumor Pkey ExAccnUnigenelD UnigeneTitle R1 100472 D90084Hs.1023 pyruvate dehydrogenase5 (lipoamide) alpha 100499 T51986Hs.283108 hemoglobin, gamma 10 G

100545 M55405gb:Homo sapiens mucin (MUC-3)5 mRNA, part 100549 BE142019Hs.222056 Homo Sapiens cDNA 10 FLJ11572 fis, clone HE

100613 X52078Hs.101047 transcription factor35 (E2A immunoglobul 25 100635 BE259039Hs.129953 Ewing sarcoma breakpoint5 region 1 100645 X16841Hs.167988 neural cell adhesion5 molecule 1 100654 A03758NM 000477*:Homo Sapiens albumin10 (ALB), m 100702 L27065gb:Human neurofibromatosis 5 2 (NF2) mRNA, 100915 M60832Hs.249239 collagen, type 5 VIII, alpha 2 30 100971 BE379727Hs.83213 fatty acid binding 10 protein 4, adipocyte 101125 AJ250562Hs.82749 transmembrane 4 5 superfamily member 2 101166 M90424Hs.2099 lipocalin 1 (protein5 migrating fasterth 101184 NM Hs.460 activating transcription10 001674 factor 3 101336 NM_006732Hs.75678 FBJ murine osteosarcoma10 viral oncogene h 35 101367 X03350Hs.4 alcohol dehydrogenase 10 1B (class I), beta 101447 M21305gb:Human alpha satellite 10 and satellite 3 101461 N98569Hs.76422 phospholipase A2, 10 group IIA (platelets, 101511 M27826Hs.267319 endogenous retroviral10 protease 101634 AV650262Hs.75765 GR02 oncogene 5 40 101736 M74447Hs.502 transporter 2, ATP-binding10 cassette, sub 102208 022961gb:Human mRNA clone with 10 similarity to L

102297 NM_001504Hs.198252 G protein-coupled 5 receptor 9 102450 048251Hs.75871 protein kinase C 10 binding protein 1 102515 089337Hs.169886 tenascin XB 10 102571 060115Hs.239069 four and a half 5 LIM domains 1 102800 AA313538gb:EST185419 Colon carcinoma10 (HCC) cell 102857 NM Hs.76461 retinol-binding 10 006744 protein 4, interstitial 102990 AA829286Hs.332053 serum amyloid A1 10 103434 X98085Hs.54433 tenascin R (restrictin,5 janusin) S0 103747 AA081995gb:zn26d06.r1 Stratagene 10 neuroepithelium 103750 AA126129gb:zm78c07.r1 Stratagene 5 neuroepithelium 103812 AA137107Hs.326391 Homo Sapiens, clone10 MGC:16638, mRNA, com 103851 AA326216Hs.8719 hypothetical protein5 104080 AB041036Hs.57771 kallikrein 11 (KLK11;5 TLSP; PRSS20; hipp SS 104093 850727Hs.336970 ESTs 10 104106 AA422123gb:zv26h12.r1 Soares_NhHMPu_S15 Homo sapi 104109 AL353957Hs.284181 hypothetical protein10 DKFZp434P0531 104250 F06638Hs.12440 Homo Sapiens clone 10 24734 mRNA sequence 104340 AA426189gb:2w11e09.r1 Soares_NhHMPu_S15 Homo sapi 60 104492 N73185Hs.94285 EST 10 104506 N91071Hs.109650 ESTs 10 104511 N99542Hs.572 orosomucoid 1 5 104532 AI498763Hs.203013 hypothetical protein10 104536 Hs.158101Homo Sapiens cDNA FLJ146735 824024 fis, clone NT

104572 Hs.132463phosphoinositide-3-kinase,5 Y11312 class 2, beta 104659 Hs.105201ESTs 5 104677 Hs.190380ESTs 10 $ 104711 Hs.32794ESTs 10 104731 Hs.125070ESTs, Moderately similar10 AA019300 to 154374 gene 104764 Hs.278585ESTs 5 105005 Hs.28805ESTs 10 105036 Hs.25549hypothetical protein 10 105105 Hs.87016hypothetical protein 5 105231 Hs.238039hypothetical protein 5 105239 gb:zr03f12.r1 Stratagene10 AA221036 NT2 neuronal pr 105921 Hs.169119ESTs, Weakly similar 5 AA421973 to T25731 hypotheti 105957 Hs.27021hypothetical protein 5 1$ 106052 Hs.6382ESTs,HighlysimilartoT00391hypotheti10 106119 Hs.11387KIAA1453 protein 5 106181 Hs.191608ESTs 10 106194 Hs.286194hypothetical protein 5 106283 Hs.25522KIAA1808 protein 10 106379 Hs.119021DKFZP434N061 protein 10 106451 Hs.313182ESTs 10 106491 Hs.10083Homo Sapiens, clone 10 AA135688 IMAGE:4139786, mRNA, 106700 Hs.3776zinc finger protein 5 106782 Hs.25682Homo sapiens mRNA for 10 AW054886 KiAA1863 protein, ~$ 106851 gbak04g09.x1 NCI_CGAP 5 AI458623 Lu24 Homo sapiens 106870 Hs.26530serum deprivation response5 AI983730 (phosphatidyl 106892 Hs.124015hypothetical protein 5 106954 Hs.204038indolethylamine N-methyltransferase5 106991 Hs.30127hypothetical protein 5 107103 Hs.9572ESTs, Highly similar 5 AI446183 to CYAS_HUMAN ADENY

107124 Hs.31442RecO protein-like 4 10 107148 Hs.334305GS1999fu11 10 107214 Hs.5394myosin IA 10 107242 Hs.175411KIAA0865 protein 10 3$ 107331 Hs.111805ESTs 10 107351 Hs.323428ESTs, Moderately similar5 U51704 to ALUB_HUMAN A

107423 Hs.6163PTEN induced putative 5 W26652 kinase 1 107447 Hs.19210hypothetical protein 10 107451 Hs.283976hypthetical protein 10 107453 Hs.334703hypothetical protein 5 107459 Empirically selected 10 W38002 from AFFX single pr 107683 Hs.47623ESTs 10 107711 Hs.220687ESTs 10 107754 Hs.269244ESTs 10 4$ 107757 Hs.280792hypothetical protein 10 BE621721 FLJ12387 similar to 107864 Hs.61246ESTs 10 107872 Hs.95110ESTs, Weakly similar 10 BE271708 to A55943 1-phospha 107888 Hs.191637ESTs 5 107997 Hs.82223chordin-like 10 $0 108056 Hs.62633ESTs 10 108081 Hs.28578muscleblind (Drosophila)-like5 108113 Hs.72531hypothetical protein 10 108238 Hs.66783EST 10 108257 Hs.144269ESTs 5 $$ 108335 gb:zm70h03,s1Stratageneneuroepithelium5 108351 gb:zf79b12.s1 Soares_pineal,~land_N3HPG10 108382 Hs.67726macrophage receptor 5 NM_006770 with collagenous str 108392 gb:zm86a01.s1 Stratagene10 AA075124 ovarian cancer 108441 gb:zm97c09.s1 Stratagene10 AA079079 colon HT29 (937 60 108446 gb:zn13g03.s1 Stratagene10 AA085383 hNT neuron (937 108497 gb:zm85a05.r1 Stratagene10 AA074897 ovarian cancer 108604 Hs.49696ESTs 5 108662 Hs.156637Cas-Br-M (murine) ectropic5 AF117646 retroviral tr 108706 Hs.74569KIAA0842 protein 10 6$ 108738 Hs.158725ESTs 10 108827 Hs.110470ESTs 10 109123 Hs.73232ESTs 10 109389 AA101325Hs.86154 hypothetical protein FLJ12457 109546 F01449Hs.26954 Homo Sapiens mRNA; cDNA DKFZp762G123 (fr 109919 840604Hs.129539 ESTs, Weakly similar to MCAT_HUMAN
MITOC

110006 A1094674Hs.30524 ring finger protein 110141 H46749Hs.31540 ESTs 110354 W22165Hs.22586 ESTs 110433 AW294162Hs.301062 UDP-N-acetyl-alpha-D~alactosamine:polyp 110448 H51276Hs.13526 hypothetical protein FLJ12688 110455 H52576gb:yt85e08.r1 Soares_pineal~land_N3HPG

1 110540 H72639Hs.167608 ESTs 110553 H60593Hs.124990 ESTs 110976 AL044174Hs.159526 patched (Drosophila) homolog 110987 AI753316Hs.26034 ESTs 111158 N66616Hs.138629 H.sapiens mRNA
for subtelomeric repeat s I 111168 AI798376gbar34b07.x1 NCI_CGAP
$ Ov23 Homo Sapiens 111187 AJ224864Hs.9688 leukocyte membrane antigen 111307 AA641636Hs.37477 ESTs, Weakly similar to T46908 hypotheti 111400 800144Hs.189771 ESTs 111498 A1168511gb:ow90h09.s1 Soares fetal_liver_spleen_ 20 111651 816733Hs.20499 ESTs 111738 826065gb:yh39d03.s1 Soares placenta Nb2HP Homo 111803 AA593731Hs.325823 ESTs, Moderately similar to ALUS_HUMAN
A

111995 842333Hs.302292 ESTs 112071 AL117490Hs.47225 Ras-associated protein Rap1 25 112204 NM Hs.25121 cytochrome P450, 006668 subfamily 46 (cholester 112258 851889Hs.24990 ESTs 112490 831094Hs.24378 ESTs 112588 877302gb:yi75h08.s1 Soares placenta Nb2HP Homo 112654 BE618629Hs.268809 ESTs 112784 T98628Hs.191290 ESTs 112817 A1057205Hs.14584 ESTs 112885 AA581428Hs.5021 EST

112913 T16837Hs.4241 ESTs 113149 T51588gb:yb27e06.s1 Stratagene fetal spleen (9 3 113174 T54659Hs.301755 Homo Sapiens S cDNA FLJ11465 fis, clone HE

113203 AA743563Hs.10305 ESTs 113299 AW207424Hs.332594 ESTs 113367 N92359Hs.14518 ESTs, Moderately similar to A48752 B-cel 113457 816763Hs.268679 ESTs 113563 AA913635Hs.326413 Homo sapiens cDNA FLJ20812 fis, clone AD

113574 806874Hs.268628 ESTs, Moderately similar to ALU1 HUMAN
A

113776 AI791905Hs.95549 hypothetical protein 113790 AI244311Hs.26912 ESTs 113807 W07586Hs.8045 ESTs 4$ 113958 W86195gb:zh54e05.s1 Soares fetal_liver_spleen_ 114211 239319Hs.27347 EST

114254 AB018263Hs.180338 tumor necrosis factor receptor superfami 114349 AA745978Hs.28273 ESTs 114449 AA020736gb:ze63b11.s1 Soares retina N2b4HR Homo 114484 AA034378Hs.267319 endogenous retroviral protease 114576 AA065096gb:zm50a02.s1 Stratagene fibroblast (937 114624 AA081507gb:zn05b10.r1 Stratagene hNT neuron (937 114844 AA234826Hs.87386 EST

114906 AA234462Hs.87350 ESTs 55 115624 AK000725Hs.50579 hypothetical protein FLJ20718 115666 AF173081Hs.178215 Vertebrate LIN7 homolog 1, Tax interacti 115712 AB020649Hs.74569 KIAA0842 protein 115889 AA398841Hs.39850 hypothetical protein FLJ20517 115949 AI478427Hs.43125 esophageal cancer related gene 4 protein 116107 AL133916Hs.172572 hypothetical protein FLJ20093 116180 AA463902Hs.13522 ESTs, Weakly similar to 138022 hypotheti 116267 AW968703Hs.30085 hypothetical protein FLJ23186 116291 AW410377Hs.41502 hypothetical protein FLJ21276 116527 AW194253Hs.68607 ESTs ()$116659 BE314852Hs.168694 Homo Sapiens clone 23763 unknown mRNA, p 116708 F10528Hs.70001 ESTs, Moderately similar to JC6169 nucle 117058 AW801806gb:ILS-UM0070-110400-062-g07 UM0070 Homo 117151 Hs.42373 ESTs 5 117226 gb:yx39b10.s1 Soares melanocyte10 N20468 2NbHM Ho 117323 Hs.43387 ESTs 5 117571 Hs.44584 ESTs 3 117624 Hs.82364 ESTs, Weakly similar5 N26627 to JC4124 pregnancy 117673 Hs.184043 Homo Sapiens Ets-110 N40551 binding protein (E1B) 117847 Hs,182391 ESTs 10 117877 Hs.44268 myelin gene expression10 AW263476 factor 2 117919 Hs.279472 ESTs 5 118049 gb:yv55f09.s1 Soaresfetalliverspleen3 118413 Hs.90960 ESTs 10 118613 Hs.49688 ESTs 5 118664 Hs.230619 EST ' 118858 Hs.102981 Homo sapiens mRNA;3 AL122040 cDNA DKFZp434G1972 (f 118902 Hs.293907 hypothetical protein5 119039 Hs.252097 pregnancy specific3 AI160570 beta-1-glycoprotein 6 119159 Hs,15020 homolog of mouse 5 AF142419 quaking QKI (KH domain 119216 Hs.221849 ESTs 5 119317 Hs.51305 v-maf musculoaponeurotic10 AK002001 fibrosarcoma (a 119366 gb:yd20f04.s1 Soaresfetal 5 T77892 liver spleen 119378 Hs.90949 EST 5 119528 Empirically selected from 10 W38051 AFFX single pr 119792 Hs.80552 dermatopontin 3 119800 Hs.58314 ESTs 10 ~,$119817 Hs.159690 ESTs 5 119835 Hs.58429 ESTs 5 119923 Hs.62954 femtin, heavy'polypeptide5 119961 Hs.337461 Human putative 5 U34249 zinc finger protein (ZNFB

120379 gb:DKFZp434B1822_r1434 (synonym:10 AL042725 htes3) 30 120931 Hs.97162 ESTs 5 121037 Hs.142373 ESTs 5 121282 Hs.97334 ESTs 5 121382 Hs.111939 Homo sapiens cDNA 5 AA405763 FLJ20470 fis, clone KA

121764 Hs.164851 ESTs, Weakly similar5 AA421452 to KIAA0926 protein 35 122034 Hs.98017 Homo sapiens cDNA 10 AK000229 FLJ20222 fis, clone CO

122441 Hs.99116 EST 10 122756 Hs.95898 ESTs 10 122771 Hs.97282 ESTs, Highly similar5 AW135093 to G100_HUMAN 110 K

123601 Hs.112645 Homo sapiens mRNA;5 AA609122 cDNA DKFZp434D2472 (f 40 123623 Hs.97508 a disintegrin and 5 A1024595 metalloproteinase doma 123941 gb:af47a02.s1 Soares_totaLfetus_Nb2HF8_10 124215 gb:yr44a01.r1 Soaresfetalliverspleen5 124276 gb:ys91a11.s1 Soares retina 5 H83465 N2b5HR Homo 124680 Hs.163953 hypothetical protein5 45 125099 Hs.112377 comic al thymocyte10 NM_014312 receptor (X. laevis 125121 Hs.48403 hypothetical protein10 125188 Hs.271749 ESTs, Moderately 5 BE299567 similar to ALUS HUMAN A

125284 Hs.103253 perilipin 10 125906 Hs.17775 p75NTR-associated 5 BE256206 cell death executor; 0 $0 128484 Hs.270503 ESTs, Weakly similar10 AA485421 to ALU7 HUMAN ALU S

128511 Hs.10082 potassium intermediatelsmall10 NM_002250 conductance 128538 Hs.101189 ESTs 5 128606 Hs.283040 hypothetical protein5 128850 Hs.180817 chromosome 11 open10 AA193106 reading frame 23 S 128870 Hs.75309 eukaryotic translation10 S H39537 elongation factor 128903 Hs.296176 STAT induced STAT 10 AW150717 inhibitor 3 128931 Hs.107242 Homo sapiens cDNA 10 N62889 FLJ12965 fis, clone NT

129001 Hs.107812 BPOZ protein 5 129091 Hs.301463 Human Chromosome 5 AA056483 16 BAC clone CIT987SK-A

60 129101 Hs.108665 zinedin 10 NM_013403 129146 Hs.108924 SH3-domain protein5 AL117472 5 (ponsin) 129213 Hs.109525 ESTs, Weakly similar3 AI146494 to IRX2 HUMAN IROQU

129228 Hs.239307 tyrosyl-tRNA synthetase5 129265 Hs.171695 dual specificity 5 AA530892 phosphatase 1 6$ 129285 Hs.11006 ESTs, Moderately 10 BE617015 similar to T17372 plasm 129346 Hs.288908 WAS protein family,10 AF110141 member 2 129368 Hs.110776 STAT induced STAT 5 NM 003877 inhibitor-2 107459 Empirically selected 10 W38002 from AFFX single pr 107683 Hs.47623ESTs 10 107711 Hs.220687ESTs 10 129371 X06828Hs.110802 von Willebrand factor 129381 AW245805Hs.110903 claudin 5 (transmembrane protein deleted 10 129440 W37944Hs.4007 Sarcolemmal-associated protein 5 129441 BE061069Hs.301943 KIAA0467 protein 10 129516 AF020038Hs.11223 isocitrate dehydrogenase 1 (NADP+), solu 10 129554 BE222078Hs.113069 ESTs 10 129684 BE622468Hs.11924 ESTs, Weakly similar to 138022 hypotheti 5 129702 AI304966Hs.12035 ESTs, Weakly similar to 138022 hypotheti 5 129778 AK001676Hs.12457 hypothetical protein 1 129893 AK000956Hs.13209 hypothetical protein ~ FLJ10094 5 129928 AI338993Hs.134535 ESTs 5 129973 AJ251760Hs.273385 guanine nucleotide binding protein (G pr 5 129977 NM Hs.1395 early growth response 000399 2 (Krox-20 (Drosop 5 130014 NM Hs.143102 amine oxidase, copper 001158 containing 2 (reti 5 1 130085 M62402Hs.274313 insulin-like growth S factor binding prote 10 130089 AA452006Hs.333199 ESTs 5 130162 W80711Hs.319946 Homo sapiens mRNA far KIAA1727 protein, 5 130243 D88435Hs.153227 cyclin G associated kinase 10 130315 AI241084Hs.154353 nonselective sodium potassiumiproton exc 5 130339 AA435746gb:zt79e03.s1 Soares_testis_NHT
Homo sap 5 130400 V00517Hs.283108 hemoglobin, gamma G

130436 NM_001928Hs.155597 D component of complement (adipsin) 10 130478 X72308Hs.251526 small inducible cytokine A7 (monocyte ch 5 130480 BE222978Hs.15760 MYG1 protein 10 2$ 130494 AW390834Hs.75874 pregnancy-associated plasma protein A 5 130563 BE270472Hs.279900 HSPC015 protein 10 130589 AL110226Hs.16441 DKFZP434H204 protein 130606 AI652143Hs.288382 hypothetical protein 130634 AI769067Hs.127824 ESTs, Weakly similar to T28770 hypotheti 3 130683 AA993269Hs.17872 Homo sapiens, clone IMAGE:3875012, mRNA 10 130689 NM_006691Hs.17917 extraceliular link domain-containing 130716 AA232075Hs.18259 XPA binding protein 1; putative ATP(GTP) 5 130718 AF263462Hs.18376 KIAA1319 protein 10 130722 N41322Hs.18441 ESTs 5 35 130798 M81349Hs.1955 serum amyloid A4, constitutive 130840 BE048821Hs.20144 small inducible cytokine subfamily A (Cy 10 131184 AB040935Hs.23954 cerebral cell adhesion molecule 10 131261 AA360419Hs.171776 inositol(myo)-1(or4)-monophosphatase 131282 X03350Hs.4 alcohol dehydrogenase 1B
(class I), beta 10 4~ 131328 AW939251Hs.25647 v-fos FBJ murine osteosarcoma viral onto 10 131340 AK000393Hs.25817 BTB (POZ) domain containing 131341 AF110908Hs.297660 TNF receptor-associated factor 3 5 131406 H83294Hs.284122 Wnt inhibitory factor-1 131489 BE394648Hs.27414 hypothetical protein 4$ 131543 AW966881Hs.41639 programmed cell death 131692 BE559681Hs.30736 KIAA0124 protein 5 131753 AA829286Hs.332053 serum amyloid A1 10 131756 AA443966Hs.31595 ESTs 10 131785 H69342Hs.26320 TRABID protein 10 131815 AA021258Hs.32753 ESTs 5 131819 BE244961Hs.173103 FE65-LIKE 2 5 131828 AJ000263Hs.278658 keratin, hair, basic, 6 (monilethrix) 10 131888 AW294659Hs.34054 Homo sapiens cDNA: FLJ22488 fis, clone H 5 131927 AJ003112Hs.34780 doublecortex; fissencephaly, X-finked (d 5 $ 131949 AK000010Hs.258798 hypothetical protein 132115 H81604Hs.178471 KIAA0798 gene product 132177 X80818Hs.178078 glutamate receptor, metabotropic 4 5 132296 AA467752Hs.195161 ESTs 5 132426 AW118072Hs.89981 diacylglycerol kinase, zeta (104kD) 10 132477 S68874Hs.170917 prostaglandin E receptor 3 (subtype EP3) 5 132675 AI291496Hs.5476 Homo sapiens, clone IMAGE:3530123, mRNA, 10 132796 NM_006283Hs.173159 transforming, acidic coiled-coil contain 10 132898 W28548Hs.224829 ESTs 10 132905 NM_004235Hs.7934 Kruppel-like factor4 (gut) 10 6$ 132953 BE175645Hs.321264 LBP protein 32 5 133116 BE563966Hs.6529 ESTs, Weakly similar to 178885 serinelth 5 133120 NM_003278Hs.65424 tetranectin (plasminogen-binding protein 10 133139 AF052138Hs.6580 Homo sapiens cDNA: 5 FLJ23227 fis, clone C

133163 AA668224Hs.6634 Homo Sapiens cDNA: 5 FLJ22547 fis, clone H

133268 AW956781Hs.293937 ESTs, Weakly similar5 to FXD2_HUMAN FORKH

133272 NM Hs.69423 kaliikrein 10 (KLK10)5 002776 (PRSSL1) (nest) _ gb:zq80h09.s1 Stratagene 5 133379 AA207059hNT neuron (937 133407 AF017987Hs.7306 secreted frizzled-related5 protein 1 133552 H21497Hs.7471 BBP-like protein 5 133702 L02321Hs.75652 glutathione S-transferase5 133719 H26904Hs.75736 apolipoprotein D 5 1 133731 N71725Hs.272572 hemoglobin, alpha 10 ~ 2 133789 T85626Hs.76239 hypothetical protein5 134007 AF072441Hs.7840 calcineurin binding 10 protein 1 134055 D86062Hs.182423 ES1 (zebrafish) 10 protein, human homolog o 134111 AI372588Hs.8022 TU3A protein 10 1$134117 AA081846Hs.7921 Homo Sapiens mRNA; 10 cDNA DKFZp566E183 (fr 134177 BE243319Hs.79672 KIAA0652 gene product5 134308 AW905827Hs.81454 ketohexokinase (fructokinase)10 134361 BE549343Hs.82208 acyl-Coenzyme A 5 dehydrogenase, very long 134369 AF207664Hs.8230 a disintegrin-like 5 and metalloprotease ( 2~134449 L34155Hs.83450 laminin, alpha 3 5 (nicein (150kD), kalini 134467 AI190413Hs.8373 ESTs 10 134496 M64936gb:Homo Sapiens retinoic 10 acid-inducible 134510 NM_002757Hs.250870 mitogen-activated 10 protein kinase kinase 134550 M26315Hs.85258 CD8 antigen, alpha 10 polypepfide (p32) 2$134577 BE244323Hs.85951 exportin, tRNA (nuclear5 export receptor 134591 073394Hs.166085 killer cell immunoglobulin-like5 receptor 134678 AL008583Hs.182595 dynein, axonemal, 5 light polypeptide 4 134728 D10216Hs.89394 POU domain, class 5 1, transcription facto 134758 NM_000078Hs.89538 cholesteryl ester 10 transfer protein, plas 134786 T29618Hs.89640 TEK tyrosine kinase,10 endothelial (venous 134912 T87521Hs.261457 ESTs 5 134963 NM_003394Hs.91985 wingless-type MMTV 10 integration site fami 134969 H22570Hs.172572 hypothetical protein5 135001 AA302517Hs.92732 KIAA1444 protein 5 3 135066 X04430Hs.93913 interieukin 6 (interferon,10 S beta 2) 135173 AL036557Hs.95910 putative lymphocyte10 GOIG1 switch gene 135197 076456Hs.190787 tissue inhibitor 5 of metalloproteinase 4 135219 AB002361Hs.96633 KIAA0363 protein 5 135250 083171Hs.97203 small inducible 5 cytokine subfamily A (Cy 135304 AA416829Hs.191597 ESTs 5 135337 AA905406Hs.9905 ESTs, Weakly similar3 to unnamed protein 135417 X55019Hs.99975 cholinergic receptor,10 nicotinic, delta p 101367 X03350Hs.4 alcohol dehydrogenase 5 1B (class I), beta 128870 H39537Hs.75309 eukaryotic translation5 elongation factor 4$129381 AW245805Hs.110903 claudin 5 (transmembrane5 protein deleted 130085 M62402Hs.274313 insulin-like growth5 factor binding prote 130689 NM_006691Hs.17917 extracellular link 10 domain-containing 1 133120 NM_003278Hs.65424 tetranectin (plasminogen-binding3 protein 133407 AF017987Hs.7306 secreted frizzled-related5 protein 1 $0133731 N71725Hs.272572 hemoglobin, alpha 5 134369 AF207664Hs.8230 a disintegrin-like 5 and metalloprotease ( 135066 X04430Hs.93913 interleukin 6 (interferon,10 beta 2) -135173 AL036557Hs.95910 putative lymphocyte5 GOIG1 switch gene 322580 AK001852Hs.274151 ligatin 5 S$408790 AW580227Hs.47860 neurotrophic tyrosine10 kinase, receptor, type 2 418043 AW377752Hs.83341 AXL receptor tyrosine5 kinase 427458 BE208364Hs.29283 ESTs, Weakly similar5 to LKHU protecglycan link 446674 AA563892Hs.306000 solute carrier 10 family 4 (anion exchanger), memb 449826 085642Hs.138506 ESTs ' 5 RC_H15814 Human apM1 mRNA for GS3109 c collagen s (novel adipose specifi 10 YEL024wIRIPI 3 EST-YEL024wIRIP1 1~$

TABLE lA
Table 1 A shows the accession numbers for those plceys lacking unigeneID's for Table 1.
For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT Number Accessions 108497 110079_2 AA074897 AA113914 AA064871 AA079329 AA071309 AA084710 AA129030 124215 1597154 1 H62570 H59063 ' 117058 1219924_1 AW801806 H90434 BE086530 111168 38585_1 A1798376 S46400 AW811617 AW811616 W00557 BE142245 AW858232 3 'J AA157718 AA157719 AA100472 AA100774 AA130756 AA157705 AA157730 AA157715 103747 117944_1 AA081995 AA101099 103750 118365_1 AA126129 AA126033 AA082561 105239 34624_1 AA221036 887170 BE537068 BE544757 C18935 AW812058 T92565 $ 0 120379 34624_3 AL042725 BE063316 AW975610 AA457591 BE062092 A1655202 114624 111686_1 AA081507 AA070071 AA070840 AA084362 106851 322947_1 A1458623 AA639708 AA485409 822065 AA485570 $ 5 108392 113549_1 AA075124 AA075208 100654 tigr_HT2969 A03758 A06977 A15293 D17029 D17107 D17171 L00132 L00133 100702 tigr_HT3413 L27065 60 102208 6735_9 U22961 AA203623 AA503337 A1174733 A1192802 C06092 AA035357 123941 genbank_AA621529 AA621529 118049 genbank_N53145 N53145 102800 14782_20 AA313538 088895 088902 104106 AA422123 i atAA422123 i 111738 genbanILR26065 826065 113149 genbank_T51588 751588 113958 genbank_W86195 W86195 108335 genbank_AA070500 AA070500 108351 genbank_AA071193 AA071193 108441 genbanhAA079079 AA079079 124276 genbank_H83465 H83465 101447 entrez M21305 M21305 117226 genbank,N20468 N20468 4$ 133379 genbanILAA207059 AA207059,AA207241 119366 genbank_T77892 777892 119528 NOT FOUND entre~,W38051 W38051 112588 genbank_R77302 877302 114449 genbank_AA020736 AA020736 S0 114576 genbanILAA065096 AA065096 107459 W38002_s_at W38002_s 130339 genbanILAA435746 AA435746 TABLE 2: Figure 2 from BRCA 001 US
Table 2 shows genes downregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: ExempIarAccession number, Genbank accession number 1 ~ UnigenelD: Unigene number Unigene Title: Unigene gene title R1: Ratio of normal breast tissue to tumor 1$ Pkey ExAccnUnigenelDUnigene Tittle R1 100499 T51986Hs.283108hemoglobin, gamma G

100549 BE142019Hs.222056Homo sapiens cDNA FLJ11572 fis, clone HE 10 100654 A03758 NM_000477*:Homo Sapiens albumin (ALB), m 10 100971 BE379727Hs.83213fatty acid binding protein 4, adipocyte 10 101184 NM Hs.460activating transcription 001674 factor 3 10 101336 NM_006732Hs.75678FBJ marine osteosarcoma viral oncogene h 10 101367 X03350Hs.4 alcohol dehydrogenase 1 B (class I), beta 101447 M21305 gb:Human alpha satellite and satellite 3 10 101461 N98569Hs.76422phospholipase A2, group IIA (platelets, 10 101511 M27826Hs.267319endogenous retroviral protease 10 101736 M74447Hs.502transporter 2, ATP-binding cassette, sub-famil 102208 U22961 gb:Human mRNA clone with similarity to 102450 U48251Hs.75871protein kinase C binding protein 1 10 30 102800 AA313538 gb:EST185419 Colon carcinoma (HCC) cell 10 102857 NM Hs.76461retinol-binding protein 006744 4, interstitial 10 102990 AA829286Hs.332053serum amyloid A1 10 103747 AA081995 gb:zn26dO6.r1 Stratagene neuroepithelium 10 103812 AA137107Hs.326391Homo Sapiens, clone MGC:16638, mRNA, com 3S 104093 850727Hs.336970ESTs 10 104109 AL353957Hs.284181hypothetical protein DKFZp434P0531 10 104250 F06638Hs.12440Homo Sapiens clone 24734 mRNA sequence 10 104492 N73185Hs.94285EST 10 104506 N91071Hs.109650ESTs 10 40 104532 A1498763Hs.203013hypothetical protein 104677 AA009764Hs.190380ESTs 10 104711 AA017245Hs.32794ESTs 10 104731 AA019300Hs.125070ESTs, Moderately similar to 154374 gene 10 105005 AI298208Hs.28805ESTs 10 45 105036 AA130390Hs.25549hypothetical protein 105239 AA221036 gb:zr03f12.r1 Stratagene NT2 neuronal pr 10 106052 N79885Hs.6382E$Ts, Highly similar to T00391 hypotheti 106181 AI803651Hs.191608ESTs 10 106283 A1085846Hs.25522KIAA1808 protein 10 106379 AL042069Hs.119021DKFZP434N061 protein 106451 AW235928Hs.313182ESTs 10 106491 AA135688Hs.10083Homo Sapiens, clone IMAGE:4139786, mRNA, 106782 AW054886Hs.25682Homo Sapiens mRNA for KIAA1863 protein, 10 107124 A8006532Hs.31442RecQ protein-like 4 SS 107148 A1005036Hs.334305GS1999fu11 10 107214 AF127026Hs.5394myosin IA 10 107242 AB020672Hs.175411KIAA0865 protein 10 107331 AI905985Hs.111805ESTs 10 107447 W28516Hs.19210hypothetical protein 107451 AL042425Hs.283976hypthetical protein 107872 BE271708Hs.95110ESTs, Weakly similar to A559431-phospha 108351 AA071193 gb:zt79b12.s1 Soares_pineal~land 109546 F01449Hs.26954Homo Sapiens mRNA; cDNA
DKFZp762G123 (fr 10 110433 AW294162Hs.301062UDP-N-acetyl-alpha-D~alactosamine:polyp 6S 110976 AL044174Hs.159526patched (Drosophila) homolog 5 111168 AI798376 gbar34b07.x1 NCI_CGAP_Ov23 Homo Sapiens 10 111651 816733Hs,20499ESTs 10 111803 AA593731Hs,325823ESTs, Moderately similar to ALUS_HUMAN A 10 114484 AA034378Hs.267319endogenous retroviral protease 10 125284 NM_002666Hs.103253perilipin 10 128850 AA193106Hs.180817chromosome 11 open reading frame 23 5 128903 AW150717Hs.296176STAT induced STAT inhibitor 129346 AF110141Hs.288908WAS protein family, member 2 10 129381 AW245805Hs.110903claudin 5 (transmembrane protein deleted 10 10129516 AF020038Hs.11223isocitrate dehydrogenase 1 (NADP+), solu 10 129554 BE222078Hs.113069ESTs 10 130085 M62402Hs.274313insulin-like growth factor binding prote 130243 D88435Hs.153227cyclin G associated kinase 10 130400 V00517Hs.283108hemoglobin, gamma G

1$130436 NM Hs.155597D component of complement 001928 (adipsin) 10 130563 BE270472Hs.279900HSPC015 protein 10 130589 AL110226Hs.16441DKFZP434H204 protein 130683 AA993269Hs.17872Homo Sapiens, clone IMAGE:3875012, mRNA

130689 NM_006691Hs.17917extracellular link domain-containing 130689 AA046747Hs.17917extracellular link domain-containing 130718 N70196Hs.18376KIAA1319 protein 10 130798 M81349Hs.1955serum amyloid A4, constitutive 130840 BE048821Hs.20144small inducible cytokine subfamily A (Cy 10 131184 AB040935Hs.23954cerebral cell adhesion molecule 10 ~5131282 X03350Hs.4 alcohol dehydrogenase 1B (class I), beta 131328 AW939251Hs.25647v-fos FBJ murine ostecsarcoma viral onco 10 131543 AW966881Hs.41639programmed cell death 131753 AA829286Hs.332053serum amyloid A1 10 131785 H69342Hs.26320TRABID protein 10 30131828 AJ000263Hs.278658keratin, hair, basic, 6 (monilethrix) 10 132426 AW118072Hs,89981diacylglycerol kinase, zeta (104kD) 10 132675 AI291496Hs.5476Homo sapiens, clone IMAGE:3530123, mRNA, 132898 W28548Hs.224829ESTs 10 132905 NM_004235Hs.7934Kruppel-like factor 4 (gut) 10 3S133120 NM_003278Hs.65424tetranectin (plasminogen-binding protein 10 133407 AF017987Hs.7306secreted frizzled-related protein 1 10 133719 H26904Hs.75736apolipoprotein D 10 134007 AF072441Hs.7840calcineurin binding protein 1 10 134055 D86062Hs.182423ES1 (zebrafish) protein, human homolog o 10 40134111 AI372588Hs.8022TU3A protein 5 134117 AA081846Hs.7921Homo Sapiens mRNA; cDNA
DKFZp566E183 (fr 5 134177 BE243319Hs.79672KIAA0652 gene product 134369 AF207664Hs.8230a distntegrin-like and metalloprotease ( 10 134496 M64936 gb:Homo sapiens retinoic acid-inducible 10 45134510 NM_002757Hs.25087Dmitogen-activated protein kinase kinase 10 134550 M26315Hs.85258CD8 antigen, alpha polypeptide (p32) 5 134758 NM_000078Hs.89538cholesteryl ester transfer protein, plas 5 134963 NIV~003394Hs.91985wingless-type MMTV integration site fami 10 135066 X04430Hs.93913interleukin 6 (interferon, beta 2) 10 $0408790 AW580227Hs.47860neurotrophic tyrosine kinase, receptor, type 446674 AA563892Hs,306000solute camer family 4 (anion exchanger), memb 10 Table 2A shows the accession numbers for those pkeys lacking unigeneID's for Table 2.
For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT number Accessions 111168 38585_1 AI798376 S46400 AW811617 AW811616 W00557 BE142245 AW858232 2$ 103747 117944_1 AA081995 AA101099 105239 34624_1 AA221036 887170 BE537068 BE544757 C18935 AW812058 T92565 100654 tigr_HT2969 A03758 A06977 A15293 D17029 D17107 D17171 L00132 L00133 102208 6735_9 022961 AA203623 AA503337 A1174733 A1192802 C06092 AA035357 4$ AI444620 752290 D16931 740012 748403 758926 769195 AI133061 750850 AI400677 AA332728 751362 AI114589 806691 AI110629 AF063503 Ai140543 AA334661 AA332720 (0 AA845518 AA719124 AA883454 768850 769115 AI935509 AI150977 762890 771374 108351 genbank_AA071193 AA071193 101447 entrez_M21305 M21305 TABLE 3: Figure 3 from BRCA 001 US
Table 3 shows genes downregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number 1 o UnigenelD: Unigene number Unigene Title: Unigene gene title R1: Ratio of normal breast tissue to tumor Pkey ExAccn UnigenelD UnigeneTitle R1 101336 NM_006732 Hs.75678 FBJ murine osteosarcoma viral oncogene h 10.0 102208 022961gb:Human mRNA clone with 10.0 similarity to L

102990 AA829286Hs.332053 serum amyloid 10.0 111168 AI798376gbar34b07,x1 NCI CGAP_Ov2310.0 Homo sapiens 111803 AA593731Hs.325823 ESTs, Moderately10.0 similar to ALU5 HUMAN
A

130085 M62402Hs.274313 insulin-like 10.0 growth factor binding prote 130840 BE048821Hs.20144 small inducible 10.0 cytokine subfamily A (Cy 2$ 131543 Hs.41639 programmed cell 10.0 AW966881 death 2 133120 NM Hs.65424 tetranectin (plasminogen-binding10.0 003278 protein 134758 NM_000078Hs,89538 cholesteryl ester10.0 transfer protein, plas Table 3A shows the accession numbers for those pkeys lacking unigeneID's for Table 3. For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
1 ~ Pkey: Unique Eos probeset identifier number CAT number Gene cluster number Accession: Genbank accession numbers 15 Pkey CAT number Accessions 2o AA157719 AA100472 AA100774 AA130756 AA157705 AA157730 AA157715 AA053524 AA045564 AI694265 H60808 AA149726 AW195620 BE081333 BE073424 AW817_662 2$ AI209170 AI186653 AI127795 AI183846 H77389 AI589465 AA629390 H94306 3o D17107 NM_000477 AF190168 850724 AI248416 AI207432 AI133684 AI133345 S$ AI312890 767751 AI174983 751679 754851 H69880 N73734 AA443453 773466 H69672 TABLE 4: Figure 4 from BRCA 001 US
Table 4 shows genes upregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: ExempIarAccession number, Genbankaccession number 1 ~ UnigenelD: Unigene number Unigene Title: Unigene gene title R1: Ratio of tumor to normal breast tissue 15 Pkey ExAccn UnigenelD Unigene Title R~

100113 NM_001269Hs.84746 chromosome condensation 1 2.3 100114 X02308 Hs.82962 thymidylate synthetase 2.9 100131 D12485 Hs.11951 ectonucleotide pyrophosphataselphosphodiesterase1.9 100146 BE185499 Hs.2471 KIAA0020 gene product 1.9 100147 D13666 Hs.136348 osteoblast specific factor 7.5 2 (fasciclin I-like) (periostin) 100154 H60720 Hs.81892 KIAA0101 gene product 9.2 100163 W44671 Hs.124 gene predicted from cDNA with 1.6 a complete coding sequence 100220 AW015534 Hs.217493 annexin A2 2.0 2$ 100265 D38521 Hs.112396 KIAA0077 protein 1.5 100271 BE160081 Hs.256290 S100 calcium-binding protein13.5 A11 (calgizzarin) 100275 BE242802 Hs.154797 KIAA0090 protein 5.1 100323 D50920 Hs.23106 KIAA0130 gene product 1.9 100335 AW247529 Hs.6793 platelet-activating factor 2.7 acetylhydrolase, isoform Ib, gamma subunit (29kD) 30 100364 NM 004341 Hs.154868 carbamoyl-phosphate synthetase2.0 2, aspartate transcarbamylase, and dihydroorotase 10D372 NM 014791 Hs.184339 KIAA0175 gene product 2.6 100393 D84145 Hs.39913 novel RGD-containing protein 3.2 100400 AW954324 Hs.75790 phosphatidylinositol glycan, 1.5 class C

100418 D86978 Hs.84790 KIAA0225 protein 2.0 3 100482 M65028 Hs.81361 heterogeneous nuclear ribonucleoprotein2.9 S AIB

100518 NM_004415Hs.74316 desmoplakin (DPI, DPII) 1.9 100666 L05424 Hs.169610 CD44 antigen (homing function 5.7 and Indian blood group system) 100667 L05424 Hs.169610 CD44 antigen (homing function 9.0 and Indian blood group system) 100668 L05424 Hs.169610 CD44 antigen (homing function 7.6 and Indian blood group system) 4~ 100678 AW502935 Hs.740 PTK2 protein tyrosine kinase 53.2 100685 AA328229 Hs.184582 ribosomal protein L24 1.8 100690 AA383256 Hs.1657 estrogen receptor 1 1.6 100783 AF078847 Hs.191356 general transcription factor5.9 IIH, polypeptide 2 (44kD subunit) 100850 AA836472 Hs.297939 cathepsin B 1.7 45 100892 BE245294 Hs.180789 S164 protein 1.7 100945 AF002225 Hs.180686 ubiquitin protein ligase 1.5 E3A (human papilloma virus E6-associated protein, Angelman syndrome) 100969 AA157634 Hs.79172 solute comer family 25 (mitochondrial6.3 carrier; adenine nucleotide translocator), member 100988 AK000405 Hs.76480 ubiquitin-like 4 11.4 100999 H38765 Hs.80706 diaphorase (NADHINADPH) (cytochrome1.6 b-5 reductase) $0 101031 J05070 Hs.151738 matrix metalloproteinase 9 8.2 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase) 101045 J05614 gb:Human proliferating cell nuclear antigen5.0 (PCNA) gene, promoter region.

101077 N99692 Hs.75227 Empirically selected from AFFX 2.6 single probeset 101093 L06419 Hs.75093 procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)1.4 101161 NM_006262Hs.37044 peripherin 16.9 $ 101186 AA020956 Hs.179881 core-binding factor, beta 2.0 5 subunit 101216 AA284166 Hs.84113 cyclin-dependent kinase inhibitor1.8 3 (CDK2-associated dual specificity phosphatase) 101228 AA333387 Hs.82916 chaperonin containing TCP1, 1.7 subunit 6A (zeta 1) 101247 AA132666 Hs.78802 glycogen synthase kinase 3 1.9 beta 101249 L18964 Hs.1904 protein kinase C, iota 1.5 101332 J04088 Hs.156346 topoisomerase (DNA) ll alpha 5.2 (170kD) ~

101332 J04088 Hs.156346 topoisomerase (DNA) II alpha 3.4 (170kD) 101352 AI494299 Hs.16297 COX17 (yeast) homolog, cytochrome6.3 c oxidase assembly protein 101396 BE267931 Hs.78996 proliferating cell nuclear 4.2 antigen 101445 M21259 gb:Human Alu repeats in the region 5' 1.9 to the small nuclear rib 65 101470 NM 000546Hs.1846 tumor protein p53 (Li-Fraumeni1.6 syndrome) 101478 NM 002890Hs.758 RAS p21 protein activator (GTPase2.5 activating protein) 1 101483 M24486 Hs.76768 procollagen-proline, 2-oxoglutarate5.5 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I

101540 J04977 Hs.84981 X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining 2.1 101573 AW248421 Hs.250758 proteasome (prosome, macropain)1.6 268 subunit, ATPase, 3 101580 NM_012151 Hs.83363 coagulation factor VIII-associated5.7 (intronic transcript) 101592 AF064853 Hs.91299 guanine nucleotide binding 1.8 protein (G protein), beta polypeptide 2 101592 AF064853 Hs.91299 guanine nucleotide binding 5.6 protein (G pr 101621 BE391804 Hs.62661 guanylate binding protein 2.4 1, interferon-inducible, 67kD

101702 AW504089 Hs.179574 protein phosphatase 2 (formerly1.3 2A), regulatory subunit 8 (PR 52), alpha isoform 10101734 M74099 Hs.147049 cut (Drosophila)-like 1 (CCAAT2.1 displacement protein) 101759 M80244 Hs.184601 solute carrier family 7 (cationic5.0 amino acid transporter, y+system), member 5 101767 M81057 Hs.180884 carboxypeptidase B1 (tissue) 14.4 101782 AA306495 Hs.1869 phosphoglucomutase 1 5.2 101805 AW409747 Hs.75612 stress-induced-phosphoprotein8.6 1 (Hsp701Hsp90-organizing protein) 1$101806 AA586894 Hs.112408 S100 calcium-binding protein8.9 A7 (psoriasin 1) 101810 NM_000318Hs.180612 peroxisomal membrane protein3.2 3 (35kD, Zellweger syndrome) 101879 AA176374 Hs.243886 nuclear autoantigenic sperm 1.6 protein (histone-binding) 101911 AA441787 Hs.119689 glycoprotein hormones, alpha31.3 polypeptide 101920 AF182645 Hs.8024 IK cytokine, down-regulator 1.8 of HLA II

101973 041514 Hs.80120 UDP-N-acetyl-alpha-D~galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GaINAo-T1) 2.4 101983 AI904232 Hs.75323 prohibitin 8.4 102009 BE245149 Hs.82643 protein tyrosine kinase 9 1.3 102036 BE250127 Hs.82906 CDC20 (cell division cycle 2.0 20, S. cerevisiae, homology 102083 T35901 Hs.75117 interieukin enhancer binding 1.6 factor 2, 45kD

2$102083 T35901 Hs.75117 interleukin enhancer binding 1.3 factor 2, 4 102107 BE258602 Hs.182366 heat shock protein 75 1.4 102123 NM 001809Hs.1594 centromere protein A (17kD) 1.8 102165 BE313280 Hs.159627 death associated protein 4.6 102198 AW950852 Hs.74598 polymerase (DNA directed), 4.3 delta 2, regulatory subunit (50kD) 102217 AA829978 Hs.301613 JTV1 gene 6.7 102220 024389 Hs.65436 lysosomal 4.3 102234 AW163390 Hs.278554 heterochromatin-like protein1.9 102260 AL039104 Hs.159557 karyopherin alpha 2 (RAG 4.4 cohort 1, imporfin alpha 1) 102302 AA306342 Hs.69171 protein kinase C-like 2 2.7 35102330 BE298063 Hs.77254 chromobox homolog 1 (Drosophila1.5 HP1 beta) 102339 BE378432 Hs.95577 cyclin-dependent kinase 4 2.3 102348 037519 Hs.87539 aldehyde dehydrogenase 3 family,2.0 member B2 102349 AU077055 Hs.289107 baculoviral IAP repeat-containing3.2 102369 039840 Hs.299867 hepatocytenuclearfactor3,alpha2.0 102374 033635 Hs.90572 PTK7 protein tyrosine kinase 6.2 102391 AA296874 Hs.77494 deoxyguanosine kinase 1.5 102455 048705 Hs.75562 discoidin domain receptor family,6.9 member 1 102465 NM 001359Hs.81548 2,4-dienoyl CoA reductase 1.8 1, mitochondria) 102488 050939 Hs.61828 amyloid beta precursor protein-binding1.5 protein 1, 59kD

4S102489 AL080116 Hs.74420 origin recognition complex, 3.3 subunit 3 (yeast homology-like 102494 AI188137 Hs.75193 COP9 homolog 2.1 102501 AF217197 Hs.74562 siah binding protein 1; FBP 3.2 interacting repressor; pyrimidine tract binding splicing 102522 BE250944 Hs.183556 solute carrier family 1 (neutral2.8 amino acid transporter), member 5 102532 AF040253 Hs.70186 suppresser of Ty (S.cerevisiae)5.7 homolog 102564 059423 Hs.79067 MAD (mothers againstdecapentaplegic,2.3 Drosophila) homolog 1 102568 W81489 Hs.223025 RAB31, member RAS oncogene 5.3 family 102580 060808 Hs.152981 CDP-diacylglycerol synthase 2.1 (phosphatidate cytidylyltransferase) 1 102581 AU077228 Hs.77256 enhancer of zeste (Drosophila)1.6 homolog 2 102582 061232 Hs.32675 tubulin-specific chaperone a 2.1 $$102617 AW161453 Hs.198767 COP9 (constitutive photomorphogenic,1.8 Arabidopsis, homology subunit 5 102618 AL037672 Hs.81071 extracellular matrix protein 5.8 102627 AL021918 Hs.158174 zinc finger protein 184 (Kn~ppel-like)1.3 102663 NM_002270Hs.168075 karyopherin (importin) beta 1.8 102676 BE262989 Hs.12045 putative protein 2.3 102687 NM_007019Hs.93002 ubiquitin carrier protein 4.3 102689 096132 Hs.171280 hydroxyacyl-Coenzyme A dehydrogenase,6.0 type II

102696 BE540274 Hs.239 forkhead box M1 4.2 102704 AU077058 Hs.54089 BRCA1 associated RING domain 1.9 102705 T97490 Hs.50002 small inducible cytokine subfamily2.3 A (Cys-Cys), member 19 65102750 AB014460 Hs.66196 nth (E.coli endonuclease III)-like1.2 102801 BE252241 Hs.38041 pyridoxal (pyridoxine, vitamin6.4 86) kinase 102812 090549 Hs.236774 high-mobility group (nonhistone1.6 chromosomal) protein 17-like 3 102827 BE244588 Hs.6456 chaperonin containing TCP1, 5.6 subunit 2 (beta) 102831 AA262170 Hs.80917 adaptor-related protein complex2.0 3, sigma 1 subunit 102844 AV653790 Hs.324275 WW domain-containing protein1.3 102868 X02419 Hs.77274 plasminogen activator, urokinase4.4 $ 102925 BE440142 Hs.2943 signal recognition particle 1.9 19kD

102935 BE561850 Hs.80506 small nuclear ribonucleoprotein2.4 polypeptide A' 102968 AU076611 Hs.154672 methylene tetrahydrofolate dehydrogenase (NAD+dependent), methenyltetrahydrofolate cyclohydrolase2.7 102983 BE387202 Hs.118638 non-metastatic cells 1, 3.1 protein (NM23A) expressed in 102965 U95742 Hs.2707 G1 to S phase transition 1 5.2 1 103023 AW500470 Hs.117950 multifunctional polypeptide1.6 ~ similar to SAICAR synthetase and AIR carboxylase 103038 AP,926960 Hs.334883 CDC28 protein kinase 1 2.5 103060 NM_005940Hs.155324 matrix metalloproteinase 4.5 11 (MMP11; stromelysin 3) 103080 AU077231 Hs.82932 cyclin D1 (PRAD1: parathyroid3.1 adenomatosis 1) 103089 D31152 Hs.179729 collagen, type X, alpha 1 2.4 (Schmid metaphyseal chondrodysplasia) 1$ 103177 BE244377 Hs.48876 famesyl-diphosphate famesyltransferase3.5 1 ' 103178 AA205475 Hs.275865 ribosomal protein S18 9.9 103179 NM_001777Hs.82685 CD47 antigen (Rh-related 1.3 antigen, integrin-associated signal transducer) 103181 X69636 Hs.334731 Homo Sapiens, clone IMAGE:3448306,2.0 mRNA, partial cds 103185 NM 006825Hs.74368 transmembrane protein (63kD),1.6 endoplasmic reticulumlG0lgi intermediate compartment 103191 AA401039 Hs.2903 protein phosphatase 4 (formerly2.5 X), catalytic subunit 103193 NM 004766Hs.75724 coatomer protein complex, 2.2 subunit beta 2 (beta prime) 103194 NM 004939Hs.78580 DEADIH (Asp-Glu-Ala-AspIHis)6.3 box polypeptide 1 103206 X72755 Hs.77367 monokine induced by gamma interferon8.8 103223 BE275607 Hs.1708 chaperonin containing TCP1, 3.0 subunit 3 (gamma) 2$ 103232 X75962 Hs.129780 tumor necrosis factor receptor1.8 superfamily, member 4 103238 AI369285 Hs.75189 death-associated protein 5.6 103297 NM 001545Hs.9078 immature colon carcinoma transcript1.9 103330 AI803447 Hs.77496 small nuclear ribonucleoprotein2.5 polypeptide G

103349 X89059 gb:H.sapiens mRNA for unknown protein 1.6 expressed in macrophage 3 103376 AL036166 Hs.323378 coated vesicle membrane 1.8 0 protein 103391 X94453 Hs.114366 pyrroline-5-carboxylate synthetase2.3 (glutamate gamma-semialdehyde synthetase) 103392 X94563 gb:H.sapiens dbilacbp gene exon 1 & 4.0 2.

103430 BE564090 Hs.20716 translocase of inner mitochondria!1.3 membrane 17 (yeast) homolog A

103491 AF264750 Hs.288971 myeloidllymphoid or mixed-lineage5.6 leukemia 3 3$ 103505 AL031224 Hs.33102 transcription factorAP-2 5.1 beta (activating enhancer-binding protein 2 beta) 103547 A1376722 Hs.180062 proteasome (prosome, macropain)9.7 subunit, beta type, 8 (large multifunctional protease 7) 103588 NM_006218Hs.85701 phosphoinosi6de-3-kinase, 2.0 catalytic, alpha polypeptide 103613 NM_000346Hs.2316 SRY (sex determining region 1.3 Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) 103621 BE379766 Hs.150675 polymerase (RNA) II (DNA 2.0 directed) polypeptide K (7.OkD) 40 103622 AA609685 Hs.278672 membrane component, chromosome2.3 11, surface marker 1 103727 AI878883 Hs.296381 growth factor receptor-bound1.3 protein 2 103749 AL135301 Hs.8768 hypothetical protein FLJ108491.8 103754 A1015709 Hs.172089 Homo Sapiens mRNA; cDNA 1.3 DKFZp58612022 (from clone DKFZp58612022) 103780 AA094752 Hs.169992 hypothetical 43.2 Kd protein7.5 4$ 103795 H26531 Hs.7367 Homo Sapiens BTB domain protein1.2 (BDPL) mRNA, partial cds 103797 AA080912 gb:zn04d03.r1 Stratagene hNT neuron 1.5 (937233) Homo sapiens cDNA clone 5' similar 103813 A1042582 Hs.181271 CGI-120 protein 1.5 103855 W02363 Hs.302267 hypothetical protein FLJ103301.5 103886 AK001278 Hs.105737 hypothetical protein FLJ104166.5 similar to constitutive photomorphogenic protein $~ 104052 NM_002407Hs.97644 mammaglobin 2 2.9 104079 AA251242 Hs.103238 ESTs 1.4 104174 AA478984 Hs.6451 PR00659 protein 5.6 104227 AB002343 Hs.98938 protocadherin alpha 9 1.6 104275 AI751970 Hs.101067 GCN5 (general control of 5.4 amino-acid synthesis, yeast, homology-like 2 $$ 104325 BE379766 Hs.150675 polymerase (RNA) II (DNA 6.3 directed) polypeptide K (7.OkD) 104370 AA324597 Hs.21851 Homo Sapiens cDNA FLJ12900 1.6 fis, clone NT2RP2004321 104423 883113 Hs.1432 protein kinase C substrate 80K-H5.2 104482 AB037762 Hs.44268 myelin gene expression factor1.2 104532 AI498763 Hs.203013 hypothetical protein FLJ127482.1 104563 AL117403 Hs.306189 DKFZP434F1735 protein 1.2 104667 AI239923 Hs.30098 ESTs 1.3 104757 AI694413 Hs.332649 olfactory receptor, family 2.3 2, subfamily 1, member 6 104804 AI858702 Hs.31803 ESTs, Weakly similar to N-WASP1.3 [H.sapiens]

104806 AB023175 Hs.22982 KIAA0958 protein 2.3 6S 104827 AW052006 Hs.8551 PRP41STKIWD splicing factor 10.9 104846 AI250789 Hs.32478 ESTs 5.6 104854 AA041276 Hs.154729 3-phosphoinositide dependent12.3 protein kinase-1 104867 AA278898 Hs.225979 hypothetical protein similar2.0 to small G proteins, especially RAP-2A

104871 T78044 Hs.28893 Homo Sapiens mRNA; cDNA DKFZp564023641.3 (from clone DKFZp56402364) 104896 AW015318 Hs.23165 ESTs 17.7 104909 AW408164 Hs.249184 transcription factor 19 (SC1)5.0 $ 104916 AW958157 Hs.155489 NS1-associated protein 1 1.7 104919 AA026880 Hs.25252 prolactin receptor 1.4 104930 AF043467 Hs.32893 neurexophilin 2 2.2 104973 NM_015310Hs.6763 KIAA0942 protein 5.0 104974 Y12059 Hs.278675 bromodomain-containing 4 1.4 1 104975 AL136877 Hs.50758 SMC4 (structural maintenance 2.4 ~ of chromosomes 4, yeast)-like 1 104975 AL136877 Hs.50758 SMC4 (structural maintenance 2.3 of chromoso 104978 A1199268 Hs.19322 Homo sapiens, Similar to R1KEN
cDNA 2010317E24 gene, clone 1MAGE;3502019, mRNA, partial cds 7.2 104979 AA937934 Hs.321062 ESTs 1.3 104994 A1499930 Hs.334885 mitochonddal GTP binding 3.5 protein 1$ 105009 BE379584 Hs.34789 dolichyl-diphosphooligosaccharide-protein5.5 glycosyltransferase 105012 AF098158 Hs.9329 chromosome 20 open reading 3.3 frame 1 105028 A1050715 Hs.2331 E2F transcription factor 5, 2.2 p130-binding 105032 AA127818 gb:z112a02.s1 Soares_pregnant_uterus_NbHPU6.8 Homo Sapiens cDNA clone IMAGE:501674 3' 105039 AA907305 Hs.36475 ESTs 2.5 105041 AB037716 Hs.26204 KIAA1295 protein 2.2 105045 BE242899 Hs.129951 speckle-type POZ protein 3.8 105079 AA151342 Hs.12677 CGI-147 protein 9.5 105087 AA147884 Hs.9812 Homo Sapiens cDNA FLJ14388 5.6 fis, clone HEMBA1002716 105088 H58589 Hs.35156 Homo sapiens cDNA FLJ11027 fis,2.2 clone PLACE1004114 ~$ 105095 278407 Hs.27023 vesicle transport-related protein2.2 105110 BE387350 Hs.33122 KIAA1160 protein 1.6 105126 AW975433 Hs.36288 ESTs 6.3 105127 AA045648 Hs.301957 nudix (nucleoside diphosphate2.1 linked moiety X)-type motif 5 105141 AA164687 Hs.177576 mannosyl (alpha-1,3-)-glycoprotein2.7 beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A

30 105158 AW976357 Hs.234545 hypothetical protein NUF2R 1.9 105169 BE245294 Hs.180789 S164 protein 1.7 105186 AA191512 Hs.28005 Homo Sapiens cDNA FLJ11309 4.8 fis, clone PLACE1010076 105254 AA071276 Hs.19469 KIAA0859 protein 1.9 105281 AA263143 Hs.24596 RAD51-interacting protein 2.8 3 105288 N99673 Hs.3585 ESTs, Weakly similar to AF12674311.9 $ DNAJ domain-containing protein MCJ [H.sapiens]

105302 AA700122 Hs.3355 sentrin-specific protease 8.0 105331 AW270037 Hs.179507 KIAA0779 protein 1.8 105359 NM_016015Hs.8054 CGI-68 protein 8.2 105366 BE264645 Hs.282093 hypothetical protein FLJ219185.0 105373 AW887701 Hs.32356 hypothetical protein FLJ206282.5 105374 BE242803 Hs.262823 hypothetical protein FLJ103262.2 105387 AW592146 Hs.108636 membrane protein CH1 2.3 105393 AF167570 Hs.256583 intedeukin enhancer binding 5.4 factor 3, 90kD

105399 BE386877 Hs.334811 Npw38-binding protein NpwBP 1.6 4$ 105400 AF198620 Hs.65648 RNA binding motif protein 1.6 105445 AA252395 gb:zs12g10.s1 NCI CGAP_GCB1 Homo Sapiens cDNA clone IMAGE;685026 3', mRNA sequence. 5.0 105507 BE268348 Hs.226318 CCR4-NOT transcription complex,1.6 subunit 7 105529 AA113449 Hs.32471 hypothetical protein FLJ203641.3 105530 AB023179 Hs.9059 KIAA0962 protein 3.4 105547 AA262640 Hs.27445 unknown 9.3 105564 BE616694 Hs.288042 hypothetical protein FLJ142991.4 105596 AA579535 Hs.18490 hypothetical protein FLJ2045210.9 105597 AF054284 Hs.334826 splicing factor 3b, subunit 2.9 1,155kD

105608 AI808201 Hs.287863 hypothetical protein FLJ124751.7 $ 105610 AA280072 Hs.99872 fetal Alzheimer antigen ~ 1.4 $

105617 AK000892 Hs.4069 glucocorticoid modulatory element1.7 binding protein 1 105620 AW302245 Hs.181390 casein kinase 1, gamma 2 5.5 105658 AA985190 Hs.246875 hypothetical protein FLJ200599.4 105697 AW499988 Hs.27801 zinc finger protein 278 2.0 105708 826944 Hs.180777 Homo Sapiens mRNA; cDNA DKFZp564M02641.7 (from clone DKFZp564M0264) 105743 BE246502 Hs.9598 sema domain, immunoglobulin 2.6 domain (Ig), transmembrane domain (TM) and short 105746 AW151952 Hs.46679 hypothetical protein FLJ207391.5 105759 AI123118 Hs.15159 chemokine-like factor, alternatively1.3 spliced 105771 AI267720 Hs.153221 synovial sarcoma, translocated1.6 to X chromosome (7$105820 AA741336 Hs.152108 transcriptional unit N143 2.2 105826 AA478756 Hs.194477 E3 ubiquitin ligase SMURF2 1.3 105856 AI262106 Hs.12653 ESTs 2.4 105858 AF151066 Hs,281428 hypothetical protein 2.9 105875 AK001708 Hs.32271 hypothetical protein FLJ108461.4 105930 AF016371 Hs.9880 peptidyl prolyl isomerase 5.2 H (cyclophilin H) 106000 AW194426 Hs.20726 ESTs 1.7 $ 106011 AW081202 Hs.12284 Homo sapiens, clone IMAGE:2989556,2.8 mRNA, partial cds 106017 AA477956 Hs.26268 ESTs 1.4 106073 AL157441 Hs.17834 downstream neighbor of SON 1.4 106078 AA130158 Hs.19977 ESTs, Moderately similar to ALU8_HUMAN ALU SUBFAMILY SX SEQUENCE CONTAMINATION
1.6 106094 AA533491 Hs.23317 hypothetical protein FLJ146816.8 1 106140 AB006624 Hs.14912 KIAA0286 protein 1.6 ~

106271 AA251393 Hs.289052 Homo sapiens, Similar to RIKEN cDNA 5430429M05 gene, clone MGC:13155, mRNA, complete cds 10.8 106288 AB037742 Hs.24336 KIAA1321 protein 1.3 106300 Y10043 Hs.19114 high-mobility group (nonhistone3.6 chromosomal) protein 4 106333 AL043114 Hs.22410 ESTs, Weakly similar to A548495.4 collagen alpha 1 (VII) chain precursor [H.sapiens]

1$ 106350 AK001404 Hs.194698 cyclin B2 5.7 106359 AW390282 Hs.31130 transmembrane 7 superfamily 6.3 member 2 106381 AB040916 Hs,24106 KIAA1483 protein 6.5 106389 AW748420 Hs.6236 Homo sapiens cDNA: FLJ21487 2.2 fis, clone COL05419 106457 AF119256 Hs.27801 zinc finger protein 278 2.7 106470 D63078 Hs.186180 Homo Sapiens cDNA: FLJ23038 2.3 fis, clone LNG02039 106531 AA454036 Hs.8832 ESTs 1.6 106586 AA243837 Hs.57787 ESTs 1.6 106589 AK000933 Hs.28661 Homo sapiens cDNA FLJ10071 2.4 fis, clone HEMBA1001702 106610 AA458882 Hs.79732 fibulin 1 7.9 ~$ 106624 NM_003595Hs.26350 tyrosylprotein sulfotransferase7.7 106650 AL049951 Hs.22370 Homo sapiens mRNA; cDNA DKFZp564001221.8 (from clone DKFZp56400122) 106669 AV657117 Hs.184164 ESTs, Moderately similar 1.3 to S65657 alpha-1C-adrenergic receptor splice form 2 [H.sapiens]

106713 BE614802 Hs.184352 hypothetical protein FLJ125494.5 106717 AA600357 Hs.239489 TIA1 cytotoxic granule-associated1.3 RNA-binding protein 106723 BE388094 Hs.21857 ESTs 1,6 106795 AF174487 Hs.293753 Bcl-2-related ovarian killer5.7 protein-like 106829 AW959893 Hs.27099 hypothetical protein FLJ2329316.2 similar to ARL-6 interacting protein-2 106831 BE564871 Hs.29463 centrin, EF-hand protein, 1.5 3 (CDC31 yeast homology 106846 A8037744 Hs.34892 KIAA1323 protein 2.2 3 106852 AF151031 Hs.300631 hypothetical protein 1.3 $

106873 N49809 Hs.11197 Homo sapiens, clone IMAGE:3343149,16.8 mRNA, partial cds 106886 W79171 Hs.9567 GL002 protein 1.5 106906 AA861271 Hs.222024 transcription factorBMAL2 2.2 106920 AK001838 Hs.296323 serumlglucocorticoid regulated3.3 kinase 106945 AK000511 Hs.6294 hypothetical protein DKFZp434L14356.8 similar to valyl tRNA synthetase 106973 BE156256 Hs.11923 hypothetical protein 6.6 106977 AL043152 Hs.50421 KIAA0203 gene product 4.8 106978 AW631480 Hs.8688 ESTs 6.0 107004 AA146872 Hs.300700 hypothetical protein FLJ207271.3 4$ 107029 AF264750 Hs.288971 myeloidllymphoid or mixed-lineage1.8 leukemia 3 107071 AW385224 Hs.35198 ectonucleotide pyrophosphataselphosphodiesterase1.7 (putative function) 107113 AK000733 Hs.23900 GTPase activating protein 2.5 107125 AK000512 Hs.69388 hypothetical protein FLJ205051.7 107136 AV661958 Hs.8207 GK001 protein 4.6 $Q 107136 AV661958 Hs.8207 GK001 protein 3.3 107146 AK001455 Hs.5198 Down syndrome critical region2.0 gene 2 107151 AW378065 Hs.8687 ESTs 6.3 107155 AW391927 Hs.7946 KIAA1288 protein 33.5 107174 BE122762 Hs.25338 ESTs 5.2 $$ 107197 W15477 Hs.64639 glioma pathogenesis-related 6.1 protein 107221 AW888411 Hs.81915 leukemia-associated phosphoprotein17.4 p18 (stathmin) 107243 BE219716 Hs.34727 ESTs, Moderately similar 7.4 to 138759 zinc fingerlleucine zipper protein [H.sapiens]

107248 AW263124 Hs.315111 nuclear receptor co-repressorIHDAC31.8 complex subunit 107263 D60341 Hs.21198 translocase of outer mitochondrial6.6 membrane 70 (yeast) homolog A

107265 BE379594 Hs.49136 ESTs, Moderately similar ON
to ALU7 HUMAN ALU SUBFAMILY SO SEQUENCE CONTAMINATI 2.5 107298 N95657 Hs.6820 ESTs, Moderately similar to 2.5 YOJ1 CAEEL HYPOTHETICAL 63.5 KD PROTEIN ZK353.1 IN

107298 N95657 Hs.6820 ESTs, Moderately similar to 1.7 107299 BE277457 Hs.30661 hypothetical protein MGC46063.2 107316 T63174 Hs.193700 Homo Sapiens mRNA; cDNA DKFZp586103242.0 (from clone DKFZp58610324) 6$ 107354 NM_006299Hs.96448 zinc finger protein 193 5.0 107392 AW299900 Hs.267632 TATA element modulatory 1.2 factor 1 107481 AA307703 Hs.279766 kinesin family member 4A 1.6 107529 BE515065 Hs.296585 nucleolar protein (KKEID 3.0 repeat) 107554 AA001386 Hs.59844 ESTs 1.3 107681 BE379594 Hs,49136 ESTs, Moderately similar to 2.2 107772 AA018587 Hs.303055 ESTs, Weakly similar to ALU12.1 HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION

$ 107859 AW732573 Hs.47584 potassium voltage-gated channel,8.4 delayed-rectifier, subfamily S, member 3 107901 L42612 Hs.335952 keratin 6B 2.5 107901 L42612 Hs.335952 keratin 6B 1.6 107922 BE153855 Hs.61460 Ig superfamily receptor LNIR 2.2 107974 AW956103 Hs.61712 pyruvate dehydrogenase kinase,6.7 isoenzyme 1 1 108040 AL121031 Hs.159971 SWIISNF related, matrix associated, ~ actin dependent regulator of chromatin, subfamily b, member 1 1.5 108230 AA054224 Hs.59847 ESTs 1.3 108274 AF129535 Hs.272027 F-box only protein 5 7.1 108296 N31256 Hs.161623 ESTs 2.5 108496 AA083069 Hs.339659 ESTs 3.5 1$ 108607 BE300380 Hs.69476 Homo Sapiens cDNA FLJ12758 3.4 fis, clone NT2RP2001328 108621 AA101809 Hs.182685 ESTs 1.6 108634 AW022410 Hs.69507 ESTs 1.7 108647 BE546947 Hs.44276 homeo box C10 9.8 108695 AB029000 Hs.70823 KIAA1077 protein 7.2 108717 AA122393 Hs.70811 hypothetical protein FLJ205161.3 108740 A1089575 Hs.9071 progesterone membrane binding 2.7 protein 108828 AK001693 Hs.273344 DKFZP56400463 protein 1.8 108859 AL121500 Hs.178904 ESTs 1.5 108872 H06720 Hs.111680 endosultine alpha 2.1 25 108891 AI801235 Hs.48480 ESTs 5.3 108894 AK001431 Hs.5105 hypothetical protein FLJ10569 4.0 108955 AA149754 Hs.195155 Homo sapiens amino acid transport5.6 system N2 (SN2) mRNA, complete cds 108982 AA151708 Hs.171980 homeo box (expressed in ES 1.6 cells) 1 108987 AA152178 Hs.23467 hypothetical protein FLJ106336.2 109002 AB028987 Hs.72134 KIAA1064 protein 1.7 109011 AA156542 Hs.72127 ESTs 1.4 109026 AA157811 gb:zo35d07.s1 Stratagene colon (937204) Homo Sapiens cDNA clone 3' similar to contains Alu repetitive 5.3 109068 AA164293 Hs.72545 ESTs 2.9 109101 AW608930 Hs.52184 hypothetical protein FLJ206181.6 35 109112 AW419196 Hs.257924 hypothetical protein FLJ137823.2 109124 AK000684 Hs.183887 hypothetical protein FLJ221041.7 109139 AJ 132592 Hs.59757 zinc finger protein 281 2.6 109166 AA219691 Hs.73625 RAB6 interacting, kinesin-like2.9 (rabkinesin 6) 109198 BE566742 Hs.58169 highly expressed in cancer, 2.0 rich in leucine heptad repeats 109213 NI1~016603Hs.82035 potential nuclear protein 5.3 C50RF5; GAP-like protein 109220 AW958181 Hs.189998 ESTs 5.7 109233 AU077281 Hs.170285 nucleoporin 214kD (CAIN) 5.3 109270 N99673 Hs.3585 ESTs, Weakly similar to AF12674311.4 DNAJ domain-containing protein MCJ [H.sapiens]

109273 AA375752 Hs.82719 Homo sapiens mRNA; cDNA DKFZp586F18222.9 (from clone DKFZp586F1822) 4S 109313 AF153201 Hs.86276 C2H2 (Kruppel-type) zinc finger1.3 protein 109341 AA213506 Hs.115099 EST 2.9 109391 AL096858 Hs.184245 KIAA0929 protein Msx2 interacting1.5 nuclear target (MINT) homolog 109420 H83603 Hs.40408 homeo box C9 2,2 109426 N30531 Hs.42215 protein phosphatase 1, regulatory3.0 subunit 6 109429 AI160029 Hs.61438 ESTs 1.9 109445 AA232103 Hs.189915 ESTs 1.8 109450 AB032969 Hs.173042 KlAA1143 protein 3.7 109468 NM_015310Hs.6763 KIAA0942 protein 3.2 109478 AW074143 Hs.87134 ESTs 2.0 $ 109570 L40027 Hs.118890 glycogen synthase kinase 3 2.1 S alpha 109662 F02614 Hs.27319 ESTs 1.4 109825 871264 Hs.16798 ESTs 1.3 110039 H11938 Hs.21907 histone acetyltransferase 2.0 110056 AA503041 Hs.279009 matrix Gla protein 2.5 60 110085 AA603840 Hs.29956 KIAA0460 protein 1.7 110110 T07353 Hs.7948 ESTs 2.9 110129 851853 Hs.226429 ESTs, Weakly similar to ALU1_HUMAN1.7 ALU SUBFAMILY J SEQUENCE CONTAMINATION

110154 NM_014521 Hs.17667 SH3-domain binding protein 4.2 110240 AI668594 Hs.176588 ESTs, Weakly similar to CP4Y_HUMAN4.2 CYTOCHROME P450 4A11 PRECURSOR [H.sapiens]

65 110242 N41744 Hs.19978 CGI-30 protein 1.3 110259 H28428 Hs.32406 ESTs, Weakly similar to 138022 2.2 hypothetical protein [H.sapiens] ' 110312 BE256986 Hs.11896 hypofihetical protein FLJ120892.1 110330 A1288666 Hs.16621 DKFZP4341116 protein 6.2 110501 H55748 gb:yq94a01,s1 Soares fetal liverspleen 6.1 1NFLS Homo Sapiens cDNA clone IMAGE:203400 3' 110504 H55915 Hs.210859 hypothetical protein FLJ11016 6.1 110525 H57330 Hs.37430 EST 6.3 $ 110568 AK001160 Hs.5999 hypothetical protein FLJ10298 1.3 110699 T97586 Hs,18090 ESTs 1.8 110705 AB007902 Hs.32168 KIAA0442 protein 1.6 110742 AW190338 Hs.28029 hypothetical protein MGC11256 7.6 110761 AL138077 Hs.16157 hypothetical protein FLJ12707 2.5 110762 BE044245 Hs.30011 hypothetical protein MGC2963 9.3 110765 AK000322 Hs.18457 hypothetical protein FLJ20315 5.5 110769 BE000831 Hs.23837 Homo sapiens cDNA FLJ11812 2.1 fis, clone HEMBA1006364 110799 A1089660 Hs.323401 dpy-30-like protein 1.5 110805 T25829 Hs.24048 FK506 binding protein precursor 6.6 1$ 110813 AA767373 Hs.35669 ESTs, Moderately similar to 5.7 110820 833261 Hs.6614 ESTs, Weakly similar to A43932 3.4 mucin 2 precursor, intestinal [H.sapiens]

110840 N31598 Hs.12727 hypothetical protein FLJ21610 1.7 110844 AI740792 Hs.167531 methylcrotonoyl-Coenryme A 1.7 carboxylase 2 (beta) 110854 BE612992 Hs.27931 hypothetical protein FLJ10607.similarto4.7 glucosamine-phosphate N-acetyltransferase 110856 AA992380 gb:ot37g06.s1 Soares testis NHT Homo 2.3 sapiens cDNA clone 3' similar to contains element 110885 BE384447 Hs.16034 hypothetical protein MGC13186 3.5 110897 AL117430 Hs.6880. DKFZP434D156 protein 2.2 110915 BE092285 Hs.29724 hypothetical protein FLJ13187 2.6 ' 110918 H04360 Hs.24283 ESTs, Moderately similar to reduced1,9 expression in cancer [H.sapiens]

2$ 110958 NM 005864Hs.24587 signal transduction protein 6.7 (SH3 containing) 110963 AK002180 Hs.11449 DKFZP5640123 protein 2.0 110981 AK001980 Hs.24284 ADP-ribosyltransferase (NAD+; 1.3 poly(ADP-ribose) polymerase)-like 2 110984 AW613287 Hs.80120 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GaINAc-T1) 1.8 111125 N63823 Hs.269115 ESTs, Moderately similar to 3.6 Z195_HUMAN ZINC FINGER PROTEIN 195 [H.sapiens]

111132 AB037807 Hs.83293 hypothetical protein 2.1 111164 N46180 Hs.122489 Homo sapiens cDNA FLJ13289 fis,2.3 clone OVARC1001170 111172 867419 Hs.21851 Homo Sapiens cDNA FLJ12900 fis, 3.7 clone NT2RP2004321 111174 AL050166 Hs.26295 Homo Sapiens mRNA; cDNA DKFZp586D11227.5 (from clone DKFZp586D1122) 111179 AK000136 Hs.10760 asporin (LRR class 1) 7.1 3 111184 AI815486 Hs.243901 Homo Sapiens cDNA FLJ20738 6.7 $ fis, clone HEP08257 111184 AI815486 Hs.243901 Homo Sapiens cDNA FLJ20738 3.3 fis, clone HE

111189 N67603 Hs.272130 ESTs, Weakly similar to S65824 3.6 reverse transcriptase homolog [H.sapiens]

111216 AW139408 Hs.152940 ESTs 1.5 111221 A8037782 Hs.15119 KIAA1361 protein 2.6 111223 AA852773 Hs.334838 KIAA1866 protein 4.6 111239 N90956 Hs.17230 hypothetical protein FLJ22087 7.9 111285 AA778711 Hs.4310 eukaryotic translation initiation6.9 factor 1A

111299 AB033091 Hs.74313 KIAA1265 protein 5.0 111312 AI523913 Hs.34504 ESTs 3,8 4$ 111318 T99755 Hs.334728 ESTs 1.2 111337 AA837396 Hs.263925 LIS1-interacting protein NUDE1,5.1 rat homolog 111352 H58589 Hs.35156 Homo sapiens cDNA FLJ11027 fis, 2.2 clone PLACE1004114 111370 AI478658 Hs.94631 brefeldin A-inhibited guanine 2.8 nucleotide-exchange protein 1 111384 N94606 Hs.288969 HSCARG protein 2.2 $0 111389 AK000987 Hs.169111 oxidation resistance 1 2.1 111391 NM 003896Hs.225939 sialyltransferase 9 (CMP-NeuAc:lactosylceramide5.1 alpha-2,3-sialyltransferase; GM3 synthase) 111392 W46342 Hs.325081 Homo Sapiens, clone IMAGE:3659680,8.4 mRNA, partial cds 111452 802354 Hs.15999 ESTs 2.7 111486 A1051194 Hs.227978 EST 6.5 $$ 111549 W90638 Hs.20321 ESTs, Moderately similar to ZRF11.4 HUMAN ZUOTIN RELATED FACTOR-1 (M-PHASE

111585 810720 Hs.20670 EST 1.6 111627 852656 Hs,21691 ESTs 1.6 111870 AB037834 Hs.18685 Homo sapiens mRNA for KIAA14132.4 protein, partial cds 111937 BE298665 Hs.14846 Homo sapiens mRNA; cDNA DKFZp564D01610.6 (from clone DKFZp564D016) 60 111944 AW083791 Hs.21263 suppressor of potassium transport6.6 defect 3 111987 NM_015310Hs.6763 KIAA0942 protein 5.1 112134 841823 Hs.7413 ESTs; calsyntenin-2 2.8 112244 AB029000 Hs.70823 KIAA1077 protein 14.6 112388 846071 Hs,301693 Homo sapiens, clone IMAGE:3638994,9.0 mRNA, partial cds li$112456 Ntv~016248Hs.232076 A kinase (PRKA) anchor protein1.4 112464 AW007287 Hs.28538 Homo sapiens cDNA: FLJ21086 1,4 fis, clone CAS03272 112506 AI742756 Hs.26079 ESTs 3.2 112513 868425 Hs.13809 hypothetical protein FLJ10648 2.0 112752 AK001635 Hs.14838 hypothetical protein FLJ107731.8 112884 AK000004 Hs.5013 Homo Sapiens mRNA for FLJ000046.6 protein, partial cds 112923 T10258 Hs.5037 EST 1.5 $ 112936 AW970826 Hs.6185 KIAA1557 protein 3.2 112958 861388 Hs.6724 ESTs 6.0 112966 244718 Hs.102548 glucocorticoid receptor DNA 6.4 binding factor 1 112978 AK000272 Hs.7099 hypothetical protein FLJ20265 1.2 112995 AA737033 Hs.7155 ESTs, Moderately similar to 5.6 2115357A TYKi protein [M.musculus]

1 112996 BE276112 Hs.7165 zinc finger protein 259 2.0 ~

113047 AI571940 Hs.7549 ESTs 1.9 113049 AW965190 Hs.7560 Homo sapiens mRNA for KIAA17292.4 protein, partial cds 113089 T40707 Hs.270862 ESTs 1.3 113196 T57317 gb:yb51a03.s1 Stratagene fetal spleen 1.7 (937205) Homo sapiens cDNA clone INIAGE:74668 3', 1$ 113248 T63857 gb:yc16e01.s1 Stratagene lung (937210) 2.8 Homo Sapiens cDNA clone 3', mRNA sequence 113254 AK002180 Hs.11449 DKFZP5640123 protein 1.3 113277 AW971049 Hs.11774 protein (peptidyl-prolyl cisltrans3.2 isomerase) NIMA-interacting, 4 (parvulin) 113429 AA688021 Hs.179808 ESTs 1.2 113499 AI467908 Hs.8882 ESTs 5.9 113547 H59588 Hs.15233 ESTs 2.0 113554 AW503990 Hs.142442 HP1-BP74 3.6 113647 AA813887 Hs.188173 Homo sapiens cDNA FLJ12187 1.3 fis, clone MAMMA1000831 113702 T97307 gb:ye53h05.s1 Soares fetal liver spleen 4.4 1NFLS Homo sapiens cDNA clone 1MAGE:121497 3', 113722 AV653556 Hs.184411 albumin 1.3 2$ 113759 AW499665 Hs.9456 SWIISNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 1.2 113777 BE266947 Hs.10590 zinc finger protein 313 13.4 113783 AL359588 Hs.7041 hypothetical protein DKFZp762B2261.7 113791 AI269096 Hs.135578 chitobiase, di-N-acetyl- 1.3 113808 W44735 Hs.9286 Homo sapiens cDNA: FLJ21278 fis,3.3 clone COL01832 30 113811 BE207480 Hs.6994 Homo Sapiens cDNA: FLJ22044 3.1 fis, clone HEP09141 113817 H13325 Hs.332795 hypothetical protein DKFZp7610171213.2 113826 AW378212 Hs.24809 hypothetical protein FLJ108262.3 113834 T26483 Hs.6059 EGF-containing fibulin-like extracellular11.3 matrix protein 2 113868 W57902 Hs.90744 proteasome (prosome, macropain)2.7 26S subunit, non-ATPase,11 3 113870 AL079314 Hs.16537 hypothetical protein, similar6.1 $ to (U06944) PRAJA1 113885 AW959486 Hs.21732 ESTs 6.6 113923 AW953484 Hs.3849 hypothetical protein FLJ22041 1.9 similar to FK506 binding proteins 113989 W87544 Hs.268828 ESTs 1.2 114022 AI539519 Hs.120969 Homo sapiens cDNA FLJ11562 5.4 fis, clone HEMBA1003197 114030 AI825386 Hs.164478 hypothetical protein FLJ219399.4 similar to 5-azacytidine induced gene 2 114060 AB029551 Hs.7910 RING1 and YY1 binding protein 1.8 114196 AF017445 Hs.150926 fucose-1-phosphate guanylyltransferase1.5 114226 AB028968 Hs.7989 KIAA1045 protein 1.8 114253 BE149866 Hs.14831 Homo sapiens, 5iinilar to zinc finger protein 136 (clone pHZ-20), clone MGC:10647, mRNA, complete cds 2.3 4$ 114262 AL117518 Hs.3686 KIAA0978 protein 1.4 114275 AW515443 Hs.306117 KIAA0306 protein 15.8 114292 AI815395 Hs.184641 fatty acid desaturase 2 1.9 114309 AA332453 Hs.20824 CGI-85 protein 2.4 114392 AA249590 Hs.100748 ESTs, Weakly similar to A289961.8 proline-rich protein M14 precursor- mouse [M.musculus]

$~ 114407 BE539976 Hs.103305 Homo Sapiens mRNA; cDNA DKFZp434B04251.2 (from clone DKFZp434B0425) 114455 H37908 Hs.271616 ESTs, Weakly similar to ALUB_HUMAN5.5 ALU SUBFAMILY SX SEQUENCE

114463 AL120247 Hs.40109 KIAA0872 protein 5.2 114464 A1091713 Hs.106597 Homo Sapiens, Similar to RIKEN cDNA 1110012M11 gene, clone IMAGE:3688605, mRNA, partial cds1.2 114471 AA028074 Hs.104613 RP42 homolog 1.8 $ 114480 BE066778 Hs.151678 UDP-N-acetyl-alpha-D-galactosamine;polypeptide $ N-acetylgalactosaminyltransferase 6 (GaINAc-T6) 13.4 114671 AA766268 Hs.266273 hypothetical protein FLJ133461.9 114698 AA476966 Hs.110857 polymerase (RNA) III (DNA 3.5 directed) polypeptide K (12.3 kDa) 114730 A1373544 Hs,331328 intermediate filament protein3.8 syncoilin 114767 AI859865 Hs.154443 minichromosome maintenance 1.6 deficient (S. cerevisiae) 4 60 114774 AV656017 Hs.184325 CGI-76 protein 3.1 114798 AA159181 Hs.54900 serologically defined colon 3.5 cancer antigen 1 114860 AL157545 Hs.42179 bromodomain and PHD finger 4.3 containing, 3 114895 AA236177 Hs.76591 KIAA0887 protein 7.1 114896 BE539101 Hs.5324 hypothetical protein 1.3 6$ 114911 AA236672 gb:zt29f02.s1 Soares ovary tumor NbHOTsequence.
Homo Sapiens cDNA clone IMAGE:723771 3', mRNA 1.5 114930 AA237022 Hs.188717 ESTs 2.0 114938 AA242834 Hs.58384 ESTs 2.9 114965 AI733881 Hs.72472 BMP-R1B 2.3 115023 AF102546 Hs.63931 dachshund (Drosophila) 1.3 homolog 115038 AA252360 Hs.87968 toll-likereceptor9 1.6 115061 AI751438 Hs.41271 Homo sapiens mRNA full 11.8 length insert cDNA clone EUROIMAGE 1913076 115062 AA253314 Hs.154103 LlM protein (similar to 1.5 rat protein king 115117 AI670847 Hs.5324 hypothetical protein 1.5 115121 AI634549 Hs.88155 ESTs 2.8 115206 AW183695 Hs.186572 ESTs 2.5 115221 AW365434 Hs.79741 hypothetical protein FLJ101161.5 1 115239 BE251328 Hs.73291 hypothetical protein FLJ 1.3 ~ 10881 115242 AI368236 Hs.283732 ESTs, Moderately similar 1.4 to ALU1 HUMAN ALU SUBFAMILY J SEQUENCE

115278 AK002163 Hs.301724 hypothetical protein FLJ113011.5 115285 AW972872 Hs.293736 ESTs 2.4 115291 BE545072 Hs.122579 hypothetical protein FLJ104616.2 1$ 115400 AI215069 Hs.89113 ESTs 6.6 115468 AA314349 Hs.48499 tumor antigen SLP-Sp 7.4 115471 AK001376 Hs.59346 hypothetical protein FLJ105141.4 115479 AW301608 Hs.278188 ESTs, Moderately similar 4.0 to 154374 gene NF2 protein [H.sapiens]

115496 AW247593 Hs.71819 eukaryotic translation 16.3 initiation factor 4E binding protein 1 2~ 115500 Y14443 Hs.88219 zinc finger protein 200 5.0 115553 AJ275986 Hs.71414 transcription factor (SMIF2.5 gene) 115581 AI540842 Hs.61082 ESTs 6.1 115587 BE081342 Hs.283037 HSPC039 protein 2~9 115590 AA399477 Hs.67896 7-60 protein 5.3 25 115646 N36110 Hs.305971 solute carrier family 2 4.7 (facilitated glucose transporter), member 10 115652 BE093589 Hs.38178 hypothetical protein FLJ2346810.6 115655 AL048269 Hs.288544 Homo Sapiens, clone MGC:16063,12.7 mRNA, complete cds 115663 AI138785 Hs.40507 ESTs 2.0 115676 AA953006 Hs.88143 ESTs 3.0 115690 AA625132 Hs.44159 hypothetical protein FLJ216151.7 115693 AF231023 Hs.55173 cadherin, EGF LAG seven-pass6.8 G-type receptor 3, flamingo (Drosophila) homolog 115715 BE395161 Hs.1390 proteasome (prosome, macropain)1.7 subunit, beta type, 2 115734 AI950339 Hs.40782 ESTs 2.6 115811 NM 015434Hs.48604 DKFZP434B168 protein 2.1 35 115823 AI732742 Hs.87440 ESTs 2.1 115837 AI675217 Hs.42761 ESTs 1.3 115844 AI373062 Hs.332938 hypothetical protein MGC53704.4 115866 AW062629 Hs.52081 KIAA0867 protein 7.2 115875 N55669 Hs.333823 mitochondrial ribosomal 1.2 protein L13 115941 AI867451 Hs.46679 hypothetical protein FLJ207395.5 115968 AB037753 Hs.62767 KIAA1332 protein 9.8 116003 BE275469 Hs.66493 Down syndrome critical 1.4 region gene 5 116011 AL359053 Hs.57664 Homo Sapiens mRNA full 2.4 length insert cDNA clone EUROIMAGE 2005735 116108 AA770688 Hs.28777 H2A histone family, member1.8 L

45 116134 BE243834 Hs.50441 CGI-04 protein 1.4 116189 N35719 Hs.44749 ESTs, Moderately similar 1.2 to T00358 hypothetical protein KIAA0684 [H.sapiens]

116195 AW821113 Hs.72402 ESTs 2.1 116238 AV660717 Hs.47144 DKFZP586N0819 protein 1.7 116246 AF265555 Hs.250646 baculoviral IAP repeat-containing1.7 5~ 116262 AI936442 Hs.59838 hypothetical protein FLJ108081.7 116298 AI955411 Hs.94109 Homo Sapiens cDNA FLJ136341.9 fis, clone PLACE1011133 116318 AF097645 Hs.58570 deleted in cancer 1; RNA 4.9 helicase HDSIDICE1 116325 AI472106 Hs.49303 Homo sapiens cDNA FLJ116631.4 fis, clone HEMBA1004631 116336 AL133033 Hs.4084 KIAA1025 protein 1.9 $ 116339 AK000290 Hs.44033 dipeptidyl peptidase 8 1.5 $

116350 AA497129 Hs.184771 nuclear factor IIC (CCAAT-binding1.9 transcription factor) 116358 AI149586 Hs.38125 interferon-induced protein1.9 75, 52kD

116365 N50174 Hs.46765 ESTs 6.1 116368 N90466 Hs.71109 KIAA1229 protein 1.6 60 116417 AW499664 Hs.12484 Human clone 23826 mRNA 7.4 sequence 116436 AA161411 Hs.58668 chromosome 21 open reading2.1 frame 57 116462 AF218313 Hs.236828 putative helicase RUVBL 1.5 116470 AI272141 Hs.83484 SRY (sex determining region2.1 Y)-box 4 116470 AI272141 Hs.83484 SRY (sex determining region1.2 Y)-box 4 6$ 116575 AA312572 Hs.6241 phosphoinositide-3-kinase, 1.5 regulatory subunit, polypeptide 1 (p85 alpha) 116637 AK001043 Hs.92033 integrin-linked kinase-associated2.7 serinelthreonine phosphatase 2C

116640 X89984 Hs.211563 B-cell CLUlymphoma 7A 2.3 116700 AI800202 Hs.317589 hypothetical protein MGC107651.4 116705 AW074819 Hs.12313 hypothetical protein FLJ145663.4 116732 AW152225 Hs.165909 ESTs, Weakly similar to 1380222.9 hypothetical protein [H.sapiens]

116921 AW068115 Hs.821 biglycan 8.3 $ 116926 H73608 Hs.290830 ESTs 1.7 117034 U72209 Hs.180324 YY1-associated factor 2 ~ 3.4 117132 AI393666 Hs.42315 p10-binding protein 5.2 117247 N21032 gb:yx46f06.s1 Soares melanocyte 2NbHM sequence.
Homo sapiens cDNA clone IMAGE:264803 3', mRNA 5.5 117276 N71183 Hs.121806 Homo sapiens cDNA FLJ11971 1.5 fis, clone HEMBB1001208 1 117284 AK001701 Hs.183779 Homo Sapiens cDNA FLJ10590 2.0 ~ fis, clone NT2RP2004392, weakly similar to MNN4 PROTEIN

117367 A1041793 Hs.42502 ESTs 2.0 117368 AI878942 Hs.90336 ATPase, H+transporting, lysosomal2.1 (vacuolar proton pump), member J

117382 AF150275 Hs.40173 ESTs 2.7 117412 N32536 Hs.42645 solute carver family 16 (monocarboxylic1.4 acid transporters), member 6 1$ 117557 AF123050 Hs.44532 diubiquitin 3.4 117588 N34895 Hs.44648 ESTs 3.4 117745 BE294925 Hs.46680 CGI-12 protein 3.0 117754 AA121673 Hs.59757 zinc finger protein 281 1.9 117879 N54706 Hs.303025 chromosome 11 open reading 1.8 frame 24 2~ 117881 AF161470 Hs.260622 butyrate-induced transcript 5.7 , 5.9 117904 BE540675 Hs.332938 hypothetical protein MGC5370 117911 AL137379 Hs.47125 hypothetical protein FLJ139121.7 117933 Y10518 Hs.116470 hypothetical protein FLJ20048 1.7 117983 AL110246 Hs.47367 KIAA1785 protein 5.4 25 118078 N54321 Hs.47790 EST 5.2 118301 AA453902 Hs.293264 ESTs 2.6 118429 AA243332 Hs.74649 cytochrome c oxidase subunit 2.5 Vlc , 118472 AL157545 Hs.42179 bromodomain and PHD finger 4.1 containing, 3 118488 AJ277275 Hs.50102 rapa-2 (rapa gene) 1.2 118509 N22617 Hs.43228 Homo Sapiens cDNA FLJ11835 fis,1.5 clone HEMBA1006595 118528 AI949952 Hs.49397 ESTs 7.4 118656 AI458020 Hs.293287 ESTs 2.5 118670 AA332845 Hs.152618 ESTs, Moderately similar 1.2 to ZN91 HUMAN ZING FINGER PROTEIN 91 [H.sapiens]

118698 AB033113 Hs.50187 KIAA1287 protein 2.1 3 118737 AA199686 gb:zq75g09.r1 Stratagene hNT neuron 5.2 S (937233) Homo sapiens cDNA clone IMAGE:647488 5' 118925 N92293 Hs.206832 ESTs, Moderately similar to ALU8_HUMAN ALU SUBFAMILY SX SEQUENCE CONTAMINATION
1.4 118984 AI668709 Hs.240722 ESTs, Moderately similar to ALUB HUMAN ALU SUBFAMILY SX SEQUENCE CONTAMINATION
3.6 118986 AF148713 Hs.125830 bladder cancer overexpressed4.8 protein 119206 W24781 Hs.293798 KIAA1710 protein 1.7 119235 AW453069 Hs.3657 activity-dependent neuroprotective2.2 protein 119235 AW453069 Hs.3657 activity-dependentneuroprotectiveprote1.6 119265 BE539706 Hs.285363 ESTs 1.4 119279 N57568 Hs.48028 EST 25.1 119298 NM 001241Hs,155478 cyclin T2 1.6 45 119338 AI417240 Hs.320836 ESTs, Weakly similar to A475821.3 B-cell growth factor precursor [H.sapiens]

119349 T65004 Hs.163561 ESTs 8.4 119403 AL117554 Hs.119908 nucleolar protein NOP51NOP586.7 119478 AI624342 Hs.170042 ESTs 2.4 119486 AI796730 Hs.55513 ESTs 2.1 $0 119513 W37933 Empirically selected from AFFX single 1.9 probeset 119601 AK000155 Hs.91684 Homo Sapiens mRNA; cDNA DKFZp66711033.7 (from clone DKFZp6671103) 119602 AW675298 Hs.233694 hypothetical protein FLJ113503.0 119676 AA243837 Hs.57787 ESTs 1.4 119682 W61019 Hs.57811 ESTs 1.2 $S 119774 AB032977 Hs.6298 KIAA1151 protein 1.8 119780 NM_016625Hs.191381 hypothetical protein 3.1 119789 BE393948 Hs.50915 kallikrein 5 (KLKS; KLK-L2; 9.2 stratum comeum tryptic enzyme) 119805 AJ223810 Hs.43213 ESTs, Weakly similar to IEFS 3.6 HUMAN TRANSFORMATION-SENSITIVE PROTEIN IEF SSP

119818 AA130970 Hs.58382 hypothetical protein FLJ111012.5 119863 AA081218 Hs.58608 Homo Sapiens cDNA FLJ14206 2.7 fis, clone NT2RP3003157 119905 AW449064 Hs.119571 collagen, type III, alpha 2.6 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) 119966 AA703129 Ns.58963 ESTs 2.7 120132 W57554 Hs.125019 lymphoid nuclear protein (LAF-4)1.2 mRNA

120206 H26735 Hs.91668 Homo Sapiens clone PP1498 unknown45.7 mRNA

65 120248 AI924294 Hs.173259 uncharacterized bone marrow 1.2 protein BM033 120253 AA131376 Hs.326401 fibroblast growth factor 38.9 120269 AW131940 Hs.104030 ESTs 9.6 120274 AA177051 gb;nc02a02.s1 NCI CGAP_Pr3 Homo sapiens4.6 cDNA clone IMAGE:194 similar to contains Alu 120280 AA190577 gb:zp52g02.s1 Stratagene HeLa cell s3 2.0 937216 Homo Sapiens cDNA clone 3', mRNA sequence 120296 AW995911 Hs.299883 hypothetical protein FLJ233991.8 120297 AA191384 Hs.104072 ESTs, Weakly similar to Z195_HUMAN15.2 ZINC FINGER PROTEIN 195 [H.sapiens]

$ 120324 AA195517 Hs.191643 ESTs 5.5 120325 AA195651 Hs.104106 ESTs 6.4 120327 AK000292 Hs.278732 hypothetical protein FLJ2028516.1 120336 N85785 Hs.181165 eukaryotic translation elongation2.9 factor 1 alpha 1 120342 AW450669 Hs.45068 hypothetical protein DKFZp43411435.7 1 120345 AA210722 Hs.104158 ESTs 4.5 ~

120349 AW969481 Hs.55189 hypothetical protein 16.8 120352 806859 Hs.193172 ESTs, Weakly similar to 138022 5.0 hypothetical protein [H.sapiens]

120356 AF000545 Hs.296433 putative purinergic receptor 28.1 120371 AA219305 Hs.104196 EST 12.4 1$ 120382 AA228026 Hs.38774 ESTs 4.0 120383 AL109963 Hs.123122 FSH primary response (LRPR1, 9.7 rat) homolog 1 120386 AW969665 Hs.154848 hypothetical protein DKFZp434D012732.6 120388 AA232874 Hs.104245 ESTs 3.1 120389 AW967985 Hs.325572 ESTs, Moderately similar to 21.7 2~ 120396 AA134006 Hs.79306 eukaryotictranslationiniGationfactor4E12.5 120404 AB023230 Hs.96427 KIAA1013 protein 7.2 120418 AW966893 Hs.26613 Homo sapiens mRNA; cDNA DKFZp586F132311.4 (from clone DKFZp586F1323) 120423 AA236453 Hs.18978 Homo sapiens cDNA: FLJ22822 1.9 fis, clone KAIA3968 120472 AI950087 gb:wq05c02.x1 NCI_CGAP_Kid12 Homo sapiens19.4 cDNA clone 3', mRNA sequence 2$ 120473 AA251973 Hs.269988 ESTs 5.4 120484 AA253170 Hs.96473 EST 10.4 120504 AA256837 gb:zr84d10.s1 Soares_NhHMPu_S1 Homo Sapiens cDNA clone IMAGE:682387 3', mRNA sequence.
3.9 120509 BE047718 Hs.96545 ESTs 9.4 120520 AA258601 Hs.161731 EST 2.4 120535 BE350244 Hs.96547 ESTs 2.5 120551 AA279160 Hs.111407 Homo sapiens, clone IMAGE:3613029,5.2 mRNA, partial cds 120570 AA280679 Hs.271445 ESTs, Weakly similar to ALU1 14.4 HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION

120582 BE244830 Hs.284228 ZNF135-like protein 10.2 120590 AW372799 Hs.125790 leucine-rich repeat-containing2.1 3$ 120596 AA282074 Hs.237323 N-acetylglucosamine-phosphate7.5 mutase 120619 AW965339 Hs.111471 ESTs 2.5 120624 AW407987 Hs.173518 M-phase phosphoprotein homolog52.0 120639 AA286942 gb:zs56f05.s1 NCI CGAP GCB1 Homo sapiens cDNA clone IMAGE:701505 3' similar to contains A1u2.4 120648 AA287095 Hs.140309 Homo Sapiens, clone IMAGE:3677194,5.0 mRNA, partial cds 4~ 120653 AW063659 Hs.191649 ESTs 2.2 120668 AW969638 Hs.112318 6.2 kd protein 2.2 120669 BE536739 Hs.109909 ESTs 1.9 120695 AA976503 gb:oq30a04.s1 NCI_CGAP_GC4 Homo Sapiens46.8 cDNA clone 3' similar to contains PTR7.t1 PTR7 120696 AI821539 Hs.97249 ESTs 2.5 4$ 120713 AW449855 Hs.96557 Homo sapiens cDNA FLJ12727 5.9 fis, clone NT2RP2000027 120718 AA292747 Hs.97296 ESTs 2.9 120750 AI191410 Hs.96693 ESTs, Moderately similar to 7.0 2109260A B cell growth factor [H.sapiens]

120774 AI608909 Hs.193985 ESTs 7.8 120807 AA346385 Hs.30002 SH3-containing protein SH3GLB2;6.8 KIAA1848 protein $ 120809 AA346495 gb:EST52657 Fetal heart II Homo sapiens4.4 ~ cDNA 3' end similar to EST containing 0 family repeat, 120938 AA386260 Hs.104632 EST 4.4 120977 AA398155 Hs.97600 ESTs 4.4 120984 BE262951 Hs.99052 ESTs 5.6 120985 A1219896 Hs.97592 ESTs 1.2 $$ 121011 AA398360 Hs.97608 EST 3.1 121026 AI439713 Hs.165295 ESTs 3.5 121081 AA398721 Hs.186749 ESTs, Highly similar to 1375505.4 mismatch repair protein MSH2 [H.sapiens]

121133 AA363307 Hs.97032 ESTs 3.7 121176 AL121523 Hs.97774 ESTs 1.7 121223 A1002110 Hs.97169 ESTs, Weakly similar to dJ667H12.2.12.9 [H.sapiens]

121320 AA403008 Hs.301927 c6.1A 1.9 121340 AW956981 Hs.97910 Homo Sapiens cDNA FLJ13383 3.5 fis, clone PLACE1001024 121408 AA406137 Hs.98019 EST 6.0 121439 AA410190 Hs.98076 ESTs, Weakly similar to A475827.4 B-cell growth factor precursor [H.sapiens]

6$ 121450 AA406430 Hs.105362 Homo Sapiens, clone MGC:18257,6.9 mRNA, complete cds 121452 AW971063 Hs.292882 ESTs 1.8 121455 H58306 Hs.15165 retinoic acid induced 14 10.5 121457 W07404 Hs.144502 hypothetical protein FLJ22055 3.4 121496 AA442224 Hs.97900 ESTs 14.4 121505 AA494172 Hs.194417 ESTs 13.1 121508 AA402515 Hs.97887 ESTs 28.0 $ 121513 AA416653 Hs.181510 ESTs 6.2 121514 AA412112 gb:zt69b02.s1 Soares_testis_NHT Homo sapiens cDNA clone IMAGE:727563 3', mRNA sequence.
2.6 121549 AA412477 Hs.98142 EST 7.4 121558 AA412497 gb:zt95g12.s1 Soares_testis_NHT Homo ns2.8 sapiens cDNA clone IMAGE:730150 3' similar to contai 121577 AA411970 Hs.98096 EST 3.5 1 121581 AA416568 gb:zu05c10.s1 Soares testis_NHT Homo 6.1 ~ sapiens cDNA clone 3', mRNA sequence 121589 AD001528 Hs.89718 spermine synthase 3.9 121594 AA626010 Hs.98247 ESTs 2.2 121622 AA416931 Hs.126065 ESTs 4.2 121655 AA421537 Hs.178072 Homo sapiens mRNA; cDNA DKFZp434B10237.8 (from clone DKFZp434B1023) I 121682 AA418160 Hs.86043 Homo Sapiens cDNA FLJ13558 2.0 fis, clone PLACE1007743 121690 AV660305 Hs.110286 ESTs 4,7 121706 055184 Hs.154145 hypothetical protein FLJ11585 12.7 121714 AA419225 Hs.98269 Homo Sapiens cDNA FLJ11953 8.1 8s, clone HEMBB1000883 121729 AI949597 Hs.98325 ESTs 1.8 121731 AA421041 Hs.180744 ESTs 4.0 121744 AA398784 Hs.97514 ESTs 7.1 121748 BE536911 Hs.234545 hypothetical protein NUF2R 19.5 121773 AB033022 Hs.158654 KIAA1196 protein 7.9 121775 AA421773 Hs.161008 ESTs 1.7 2$ 121776 AA292579 Hs.125133 hypothetical protein FLJ225016.6 121786 AI810774 Hs.98376 ESTs 10.5 121832 AW340797 Hs.98434 ESTs 5.8 121836 AA328348 Hs.218289 ESTs 3.8 121839 AA425691 Hs.191606 ESTs, Highly similar to KIAA10485.0 protein [H.sapiens]

121842 AF027406 Hs.104865 serinelthreonine kinase 23 2.7 121847 AA446628 Hs.2799 cartilage linking protein 1 2.3 121871 AW972668 Hs.293044 ESTs 2.9 121882 AA426376 Hs.98459 ESTs 5.0 121911 AA427950 gb:zw50f02.s1 Soares total_fetus Nb2HF87.2 9w Homo Sapiens cDNA clone IMAGE:773499 3' 3 121915 AA428179 Hs.223405 ESTs, Moderately similar 2.5 $ to A46010 X-linked retinopathy protein [H.sapiens]

121935 AA428647 Hs.98611 EST 2.3 121983 AA298760 Hs.180191 hypothetical protein FLJ149043.4 121985 AI862570 Hs.299214 Homo sapiens, clone IMAGE:2822295,11.4 mRNA, partial cds 121995 AA210863 Hs.3532 nemo-like kinase 3.8 121999 AA430211 Hs.98668 EST 6.4 122009 AW292763 Hs.160822 Homo sapiens cDNA: FLJ20863 2.2 fis, clone ADKA01804 122013 AA431085 Hs.98706 ESTs 6.5 122036 W92142 Hs.271963 ESTs, Weakly similar to ALU5_HUMAN13.1 ALU SUBFAMILY SC SEQUENCE CONTAMINATION

122050 AI453076 Hs.166109 ELAV (embryonic lethal, abnormal9.1 vision, Drosophila)-like 2 4$ 122060 AAd31738 Hs.98750 EST 13.1 122114 AW161023 Hs.104921 ESTs 1.5 122188 AA398838 gb:zt80d01.r1 Soares testis_NHT Homo 3.3 Sapiens cDNA clone 5', mRNA sequence 122204 AA435936 Hs.98842 EST 5.6 122246 AA329550 Hs.29417 HCF-binding transcription 5.1 factor Zhangfei $~ 122257 AA436819 Hs.98899 ESTs 5.6 122302 AA441801 Hs.104947 ESTs 5.8 122341 AW601969 Hs.99010 hypothetical protein FLJ222632.0 similar to nuclear receptor-binding SET-domain protein 1 .

122356 AA443794 Hs.98390 ESTs 7.3 122369 AA443985 Hs.303222 ESTs 12.2 $$ 122371 AA868555 Hs.178222 ESTs 5.0 122372 AA446008 Hs.336677 EST 7.6 122378 AB032948 Hs.21356 hypothetical protein DKFZp762K20152.5 122405 AA446572 Hs.303223 EST 2.8 122412 AA446869 Hs.119316 ESTs 7.3 122415 AA446918 Hs.99088 EST 1.9 122418 AA446966 Hs.99090 ESTs, Moderately similar to 6.8 similar to KIAA0766 [H.sapiens) 122440 AW505139 Hs,9460 Homo Sapiens mRNA; cDNA DKFZp547C2442.6 (from clone DKFZp547C244) 122446 AA447603 Hs,99123 EST 1.8 122448 AA447626 Hs.99127 EST 3.5 ()$122458 AI266159 Hs.104980 ESTs 1.5 122460 AW418788 Hs.99148 ESTs, Weakly similar to S435699.7 R01H10.6 protein - Caenorhabditis elegans [C.elegans]

122464 AA448158 Hs.99152 EST 4.8 12$

121439 AA410190 Hs.98076 ESTs, Weakly similar to A475827.4 B-cell growth factor precursor [H.sapiens]

122490 AA448349 Hs.238151 EST 6.1 122492 AA448417 Hs.104990 ESTs 5.4 122502 AA204969 Hs.234863 Homo sapiens cDNA FLJ12082 1.3 fis, clone HEMBB1002492 122510 AA449232 Hs.99195 ESTs 11.2 $ 122530 AW959741 Hs.40368 adaptor-related protein complex10.1 1, sigma 2 subunit 122547 AA779725 Hs.164589 ESTs 2.5 , 122555 AA194055 Hs.293858 ESTs 1.9 122570 AA452578 Hs.262907 ESTs 9.5 122572 AA452601 Hs.99287 EST 11.0 1 122586 AK001910 Hs.99303 Homo Sapiens cDNA FLJ11048 3.4 ~ fis, clone PLACE1004516 122587 AB040893 Hs.6968 KIAA1460 protein 2.0 122598 A1028173 Hs.99329 ESTs 1.7 122599 AL355841 Hs.99330 hypothetical protein FLJ235884.4 122602 AA411925 Hs.301960 ESTs 4.6 1 122607 AA453518 Hs.98023 ESTs 61.5 S

122614 AA453630 Hs.99339 EST 10.7 122616 AA453638 Hs.161873 ESTs 107.3 122617 A1681535 Hs.148135 serinelthreonine kinase 33 121.4 122618 AA453641 gb:zx48e06.s1 Soares testis_NHT Homo 31.1 sapiens cDNA clone 3', mRNA sequence 2~122622 AA453987 Hs.144802 ESTs 5.6 122717 AA456859 Hs.178358 ESTs 8.5 122762 Ai376875 Hs.105119 ESTs 10.4 122829 AW204530 Hs.99500 ESTs 81.8 122834 AA461492 Hs.99545 Homo Sapiens cDNA FLJ 10658 3.6 fis, clone NT2RP2006052 2S122836 AA460581 Hs.290996 ESTs 4.5 122837 AA461509 Hs.293565 ESTs, Weakly similar to putative2.7 p150 [H.sapiens]

122838 AA460584 Hs.334386 ESTs 75.3 122854 AA600235 Hs.9625 NIMA (never in mitosis gene 7.7 a)-related kinase 6 122856 AI929374 Hs.75367 Src-like-adapter 5.8 30122861 AA335721 Hs.119394 ESTs 1.3 122866 BE539656 Hs.283705 ESTs 4.1 122868 AF005216 Hs.115541 Janus kinase 2 (a protein 5.3 tyrosine kinase) 122870 AW576312 Hs.318722 Homo sapiens cDNA: FLJ21766 9.9 fis, clone COLF7179 122872 AW081394 Hs.97103 ESTs 5.3 35122879 AA769410 Hs.128654 ESTs 13.9 122907 AA470074 Hs.169896 ESTs - 11.5 122916 AA470140 Hs.229170 EST 1.7 122981 AA478951 Hs.105629 ESTs 5.0 123013 AW968324 Hs.17384 ESTs 15.4 123016 AW338067 Hs.323231 Homo Sapiens cDNA FLJ11946 2.8 fis, clone HEMBB1000709 123034 AL359571 Hs.44054 ninein (GSK3B interacting 8.7 protein) 123072 AI382600 Hs.104308 ESTs, Weakly similar to KIAA13958.8 protein [H.sapiens]

123082 AA485360 Hs.105661 ESTs 3.9 123088 AI343652 Hs.105667 ESTs 3.8 45123110 AA486256 Hs.193510 EST 7.4 123114 BE304942 Hs.265848 myomegalin 2.8 123131 T52027 Hs.271795 ESTs, Weakly similar to 1380222.4 hypothetical protein [H.sapiens]

123132 A1061582 Hs.324179 Homo Sapiens cDNA FLJ12371 15.6 fis, clone MAMMA1002434 123136 AW451999 Hs.194024 ESTs 5.1 123149 AI734179 Hs.105676 ESTs 23.8 123152 AW601773 Hs.270259 ESTs 5.2 123258 AA490929 Hs.105274 ESTs, Weakly similar to RMS1 HUMAN REGULATOR OF MITOTIC SPINDLE ASSEMBLY 1 [H.sapiens]
9.3 123315 AA496369 gb:zv37d10.s1 Soares ovary tumor NbHOT
Homo Sapiens cDNA clone IMAGE:755827 3' similar to4.1 123369 AA504757 Hs.105738 ESTs 6.9 123394 AA731404 Hs.105510 ESTs 3.6 123433 AW450922 Hs.112478 ESTs 3.7 123466 AA599042 Hs.112503 EST 7.4 123470 AW303285 Hs.303632 Human DNA sequence from clone RP11-110H4 on chromosome 5 Contains a pseudogene similar to 3.5 123471 A8021644 Hs.197219 zinc finger protein 14 (KOX 5.2 6) 123475 BE439553 Hs.250528 Homo sapiens, clone IMAGE:4098694,1.7 mRNA, partial cds 123482 N95059 Hs.55098 ESTs 1.6 123486 BE019072 Hs.334802 Homo sapiens cDNA FLJ14680 2.4 fis, clone NT2RP2004242, weakly similar to 123508 AW380388 Hs.155546 KIAA1080 protein; Golgi-associated,2,2 gamma-adaptin ear containing, ARF-binding protein 123615 AA609170 gb:af12a12.s1 Soares testis NHT Homo 7.8 sapiens cDNA clone 3', mRNA sequence 6$123619 AA602964 gb:no97c02.s1 NCI_CGAP_Pr2 Homo Sapiens2.8 cDNA clone, mRNA sequence 123658 AA609364 gb:zu71d09.s1 Soares tesGs_NHT Homo Sapiens cDNA clone IMAGE:743441 3' similar to contains Alu. 1.7 123674 AI269609 Hs.105187 kinesin protein 9 gene 5.7 123735 NM_013241Hs.95231 FH11FH2 domain-containing prote!n10.0 123738 AA609891 Hs.112777 EST 5.2 123753 AA609955 Hs.234961 Huntingtin interacting protein30.6 E

123804 AA620464 Hs.261915 EST, Weakly s!milar to S656572.1 alpha-1 C-adrenergic receptor splice form 2 [H.sapiens]

S 123811 AA620586 gb:ae60g05.s1 Stratagene lung carcinoma2.7 937218 Homo sapiens cDNA clone IMAGE:951320 3' 123951 AB012922 Hs.173043 metastasis-assoc!ated 1-like 6.2 123983 AJ272267 Hs.146178 choline dehydrogenase , 4.4 124001 L42542 Hs.75447 ralA binding protein 1 7.0 124006 AI147155 Hs.270016 ESTs 8.1 1 124070 AI950314 Hs.154762 HIV-1 rev b!nding protein 3.7 ~ 2 124074 H05635 Hs.294030 topoisomerase-related function 1.2 protein 4-2 124178 BE463721 Hs.97101 putative G prote!n-coupled 3.1 receptor 124203 AA372796 Hs.269339 ESTs, Weakly similar to AF16135615.7 HSPC093 [H.sapiens]

124352 AA640891 Hs.102406 ESTs 3.1 1 124375 D87454 Hs.192966 KIAA0265 protein 3.5 S

124385 AI267847 gb:aq49a10.x1 Stanley Frontal N8 pool 57.1 2 Homo Sapiens cDNA clone similar to conta!ns 124390 AA317338 Hs.7535 COBW-like protein 2.8 124391 AF155099 Hs.279780 NY-REN-18 antigen 7.1 124417 N34059 gb:yv28h09.s1 Soares fetal liver spleen 1 NFLS Homo Sapiens cDNA clone 3' s!milar to contains Alu 3.3 124428 H13540 Hs.82202 ribosomal protein L17 2.9 124440 AA532519 Hs.129043 Human DNA sequence from clone7.8 989H11 on chromosome 22q13.1-13.2. Contains part of a 124466 810084 Hs.113319 kinesin heavy chain member 2 2.6 124482 N53935 gb:yv59d09.s1 Soares fetal liver spleen 7.9 1NFLS Homo Sapiens cDNA clone 3', mRNA sequence 124498 H79433 Hs.268997 ESTs 7.8 25 124515 AA669097 Hs.109370 ESTs 3.3 124608 N71076 Hs.102800 ESTs, Weakly s!milar to neuronal4.5 thread protein AD7c-NTP [H.sapiens]

124631 NM_014053Hs.270594 FLVCR protein 3.2 124634 AI765123 Hs.143671 Homo sapiens cDNA FLJ13533 5.8 fis, clone PLACE1006371 124637 AA160474 Hs.75798 hypothetical protein 9.3 124642 AW968856 Hs.278569 sorting nex!n 17 3.5 124649 N92593 Hs.313054 ESTs 6.1 124656 AW297702 Hs.102915 ESTs 8.3 124661 848170 Hs.78436 EphB1 5.6 124683 AA381661 Hs.119878 ESTs, Weakly similar to M3K9_HUMAN7.9 MITOGEN-ACTIVATED PROTEIN KINASE KINASE

3 124712 809166 Hs.191148 ESTs 5.7 S

124735 822952 Hs.268685 ESTs 11.3 124761 AA374756 Hs.93560 Homo Sapiens mRNA for KIAA17719.0 protein, partial cds 124768 AW368528 Hs.100855 ESTs 8.1 124775 841772 Hs.100878 ESTs 4.9 124777 841933 Hs.140237 ESTs, Weakly s!milar to ALU1 2.8 HUMAN ALU SUBFAMILY J SEQUENCE

124788 843543 Hs.100912 Homo Sapiens cDNA: FLJ22726 5.1 fis, clone HSI15005 124809 AL355722 Hs.106875 Homo sapiens EST from clone 4.2 35214, full insert 124811 846068 Hs.288912 hypothetical protein FLJ22604 14.2 124812 847948 Hs.188732 ESTs 7.9 4$ 124822 AA418160 Hs.86043 Homo sapiens cDNA FLJ13558 6.6 fis, clone PLACE1007743 124825 AA501669 Hs.336693 ESTs 2.3 124833 AW975868 Hs.294100 ESTs 2.7 124857 863652 Hs.137190 ESTs 2.3 124860 865763 Hs.101477 EST 23.9 5~ 124863 AI382555 Hs.127950 bromodomain-conta!ning 1 2.0 124876 AF135422 Hs.27059 GDP-mannose pyrophosphorylase 4.4 A

124878 BE397530 Hs.288057 hypothetical protein FLJ222422.7 124902 H37941 Hs.101883 ESTs 5.7 124903 AW296713 Hs.221441 ESTs 32.4 $$ 124930 A1076343 Hs.173939 ESTs, Weakly similar to ALUB_HUMAN22.8 !!!! ALU CLASS B WARNING ENTRY !!! [H.sapiens]

124942 899978 Hs.268892 ESTs, Moderately similar to 6.1 834087 hypothetical prote!n [H.sapiens]

124958 A1078645 Hs.431 murine leukemia viral [bmi-1) 1.9 oncogene homolog 124980 T40841 Hs.98681 ESTs 4.5 1250D2 T59338 Hs.269463 ESTs, Weakly similar to ALU1 4.9 HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION

125047 T79815 Hs.279793 ESTs 5.0 125051 T79956 Hs.100588 EST 135.3 125056 T81310 Hs.100592 ESTs 5.4 125101 AI472068 Hs.286236 KIAA1856 protein 5.6 125113 T96595 Hs.302270 ESTs, Weakly similar to ALUF_HUMAN1.8 !!!! ALU CLASS F WARNING ENTRY !!! [H.sapiens]

6$ 125115 T97341 gb:ye57e05.s1 Soares fetal liver spleen lar to 1 NFLS Homo Sapiens cDNA clone IMAGE:121856 3' sim! 9.6 125125 AI222382 Hs.240767 Human DNA sequence from cloneof the RP1-12614 on chromosome 6q24.1-25.2. Contains the 5' gene end 1.5 125147 W38150 Empirically selected from AFFX single 1.7 probeset 1~~

125161 W44657 Hs.144232 EST 10.7 125249 AA630863 Hs.131375 ESTs, Moderately similar 1.3 to ALUB_HUMAN I!!! ALU CLASS B WARNING ENTRY !!! [H.sapiensj 125255 AF098162 Hs.118631 timeless (Drosophila) homolog9.4 125279 AW401809 Hs.4779 KIAA1150 protein 1.5 125280 AI123705 Hs.106932 ESTs 8.0 125298 AW972542 Hs.289008 Homo Sapiens cDNA: FLJ21814 1.5 fis, clone HEP01068 125660 AW292171 Hs.23978 scaffold attachment factor 5.9 B

125827 NM_003403Hs.97496 YY1 transcription factor 1.2 125891 U29589 Hs.7138 cholinergic receptor, muscarinic6.4 1 126005 AW409701 Hs.1578 baculoviral IAP repeat-containing14.3 ~ 5 (survivin) 126202 AA157632 Hs.272630 vacuolar proton pump delta 2.4 polypeptlde 126695 AA643322 Hs.172028 a disintegrin and metalloproteinase9.1 domain 10 127050 AW411066 Hs.274351 GGI-89 protein 17.0 127274 AW966158 Hs.58582 Homo Sapiens cDNA FLJ12789 12.8 fis, clone NT2RP2001947 15 128355 AW293012 Hs.161623 ESTs 7.3 128493 D87466 Hs.240112 KIAA0276 protein 3.1 128493 D87466 Hs.240112 KIAA0276 protein 1.3 128522 BE173977 Hs.10098 putative nucleolar RNA helicase9.4 128527 AA504583 Hs.101047 transcription factor 3 (E2A 1.5 immunoglobulin enhancer binding factors E121E47) 20 128528 839234 Hs.251699 ESTs, Weakly similar to IDN4-GGTR142.8 [H.sapiensj 128595 U31875 Hs.272499 short-chain alcohol dehydrogenase12.1 family member 128599 NM_015366Hs.102336 Rho GTPase activating protein2,3 128604 AI879099 Hs.102397 GIOT-3 for gonadofropin inducible1.3 franscripfion repressor-3 ~

128608 BE267994 Hs.102419 zinc finger protein 7.1 2$ 128625 AB037841 Hs.102652 hypothetical protein ASH1 1.3 .

128629 AL096748 Hs.102708 DKFZP434A043 protein 3.2 128639 AW582962 Hs.102897 CGI-47 protein 2.0 128656 AA458542 Hs.10326 coatomer protein complex, 1.4 subunit epsilon ' 128656 AA458542 Hs.10326 coatomer protein complex, 1.3 subunit epsilo 128658 BE397354 Hs.324830 diptheria toxin resistance 2.4 protein required for diphthamide biosynthesis (Saccharomyces)-like 128670 AA975486 Hs.103441 Homo sapiens, Similar to RIKEN cDNA 1700010L19 gene, clone MGC:16214, mRNA, complete cds 7.1 128691 W27939 Hs.103834 hypothetical protein MGC5576 7.7 128696 BE081143 Hs.225977 nuclear receptorcoactivator33.8 128700 Y15221 Hs.103982 small inducible cytokine subfamily1.6 B (Cys-X-Cys), member 11 35 128714 T85231 Hs.179661 tubulin,beta5 7.6 128717 AK001564 Hs.104222 hypothetical protein FLJ107025.5 128733 BE147740 Hs.104558 ESTs, Moderately similar 2.7 to 138022 hypothetical protein [H.sapiensj 128737 AF292100 Hs.104613 RP42 homolog 2.8 128742 AA307211 Hs.251531 proteasome (prosome, macropain)4.4 subunit, alpha type, 4 4~ 128746 AI470163 Hs.323342 actin related protein 213 2.2 complex, subunit 4 (20 kD) 128747 AB027249 Hs.104741 PDZ-binding kinase; T-cell 2.8 originated protein kinase 128772 BE302796 Hs.105097 thymidine kinase 1, soluble 5.3 128781 N71826 Hs.105465 small nuclear ribonucleoprotein53.9 polypeptide F

128797 NM 002975Hs.105927 stem cell growth factor; 13.3 lymphocyte secreted C-type lectin 45 128806 AW630942 Hs.106061 RD RNA-binding protein 2.6 128814 AW248431 Hs.256526 nuclear prelamin A recognition2.2 factor 128830 BE281170 Hs.106357 valosin-containing protein 5.9 128835 AK001731 Hs.106390 Homo Sapiens mRNA; cDNA DKFZp586H09241.6 (from clone DKFZp586H0924) 128854 BE159181 Hs.168232 hypothetical protein FLJ138552.2 128854 BE159181 Hs.168232 hypothetical protein FLJ138551.9 128868 AA419008 Hs.f06730 chromosome 22 open reading 3.0 frame 3 128868 AA419008 Hs.106730 chromosome 22 open reading 2.2 frame 3 128871 AF189723 Hs.106778 ATPase, Ca++transporting, 1.5 type 2C, member 1 128891 F34856 Hs.292457 Homo Sapiens, clone MGC:16362,13.3 mRNA, complete cds $ 128906 857988 Hs.10706 epithelial protein lost in neoplasm4.7 S beta 128920 AA622037 Hs.166468 programmed cell death 5 1.4 128925 867419 Hs.21851 Homo Sapiens cDNA FLJ12900 fis,1.9 clone NT2RP2004321 128946 Y13153 Hs.107318 kynurenine 3-monooxygenase 7.2 (kynurenine 3-hydroxylase) 128949 AA009647 Hs.8850 a disintegrin and metalloproteinase2.4 domain 12 (meltrin alpha) (ADAM-12) 60 128958 AW139032 Hs.107376 hypothetical protein DKFZp434N0351.3 128959 AI580127 Hs.107381 hypothetical proteinFLJ1120010.9 128965 AW150697 Hs.107418 ESTs 1.4 128970 AI375672 Hs.165028 ESTs 1.3 128975 BE560779 Hs.284233 NICES protein 14.0 65 128979 AW271217 Hs.281434 Homo sapiens cDNA FLJ14028 1.6 fis, clone HEMBA1003838 128995 AI816224 Hs.107747 DKFZP566C243 protein 1.9 129019 AI950087 gb:wq05c02.x1 NCI_CGAP_Kid12 Homo Sapiens2.9 cDNA clone 3', mRNA sequence 129021 AL044675 Hs.173081 KIAA0530 protein 3.8 129021 AL044675 Hs.173081 KIAA0530 protein 2.5 129032 880088 Hs.108104 ubiquitin-conjugating enzyme3.4 129076 AW296806 Hs.326234 ESTs, Highly similar to 5.0 T46422 hypothetical protein DKFZp434M2023.1 [H.sapiens]

$ 129078 AI351010 Hs.102267 lysosomal 2.1 129088 AA744610 Hs.194431 palladin 17.1 129095 L12350 Hs.108623 thrombospondin 2 2.7 129096 AA463189 Hs.288906 WW Domain-Containing Gene 20.9 129097 BE243933 Hs.108642 z'snc finger protein 22 3.0 (KOX 15) 1 129099 AF146074 Hs.108660 ATP-binding cassette, sub-family5.8 ~ C (CFTRIMRP), member 5 129136 W93048 Hs.250723 hypothetical protein MGC27475.9 129149 AA356620 Hs.108947 KIAA0050 gene product 6.3 129172 AW162916 Hs.241576 hypothetical protein PR025771.8 129192 AA286914 Hs.183299 ESTs 2.1 1$ 129194 AA150797 Hs.109276 latexin protein 3.2 129198 N57532 Hs.109315 KIAA1415 protein 5.8 129207 AI934365 Hs.109439 osteoglycin (osteoinductive8.0 factor, mimecan) 129228 040714 Hs.239307 tyrosyl-tRNA synthetase 2.9 129229 AF013758 Hs.109643 polyadenylate binding protein-interacting3.2 protein 1 2~ 129254 AA252468 Hs.1098 DKFZp434J1813 protein 2.6 129255 A1961727 Hs.109804 H1 histone family, memberX7.3 129288 W26392 Hs.110080 ESTs, Weakly similar to S134959.6 pregnancy zone protein [H.sapiens]

129296 A1051967 Hs.110122 ESTs 1.2 129323 AA287239 Hs.5518 Homo Sapiens cDNA FLJ11311 5.1 fis, clone PLACE1010102 2$ 129340 H75334 Hs.11050 F-box only protein 9 4.6 129347 BE614192 Hs.279869 melanoma-associated antigen7.6 recognised by cytotoxic T lymphocytes 129362 030246 Hs.110736 solute carrier family 12 6.7 (sodiumlpotassiumlchloride transporters), member 129366 BE220806 Hs.184697 Homo sapiens clone 23785 8.6 mRNA sequence 129370 AI686379 Hs.110796 SAR1 protein 1.4 129372 NM 016039Hs.110803 CGI-99 protein 2.0 129403 AF149785 Hs.111126 pituitary tumor-transforming7.4 1 interacting protein 129404 AI267700 Hs.317584 ESTs 5.0 129404 AI267700 Hs.317584 ESTs 2.5 129423 AA204686 Hs.234149 hypothetical protein FLJ2064710.2 3 129449 A1096988 Hs.111554 ADP-ribosylation factor-like8.0 $ 7 129453 AW974265 Hs.111632 Lsm3 protein 3.2 129482 AA188185 Hs.289043 spindlin 6.7 129482 AA188185 Hs.289043 spindlin 3.6 129513 AW843633 Hs.306163 hypothetical protein AL1101157.1 129515 AF255303 Hs.112227 membrane-associated nucleic2.5 acid binding protein 129527 AA769221 Hs.270847 delta-tubulin 3.2 129559 W01296 Hs.11360 hypothetical protein FLJ147847.5 129560 AA317841 Hs.7845 hypothetical protein MGC27526.8 129570 AI923097 Hs.11441 chromosome 1 open reading 2.0 frame 8 4$ 129575 F08282 Hs.278428 progestin induced protein 1.6 129587 H14718 Hs.11506 Human clone 23589 mRNA sequence6.8 129588 BE408300 Hs.301862 postmeiotic segregation 1.4 increased 2-like 9 129591 N57423 Hs.179898 HSPC055 protein 7.3 129594 AW403724 Hs.36989 coagulation factor VII (serum9.0 prothrombin conversion accelerator) $0 129596 AF035537 Hs.115521 REV3 (yeast homology-like,1.6 catalytic subunit of DNA polymerise zeta 129628 038945 Hs.1174 cyclin-dependent kinase inhibitor2.2 2A (melanoma, p16, inhibits CDK4) 129628 038945 Hs.1174 cyclin-dependent kinase inhibitor1.4 2A (me 129629 AK000398 Hs.11747 hypothetical protein FLJ203913.8 129649 AD000092 Hs.16488 calreticulin 3.3 $$ 129675 NM_015556Hs.172180 KIAA0440 protein 13.4 129680 003749 gb:Human chromogranin A (CHGA) gene, 14.1 promoter an 129689 AW748482 Hs.77873 B7 homolog 3 2.6 129702 AI304966 Hs.12035 ESTs, Weakly similar to 7.4 138022 hypothetical protein [H.sapiens]

129720 AA156214 Hs.12152 APMCF1 protein 2.0 129721 NM_001415Hs.211539 eukaryotic translation 1.7 initiation factor 2, subunit 3 (gamma, 52kD) 129726 H15474 Hs.132898 fatty acid desaturase 1 8.3 129778 AK001676 Hs.12457 hypothetical protein FLJ108141.8 129779 AA394090 Hs.12460 Homo sapiens clone 23870 5.4 mRNA sequence 129800 AF052112 Hs.12540 lysosomal 1.7 6$ 129806 AB023148 Hs.173373 KIAA0931 protein 1.2 129815 BE565817 Hs.26498 hypothetical protein FLJ216573.1 129840 NM_006590Hs.12820 SnRNP assembly defective 1.8 1 homolog 129861 AL049999 Hs,85963 DKFZP564M182 protein 2.2 129864 A1393237 Hs.129914 runt-related transcription 1.7 factor 1 (acute myef0id leukemia 1; aml1 oncogenej 129869 AI222069 Hs.13015 hypothetical protein similar2.7 to mouse Dnajl1 129922 AF042379 Hs.13386 gamma-tubulin complex protein4.5 $ 129945 BE514376 Hs.165998 PAI-1 mRNA-binding protein 1.8 129953 AA412195 Hs.13740 ESTs 2.5 129972 AW753185 Hs.180628 dynamin 1-like 1.8 129983 009848 Hs.132390 zinc finger protein 36 (KOX 1.3 18) 129989 A8015856 Hs.247433 activating transcription 4.0 factor 6 130010 AA301116 Hs.142838 nucleolar phosphoprotein 1.6 Nopp34 130081 AA287325 Hs.14713 ESTs 4.0 130082 S73265 Hs.1473 gastrin-releasing peptide 1.8 130097 AL046962 Hs.14845 forkhead box 03A 2.8 130100 AL135561 Hs.14891 hypothetical protein FLJ210472.3 1$ 130111 X53002 Hs.149846 integrin, beta 5 2.3 130112 AA916785 Hs.180610 splicing factor prolinelglutamine3.0 rich (polypyrimidine tract-binding protein-associated) 130112 AA916785 Hs.180610 splicing factor prolinelglutamine2.1 rich ( 130128 L76937 Hs.150477 Wemersyndrome 1.8 130135 AA311426 Hs.21635 tubulin, gamma 1 6.1 130211 NM_003358Hs.23703 ESTs, Moderately similar to CEGT_HUMAN CERAMIDE GLUCOSYLTRANSFERASE [H.sapiensj 1.6 130212 D80001 Hs.152629 KIAA0179 protein 1.3 130236 885367 Hs.51957 splicing factor, argininelserine-rich2.0 2, interacting protein 130241 AL035588 Hs,153203 MyoD family inhibitor 3.2 130242 X79201 Hs.153221 synovial sarcoma, translocated5.4 to X chromosome ~$ 130249 D81983 Hs.322852 GAS2-related on chromosome 4.8 130263 NM 002497Hs.153704 NIMA (never in mitosis gene1.4 a)-related kinase 2 130287 AA479005 Hs.154036 tumor suppressing subtransferable2.6 candidate 3 130310 AB011121 Hs.154248 amyotrophic lateral sclerosis6.3 2 (juvenile) chromosome region, candidate 3 130353 219084 Hs.172210 MUF1 protein 6.2 30 130356 AF127577 Hs,155017 nuclear receptor interacting2.4 protein 1 130357 AJ224442 Hs.155020 putative methyltransferase 3.4 130359 NM_013449Hs.277401 bromodomain adjacent to 8.5 zinc finger domain, 2A

130367 AL135301 Hs.8768 hypothetical protein FLJ108491.4 130372 A1077464 Hs,5011 RNA binding motif protein 3.3 3 130393 N89487 Hs.155291 KIAA0005 gene product 1.8 $

130399 AW374106 Hs.155356 hypothetical protein MGC28403.4 similar to a putative glucosyltransferase 130407 BE385099 Hs,334727 hypothetical protein MGC30172.3 130409 NM 001197Hs.155419 BCL2-interactingkiller(apoptosis-inducing)2.7 130419 AF037448 Hs.155489 NS1-associated protein 1 1.8 40 130441 063630 Hs.155637 protein kinase, DNA-activated,2.3 catalytic polypeptide 130448 BE513202 Hs.15589 PPAR binding protein 3.9 130455 D90041 Hs.155956 N-acetyltransferase 1 (arylamine33.6 N-acetyltransferase) 130455 D90041 Hs.155956 N-acetyltransferase 1 (arylamine4.6 N-acety 130471 AL121438 Hs.183706 adducin 1 {alpha) 2.7 4$ 130485 BE245851 Hs.180779 H2B histone family, member 5.0 B

130487 049844 Hs.77613 ataxia telangiectasia and Rad34.3 related 130498 L38951 Hs.180446 karyopherin (importin) beta 1.6 130503 BE208491 Hs.295112 KIAA0618 gene product 16.1 130511 L32137 Hs.1584 cartilage oligomeric matrix 6.1 protein {pseudoachondroplasia, epiphyseal dysplasia 1, multiple) $0 130511 L32137 Hs.1584 cartilage oligomeric matrix 5.3 protein (pse 130526 AW876523 Hs.15929 hypothetical protein FLJ129102.1 130542 064675 Hs.179825 RAN binding protein 2-like 7.8 130544 AA321238 Hs.4310 eukaryotic translation initiation1.5 factor 1A

130553 AF062649 Hs,252587 pituitary tumor-transforming14.4 $ 130556 AI907018 Hs.15977 Empirically selected from 4.7 $ AFFX single probeset 130567 AA383092 Hs.1608 replication protein A3 (14kD)7.9 130568 AA232119 Hs.16085 putative G-protein coupled 3.3 receptor 130574 AF083208 Hs.16178 apoptosis antagonizing transcription1.2 factor 130586 AB007891 Hs.16349 KIAA0431 protein 5.6 60 130598 AL042210 Hs.16493 hypothetical protein DKFZp762N2316;1.4 KIAA1803 protein 130601 AA609738 Hs.16525 ESTs 1.5 130614 AI354355 Hs.16697 down-regulator of transcription1.3 1, TBP-binding {negative cofactor 2) 130617 M90516 Hs.1674 glutamine-fructose-6-phosphate 12.1 transaminase 1 130617 M90516 Hs.1674 glutamine-fructose-6-phosphate 2.4 transamin 6$ 130618 AA383439 Hs.16758 Spir-1 protein 15.9 130667 BE246961 Hs.17639 Homo Sapiens ubiqui6n protein13.9 ligase (UBE3B) mRNA, partial cds 130674 AL048842 Hs.194019 attractin 1.5 130675 AA442233 Hs.17731 hypothetical protein FLJ128925.4 130692 AA652501 Hs.13561 hypothetical protein MGC46925.0 130693 868537 Hs.17962 ESTs 2.0 130712 AJ271881 Hs.279762 bromodomain-containing 7 1.8 130714 AI348274 Hs.18212 DNA segment on chromosome 2.0 X (unique) 9879 expressed sequence 130730 AB007920 Hs.18586 KIAA0451 gene product 3.7 130744 H59696 Hs.18747 POP7 (processing of precursor,3.1 S. cerevisiae) homolog 130751 AF052105 Hs.18879 chromosome 12 open reading 1.4 frame 130757 AL036067 Hs.18925 protein x 0001 5.7 1 130768 AF258627 Hs.211562 ATP-binding cassette, sub-family5.1 ~ A (ABC1), member 1 130789 AK000355 Hs.8899 sirtuin (silent mating type 5.2 information regulation 2, S.cerevisiae, homology 130815 AB018298 Hs.19822 SEC24 (S. cerevisiae) related1.5 gene family, member D

130836 J05068 Hs.2012 transcobalamin I (vitamin 812 15.7 binding protein, R binder family) 130841 AL157468 Hs.325825 Homo Sapiens cDNA FLJ20848 2.8 fis, clone ADKA01732 1$ 130843 AA447492 Hs.20183 ESTs, Weakly similar to AF16479311.5 protein x 013 [H.sapiens]

130844 U76248 Hs.20191 seven in absentia (Drosophila)3.4 homolog 2 130855 AJ243706 Hs.143323 putative DNAlchromatin binding1.7 motif 130861 NM_016578Hs.20509 HBV pX associated protein-8 1.9 130879 NM_003416Hs.2076 zinc finger protein 7 (KOX 1.4 4, clone HF.16) 130880 BE514434 Hs.20830 kinesin-like 2 2.1 130892 AL120837 Hs.20993 high-glucose-regulated protein2.4 130898 AB033078 Hs.186613 sphingosine-1-phosphate 1.7 lyase 1 130911 BE409769 Hs.21189 DnaJ (Hsp40) homolog, subfamily1.8 A, member 2 130919 N79110 Hs.21276 collagen, type IV, alpha 3 2.3 (Goodpasture antigen) binding protein 2S 130944 BE382657 Hs.21486 signal transducer and activator5.4 oftranscription1,91kD

130971 N39842 Hs.301444 KIAA1673 2.2 130992 BE398091 Hs.74316 desmoplakin (DPI, DPII) 1.8 130993 T97401 Hs.21929 ESTs 1.6 131005 AV658308 Hs.2210 thyroid hormone receptor interactor1.6 30 131028 AI879165 Hs.2227 CCAATIenhancer binding protein1.2 (CIEBP), gamma 131042 AI826288 Hs.171637 hypothetical protein MGC26281.6 131046 AA321649 Hs.2248 small inducible cytokine subfamily7.4 B (Cys-X-Cys), member 10 131046 AA321649 Hs.2248 small inducible cytokine subfamily3.0 B (Cy 131047 H23230 Hs.22481 ESTs, Moderately similar to 1.7 A46010 X-linked retinopathy protein [H.sapiens]

3 131060 AA194422 Hs.22564 myosin VI 5.1 $

131060 AA194422 Hs.22564 myosin VI 2.5 131070 N53344 Hs.22607 ESTs 7.1 131076 AA749230 Hs.26433 dolichyl-phosphate (UDP-N-acetylglucosamine)2.0 N-acetylglucosaminephosphotransferase 1 ( 131076 AA749230 Hs.26433 dolichyl-phosphate (UDP-N-acetylglucosam1.9 131099 AL133353 Hs.226581 COX15 (yeast) homolog, cytochrome7.0 c oxidase assembly protein 131174 NM_006540Hs.29131 nuclear receptor coacGuator 1.9 131185 8E280074 Hs.23960 cyclin B1 5.8 131206 AW138839 Hs.24210 ESTs 2.0 131213 AA885699 Hs.24332 CGI-26 protein 7.0 4$ 131225 H62087 Hs.31659 thyroid hormone receptor-associated7.5 protein, 95-kD subunit 131231 N47468 Hs.59757 zinc finger protein 281 2.9 131233 D89053 Hs.268012 fatty-acid-Coenzyme A ligase,3.5 long-chain 3 131243 AW383256 Hs.24752 spectrin SH3 domain binding 2.8 protein 1 131245 AL080080 Hs.24766 thioredoxin domain-containing2.8 S~ 131247 AL043100 Hs.326190 fatty acid amide hydrolase 5.6 131281 AA251716 Hs.25227 ESTs 5.7 131283 X80038 Hs.339713 Homo Sapiens clone F19374 1.3 APO E-C2 gene cluster 131305 AV656017 Hs.184325 CGI-76 protein 5.0 131320 AA505691 Hs.145696 splicing factor (CC1.3) 1.8 55 131339 AF058696 Hs.25812 Nijmegen breakage syndrome 2.6 1 (nibrin) 131339 AF058696 Hs.25812 Nijmegen breakage syndrome 2.6 1 (nibrin) 131375 AW293165 Hs.143134 ESTs 5.4 131390 BE269388 Hs.182698 mitochonddal ribosomal protein5.3 131410 BE259110 Hs.279836 HSPC166 protein 2.2 131412 NM_012247Hs.124027 SELENOPHOSPHATE SYNTHETASE 2.0 ; Human selenium donor protein 131429 AL046302 Hs.26750 hypothetical protein FLJ219081.4 131458 BE297567 Hs.27047 hypothetical protein FLJ203921.7 131475 AA992841 Hs.27263 KIAA1458 protein 2.0 131501 AV661958 Hs.8207 GK001 protein 2.6 6S 131501 AV661958 Hs.8207 GK001 protein 1.6 131511 AA732153 Hs.27865 Homo Sapiens cDNA: FLJ21333 2.0 fis, clone COL02535 131528 AU076408 Hs.28309 UDP-glucose dehydrogenase 1.6 131532 BE268278 Hs.28393 hypothetical protein MGC2592 7.4 131543 AW966881 Hs.41639 programmed cell death 2 2.2 131544 AL355715 Hs.28555 programmed cell death 9 (PDCD9)2.1 131562 NM_003512Hs.28777 H2A histone family, member 1.7 L

$ 131564 T93500 Hs.28792 Homo sapiens cDNA FLJ11041 fis,5.1 clone PLACE1004405 131564 T93500 Hs.28792 Homo sapiens cDNA FLJ11041 fis,1.8 clone PL

131569 AL389951 Hs.271623 nucleoporin 50kD 5,0 131618 BE393822 Hs.29645 Homo sapiens mRNA; cDNA DKFZp7611.8 C029 (from clone DKFZp761 C029); partial cds 131622 878195 Hs.29692 Homo sapiens cDNA FLJ11436 fis,1.3 clone HEMBA1001213 131623 A8037791 Hs.29716 hypothetical protein FLJ109802.2 131623 AB037791 Hs.29716 hypothetical protein FLJ109801.9 131643 AW410601 Hs.30026 HSPC182 protein 2.9 131653 AW960597 Hs.30164 ESTs 1.3 131656 AI218918 Hs.30209 KIAA0854 protein 2.8 1$ 131669 X52486 Hs.3041 uracil-DNA glycosylase 2 2.8 131692 BE559681 Hs.30736 KIAA0124 protein 5.6 131714 AA642831 Hs.31016 putative DNA binding protein 2.9 131722 D13757 Hs.311 phosphoribosyl pyrophosphate amidotransferase3.4 131737 AK001641 Hs.31323 inhibitor of kappa light polypeptide3.8 gene enhancer in B-cells, kinase complex-associated protein 2~ 131760 X76732 Hs.3164 nucleobindin 2 2.9 131760 X76732 Hs.3164 nucleobindin 2 2.8 131763 AI878932 Hs.317 topoisomerase (DNA) I 3.4 131772 AA382590 Hs.170980 KIAA0948 protein 25.5 131774 BE267158 Hs.169474 DKFZP586J0119 protein 5.5 2$ 131787 D87077 Hs.196275 KIAA0240 protein 2.4 131793 AW966127 Hs.32246 Homo Sapiens cDNA FLJ14656 7.9 fits, clone NT2RP2002439 131795 BE501849 Hs.32317 high-mobility group 20B 1.4 131798 X86098 Hs.301449 adenovirus 5 E1A binding protein4.1 131817 U20536 Hs.3280 caspase 6, apoptosis-related 4.2 cysteine protease 3~ 131824 U28838 Hs.32935 TATA box binding protein (TBP)-associated3.5 factor, RNA polymerise III, GTF3B subunit 2 131850 AI251317 Hs.33184 ESTs 5.1 131878 AA083764 Hs.6101 hypothetical protein MGC3178 5.8 131885 BE502341 Hs.3402 ESTs 13.7 131885 BE502341 Hs.3402 ESTs 2.4 3 131887 W17064 Hs.332848 SWIISNF related, matrix associated, $ actin dependent regulator of chromatin, subfamily e, member 1 3.2 131900 AA099014 Hs.231029 Homo sapiens, clone MGC:15961,8.7 mRNA, complete cds 131900 AA099014 Hs.231029 Homo Sapiens, clone MGC:15961,2.0 mRNA, com 131904 AF078866 Hs.284296 Homo Sapiens cDNA: FLJ22993 5.5 fis, clone KAT11914 131905 AA179298 Hs.3439 stomatin-like 2 11.3 4~ 131913 AW207440 Hs.185973 degenerative spermatocyte 1.7 (homolog Drosophila; lipid desaturase) 131916 AA025976 Hs.34569 ESTs . 5.2 131925 AF151048 Hs.183180 anaphase promoting complex 2.7 subunit 11 (yeast APC11 homology 131929 BE541211 Hs.34804 Homo Sapiens cDNA FLJ11472 5.3 fis, clone HEMBA1001711 131941 BE252983 Hs.35086 ubiquitin specific protease 2.3 4$ 131950 AA355113 Hs.35380 x 001 protein 1.5 131962 AK000046 Hs.267448 hypothetical protein FLJ200392.3 131965 W79283 Hs.35962 ESTs 1.4 131971 BE567100 Hs.154938 hypothetical protein MDS025 3.5 131977 U90441 Hs.3622 procollagen-proline, 2-0xoglutarate6.5 4~iioxygenase (proline 4-hydroxylase), alpha polypeptide II

$Q 131985 AA503020 Hs.36563 hypothetical protein FLJ224182.4 131991 AF053306 Hs.36708 budding uninhibited by benzimidazoles2.1 1 (yeast homology, beta 132019 H56995 Hs.37372 Homo sapiens DNA binding peptide3.2 mRNA, partial cds 132031 AF193844 Hs.3758 COP9 complex subunit 7a 5.8 132062 BE266155 Hs.3832 clathrin-associated protein 1.5 $ 132084 NM 002267Hs.3886 karyopherin alpha 3 (importin 3.7 $ alpha 4) 132103 BE171921 Hs.3991 ESTs ~ 1.4 132105 AV646076 Hs.39959 ESTs 5.8 132116 AW960474 Hs.40289 ESTs 1.7 132176 AA857025 Hs.8878 kinesin-like 1 3.3 132180 NM_004460Hs.418 fibroblast activation protein, 14.7 alpha 132192 AA206153 Hs.4209 mitochondrial ribosomal protein5.5 132194 842432 Hs.4212 ESTs 4.4 132203 NM_004782Hs.194714 synaptosomal-associated protein,2.2 29kD

132207 BE206939 Hs.42287 E2F transcription factor 6 2.2 6$ 132235 AV658411 Hs.42656 KIAA1681 protein 7.8 132240 AB018324 Hs.42676 KIAA0781 protein 1.5 132252 AI566004 Hs.141269 Homo Sapiens cDNA: FLJ21550 1.3 fis, clone COL06258 132266 AA301228 Hs.43299 hypothetical protein FLJ128905.7 132273 AA227710 Hs.43658 DKFZP586L151 protein 4.2 132276 AA653507 Hs.285711 hypothetical protein FLJ130892.1 132288 N36110 Hs.305971 solute carrier family 2 (facilitated1.5 glucose transporter), member 10 132294 A8023191 Hs.44131 KIAA0974 protein 10.0 132298 NM_015986Hs.7120 cytokine receptor-like molecule1.9 132299 AW405882 Hs.44205 cortistatin 9.2 132325 N37065 Hs.44856 hypothetical protein FLJ121162.0 132346 AW067708 Hs.170311 heterogeneous nuclear ribonucleoprotein6.5 D-like 1 132370 AW572805 Hs.46645 ESTs 3.8 ~

132374 AF155582 Hs.46744 core1 UDP-galactose:N-aceiylgalactosamine-alpha-R1.5 beta 1,3-galactosyltransferase 132376 AI279892 Hs.46801 sorting nexin 14 12.5 132384 AA312135 Hs.46967 HSPC034 protein 28.3 132393 AL135094 Hs.47334 hypothetical protein FLJ144951.9 1$ 132450 AA100012 Hs.48827 hypothetical protein FLJ120851.9 132452 AW973521 Hs.247324 mitochondrial ribosomal 6.1 protein S14 132456 A8011084 Hs.48924 KIAA0512 gene product; ALEX21.7 132465 AW169847 Hs.49169 KIAA1634 protein 8.6 132470 AI224456 Hs.4934 H.sapiens polyA site DNA 5.2 132484 X16660 Hs.119007 RAB4, member RAS oncogene 1.4 family 132518 AW885606 Hs.5064 ESTs 6.1 132528 T78736 Hs.50758 SMC4 (structural maintenance 3.3 of chromosomes 4, yeast)-like 1 132530 AA306105 Hs.50785 SEC22, vesicle trafficking 2.0 protein (S. cerevisiae)-like 1 132532 AA454132 Hs.5080 mitochondrial ribosomal protein2.9 132534 BE388673 Hs.5086 hypothetical protein MGC104332.2 132543 BE568452 Hs.5101 protein regulator of cytokinesis7.3 132571 AW674699 Hs.5169 suppressor of G2 allele of 1.7 SKP1, S. cerevisiae, homolog of 132574 AW631437 Hs.5184 TH1 drosophila homolog 7.1 132596 AK001484 Hs.5298 CGI-45 protein 2.2 3~ 132611 AA345547 Hs.53263 hypothetical protein FLJ13287, 2.2 132612 H12751 Hs.5327 PR01914 protein 6.8 132616 BE262677 Hs.283558 hypothetical protein PR0185514.0 132638 AI796870 Hs.54277 DNA segment on chromosome 11.4 X (unique) 9928 expressed sequence 132648 U51127 Hs.54434 hypothetical protein MGC1715 1.9 3$ 132668 AB018319 Hs.5460 KIAA0776 protein 2.6 132692 AW191962 Hs.249239 collagen, type VIII, alpha2.0 132715 F11875 Hs.5534 Homo Sapiens cDNA FLJ12961 1.5 fis, clone NT2RP2005645 132718 NM 004600Hs.554 Sjogren syndrome antigen A2 3.0 (60kD, ribonucleoprotein autoantigen SS-AIRo) 132724 AI142265 Hs.55498 geranylgeranyl diphosphate 2.4 synthase 1 132731 AI189075 Hs.301872 hypothetical protein MGC484012.4 132744 AA010233 Hs.55921 glutamyl-prolyl-tRNA synthetase14.6 132760 AA125985 Hs.56145 thymosin, beta, identified 2.7 in neuroblastoma cells 132771 Y10275 Hs.56407 phosphoserine phosphatase 3.0 132773 AA459713 Hs.295901 KIAA0493 protein 2.3 45 132784 AI142133 Hs.56845 GDP dissociation inhibitor21.8 132798 A1026701 Hs.5716 KIAA0310 gene product 3.7 132807 U07418 Hs.57301 mutt (E, coli) homolog 1 (colon1.8 cancer, nonpolyposis type 2) 132810 AB007944 Hs.5737 KIAA0475 gene product 5.9 132813 BE313625 Hs.57435 solute camerfamily 11 (proton-coupled8.7 divalent metal ion transporters), member 2 SD 132815 AI815189 Hs.57475 sex comb on midleg homolog 6.4 132817 N27852 Hs.57553 tousled-like kinase 2 3.6 132821 AJ251595 Hs.169610 CD44 antigen (homing function2.8 and Indian blood group system) 132833 U78525 Hs.57783 eukaryotic translation initiation14.6 factor 3, subunit 9 (eta,116kD) 132842 NM 016154Hs.279771 Homo Sapiens clone PP1596 1.6 unknown mRNA

55 132844 F12200 Hs.5811 chromosome 21 open reading 2.5 frame 59 132851 U09716 Hs.287912 lectin, mannose-binding,1 1.4 132863 BE268048 Hs.236494 RA810, member RAS oncogene4.2 family 132869 AW963217 Hs.203961 ESTs, Moderately similar 2.8 to AF11672189 PR02168 [H.sapiens]

132873 AW007683 Hs.58598 KIAA1266 protein 2.0 132875 NM_004850Hs.58617 Rho-associated, coiled-coil1.6 containing protein kinase 2 132891 BE267143 Hs.59271 U2(RNU2) small nuclear RNA 1.4 auxiliary factor 1 (non-standard symbol) 132897 AW503667 Hs.59545 ring finger protein 15 5.4 132902 A1936442 Hs.59838 hypothetical protein FLJ108086.1 132912 AW732760 Hs.167578 Homo Sapiens cDNA FLJ110957.1 fis, clone PLACE1005374 6S 132913 W78714 Hs.60257 Homo Sapiens cDNA FLJ13598 2.8 fis, clone PLACE1009921 132940 T79136 Hs.127243 Homo sapiens mRNA for KIAA17246.1 protein, partial cds 132941 AI817165 Hs.6120 hypothetical protein FLJ1322210.3 132942 AA554458 Hs.197751 KIAA0666 protein 1.8 132952 AI658580 Hs.61426 Homo sapiens mesenchymal stem2.2 cell protein DSC96 mRNA, partial cds 132962 AA576635 Hs.6153 CGI-48 protein 4.9 132972 AA034365 Hs.288924 Homo Sapiens cDNA FLJ11392 2.7 fis, clone HEMBA1000575 $ 132973 AA035446 Hs.323277 ESTs 5.3 132977 AA093322 Hs.301404 RNA binding motif protein 3.2 132980 AA040696 Hs.62016 ESTs 1.3 132994 AA112748 Hs.279905 clone HQ0310 PR00310p1 3.0 133012 AA847843 Hs.62711 Homo sapiens, clone IMAGE:3351295,10.3 mRNA

1 133015 AJ002744 Hs.246315 UDP-N-acetyl-alpha-D-galactosamine:polypeptide ~ N-acefylgalactosaminyftransferase 7 (GaINAc-T7) 2.1 133016 AI439688 Hs.6289 hypothetical protein FLJ20886 1.3 133053 A1065016 Hs.6390 Homo Sapiens clone FLB3344 6.0 PR00845 mRNA, complete cds 133062 AW500374 Hs.64056 PR00149 protein 5.3 133069 BE247441 Hs.6430 protein with polyglutamine 4.9 repeat; calcium (cat+) homeostasis endoplasmic reticulum protein 1$ 133091 AK001628 Hs.64691 KIAA0483 protein 3.5 133110 AA808177 Hs.65228 ESTs 13.1 133134 AF198620 Hs.65648 RNA binding motif protein 1.3 SA

133145 H94227 Hs.6592 Homo Sapiens, clone IMAGE:2961368,2.2 mRNA, partial cds 133152 211695 Hs.324473 mitogen-activated protein kinase1.3 133174 AA431620 Hs.324178 hypothetical protein MGC274517.1 133175 AW955632 Hs.66666 ESTs, Weakly similar to S195601.8 proline-rich protein MP4 - mouse [M.musculus]

133177 X97795 Hs.66718 RAD54 (S.cerevisiae)-like 4.9 133197 AI275243 Hs.180201 hypothetical protein FLJ206713.1 133208 AI801777 Hs.6774 ESTs 4.4 133226 AW954569 Hs.296287 Homo Sapiens, Similar to 1.7 bromodomain-containing 4, clone IMAGE:3542455, mRNA, partial cds 133228 AI492924 Hs.6831 golgi phosphoprotein 1 6.0 133240 AK001489 Hs.242894 ADP-ribosylation factor-like1.5 133254 AI567421 Hs.273330 Homo Sapiens, clone IMAGE:3544662,1.4 mRNA, partial cds 133266 AI160873 Hs.69233 zinc finger protein ~ 5.6 30 HUMAN FORKHEAD BOX PROTEIN D2 [H.sapiens] 1.9 133268 AW956781 Hs.293937 ESTs, Weakly similar to FXD2 _ 4.7 133285 M76477 Hs.289082 GM2 ganglioside activator protein , 133291 BE297855 Hs.69855 NRAS-related gene 5.0 133314 AA102670 Hs.70725 gamma-aminobutyric acid (GABA)2.7 A receptor, pi 133321 T79526 Hs.179516 integral type I protein 9.3 3 133327 AL390127 Hs.7104 Kruppel-like factor 13 4.4 $

133347 BE257758 Hs.71475 acid cluster protein 33 1.8 133360 A1016521 Hs.71816 v-akt murine thymoma viral 5.5 oncogene homolog 1 133366 AA292811 Hs.72050 non-metastatic cells 5, protein2.7 expressed in (nucleoside-diphosphate kinase) 133367 AF231919 Hs.18759 KIAA0539 gene product 1.7 4~ 133370 AF245505 Hs.72157 DKFZP56411922 protein 1.8 133383 BE313555 Hs.7252 KIAA1224 protein 1.7 133390 AI950382 Hs.72660 phosphatidylserine receptor 1.3 133391 AW103364 Hs.727 inhibin, beta A (activin A, 16.1 activin AB alpha polypeptide) 133394 AA305127 Hs.237225 hypothetical protein HT023 12.2 4S 133437 AL031591 Hs.7370 phosphofidylinosifol transfer 10.4 protein, beta 133452 NM_002759Hs.274382 protein kinase, interferon-inducible1.2 double stranded RNA dependent 133453 AI659306 Hs.73826 protein tyrosine phosphatase,1.7 non-receptor type 4 (megakaryocyte) 133500 AW964804 Hs.74280 hypothetical protein FLJ2223711.1 133529 W45623 Hs.74571 ADP-ribosylation factor 1 2.8 133540 AL037159 Hs.74619 proteasome (prosome, macropain)2.9 26S subunit, non-ATPase, 2 133543 AU077073 Hs.108327 damage-specific DNA binding 2.5 protein 1 (127kD) 133578 AU077050 Hs.75066 translin 1.5 133579 X75346 Hs.75074 mitogen-activated protein kinase-activated2.1 protein kinase 2 133582 BE391579 Hs.75087 Fas-activated serinelthreonine1.3 kinase $ 133594 AW160781 Hs.172589 nuclear phosphoprotein similar2.2 S to S. cerevisiae PWP1 133595 AA393273 Hs.75133 transcription factor 6-like 1.5 1 (mitochondria) transcription factor 1-like) 133599 NM_002885Hs.75151 RAP1, GTPase activating protein5.7 133621 NM_004893Hs.75258 H2A histone family, memberY 25.5 133627 NM_002047Hs.75280 glycyl-tRNA synthetase 15.8 133631 NM_000401 Hs.75334 exostoses (multiple) 2 3.3 133649 025849 Hs.75393 acid phosphatase 1, soluble 1.6 133690 AV661185 Hs.75574 mitochondria) ribosomal protein4.1 133720 L27841 Hs.75737 pericentriolar material 1 1.5 133722 AW969976 Hs.279009 matrix Gla protein 6.3 65 133751 AW402048. Hs.334787 Homo Sapiens, Similar to 3.9 likely ortholog ofyeastARV1, clone IMAGE:3506392, mRNA

133757 T52946 Hs.196209 RAE1 (RNA export 1, S.pombe) 1.7 homolog 133760 BE271766 Hs.181357 laminin receptor 1 (67kD, 1.8 ribosomal protein SA) 133765 M62194 Hs.75929 1.5 cadherin 11, type 2, OB-cadherin (osteoblast) 133780 AA557660 Hs.76152 3.5 decorin 133784 BE622743 Hs.301064 6.8 arfaptin 1 133791 M34338 Hs.76244 2.6 spermidine synthase $ 133797 AL133921 Hs.76272 1.4 retinoblastoma-binding protein 2 133822 D50525 Hs.699 8.0 peptidylprolyl isomerase B (cyclophilin B) 133842 AW797468 Hs.285013 13.5 putative human HLA
class II associated protein I

133845 AA147026 Hs.76704 2.2 ESTs 133850 W29092 Hs.7678 1.8 cellular retinoic acid-binding protein 1 133859 086782 Hs.178761 2.0 ~ 26S proteasome-associated pad1 homolog 133865 AB011155 Hs.170290 2.8 discs, large (Drosophila) homolog 5 133867 AW340125 Hs.76989 6.7 KIAA0097 gene product 133868 AB012193 Hs.183874 2.5 cullin 4A

133881 030872 Hs.77204 3.0 centromere protein F (3501400kD, mitosin) 1$ 133922 030825 Hs.77608 1.4 splicing factor, argininelserine-rich 133924 D86326 Hs.325948 5.4 vesicle docking protein p115 133929 NM_006306Hs.211602 4.9 SMC1 (structural maintenance of chromosomes 1, yeast)-like 1 133936 L17128 Hs.77719 3.7 gamma-glutamyl carboxylase 133941 BE244332 Hs.77770 12.1 adaptor-related protein complex 3, mu 2 subunit 2~ 133959 X81789 Hs.77897 9.7 splicing factor 3a, subunit 3, 60kD

133976 AI908165 Hs.169946 3.1 GATA-binding protein 3 (T-cell receptor gene activator) 133989 AL040328 Hs.78202 1.3 SWI/SNF related, matrix associated, actin dependent regulator of chromatin 133997 AI824113 Hs.78281 9.7 regulator of G-protein signalling 12 134010 AB016092 Hs.197114 2.4 RNA binding protein;
AT-rich element binding factor ~$ 134015 D31764 Hs.278569 2.5 sorting nexin 17 134070 NM 003590Hs.78946 1.3 cullin 3 134110 041060 Hs.79136 4.2 LIV-1 protein, estrogen regulated 134129 NM 014742Hs.79305 2.2 KIAA0255 gene product 134134 H86504 Hs.173328 5.0 protein phosphatase 2, regulatory subunit 8 (B56), epsilon isoform 3 134200 BE559598 Hs.197803 3.2 ~ KIAA0160 protein 134206 AF107463 Hs.79968 2.5 splicing factor 30, survival of motor neuron-related 134208 NM_000288Hs.79993 2.1 peroxisomal biogenesis factor 7 134219 NM_000402Hs.80206 9.1 glucose-6-phosphate dehydrogenase 134234 BE300078 Hs.80449 2.B
Homo Sapiens, clone 1MAGE:3535294, mRNA, partial cds 3 134275 AI878910 Hs.3688 1.8 $ cisplatin resistance-associated overexpressed protein 134292 AI906291 Hs.81234 2.0 immunoglobulin superfamily, member 3 134301 AW502505 Hs.81360 2.5 Homo Sapiens cDNA:
FLJ21927 fis, clone HEP04178, highly similar to HSU90909 134305 061397 Hs.81424 2.8 ubiquitin-like 1 (sentrin) 134324 AB029023 Hs.179946 10.4 KIAA1100 protein 134326 AW903838 Hs.81800 1.9 chondroitin sulfate proteoglycan 2 (versican) 134329 N92036 Hs.81848homolog 2.6 RAD21 (S. pombe) 134337 NM_004922Hs.81964ae) related gene family, member2.3 SEC24 (S. cerevisi C

134348 AW291946 Hs.82065 13.0 interleukin 6 signal transducer (gp130, oncostatin M receptor) 134367 AA339449 Hs.82285 8.8 phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, 4$ 134376 X06560 Hs.82396 1.5 2',5'-oligoadenylate synthetase 1 (40-46 kD) 134379 AW362124 Hs.323193 8.1 hypothetical protein 134384 AI589941 Hs.8254 Homo Sapiens, Similar to tumor differentially expressed 1, clone IMAGE:3639252, mRNA, partial cds 2.6 134391 AA417383 Hs.82582 4.1 integrin, beta-like 1 (with EGF-like repeat domains) 134395 AA456539 Hs.8262 1.7 lysosomal $0 134403 AA334551 Hs.82767 2.6 sperm specific antigen 134405 AW067903 Hs.82772 1.3 collagen, type XI, alpha 1 134411 BE272095 Hs.167791 3.2 reticulocalbin 1, EF-hand calcium binding domain 134415 AI750762 Hs.82911 1.9 protein tyrosine phosphatase type IVA, member 2 134421 AU077196 Hs.82985 10.3 collagen, type V, alpha 2 $$ 134424 244190 Hs.83023 2.4 peroxisomal biogenesis factor 118 134446 AA112036 Hs.83419 1.2 KIAA0252 protein 134447 M58603 Hs.83428 1.6 nuclear factor of kappa light polypeptide gene enhancer in 8-cells 1 (p105) 134470 X54942 Hs.83758 2.1 CDC28 protein kinase 134480 NM_005000Hs.83916 5.3 Empirically selected from AFFX single probeset 134485 X82153 Hs.83942 2.5 cathepsin K (pycnodysostosis) 134498 AW246273 Hs.84131 2.1 threonyl-tRNA synthetase 134513 AA425473 Hs.84429 3.8 KIAA0971 protein 134516 AK001571 Hs.273357 2.4 hypothetical protein 134520 BE091005 Hs.74861 6.7 activated RNA polymerase II transcription cofactor 6$ 134529 AW411479 Hs.848 2.3 FK506-binding protein 4 (59kD) 134577 BE244323 Hs.85951 5.5 exportin, tRNA (nuclear export receptor fortRNAs) 134582 AA927177 Hs.86041 5.8 CGG triplet repeat binding protein 1 13$

134612 AW068223 Hs.171581 ubiquitin C-terminal hydrolase2.2 134624 AF035119 Hs.8700 deleted in liver cancer 1 2.0 134632 X78520 Hs.174139 chloride channel 3 2.3 134654 AK001741 Hs.8739 hypothetical protein FLJ108791.4 $ 134664 AA256106 Hs.87507 ESTs ~ 72.9 134666 BE391929 Hs.8752 transmembrane protein 4 8.5 134687 062317 Hs.88251 arylsulfatase A 6.0 134692 NM 003474Hs.8850 a disintegrin and metalloproteinase4.3 domain 12 (meltrin alpha) 134705 BE161887 Hs.88799 anaphase-promoting complex 2.3 subunit 10 1 134714 Y14768 Hs.890 lysosomal 6.7 ~

134719 AA852985 Hs.89232 chromobox homolog 5 (Drosophila2.3 HP1 alpha) 134722 AF129536 Hs.284226 F-box only protein 6 2~9 134724 AF045239 Hs.321576 ring finger protein 22 6.6 134746 X07871 Hs.89476 CD2 antigen (p50), sheep red 2.3 blood cell receptor 15 134751 AW630803 Hs.89497 lamin B1 6.2 134790 BE002798 Hs.287850 integral membrane protein 1.9 134806 AD001528 Hs.89718 spermine synthase 1.8 134834 AW451370 Hs.8991 adaptor-related protein complex1.4 1, gamma 2 subunit 134850 AI701162 Hs.90207 hypothetical protein MGC111381.4 134853 BE268326 Hs.90280 5-aminoimidazole-4-carboxamide5.6 ribonucleotide formyltransferaseIIMP cyclohydrolase 134859 026488 Hs.90315 KIAA0007 protein 2.8 134880 AI879195 Hs.90606 15 kDa selenoprotein 1.7 134910 AA532963 Hs.9100 Homo sapiens cDNA FLJ13100 1.7 fis, clone NT2RP3002255 134925 AW885909 Hs.6975 PR01073 protein 2.1 134955 AW401361 Hs.91773 protein phosphatase 2 (formerly1.3 2A), catalytic subunit, alpha isoform 134971 A1097346 Hs.286049 phosphoserine aminotransferase2.1 134975 850333 Hs.92186 Leman coiled-coil protein 2.3 135011 AB037835 Hs.92991 KIAA1414 protein 1.6 135022 NM_000408Hs.93201 glycerol-3-phosphate dehydrogenase3.9 2 (mitochondrial) 3~ 135032 AW301984 Hs.173685 hypothetical protein FLJ126196.2 135077 AW503733 Hs.9414 KIAA1488 protein 2.0 135083 AB036063 Hs.94262 p53-inducible ribonucleotide1.3 reductase small subunit 2 homolog 135095 AF027219 Hs.9443 zinc finger protein 202 7.1 135096 AA081258 Hs.132390 zinc finger protein 36 (KOX3.2 18) 35 135153 A1093155 Hs.95420 JM27 protein 2.5 135181 BE250865 Hs.279529 pxl9-like protein 1.4 135199 AA477514 Hs.96247 translin-associated factorX 5.0 135207 N26427 Hs.9634 ESTs, Highly similar to C10_HUMAN6.1 PUTATIVE C10 PROTEIN [H.sapiens]

135214 T78802 Hs.96560 hypothetical protein FLJ11656 4.6 135243 BE463721 Hs.97101 putative G protein-coupled 5.6 receptor 135245 A1028767 Hs.262603 ESTs 3.5 135257 AW291023 Hs.97255 ESTs, Weakly similar to A460101.2 X-linked retinopathy protein [H.sapiens]

135263 A1088775 Hs.55498 geranylgeranyl diphosphate 2.6 synthase 1 135274 AA448460 Hs.112017 GE36 gene 5.3 ' 9.1 135294 AA150320 Hs.9800 protein kinase Njmu-R1 135295 A1090838 Hs.98006 ESTs 2.4 135307 AI743770 Hs.98368 ESTs, Weakly similar to KIAA082213.3 protein [H.sapiens]

135321 AI652069 Hs.98614 ribosome binding protein 2.6 1 (dog 180kD homology 135354 AA456454 Hs.183415 cell division cycle 2-like 8.3 1 (PITSLRE proteins) 135361 AA373452 Hs.167700 Homo sapiens cDNA FLJ10174 1.5 fis, clone HEMBA1003959 135389 005237 Hs.99872 fetal Alzheimer antigen 4~9 135400 X78592 Hs.99915 androgen receptor (dihydrotestosterone2.0 receptor; testicular feminization; spinal and bulbar 134975 850333 Hs.92186 Leman coiled-coil protein 2.6 135011 A8037835 Hs.92991 KIAA1414 protein 1.4 55 135022 NM_000408Hs.93201 glycerol-3-phosphate dehydrogenase1.6 2 (mi 135032 AW301984 Hs.173685 hypothetical protein FLJ126191.4 135077 AW503733 Hs.9414 KIAA1488 protein 1.8 135083 AB036063 Hs.94262 p53-inducible ribonucleotide2.5 reductase s 135095 AF027219 Hs.9443 zinc finger protein 202 1.5 135096 AA081258 Hs.132390 zinc finger protein 36 (KOX2.1 18) 135153 A1093155 Hs.95420 JM27 protein 4.4 135181 BE250865 Hs.279529 px19-like protein 14.9 135199 AA477514 Hs.96247 translin-associatedfactorX 1.3 135207 N26427 Hs.9634 ESTs, Highly similar to C10_HUMAN1.7 PUTATI

65 135214 T78802 Hs.96560 hypothetical protein FLJ11656 6.1 135243 BE463721 Hs.97101 putative G protein-coupled 2.7 receptor 135245 A1028767 Hs.262603 ESTs 12.2 135257 AW291023 Hs.97255 ESTs, Weakly similar7.6 to A46010 X-linked 135263 A1088775 Hs.55498 geranylgeranyl diphosphate1.8 synthase 1 135274 AA448460 Hs.112017 GE36 gene 4.1 135294 AA150320 Hs.9800 protein kinase Njmu-R11.2 $ 135295 A1090838 Hs.98006 ESTs 4.8 135307 AI743770 Hs.98368 ESTs, Weakly similar5.8 to KIAA0822 protein 135321 AI652069 Hs.98614 ribosome binding 12.3 protein 1 (dog 180kD ho 135354 AA456454 Hs.183418 cell division cycle5.7 2-like 1 (PITSLRE pr 135361 AA373452 Hs.167700 Homo sapiens cDNA 7.9 FLJ10174 fis, clone HE

1 135389 U05237 Hs.99872 fetal Alzheimer antigen1.9 ~

135400 X78592 Hs.99915 androgen receptor (dihydrotestosterone13.9 r 302256 AA857131 Hs.171595 HIV TAT specific 5.3 factor 1 302276 AW057736 Hs.323910 HER2 receptor tyrosine2.2 kinase (o-erb-b2, 303135 AW592789 Hs.279474 HSPC070 protein 1.4 1$ 303686 AK000714 Hs.109441 MSTP033 protein 5.2 310085 843191 Hs.101248 Homo sapiens clone 2.3 IMAGE:32553, mRNA seq 315518 AA808229 Hs.167771 ESTs 2.8 317781 NM 007057Hs.42650 ZW10 interactor 2.0 320836 AI268997 Hs.197289 rab3 GTPase-activating5.5 protein, non-rata 321114 AA902256 Hs.78979 Golgi apparatus protein1.4 322221 N24236 Hs.179662 nucleosome assembly 1.3 protein 1-like 1 322474 AF118083 Hs.29494 PR01912 protein 2.9 322556 BE041451 Hs.177507 hypothetical protein1.6 323541 AF292100 Hs.104613 RP42 homolog 1.8 2$ 407827 BE278431 Hs.40323 BUB3 (budding uninhibited1.6 by benzimidazo 408196 AL034548 Hs.43627 SRY (sex determining6.1 region Y)-box 22 408813 AI580090 Hs.48295 RNA helicase family 5.6 409176 873727 Hs.101617 ESTs, Weakly similar 2.6 to T32527 hypotheti 413670 AB000115 Hs.75470 hypothetical protein,2.4 expressed in osteo 3 414108 AI267592 Hs.75761 SFRS protein kinase 1.5 ~ 1 414846 AW304454 Hs.77495 UBX domain-containing4.2 416980 AA381133 Hs.80684 high-mobility group 23.6 (nonhistone chromoso 417378 857256 Hs.82037 TATA box binding protein5.8 (TBP)-associate 418283 S79895 Hs.83942 cathepsin K (pycnodysostosis)1.3 3$ 418467 NM_006910Hs.85273 retinoblastoma-binding1.6 protein 6 420269 U72937 Hs.96264 alpha thalassemialmental2.3 retardation syn 420802 U22376 Hs.1334 v-myb avian myeloblastosis1.6 viral oncogen 421225 AA463798 Hs.102696 MCT-1 protein 3.5 421642 AF172066 Hs.106346 retinoic acid repressible4.9 protein 40 421828 AW891965 Hs.279789 histone deacetylase3.1 421983 AI252640 Hs.110364 peptidylprolyl isomerase1.9 C (cyclophilin 422052 AA302744 Hs.104518 ESTs 2.4 422055 NM_014320Hs.111029 putative heme-binding4.1 protein 423750 AF165883 Hs.298229 prefoldin 2 7.0 4$ 424001 W67883 Hs.137476 paternally expressed 4.9 (PEG10; KIAA105 425182 AF041259 Hs.155040 zinc finger protein3.4 425284 AF155568 Hs.155489 NS1-associated protein2.1 426372 BE304680 Hs.169531 DEADIH (Asp-Glu-Ala-AspIHis)7.5 box polypep 428049 AW183765 Hs.182238 GW128 protein 1.7 428477 AW500533 Hs.11482 splicing factor, 2.4 argininelserine-rich 11 437562 AB001636 Hs.5683 DEADIH (Asp-Glu-Ala-AspIHis)3.8 box polypep 438449 AK001333 Hs.6216 Homo sapiens hepatocellular5.6 carcinoma-as 441560 F13386 Hs.7888 Homo sapiens clone 237362.0 mRNA sequence 445580 AF167572 Hs.12912 skb1 (S. pombe) homolog7.5 $$ 446999 AA151520 Hs.334822 hypothetical protein2.2 447111 A1017574 Hs.17409 cysteine-rich protein2.8 1 (intestinal) 447778 BE620592 Hs.71190 ESTs, Weakly similar1.7 to S16506 hypotheti 448873 NM 003677Hs.22393 density-regulated 5.9 protein 449687 W68520 Hs.331328 intermediate filament5.6 protein syncoilin 450701 H39960 Hs.288467 Homo sapiens cDNA 1.4 FLJ12280 fis, clone MA

450703 AA011202 Hs.184771 nuclear factorIIC 4.7 (CCAAT-binding transc 452461 N78223 Hs.108106 transcription factor 2.9 452511 BE408178 Hs.285165 Homo Sapiens cDNA 12.1 FLJ208'45 fis, clone AD

453157 AF077036 Hs.31989 DKFZP586G1722 protein4.7 6$ 453658 BE541906 Hs.87819 Homo Sapiens, clone 1.3 MGC:2492, mRNA, comp 100833 AF135168 Hs.108802 N-ethylmaleimide-sensitive3.2 factor 102481 U50360 gb:Human calcium, calmodulin~dependent6.2 p 102827 BE244588 Hs.6456 chaperonin containing7.9 TCP1, subunit 2 (b 103549 BE270465 Hs.78793 protein kinase C, 2.0 zefa 104331 AB040450 Hs.279862 cdk inhibitor p21 5,3 binding protein 110018 AW579842 Hs.104557 hypothetical protein2.0 115008 AK001827 Hs.87889 helicase-moi 5.7 119075 M10905 Hs.287820 fibronectin 1 1.3 119615 AL034423 Hs.75875 ubiquiGn-conjugating2.9 enzyme E2 variant 125006 BE065136 Hs,145696 splicing factor(CC1,3)1.7 127609 X80031 Hs.530 collagen, type IV, alpha2.4 3 (Goodpasture 1 129209 862676 Hs.17820 Rho-associated, coiled-coil5.2 ~ containing p 129917 M30773 Hs.278540 protein phosphatase 4.5 3 (formerly 2B), reg 130182 BE267033 Hs.192853 ubiquitin-conjugating11.0 enzyme E2G 2 (homo 130365 W56119 Hs.155103 eukaryotic translation3.3 initiation factor 131135 NM_016569Hs.267182 TBX3-iso protein 1.3 1$131853 AI681917 Hs.3321 ESTs, Highly similar 3.2 to IRX1 HUMAN IROQU

131881 AW361018 Hs.3383 upstream regulatory 14.3 element binding prot 132726 N52298 Hs.55608 hypothetical protein 3.0 135193 X95525 Hs.96103 TATA box binding protein2.7 (TBP)-associate 409487 H19886 gb:yn57a05.r1 Soares adult brain2.3 N2b5H

416040 AW819158 Hs.289044 Homo Sapiens cDNA 7.4 FLJ 12048 fis, clone HE

Table 4A shows the accession numbers for those pkeys lacking unigeneID's for Table 4. For $ each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number. Gene cluster number Accession: Genbank accession numbers 1$
Pkey CAT number Accessions 1014451650= M21259 1244171642364_1N34059 N46979 2$ 10334911052_X89059 11085619346_14AA992380 N33063 N21418 H79958 821911 H79957 .

103797 109699_1 AA080912 AA075318 AA083403 AA076594 12047244573_2AI950087 N70208 897040 N36809 AI308119 AW967677 N35320 $ AA642789 AA856975 AW505512 AI961530 AW629970 ~$ BE612881 AW276997 AW513601 AW512843 AA044209 AW856538 1206959683_3AA976503 AI917802 AA953664 AA404613 AA428771 BE280542 $0 AA970201 AI633384 AA425910 A1017004 AI241295 AA402816 122618305217_1AA453641 AA454061 $$ 123658genbanILAA609364 123811genbank_AA620586 125115genbank_T97341 125147NOT_FOUND_entre~W38150 W38150 60 120274genbank_AA177051 113196genbank_T57317 120504genbanhAA256837 120639genbank_AA286942 120809genbank_AA346495 AA346495 113702genbank_T97307 T97307 12968023162_1 U03749 NM_001275 J03483 J03915 A1214509 AW245744 AW470949 AA843095 AA772028 Ai148432 101045entrez J05614 J05614 117247genbank N21032 110501genbank H55748 103392entrez X94563X94563 105032genbank AA127818 1 119513NOT_FOUND_entrez W37933 S

105445genbank AA252395 121514genbank AA412112 121558genbank AA412497 121911genbank AA427950 114911genbank AA236672 4094871134778_1 H19886 AW402806 T10231 TABLE 5: Figure 5 from BRCA 001 US
Table 5 shows genes upregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: ExempIarAccession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title R1: Ratio of tumor to normal breast tissue Pkey ExAccn UnigenelDUnigeneTitle R1 100114 X02308 thymidylafe synthetase2.9 Hs.82962 100147 D13666 osteoblast specific7.5 Hs.136348 factor 2 (fasciclin 100154 H60720 KIAA0101 gene product9.2 Hs.81892 100335 AW247529 platelet-activating2.7 Hs.6793 factor acetylhydrola 100666 L05424 CD44 antigen (homing5.7 Hs.169610 function and Indian 100667 L05424 CD44 antigen (homing9 Hs.169610 function and Indian 100668 L05424 CD44 antigen (homing7.6 Hs.169610 function and Indian 100678 AW502935 PTK2 protein tyrosine53.2 Hs.740 kinase 2 100988 AK000405 ubiquitin-like 4 11.4 Hs.76480 101031 J05070 matrix metalloproteinase8.2 Hs.151738 9 (gelatinase B

101045 J05614 gb:Human proliferating5 cell nuclear anti 101332 J04088 topoisomerase (DNA)3.4 Hs.156346 II alpha (170kD) 101352 AI494299 COX17 (yeast) homolog,6.3 Hs.16297 cytochrome c oxid 101580 NM 012151Hs.83363coagulation factorVlll-associated(intr5.7 101592 AF064853 guanine nucleotide 5.6 Hs.91299 binding protein ( 101767 M81057 carboxypeptidase 14.4 Hs.180884 B1 (tissue) 101806 AA586894 S100 calcium-binding8.9 Hs.112408 protein A7 (psorias 101810 NM 000318Hs.180612peroxisomal membrane3.2 protein 3 (35kD, Ze 101983 AI904232 prohibitin 8.4 Hs.75323 3 102107 BE258602 heat shock protein 1.4 $ Hs.182366 75 102165 BE313280 death associated 4.6 Hs.159627 protein 3 102198 AW950852 polymerase (DNA 4.3 Hs.74598 directed), delta 2, regu 102217 AA829978 JTV1 gene 6.7 Hs.301613 102220 U24389 lysosomal 4.3 Hs.65436 4~ 102302 AA306342 protein kinase C-like2.7 Hs.69171 2 102348 U37519 aldehyde dehydrogenase2 Hs.87539 3 family, member 102374 U33635 PTK7 protein tyrosine8.2 Hs.90572 kinase 7 102455 U48705 discoidin domain 6.9 Hs.75562 receptor family, member 102568 W81489 RAB31, member RAS 5.3 Hs.223025 oncogene family 45 102618 AL037672 extracellular matrix5.8 Hs.81071 protein 1 102687 NM_007019Hs.93002ubiquitin carrier 4.3 protein E2-C

102689 U96132 hydroxyacyl-Coenzyme6 Hs.171280 A dehydrogenase, ty 102704 AU077058 BRCA1 associated 1.9 Hs.54089 RING domain 1 102705 T97490 small inducible 2.3 Hs.50002 cytokine subfamily A (Cy 102801 BE252241 pyridoxal (pyridoxine,6.4 Hs.38041 vitamin B6) kinas 102827 BE244588 chaperonin containing5.6 Ns.6456 TCP1, subunit 2 (b 103060 NM 005940Hs.155324matrix metalloproteinase4.5 11 (MMP11; stro 103080 AU077231 cyclin D1 (PRAD1: 3.1 Hs.82932 parathyroid adenomatos 103178 AA205475 ribosomal protein 9.9 Hs.275865 S18 S 103206 X72755 monokine induced 8.8 $ Hs.77367 by gamma interferon 103238 AI369285 death-associated 5.6 Hs.75189 protein 103547 AI376722 proteasome (prosome,9.7 Hs.180062 macropain) subunit, 103549 BE270465 protein kinase C, 7.9 Hs.78793 zeta 103886 AK001278 hypothetical protein6.5 Hs.105737 FLJ10416 similar to 104325 BE379766 polymerase (RNA) 6.3 Hs.150675 II (DNA directed) polyp 104827 AW052006 PRP41STKIWD splicing10.9 Hs.8551 factor 104846 AI250789 ESTs 5.6 Hs.32478 104854 AA041276 3-phosphoinositide 12.3 Hs.154729 dependent protein kin 104867 AA278898 hypothetical protein2 Hs.225979 similar to small G

104896 AW015318ESTs 17.7 Hs.23165 104909 AW408164transcription factor5 Hs.249184 19 (SC1) 104916 AW958157NS1-associated protein1.7 Hs.155489 1 104919 AA026880prolactin receptor 1.4 Hs.25252 $ 104974 Y12059 bromodomain-containing1.4 Hs.278675 4 104978 AI199268Homo sapiens, Similar7.2 Hs.19322 to RIKEN cDNA 2010 105012 AF098158chromosome 20 open 3.3 Hs.9329 reading frame 1 105039 AA907305ESTs 2.5 Hs.36475 105079 AA151342CGi-147 protein 9.5 Hs.12677 1 105088 H58589 Homo sapiens cDNA 2.2 ~ Hs.35156 FLJ11027 fis, clone PL

105393 AF167570interleukin enhancer5.4 Hs.256583 binding factor 3, 9 105547 AA262640unknown 9.3 Hs.27445 105564 BE616694hypothetical protein1.4 Hs.288042 FLJ14299 105658 AA985190hypothetical protein9.4 Hs.246875 FLJ20059 1$ 105746 AW151952hypothetical protein1.5 Hs.46679 FLJ20739 105858 AF151066hypothetical protein2.9 Hs.281428 105930 AF016371peptidyl prolyl 5.2 Hs.9880 isomerase H (cyclophilin 106094 AA533491hypothetical protein6.8 Hs.23317 FLJ14681 106350 AK001404cyclin B2 5.7 Hs.194698 2~ 106359 AW390282transmembrane 7 6.3 Hs.31130 superfamily member 106610 AA458882fibulin 1 7.9 Hs.79732 106624 NM 003595Hs.26350tyrosylprotein sulfotransferase7.7 106713 BE614802hypothetical protein4.5 Hs.184352 FLJ12549 106829 AW959893hypothetical protein16.2 Hs.27099 FLJ23293 imilar to 2$ 106846 AB037744KIAA1323 protein 2.2 Hs.34892 106873 N49809 Homo Sapiens, clone Hs.11197 1MAGE:3343149, mRNA, 16.8 106973 BE156256hypothetical protein6.6 Hs.11923 107029 AF264750myeloidhymphoid 1.8 Hs.288971 or mixed-lineage leukem 107197 W15477 glioma pathogenesis-related6.1 Hs.64639 protein 107859 AW732573potassium voltage-gated8.4 Hs.47584 channel, delayed 107901 L42612 keratin 68 2.5 Hs.335952 107922 BE153855Ig superfamily receptor2.2 Hs.61460 LNIR

107974 AW956103pyruvate dehydrogenase6.7 Hs.61712 kinase, isoenzyme 108274 AF129535F-box only protein 7.1 Hs.272027 5 3 108647 BE546947homeo box C10 9.8 $ Hs.44276 108695 AB029000KIAA1077 protein 7.2 Hs.70823 108894 AK001431hypothetical protein4 Hs.5105 FLJ10569 109011 AA156542ESTs 1.4 Hs.72127 109068 AA164293ESTs 2.9 Hs.72545 4~ 109273 AA375752Homo Sapiens mRNA;
Hs.82719 cDNA DKFZp586F1822 (f 2.9 109468 NM 015310Hs.6763KIAA0942 protein 3.2 110240 AI668594ESTs, Weakly similar Hs.176588 to CP4Y_HUMAN CYTOC
4.2 110330 AI288666DKFZP4341116 protein6.2 Hs.16621 110501 H55748 gb:yq94a01.s1 Soaresfetalliverspleen6.1 4$ 110742 AW190338hypothetical protein7.6 Hs.28029 MGC11256 110762 BE044245hypothetical protein9.3 Hs.30011 MGC2963 110856 AA992380gb:ot37g06.s1 Snares iesiis NHT Homo sap 2.3 110958 NM_005864Hs.24587signal transduction6.7 protein (SH3 contain 111125 N63823 ESTs, Moderately 3.6 Hs.269115 similar to Z195_HUMAN
Z

$~ 111179 AK000136asporin (LRR class 7.1 Hs.10760 1) 111239 N90956 hypothetical protein7.9 Hs.17230 FLJ22087 111285 AA778711eukaryotic translation6.9 Hs.4310 initiation factor 111392 W46342 Homo sapiens, clone Hs.325081 IMAGE:3659680, mRNA, 8.4 111937 BE298665Homo sapiens mRNA;
Hs.14846 cDNA DKFZp564D016 (fr 10.6 $ 112244 A8029000KIAA1077 protein 14.6 $ Hs.70823 112995 AA737033ESTs, Moderately 5.6 Hs.7155 similar to 2115357A
TYK

113777 BE266947zinc finger protein13.4 Hs.10590 313 113791 AI269096chitobiase, di-N-acetyl-1.3 Hs.135578 113811 BE207480Homo Sapiens cDNA: 3.1 Hs.6994 FLJ22044 fis, clone H

113834 T26483 EGF-containing fibulin-like11.3 Hs.6059 extracellula 113868 W57902 proteasome (prosome,2.7 Hs.90744 macropain) 26S
subu 113870 AL079314hypothetical protein,6.1 Hs.16537 similar to (U06944 113923 AW953484hypothetical protein1.9 Hs.3849 FLJ22041 similar to 114275 AW515443KIAA0306 protein 15.8 Hs.306117 6$ 114895 AA236177KIAA0887 protein 7.1 Hs.76591 114965 AI733881BMP-R18 2.3 Hs.72472 115061 AI751438Homo Sapiens mRNA 11.8 Hs.41271 full length insert cDN

142 .

115278 AK002163 hypothetical protein1.5 Hs.301724 FLJ11301 115291 BE545072 hypothetical protein6.2 Hs.122579 FLJ10461 115652 BE093589 hypothetical protein10.6 Hs.38178 FLJ23468 115693 AF231023 cadherin, EGF LAG 6.8 Hs.55173 seven-pass G-type rece $ 115941 AI867451 hypothetical protein5.5 Hs.46679 FLJ20739 115968 AB037753 KIAA1332 protein 9.8 Hs.62767 116011 AL359053 Homo Sapiens mRNA 2.4 Hs.57664 full length insert cDN

116417 AW499664 Human clone 23826 7.4 Hs.12484 mRNA sequence 116470 AI272141 SRY (sex determining2.1 Hs.83484 region Y)-box 4 1~ 116637 AK001043 integrin-linked 2.7 Hs.92033 kinase-associated serine 117132 AI393666 p10-binding protein5.2 Hs.42315 117881 AF161470 butyrate-induced 5.7 Hs.260622 transcript 1 ~

Hs.49397 ESTs 7.4 119075 M10905 fibronectin 1 5.7 Hs.287820 1$ 119265 BE539706 ESTs 1.4 Hs.285363 119349 T65004 ESTs 8.4 Hs.163561 119403 AL117554 nucleolar.protein 6.7 Hs.119908 NOP51NOP58 119789 BE393948 kallikrein 5 (KLK5;9.2 Hs.50915 KLK-L2; stratum com 120206 H26735 Homo Sapiens clone Hs.91668 PP1498 unknown mRNA 45.7 120253 AA131376 fibroblast growth 38.9 Hs.326401 factor 12B

120297 AA191384 ESTs, Weakly similar15.2 Hs.104072 to Z195_HUMAN ZINC

120325 AA195651 ESTs 6.4 Hs.104106 120327 AK000292 hypothetical protein16.1 Hs.278732 FLJ20285 120349 AW969481 hypothetical protein16.8 Hs.55189 2$ 120356 AF000545 putative pudnergic 28.1 Hs.296433 receptor 120371 AA219305 EST 12.4 Hs.104196 120383 AL109963 FSH primary response9.7 Hs.123122 (LRPR1, rat) homolo 120386 AW969665 hypothetical protein32.6 Hs.154848 DKFZp434D0127 120389 AW967985 ESTs, Moderately Hs.325572 similar to ALU7 HUMAN A 21.7 30 120396 AA134006 eukaryotic translation12.5 Hs.79306 initiation factor 120418 AW966893 Homo sapiens mRNA;
Hs.26613 cDNA DKFZp586F1323 (f 11.4 120472 AI950087 gb:wq05c02.x1 NCI_CGAP_Kid12 Homo sapien 19.4 120484 AA253170 EST 10.4 Hs.96473 120570 AA280679 ESTs, Weakly similarS
Hs.271445 to ALU1 HUMAN ALU 14.4 3$ 120582 BE244830 ZNF135-like protein10.2 Hs.284228 120596 AA282074 N-acetylglucosamine-phosphate7.5 Hs.237323 mutase 120624 AW407987 M-phase phosphoprotein52 Hs.173518 homolog 120695 AA976503 gb:oq30a04.s1 NCI_CGAP
GC4 Homo Sapiens 46.8 120713 AW449855 Homo Sapiens cDNA 5.9 Hs.96557 FLJ12727 fis, clone NT

40 120750 AI191410 ESTs, Moderately 7 Hs.96693 similar to 2109260A
B c 120774 AI608909 ESTs 7.8 Hs.193985 120807 AA346385 SH3-containing protein6.8 Hs.30002 SH3GL82; KIAA1848 120809 AA346495 gb:EST52657 Fetal 4.4 heart II Homo Sapiens 120984 BE262951 ESTs 5.6 Hs.99052 4$ 121081 AA398721 ESTs, Highly similar5.4 Hs.186749 to 137550 mismatch Hs.98019 121505 AA494172 ESTs 13.1 Hs.194417 121508 AA402515 ESTs 28 Hs.97887 121513 AA416653 ESTs 6.2 Hs.181510 121549 AA412477 EST 7.4 Hs.98142 121558 AA412497 gb:zt95g12.s1 Soares testis_NHT Homo sap 2.8 121655 AA421537 Homo Sapiens mRNA;
Hs.178072 cDNA DKFZp434B1023 (f 7.8 121744 AA398784 ESTs 7.1 Hs.97514 121748 BE536911 hypothetical protein19.5 Hs.234545 NUF2R

$$ 121773 AB033022 KIAA1196 protein 7.9 Hs.158654 121832 AW340797 ESTs 5.8 Hs.98434 121839 AA425691 ESTs, Highly similar5 Hs.191606 to KIAA1048 protein 121882 AA426376 ESTs 5 Hs.98459 121911 AA427950 gb:zw50f02.s1 Soares7.2 total_fetus_Nb2HF8_ 60 121999 AA430211 EST 6.4 Hs.98668 122013 AA431085 ESTs 6.5 Hs.98706 122036 W92142 ESTs, Weakly similarS
Hs.271963 to ALUS_HUMAN ALU 13.1 122356 AA443794 ESTs 7.3 Hs.98390 122371 AA868555 ESTs 5 Hs.178222 6$ 122372 AA446008 EST 7.6 Hs.336677 122460 AW418788 ESTs, Weakly similar9.7 Hs.99148 to S43569 R01H10.6 122490 AA448349 EST 6.1 Hs.238151 122492 AA448417 ESTs 5.4 Hs.104990 122510 AA449232 ESTs 11.2 Hs.99195 122530 AW959741 adaptor-related 10.1 Hs.40368 protein complex 1, sigma Hs.99287 $ 122607 AA453518 ESTs 61.5 Hs.98023 122614 AA453630 EST 10.7 Hs.99339 122616 AA453638 ESTs 107.3 Hs.161873 122618 AA453641 gb:zx48e06.s1 Soares31.1 testis_NHT Homo sap 122622 AA453987 ESTs 5.6 Hs.144802 122717 AA456859 ESTs 8.5 Hs.178358 122829 AW204530 ESTs 81.8 Hs.99500 122838 AA460584 ESTs 75.3 Hs.334386 122856 AI929374 Src-like-adapter 5.8 Hs.75367 122868 AF005216 Janus kinase 2 (a 5.3 Hs.115541 protein tyrosine kinas 1$ 122907 AA470074 ESTs 11.5 Hs.169896 123016 AW338067 Homo Sapiens cDNA 2.8 Hs.323231 FLJ11946 fis, clone HE

123034 AL359571 ninein (GSK3B interacting8.7 Hs.44054 protein) 123136 AW451999 ESTs 5.1 Hs.194024 123152 AW601773 ESTs 5.2 Hs.270259 123394 AA731404 ESTs 3.6 Hs.105510 123466 AA599042 EST 7.4 Hs.112503 123486 BE019072 Homo sapiens cDNA 2.4 Hs.334802 FLJ14680 fis, clone NT

123615 AA609170 gb:af12a12.s1 Soares7.8 testis_NHT Homo sap 123735 NM_013241Hs.95231FH1/FH2domain-containing10 protein 2$ 123753 AA609955 Huntingtin interacting30.6 Hs.234961 protein E

124006 AI147155 ESTs 8.1 Hs.270016 124385 AI267847 gb:aq49a10.x1 Stanley57.1 Frontal NB pool 124440 AA532519 Human DNA sequence 7.8 Hs.129043 from clone 989H11 on 124656 AW297702 ESTs 8.3 Hs.102915 124683 AA381661 ESTs, W,eaklysimilartoG
Hs.119878 M3K9_HUMAN MITO 7.9 124735 822952 ESTs 11.3 Hs.268685 124761 AA374756 Homo Sapiens mRNA 9 Hs.93560 for KIAA1771 protein, 124768 AW368528 ESTs 8.1 Hs.100855 124788 843543 Homo sapiens cDNA: 5.1 Hs.100912 FLJ22726 fis, clone H

3 124811 846068 hypothetical protein14.2 $ Hs.288912 FLJ22604 124812 847948 ESTs 7.9 Hs.188732 124822 AA418160 Homo Sapiens cDNA 6.6 Hs.86043 FLJ13558 fis, clone PL

124860 865763 EST 23.9 Hs.101477 124903 AW296713 ESTs 32.4 Hs.221441 4~ 124930 A1076343 ESTs,WeaklysimilartoALUB22.8 Hs.173939 HUMANIIII

124942 899978 ESTs, Moderately 6.1 Hs.268892 similar to 834087 hypot 125051 T79956 EST 135.3 Hs.100588 125056 T81310 ESTs 5.4 Hs.100592 125101 AI472068 KIAA1856 protein 5.6 Hs.286236 4$ 125115 T97341 gb;ye57e05.s1 Soaresfetal9.6 liver spleen 125280 AI123705 ESTs 8 Hs.106932 127274 AW966158 Homo sapiens cDNA 12.8 Hs.58582 FLJ12789 fis, clone NT

128528 839234 ESTs, Weakly similar2.8 Hs.251699 to IDN4-GGTR14 [H.s 128670 AA975486 Homo sapiens, Similar7.1 Hs.103441 to RIKEN cDNA 1700 $Q 128691 W27939 hypothetical protein7.7 Hs.103834 MGC5576 128772 BE302796 thymidine kinase 5.3 Hs.105097 1, soluble 128781 N71826 small nuclear ribonucleoprotein53.9 Hs.105465 polypept 128797 NM 002975Hs.105927stem cell growth 13.3 factor; lymphocyte secr 128868 AA419008 chromosome 22 open 3 Hs.106730 reading frame 3 $$ 128891 F34856 Homo Sapiens, clone Hs.292457 MGC:16362, mRNA, com 13.3 128946 Y13153 kynurenine 3-monooxygenase7.2 Hs.107318 (kynurenine 3 128975 BE560779 NICE-5 protein 14 Hs.284233 128995 AI816224 DKFZP566C243 protein1.9 Hs.107747 129019 AI950087 gb:wq05c02.x1 NCI_CGAP
Kid12 Homo sapien 2.9 129076 AW296806 ESTs, Highly similar5 Hs.326234 to T46422 hypotheti 129088 AA744610 palladin 17.1 Hs.194431 129096 AA463189 WW Domain-Containing20.9 Hs.288906 Gene 129198 N57532 KIAA1415 protein 5.8 Hs.109315 129347 BE614192 melanoma-associated7.6 Hs.279869 antigen recognised b 6$ 129362 030246 solute carrierfamily6.7 Hs.110736 12 (sodium/potassi 129372 NM 016039Hs.110803CGI-99 protein 2 129404 AI267700 ESTs 5 Hs.317584 129482 Hs.289043spindlin 6.7 129559W01296Hs.11360hypothetical protein7.5 129587H14718Hs.11506Human clone 23589 6.8 mRNA sequence 129629AK000398Hs.11747hypothetical protein3,8 129649AD000092Hs.16488calreticulin 3.3 129680003749 gb:Human chromogranin A (CHGA) gene, pro 14,1 129689AW748482Hs.7787387 homolag 3 2.6 129702AI304966Hs.12035ESTs, Weakly similar7.4 to 138022 hypotheti 129720AA156214Hs.12152APMCF1 protein 2 1 130010AA301116Hs.142838nucleolar phosphoprotein1.6 ~ Nopp34 130097AL046962Hs.14845forkhead box 03A 2.8 130135AA311426Hs.21635tubulin, gamma 1 6.1 130211NM_003358Hs.237D3 ESTs, Moderately C1.6 similar to CEGT_HUMAN

130242X79201Hs.153221synovial sarcoma, 5.4 translocated to X chro 1$130359NM_013449Hs.277401 bromodomain adjacent8.5 to zinc finger doma 130365W56119Hs.155103eukaryotic translation11 initiation factor 130448BE513202Hs.15589PPAR binding protein3.9 130455D90041Hs.155956N-acetyltransferase33.6 1 (arylamine N-acety 130471AL121438Hs.183706adducin 1 (alpha) 2.7 130503BE208491Hs.295112KIAA0618 gene product16.1 130511L32137Hs.1584cartilage oligomeric6.1 matrix protein (pse 130542064675Hs.179825RAN binding protein7.8 2-like 1 130553AF062649Hs.252587pituitary tumor-transforming14.4 130556AI907018Hs.15977Empirically selected4.7 from AFFX single pr 130567AA383092Hs.1608replication protein7.9 A3 (14kD) 130574AF083208Hs.16178apoptosis antagonizing1.2 transcription fat 130617M90516Hs.1674glutamine-fructose-6-phosphate12.1 transamin 130667BE246961Hs.17639Homo Sapiens ubiquitin13.9 protein ligase (U

130693868537Hs.17962ESTs 2 30130744H59696Hs.18747POP7 (processing 3.1 of precursor, S.
cerevi 130757AL036067Hs.18925protein x 0001 5.7 130880BE514434Hs.20830kinesin-like 2 2.1 130944BE382657Hs.21486signal transducer 5.4 and activator of traps 131046AA321649Hs.2248small inducible 7.4 cytokine subfamily B (Cy 3$131060AA194422Hs.22564myosin VI 5.1 131099AL133353Hs.226581COX15 (yeast) homolog,7 cytochrome c oxid 131135NM_016569Hs.267182 TBX3-iso protein 3.3 131185BE280074Hs.23960cyclin B1 5.8 131225H62087Hs.31659thyroid hormone 7.5 receptor-associated prot 40131245ALO80080Hs.24766thioredoxin domain-containing2.8 131283X80038Hs.339713Homo sapiens clone gene 1.3 131569AL389951Hs.271623nucleoporin 50kD 5 131643AW410601Hs.30026HSPC182 protein 2.9 131714AA642831Hs.31016putative DNA binding2.9 protein 45131722D13757Hs.311phosphoribosyl pyrophosphate3.4 amidotransf 131760X76732Hs.3164nucleobindin 2 2.9 131793AW966127Hs.32246Homo Sapiens cDNA
FLJ 14656 fis, clone NT 7.9 131885BE502341Hs.3402ESTs 13.7 131900AA099014Hs.231029Homo Sapiens, clone MGC:15961, mRNA, tom 8.7 131905AA179298Hs.3439stomatin-like 2 11.3 131941BE252983Hs.35086ubiquitin specific 2.3 protease 1 131971BE567100Hs.154938hypothetical protein3.5 132180NM_004460Hs.418 fibroblast activation14.7 protein, alpha 132203NM_004782Hs.194714 synaptosomai-associated7.8 protein, 29kD

$$132273AA227710Hs.43658DKFZP586L151 protein10 132288N36110Hs.305971solute tamer family9.2 2 (facilitated glu 132294AB023191Hs.44131KIAA0974 protein 2 13234BAW067708Hs.170311heterogeneous nuclear12.5 ribonucleoprotein 132370AW572805Hs.46645ESTs 28.3 132384AA312135Hs.46967HSPC034 protein 6.1 132450AA100012Hs.48827hypothetical protein8.6 132465AW169847Hs.49169KIAA1634 protein 6.1 132532AA454132Hs.5080mitochondtial ribosomal7.1 protein L16 132574AW631437Hs.5184TH1 drosophila homolog14 6$132638AI796870Hs.54277DNA segment on chromosome X (unique) 99212.4 132718NM_004600Hs.554 Sjogren syndrome 3.7 antigen A2 (60kD, ribon 132726N52298Hs.55608hypothetical protein14.3 132731AI189075Hs.301872hypothetical protein5.9 132744AA010233Hs.55921glutamyl-prolyl-tRNA6.4 synfhefase 132773AA459713Hs.295901KIAA0493 protein 14.6 132798A1026701Hs.5716KIAA0310 gene product2.5 $ 132810AB007944Hs.5737KIAA0475 gene product4.2 132833078525Hs.57783eukaryotic translation6.1 initiation factor 132842NM_016154Hs.279771Homo Sapiens clone PP1596 unknown mRNA7.1 132851009716Hs.287912lectin, mannose-binding,16.1 132891BE267143Hs.59271U2(RNU2) small nuclear2.7 RNA auxiliary fac 1 132941AI817165Hs.6120hypothetical protein2.1 ~ FLJ13222 132972AA034365Hs.288924Homo Sapiens cDNA 3.5 FLJ11392 fis, clone HE

132980AA040696Hs.62016ESTs 1.3 132994AA112748Hs.279905clone HQ0310 PR00310p117.1 133016AI439688Hs.6289hypothetical protein4.4 ~$'133177X97795Hs.66718RAD54(S.cerevisiae)-like4.4 133208AI801777Hs.6774ESTs 5.5 133254AI567421Hs.273330Homo sapiens, clone IMAGE:3544662, mRNA, 1.3 133266AI160873Hs.69233zinc finger protein16.1 133268AW956781Hs.293937ESTs, Weakly similar to FXD2_HUMAN FORKH
12.2 133285M76477Hs.289082GM2 ganglioside 10.4 activator protein 133390AI950382Hs.72660phospha6dylserine 5.7 receptor 133391AW103364Hs.727inhibin, beta A 25.5 (activin A, acEivin AB a 133540AL037159Hs.74619proteasome (prosome,1.7 macropain) 26S
subu 133594AW160781Hs.172589nuclear phosphoprotein2.6 similar to S. cer ~$ 133621NM_004893Hs.75258 H2A histone family,13.5 memberY

133720L27841Hs.75737pericentriolar material6.7 133760BE271766Hs.181357laminin receptor 5.4 1 (67kD, ribosomal prot 133784BE622743Hs.301064arfaptin 1 12.1 133791M34338Hs.76244spermidine synthase9.7 30 133797AL133921Hs.76272retinoblastoma-binding1.3 protein 2 133822D50525Hs.699peptidylprolyl isomerase9.7 8 (cyclophilin 133850W29092Hs.7678cellular retinoic 4.2 acid-binding protein 133865AB011155Hs.170290discs, large (Drosophila)5 homolog 5 133881030872Hs.77204centromere protein 9.1 F (3501400kD, mitosin 3 133924D86326Hs.325948vesicle docking 1.8 $ protein p115 133959X81789Hs.77897splicing factor 10.4 3a, subunit 3, 60kD

133989AL040328Hs.78202SWIISNF related, 2.6 matrix associated, acti 133997AI824113Hs.78281regulator of G-protein13 signalling 12 134234BE300078Hs.80449Homo sapiens, clone IMAGE:3535294, mRNA, 10.3 4~ 134348AW291946Hs.82065interleukin 6 signal6.7 transducer (gp130, 134376X06560Hs.823962',5'-oligoadenylate5.5 synthetase 1 (40-46 134379AW362124Hs.323193hypothetical protein5.8 134405AW067903Hs.82772collagen, type XI, 72.9 alpha 1 134421AU077196Hs.82985collagen, type V, 6.7 alpha 2 4$ 134480NI~005000Hs.83916 Empirically selected6.2 from AFFX single pr 134516AK001571Hs.273357hypothetical protein1.4 134529AW411479Hs.848FK506-binding protein2.8 4 (59kD) 134751AW&30803Hs.89497lamin B1 6.1 134790BE002798Hs.287850integral membrane 1.2 protein 1 ~

$~ 134806AD001528Hs.89718sperminesynthase 2.6 134850AI701162Hs.90207hypothetical protein9.1 134859D26488Hs.90315KIAA0007 protein 13.3 ~

134971A1097346Hs.286049phosphoserine aminotransferase2 135181BE250865Hs.279529px19-like protein 14.9 $$ 135207N26427Hs.9634ESTs,HighlysimilartoClO_HUMANPUTATI1.7 135245A1028767Hs.262603ESTs 12.2 135257AW291023Hs.97255ESTs, Weakly similar7.6 to A46010 X-linked 135307AI743770Hs.98368ESTs, Weakly similar5.8 to KIAA0822 protein 135321AI652069Hs.98614ribosome binding 12.3 protein 1 (dog 180kD ho 135354AA456454Hs.183418cell division cycle5.7 2-like 1 (PITSLRE
pr 135400X78592Hs.99915androgen receptor 13.9 (dihydrotestosterone r 302276AW057736Hs.323910HER2 receptor tyrosine5.3 kinase (c 317781NM ZW10 interactor 2.8 007057Hs.42650 321114AA902256Hs.78979G0lgi apparatus 5.5 protein 1 6$ 322556BE041451Hs.177507hypothetical protein2.9 420802022376Hs.1334v-myb avian myeloblastosis2.3 viral oncogen 424001W67883Hs.137476paternally expressed7 10 (PEG10; KIAA105 425182 AF041259 . Hs.155040 zinc finger protein 217 2.3 446999 AA151520 Hs.334822 hypothetical protein MGC4485 7.5 450701 H39960 Hs.288467 Homo Sapiens cDNA FLJ12280 fis, clone MA 5.6 452461 N78223 Hs.108106 transcription factor 4.7 453157 AF077036 Hs.31989 DKFZP586G1722 protein 12.1 TABLE SA
Table SA shows the accession numbers for those pkeys lacking unigenelD's for Table 5. For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
1 ~ Pkey: Unique Eos probeset identifier number CAT number. Gene cluster number Accession: Genbank accession numbers 15 Pkey CAT number Accessions 124385 656394_1 A1267847 N27351 20 120472 44573_2 AI950087 N70208 897040 N36809 AI308119 AW967677 N35320 30 129019 44573_2 A1950087 N70208 897040 N36809 A1308119 AW967677 N35320 4~ 120695 9683 3 AA976503 A1917802 AA953664 AA404613 AA428771 BE280542 125115 genbank_T97341 T97341 120809 genbank_AA346495 AA346495 4$ 129680 23162_1 U03749 NIVL001275 J03483 J03915 A1214509 AW245744 AL046455 101045 entrez_J05614J05614 110501 genbank_H55748 H55748 121558 genbank_AA412497 AA412497 $$ 121911 genbank_AA427950 AA427950 TABLE 6: Figure 6 from BRCA 001 US
Table 6 shows genes upregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number 1 o Unigene Title: Unigene gene title R1: Ratio of tumor to normal breast tissue Pkey ExAccn UnigenelD UnigeneTitleR1 1$

100147 D13666 Hs.136348 osteoblast7.5 specific factor 2 (fasciclin 100678 AW502935 Hs.740 PTK2 protein53.2 tyrosine kinase 2 101806 AA586894 Hs.112408 S100 8.9 calcium-binding protein A7 (psorias 102455 U48705 Hs.75562 discoidin 6.9 domain receptor family, member 103206 X72755 Hs.77367 monokine 8.8 induced by gamma interferon 105743 BE246502 Hs.9598 sema domain,2.6 immunoglobulin domain (Ig), 105746 AW151952 Hs.46679 hypothetical1.5 protein FLJ20739 106373 AW503807 Hs.21907 histone 1.8 acetyltransferase 110240 AI668594 Hs.176588 ESTs, Weakly similar to CP4Y HUMAN CYTOC
4.2 2$ 119260 AK001724 Hs.102950 coat 3.2 protein gamma-cop 120206 H26735 Hs.91668 Homo Sapiens45.7 clone PP1498 unknown mRNA

120253 AA131376 Hs.326401 fibroblast38.9 growth factor 12B

120297 AA191384 Hs.104072 ESTs, 15.2 Weakly similar to 2195 HUMAN ZINC

120624 AW407987 Hs.173518 M-phase 52 phosphoprotein homolog 3 120695 AA976503 gb:oq30a04.s1 NCI_CGAP_GC446.8 ~ Homo sapiens 120807 AA346385 Hs.30002 SH3-containing6.8 protein SH3GLB2; KIAA1848 121508 AA402515 Hs.97887 ESTs 28 122607 AA453518 Hs.98023 ESTs 61.5 122616 AA453638 Hs.161873 ESTs 107.3 3 122618 AA453641 gb:zx48e06.s1 Soares_testis_NHT31.1 $ Homo sap 122829 AW204530 Hs.99500 ESTs 81.8 122838 AA460584 Hs.334386 ESTs 75.3 123753 AA609955 Hs.234961 Huntingtin30.6 interacting protein E

124385 AI267847 gb:aq49a10.x1 Stanley57.1 Frontal NB pool 2 4~ 124860 865763 Hs.101477 EST 23.9 124930 A1076343 Hs.173939 ESTs, 22.8 Weakly similar to ALUB_HUMAN !lll 125051 T79956 Hs.100588 EST 135.3 128781 N71826 Hs.105465 small nuclear53.9 ribonucleoprotein polypept 129096 AA463189 Hs.288906 WW Domain-Containing20.9 Gene 4$ 129347 BE614192 Hs.279869 melanoma-associated7.6 antigen recognised b 129689 AW748482 Hs.77873 B7 homolog2.6 130503 BE208491 Hs.295112 KIAA061816.1 gene product 130511 L32137 Hs.1584 cartilage 6.1 oligomeric matrix protein (pse 131046 AA321649 Hs.2248 small inducible7.4 cytokine subfamily B (Cy $0 131643 AW410601 Hs.30026 HSPC182pratein2.9 131925 AF151048 Hs.183180 anaphase2.7 promoting complex subunit 11 (y 132180 NM 004460Hs.418 fibroblastactivation14.7 protein, alpha 132370 AW572805 Hs.46645 ESTs 28.3 132994 AA112748 Hs.279905 clone 17.1 HQ0310 PR00310p1 $$ 133016 A1439688 Hs.6289 hypothetical4.4 protein FLJ20886 133266 AI160873 Hs.69233 zinc finger16.1 protein 133391 AW103364 Hs.727 inhibin, 25.5 beta A (activin A, activin AB
a 134169 AI690916 Hs.178137 transducer1.2 of ERBB2,1 134219 NM_000402Hs.80206 glucose-6-phosphate1.9 dehydrogenase (70134405 AW067903 Hs.82772 collagen,72.9 type XI, alpha 1 134529 AW411479 Hs.848 FK506-binding2.8 protein 4 (59kD) 134975 850333 Hs.92186 Lemon coiled-coil2.6 protein 135181 BE250865 Hs.279529 px19-like14.9 protein 322556 BE041451 Hs.177507 hypothetical2.9 protein Table 6A shows the accession numbers for those pkeys lacking unigenelD's for Table 6. For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT number Accessions 124385 656394_1 AI267847 N27351 120695 9683_3 AA976503 A1917802 AA953664 AA404613 AA428771 BE280542 AW194691 TABLE 7: Figure 7 from BRCA 001-1 US
Table 7 shows genes upregulated in tumor tissue compared to normal breast tissue. Open reading frames in the sequences have been characterized as having a signal sequence (SS), a transmembrane domain (TM) or other.
l0 Pkey: Unique Eos probeset identifier number ExAccn;
ExempIarAccession number, Genbankaccession number UnigenelD:
Unigene number Unigene Title:
Unigene gene title R1: Ratio rmal breast tissue of tumor to no 1$ ORF struct info:
Structural characterization of open reading frame for the sequence of the gene Pkey ExAccnUnigenelDUnigeneTitle R1 ORF struct info 100113 Hs.84746chromosome condensation2.3 TM

100114 Hs.82962thymidylate synthefase2.9 other 100131 Hs.11951ectonucleotide pyrophosphataselphosphodi1.9 other 100146 Hs.2471KIAA0020 gene product1.9 TM

100147 Hs.136348osteoblast specific 7.6 other D13666 factor 2 (fasciclin 100154 Hs.81892KiAA0101 gene product9.2 other 2$ 100163 Hs.124gene predicted from 1.6 other W44671 cDNA with a complete 100220 Hs.217493annexin A2 2 other 100265 Hs.112396KIAA0077 protein 1.5 other 100271 Hs.256290S100 calcium-binding 13.5other BE160081 protein A11 (calgiz 100275 Hs.154797KIAA0090 protein 5.1 other 100323 Hs.23106KIAA0130 gene product1.9 TM

100335 Hs.6793platelet-activating 2.7 other AW247529 factor acetylhydrola 100364 Hs.154868carbamoyl-phosphate 2 ofher NM_004341 synfhetase 2, aspart 100372 Hs.184339KIAA0175 gene product2.6 other 100393 Hs.39913novel RGD-containing 3.2 other D84145 protein 3 100400 Hs.75790phospha6dylinositol 1.5 other $ AW954324 glycan, class C

100418 Hs.84790KIAA0225 protein 2 other 100482 Hs.81361heterogeneous nuclear2.9 other M65028 ribonucleoprotein 100518 Hs.74316desmoplakin (DPI, 1.9 other NM 004415 DPII) 100666 Hs.169610CD44 antigen (homing 5.7 other L05424 function and Indian 100667 Hs.169610CD44 antigen (homing 9 ?
L05424 function and Indian 100668 Hs.169610CD44 antigen (homing 7.7 other L05424 function and Indian 100678 Hs.740PTK2 protein tyrosine53.2other AW502935 kinase 2 100783 Hs.191356general transcription6 other AF078847 factor IIH, polype 100892 Hs.180789S164 protein 1.7 ?

4$ 100945 Hs.180686ubiquitin protein 1.5 other AF002225 ligase E3A (human papi 100969 Hs.79172solute carrier family6.3 other AA157634 25 (mitochondrial 100988 Hs.76480ubiquitin-like 4 11.4?

100999 Hs.80706diaphorase (NADHINADPH)1.6 other H38765 (cytochrome b-5 101031 Hs.151738matrix metalloproteinase8.4 other J05070 9 (gelatinase B

$0 101045 gb:Human proliferating5 ?
J05614 cell nuclear anti 101077 Hs.75227Empirically selected 2.6 other N99692 from AFFX single pr 101093 Hs.75093procollagen-lysine, 1.4 ?
L06419 2-oxoglutarate 5-dio 101186 Hs.179881core-binding factor, 2 TM
AA020956 beta subunit 101216 Hs.84113cyclin-dependent kinase1.8 other AA284166 inhibitor 3 (CDK

$ 101228 Hs.82916chaperonin containing1.7 TM
$ AA333387 TCP1, subunit 6A
( 101247 Hs.78802glycogen synthase 1.9 other AA132666 kinase 3 beta 101249 Hs.1904protein kinase C, 1.5 other L18964 iota 101332 Hs.156346topoisomerase (DNA) 5.3 other J04088 II alpha (170kD) 101352 Hs.16297COX17 (yeast) homolog,4.2 other AI494299 cytochrome c oxid 60 101396 Hs.78996proliferating cell 1.9 TM
BE267931 nuclear antigen 101445 gb:Human Alu repeats 1.6 TM
M21259 in the region 5' to 101470 Hs.1846tumor protein p53 2.5 other NM_000546 (Li-Fraumeni syndrome) 101478 Hs.758RAS p21 protein activator5.5 other NM_002890 (GTPase activa 1$1 101483 Hs.76768procollagen-proline, 2.1 other M24486 2-oxoglutarate 4-di 101540 Hs.84981X-ray repair complementing1.6 other J04977 defective rep 101573 Hs.250758proteasome (prosome, 5.7 other AW248421 macropain) 268 subu 101580 Hs.83363coagulation factor 1.8 other NM_012151 VIII-associated (intr $ 101592 Hs.91299guanine nucleotide 5.6 ?
AF064853 binding protein (G
pr 101621 Hs.62661guanylate binding 2.4 other BE391804 protein 1, interferon-101702 Hs.179574protein phosphatase 1.3 other AW504089 2 (formerly 2A), reg 101734 Hs.147049cut (Drosophila)-like2.1 ?
M74099 1 (CCAAT displacem 101759 Hs.184601solute carrier family5 TM
M80244 7 (cationic amino 1 101767 Hs.180884carboxypeptidase B1 14.4SS, ~ M81057 (tissue) 101782 Hs.1869phosphoglucomutase 5.2 other 101805 Hs.75612stress-induced-phosphoprotein8.6 other AW409747 1 (Hsp701H

101806 Hs.112408S100 calcium-binding 8.9 SS,TM
AA586894 protein A7 (psorias 101810 Hs.180612peroxisomal membrane 3.2 TM
NM 000318 protein 3 (35kD, Ze 1$ 101879 Hs.243886nuclear autoantigenic1.6 other AA176374 sperm protein (his 101911 Hs.119689glycoprotein hormones,31.3?
AA441787 alpha polypeptide 101920 Hs.8024IK cytokine, down-regulator1.8 other AF182645 of HLA II

101973 Hs.80120UDP-N-acetyl-alpha-D~alactosamine;polyp2.4 other 102009 Hs.82643protein tyrosine kinase1.3 other 102036 Hs.82906CDC20 (cell division 2 ?
BE250127 cycle 20, S. cerevi 102083 Hs.75117interleukin enhancer 1.6 other T35901 binding factor 2, 102107 Hs.182366heat shock protein 1.4 other 102123 Hs.1594centromere protein 1.8 other NM_001809 A (17kD) 102165 Hs.159627death associated protein4.6 7 2$ 102198 Hs.74598polymerase (DNA directed),4.4 ?
AW950852 delta 2, regu 102217 Hs.301613JTV1 gene 6.7 other 102220 Hs.65436lysosomal 4.4 TM

102234 Hs.278554heterochromatin-like 1.9 TM
AW163390 protein 1 102260 Hs.159557karyopherin alpha 4.4 other AL039104 2 (RAG cohort 1, impor 102302 Hs.69171protein kinase C-like2.7 ?

102330 Hs.77254chromobox homolog 1.5 other BE298063 1 (Drosophila HP1 beta 102339 Hs.95577cyclin-dependent kinase2.3 TM

102348 Hs.87539aldehyde dehydrogenase2 TM
037519 3 family, member 102349 Hs.289107baculoviral IAP repeat-containing3.2 other 3$ 102369 Hs.299867hepatocytenuclearfactor3,alpha2 other 102374 Hs.90572PTK7 protein tyrosine6.2 other 033635 kinase 7 102391 Hs.77494deoxyguanosine kinase1.5 TM

102455 Hs.75562discoidin domain receptor7 other 048705 family, member 102465 Hs.815482,4-dienoyl CoA reductase1.8 SS, NM_001359 1, mitochondri 102488 Hs.61828amyloid beta precursor1.5 ?
050939 protein-binding p 102489 Hs.74420origin recognition 3.3 other AL080116 complex, subunit 3 (y 102494 Hs.75193COP9 homolog 2.1 other 102501 Hs.74562siah binding protein 3.2 other AF217197 1; FBP interacting 102522 Hs.183556solute tamer family 2.8 ?
BE250944 1 (neutral amino a 4$ 102532 Hs.70186suppresser of Ty (S.cerevisiae)5.7 ?
AF040253 5 homolo 102564 Hs.79067MAD (mothers against 2.3 other 059423 decapentaplegic, Dr 102568 Hs.223025RAB31, member RAS 5.3 other W81489 oncogene family ~

102580 Hs.152981CDP-diacylglycerol 2.1 other 060808 synthase (phosphatida 102581 Hs.77256enhancer of zeste 1.6 ?
AU077228 (Drosophila) homolog $~ 102582 Hs.32675tubulin-specific chaperone2.1 other 061232 a 102617 Hs.198767COP9 (constitutive 1.8 other AW161453 photomorphogenic, Ara 102618 Hs.81071extracellular matrix 5.8 other AL037672 protein 1 102627 Hs.158174zinc finger protein 1.3 other AL021918 184 (Kruppel-like) 102663 Hs.168075karyopherin (importin)1.8 TM
NM_002270 beta 2 $$ 102676 Hs.12045putative protein 2.3 other 102687 Hs.93002ubiquitin tamer protein4.4 ?
NM_007019 E2-C

102689 Hs.171280hydroxyacyl-Coenzyme 6 ?
096132 A dehydrogenase, ty 102696 Hs.239forkhead box M1 4.2 other 102704 Hs.54089BRCA1 associated RING1.9 other AU077058 domain 1 102705 Hs.50002small inducible cytokine2.3 SS,TM
T97490 subfamily A (Cy 102750 Hs.66196nth (E.coli endonuclease1.2 TM
AB014460 III)-like 1 102801 Hs.38041pyddoxal (pyridoxine,6.5 other BE252241 vitamin 86) kings 102812 Hs.236774high-mobility group 1.6 other 090549 (nonhistone chromoso 102827 Hs.6456chaperonin containing5.6 TM
BE244588 TCP1, subunit 2 (b 6$ 102844 Hs.324275WW domain-containing 1.3 TM
AV653790 protein 1 102868 Hs.77274plasminogen activator,4.4 other X02419 urokinase 102925 Hs.2943signal recognition 1.9 other BE440142 particle 19kD

1$2 102935BE561850Hs.80506small nuclear ribonucleoprotein2.4?
polypept 102968AU076611Hs.154672methylene tetrahydrofolate2.7other dehydrogenase 102983BE387202Hs.118638non-metastatic cells 3.1other 1, protein (NM23A) 102985U95742Hs.2707G1 to S phase transition5.2?

$ 103023AW500470Hs.117950multifunctional polypeptide1.6other similar to S

103038AA926960Hs.334883CDC28 protein kinase 2.5TM

103060NM_005940Hs.155324matrix metalloproteinase4.5other 11 (MMP11; stro 103080AU077231Hs.82932cyclin D1 (PRAD1: parathyroid3.1other adenomatos 103089031152Hs.179729collagen, type X, alpha2.4other 1 (Schmid metaph 1 103177BE244377Hs.48876famesyl-diphosphate 3.5ofher ~ famesyltransferase 103178AA205475Hs.275865ribosomal protein S18 9.9?

103179NM Hs.82685CD47 antigen (Rh-related1.3other 001777 antigen, integr 103181X69636Hs.334731Homo sapiens, clone 2 other IMAGE:3448306, mRNA, 103185NM_006825Hs.74368transmembrane protein 1.6other (63kD), endoplasmi 15103191AA401039Hs.2903protein phosphatase 2.5other 4 (formerly X), cata 103193NM_004766Hs.75724coatomer protein complex,2.2TM
subunit beta 2 103194NM Hs.78580DEADIH (Asp-Glu-Ala-AspIHis)6.3TM
004939 box polypep 103206X72755Hs.77367monokine induced by 8.8TM
gamma interferon 103223BE275607Hs.1708chaperonin containing 3 other TCP1, subunit 3 (g 103232X75962Hs.129780tumor necrosis factor 1.8other receptor superfami 103238AI369285Hs.75189death-associated protein5.6TM

103297NM_001545Hs.9078immature colon carcinoma1.9?
transcript 1 103330AI803447Hs.77496small nuclear ribonucleoprotein2.5other polypept t 103349X89059 gb:H.sapiens mRNA for 1.6other unknown protein ex 2S103376AL036166Hs.323378coated vesicle membrane1.8other protein 103391X94453Hs.114366pyrroline-5-carboxylate2.3other synthetase (glut 103392X94563 gb:H.sapiens dbilacbp 4 TM
gene exon 1 & 2.

103430BE564090Hs.20716translocase of inner 1.3other mitochondria) membr 103491AF264750Hs.288971myeloidllymphoid or 5.7?
mixed-lineage leukem 3 103505AL031224Hs.33102transcription factor 5.1other ~ AP-2 beta (activati 103547AI376722Hs.180062proteasome (prosome, 9.7?
macropain) subunit, 103588NM_006218Hs.85701phosphoinositide-3-kinase,2 other catalytic, al 103613NM Hs.2316SRY (sex determining 1.3?
000346 region Y)-box 9 (ca 103621BE379766Hs.150675polymerase (RNA) II 2 other (DNA directed) polyp 35103622AA609685Hs.278672membrane component, 2.3TM
chromosome 11, surfa 103727AI878883Hs.296381growth factor receptor-bound1.3other protein 2 103754A1015709Hs.172089Homo sapiens mRNA; 1.3other cDNA DKFZp58612022 (f 103780AA094752Hs.169992hypothetical 43.2 Kd 7.6?
protein 103795H26531Hs.7367Homo sapiens BTB domain1.3SS,TM
protein (BDPL) m 103797AA080912 gb:zn04d03.r1 Stratagene1.6other hNT neuron (937 103813A1042582Hs.181271CGI-120 protein 1.6other 103855W02363Hs.302267hypothetical protein 1.6other 103886AK001278Hs.105737hypothetical protein 6.6TM
FLJ10416 similar to 104052NM_002407Hs.97644mammaglobin 2 2.9other 45104079AA251242Hs.103238ESTs 1.4other 104174AA478984Hs.6451PR00659 protein 5.6TM

104227AB002343Hs.98938protocadherin alpha 1.6other 104275AI751970Hs.101067GCN5 (general control 5.4other of amino-acid synt 104325BE379766Hs.150675polymerase (RNA) II 6.4other (DNA directed) polyp 104370AA324597Hs.21851Homo sapiens cDNA FLJ129001.6other fis, clone NT

104423883113Hs.1432protein kinase C substrate5.2other 104482AB037762Hs.44268myelin gene expression1.2other factor 2 104667AI239923Hs.30098ESTs 1.4other 104757AI694413Hs.332649olfactory receptor, 2.4other family 2, subfamily $ 104804AI858702Hs.31803ESTs, Weakly similar 1.4other $ to N-WASP [H.sapien 104806AB023175Hs.22982KIAA0958 protein 2.4other 104827AW052006Hs.8551PRP41STKIWD splicing 10.9other factor 104846AI250789Hs.32478ESTs 5.7other 104854AA041276Hs.1547293-phosphoinositide 12.3?
dependent protein kin 104867AA278898Hs.225979hypothetical protein 2.1other similar to small G

104871T78044Hs.28893Homo sapiens mRNA; 1.4other cDNA DKFZp56402364 (f 104896AW015318Hs.23165ESTs 17.7other 104909AW408164Hs.249184transcription factor 5.1TM
19 (SC1) 104916AW958157Hs.155489NS1-associated protein1.8other 6$104919AA026880Hs.25252prolactin receptor 1.5other 104930AF043467Hs.32893neurexophilin 2 2.3other 104973NM_015310Hs.6763KIAA0942 protein 5.1other 104974 Y12059Hs.278675bromodomain-containing1.5other 104975 AL136877Hs.50758SMC4 (structural maintenance2.4other of chromoso 104978 AI199268Hs.19322Homo sapfens, Similar 7.3other to RIKEN cDNA 2010 104979 AA937934Hs.321062ESTs 1.3other $ 104994 AI499930Hs.334885mitochondrial GTP binding3.6?
protein 105009 BE379584Hs.34789dolichyl-diphosphooligosaccharide-protei5.6other 105012 AF098158Hs.9329chromosome 20 open 3.4other reading frame 1 105028 A1050715Hs.2331E2F transcription factor2.2other 5, p130-binding 105041 AB037716Hs.26204KIAA1295 protein 2.2other .

1 105045 BE242899Hs.129951speckle-type POZ protein3.9?
~

105079 AA151342Hs.12677CGI-147 protein 9.5TM

105087 AA147884Hs.9812Homo sapiens cDNA FLJ143885.7other fis, clone HE

105088 H58589Hs.35156Homo Sapiens cDNA FLJ110272.2other fis, clone PL

105095 278407Hs.27023vesicle transport-related2.2other protein 15105110 BE387350Hs.33122KIAA1160 protein 1.6other 105126 AW975433Hs.36288ESTs 6.4?

105127 AA045648Hs.301957nudix (nucleoside diphosphate2.2other linked moi 105141 AA164687Hs.177576mannosyl (alpha-1,3-)-glycoprotein2.8other beta-105158 AW976357Hs.234545hypothetical protein 2 other 20105169 BE245294Hs.180789S164 protein 1.7other 105186 AA191512Hs.28005Homo sapiens cDNA FLJ113094.9SS,TM
fis, clone PL

105254 AA071276Hs.19469KIAA0859 protein 2 TM

105281 AA263143Hs.24596RAD51-interacting protein2.9?

105288 N99673Hs.3585ESTs, Weakly similar 1.9TM
to AF1267431 DNAJ

2$105302 AA700122Hs.3355sentrin-specific protease8.2?

105331 AW270037Hs.179507KIAA0779 protein 1.8SS, 105359 NM_016015Hs.8054CGI-68 protein 8.4other 105366 BE264645Hs.282093hypothetical protein 5.1other 105373 AW887701Hs.32356hypothetical protein 2.6other 105374 BE242803Hs.262823hypothetical protein 2.2TM

105387 AW592146Hs.108636membrane protein CH1 2.3SS,TM

105393 AF167570Hs.256583interleukin enhancer 5.5SS, binding factor 3, 105399 BE386877Hs.334811Npw38-binding protein 1.6other NpwBP

105400 AF198620Hs.65648RNA binding motif protein1.6other 3$105445 AA252395 gb:zs12g10.s1 NCI CGAP_GCB15.1?
Homosapiens 105507 BE268348Hs.226318CCR4-NOT transcription1.6other complex, subunit 105529 AA113449Hs.32471hypothetical protein 1.3other 105530 AB023179Hs.9059KIAA0962 protein 3.5other 105547 AA262640Hs.27445unknown 9.3other 4~105564 BE616694Hs.288042hypothetical protein 1.4other 105596 AA579535Hs.18490hypothetical protein 10.9TM

105597 AF054284Hs.334826splicing factor 3b, 2.9TM
subunit 1,155kD

105608 AI808201Hs.287863hypothetical protein 1.7?

105610 AA280072Hs.99872fetal Alzheimer antigen1.4other 45105617 AK000892Hs.4069glucocorticoid modulatory1.7TM
element bindin 105620 AW302245Hs.181390casein kinase 1, gamma5.6other 105658 AA985190Hs.246875hypothetical protein 9.4other 105697 AW499988Hs.27801zinc finger protein 2 TM

105708 826944Hs.180777Homo Sapiens mRNA; 1.7other cDNA DKFZp564M0264 (f 105743 BE246502Hs.9598sema domain, immunoglobulin2.7other domain (Ig), 105746 AW151952Hs.46679hypothetical protein 1.5?

105759 AI123118Hs.15159chemokine-like factor,1.3other alternatively spl 105771 AI267720Hs.153221synovial sarcoma, translocated1.6other to X chro 105820 AA741336Hs.152108transcriptional unit 2.2other S 105826 AA478756Hs.194477E3 ubiquitin ligase 1.3other 105856 AI262106Hs.12653ESTs 2.4other 105858 AF151066Hs.281428hypothetical protein 2.9other 105875 AK001708Hs.32271hypothetical protein 1.4other 105930 AF016371Hs.9880peptidyl prolyl isomerase5.3other H (cyclophilin 106000 AW194426Hs.20726ESTs 1.7other 106011 AW081202Hs.12284Homo Sapiens, clone 2.8other INIAGE:2989556, mRNA, 106017 AA477956Hs.26268ESTs 1.4other 106073 AL157441Hs.17834downstream neighbor 1.4other of SON

106078 AA130158Hs.19977ESTs, Moderately similar1.6?
to ALUB_HUMAN A

65106094 AA533491Hs.23317hypothetical protein 6.9other 106140 AB006624Hs.14912KIAA0286 protein 1.6other 106271 AA251393Hs.289052Homo Sapiens, Similar , ?
to RIKEN cDNA 5430 10.8 106288 Hs.24336KIAA1321 protein 1.3other 106300 Hs.19114high-mobility group 3.7other Y10043 (nonhistone chromoso 106333 Hs.22410ESTs, Weakly similar 5.5SS, AL043114 to A54849 collagen 106350 Hs.194698cyclin B2 5.8other $ 106359 Hs.31130transmembrane 7 superfamily6.4other AW390282 member 2 106381 Hs.24106KIAA1483 protein 6.6other 106389 Hs.6236Homo sapiens cDNA: 2.2TM
AW748420 FLJ21487 fis, clone C

106457 Hs.27801zinc finger protein 2.7other 106470 Hs.186180Homo Sapiens cDNA: 2.3other D63078 FLJ23038 fis, clone L

1~ 106586 Hs.57787ESTs 1.6other 106589 Hs.28661Homo sapiens cDNA FLJ100712.4?
AK000933 fis, clone HE

106610 Hs.79732fibulin 1 8 SS, 106624 Hs.26350tyrosylprotein sulfotransferase7.8other NM_003595 2 106650 Hs.22370Homo sapiens mRNA; 1.8other AL049951 cDNA DKFZp56400122 (f 1 106669 Hs.184164ESTs, Moderately similar1.3TM
S AV657117 to S65657 alpha 106713 Hs.184352hypothetical protein 4.6other 106717 Hs.239489TIA1 cytotoxic granule-associated1.3other AA600357 RNA-bi 106723 Hs.21857ESTs 1.6SS, 106795 Hs.293753Bcl-2-related ovarian 5.7other AF174487 killer protein-lik 106829 Hs.27099hypothetical protein 16.2TM
AW959893 FLJ23293 similar to 106831 Hs.29463cenfdn, EF-hand protein,1.5other 8E564871 3 (CDC31 yeasf 106846 Hs.34892KIAA1323 protein 2.2other 106852 Hs.300631hypothetical protein 1.3other 106873 Hs.11197Homo Sapiens, clone 16.8other N49809 IMAGE:3343149, mRNA, ~$ 106886 Hs.9567GL002 protein 1.5TM

106906 Hs.222024transcription factor 2.2other 106920 Hs.296323serumlglucocorticoid 3.4other AK001838 regulated kinase 106945 Hs.6294hypothetical protein 6.8?
AK000511 DKFZp434L1435 simil 106973 Hs.11923hypothetical protein 6.7other 106978 Hs.8688ESTs 6.1SS, 107004 Hs.300700hypothetical protein 1.3other 107029 Hs.288971myeloidllymphoid or 1.8other AF264750 mixed-lineage leukem 107071 Hs.35198ectonucleotide pyrophosphataselphosphodi1.7other 107113 Hs.23900GTPase activating protein2.5other ' AK000733 35 107125 Hs.69388hypothetical protein 1.7other 107136 Hs.8207GK001 protein 4.7other 107146 Hs.5198Down syndrome critical2 other AK001455 region gene 2 107151 Hs.8687ESTs 6.4TM

107155 Hs.7946KIAA1288 protein 33.5other 107174 Hs.25338ESTs 5.2?

107197 Hs.64639glioma pathogenesis-related6.1other W15477 protein 107221 Hs.81915leukemia-associated 17.4other AW888411 phosphoprotein p18 ( 107243 Hs.34727ESTs, Moderately similar7.4?
BE219716 to 138759 zinc 107248 Hs.315111nuclear receptor co-repressorIHDAC31.8other AW263124 comp 45 107263 Hs.21198translocase of outer 6.7other D60341 mitochondrial membr 107265 Hs.49136ESTs, Moderately similar2.5other BE379594 to ALU7_HUMAN A

107299 Hs.30661hypothetical protein 3.2TM

107316 Hs.193700Homo Sapiens mRNA; 2 TM
T63174 cDNA DKFZp58610324 (f 107354 Hs.96448zinc finger protein 5 ?
Nlu[_006299 193 107392 Hs.267632TATA element modulatory1.2other ~ AW299900 factor 1 107481 Hs.279766kinesin family member 1.6other 107529 Hs.296585nucleolar protein (KKEID3 TM
BE515065 repeat) 107554 Hs.59844ESTs 1.4other 107681 Hs.49136ESTs, Moderately similar2.3SS,TM
BE379594 to ALU7_HUMAN A

S$ 107772 Hs.303055ESTs, Weakly similar 2.2?
AA018587 to ALU1 HUMAN ALU
S

107859 Hs.47584potassium voitage~gated8.4TM
AW732573 channel, delayed 107901 Hs.335952keratin 6B 2.5other 107922 Hs.61460Ig superfamily receptor2.3other 107974 Hs.61712pyruvate dehydrogenase6.8other AW956103 kinase, isoenzyme 108040 Hs.159971SWIISNF related, matrix1.6other AL121031 associated, acti 108230 Hs.59847ESTs 1.3other 108274 Hs.272027F-box only protein 7.27 108296 Hs.161623ESTs 2.6other 108496 Hs.339659ESTs 3.6other 65 108607 Hs.69476Homo sapiens cDNA FLJ127583.5other BE300380 fis, clone NT

108621 Hs.182685ESTs 1.7other 108634 Hs.69507ESTs 1.8SS,TM

108647 Hs.44276homeo box C10 9.8other 108695 Hs.70823KIAA1077 protein 7.3ofher 108740 Hs.9071progesterone membrane 2.8?
A1089575 binding protein 108828 Hs.273344DKFZP56400463 protein 1.9other 108859 Hs,178904ESTs 1.6TM

108872 Hs.111680endosulfine alpha 2.2other 108891 Hs.48480ESTs 5,4other 108894 Hs.5105hypothetical protein 4.1TM

108955 Hs.195155Homo sapiens amino 5.7?
AA149754 acid transport system 1 108982 Hs.171980homeo box (expressed 1.7other ~ AA151708 in ES cells) 1 108987 Hs,23467hypothetical protein 6.3other 109002 Hs.72134KIAA1064 protein 1.7other 109011 Hs.72127ESTs 1.5other 109026 gb:zo35d07.s1 Stratagene5.4other AA157811 colon (937204) 1$ 109068 Hs.72545ESTs 3 other 109101 Hs.52184hypothetical protein 1.6SS, 109112 Hs.257924hypothetical protein 3.3TM

109124 Hs.183887hypothetical protein 1.7other 109139 Hs.59757zinc finger protein 2.7other 109166 Hs.73625RAB6 interacting, kinesin-like3 TM
AA219691 (rabkines 109198 Hs.58169highly expressed in 2.1other BE566742 cancer, rich in leuc 109213 Hs.82035potential nuclear protein5.4other NM 016603 C50RF5; GAP-li 109220 Hs.189998ESTs 5.8other 109233 Hs.170285nucleoporin 214kD (CAIN)5.3other ZS 109270 Hs.3585ESTs, Weakly similar 1.4other N99673 to AF1267431 DNAJ

109273 Hs.82719Homo Sapiens mRNA; 3 other AA375752 cDNA DKFZp586F1822 (f 109313 Hs.86276C2H2 (Kruppel-type) 1.3other AF153201 zinc finger protein 109341 Hs.115099EST 3 ?

109391 Hs.184245KIAA0929 protein Msx2 1.5other AL096858 interacting nuclea 3~ 109420 Hs.40408homeo box C9 2.2SS, 109426 Hs.42215protein phosphatase 3.1TM
N30531 1, regulatory subuni 109429 Hs.61438ESTs 2 ?

109445 Hs.189915ESTs 1.8other 109450 Hs.173042KIAA1143 protein 3.8other 35 109468 Hs.6763KIAA0942 protein 3.3other NM_015310 109478 Hs.87134ESTs 2 TM

109570 Hs.118890glycogen synthase kinase2.1other L40027 3 alpha 109662 Hs.27319ESTs 1,4other 109825 Hs.16798ESTs 1.3other 110039 Hs.21907histone acetyltransferase2 other 110056 Hs.279009matrix Gla protein 2.5other 110085 Hs.29956KIAA0460 protein 1.7other 110110 Hs,7948ESTs 2.9other 110129 Hs.226429ESTs, Weakly similar 1.7SS, 851853 to ALU1_HUMAN ALU
S

4S 110154 Hs.17667SH3-domain binding 4.3other NM_014521 protein 4 110240 Hs.176588ESTs, Weakly similar 4.3?
AI668594 to CP4Y_HUMAN CYTOC

110242 Hs.19978CGI-30 protein 1.3other 110259 Hs.32406ESTs, Weakly similar 2.2other H28428 to 138022 hypotheti 110312 Hs.11896hypothetical protein 2.1other S 110501 gb:yq94a01.s1 Soares 6.1?
~ H55748 fetal liver spleen 110504 Hs.210859hypothetical protein 6.1TM

110525 Hs.37430EST 6.4other 110568 Hs.5999hypothetical protein 1.3?

110699 Hs.18090ESTs 1.8other $$ 110705 Hs.32168KIAA0442 protein 1.6TM

110742 Hs,28029hypothetical protein 7,8other 110761 Hs.16157hypothetical protein 2.5other 110762 Hs.30011hypothetical protein 9.3?

110765 Hs.18457hypothetical protein ~ SS, AK000322 FLJ20315 5.5 110769 Hs.23837Homo Sapiens cDNA FLJ118122.1TM
BE000831 fis, clone HE

110799 Hs.323401dpy-30-like protein 1.5TM

110805 Hs.24048FK506 binding protein 6.7TM
T25829 precursor 110813 Hs.35669ESTs, Moderately similar5.7other AA767373 to ALU1 HUMAN A

110820 Hs.6614ESTs, Weakly similar 3.4other 833261 to A43932 mucin 2 p 65 110840 Hs.12727hypothetical protein 1.7TM

110844 Hs.167531methylcrotonoyl-Coenzyme1.7other AI740792 A carboxylase 2 110854 Hs,27931hypothetical protein 4.7other BE612992 FLJ10607 similar to 110856 gb:ot37g06.s1 Soares_testis_NHT2.3other AA992380 Homo sap 110885 Hs.16034hypothetical protein 3.5?

110897 Hs.6880DKFZP434D156 protein 2.2?

110915 Hs.29724hypothetical protein 2.6SS, 110918 Hs.24283ESTs, Moderately similar1.9TM
H04360 to reduced expr 110958 Hs.24587signal transduction 6.7other NM_005864 protein (SH3 contain 110963 Hs.11449DKFZP5640123 protein 2 other 110981 Hs.24284ADP-ribosyltransferase1.3other AK001980 (NAD+; poly(ADP-r 110984 Hs.80120UDP-N-acetyl-alpha-D~alactosamine:polyp1.8?

111125 Hs.269115ESTs, Moderately similarto3.7other N63823 Z195_HUMAN Z

111132 Hs.83293hypothetical protein 2.1TM

111164 Hs.122489Homo Sapiens cDNA FLJ132892.3other N46180 fis, clone OV

111172 Hs.21851Homo sapiens cDNA FLJ129003.7other 867419 fis, clone NT

111174 Hs.26295Homo sapiens mRNA; 7.5other AL050166 cDNA DKFZp586D1122 (f I 111179 Hs.10760asporin (LRR class 7.1other S AK000136 1) 111184 Hs.243901Homo sapiens cDNA FLJ207386.8other AI815486 fis, clone HE

111189 Hs.272130ESTs, Weakly similar 3.6SS, N67603 to S65824 reverse t 111216 Hs.152940ESTs 1.5other 111221 Hs.15119KIAA1361 protein 2.6other 111223 Hs.334838KIAA1866 protein 4.7other 111239 Hs.17230hypothetical profein 7.9?

111285 Hs.4310eukaryotic translation7 other AA778711 initiation factor 111299 Hs.74313KIAA1265 protein 5 other 111312 Hs.34504ESTs 3.8other ZS 111318 Hs.334728ESTs 1.2TM

111337 Hs.263925LIS1-interacting protein5.1other AA837396 NUDE1, rat homo 111352 Hs.35156Homo sapiens cDNA FLJ110272.2other H58589 fis, clone PL

111370 Hs.94631brefeldin A-inhibited 2.8?
AI478658 guanine nucleotide 111384 Hs.288969HSCARG protein 2.2other 111389 Hs.169111oxidation resistance 2.1other 111452 Hs.15999ESTs 2.7TM

111486 Hs.227978EST 6.6other A1051194 ~

111549 Hs.20321ESTs, Moderately similar1.4other W90638 to ZRF1 HUMAN Z

111585 Hs.20670EST 1.6?

111627 Hs.21691ESTs 1.6other 111870 Hs.18685Homo Sapiens mRNA for 2.4other AB037834 KIAA1413 protein, 111937 Hs.14846Homo Sapiens mRNA; 10.6other BE298665 cDNA DKFZp564D016 (fr 111944 Hs.21263suppressor of potassium6.6TM
AW083791 transport defect 111987 Hs.6763KIAA0942 protein 5.1other NM_015310 112134 Hs.7413ESTs; calsyntenin-2 2.8other 112244 Hs.70823KIAA1077 protein 14.6other 112388 Hs.301693Homo sapiens, clone 9 other 846071 IMAGE:3638994, mRNA, 112456 Hs.232076A kinase (PRKA) anchor1.4other NM 016248 protein 11 112464 Hs.28538Homo Sapiens cDNA: 1.4TM
AW007287 FLJ21086 fis, clone C

4S 112506 Hs.26079ESTs 3.2other 112513 Hs.13809hypothetical protein 2 TM

112752 Hs.14838hypothetical protein 1.8other 112884 Hs.5013Homo Sapiens mRNA for 6.6other AK000004 FLJ00004 protein, 112923 Hs.5037EST 1.5?

112936 Hs.6185KIAA1557 protein 3.2other 112958 Hs.6724ESTs 6.1other 112966 Hs.102548glucocorticoid receptor6.5other 244718 DNA binding fact 112978 Hs.7099hypothetical protein 1,2other 112995 Hs.7155ESTs, Moderately similar5.6other AA737033 to 2115357A TYK

S 112996 Hs.7165zinc finger protein 2 other 113047 Hs.7549ESTs 1.9other 113049 Hs.7560Homo sapiens mRNA for 2.4TM
AW965190 KIAA1729 protein, 113089 Hs.270862ESTs 1.3SS, 113196 gb:yb51a03.s1 Stratagene1.7other T57317 fetal spleen (9 113248 gb:yc16e01.s1 Stratagene2.8other T63857 lung (937210) H

113254 Hs.11449DKFZP5640123 protein 1.3other 113277 Hs.11774protein (peptidyl-prolyl3.2other AW971049 cisltrans isome 113429 Hs.179808ESTs 1.2other 113499 Hs.8882ESTs 6 other 65 113547 Hs.15233ESTs 2 SS, 113647 Hs.188173Homo Sapiens cDNA FLJ121871.3SS, AA813887 fis, clone MA

113702 gb:ye53h05.s1 Soares 4.4other T97307 fetal liver spleen 113759 Hs.9456SWIISNF related, matrix1.2other AW499665 associated, acti 113777 Hs.10590zinc finger protein 13.4other 113783 Hs.7041hypothetical protein 1.7other AL359588 DKFZp762B226 113791 Hs.135578chitobiase, di-N-acetyl-1.3other $ 113808 Hs.9286Homo sapiens cDNA: 3.3other W44735 FLJ21278 fis, clone C

113811 Hs.6994Homo Sapiens cDNA: 3.1other BE207480 FLJ22044 fis, clone H

113817 Hs.332795hypothetical protein 3.2other H13325 DKFZp761017121 113826 Hs.24809hypothetical protein 2.3?

113834 Hs.6059EGF-containing fibulin-like11.3TM
T26483 extracellula 1 113868 Hs.90744proteasome (prosome, 2.7other ~ W57902 macropain) 26S subu 113870 Hs.16537hypothetical protein, 6.1other AL079314 similar to (U06944 113885 Hs.21732ESTs 6.6other 113923 Hs.3849hypothetical protein 1.9?
AW953484 FLJ22041 similar to 113989 Hs.268828ESTs 1.2other 1$ 114022 Hs.120969Homo Sapiens cDNA FLJ115625.4other AI539519 fis, clone HE

114030 Hs.164478hypothetical protein 9.4other AI825386 FLJ21939 similar to 114060 Hs.7910RING1 and YY1 binding 1.8other A8029551 protein 114196 Hs.150926fucose-1-phosphate 1.5other AF017445 guanylyltransferase 114226 Hs.7989KIAA1045 protein 1.8other 114253 Hs.14831Homo Sapiens, Similarto2.3other BE149866 zinc finger pro 114262 Hs.3686KIAA0978 protein 1.4TM

114275 Hs.306117 KIAA0306 AW515443.comp protein 15.8 ~
other 114292 Hs.184641fatty acid desaturase 1.9TM

114309 Hs.20824CGI-85 protein 2.4other ~$ 114392 Hs.100748ESTs, Weakly similar 1.9other AA249590 toA28996 proline-r 114407 Hs.103305Homo sapiens mRNA; 1.3TM
BE539976 cDNA DKFZp434B0425 (f 114455 Hs.271616ESTs, Weakly similar 5.6other H37908 to ALUB_HUMAN ALU
S

114463 Hs.40109KIAA0872 protein 5.3TM

114464 Hs.106597Homo Sapiens, Similar 1.3other A1091713 to RIKEN cDNA 1110 114471 Hs.104613RP42 homolog 1.9?

114480 Hs.151678UDP-N-acetyl-alpha-D-galactosamine:polyp13.4other 114671 Hs.266273hypothetical protein 2 other 114698 Hs.110857polymerase (RNA) III 3.6other AA476966 (DNA directed) poly 114730 Hs.331328intermediate filament 3.9other A1373544 protein syncoilin 3 114767 Hs.154443minichromosome maintenance1.7other $ AI859865 deficient (S.

114774 Hs.184325CGI-76 protein 3.2other 114798 Hs.54900serologically defined 3.6other AA159181 colon cancer antig 114860 Hs.42179bromodomain and PHD 4.4other AL157545 finger containing, 114895 Hs.76591KIAA0887 protein 7.2other 114896 Hs.5324hypothetical protein 1.3other 114911 gb:zt29f02.s1 Soares 1.5other AA236672 ovary tumor NbHOT
H

114930 Hs.188717ESTs 2 SS, 114938 Hs.58384ESTs 2.9other 114965 Hs.72472BMP-R1B 2.3?

4$ 115023 Hs.63931dachshund (Drosophila)1.3other AF102546 homolog 115038 Hs.87968toll-like receptor 1.6other 115061 Hs.41271Homo sapiens mRNA foil11.8other AI751438 length insert cDN

115117 Hs.5324hypothetical protein 1.5other 115206 Hs.186572ESTs 2.5other $~ 115221 Hs.79741hypothetical protein 1.5other 115239 Hs.73291hypothetical protein 1.3TM

115242 Hs.283732ESTs, Moderately similar1.4other AI368236 to ALU1 HUMAN A

115278 Hs.301724hypothetical protein 1.5other 115285 Hs.293736ESTs 2.4other $$ 115291 Hs.122579hypothetical protein 6.3SS, 115400 Hs.89113ESTs 6.7?

115468 Hs.48499tumor antigenSLP-8p 7.5?

115471 Hs.59346hypothetical protein 1.4TM

115479 Hs.278188ESTs, Moderately similar4.1TM
AW301608 to 154374 gene 115496 Hs.71819eukaryotic translation16.3other AW247593 initiation factor 115500 Hs.88219zinc finger protein 5 other 115553 Hs.71414transcription factor 2.5other AJ275986 (SMIF gene) 115581 Hs.61082ESTs 6.2other 115587 Hs.283037HSPC039 protein 2.9other 6$ 115590 Hs.678967-60 protein 5.3TM

115646 Hs.305971solute carver family 4.8?
N36110 2 (facilitated glu 115652 Hs.38178hypothetical protein 10.6other 1$8 115655 Hs.288544Homo sapiens, clone 12.7TM
AL048269 MGC:16063, mRNA, com 115663 Hs.40507ESTs 2 other 115676 Hs.88143ESTs 3.1 other 115690 Hs.44159hypothetical protein 1.7 TM

115693 Hs.55173cadherin, EGF LAG 6.9 other AF231023 seven-pass G-type rece 115715 Hs.1390proteasome (prosome, 1.7 other BE395161 macropain) subunit, 115734 Hs.40782ESTs 2.7 TM

115811 Hs.48604DKFZP434B168 protein 2.1 other NM_015434 115823 Hs.87440ESTs 2.1 other 1 115837 Hs.42761ESTs 1.3 other ~ AI675217 115844 Hs.332938hypothetical protein 4.4 other 115866 Hs.52081KIAA0867 protein 7.3 other 115875 Hs.333823mitochondrial ribosomal1.2 other N55669 protein L13 115941 Hs.46679hypothetical protein 5.5 other 15 115968 Hs.62767KIAA1332 protein 9.8 other 116003 Hs.66493Down syndrome critical1.4 other BE275469 region gene 5 116011 Hs.57664Homo Sapiens mRNA 2.4 other AL359053 full length insert cDN

116108 Hs.28777H2A histone family, 1.8 other AA770688 member L

116134 Hs.50441CGI-04 protein 1.4 other 116189 Hs.44749ESTs, Moderately similar1.2 other N35719 to T00358 hypot 116195 Hs.72402ESTs 2.1 other 116238 Hs.47144DKFZP586N0819 protein1.7 other 116246 Hs.250646baculoviral IAP repeat-containing1.7 other 116262 Hs.59838hypothetical protein 1.8 ?

~$ 116298 Hs.94109Homo Sapiens cDNA 1.9 other AI955411 FLJ13634 fis, clone PL

116318 Hs.58570deleted in cancer 5 SS, AF097645 1; RNA helicase HDBIDI

116325 Hs.49303Homo sapiens cDNA 1.4 SS, AI472106 FLJ11663 fis, clone HE

116336 Hs.4084KIAA1025 protein 1.9 ?

116339 Hs.44033dipeptidyl peptidase 1.5 other 116350 Hs.184771nuclear factor IIC 1.9 ?
AA497129 (CCAAT binding transc 116358 Hs.38125interferon-induced 1,9 ?
AI149586 protein 75, 52kD

116365 Hs.46765ESTs 6.1 other 116368 Hs.71109KIAA1229 protein 1,6 ?

116417 Hs.12484Human clone 23826 7.4 other AW499664 mRNA sequence 3 116436 Hs.58668chromosome 21 open 2,1 other $ AA161411 reading frame 57 116462 Hs.236828putative helicase 1.5 TM

116470 Hs.83484SRY (sex determining 2.1 TM
AI272141 region Y)-box 4 116575 Hs.6241phosphoinositide-3-kinase,1.5 other AA312572 regulatory su 116637 Hs.92033integrin-linked kinase-associated2.7 other AK001043 serine 116640 Hs.211563B-cell CLUlymphoma 2.3 other 116700 Hs.317589hypothetical protein 1.4 other 116705 Hs.12313hypothetical protein 3.4 other 116732 Hs.165909ESTs, Weakly similar 2.9 other AW152225 to 138022 hypotheti 116926 Hs.290830ESTs 1.7 TM

45 117034 Hs.180324YY1-associatedfactor23.4 TM

117132 Hs.42315p10-binding protein 5.2 ?

117247 gb:yx46f06.s1 Soares 5.5 TM
N21032 melanocyte 2NbHM
Ho 117276 Hs.121806Homo sapiens cDNA 1.5 TM
N71183 FLJ11971 fis, clone HE

117284 Hs.183779Homo sapiens cDNA 2 other AK001701 FLJ10590 fis, clone NT

$0 117367 Hs.42502ESTs 2 other 117368 Hs.90336ATPase, H+transporting,2.1 ?
AI878942 lysosomal (vacu 117382 Hs.40173ESTs 2.7 TM

117412 Hs.42645solute carrier family1.4 other N32536 16 (monocarboxylic 117557 Hs.44532diubiquitin 3.4 TM

117588 Hs.44648ESTs 3.4 ?

117745 Hs.46680CGI-12 protein 3 SS, 117754 Hs.59757zinc finger protein 1.9 other 117879 Hs.303025chromosome 11 open 1.8 other N54706 reading frame 24 117904 Hs.332938hypothetical protein 6 ?

117911 Hs.47125hypothetical protein 1.7 other 117933 Hs.116470hypothetical protein 1.7 other 117983 Hs.47367KIAA1785 protein 5.4 other 118078 Hs.47790EST 5.2 other 118301 Hs.293264ESTs 2.6 other 6S 118429 Hs.74649cytochrome c oxidase 2.5 TM
AA243332 subunit Vlc 118472 Hs.42179bromodomain and PHD 4.1 other AL157545 finger containing, 118488 Hs.50102rapa-2 (rapa gene) 1.2 other 118509 Hs.43228Homo Sapiens cDNA FLJ118351.5other N22617 fis, clone HE

118528 Hs.49397ESTs 7.4?

118656 Hs.293287ESTs 2.5other 118670 Hs.152618ESTs, Moderately similar1.2TM
AA332845 to ZN91 fiUMAN Z

118698 Hs.50187KIAA1287 protein 2.1TM

118737 gb:zq75g09.r1 Stratagene5.2other AA199686 hNT neuron (937 118925 Hs.206832ESTs, Moderately similar1.4other N92293 to ALU8_HUMAN A

118984 Hs.240722ESTs, Moderately similar3.6other AI668709 to ALUB HUMAN A

118986 Hs.125830bladder cancer overexpressed4.9?
AF148713 protein 119206 Hs.293798KIAA1710 protein 1.7TM

119235 Hs.3657activity-dependent 2.2other AW453069 neuroprotective prote 119265 Hs.285363ESTs 1.4?

119279 Hs.48028EST 25.1other 119298 Hs.155478cyclin T2 1.6?
NM_001241 119338 Hs.320836ESTs, Weakly similar 1.3other AI417240 to A47582 B-cell gr 119403 Hs.119908nucleolar protein NOP51NOP586.7TM

119478 Hs.170042ESTs 2.4other 119486 Hs.55513ESTs 2.1other 119513 Empirically selected 1.9other W37933 from AFFX single pr 119601 Hs.91684Homo Sapiens mRNA; 3.7TM
AK000155 cDNA DKFZp6671103 (fr 119602 Hs.233694hypothetical protein 3 other 119676 Hs.57787ESTs 1.4other 119682 Hs.57811ESTs 1.2?

119774 Hs.6298KIAA1151 protein 1.8TM

2S 119780 Hs.191381hypothetical protein 3.1other NM_016625 119789 Hs.50915kallikrein 5 (KLKS; 9.2other BE393948 KLK-L2; stratum com 119805 Hs.43213ESTs, Weakly similar 3.6TM
AJ223810 to IEFS HUMAN TRANS

119818 Hs.58382hypothetical protein 2.5?

119863 Hs.58608Homo sapiens cDNA FLJ142062.7TM
AA081218 fis, clone NT

119905 Hs.119571collagen, type III, 2.6other AW449064 alpha 1 (Ehlers-Danl 119966 Hs.58963ESTs 2.7other 120132 Hs,125019lymphoid nuclear protein1.2other W57554 (LAF-4) mRNA

120206 Hs.91668Homo sapiens clone 45.7other H26735 PP1498 unknown mRNA

120248 Hs.173259uncharacterized bone 1.2other AI924294 marrow protein BM03 120269 Hs.104030ESTs 9.6other 120274 gb:nc02a02.s1 NCI CGAP_Pr34.7other AA177051 Homo Sapiens 120280 gb:zp52g02.s1 Sfratagene2.1other AA190577 HeLa cell s3 93 120296 Hs.299883hypothetical protein 1.9TM

120297 Hs.104072ESTs, Weakly similar 15.2other AA191384 to Z195_HUMAN ZINC

120324 Hs.191643ESTs 5.6?

120325 Hs.104106ESTs 6.5other 120327 Hs.278732hypothetical protein 16.1other 120336 Hs.181165eukaryotic translation3 other N85785 elongation factor 120342 Hs.45068hypofhetical profein 5.8other AW450669 DKFZp434I143 120345 Hs.104158ESTs 4.6SS,TM

120349 Hs.55189hypothetical protein 16.8other 120352 Hs.193172ESTs, Weakly similar 5.1other 806859 to 138022 hypotheti 120356 Hs.296433putative purinergic 28.1TM
AF000545 receptor 120371 Hs.104196EST 12.4?

S0 120382 Hs.38774ESTs 4.1TM

120383 Hs.123122FSH primary response 9.7TM
AL109963 (LRPR1, rat) homolo 120386 Hs.154848hypothetical protein 32.6other AW969665 DKFZp434D0127 120388 Hs.104245ESTs 3.2other 120389 Hs.325572ESTs, Moderately similar21.7other AW967985 to ALU7 HUMAN A

120396 Hs.79306eukaryotictranslationinitiationfactor12.5other 120404 Hs.96427KIAA1013 protein 7.3other 120418 Hs.26613Homo Sapiens mRNA; 11.4other AW966893 cDNA DKFZp586F1323 (f 120423 Hs.18978Homo Sapiens cDNA: 1.9other AA236453 FLJ22822 fis, clone K

120472 gb:wq05c02.x1 NCI_CGAP_Kidl219.4other A1950087 Homo sapien 120473 Hs.269988ESTs 5.5?

120484 Hs.96473EST 10.4?

120504 gb:zr84d10.s1 Soares_NhHMPu_S14 ?
AA256837 Homo sapi 120509 Hs.96545ESTs 9.4other 120520 Hs.161731EST 2.4other 120535 Hs.96547ESTs 2.5?

120551 Hs.111407Homo Sapiens, clone 5.3other AA279160 IMAGE:3613029, mRNA, 120570 Hs.271445ESTs, Weakly similar 14.4?
AA280679 to ALU1 HUMAN ALU
S

120582 Hs.284228ZNF135-like protein 10.2?

120590 Hs.125790leucine-rich repeat-containing2.2 ?

120596 Hs.237323N-acetylglucosamine-phosphate7.6 other AA282074 mutase 120619 Hs.111471ESTs 2.5 other $ 120624 Hs.173518M-phase phosphoprotein52 other AW407987 homolog 120639 gb:zs56f05.s1 NCI_CGAP2.4 other AA286942 GCB1 Homo Sapiens 120648 Hs.140309Homo Sapiens, clone 5 other AA287095 IMAGE:3677194, mRNA, 120653 Hs.191649ESTs 2.2 other 120668 Hs.1123186.2 kd protein 2.2 TM

1 120669 Hs.109909ESTs 1.9 TM
~ BE536739 120695 gb:oq30a04.s1 NGI_CGAP_GC446.8TM
AA976503 Homo sapiens 120696 Hs.97249ESTs 2.5 other 120713 Hs.96557Homo Sapiens cDNA 6 other AW449855 FLJ12727 fis, clone NT

120718 Hs.97296ESTs 2.9 other 1$ 120750 Hs.96693ESTs, Moderately similar7.1 SS, AI191410 to 2109260A B c 120774 Hs.193985ESTs 7.9 other 120807 Hs.30002SH3-containing protein7 TM
AA346385 SH3GLB2; KIAA1848 120809 gb:EST52657 Fetal 4.5 other AA346495 heart II Homo Sapiens 120938 Hs.104632EST 4.5 ?

120977 Hs.97600ESTs 4.5 other 120984 Hs.99052ESTs 5.6 other 120985 Hs.97592ESTs 1.3 other 121011 Hs.97608EST 3,2 other 121026 Hs.165295ESTs 3.6 other ~$ 121081 Hs.186749ESTs, Highly similar 5.5 other AA398721 to 137550 mismatch 121133 Hs.97032ESTs 3.8 other 121176 Hs.97774ESTs 1.7 TM

121223 Hs.97169ESTs, Weakly similar 2.9 other A1002110 to dJ667H12.2.1 [H.

121320 Hs.301927c6.1A 1.9 other 121340 Hs.97910Homo sapiens cDNA 3.5 other AW956981 FLJ13383 fis, clone PL

121408 Hs.98019EST 6.1 ?

121439 Hs.98076ESTs, Weakly similar 7.5 other AA410190 to A47582 B-cell gr 121450 Hs.105362Homo sapiens, clone 7.1 other AA406430 MGC:18257, mRNA, com 121452 Hs.292882ESTs 1.8 other 3 121455 Hs.15165retinoic acid induced10.5other $ H58306 14 121457 Hs.144502hypothetical protein 3.5 TM

121496 Hs.97900ESTs 14.4other 121505 Hs.194417ESTs 13.1other 121508 Hs.97887ESTs 28 other 121513 Hs.181510ESTs 6.3 other 121514 gb:zt69b02.s1 Soares_testis_NHT2.7 SS, AA412112 Homo sap 121549 Hs.98142EST 7.5 ?

121558 gb:zt95g12.s1 Soares 2.8 other AA412497 testis_NHT Homo sap 121577 Hs.98096EST 3.5 ?

4$ 121581 gb:zu05c10.s1 Soares_testis_NHT6.2 TM
AA416568 Homo sap 121589 Hs.89718spermine synthase 4 other 121594 Hs.98247ESTs 2.2 other 121622 Hs.126065ESTs 4.3 TM

121655 Hs.178072Homo Sapiens mRNA; 7.9 other AA421537 cDNA DKFZp434B1023 (f $0 121682 Hs.86043Homo sapiens cDNA 2 other AA418160 FLJ13558 fis, clone PL

121690 Hs.110286ESTs 4.7 ?

121706 Hs.154145hypothetical protein 12.7other 121714 Hs.98269Homo Sapiens cDNA 8.3 ?
AA419225 FLJ11953 fis, clone HE

121729 Hs.98325ESTs 1.8 TM

$$ 121731 Hs.180744ESTs 4.1 TM

121744 Hs.97514ESTs 7.1 5S, 121748 Hs.234545hypothetical protein 19.5other 121773 Hs.158654KIAA1196 protein 8 ocher 121775 Hs.161008ESTs 1.7 other 121776 Hs.125133hypothetical protein 6.7~other 121786 Hs.98376ESTs 10.5other 121832 Hs.98434ESTs 5.9 other 121836 Hs.218289ESTs 3.9 other 121839 Hs.191606ESTs, Highly similar 5 other AA425691 to KIAA1048 protein 6$ 121842 Hs.104865serinelthreonine kinase2.7 ?

121847 Hs.2799cartilage linking 2.3 other AA446628 protein 1 121871 Hs.293044ESTs 2.9 TM

121882 Hs.98459ESTs 5 other AA426376 , 121911 gb:zw50f02.s1 Soares 7.3 TM
AA427950 tofai_fetus_Nb2HF8_ 121915 Hs.223405ESTs, Moderately similar2.5 other AA428179 to A46010 X-lin 121935 Hs.98611EST 2.3 other $ 121983 Hs.180191hypothetical protein 3.4 other 121985 Hs.299214Homo sapiens, clone 11.4other AI862570 IMAGE:2822295, mRNA, 121995 Hs.3532nemo-like kinase 3.8 ?

121999 Hs.98668EST 6.5 other 122009 Hs.160822Homo sapiens cDNA: 2.2 other AW292763 FLJ20863 fis, clone A

1 122013 Hs.98706ESTs 6.6 other ~ AA431085 122036 Hs.271963ESTs, Weakly similar 13.1other W92142 to ALU5_HUMAN ALU
S

122050 Hs.166109ELAV (embryonic lethal,9.1 other AI453076 abnormal vision, 122060 Hs.98750EST 13.1?

122114 Hs.104921ESTs 1.5 other 1$ 122188 gb:zt80d01.r1 Soares_testis_NHT3.4 other AA398838 Homo sap 122204 Hs.98842EST 5.6 other 122246 Hs.29417HCF-binding transcription5.2 other AA329550 factor Zhangfe 122257 Hs.98899ESTs 5.6 other 122302 Hs.104947ESTs ~ 5.8 other 122341 Hs.99010hypothetical protein 2 other AW601969 FLJ22263 similar to 122356 Hs.98390ESTs 7.4 SS,TM

122369 Hs.303222ESTs 12.2?

122371 Hs.178222ESTs 5 ?

122372 Hs.336677EST 7.8 ?

2$ 122378 Hs.21356hypothetical protein 2.5 ?
AB032948 DKFZp762K2015 122405 Hs.303223EST 2.8 TM

122412 Hs.119316ESTs 7.4 other 122415 Hs.99088EST 1.9 other 122418 Hs.99090ESTs, Moderately similar6.9 ?
AA446966 to similar to K

122440 Hs.9460Homo sapiens mRNA; 2.6 other AW505139 cDNA DKFZp547C244 (fr 122446 Hs.99123EST 1.8 TM

122448 Hs.99127EST 3.5 other 122458 Hs.104980ESTs 1.5 other 122460 Hs.99148ESTs, Weakly similarto9.7 other AW418788 S43569 R01H10.6 3 122464 Hs.99152EST 4.9 other $ AA448158 122490 Hs.238151EST 6.2 ?

122492 Hs.104990ESTs 5.5 other 122502 Hs.234863Homo Sapiens cDNA 1.3 other AA204969 FLJ12082 fis, clone HE

122510 Hs.99195ESTs 11.2?

122530 Hs.40368adaptor-related protein10.1other AW959741 complex 1, sigma 122547 Hs.164589ESTs 2.5 SS, 122555 Hs.293858ESTs 1.9 other 122570 Hs.262907ESTs 9.5 other 122572 Hs.99287EST 11 ?

4$ 122586 Hs.99303Homo sapiens cDNA 3.4 other AK001910 FLJ11048 fis, clone PL

122587 Hs.6968KIAA1460 protein 2 other 122598 Hs.99329ESTs 1.7 ?

122599 Hs.99330hypothetical protein 4.4 ?

122602 Hs.301960ESTs 4.7 other $0 122607 Hs.98023ESTs 61.5other 122614 Hs.99339EST 10.7?

122616 Hs.161873ESTs 107.3?

122617 Hs.148135serinelthreonine kinase121.4other 122618 gb:zx48e06.s1 Soares_testis_NHT31.1SS, AA453641 Homo sap $$ 122622 Hs.144802ESTs 5.6 other 122717 Hs.178358ESTs 8.5 SS, 122762 Hs.105119ESTs 10.4other 122829 Hs.99500ESTs 81.8?

122834 Hs.99545Homo Sapiens cDNA 3.7 ?
AA461492 FLJ10658 fis, clone NT

122836 Hs.290996ESTs 4.6 other 122837 Hs.293565ESTs, Weakly similar 2.7 TM
AA461509 to putative p150 [H

122838 Hs.334386ESTs 75.3other 122854 Hs.9625NIMA (never in mitosis7.8 other AA600235 gene a)-related k 122856 Hs.75367Sro-like-adapter 5.8 other 6$ 122861 Hs.119394ESTs 1.3 other 122866 Hs.283705ESTs 4.2 other 122868 Hs.115541Janus kinase 2 (a 5.3 other AF005216 protein tyrosine kinas 122870 AW576312Hs.318722Homo sapiens cDNA: 9.9 ?
FLJ21766 fis, clone C

122872 AW081394Hs.97103ESTs 5.3 other 122879 AA769410Hs.128654ESTs 13.9other 122907 AA470074Hs.169896ESTs 11.5other $ 122916 AA470140Hs.229170EST 1.7 TM

122981 AA478951Hs.105629ESTs 5 other 123013 AW968324Hs.17384ESTs 15.4other 123016 AW338067Hs.323231Homo sapiens cDNA 2.8 other FLJ11946 fis, clone HE

123034 AL359571Hs.44054ninein (GSK3B interacting8.7 other protein) 10123072 AI382600Hs.104308ESTs, Weakly similar 8.8 other to KIAA1395 protein 123082 AA485360Hs.105661ESTs 4 ?

123088 A1343652Hs.105667ESTs 3.8 other 123110 AA486256Hs.193510EST 7.4 other 123114 BE304942Hs.265848myomegalin 2.8 ?

1$123131 T52027Hs.271795ESTs, Weakly similar 2.4 other to 138022 hypotheti 123132 A1061582Hs.324179Homo sapiens cDNA 15.6TM
FLJ12371 fis, clone MA

123136 AW451999Hs.194024ESTs 5.2 other 123149 AI734179Hs.105676ESTs 23.8TM

123152 AW601773Hs.270259ESTs 5.2 other 123258 AA490929Hs.105274ESTs, Weakly similarto9.3 ?

123315 AA496369 gb:zv37d10.s1 Soares 4.2 TM
ovary tumor NbHOT
H

123369 AA504757Hs.105738ESTs 7 other 123394 AA731404Hs.105510ESTs 3.7 other 123433 AW450922Hs.112478ESTs 3.8 other 2$123466 AA599042Hs.112503EST 7.4 other 123470 AW303285Hs.303632Human DNA sequence 3.5 other from clone RP11-110H4 123471 A8021644Hs.197219zinc finger protein 5.2 ?

14 (KOX 6) 123475 BE439553Hs.250528Homo sapiens, clone 1.7 other IMAGE:4098694, mRNA, 123482 N95059Hs.55098ESTs 1.6 other 3 123486 BE019072Hs.334802Homo sapiens cDNA 2.4 other ~ FLJ14680 fis, clone NT

123508 AW380388Hs.155546KIAA1080 protein; 2.2 TM
Golgi-associated, gamm 123615 AA609170 gb:af12a12.s1 Soares 7.9 other testis_NHT Homo sap 123619 AA602964 gb:no97c02.s1 NCI_CGAP2.8 other P~1 Homo sapiens 123658 AA609364 gb:zu71d09.s1 Soares_testis_NHT1.7 ?
Homo sap 3 123674 AI269609Hs.105187kinesin protein 9 5.7 ?
$ gene 123735 NM_013241Hs.95231FH11FH2 domain-containing10 other protein 123738 AA609891Hs.112777EST 5.2 other 123753 AA609955Hs.234961Huntingtin interacting30.6TM
protein E

123804 AA620464Hs.261915EST, Weakly similar 2.1 other to S65657 alpha-1 C-a 123811 AA620586 gb:ae60g05.s1 Stratagene2.7 other lung carcinoma 123951 AB012922Hs.173043metastasis-associated6.3 ?
1-like 1 123983 AJ272267Hs.146178choline dehydrogenase4.4 other 124001 L42542Hs.75447ralA binding protein 7.1 ?

124006 AI147155Hs.270016ESTs 8.3 SS, 4$124070 AI950314Hs.154762HIV-1 rev binding 3.8 other protein 2 124074 H05635Hs.294030topoisomerase-related1.2 SS, function protein 124178 BE463721Hs.97101putative G protein-coupled3.2 ?
receptor 124203 AA372796Hs.269339ESTs, Weakly similar 5.7 other to AF1613561 HSPCO

124352 AA640891Hs.102406ESTs 3.1 TM

$~124375 D87454Hs.192966KIAA0265 protein 3.5 other 124385 AI267847 gb:aq49a10.x1 Stanley57.1?
Frontal NB pool 2 124390 AA317338Hs.7535COBW-like protein 2.8 other 124391 AF155099Hs.279780NY-REN-18 antigen 7.1 other ~

124417 N34059 gb:yv28h09.s1 Soares 3.3 other fetal liver spleen $$124428 H13540Hs.82202ribosomal protein 2.9 other 124440 AA532519Hs.129043Human DNA sequence 7.9 other from clone 989H11 on 124466 810084Hs.113319kinesin heavy chain 2.6 TM
member 2 124482 N53935 gb:yv59d09.s1 Soares 7.9 TM
fetal liver spleen 124498 H79433Hs.268997ESTs 7.8 other 60124515 AA669097Hs.109370ESTs 3.3 other 124608 N71076Hs.102800ESTs, Weakly similarto4.6 ?
neuronal thread 124631 NM_014053Hs.270594FLVCR protein 3.2 other 124634 AI765123Hs.143671Homo sapiens cDNA 5.8 other FLJ13533 fis, clone PL

124637 AA160474Hs.75798hypothetical protein 9.3 other 6$124642 AW968856Hs.278569sorting nexin 17 3.5 other 124649 N92593Hs.313054ESTs 6.1 TM

124661 848170Hs.78436EphB1 5.6 other 124683 AA381661Hs.119878ESTs, Weakly similar 7.9 TM
to M3K9_HUMAN MITOG

124712 809166Hs.191148ESTs 5.7 other 124735 822952Hs.268685ESTs 11.3?

124761 AA374756Hs.93560Homo sapiens mRNA 9 other for KIAA1771 protein, $ 124768 AW368528Hs.100855ESTs 8.3 other 124775 841772Hs.100878ESTs 4.9 other 124777 841933Hs.140237ESTs, Weakly similar 2.8 other to ALU1 HUMAN ALU
S

124788 843543Hs.100912Homo sapiens cDNA: 5.1 other FLJ22726 fis, clone H

124809 AL355722Hs.106875Homo Sapiens EST from4.2 other clone 35214, full 1 124811 846068Hs.288912hypothetical protein 14.2other ~ FLJ22604 124812 847948Hs.188732ESTs 7.9 other 124822 AA418160Hs.86043Homo sap!ens cDNA 6.6 other FLJ13558 fis, clone PL

124825 AA501669Hs.336693ESTs 2.3 SS,TM

124833 AW975868Hs.294100ESTs 2.7 SS,TM

1$124857 863652Hs.137190ESTs 2.3 other 124860 865763Hs.101477EST 23.9?

124863 AI382555Hs.127950bromodomain-containing2 other 124876 AF135422Hs.27059GDP-mannose pyrophosphorylase4.4 SS, A

124878 BE397530Hs.288057hypothetical protein 2.7 other 124902 H37941Hs.101883ESTs 5.7 other 124903 AW296713Hs.221441ESTs 32.4other 124930 A1076343Hs.173939ESTs, Weakly similar 22.8other to ALUB HUMAN !!!!

124942 899978Hs.268892ESTs, Moderately similar6.1 other to 834087 hypot 124958 A1078645Hs.431murine leukemia viral1.9 other (bmi-1) oncogene h ~$124980 T40841Hs.98681ESTs 4.5 ?

125002 T59338Hs.269463ESTs, Weakly similar 4.9 other to ALU1 HUMAN ALU
S

125047 T79815Hs.279793ESTs 5 ?

125051 T79956Hs.100588EST 135.3?

125056 T81310Hs.100592ESTs 5.4 other 30125101 A1472068Hs.286236KIAA1856 protein 5.6 other 125113 T96595Hs.302270ESTs, Weakly similar 1.8 other to ALUF_HUMAN !!!!

125115 T97341 gb:ye57e05.s1 Soaresfetal9.6 ?
liver spleen 125125 AI222382Hs.240767Human DNA sequence 1.5 TM
from clone RP1-12614 125147 W38150 Empirically selected 1.7 ?
from AFFX single pr 125161 W44657Hs.144232EST 10.7?

125249 AA630863Hs.131375ESTs, Moderately similar1.3 other to ALUB HUMAN !

125255 AF098162Hs.118631timeless (Drosophila)9.4 other homolog 125279 AW401809Hs.4779KIAA1150 protein 1.5 ?

125280 AI123705Hs.106932ESTs 8.1 ?

4~125298 AW972542Hs.289008Homo Sapiens cDNA: 1.5 other FLJ21814 fis, clone H

125660 AW292171Hs.23978scaffold attachment 5.9 other factor B

125827 NM Hs.97496YY1 transcription 1.2 ?
003403 factor 125891 U29589Hs.7138cholinergic receptor,6.5 ?
muscarinic 3 126005 AW409701Hs.1578baculoviral IAP repeat-contain!ng14.3?
5 (sur 4$126202 AA157632Hs.272630vacuolar proton pump 2.5 SS, delta polypeptide 126695 AA643322Hs.172028a disintegrin and 9.1 SS,TM
metalloproteinase doma 127050 AW411066Hs.274351CGI-89 protein 17 other 127274 AW966158Hs.58582Homo Sapiens cDNA 12.8other FLJ12789 fis, clone NT

128355 AW293012Hs.161623ESTs 7.4 SS, $~128493 D87466Hs.240112KIAA0276 protein 3.1 TM

128522 BE173977Hs.10098putative nucleolar 9.4 other RNA helicase 128527 AA504583Hs.101047transcript!on factor 1.5 other 3 (E2A immunoglobul 128528 839234Hs.251699ESTs, Weaklysim!larto2.8 other IDN4-GGTR14 [H.s 128595 U31875Hs.272499short-chain alcohol 12.1TM
dehydrogenase family $$128599 NM_015366Hs.102336Rho GTPase activating2.4 ?
protein 8 128604 AI879099Hs.102397GIOT-3 for gonadotropin1.3 other inducible transc 128608 BE267994Hs.102419zinc finger protein 7.2 other 128625 AB037841Hs.102652hypothetical protein 1.3 other 128629 AL096748Hs.102708DKFZP434A043 protein 3.2 other 128639 AW582962Hs.102897CGI-47 protein 2 TM

128656 AA458542Hs.10326coatomer protein complex,1.4 other subunit epsilo 128658 BE397354Hs.324830diptheria toxin resistance2.5 other protein requi 128670 AA975486Hs.103441Homo sapiens, Similar7.1 ?
to RIKEN cDNA 1700 128691 W27939Hs.103834hypothetical protein 7.8 ?

6$128696 BE081143Hs.225977nuclear receptor coactivator3.8 other 128700 Y15221Hs.103982small inducible cytokine1.6 other subfamily B (Cy 128714 T85231Hs.179661tubulin, beta 5 7.8 other 128717 AK001564Hs.104222hypothetical protein 5.5 other 128733 BE147740Hs.104558ESTs, Moderately similar2.7 TM
to 138022 hypot 128737 AF292100Hs.104613RP42 homolog 2.8 TM

128742 AA307211Hs.251531proteasome (prosome, 4.5 ?
macropain) subunit, $ 128746 AI470163Hs.323342actin related protein2.2 other 213 complex, subun 128747 AB027249Hs.104741PDZ-binding kinase; 2.8 other T-cell originated pr 128772 BE302796Hs.105097thymidine kinase 1, 5.4 other soluble 128781 N71826Hs.105465small nuclear dbonucleoprotein53.9TM
polypept 128797 NM Hs.105927stem cell growth factor,13.3other 002975 lymphocyte secr 10_ Hs.106061RD RNA-binding protein2.6 other 128814 AW248431Hs.256526nuclear prelamin A 2.2 other recognition factor 128830 BE281170Hs.106357valosin-containing 6 other protein 128835 AK001731Hs.106390Homo sapiens mRNA; 1.6 SS, cDNA DKFZp586H0924 (f 128854 BE159181Hs.168232hypothetical protein 2.3 other 1$128871 AF189723Hs.106778ATPase, Ca++transporting,1.5 ?
type 2C, memb 128906 857988Hs.10706epithelial protein 4.8 other lost in neoplasm beta 128920 AA622037Hs.166468programmed cell death1.4 other 128925 867419Hs.21851Homo Sapiens cDNA 1.9 other FLJ12900 fis, clone NT

128946 Y13153Hs.107318kynurenine 3-moncoxygenase7.3 ?
(kynurenine 3 128949 AA009647Hs.8850a disintegrin and 2.5 other metalloproteinase doma 128959 AI580127Hs.107381hypothetical protein 1.3 other 128965 AW150697Hs.107418ESTs 1.4 ?

128970 AI375672Hs.165028ESTs 1.3 other 128975 BE560779Hs.284233NICE-5 protein 14 other 2$128979 AW271217Hs.281434Homo Sapiens cDNA 1.6 TM
FLJ14028 fis, clone HE

128995 AI816224Hs.107747DKFZP566C243 protein 1.9 other 129019 AI950087 gb:wq05c02.x1 NCI_CGAP_Kidl22.9 other Homo sapien 129021 AL044675Hs.173081KIAA0530 protein 3.8 other 129032 880088Hs.108104ubiquitin-conjugating3.4 other enzyme E2L 3 30129076 AW296806Hs.326234ESTs, Highly similar 5 other to T46422 hypotheti 129078 AI351010Hs.102267lysosomal 2.1 other 129088 AA744610Hs.194431palladin 17.1other 129095 L12350Hs.108623thrombospondin 2 2.7 other 129096 AA463189Hs.288906WW Domain-Containing 20.9TM
Gene 3 129097 8E243933Hs.108642zinc finger, protein 3 other $ 22 (KOX 15) 129099 AF146074Hs.108660ATP-binding cassette,5.8 TM
sub-family C (CFTR

129136 W93048Hs.250723hypothetical protein 6 other 129149 AA356620Hs.108947KIAA0050 gene product6.4 TM

129172 AW162916Hs.241576hypothetical protein 1.8 TM

129192 AA286914Hs.183299ESTs 2.1 ?

129194 AA150797Hs.109276latexin protein 3.3 SS,TM

129198 N57532Hs.109315KIAA1415 protein 5.9 other 129207 AI934365Hs.109439osteoglycin (osteoinductive8.1 other factor, mime 129228 U40714Hs.239307tyrosyl-tRNA synthetase2.9 other 4$129229 AF013758Hs.109643polyadenylate binding3.3 ?
protein-interac6n 129254 AA252468Hs.1098DKFZp434J1813 protein2.6 SS,TM

129255 AI961727Hs.109804H1 histone family, 7.4 other member X

129288 W26392Hs.110080ESTs, Weakly similarto9.6 other S13495 pregnancy 129296 A1051967Hs.110122ESTs 1.2 ofher $0129323 AA287239Hs.5518Homo Sapiens cDNA 5.2 other FLJ11311 fis, clone PL

129340 H75334Hs.11050F-box only protein 4.7 SS, 129347 BE614192Hs.279869melanoma-associated 7.7 TM
antigen recognised b 129362 U30246Hs.110736solute tamer family 6.7 TM
12 (sodiumlpotassi 129366 BE220806Hs.184697Homo sapiens done 8.6 SS, 23785 mRNA sequence $$129370 AI686379Hs.110796SAR1 protein 1.4 TM

129372 NM_016039Hs.110803CGI-99 protein 2 other 129403 AF149785Hs.111126pituitary tumor-transforming7.5 other 1 interacti 129404 AI267700Hs.317584ESTs 5.1 other 129423 AA204686Hs.234149hypothetical protein 10.2other 129482 AA188185Hs.289043spindlin 6.8 other 129513 AW843633Hs.306163hypothetical protein 7.1 SS, 129515 AF255303Hs.112227membrane-associated 2.5 other nucleic acid binding 129527 AA769221Hs.270847delta-tubulin 3.2 other 129559 W01296Hs.11360hypothetical protein 7.5 other 6$129560 AA317841Hs.7845hypothetical protein 6.8 other 129570 AI923097Hs.11441chromosome 1 open 2.1 other reading frame 8 129575 F08282Hs.278428progestin induced 1.6 other protein 16$

129587 Hs.11506Human clone 23589 6.8 other H14718 mRNA sequence 129588 Hs.301862postmeiotic segregation1.4 TM
BE408300 increased 2-like 129591 Hs.179898HSPC055 protein 7.4 other 129594 Hs.36989coagulation factor 9 ?
AW403724 VII (serum prothrombi 129596 Hs.115521REV3 (yeast homology-like,1.6 other AF035537 catalytic sub 129628 Hs.1174cyclin-dependent kinase2.2 other U38945 inhibitor 2A (me 129649 Hs.16488calreticulin 3.3 other 129675 Hs.172180KIAA0440 protein 13.4other NM_015556 129680 gb:Human chromogranin14.1?
U03749 A (CHGA) gene, pro 1 129689 Hs.77873B7 homolog 3 2.6 other ~ AW748482 129702 Hs.12035ESTs, Weakly similar 7.5 TM
AI304966 to 138022 hypotheti 129720 Hs.12152APMCF1 protein 2 other 129721 Hs.211539eukaryotic translation1.7 TM
NM_001415 initiation factor 129778 Hs.12457hypothetical protein 1.8 other 1$ 129779 Hs.12460Homo sapiens clone 5.5 TM
AA394090 23870 mRNA sequence 129800 Hs.12540lysosomal 1.7 ?

129806 Hs.173373KIAA0931 protein 1.2 other 129815 Hs.26498hypothetical protein 3.1 other 129840 Hs.12820SnRNP assembly defective1.8 other NM_006590 1 homolog 129861 Hs.85963DKFZP564M182 protein 2.3 other 129864 Hs.129914runt-related transcription1.7 SS, AI393237 factor 1 (acu 129869 Hs.13015hypothetical protein 2.8 TM
AI222069 similar to mouse Dn 129945 Hs.165998PAI-1 mRNA-binding 1.8 other BE514376 protein 129953 Hs.13740ESTs 2.5 other 25 129972 Hs.180628dynamin 1-like 1.8 ?

129983 Hs.132390zinc finger protein 1.3 other U09848 36 (KOX 18) 130010 Hs.142838nucleolar phosphoprotein1.6 other AA301116 Nopp34 130081 Hs.14713ESTs 4.1 other 130082 Hs.1473gastrin-releasing 1.9 other S73265 peptide 130097 Hs.14845forkhead box 03A 2.8 other 130100 Hs.14891hypothetical protein 2.3 other 130111 Hs.149846integrin, beta 5 2.3 other 130112 Hs.180610splicing factor prolinelglutamine3 other AA916785 rich ( 130128 Hs.150477Wemersyndrome 1.8 other 35 130135 Hs.21635tubulin, gamma 1 6.1 other 130211 Hs.23703ESTs, Moderately similar1.6 other NM_003358 to CEGT_HUMAN C

130212 Hs.152629KIAA0179 protein 1.3 other 130236 Hs.51957splicing factor, argininelserine-rich2 other 885367 2, 130241 Hs.153203MyoD family inhibitor3.2 other 130242 Hs.153221synovial sarcoma, 5.4 ?
X79201 translocated to X
chro 130249 Hs.322852GAS2-related on chromosome4.9 other 130263 Hs.153704NIMA (never in mitosis1.4 other NM_002497 gene a)-related k 130287 Hs.154036tumor suppressing 2.6 other AA479005 subtransferable candid 130310 Hs.154248amyotrophic lateral 6.3 other AB011121 sclerosis 2 (juvenil 4$ 130353 Hs.172210MUF1 protein 6.2 other 130356 Hs.155017nuclear receptor interacting2.4 other AF127577 protein 1 130357 Hs.155020putative methyltransferase3.5 TM

130359 Hs.277401bromodomain adjacent 8.5 other NM_013449 to zinc finger doma 130367 Hs.8768hypothetical protein 1.4 other 130372 Hs.5011RNA binding motif 3.3 ?
AI077464 protein 9 130393 Hs.155291KIAA0005 gene product1.8 other 130399 Hs.155356hypothetical protein 3.4 other AW374106 MGC2840 similar to 130407 Hs.334727hypothetical protein 2.3 other 130409 Hs.155419BCL2-interactingkiller(apoptosis-induc2.7 TM
NM_001197 $$ 130419 Hs.155489NS1-associated protein1.8 other 130441 Hs.155637protein kinase, DNA-activated,2.3 other U63630 catalytic 130448 Hs.15589PPAR binding protein 4 TM

130455 Hs.155956N-acetylUansferase 33.6?
D90041 1 (arylamine N-acety 130485 Hs.180779H2B histone family, 5 other BE245851 member B

60 130487 Hs.77613ataxia telangiectasia4.4 other U49844 and Rad3 related 130498 Hs.180446karyopherin (importin)1.6 SS,TM
L38951 beta 1 130503 Hs.295112KIAA0618 gene product16.1other 130511 Hs.1584cartilage oligomeric 6.1 other L32137 matrix protein (pse 130526 Hs.15929hypothetical protein 2.1 other 65 130544 Hs.4310eukaryotic translation1.5 other AA321238 initiation factor 130553 Hs.252587pituitary tumor-transforming14.4?

130556 Hs.15977Empirically selected 4.8 other AI907018 from AFFX single pr 130567 AA383092Hs.1608replication protein 8 other A3 (14kD) 130568 AA232119Hs.16085putative G-protein 3.4 other coupled receptor 130574 AF083208Hs.16178apoptosis antagonizing1.2 other transcription fac 130598 AL042210Hs.16493hypothetical protein 1.4 other DKFZp762N2316; KIAA

130601 AA609738Hs.16525ESTs 1.5 TM

130614 AI354355Hs.16697down-regulator of 1.3 other transcription 1, TBP-b 130617 M90516Hs.1674glutamine-fructose-6-phosphate12.1TM
transamin 130618 AA383439Hs.16758Spir-1 protein 15.9other 130667 BE246961Hs.17639Homo Sapiens ubiquitin13.9other protein ligase (U

1 130674 AL048842Hs.194019attractin 1.5 other ~

130675 AA442233Hs.17731hypothetical protein 5.4 other 130692 AA652501Hs.13561hypothetical protein 5 other 130693 868537Hs.17962ESTs 2 other 130712 AJ271881Hs.279762bromodomain-containing1.8 TM

15130714 AI348274Hs.18212DNA segment on chromosome2 TM
X (unique) 987 130730 AB007920Hs.18586KIAA0451 gene product3.8 ?

130744 H59696Hs.18747POP7 (processing of 3.2 ?
precursor, S. cerevi 130751 AF052105Hs.18879chromosome 12 open 1.4 other reading frame 130757 AL036067Hs.18925protein x 0001 5.7 other 130768 AF258627Hs.211562ATP-binding cassette,5.2 ?
sub-family A (ABC1 130789 AK000355Hs.8899sirtuin (silent mating1.6 other type information 130836 J05068Hs.2012transcobalamin I (vitamin15.75S, B12 binding pr 130841 AL157468Hs.325825Homo Sapiens cDNA 2.8 other FLJ20848 fis, clone AD

130843 AA447492Hs.20183ESTs, Weakly similar 1.5 other to AF1647931 prote 130844 076248Hs.20191seven in absentia 3.5 other (Drosophila) homolog 130855 AJ243706Hs.143323putative DNAlchromatin1.7 other binding motif 130861 NM_016578Hs.20509HBV pX associated 1.9 other protein-8 130879 NM_003416Hs.2076zinc finger protein 1.4 other 7 (KOX 4, clone HF.1 130880 BE514434Hs.20830kinesin-like 2 2.1 TM

130892 AL120837Hs.20993high-glucose-regulated2.5 other protein 8 130898 AB033078Hs.186613sphingosine-1-phosphate1.7 other lyase 1 130911 BE409769Hs.21189DnaJ (Hsp40) homolog,1.8 other subfamily A, membe 130919 N79110Hs.21276collagen, type IV, 2.3 TM
alpha 3 (Goodpasture 130944 BE382657Hs.21486signal transducer 5.4 other and activator of traps 35130971 N39842Hs.301444KIAA1673 2.2 SS, 130993 T97401Hs.21929ESTs 1.6 other 131005 AV65830$Hs.2210thyroid hormone receptor1.6 ?
interactor 3 131028 AI879165Hs.2227CCAATIenhancer binding1.2 other protein (CIEBP), 131042 AI826288Hs.171637hypothetical protein 1.6 other 131046 AA321649Hs.2248small inducible cytokine7.4 ?
subfamily B (Cy 131060 AA194422Hs.22564myosin VI 5.1 other 131070 N53344Hs.22607ESTs 7.1 other 131076 AA749230Hs.26433dolichyl-phosphate 2.1 TM
(UDP-N-acetylglucosam 131099 AL133353Hs.226581COX15 (yeast) homolog,7.1 other cytochrome c oxid 45131174 NM Hs.29131nuclear receptor coactivator1.9 ?

131185 BE280074Hs.23960cyclin B1 5.8 ?

131206 AW138839Hs.24210ESTs 2 other 131213 AA885699Hs.24332CGI-26 protein 7.1 TM

131225 H62087Hs.31659thyroid hormone receptor-associated7.6 ?
prot $0131231 N47468Hs.59757zinc finger protein 2.9 other 131233 D89053Hs.268012fatty-acid-Coenzyme 3.5 other A ligase, long-chain 131243 AW383256Hs.24752spectrin SH3 domain 2.8 ?
binding protein 1 131245 AL080080Hs.24766thioredoxin domain-containing2.8 SS,TM

131247 AL043100Hs.326190fatty acid amide hydrolase5.6 other S 131281 AA251716Hs.25227ESTs 5.8 other $

131283 X80038Hs.339713Homo Sapiens clone 1.3 other F19374 APO E-C2 gene 131305 AV656017Hs.184325CGI-76 protein 5 ?

131320 AA505691Hs.145696splicing factor (CC1.3)1.8 TM

131339 AF058696Hs.25812Nijmegen breakage 2.6 other syndrome 1 (nibrin) 131375 AW293165Hs.143134ESTs 5.4 other 131390 BE269388Hs.182698mitochondria) ribosomal5.3 other protein L20 131410 BE259110Hs.279836HSPC166 protein 2.2 other 131412 NIv~012247Hs.124027SELENOPHOSPHATE SYNTHETASE 2 ; Human selen 131429 AL046302Hs.26750hypothetical protein 1.4 other 6$131458 BE297567Hs.27047hypothetical protein 1.7 other 131475 AA992841Hs.27263KIAA1458 protein 2 other 131501 AV661958Hs.8207GK001 protein 2.6 other 131511 Hs.27865Homo Sapiens cDNA: 2 other AA732153 FLJ21333 fis, clone C

131528 Hs.28309UDP-glucose dehydrogenase1.6TM

131532 Hs.28393hypothetical protein 7.4other 131543 Hs.41639programmed cell death 2.2other 131544 Hs.28555programmed cell death 2.1other AL355715 9 (PDCD9) 131562 Hs.28777H2A histone family, 1.7other NM_003512 member L

131564 Hs.28792Homo sapiens cDNA FLJ110415.2other T93500 fis, clone PL

131569 Hs.271623nucleopodn 50kD 5 other 131618 Hs.29645Homo Sapiens mRNA; 1.8other BE393822 cDNA DKFZp761 C029 (fr 1 131622 Hs.29692Homo Sapiens cDNA FLJ114361.3other ~ 878195 fis, clone HE

131623 Hs.29716hypothetical protein 2.2TM

131643 Hs.30026HSPC182 protein 3 other 131653 Hs.30164ESTs 1.3other AW960597 ' 131656 Hs.30209KIAA0854 protein 2.8other 15 131669 Hs.3041uracil-DNA glycosylase2.8other 131692 Hs.30736KIAA0124 protein 5.6?

131714 Hs.31016putative DNA binding 2.9?
AA642831 protein 131722 Hs.311phosphoribosyl pyrophosphate3.4other D13757 amidotransf 131737 Hs.31323inhibitor of kappa 3.9?
AK001641 light polypeptide gen 131763 Hs.317topoisomerase (DNA) 3.4other 131772 Hs.170980KIAA0948 protein 25.5other 131787 Hs.196275KIAA0240 protein 2.4SS, 131793 Hs.32246Homo Sapiens cDNA FLJ146568 TM
AW966127 fis, clone NT

131795 Hs.32317high-mobility group 1.5other 2$ 131798 Hs.301449adenovirus 5 E1A binding4.2other X86098 protein 131817 Hs.3280caspase 6, apoptosis-related4.3other U20536 cysteine pr 131824 Hs.32935TATA box binding protein3.5other U28838 (TBP)-associate 131850 Hs.33184ESTs 5.2TM

131878 Hs.6101hypothetical protein 5.9other 131885 Hs.3402ESTs 13.7other 131900 Hs.231029Homo sapiens, clone 8.7other AA099014 MGC:15961, mRNA, tom 131904 Hs.284296Homo sapiens cDNA: 5.5other AF078866 FLJ22993 fis, clone K

131905 Hs.3439stomatin-like 2 11.3other 131913 Hs.185973degenerative spermafocyte1.7SS, AW207440 (homolog Droso 3 131916 Hs.34569ESTs 5.2TM
$ AA025976 131925 Hs.183180anaphase promoting 2.8other AF151048 complex subunit 11 (y 131929 Hs.34804Homo sapiens cDNA FLJ114725.4TM
BE541211 fis, clone HE

131941 Hs.35086ubiquitin specific 2.4other BE252983 protease 1 131950 Hs.35380x 001 protein 1.5?

131962 Hs.267448hypothetical protein 2.3other 131965 Hs.35962ESTs 1.4other 131971 Hs.154938hypothetical protein 3.5other 131977 Hs.3622procollagen-proline, 6.6TM
U90441 2-oxoglutarate 4-di 131985 Hs.36563hypothetical protein 2.4?

45 131991 Hs.36708budding uninhibited 2.2SS,TM
AF053306 by benzimidazoles 132019 Hs.37372Homo Sapiens DNA binding3.3TM
H56995 peptide mRNA, p 132062 Hs.3832clathdn-associated 1.5other BE266155 protein AP47 132084 Hs.3886karyopherin alpha 3 3.7other NM 002267 (impor8n alpha 4) 132103 Hs.3991ESTs 1.5other $0 132105 Hs.39959ESTs 5.8TM

132116 Hs.40289ESTs 1.7other 132176 Hs.8878kinesin-like 1 3.4other 132180 Hs.418fibroblast activation 14.7SS, NM 004460 protein, alpha 132194 Hs.4212ESTs 2.2other $ 132207 Hs.42287E2F transcription factor1.5other $ BE206939 6 132235 Hs.42656KIAA1681 protein 5.7other 132252 Hs.141269Homo Sapiens cDNA: 2.1other AI566004 FLJ21550 fis, clone C

132266 Hs.43299hypothetical protein 1.5other 132273 Hs.43658DKFZP586L151 protein 10 other 132276 Hs.285711hypothetical protein 2 other 132288 Hs.305971solute tamer family 9.2other N36110 2 (facilitated glu 132294 Hs.44131KIAA0974 protein 2 other 132298 Hs.7120cytokine receptor-like6.6SS, NM 015986 molecule 9 132299 Hs.44205cortistatin 3.8other 65 132325 Hs.44856hypothetical protein 1.5other 132370 Hs.46645ESTs 28.3?

132374 Hs.46744core1 UDP-galactose:N-acetylgalactosamin1.9other 132376 AI279892Hs.46801sorting nexin 14 2 ?

132384 AA312135Hs.46967HSPC034 protein 6.1 ?

132393 AL135094Hs.47334hypothetical protein 1.7 other 132450 AA100012Hs.48827hypothetical protein 8.6 other $ 132452 AW973521Hs.247324mitochondria) ribosomal5.3 other protein S14 132456 AB011084Hs.48924KIAA0512 gene product;1.5 other 132470 AI224456Hs.4934H.sapiens polyA site 2 other DNA

132484 X16660Hs.119007RAB4, member RAS oncogene2.9 SS, family 132518 AW885606Hs.5064ESTs 2.2 other 132530 AA306105Hs.50785SEC22, vesicle trafficking1.7 other protein (S. c 132532 AAd54132Hs.5080mitochondria( ribosomal7.2 TM
protein L16 132534 BE388673Hs.5086hypothetical protein 2.2 SS, 132543 BE568452Hs.5101protein regulator 2.2 other of cytokinesis 1 132574 AW631437Hs.5184TH1 drosophila homolog14 ?

15132596 AK001484Hs.5298CGI-45 protein 1.9 other 132611 AA345547Hs.53263hypothetical protein 2.6 TM

132612 H12751Hs.5327PR01914 protein 2 other 132616 BE262677Hs.283558hypothetical protein 3.1 other 132638 AI796870Hs.54277DNA segment on chromosome12.4TM
X (unique) 992 132668 AB018319Hs.5460KIAA0776 protein . 2.8 SS, 132692 AW191962Hs.249239collagen, type VIII, 3 other alpha 2 132715 F11875Hs.5534Homo Sapiens cDNA 1.8 other FLJ12961 fis, clone NT

132718 NM_004600Hs.554Sjogren syndrome antigen3.7 other A2 (60kD, ribon 132724 AI142265Hs.55498geranylgeranyl diphosphate1.8 TM
synthase 1 132731 AI189075Hs.301872hypothetical protein 5.9 other 132744 AA010233Hs.55921glutamyl-prolyl-tRNA 8.7 other synthetase 132760 AA125985Hs.56145thymosin, beta, identified3.6 other in neuroblast 132771 Y10275Hs.56407phosphoserine phosphatase2.8 TM

132773 AA459713Hs.295901KIAA0493 protein 14.6other 132784 AI142133Hs.56845GDP dissociation inhibitor1.7 other 132798 A1026701Hs.5716KIAA0310 gene product2.5 other 132807 007418Hs.57301mutt (E. toll) homolog1.4 other 1 (colon cancer, 132810 AB007944Hs.5737KIAA0475 gene product4.3 SS, 132813 BE313625Hs.57435solute comer family 2.8 other 11 (proton-coupled 35132815 AI815189Hs.57475sex comb on midleg 1.6 other homolog 1 132817 N27852Hs.57553tousled-like kinase 1.4 other 132821 AJ251595Hs.169610CD44 antigen (homing 5.4 other function and Indian 132833 078525Hs.57783eukaryotic translation6.1 ?
initiation factor 132842 NM Hs.279771Homo sapiens clone 7.2 other 016154 PP1596 unknown mRNA

132844 F12200Hs.5811chromosome 21 open 2.9 other reading frame 59 132851 009716Hs.287912lectin, mannose-binding,6.1 other 132869 AW963217Hs.203961ESTs, Moderately similar1.8 other to AF116721 89 132873 AW007683Hs.58598KIAA1266 protein 2.2 other 132875 NM Hs.58617Rho-associated, coiled-coil5 TM
004850 containing p 132891 BE267143Hs.59271U2(RNU2) small nuclear2.7 ?
RNA auxiliary fat 132897 AW503667Hs.59545ring finger protein 5.4 ?

132902 AI936442Hs.59838hypothetical protein 3.2 other 132912 AW732760Hs.167578Homo Sapiens cDNA 1.4 other FLJ11095 fis, clone PL

132913 W78714Hs.60257Homo sapiens cDNA 3 other FLJ13598 fis, clone PL

50132940 T79136Hs.127243Homo Sapiens mRNA 10.3other for KIAA1724 protein, 132942 AA554458Hs.197751KIAA0666 protein 2.1 SS, 132952 AI658580Hs.61426Homo Sapiens mesenchymal1.3 other stem cell prote 132962 AA576635Hs.6153CGI-48 protein 4.9 other 132972 AA034365Hs.288924Homo sapiens cDNA 3.6 TM
FLJ11392 fis, clone HE

$S132973 AA035446Hs.323277ESTs 13.1other 132977 AA093322Hs.301404RNA binding motif 1.3 other protein 3 132980 AA040696Hs.62016ESTs 2.3 ?

132994 AA112748Hs.279905clone H00310 PR00310p117.1other 133012 AA847843Hs.62711Homo Sapiens, clone 1.9 other IMAGE:3351295, mRNA

133015 AJ002744Hs.246315UDP-N-acetyl-alpha-D-galactosamine:polyp5 TM

133062 AW500374Hs.64056PR00149 protein 6.1 other 133069 BE247441Hs.6430protein with polyglutamine1.5 TM
repeat; calci 133091 AK001628Hs.64691KIAA0483 protein 1.4 other 133110 AA808177Hs.65228ESTs 5.6 other f 133134 AF198620Hs.65648RNA binding motif 1.9 other protein 8A

133145 H94227Hs.6592Homo Sapiens, clone 4.8 ?
IMAGE:2961368, mRNA, 133152 211695Hs.324473mitogen-activated 5 other protein kinase 1 133174 AA431620Hs.324178hypothetical protein 2.7 other 133175 AW955632Ns.66666ESTs, Weakly similar 9.3 other to S19560 proline-r 133177 X97795Hs.66718RAD54 (S.cerevisiae)-like4.5 TM

133208 AI801777Hs.6774ESTs 5.5 TM

133226 AW954569Hs.296287Homo sapiens, Similar2.7 other to bromodomain-con 133228 AI492924Hs.6831golgi phosphoprotein 1.7 ?

133254 AI567421Hs.273330Homo sapiens, clone 1.3 other IMAGE:3544662, mRNA, 133268 AW956781Hs.293937ESTs, Weakly similar 12.2other to FXD2_HUMAN FORKH

133291 BE297855Hs.69855NRAS-related gene 1.2 other 1 133314 AA102670Hs.70725gamma-aminobutyric 1.7 TM
~ acid (GABA) A recepto 133321 T79526Hs.179516integral type I protein11.1?

133327 AL390127Hs.7104Kruppel-like factor 2.9 other 133347 BE257758Hs.71475acid cluster protein 2.5 ?

133360 A1016521Hs.71816v-akt murine thymoma 1.5 other viral oncogene homo 1 133366 AA292811Hs.72050non-metastatic cells 2.1 other S 5, protein expresse 133367 AF231919Hs.18759KIAA0539 gene product1.3 other 133370 AF245505Hs.72157DKFZP56411922 protein2.2 other 133390 AI950382Hs.72660phosphatidylserine 5.7 TM
receptor 133391 AW103364Hs.727inhibin, beta A (activin25.5other A, activin AB a 20133394 AA305127Hs.237225hypothetical protein 3.3 other 133437 AL031591Hs.7370phosphotidylinositol 1.6 other transfer protein, b -133452 NN>_,002759Hs.274382protein kinase, interferon-inducible4.1 other dou 133453 AI659306Hs.73826protein tyrosine phosphatase,1.5 other non-recept 133500 AW964804Hs.74280hypothetical protein 6.3 TM

25133529 W45623Hs.74571ADP-ribosylation factor4 ?

133543 AU077073Hs.108327damage-specific DNA 1.8 ?
binding protein 1 (1 133578 AU077050Hs.75066translin 1.5 other 133579 X75346Hs.75074mitogen-activated 3.5 TM
protein kinase-activat 133582 BE391579Hs.75087Fas-activated serinelthreonine6.8 TM
kinase 3 133594 AW160781Hs.172589nuclear phosphoprotein2.6 TM
~ similar to S. cer 133595 AA393273Hs.75133transcription factor 1.4 other 6-like 1 (mitochond 133599 NM_002885Hs.75151RAP1, GTPase activating8.1 other protein 1 133621 NM_004893Hs.75258H2A histone family, 13.5other member Y

133627 NM_002047Hs.75280glycyl-tRNA synthetase2.2 other 35133631 NM_000401Hs.75334exostoses (multiple) 1.8 other 133649 025849Hs.75393acid phosphatase 1, 2 other soluble 133690 AV661185Hs.75574mitochondria) ribosomal2.8 other protein L19 133720 L27841Hs.75737pericentriolar material6.8 other 133722 AW969976Hs.279009matrix Gla protein 2.5 other 133751 AW402048.comp Hs.334787 Homo sapiens, Similar to likely ortholog 3.1 TM

133757 T52946Hs.196209RAE1 (RNA export 1, 1.4 ?
S.pombe) homolog 133760 BE271766Hs.181357laminin recepfor 1 5.4 other (67kD, ribosomal prot 133765 M62194Hs.75929cadherin 11, type 5 other 2, OB-cadherin (osteob 133780 AA557660Hs.76152decorin 3.8 other 133797 AL133921Hs.76272retinoblastoma-binding3.1 ?
protein 2 133822 D50525Hs.699peptidylprolyl isomerase9.7 ?
B (cyclophilin 133842 AW797468Hs.285013putative human HLA 2.4 other class II associated p 133845 AA147026Hs.76704ESTs 2.5 other 133865 A8011155Hs.170290discs, large (Drosophila)5 other homolog 5 $0133867 AW340125Hs.76989KIAA0097 gene product2.5 ?

133868 AB012193Hs.183874cullin 4A 2.1 other 133922 030825Hs.77608splicing factor, argininelserine-rich2.8 TM

133924 D86326Hs.325948vesicle docking protein1.8 SS, p115 133929 NM_006306Hs.211602SMC1 (structural maintenance2 ?
of chromoso 55133936 L17128Hs.77719gamma-glutamyl carboxylase2.6 other 133941 BE244332Hs.77770adaptor-related protein2.9 other complex 3, mu 2 133959 X81789Hs.77897splicing factor 3a, 10.4other subunit 3, 60kD

133976 AI908165Hs.169946DATA-binding protein 1.9 other 3 (T-cell receptor 133989 AL040328Hs.78202SWIISNF related, matrix2.6 SS, associated, acti 133997 AI824113Hs.78281regulator of G-protein13 other signalling 12 134010 AB016092Hs.197114RNA binding protein; 8.8 other AT-rich element bin 134015 D31764Hs.278569sorting nexin 17 1.5 SS, 134070 NM Hs.78946cullin 3 8.3 other 134110 041060Hs.79136LIV-1 protein, estrogen2.7 other regulated 6$134129 NM_014742Hs.79305KIAA0255 gene product4.2 other 134134 H86504Hs.173328protein phosphatase 1.7 other 2, regulatory subuni 134200 BE559598Hs.197803KIAA0160 protein 2.6 other l~~

134206 AF107463Hs.79968splicing factor 30, 1.3 other survival of motor ne 134219 NM Hs.80206glucose-6-phosphate 1.9 other 000402 dehydrogenase 134234 BE300078Hs.80449Homo sapiens, clone 10.3SS, IMAGE:3535294, mRNA, 134275 AI878910Hs.3688cisplatin resistance-associated2.5 other overexpr $ 134292 AI906291Hs.81234immunoglobulin superfamily,1.3 TM
member3 134301 AW502505Hs.81360Homo Sapiens cDNA: 1.6 TM
FLJ21927 fis, clone H

134305 U61397Hs.81424ubiquitin-like 1 (sentrin)2.1 TM

134324 AB029023Hs.179946KIAA1100 protein 5.3 ?

134326 AW903838Hs.81800chondroitin sulfate 2.5 TM
proteoglycan 2 (vers 1 134329 N92036Hs.81848RAD21 (S. pombe) homolog3.9 ?
~

134337 NM_004922Hs.81964SEC24 (S. cerevisiae)2.4 TM
related gene famil 134348 AW291946Hs.82065interieukin 6 signal 6.8 TM
transducer (gp130, 134367 AA339449Hs.82285phosphoribosylglycinamide2.3 TM
formyltransfer 134376 X06560Hs.823962',5'-oligoadenylate 5.5 other synthetase 1 (40-46 1$ 134379 AW362124Hs.323193hypothetical protein 5.9 TM

134384 AI589941Hs.8254Homo Sapiens, Similar2.2 other to tumor different 134391 AA417383Hs.82582integrin, beta-like 2.1 other 1 (with EGF-like rep 134395 AA456539Hs.8262lysosomal 2.3 other 134405 AW067903Hs.82772collagen, type XI, 72.9other alpha 1 20 134411 BE272095Hs.167791reticulocalbin 1, 4.4 other EF-hand calcium bindin 134415 AI750762Hs.82911protein tyrosine phosphatase2.3 other type IVA, m 134421 AU077196Hs.82985collagen, type V, 6.8 ?
alpha 2 134424 244190Hs.83023peroxisomal biogenesis2.4 other factor 11 B

134446 AA112036Hs.83419KIAA0252 protein 2.9 other 2.$134447 M58603Hs.83428nuclear factor of 6.7 other kappa light polypeptid 134470 X54942Hs.83758CDC28 protein kinase 2.4 other 134480 NM_005000Hs.83916Empirically selected 6.3 ?
from AFFX single pr 134485 X82153Hs.83942cathepsin K (pycnodysostosis)1.9 other 134498 AW246273Hs.84131threonyl-tRNA synthetase1.8 other 30 134513 AA425473Hs.84429KIAA0971 protein 1.4 other 134516 AK001571Hs.273357hypothetical protein 1.4 other 134520 BE091005Hs.74861activated RNA polymerise5.6 other II transcriptio 134529 AW411479Hs.848FK506-binding protein2.8 ?
4 (59kD) 134577 BE244323Hs.85951exportin, tRNA (nuclear1.7 other export receptor 3 134582 AA927177Hs.86041CGG triplet repeat 1.7 TM
$ binding protein 1 134612 AW068223Hs.171581ubiquitin C-terminal 2.1 other hydrolase UCH37 134624 AF035119Hs.8700deleted in liver cancer1.3 other 134632 X78520Hs.174139chloride channel 3 2.1 ?

134654 AK001741Hs.8739hypothetical protein 2.3 other 134666 BE391929Hs.8752transmembrane protein4 other 134687 U62317Hs.88251arylsulfatase A 6.2 other 134692 NM Hs.8850a disintegrin and 2 other 003474 metalloproteinase doma 134705 BE161887Hs.88799anaphase-promoting 1.3 SS, complex subunit 10 134714 Y14768Hs.890lysosomal 7.2 ?

4$ 134719 AA852985Hs.89232chromobox homolog 3.2 other 5 (Drosophila HP1 alph 134722 AF129536Hs.284226F-box only protein 2.5 other 134746 X07871Hs.89476CD2 antigen (p50), 5 other sheep red blood cell 134751 AW630803Hs.89497lamin B1 6.1 other 134790 BE002798Hs.287850integral membrane 5.6 TM
protein 1 $0 134834 AW451370Hs.8991adaptor-related protein5.3 other complex 1, gamma 134850 AI701162Hs.90207hypothetical protein 9.1 other 134853 BE268326Hs.902805-aminoimidazole-4-carboxamide2.4 other ribonucle 134880 AI879195Hs.9060615 kDa selenoprotein 2.7 other 134925 AW885909Hs.6975PR01073 protein 1.5 other $ 134955 AW401361Hs.91773protein phosphatase 4.9 other $ 2 (formerly 2A), cat 134971 A1097346Hs.286049phosphoserine aminotransferase2 other 134975 850333Hs.92186Leman coiled-coil 2.6 TM
protein 135011 AB037835Hs.92991KIAA1414 protein 1.4 ?

135022 NM Hs.93201glycerol-3-phosphate 1.6 ?
000408 dehydrogenase 2 (mi 135032 AW301984Hs.173685hypothetical protein 1.4 other 135077 AW503733Hs.9414KIAA1488 protein 1.8 other 135083 AB036063Hs.94262p53-inducible ribonucleotide2.5 other reductase s 135095 AF027219Hs.9443zinc finger protein 1.5 TM

135096 AA081258Hs.132390zinc finger protein 2.1 other 36 (KOX 18) 6$ 135153 A1093155Hs.95420JM27 protein 4.4 ?

135181 BE250865Hs.279529px19-like protein 14.9?

135199 AA477514Hs.96247translin-associatedfactorX1.3 other 135207 Hs.9634ESTs, Highly similar 1.7 other N26427 to C10 HUMAN PUTATI

135214 Hs.96560hypofhetical profein 6.2 other 135243 Hs.97101putative G protein-coupled2.8 TM
BE463721 receptor 135245 Hs.262603ESTs 12.2TM

135257 Hs.97255ESTs, Weakly similar 7.7 TM
AW291023 to A46010 X-linked 135263 Hs.55498geranylgeranyl diphosphate1.8 other A1088775 synthase 1 135274 Hs.112017GE36 gene 4.2 SS, 135294 Hs.9800protein kinase Njmu-R11.2 other 135295 Hs.98006ESTs 4.9 other 1 135307 Hs.98368ESTs, Weakly similar 5.9 ?
~ AI743770 to KIAA0822 protein 135321 Hs.98614ribosome binding protein12.3TM
AI652069 1 (dog 180kD ho 135354 Hs.183418cell division cycle 5.8 ?
AA456454 2-like 1 (PITSLRE
pr 135361 Hs.167700Homo Sapiens cDNA 8.1 other AA373452 FLJ10174 fis, clone HE

135389 Hs.99872fetal Alzheimer antigen1.9 other 1$ 135400 Hs.99915androgen receptor 13.9TM
X78592 (dihydrotestosterone r 302256 Hs.171595HIV TAT specific factor1.6 other 302276 Hs.323910HER2 receptor tyrosine5.3 other AW057736 kinase (c-erb-b2, 303135 Hs.279474HSPC070 protein 2.2 TM

303686 Hs.109441MSTP033 protein 1.4 SS, 310085 Hs.101248Homo sapiens clone 5.2 other 843191 IMAGE:32553, mRNA
seq 315518 Hs.167771ESTs 2.3 ?

317781 Hs.42650ZW10 interactor 2.9 ?
NM_007057 320836 Hs.197289rab3 GTPase-activating2 other AI268997 protein, non-cata 321114 Hs.78979Golgi apparatus protein5.6 SS, 322221 Hs.179662nucleosome assembly 1.4 ?
N24236 protein 1-like 1 322474 Hs.29494PR01912 protein 1.3 other 322556 Hs.177507hypothetical protein 2.9 SS, 323541 Hs.104613RP42 homolog 1.6 other 407827 Hs.40323BUB3 (budding uninhibited1.8 other BE278431 by benzimidazo 408196 Hs.436275RY (sex determining 1.6 other AL034548 region Y)-box 22 408813 Hs.48295RNA helicase family 6.2 other 409176 Hs.101617ESTs, Weakly similarto5.7 other 873727 T32527 hypotheti 409487 gb:yn57a05.r1 Soares 2.7 other H19886 adult brain N2b5HB5 413670 Hs.75470hypothetical protein,2.6 ?
AB000115 expressed in osteo 3 414108 Hs.75761SFRS protein kinase 2.4 TM
$ AI267592 1 414846 Hs.77495UBX domain-containing2.4 other 416040 Hs.289044Homo sapiens cDNA 2.3 other AW819158 FLJ12048 fis, clone 416980 Hs.80684high-mobility group 4.2 TM
AA381133 (nonhistone chromoso 417378 Hs.82037TATA box binding protein23.6other 857256 (TBP)-associate 4O 418283 Hs.83942cathepsin K (pycnodysostosis)5.8 other 418467 Hs.85273re6noblastoma-binding1.3 other NM_006910 protein 6 420269 Hs.96264alpha thalassemialmental1.6 ?
072937 retardation syn 420802 Hs.1334v-myb avian myeloblastosis2.3 ?
022376 viral oncogen 421225 Hs.102696MCT-1 protein 1.6 ?

4S 421642 Hs.106346retinoic acid repressible3.5 other AF172066 protein 421828 Hs.279789histone deacetylase 5 other 421983 Hs.110364pepGdylprolyl isomerase3.1 TM
AI252640 C (cyclophilin 422052 Hs.104518ESTs 1.9 TM

422055 Hs.111029putative heme-binding2.4 other NM_014320 protein 423750 Hs.298229prefoldin 2 4.2 ?

424001 Hs.137476paternally expressed 7.1 ?
W67883 10 (PEG10; KIAA105 425182 Hs.155040zinc finger protein 2.3 other 425284 Hs.155489NS1-associated protein3.5 other 426372 Hs.169531DEADIH (Asp-Glu-Ala-AspIHis)1.9 ?
BE304680 box polypep $5 428049 Hs.182238GW128 protein 7.6 ?

428477 Hs.11482splicing factor, argininelserine-rich1.7 other 437562 Hs.5683DEADIH (Asp-Glu-Ala-AspIHis)2.4 other AB001636 box polypep 438449 Hs.6216Homo Sapiens hepatocellular3.8 other AK001333 carcinoma-as 441560 Hs.7888Homo sapiens clone 5.6 other F13386 23736 mRNA sequence 445580 Hs.12912skbl (S. pombe) homolog2 TM

446999 Hs.334822hypothetical protein 7.6 other 447111 Hs.17409cysteine-rich protein2.2 other A1017574 1 (intestinal) 447778 Hs.71190ESTs, Weakly similar 2.9 other BE620592 to S16506 hypotheti 448873 Hs.22393density-regulated 1.8 other NM_003677 protein 65 449687 Hs.331328intermediate filament5.9 other W68520 protein syncoilin 450701 Hs.288467Homo Sapiens cDNA 5.7 other H39960 FLJ12280 fis, clone MA

450703 Hs.184771nuclear factor IIC 1.4 other AA011202 (CCAAT-binding transc 1~~

452461 N78223Hs.108106transcription factor 4.8 ?

452511 BE408178Hs.285165Homo sapiens cDNA 2.9 other FLJ20845 fis, clone AD

453157 AF077036Hs.31989DKFZP586G1722 protein12.1SS,TM

453658 BE541906Hs.87819Homo sapiens, clone 4.8 other MGC:2492, mRNA, comp $ 100685 AA328229Hs.184582ribosomal protein 1.8 TM

100690 AA383256Hs.1657estrogen receptor 1.6 other 100833 AF135168Hs.108802N-ethylmaleimide-sensitive1.3 other factor 100850 AA836472Hs.297939cathepsin B 1.7 ?

101161 NM Hs.37044periphedn 16.9other 1 102481 050360 gb:Human calcium, 3.2 other ~ calmodulin-dependent p 102831 AA262170Hs.80917adaptor-related protein2 ?
complex 3, sigma 103549 BE270465Hs.78793protein kinase C, 8 other zeta 103749 AL135301Hs.8768hypothetical protein 1.8 other 104331 AB040450Hs.279862cdk inhibitor p21 2 ?
binding protein 15 104532 AI498763Hs.203013hypothetical protein 2.1 other 104563 AL117403Hs.306189DKFZP434F1735 protein1.2 other 105032 AA127818 gb:z112a02.s1 Soares_pregnant_uterus_NbH7 ?

105039 AA907305Hs.36475ESTs 2.6 ?

106531 AA454036Hs.8832ESTs 1.6 other 106977 AL043152Hs.50421KIAA0203 gene product4.9 other 107298 N95657Hs.6820ESTs, Moderately similar2.5 TM
to YOJ1 CAEEL H

108717 AA122393Hs.70811hypothetical protein 1.3 other 110018 AW579842Hs.104557hypothetical protein 5.3 TM

110330 AI288666Hs.16621DKFZP4341116 protein 6.3 other 2$ 111391 NM_003896Hs.225939sialyltransferase 5.1 SS, 9 (CMP-NeuAc:lactosylc 111392 W46342Hs.325081Homo sapiens, clone 8.4 other IMAGE:3659680, mRNA, 113554 AW503990Hs.142442HP1-BP74 3.7 TM

113722 AV653556Hs.184411albumin 1.3 other 115008 AK001827Hs.87889helicase-moi 2 other 30 115062 AA253314Hs.154103LIM protein (similar 1.5 other to rat protein kina 115121 AI634549Hs.88155ESTs 2.8 other 117881 AF161470Hs.260622butyrate-induced transcript5.8 TM

119075 M10905Hs.287820fibronectin 1 5.7 other 119615 AL034423Hs.75875ubiquitin-conjugating1.3 other enzyme E2 variant 3 120253 AA131376Hs.326401fibroblast growth 38.9other $ factor 12B

125006 BE065136Hs.145696splicing factor (CC1.3)2.9 ?

127609 X80031Hs.530collagen, type IV, 1.8 other alpha 3 (Goodpasture 128868 AA419008Hs.106730chromosome 22 open 3 other reading frame 3 128891 F34856Hs.292457Homo sapiens, clone 13.3other MGC:16362, mRNA, com 128959 AI580127Hs.107381hypothetical protein 10.9other 129209 862676Hs.17820Rho-associated, coiled-coil2.4 other containing p 129449 A1096988Hs.111554ADP-ribosylation factor-like8.2 TM

129453 AW974265Hs.111632Lsm3 protein 3.3 ?

129629 AK000398Hs.11747hypothetical protein 3.9 other 4$ 129917 M30773Hs.278540protein phosphatase 5.3 TM
3 (formerly 2B), reg 129922 AF042379Hs.13386gamma-tubulin complex4.6 other protein 2 129989 AB015856Hs.247433activating transcription4 SS, factor 6 130182 BE267033Hs.192853ubiquitin-conjugating4.6 other enzyme E2G 2 (homo 130365 W56119Hs.155103eukaryotic translation11 other initiation factor 50 130471 AL121438Hs.183706adducin 1 (alpha) 2.7 ofher 130542 064675Hs.179825RAN binding protein 7.9 other 2-like 1 130586 AB007891Hs.16349KIAA0431 protein 5.6 TM

130768 AF258627Hs.211562ATP-binding cassette,5.2 other sub-family A (ABC1 130992 BE398091Hs.74316desmoplakin (DPI, 1.8 TM
DPII) 55 131047 H23230Hs.22481ESTs, Moderately similar1.7 ?
to A46010 X-lin 131135 NM Hs.267182TBX3-iso protein 3.3 TM

131339 AF058696Hs.25812Nijmegen breakage 2.6 other syndrome 1 (nibrin) 131760 X76732Hs.3164nucleobindin 2 2.9 TM

131774 BE267158Hs.169474DKFZP586J0119 protein5.6 other 131853 AI681917Hs.3321ESTs, Highly similar 1.3 other to 18X1 HUMAN IROQU

131881 AW361018Hs.3383upstream regulatory 3.2 TM
element binding prot 131887 W17064Hs.332848SWIISNF related, matrix3.2 other associated, acti 132031 AF193844Hs.3758COP9 complex subunit 5.9 ?
7a 132192 AA206153Hs.4209mitochondrial ribosomal2.2 TM
protein L37 tiS132203 NM_004782Hs.194714synaptosomal-associated7.9 ?
protein, 29kD

132240 AB018324Hs.42676KIAA0781 protein 4.3 other 132348 AW067708Hs.170311heterogeneous nuclear12.5other ribonucleoprotein 132528 T78736Hs.50758SMC4 (structural maintenance7.4?
of chromoso 132571 AW674699Hs.5169suppressor of G2 allele6.9other of SKP1, S. cere 132726 N52298Hs.55608hypothetical protein 1437 132863 BE268048Hs.236494RAB10, member RAS oncogene10.3other family 133016 AI439688Hs.6289hypothetical protein 4.4other 133053 A1065016Hs.6390Homo Sapiens clone 1.8SS,TM
FLB3344 PR00845 mRNA, 133197 AI275243Hs.180201hypothetical protein 1.8other 133240 AK001489Hs.242894ADP-ribosylation factor-like1.8other 133266 AI160873Hs.69233zinc finger protein 16.1other 1 ~ 133285 Hs.289082GM2 ganglioside activator10.4SS, M76477 protein 133383 BE313555Hs.7252KIAA1224 protein 1.5?

133540 AL037159Hs.74619proteasome (prosome, 1.7other macropain) 26S subu 133784 BE622743Hs.301064arfaptin 1 12.1other 133791 M34338Hs.76244spermidine synthase 9.7other 1$ 133850 Hs.7678cellular retinoic acid-binding4.2SS, W29092 protein 1 133859 U86782Hs.17876126S proteasome-associated2.2other pad1 homolog 133881 U30872Hs.77204centromere protein 9.1other F (3501400kD, mitosin 134208 NM Hs.79993peroxisomal biogenesis3.2other 000288 factor 7 134403 AA334551Hs.82767sperm specific antigen1.4other ZQ 134724 Hs.321576ring finger protein 1.4other 134806 AD001528Hs.89718spermine synthase 2.6other 134859 D26488Hs.90315KIAA0007 protein 13.3other 135193 X95525Hs.96103TATA box binding protein3.1other (TBP)-associate AA243007 ESTs 1.6?

25 T70541 ESTs 2.5SS, X57766 Human stromelysin-3 4.5other mRNA

S66431 Homo Sapiens clone 3.1other 23592 mRNA sequence AA453483 ESTs 4.6TM

863925 ESTs 1.4other AA173417 ESTs 1.9other AA280588 ESTs 2.2other AA504223 ESTs Highly similar 2.4other to CHROMOSOME

AA609996 ESTs Highly similar 5.5?
to Surf-4 protein [M.musculus]

F02907 ESTs 2.3TM

35 AA480103 ESTs Weakly similar 2.8TM
to 1111 ALU SUBFAMILY
J

AA024664 Human NADH:ubiquinone 6.2other oxidoreductase subunit AA251776 ESTs 2.3other AA399047 ESTs 2.4other N34059 EST - RC_N34059 3.3other 4~ U95367 Human GABA-A receptor 1.7 TM
pi subunit mRNA complete cds AA490899 ~ ESTs 3.3other T54762 ESTs 2.9?

241963 Homo sapiens HP protein 7 (HP) mRNA complete cds 1.3 AA521186 ESTs 1.6TM

4S AA400195 ESTs 1.3other AA045083 VITAMIN K-DEPENDENT E 2.5 other GAMMA-CARBOXYLAS

AA099589 Homo Sapiens mRNA for 1.6 TM
GDP dissociation inhibitor beta W85712 ESTs Weakly similar 2.6 TM
to PROCOLLAGEN ALPHA
2(IV

W45728 ESTs Highly similar 3.7other to HETEROGENEOUS

U61232 Human tubulin-folding 2.1 other cofactor E mRNA complete cds AA425154 ESTs 5.3other T39176 ESTs Weakly similar 2.6SS,TM
to ZK1058.4 [C.elegansj AA496000 ESTs 1.9SS, W38150 EST - RC_W38150 1.7?

S T96595 EST - RC T96595 1.8TM

AA227463 ESTs Weakly similar 1.9 ?
to No definition line found [C.elegans]

846025 ESTs 2.8SS, AA233177 ESTs 2 other AA338760 ESTs 1.3?

(o AA412106 ESTs 6.2other L47276 EST - L47276 3.4other D82307 ESTs Weakly similar 11.4other to TH1 protein [D.melanogaster]

AA293568 ESTs 1.5other 837778 ESTs 2.4other ($ AA250843 Interferon regulatory 14.6?
factor 5 W49521 Human prolyl 4-hydroxylase6.5?
alpha (II) subunit D80000 Human mRNA for KIAA01782 other gene partial cds 899978 ESTs Weakly similar to line-16.1 ?
protein ORF2 [H.sapiens]

AA195036 Human RoISSA ribonucleoprotein?
homolog (RoRet 5.3 238501 ESTs Weakly similar to PROBABLEother E5 1.4 U37547 Human IAP homolog 8 (MIHB) other mRNA complete cds 3.2 AA479961 ESTs 1.7 other X57579 Inhibin beta A (activin A 15.8 activin AB alpha polypeptide)?

AA449071 ESTs 1.3 TM

N51855 ESTs Moderately similar to other NAD(+) ADP- 1.3 AA421213 ESTs Weakly similar to F28F8.3other [C.elegans] 3.2 1 AA355201 ESTs 1.2 SS,TM
~

N78717 H.sapiens mRNA for translin ?
1.5 N73808 ESTs 5 ?

U86782 Human 26S proteasome-associatedother pad1 2.2 AA234817 ESTs ~ 1.3 other 15 D13666 Homo sapiens mRNA for osteoblastSS, specific 7.5 AA236177 ESTs 7.1 ?

U50648 Protein kinase interferon-inducible?
double 4.1 M28211 Homo sapiens GTP-binding other protein (RAB4) 2.9 AA446949 ESTs 2.2 other 2~ W03007 ESTs 1.2 other W61011 ESTs 1.2 other W87544 ESTs 1.2 other X02751 Neuroblastoma RAS viral (v-ras)?
oncogene homolog 1.2 214077 YY1 transcription factor other 1.2 238839 ESTs 1.2 ?

AA410894 ESTs 1.7 other AA504499 ESTs Highly similar to probable1.3 other chloride channel 3 [H.sap Table 7 A shows the accession numbers for those pkeys lacking unigeneID's for Table 7.
For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number Gene cluster number Accession: Genbank accession numbers Pkey CAT number Accession 105032 genbank_AA127818 AA127818 409487 1134778_1 H19886 AW402806 T10231 TABLE 8: Figure 8 from BRCA 001-1 US
Table 8 shows genes upregulated in tumor tissue compared to normal breast tissue.
Specifically, one column shows the ratio of expression of the indicated gene in breast tumor tissue compared to other body tissues, and another column shows the ratio of expression of the indicated gene in breast tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: ExempIarAccession number, Genbank accession number UnigenelD: Unigene number Unigene Titie: Unigene gene title 1$ R1: Ratio of tumor to normal body tissue R2: Ratio of tumor to normal breast tissue Pkey ExAccn UnigenelD UnigeneTitle R1 R2 100075 Hs.284160 protocadherin 1 3.8 AF152333 gamma subfamily B, 4 100229 Hs.180107 polymerase 1.7 5.3 AV652249 (DNA directed), beta 100262 Hs.278468 postmeiotic 0.8 4.8 D38500 segregation increased 2-like 100271 Hs.256290 S100 calcium-binding3.2 2.3 BE160081 protein A11 (calgiz 100355 Hs.71465 squalene epoxidase3.3 1.4 ~S 100522 Hs.99949 prolactin-induced11.90.4 X51501 protein 100552 Hs.301946 lysosomal 3.8 1.2 100599 Hs.334334 transcription 9.4 9.4 X77343 factorAP-2 alpha (activat 100676 Hs.287820 fibronectin 3 7.8 100690 Hs.1657 estrogen receptor4.4 4.4 100895 Hs.75772 nuclear receptor1 3.9 001351 subfamily 3, group C, m 101046 NM_002122:Homo sapiens 4 K01160 major histocompat1.7 101086 Hs.250959 histatin 1 0.8 4.1 101148 Hs.78944 regulator of 1.2 12 NM_002923 G-protein signalling 2, 24k 101161 Hs.37044 peripherin 3.1 1.1 101201 Hs.2256 matrix metalloproteinase4.4 0.6 L22524 7 (MMP7; uterin 101212 Hs.83164 collagen, type 3.1 3.4 AI186220 XV, alpha 1 101441 Hs.100000 S100 calcium-binding0.9 4.2 AW468397 protein A8 (calgran 101447 gb:Human alpha satellite29.90.3 M21305 and satellite 3 101469 Hs.169248 cytochrome 0.8 4.9 AA310162 c 101567 Hs.56729 lysosomal 1 5.9 101600 Hs.119192 H2A histone 2.8 4 BE561617 family, member Z

101624 gb:Human alpha-1 collagen3.1 1.7 M55998 type I gene, 3 101674 Hs.82124 laminin, beta 1.5 4.1 NM_002291 1 101861 Hs.83347 angio-associated,3.1 1.4 AA350659 migratory cell protein 101977 Hs.184062 putative Rab5-interacting1.3 6.9 AF112213 protein 102193 Hs.313 secreted phosphoprotein1.9 4.9 AL036335 1 (osteopontin, 102199 Hs.79914 lumican 2.2 3.8 102304 Hs.46452 mammaglobin 4.2 0.7 102345 Hs.300946 Microfibdl-associated1.1 4.2 NM_003480 glycoprotein-2 $0 102457 Hs.2359 dual specificity4.5 0.5 NM 001394 phosphatase 4 102534 Hs.198307 von Hippel-Lindau1.4 4.2 096759 binding protein 1 102541 Hs.79025 KIAA0096 protein0.9 3.9 102827 Hs.6456 chaperonin containing1.5 10.9 BE244588 TCP1, subunit 2 (b 102962 Hs.159263 collagen, type2.2 6.2 850032 VI, alpha 2 $ 102991 Hs.75309 eukaryotic translation5.6 5.7 5 AW293542 elongation factor 103119 Hs.2877 cadherin 3, type3.7 0.5 X63629 1, P-cadherin (placenta 103175 Hs.79227 myomesin (M-protein)1.3 4 X69089 2 (165kD) 103286 Hs.54941 phosphorylase 1.3 3.8 D38616 kinase, alpha 2 (liver) 103319 Hs.82359 tumor necrosis 0.8 4.6 X83492 factor receptor superfami 60 103372 Hs.4888 Beryl-tRNA synthetase0.9 8 103419 Hs.272927 Sec23 (S. cerevisiae)1.1 5.1 T34708 homolog A

103471 Hs.75216 protein tyrosine3.7 1.2 Y00815 phosphatase, receptor t 103546 Hs.75752 cytochrome c 0.9 4.4 214244 oxidase subunit Vllb 103658 Hs.172928 collagen, type3.2 3 NM 000088 I, alpha 1 103758 gb:zn13e04.r1 Stratagene0.9 10 AA084874 hNT neuron (937 103774 Hs.92918 hypothetical 1.9 15.9 H24185 protein 103821 Hs.198793 Homo Sapiens 1.2 3.9 AA095971 cDNA: FLJ22463 fis, clone H

103869 Hs.24322 ATPase, H+transporting,1.4 3.9 BE439604 lysosomal (vacu 103980 Hs.293476 hypothetical 1.6 4.1 AW130242 protein FKSG44 104054 Hs.7100 hypothetical 1.5 4.3 AK001913 protein 104115 Hs.26102 opposite strand7 7 AF183810 to trichorhinophalangeal 104189 Hs.301804 KIAA1494 protein2 4.6 1 104230 Hs.15303 KIAA0349 protein0.7 4.5 ~ AB002347 104278 Hs.109253 N-terminal 3.3 3.3 AW583693 acetyltransferase complex and 104295 Hs.103657 hypothetical 2.3 4.2 AW365522 protein PR02219 104319 Hs.9950 Sec61 gamma 3.1 7 104425 Hs.35380 x 001 protein 4 1.3 104432 Hs.99949 prolactin-induced3.8 0.6 X51501 protein 104464 Hs.54642 methionine adenosyltransferase0.8 6.7 AW966728 II, beta 104479 Hs.106390 Homo Sapiens 1.7 4.8 AK001731 mRNA; cDNA DKFZp586H0924 (f 104505 Hs.11565 RIKEN cDNA 20101000122 7.5 W94824 gene 104592 Hs.325820 protease, serine,1.9 7.4 104613 Hs.24713 hypothetical 1.1 6.3 AF123303 protein 104636 Hs.106106 protein kinase1.2 4 882252 (CAMP-dependent, catalyti 104782 Hs.171774 hypothetical 1.4 3.9 AW270555 protein 104792 Hs.305953 zinc finger 1.5 4.2 AA960961 protein 83 (HPF1) 104848 Hs.274369 uncharacterized1.1 4.1 AA305351 hypothalamus protein HAR

104849 Hs.241507 ribosomal protein1.3 4.6 104850 Hs.8728 hypothetical 1.2 3.6 AL133035 protein DKFZp434G171 104852 Hs.20107 ESTs 0.8 4.2 104861 Hs.29759 RNA POLYMERASE 1.7 5.1 104873 Hs.20597 host cell factor0.8 5.4 W03831 homolog 104891 Hs.30627 ESTs 0.7 6.8 104920 Hs.306083 Novel human 2 1 AW955089 gene mapping to chomosome 3.9 104926 Hs.33363 DKFZP434N093 3.3 3.3 BE298808 protein 104952 Hs.74316 desmopiakin 1.2 3.7 AW076098 (DPI, DPII) 104963 Hs.173694 KIAA1097 protein1.1 5.5 104977 Hs.18272 amino acid transporter3.2 1.4 AI392640 system A1 105030 Hs.337772 Homo sapiens, 1.6 11.4 BE613061 Similar to RIKEN cDNA

105035 Hs.8859 Homo sapiens, 1.5 7.2 N39760 Similar to RIKEN cDNA

105068 Hs.9006 VAMP (vesicle-associated1.1 3.5 BE410438 membrane protei 105159 Hs.265561 CD2-associated1.2 10 AF146277 protein 105178 Ns.21941 AD036 protein 3.6 8.3 105182 Hs.18271 golgi phosphoprotein1.7 6.8 105274 Hs.281866 ATPase, H+transporting,1.1 3.7 AI554929 lysosomal (vacu 105303 Hs.182626 chromosome 1.5 4 BE243327 22 open reading frame 105413 Hs.172089 Homo sapiens 1.5 14 A1015709 mRNA; cDNA DKFZp58612022 (f 4S 105426 Hs.23439 ESTs 4.3 2.9 105432 Hs.76698 stress-associated1.5 5 W03516 endoplasmic reticulum 105443 Hs.12144 KIAA1033 protein1.2 3.6 105483 Hs.23458 Homo sapiens 1.7 15.8 AL137257 cDNA: FLJ23015 fis, clone L

105492 Hs.289112 CGI-03 protein2 4.8 105495 Hs.28785 microfibrillar-associated1.3 3.9 AL037715 protein 3 105539 Hs.109694 KIAA1451 protein2.7 11.4 105594 Hs.25001 tyrosine 3-monooxygenaseltryptophan1.3 6.1 AB024334 5-mo 105623 Hs.30127 hypothetical 1.7 4.5 BE504200 protein 105807 Hs.16869 ESTs, Moderately3.9 24.6 AA788946 similar to CA1C RAT
COL

5$ 105812 Hs.20814 CGI-27 protein 1.8 3.6 105823 Hs.293960 ESTs 1.9 6.6 105831 Hs.247302 twisted gastrulation1.5 4.3 105851 Hs.24391 hypothetical 3.8 1.9 AI827976 protein FLJ13612 105879 Hs.30503 Homo sapiens 1.7 4 BE392914 cDNA FLJ11344 fis, clone PL

105918 Hs.26136 hypothetical 1.7 7.4 AW028485 protein MGC14156 105939 Hs.12258 Homo Sapiens 1.2 3.8 AL137728 mRNA; cDNA DKFZp434B0920 (f 105941 Hs.10669 development 1.3 4.6 AB033075 and differentiation enhancin 105969 Hs.17377 coronin, actin-binding1.1 5.9 AB030656 protein,1C

105990 Hs.29403 hypothetical 2 4.6 AI690586 protein FLJ22060 65 106012 Hs.8895 ESTs 4.1 1.2 106060 Hs.171391 C-terminal 2.6 7 NM_001329 binding protein 2 106070 Hs.5957 Homo Sapiens 1.4 10.7 T74445 clone 24416 mRNA sequence 106083 H62087Hs.31659 thyroid hormone1.53.6 receptor-associated prot 106155 AA425414Hs.33287 nuclear factor 5.41,2 IIB

106255 BE613206Hs.279607 calpastatin 1.84 106414 BE568205Hs.28827 mitogen-activated5.16.1 protein kinase kinase $ 106538 AK000274Hs,278635 HDCMA18P protein1.25.9 106568 AW051564Hs.28285 patched related1.85.4 protein translocated in 106574 BE044325Hs,227280 U6 snRNA-associated2.311.2 Sm-like protein 106613 N88604Hs,30212 thyroid receptor1.23,6 interacting protein 106617 H09548Hs.5367 ESTs, Weakly 0.94.4 similar to 138022 hypotheti 1 106619 AA459480Hs,23956 hypothetical 1.33.6 ~ protein FLJ20502 106701 BE387614Hs.25797 splicing factor1.67.3 3b, subunit 4, 49kD

106721 AA741038Hs,6670 ESTs 1.76.1 106776 AA206079Hs.6693 hypothetical 1 5.4 protein FLJ20420 106866 AA487416Hs.268231 Homo sapiens 1,65.4 cDNA: FLJ23111 fis, clone L

1$ 106868 BE185536Hs.301183 molecule possessing3,31.2 ankyrin repeats indu 106887 BE503373Hs.334335 hypothetical 1.46.3 protein FLJ13576 106940 T85594Hs.339808 hypothetical 3.31.8 protein FLJ10120 106968 AF216751Hs.26813 CDA14 3 3 107052 BE391904Hs.12482 glyceronephosphate1.77.6 0-acyltransferase 107061 BE147611Hs.6354 stromal cell 1.24.3 derived factor receptor 107149 AI289507Hs.299883 hypothetical 1.86.5 protein FLJ23399 107222 BE172058Hs.82689 tumor rejection1.26.9 antigen (gp96) 1 107233 BE267795Hs.22595 hypothetical 1.43.5 protein FLJ10637 107295 AA186629Hs.80120 UDP-N-acetyl-alpha-D-galactosamine:polyp2.64.3 ~$ 107679 AA011510Hs.60512 ESTs 1.84 107914 AA027229Hs.61329 ESTs, Weakly 1.33.5 similar to T16370 hypotheti 107965 AF109219Hs.108787 phospha6dylinositol1.63.5 glycan, class N

108033 AW368993Hs.323748 Homo sapiens uen1.8 8,1 clone CDABP0086 mRNA
seq 108060 AA291440Hs,73149 paired box gene1.13.5 108081 AA093668Hs,28578 muscleblind 0.75.6 (Drosophila)-like 108137 AI283611Hs,263479 ESTs, Weakly H 1.2 5.6 similar to HMG1 HUMAN
HIG

108186 AW068579Hs.7780 Homo sapiens 3.1 6.9 mRNA; cDNA DKFZp564A072 (fr 108215 AI879238Hs.299315 collapsin response1.54.6 mediator protein-5;
C

108297 AA333660Hs,71331 hypothetical 1.54 protein MGC5350 3 108339 AW151340Hs,51615 ESTs, Weakly S 6.3 4.7 $ similar to ALU7_HUMAN
ALU

108371 AA074374Hs,67639 ESTs 1.33.8 108399 AF086070Hs,237519 EST 1 3.6 108469 AA079487gb:zm97f08.s1 Stratagene1.53.6 colon HT29 (937 108470 AA079500gb:zm96h10.s1 Stratagene1.14.3 colon HT29 (937 40 108564 M23114Hs.1526 ATPase, Ca++transporting,2 4.9 cardiac muscl 108641 AA112059Hs.429 ATP synthase, 1.13.5 H+transporting, mitochond 108668 AA058522Hs.185751 ESTs 1.23.6 108694 AA036725Hs.61847 ESTs 1.43.6 108824 AK001332Hs.44672 hypothetical 1.43.5 protein FLJ10470 4$ 108863 AA133456Hs.102548 glucocorticoid1.24 receptor DNA binding fact 108893 BE276891Hs.194691 reGnoic acid 1.33.6 induced 3 108992 AA152312Hs.72047 ESTs 1.14.1 109072 AI732585Hs.22394 hypothetical 1.23.5 protein FLJ10893 109097 AA167512gb:zp10f12.s1 Stratagene1.35 fetal retina 93 $0 109160 BE220601Hs,301997 hypothetical 4 6.1 protein FLJ13033 109244 BE179030Hs,64239 Human DNA sequence 1.7 7.4 from clone RP5-1174N9 109481 AA878923Hs,289069 hypothetical 3.87.7 protein FLJ21016 109484 AA366263Hs.72531 hypothetical 1.94 protein FLJ11838 109795 AA173942Hs.326416 Homo Sapiens 6 3.7 1.3 mRNA; cDNA DKFZp564H191 (f $$ 110009 BE075297Hs.6614 ESTs, Weakly 4.67.4 similar to A43932 mucin 2 p 110107 AW151660Hs,31444 ESTs 1.23.5 110411 AW001579Hs.9645 Homo Sapiens 3.73.3 mRNA for KIAA1741 protein, 110731 NM_014899Hs.188006 KIAA0878 protein2.83.7 110756 N21207Hs.182999 ESTs 1.63.5 60 110930 BE242691Hs.14947 ESTs 3.11.2 110935 AI753230Hs.323562 hypothetical 1.97.5 protein DKFZp564K142 111051 AI681293Hs.12186 hypothetical 2 4 protein FLJ22558 111110 AK001566Hs.23618 hypothetical 1.13.8 protein FLJ10704 111356 BE301871Hs.4867 mannosyl (alpha-1,3-)-glycoprotein1 8,2 beta-6$ 111357 BE314949Hs.87128 hypothetical 3.36.1 protein FLJ23309 111770 827975Hs.269401 ESTs, Moderately1.25.4 similar to S65657 alpha 111900 AF131784Hs.25318 Homo Sapiens 3.20.8 clone 25194 mRNA sequence 111903 NM Hs.166351 KIAA1072 protein1 5.4 111951 NM_014927Hs.100527 KIAA0902 protein1 3.8 112141 AW137198Hs.278682 Phosphatidylglycerophosphate1.43.5 Synthase ,192193 Hs.138238 ESTs 1.53.6 $ 112197 NM_003655Hs.5637 ESTs 4.62 112610 AW500106Hs.23643 serinelthreonine3.310.5 protein kinase MASK

112971 242387Hs.83883 transmembrane, 3.23 prostate androgen induced 112984 T16971Hs.289014 ESTs, Weakly 3,710.8 similar to A43932 mucin 2 p 113056 AF019226Hs.8036 glioblastoma 4.53.7 overexpressed 1 113449 AW160683Hs.158006 hypothetical 1.24.4 ~ protein 113497 AF143321Hs.15572 hypothetical 0.93.6 protein IMAGE 109914 113508 AL042936Hs.211571 holocytochrome1.13.5 c synthase (cytochrome c 113531 AK001898Hs.16740 hypothetical 1.23.9 protein FLJ11036 113604 A1075407Hs.296083 ESTs, Moderately1.75.3 similar to 154374 gene IS113674 NM_014214Hs.5753 inositol(myo)-1(or4)-monophosphatase20.86.1 113841 W30681Hs.146233 Homo Sapiens 1.76.2 cDNA: FLJ22130 fis, clone H

113857 AW243158Hs.5297 DKFZP564A2416 1.24.6 protein , 113931 BE255499Hs.3496 hypothetical 1.54 protein MGC15749 113936 W17056Hs.83623 nuclear receptor3.81 subfamily 1, group I, m 113987 AA345519Hs.9641 complement component1.24.7 1, q subcomponent, 114132 AI342493Hs.24192 Homo Sapiens 0.34.3 cDNA FLJ20767 fis, clone CO

114156 BE179882Hs.336920 glutathione 1.14.3 peroxidase 3 (plasma) 114213 N58309Hs.19575 CGI-11 protein 1.69.2 114636 AA075488gb:zm88d01.s1 Stratagene1.63.7 ovarian cancer ' 25114760 AI929382Hs.252692 hypothetical 1.44 protein FLJ20343 114781 T10446Hs.95388 ESTs 1 4.3 114795 AB037858Hs.173484 hypothetical 1.69.2 protein FLJ10337 114901 AV660012Hs.196437 hypothetical 1.45.2 protein FLJ10788 115096 AI683069Hs.175319 ESTs 3.71 30115518 BE541042Hs.23240 Homo Sapiens 3.24.2 cDNA: FLJ21848 fis, clone H

115646 N36110Hs.305971 solute camer 1.53.9 family 2 (facilitated glu 115764 AW582256Hs.91011 anterior gradient1.35.9 2 (Xenepus laevis) hom 115802 AW410233Hs.206521 YME1 (S.cerevisiae)-like1.76.6 115994 AB037836Hs.109315 KIAA1415 protein1.59.1 35116032 BE383668Hs.42484 hypothetical 0.94.3 protein FLJ10618 116046 BE395293Hs.94491 hypothetical 1.65.5 protein FLJ20297 116274 AI129767Hs.182874 guanine nucleotide3.22.4 binding protein (G pr 116310 224854Hs.42299 ESTs 0.84.7 116356 AI371223Hs.288671 Homo Sapiens 2.43.9 cDNA FLJ11997 fis, clone HE

116429 AF191018Hs.279923 putative nucleotide5.55.5 binding protein, est 116461 AA313607Hs.58633 Homo Sapiens 5 1.3 cDNA: FLJ22145 fis, clone H

116470 AI272141Hs.83484 SRY (sex determining8.74,5 region Y)-box 4 116578 D21262Hs.75337 nucleolar and 3.26.9 coiled-body phosphprotein 116579 AW888411Hs.81915 leukemia-associated3.23 phosphoprotein p18 ( 45116589 AI557212Hs.17132 ESTs, Moderately3.18.3 similar to 154374 gene 116786 H25836Hs.301527 ESTs, Moderately3.24.5 similar to unknown [H.s 117170 N25929Hs.42500 ADP-ribosylation7 5.5 factor-like 5 117215 N20066Hs.133207 PTPRF interacting1.26.2 protein, binding prote 117280 M18217Hs.172129 Homo sapiens 4.52.4 cDNA: FLJ21409 fis, clone C

50117576 AI383467Hs,44597 ESTs 1.44.2 117667 U59305Hs.44708 Ser-Thr protein4.30.5 kinase related to the my 117881 AF161470Hs.260622 butyrate-induced2.15.7 Uanscript 1 118336 BE327311Hs.47166 HT021 3.67.7 118475 N66845gb:za46c11.s1 Soares 4.20.5 fetal liver spleen SS118493 AL353944Hs.50115 Homo sapiens 2 3.5 3.3 mRNA; cDNA DKFZp761J111 (f 118505 N67343gb:yz50b07.s1 Morton 2.13.8 Fetal Cochlea Homo 119159 AF142419Hs.15020 homolog of mouse3.71.5 quaking QKI (KH domain 119307 BE048061Hs.37054 ephrin-A3 3 1.1 119355 BE218319Hs.5807 GTPase Rab14 1.15.6 119462 BE041667Hs.314544 Homo sapiens 1.44.3 cervical cancer suppressor-119771 AI905687Hs.2533 EST 3.21 119940 AL050097Hs.272531 DKFZP586B0319 4.30.7 protein 119943 BE565849Hs.14158 copine III 3.51.9 120407 AA235207Hs.250456 hypothetical 1.53.7 protein DKFZp762F2011 6$120493 AW968080Hs.152939 Homo sapiens 4 1.4 clone 24630 mRNA sequence 120677 AF150208Hs.108327 damage-specific1.66.8 DNA binding protein 1 (1 120867 AA350781Hs.96967 ESTs 1.13.6 1~0 121368 Hs.178292 KIAA0180 protein1.5 4.1 121603 Hs.249495 heterogeneous 2.2 5.5 AA416785 nuclear ribonucleoprotein 121723 Hs.104800 hypothetical 3.4 3.2 AA243499 protein FLJ10134 122223 Hs.27413 adaptor protein3.9 3.9 AF169797 containing pH domain, PT

$ 122378 Hs.21356 hypothetical 1.4 7.1 AB032948 protein DKFZp762K2015 122946 Hs.308026 major histocompatibility1.4 3.7 AI718702 complex, class 123155 Hs.284291 sorting nexin 1.2 4.9 123158 Hs.218329 hypothetical 2.4 3.6 AF161426 protein 123327 Hs.178443 ESTs 0.9 5.2 1 123495 Hs.106747 serine carboxypeptidase1.3 5.1 ~ W28673 1 precursor prot 123526 gb:ae55d04.s1 Stratagene2.1 5.2 AA608657 lung carcinoma 123533 gb:ae56h07.s1 Stratagene2.1 9.3 AA608751 lung carcinoma 123768 Hs.188762 ESTs, Moderately 3.6 AI932318 similar to H2BL_HUMAN
H 1.1 123961 Hs.21610 DKFZP434B203 1.1 3.5 AL050184 protein 1$ 123999 Hs.7351 cyclic AMP phosphoprotein,191.4 3.8 AF084555 kD

124000 Hs.74861 activated RNA 1.9 11.2 BE563957 polymerise II transcriptio 124038 Hs.173933 nuclear factorllA1.5 4.4 124059 Hs.283713 ESTs, Weakly 14.811.5 BE387335 similar to S64054 hypotheti 124083 Hs.7734 hypothetical 1.2 6.2 AW195237 protein FLJ22174 124148 Hs.227751 lectin, galactoside-binding,2.5 12.7 BE300094 soluble,1 124153 Hs.160483 erythrocyte 1 4.1 AU077333 membrane protein band 7.2 (s 124252 Hs.334725 Homo sapiens, 1.5 8.4 BE613340 Similar to RIKEN cDNA

124314 Hs.215766 GTP-binding 1.8 10.2 AK001552 protein 124375 Hs.192966 KIAA0265 protein1.1 4.8 2$ 124432 Hs.268869 ESTs,WeaklysimilartoALUC1.3 4.1 N39016 HUMANhII

124447 gb:yy98e12.s1 Soares 2.7 4.3 N48000 multiple_sclerosis_ 124539 Hs.146409 cell division 2.1 5.7 D54120 cycle 42 (GTP-binding prot 124543 Hs.104573 ESTs 1 4.1 124564 Hs.108275 ESTs 1.4 4 124574 Hs.42322 A kinase (PRKA)0.7 4 AL036596 anchor protein 2 124605 Hs.77171 minichromosome 1.1 3.5 AA749315 maintenance deficient (S.

124639 Hs.21143 DKFZP586C1324 1.4 3.6 H60193 protein 124659 Hs.289068 Homo sapiens 1.5 9.9 AI680737 cDNA FLJ11918 fis, clone HE

124737 Hs.78793 protein kinase 0.7 4 BE270465 C, zeta 3 124760 Hs.91052 ESTs, Moderately 3.6 $ AW408586 similar to ALUS_HUMAN
A 0.9 124763 Hs.76288 calpain 2, (mlll)1.3 3.9 BE410405 large subunit 124792 Hs.48712 hypothetical 1.8 4.2 844357 protein FLJ20736 124842 gb:yg93h09.s1 Soares 1 3.6 856485 infant brain 1NIB H

124940 Hs.103804 heterogeneous 3.2 3.4 AF068846 nuclear ribonucleoprotein 124949 Hs.336780 tubulin, beta 1 4.4 AI903210 polypeptide 124960 Hs.194766 seizure related0.9 5.2 AL023513 gene 6 (mouse)-like 124995 Hs.110044 ESTs 0.9 3.5 125030 Hs.187775 ESTs 1.2 5 125034 Hs.5167 Homo Sapiens 1.5 3.7 BE548446 mRNA; cDNA DKFZp434F152 (fr 4$ 125058 Hs.3343 phosphoglycerate0.9 6 T83731 dehydrogenase 125076 gb:oq02h08.s1 NCI_CGAP_Lu5 1 3.7 AA973971 Homo sapiens 125090 gb:ye20f05.s1 Stratagene3.2 2.5 T91518 lung (937210) H

125103 Hs.122730 ESTs, Moderately5.3 6.6 AA570056 similar to KIAA1215 pro 125154 gb:zc78a07.s1 Pancreatic0.9 6.1 W38419 Islet Homo sapi $~ 125155 Hs.143669 ESTs 1.1 4.3 125159 Hs.274428 TRF2-interacting1.1 4.1 AK000669 telomeric RAP1 protein 125170 Hs.8518 selenoprotein 1.1 3.8 125181 Hs.12396 ESTs, Weakly 1 3.6 840815 similar to 2004399A
chromos 125193 Hs.84298 CD74 antigen 1.2 7.8 W67577 (invariant polypeptide of m $ 125260 Hs.294030 topoisomerase-related1 4.9 $ H05635 function protein 4 125262 Hs.171957 triple functional1.3 4.8 AW884980 domain (PTPRF interact 125272 Hs.180224 myosin regulatory1.1 16.1 BE612888 light chain 125388 Hs.64311 a disintegrin 1.4 5.3 W27235 and metalloproteinase doma 125824 Hs.286013 short coiled-coil2.4 8.7 245258 protein 125852 Hs.76550 Homo sapiens 1.8 4.6 AW630088 mRNA; cDNA DKFZp564B1264 (f 125970 Hs.177516 high density 1.9 3.8 AW504721 lipoprotein binding protein 126192 Hs.30376 hypothetical 1.4 4.1 AW160399 protein 126469 Hs.182885 ESTs, Weakly 2 3.7 BE384361 similar to JC5024 UDP~alac 126510 Hs.334762 hypothetical 1.3 4.1 AA057593 protein FLJ14735 6$ 127095 Hs.10248 Homo Sapiens 5 AA340277 cDNA FLJ20167 fis, clone CO 1.3 127524 Hs.94830 ESTs, Moderately4.3 0.9 AI243596 similar to T03094 A-kin 128312 Hs.150101 lysosomal 1.5 4.7 128453 X02761Hs.287820 fibronectin 1.24.3 128460 T16206Hs.237164 ESTs, Highly 44.4 similar to LDHH HUMAN
L-LAC3.1 128491 H08379Hs.165563 hypothetical 0.613.1 protein DKFZp434N1429 128495 NM Hs.100602 MAD (mothers 1.34 005904 against decapentaplegic, Dr $ 128546 NN~,003478Hs.101299 cullin 5 1 5.1 128574 AI185977Hs.38260 ubiquitin specific0.84 protease 18 128611 NM_014721Hs.102471 KIAA0680 gene 1.33.7 product 128652 AA432202Hs.103147 hypothetical 1.43.9 protein FLJ21347 128653 D87432Hs.10315 solute carver 1.23.6 family 7 (cationic amino 1 128655 AI246669Hs.324275 WW domain-containing0.84.1 ~ protein 1 128684 BE246444Hs.283685 hypothetical 3 1.6 protein FLJ20396 128717 AK001564Hs.104222 hypothetical 2.84.8 protein FLJ10702 128774 AA476220Hs.54457 CD81 antigen 1.110.6 (target of antiproliferativ 128790 AF026692Hs.105700 secreted frizzled-related1 3.8 protein 4 1 128805 AA194554Hs.183434 ATPase, H+transporting,5.35.3 ~ lysosomal (vacu 128827 AI638184Hs.106334 Homo Sapiens 2.25.3 clone 23836 mRNA sequence 128840 AI917602Hs.106440 ESTs 1 4.5 128869 AA768242Hs.80618 hypothetical 0.83.6 protein 128889 D60985Hs.106909 DKFZP566D193 4.63.7 protein 128890 AI222020Hs.182364 CocoaCrisp 3 1.5 128915 AK000140Hs.107139 hypothetical 0.23.9 protein 128920 AA622037Hs.166468 programmed 2.515.2 cell death 5 128926 AF155096Hs.107213 hypothetical 4 4 protein FLJ20585 128930 AA298958Hs.10724 MDS023 protein 1.24.5 2$ 128942 AW247536Hs.10729 hypothetical 1.45 protein 128948 AW953622Hs.223025 RAB31, member 2.35.6 RAS oncogene family 128953 AB020716Hs.107362 KIAA0909 protein0.93.9 128979 AW271217Hs.281434 Homo sapiens 1.53.6 cDNA FLJ14028 fis, clone HE

128980 AA258924Hs.10758 NM_002495*:Homo 0.8 3.8 Sapiens NADH dehydrogena 30 129005 AI770025Hs.13323 hypothetical 1.25.7 protein FLJ22059 129009 C15105Hs.330716 Homo Sapiens 2.19.9 cDNA FLJ14368 fis, clone HE

129013 AA371156Hs.107942 DKFZP564M112 2.43.8 protein 129068 AI634522Hs.152925 KIAA1268 protein1.23.8 129106 AW504486Hs.108689 sterol regulatory1.25.5 element binding transc 3$ 129113 BE543205Hs.288771 DKFZP586A0522protein0.53.7 129125 AB002450Hs.278391 CGI-109 protein1 5.2 129126 AW881089Hs.108806 Homo Sapiens 1.5 7 mRNA; cDNA DKFZp566M0947 (f 129151 N23018-Hs.171391 C-terminal 2.19.7 binding protein 2 129230 AA335362Hs.109646 Empirically 0.98.6 selected from AFFX single pr 4~ 129234 M18916Hs.282997 glucosidase, 1.13.5 beta; acid (includes glucos 129238 BE542214Hs.109697 ESTs 1.112.8 129239 W57656Hs.109701 ubiquitin-like3.25.1 129241 AI878857Hs.109706 hematological 1.95.7 and neurological expressed 129243 BE169531Hs.109727 TAK1-binding 1.26.6 protein 2; KIAA0733 protein 4$ 129247 849920Hs.109733 CGI-131 protein1.53.5 129250 AA344367Hs.109760 Empirically 1 5.4 selected from multiple AFFX

129258 AA250970Hs.251946 poly(A)-binding1.34.1 protein, cytoplasmic 129260 AF077200Hs.279813 hypothetical 1.63.9 protein 129270 AA357185Hs.109918 ras homolog 1.84.2 gene family, member H

$ 129277 AB007896Hs.110 putative L-type 1.16.1 ~ neutral amino acid traps 129284 AA318224Hs.296141 ESTs 2.54.8 129300 W94197Hs.110165 ribosomal protein1.65.1 L26 homolog 129318 AF189062Hs.285976 tumor metastasis-suppressor1.86.5 129352 AW511656Hs.170177 Meis1 (mouse] 0.94 hamolog $$ 129362 U30246Hs.110736 solute carrier1.49.2 family 12 (sodiumlpotassi 129379 BE278964Hs.11085 CGI-111 protein1 4.8 129390 AA318271Hs.250905 hypothetical 1 4.1 protein 129416 AA016188Hs.111244 hypothetical 1.810.7 protein 129427 AI498631Hs.111334 femtin, light 1.14.8 polypeptide 129470 W92931Hs.250899 heat shock 1.89.3 factor binding protein 129472 AL050260Hs.323817 DKFZP547E1010 1 5 protein 129475 NM_004477Hs.203772 FSHD region 1.14.2 gene 1 129498 AA449789Hs.75511 connective tissue1.96.8 growth factor 129501 AI631811Hs.180403 STRIN protein 1.19.7 6$ 129527 AA769221Hs.270847 delta-tubulin 1.14.3 129545 818087Hs.323769 cisplatin resistance1 4.2 related protein CRR

129579 AW517695Hs.286218 functional 2.33.5 adhesion molecule 1 1$~

129606 AW968941Hs.166254 hypothetical 2.4 4.4 protein DKFZp5661133 129619 AA209534Hs.284243 tetraspan 3.2 13 NET-6 protein 129620 D79338Hs.239720 CCR4-NOT transcription1.6 4.6 complex, subunit 129621 AL110212Hs.301005 purine-rich 1.1 5.7 element binding protein B

$ 129634 AB020335Hs.181300 sel-1 (suppressor0.9 4.3 of lin-12, C.elegans)-129663 AI207406Hs.11866 translocase 1.9 4.8 of inner mitochondrial membr 129679 AW889132Hs.11916 ribokinase 0.9 4.1 129688 U53209Hs.24937 transformer-2 1.3 4.7 alpha (htra-2 alpha) 129691 M26939Hs.119571 collagen, 4.7 3.7 type III, alpha 1 (Ehlers-Danl 1 129712 U46386Hs.12102 sorting nexin 1.2 3.6 ~ 3 129747 AL050272Hs.12305 DKFZP566B183 1 8.9 protein 129788 BE397454Hs.124969 Homo Sapiens 3.6 clone 24707 mRNA sequence 1.4 129796 BE218319Hs.5807 GTPase Rab14 2.9 5.1 129797 M62839Hs.1252 apolipoprotein 0.3 5.1 H (beta-2-glycoprotein I) 1$ 129800 AF052112Hs.12540 lysosomal 1.6 8.8 129834 AL080084Hs.296155 CGI-100 protein0.9 5.3 129836 AW410233Hs.206521 YME1 (S.cerevisiae)-like1.8 9.9 129843 NM_014840Hs.200598 KIAA0537 gene0.9 3.6 product 129874 AA626937Hs.181551 hypothetical 1.4 9.5 protein MGC2594 129878 243161Hs.283714 30 kDa protein1.1 6.3 129904 AL119499Hs.13285 neuronal potassium1 3.5 channel alpha subunit 129917 M30773Hs.278540 protein phosphatase2 5.1 3 (formerly 2B), reg 129976 X14008Hs.234734 lysosomal 0.9 4.9 129982 214221gb:H.sapiens germline 1.2 3.6 transcript of Ig h 2$ 130007 815917Hs.142570 Homo sapiens 1.3 clone 24629 mRNA sequence 4.3 130060 BE277024Hs.146381 RNA binding 1.6 3.8 motif protein, X chromosome 130064 X57815.compEmpirically selected 1.2 8.2 from AFFX single pr 130068 M93143Hs.262869 plasminogen-like1.4 7.9 130090 H97878Hs.132390 zinc finger 1.4 12.3 protein 36 (KOX 18) 130095 AK001635Hs.14838 hypothetical 0.2 4.6 protein FLJ10773 130102 W61005Hs.14896 DHHC1 protein 1 4.1 .

130112 AA916785Hs.180610 splicing factor1.2 5.3 prolinelglutamine rich ( 130115 T47294Hs.149923 X-box binding3.8 0.8 protein 1 130123 NM Hs.150390 zinc finger 1 4.2 005095 protein 262 3$ _ Hs.15113 homogentisate 0.5 4 130150 BE0948481,2-dioxygenase (homogenti 130161 842678Hs.151385 KIAA0564 protein1 3.7 130210 M23115Hs.1526 ATPase, Cai+transporfing,0.4 4.4 cardiac muscl 130213 BE278370Hs.15265 heterogeneous 1.7 7.5 nuclear ribonucleoprotein 130215 BE301883Hs.152707 glioblastoma 1 5.6 amplified sequence 130232 U29463gb:Human cytochrome 1.2 4.2 b561 gen 130252 U92014Hs.153527 Homo sapiens 1.3 3.6 pTM5 mariner-like transposo 130281 W78907Hs.15395 similar to 1.5 4.4 arginyl-tRNA synthetase (argi 130343 AB040914Hs.278628 KIAA1481 protein2.9 7.5 130385 AW067800Hs.155223 stanniocalcin3.2 0.2 4$ 130414 AW842182Hs.241392 small inducible1.4 10.6 cytokine A5 (RANTES) 130417 AW163518Hs.155485 huntingtin 1.7 11.7 interacting protein 130440 AA852868Hs.132853 KIAA0171 gene1.1 5 product 130442 NM_006245Hs.118244 protein phosphatase1.4 4.3 2, regulatory subuni 130465 AW362955Hs.15641 Homo Sapiens 1.6 7.6 cDNA FLJ14415 fis, clone HE

130479 844163Hs.12457 hypothetical 0.9 4.1 protein FLJ10814 130499 AB007915Hs.158286 KIAA0446 gene1 3.8 product 130546 AI598022Hs.193989 TAR DNA binding1.3 4.7 protein 130568 AA232119Hs.16085 putative G-protein1.2 9.4 coupled receptor 130606 AI652143Hs.288382 hypothetical 1 4.1 protein FLJ13111 $ 130612 BE242873Hs.16677 WD repeat domain1.1 3.6 $ 15 130616 AL049963Hs.284205 up-regulated 0.6 3.8 by BCG-CWS

130623 AL045128Hs.1691 glucan (1,4-alpha-),0.9 6.6 branching enzyme 1 130629 AL042896Hs.1697 ATPase, H+transporting,0.9 3.9 lysosomal (vacu 130632 AW073971Hs.238954 ESTs, Weakly 0.9 6.9 similar to KIAA1204 protein 60 130639 AI557212Hs.17132 ESTs, Moderately2.6 3.9 similar to 154374 gene 130641 AF158555Hs.239189 glufaminase 1.2 13.8 130653 AI861791Hs.278479 TSPY-like 1.3 4 130655 AI831962Hs.17409 cysteine-rich 2.5 4 protein 1 (intestinal) 130666 AL117508Hs.194035 KIAA0737 gene1.3 6.2 product 6$ 130669 AI928985Hs.17680 hypothetical 1.4 3.9 protein MGC1314 similar to 130693 868537Hs.17962 ESTs 3.2 0.8 130694 NM_014827Hs.17969 KIAA0663 gene 1.1 4.8 product 1~3 130696 AA325308Hs.18016 Homo sapiens 1.8 mRNA; cDNA DKFZp586H0324 (f 130701 298883Hs.18079 phosphatidylinositol1.1 6.7 glycan, class Q

130707 AW190925Hs.203559 hypothetical 1.2 4.1 protein FLJ12701 130731 AI932971Hs.18593 Homo sapiens 1,4 6.9 cDNA: FLJ21449 fis, clone C

130787 AF072813Hs.252831 reticulon 3 1.2 11.2 130796 AA088809Hs.19525 hypothetical 1.8 6.8 protein FLJ22794 130808 NM Hs.1973 cyclin F 1.3 4.1 130863 Y10805Hs.20521 HMT1 (hnRNP 3.2 5.9 methyltransferase, S.
cerevi 130902 AB037750Hs.21061 KIAA1329 protein1 3.8 130908 AW195747Hs.21122 hypothetical 1.3 7.9 protein FLJ11830 similar to 130911 BE409769Hs.21189 DnaJ (Hsp40) 2.7 3.7 homolog, subfamily A, membe 130913 BE390905Hs.21198 translocase 1.9 4 of outer mitochondrial membr 130923 H96115Hs.21293 UDP-N-acteylglucosamine1.9 10.3 pyrophosphorylas 130959 AB023182Hs.184523 KIAA0965 protein1.5 6.8 I 130967 AA393071Hs.182579 leucine aminopeptidase1.4 5.5 S

130975 AA099923Hs.283728 PEST-containing1.3 3.8 nuclear protein 131037 BE243101Hs.22391 chromosome 20open1.9 4.1 reading frame 3 131039 D87436Hs.166318 lipin 2 1.6 3.5 131060 AA194422Hs.22564 myosin VI 4.5 5 131097 AL137682Hs.22937 I-kappa-B-interacting2 3.7 Ras-like protein 2 131101 BE387561Hs.22981 DKFZP586M1523 1.6 ~
protein 4.5 131104 W27770Hs.301756 ESTs, Weakly 0.9 3.5 similar to T31475 hypotheti 131107 BE620886Hs.75354 GCN1 (general 2.1 4.5 control of amino-acid synt 131109 BE564123Hs.23060 DKFZP564F0522 1.1 4.6 protein 2S 131136 A8033099Hs.23413 KIAA1273 protein1.2 4.2 131148 AW953575Hs.303125 p53-induced 4.5 13.5 protein PIGPC1 131150 X77753Hs.23582 tumor-associated3.4 0.4 calcium signal transduc 131156 AI472209Hs.323117 ESTs 0.8 4.9 131164 AW013807Hs.182265 keratin 19 3.3 2.4 131181 H25094Hs.293663 ESTs, Moderately0.6 4 similar to 138022 hypot 131194 AW864222Hs.24083 KIAA0997 protein1.4 3.8 131199 AW979155Hs.298275 amino acid 1.2 8.5 transporter 2 131215 AL050107Hs.24341 transcriptional0.7 4.7 co-activatorwith PDZ-bi 131216 AI815486Hs.243901 Homo sapiens 2.1 8.2 cDNA FLJ20738 fis, clone HE

3 131233 D89053Hs.268012 fatty-acid-Coenzyme1.7 3.5 $ A ligase, long-chain 131237 AW956868Hs.24608 DKFZP564D177 1.3 5.4 protein 131262 AU077158Hs.24930 tubulin-specific1.6 4.8 chaperone a 131263 AU077002Hs.24950 regulator of 1.4 4.4 G-protein signalling 131367 AI750575Hs.173933 nuclear factor3.3 2.2 IIA

131372 AW293399Hs.144904 nuclear receptor1.6 3.9 co-repressor 1 131373 NIv~006052Hs.26146 Down syndrome 1 11.1 critical region gene 131388 NM Hs.92200 KIAA0480 gene 5 2 014810 product 131492 AI452601Hs.288869 nuclear receptor0.9 3.5 subfamily 2, group F, m 131493 AW960146Hs.284137 hypothetical 1 3.5 protein FLJ12888 ~5 131514 BE270734Hs.2795 lactate dehydrogenase2 6.5 A

131524 AB040927Hs.301804 KIAA1494 protein1.5 10.7 131528 AU076408Hs.28309 UDP-glucose 1.3 4.7 dehydrogenase 131534 AF157326Hs.184786 TBP-interacting1.3 4.9 protein 131555 T47364Hs.278613 interferon, 1.5 8 alpha-inducible protein 131578 AA936296Hs.234265 DKFZP586G011 1.8 3.5 protein 131589 C18825Hs.29191 epithelial membrane1.3 8.2 protein 2 131609 D83032Hs.169984 nuclear protein2.8 3.9 131626 BE514605Hs.289092 Homo sapiens 1.3 11.2 cDNA: FLJ22380 fis, clone H

131670 H03514Hs.10130 ESTs 1.3 4.8 $5 131697 C19034Hs.288613 Homo sapiens 3.2 9.7 cDNA FLJ14175 fls, clone NT

131701 AF103798Hs.30819 hypothetical 1.3 5.2 protein 131703 AW160865Hs.30888 cytochrome c 1.3 7.8 oxidase subunit Vlla polype 131739 AF017986Hs.31386 secreted friuled-related10.614.7 protein 2 131764 AI805664Hs.31731 peroxiredoxin 1.1 3.6 131781 AF077036Hs.31989 DKFZP586G1722 1.6 3.7 protein 131791 X62111gb:H.sapiens VII-5 gene 1.1 3.5 for immunoglobul 131853 AI681917Hs.3321 ESTs, Highly 1.2 similar to IRX1 HUMAN
IROQU 5.3 131870 NM_014874Hs.3363 KIAA0214 gene 0.6 4,2 product 131903 NM Hs.3436 deleted in oral 2.4 4.9 004642 cancer (mouse, homology 6S 131913 AW207440Hs.185973 degenerative 2.4 6 spermatocyte (homolog Droso 131930 AA772603Hs.69476 Homo sapiens 1.7 9.2 cDNA FLJ12758 fis, clone NT

131941 BE252983Hs.35086 ubiquitin specific0.5 5.2 protease 1 1~4 131947 AI123939Hs.182997 ESTs 0.7 4.1 131961 AA129782Hs.3576 Homo Sapiens 0.9 4.8 mRNA full length insert cDN

131964 AW381148Hs.198365 2,3-bisphosphoglycerate1.1 6.1 mutase 131974 AF208856Hs.268122 hypothetical 1.3 3.9 protein 131983 AF119665Hs.184011 pyrophosphatase3.3 6.9 (inorganic) 131997 AF229181Hs.136644 CS box-containing0.9 5.2 WD protein 132006 AW162336Hs.3709 low molecular 1.2 3.6 mass ubiquinone-binding pr 132063 BE277910Hs.3833 3'-phosphoadenosine3.2 1.8 5'-phosphosulfate sy 132065 BE379335Hs.211594 proteasome 1.2 3.6 (prosome, macropain) 268 subu 1 132071 AF217798Hs.3850 LIS1-interacting0.7 5.2 ~ protein NUDEL; endoolig 132079 A1701457Hs.38694 ESTs 2 5.3 132094 NM_016045Hs.3945 CGI-107 protein 1.2 4.3 132116 AW960474Hs.40289 ESTs 3.1 3.1 132164 AI752235Hs.41270 procollagen-lysine,1.8 3.7 2-oxoglutarate 5-dio 1 132181 AW961231Hs.16773 Homo sapiens 1.2 S clone TCCCIA00427 mRNA
sequ 132208 AL031709Hs.241575 hypothetical 1.4 4.2 protein CA856184 132258 AA306325Hs.4311 SUMO-1 activating2 10.3 enryme subunit 2 132303 BE177330Hs.325093 Homo sapiens 1.2 4.1 cDNA: FLJ21210 fis, clone C

132316 028831Hs.44566 KIAA1641 protein5.9 1.6 132358 NM Hs.46423 H4 histone family,5.8 1.5 003542 member G

132384 AA312135Hs.46967 HSPC034 protein2.1 9.3 132397 AA021160Hs.4750 hypothetical 1.3 4.6 protein DKFZp564K0822 132413 AW361383Hs.260116 metalloprotease2 4.9 1 (pitrilysin family) 132442 AW970859Hs.313503 ESTs 1.2 5 ~$ 132534 BE388673Hs.5086 hypothetical 2 3.9 protein MGC10433 132540 BE396290Hs.5097 synaptogyrin 1.4 5.1 132554 AF065391Hs.194718 zinc finger 1.2 4 protein 265 132575 AV660538Hs.284162 60S ribosomal 3 1.7 protein L30 isolog 132585 AF029750Hs.179600 TAP binding 1.8 4.7 protein (tapasin) 30 132602 AW606927Hs.5306 hypothetical 1.6 4.9 protein DKFZp586F1122 simil 132608 AA353044Hs.5321 ARP3 (actin-related1.8 8.1 protein 3, yeast) ho 132718 NM Hs.554 Sjogren syndrome 4.2 2 004600 antigen A2 (60kD, ribon 132719 AI264357Hs.55405 hypothetical 1.1 5.3 protein MGC16212 132730 AK000868Hs.5570 hypothetical 1.4 5.2 protein FLJ10006 3 132765 BE222975Hs.56205 insulin induced1.1 5.8 S gene 1 132782 F07424Hs.279840 zinc finger 1.3 3.7 protein 222 132793 AB020713Hs.56966 KIAA0906 protein2.3 6.3 132805 AW975748Hs.5724 sclerostin 0.7 7.7 132863 BE268048Hs.236494 RA810, member 1.8 6.2 RAS oncogene family 40 132894 D63209Hs.5944 solute comer 1.5 20.8 family 11 (proton-coupled 132930 AA579258Hs.6083 Homo sapiens 1 3.8 cDNA: FLJ21028 fis, clone C

132932 AW118826Hs.6093 Homo sapiens 0.7 5.4 cDNA: FLJ22783 fis, clone K

132933 BE263252Hs.6101 hypothetical 1.6 4.1 protein MGC3178 132965 AI248173Hs.191460 hypothetical 1 4.2 protein MGC12936 45 132984 BE539199Hs.62112 zinc finger 1.5 4.4 protein 207 132990 X77343Hs.334334 transcription 13.90.8 factor AP-2 alpha (activat 132998 Y00062Hs.170121 protein tyrosine0.6 4.6 phosphatase, receptor t 133002 AW499985Hs.42915 ARP2 (actin-related1.5 11.1 protein 2, yeast) ho 133011 NM_006379Hs.171921 sema domain, 3.5 1 immunoglobulin domain (Ig) 50 133012 AA847843Hs.62711 Homo Sapiens, 4.5 clone INIAGE:3351295, mRNA1 133040 AW502761Hs.30909 KIAA0430 gene 0.9 5.5 product 133056 H12028Hs.6396 jumping translocation1.7 5.3 breakpoint 133063 AI654133Hs.30212 thyroid receptor0.6 4.9 interacting protein 133067 AK000708Hs.169764 hypothetical 1.2 3.5 protein FLJ20701 55 133080 AF089816Hs.6454 chromosome 19 1.2 17.5 open reading frame 3 133110 AA808177Hs.65228 ESTs 0.9 5.1 133150 AV655783Hs.661 Empirically selected1.1 4.5 from AFFX single pr 133175 AW955632Hs.66666 ESTs, Weakly 1.5 4.8 similar to S19560 proline-r 133199 AF231981Hs.250175 homolog of 5.5 5.9 yeast long chain polyunsatura 133203 AA464362Hs.6748 hypothetical 1.2 3.7 protein PP1665 133206 AB037773Hs.6762 hypothetical 1.6 8.6 protein 133221 W32474Hs.301746 RAP2A, member 2.4 4.8 of RAS oncogene family 133229 AL137480Hs.6834 KIAA1014 protein1 4.2 133241 AW796524Hs.68644 Homo sapiens 1.3 3.9 microsomal signal peptidase ())$133257 BE617892Hs.6895 actin related 1.4 5.4 protein 213 complex, subun 133271 248633Hs.283742 H.sapiens mRNA3.1 0.7 for retrotransposon 133273 N27672Hs.69469 dendritic cell 2.5 6.5 protein 133287AW797437Hs.69771B-factor, properdin1.34 133291BE297855Hs.69855NRAS-related gene 1.45 133292AA304961Hs.699peptidylprolyl isomerase2.26.8 B (cyclophilin 133294AJ001388Hs.69997zinc finger protein1.54.3 $ 133300AF116666Hs.70333hypothetical protein1.46.3 133302X04898Hs.237658apolipoprotein A-II0.23.6 133308U56979Hs.250651H factor 1 (complement)0.65 133347BE257758Hs.71475acid cluster protein1.24.2 133370AF245505Hs.72157DKFZP56411922 protein3.75.8 1 133404AB007916Hs.214646KIAA0447 gene product1.45.1 ~

133408AI738719Hs.198427hexokinase 2 0.96.3 133422AB033061Hs.73287KIAA1235 protein 1.23.7 133442AL137663Hs.7378Homo sapsens mRNA; 0.7 4.8 cDNA DKFZp434G227 (fr 133448M27749Hs.288168immunoglobulin lambda-like1.14.3 polypeptide 1 1$133449AF038962Hs.7381voltage-dependent 0.74.2 anion channel 3 133501AI962602Hs.74284hypothetical protein3.15.9 133504NM_004415Hs.74316desmoplakin (DPI, 4,311.5 DPII) 133506BE562958Hs.74346hypothetical protein1.819.7 133532D87452Hs.74579KIAA0263 gene product1.25.4 20133574H97991Hs.193313Empirically selected1.43.9 from AFFX single pr 133586AI929645Hs.225936synapsin I 0.84.9 133589L37368Hs.75104RNA-binding protein2 10.8 S1, serine-rich doma 133591AI423369Hs.75111protease, serine,112.14.5 (IGF binding) 133606U10564Hs.75188wee1+(S. pombe) 3.31.1 homosog 2$133617BE244334Hs.75249ADP-ribosylaGon 2.35.6 factor-like 6 interacts 133651AI301740Hs.173381dihydropyrimidinase-like0.813.5 133660H14843Hs.303154popeye protein 3 1 9.1 133663AJ006239Hs.75438qusnosd dihydropteridine0.55.8 reductase 133668L77964Hs.271980mitogen-activated 1.16.9 protein kinase 133671AW503116Hs.301819zinc finger protein1.83.8 133681AI352558Hs.75544tyrosine 3-monooxygenaseltryptophan1.511.1 5-mo 133694W17187.compHs.232400heterogeneous nuclear2 3.9 ribonucleoprotein 133708A1018666Hs.75667synaptophysin 0.63.5 , 133737AW001130Hs.75824KIAA0174 gene product1.27.2 3$133743AI929587Hs.75847CREBBPIEP300 inhibitory1.55 protein 1 133750BE410769Hs.75873zyxin 1.24.8 133765M62194Hs.75929cadherin 11, type 3.24.1 2, OB-cadherin (osteob 133776BE268649Hs.177766ADP-ribosyltransferase2.13.8 (NAD+; poly (ADP-133799W24087Hs.76285DKFZP564B167 protein1.912.6 40133800AF075337Hs.76293thymossn, beta 10 2.66.6 133802AW239400Hs.76297G protein-coupled 1 4.9 receptor ksnase 133806D25969Hs.76325step II splicing 0.53.8 factor SLU7 133817AW578716Hs.7644H1 hsstone famsly, 1.54.5 member 2 133829AW630088Hs.76550Homo sapsens mRNA; 3.7 5.6 cDNA DKFZp564B1264 (f 4$133841AA345824Hs.76688carboxylesterase 0.34.4 1 (monocyte/macrophage 133845AA147026Hs.76704ESTs 5.52.9 133863AI815523Hs.76930synuclein, alpha 0.64.8 (non A4 component of am 133887X07767Hs.77271protein kinase, 1 10.2 cAMP-dependent, catalyti 133892AW859528Hs.301497arginyltransferase 0.94.8 133913AU076964Hs.7753calumenin 2.810.5 133914AI458213Hs.77542ESTs 1.85.6 133917AL031177Hs.7756proteasome (prosome,1.56.6 macropain) 268 subu 133947L41066Hs.77810nuclear factor of 1.53.8 activated T-cells, cyt 133986M54968Hs.184050v-Ki-ras2 Kirsten 0.94.3 rat sarcoma 2 viral on $$133987L15409Hs.174007von Hippel-Lsndau 2.34.3 syndrome 133989AL040328Hs.78202SWIISNF related, 3.33.4 matrix associated, acts 133990848316Hs.7822Homo sapiens mRNA; 6 1.3 5.7 cDNA DKFZp564C121 (f 134029BE150882Hs.143601hypothetical protein1 6.5 hCLA-iso 134040NM_003470Hs.78683ubiquitin specific 1.73.6 protease 7 (herpes vi 134042A1027881Hs.7869lysosomal 1 7.5 134049AF117236Hs.78825matrin 3 1.24 134095NM_004354Hs.79069cyclin G2 2.74.8 134098BE513171Hs.79086mitochondrial ribosomal3.32.1 protein L3 134207243039Hs.170198KIAA0009 gene product1.33.5 6$134210AF035606Hs.80019programmed cell 1.76.9 death 6 134218U77735Hs.80205pim-2 oncogene 0.85.3 134270X68194Hs.80919synaptophysin-like 1.411.4 protein 1~6 134277 NM Hs.80988 collagen, type 2.63.5 004369 VI, alpha 3 134280 NM Hs.81029 biliverdin reductase1.85.8 134288 A1022650Hs.8117 erbb2-interacting1.13.6 protein ERBIN

134296 800603Hs.8128 phosphatidylserine1.15.9 decarboxylase $ 134300 NM_001430Hs.8136 endothelial PAS 0.54.8 domain protein 1 134310 AL037800Hs.8148 selenoprotein 1.77.9 T

134343 D50683Hs.82028 transforming 0.87.6 growth factor, beta recepto 134364 X76534Hs.82226 glycoprotein 2.23.6 (transmembrane) nmb 134374 N22687Hs.8236 ESTs 1.93.6 1 134378 AL035786Hs.82425 actin related 1.5S.3 ~ protein 213 complex, subun 134382 BE512856Hs.109051 SH3 domain 1.13.6 binding glutamic acid-rich pr 134415 AI750762Hs.82911 protein tyrosine1.94.6 phosphatase type IVA, m 134417 NM Hs.82921 solute comer 1.27.5 006416 family 35 (CMP-sialic aci 134421 AU077196Hs.82985 collagen, type 6.68.7 V, alpha 2 1 134439 223024Hs.138860 Rho GTPase 2 3.9 S activating protein 1 134454 NM_013230Hs.286124 CD24 antigen 3.51.1 (small cell lung carcinoma 134494 D86981Hs.84084 amyloid beta 1.54.4 precursor protein (cytoplas 134501 W84869Hs.211568 eukaryotic 1.25.7 translation initiation factor 134505 AW960673Hs.177530 ATP synthase, 1.33.9 H+transporting, mitochond 134520 BE091005Hs.74861 activated RNA 1.84.3 polymerise II transcriptio 134528 M23161Hs.84775 Human transposon-like0.85.6 element mRNA

134545 AI902899Hs.85155 butyrate response1.45 factor 1 (EGF-response 134553 AI203545Hs.296169 S-phase response0.83.9 (cyclin-related) 134573 NM_016142Hs.279617 steroid dehydrogenase1.35.7 homolog ~$134576 AB033017Hs.8594 KIAA1191 protein0.93.7 134577 BE244323Hs.85951 exportin, tRNA 4 6.8 (nuclear export receptor 134579 AW936928Hs.85963 DKFZP564M182 2.24.3 protein 134582 AA927177Hs.86041 CGG triplet 1.63.6 repeat binding protein 134600 AF078859Hs.86347 hypothetical 2.13.5 protein 30134655 AF265208Hs.123090 SWIISNF related,1.74.2 matrix associated, acti 134700 AK000606Hs.8868 golgi SNAP receptor4.40.9 complex member 1 134737 D17530Hs.89434 drebrin 1 3.11.6 134762 T51986Hs.283108 hemoglobin, 0.54.6 gamma G

134843 AA428520Hs.90061 progesterone 1.33.7 binding protein 134854 J03464Hs.179573 collagen, type8.717.3 I, alpha 2 134865 AA587775Hs.66295 multi-PDZ-domain-containing1.74 protein 134868 AB020689Hs.90419 KIAA0882 protein3.40.9 134874 AI803761Hs.90458 serine palmitoyltransferase,1.36.9 long chain 134885 AJ002030Hs.9071 progesterone 1.49.6 membrane binding protein 40134891 851083Hs.90787 ESTs 1 10.1 134908 BE089782Hs.9877 hypothetical 1.93.9 protein 134934 AF005043Hs.91390 poly (ADP-ribose)1 4.3 glycohydrolase 134970 BE560779Hs.284233 NICE-5 protein1.410.4 134982 AK002085Hs.92308 Homo Sapiens 1.64.1 cDNA FLJ11223 fis, clone PL

45135011 AB037835Hs.92991 KIAA1414 protein1.25.6 135032 AW301984Hs.173685 hypothetical 1.77.6 protein FLJ12619 135035 AL034344Hs.284186 forkhead box 3.20.6 135051 AI272141Hs.83484 SRY (sex determining4.24.1 region Y)-box 4 135060 AK001887Hs.259842 protein kinase,1.34.8 AMP-activated, gamma 2 n 135062 AK000967Hs.93872 KIAA1682 protein2 3.7 135077 AW503733Hs.9414 KIAA1488 protein2.83.7 135082 AB017363Hs.94234 frizzled (Drosophila)2.44.8 homolog 1 135107 T97257Hs.337531 ESTs, Moderately1.45.8 similar to 138022 hypot 135143 AA132813Hs.69559 KIAA1096 protein1.88.5 $ - 135156 Hs.9552 binder of Ari 1.26.8 $ BE563088 Two 135172 AB028956Hs.12144 KIAA1033 protein3.11.4 135181 BE250865Hs.279529 pxl9-like protein1.37.5 135222 AA534009Hs.183487 interferon 1.33.8 stimulated gene (20kD) 135232 AL038812Hs.96800 ESTs, Moderately 3.9 similarto ALU7_HUMAN
A 2.1 135289 AW372569Hs.9788 hypothetical 0.98.4 protein MGC10924 similar to 135290 AA331901Hs.184736 hypothetical 1 3.8 protein FLJ10097 135291 T83882Hs.97927 ESTs 1.23.5 135349 AA114212Hs.9930 serine (or cysteine)2.68.9 proteinase inhibito 135357 AI565004Hs.79572 cathepsin D 2.55.4 (lysosomal aspartyl protease 6S135398 M16029Hs.287270 ret proto-oncogene0.47.9 (multiple endocrine n 135399 W79431Hs.326249 ribosomal protein1.54.5 135400 X78592Hs.99915 androgen receptor3.21.8 (dihydrotestosterone r 302665 Hs.224410 3.6 899693 Homo sapiens cDNA

fis, clone NT
3.6 302892 Hs.42346 3.3 1.6 AW176909 calcineurin-binding protein calsarcin-1 302963 Hs.151945 0.9 4.2 AW673106 mitochondria) ribosomal protein 303131 Hs.103180 3 17.3 protein $ 303150 Hs.8217 6.2 4 AA887146 stromal antigen 310125 Hs.285005 1.2 6.6 AA147979 mitochondrialimportreceptorTom22 312662 Hs.286241 1 3.5 AA233808 protein kinase, cAMP-dependent, regulato 319429 Hs.286218unctional adhesion1.5 4.7 BE616412 f molecule 1 320591 Hs.169149karyopherin alpha 1.2 ., AA054761 1 (importin alpha 5.6 5) 1 406779 Hs.279574 1.3 3.5 ~ AA412048 CGI-39 protein;
cell death-regulatory pr 410691 Hs.65450 1.2 13.9 AW239226 reticulon 410763 Hs.8966 2 5.1 AF279145 hypothetical protein 415738 Hs.295953 1.3 3.9 BE539367 ESTs, Weakly similar to uncha 420186 Hs.95697 1.5 6.2 NM_015925 liver-specific bHLH-Zip transcription fa 1$ 422055 Hs.111029 2 11.3 NM_014320 putative heme-binding protein 425815 Hs.337531 1.7 3.6 894023 ESTs, Moderately similar to hypot 426218 Hs.168005 3.3 2.8 AF119043 Homo Sapiens cDNA

fis, clone PL

427397 Hs.177656 1.3 4.7 AI929685 calmodulin (phosphorylase kinase, delt 427466 Hs.7678 1.1 3.7 AA523543 cellular retinoic acid-binding protein 427505 Hs.178761 3.2 2.5 proteasome-associated pad1 homolog 427723 Hs.279789 2.8 22 A1355260 histone deacetylase 428673 Hs.324278 1.1 5.2 AW601325 Homo Sapiens mRNA;
cDNA
DKFZp566M063 (fr 430219 Hs.235887 1.8 8.8 (hnRNP
methyltransferase, S.
cerevi 430450 Hs.241489 1.1 5.6 823553 hypothetical protein 432866 Hs.279609 1.5 6.1 BE395875 mitochondria) carrier homolog 433423 Hs.8997 1.3 7.6 BE407127 heatshock70kD
protein 437562 Hs.5683 1.6 6.5 (Asp-Glu-Ala-AspIHis) box polypep 437667 Hs.286218unctional adhesion1.3 3.5 BE616412 f molecule 1 437754 Hs.5822Homo sapiens cDNA:2 5.7 860366 FLJ22120 fis, clone H

30 440252 Hs.6101 1.1 6.2 BE513940 hypothetical protein 441471 Hs.7857 0.5 3.7 AL042986 erythrocyte membrane protein band 448292 Hs.47334 2.5 4.9 BE281316 hypothetical protein 449404 Hs.23581 1.1 3.6 H51066 leptin receptor gene-related protein 449964 Hs.273193 1.4 3.5 AW001741 hypothetical protein 3 451389 Hs.279009 4 11.2 $ N73222 matrix Gla protein 452685 Hs.30250 0.8 5.6 AI634651 v-maf musculoaponeurotic fibrosarcoma (a RC H15847 peptidylprolyl 1.8 4.8 s isomerase B
(cyclophilin B) RC W84712 calumenin 3.5 4.6 X14008 lysozyme 0.9 4.5 mat f (renal amyloidosis) 4~ RC H86543 ESTs 1.8 6.6 f H07011 ESTs; 1.8 3.9 Weakly similar to SAS
[H.sapiens]

RC AA164586 ESTs6.2 0.8 s RC_AA070485Homo 3.4 2.6 Sapiens clone RC H98714 ESTs 1.6 3.5 s 4$ RC_AA406145 ESTs4.6 3 f ~

AA458584 SRY 3.4 0.4 (sex determining region Y)-box AA031548 cell 3.1 3.9 division cycle (GTP-binding protein;
25kD) X02761 fibronectin 3.6 15.2 RC_AA487193secreted 4.7 4 frizzled-related protein $0 825326 Homo 0.9 5 sapiens mRNA
for putative vacuolar RC_AA393805ESTs; 1.1 8.4 Weakly similar to (defline not RC_AA449333ESTs 2.9 4.6 RC_AA287681s ESTs1.3 4 AA490864 ESTs; 1.4 5 RC Highly similar to heat shock factor $$ _ ESTs;Highlysimilartoheatshockfactor 1.7 5 RC_C14243_f 821443 ESTs 1.6 3.7 RC_AA251902Homo 2.2 3.8 Sapiens lysophospholipase (LPL1) M21121 small 0.9 9.9 s inducible cytokine (RANTES) C00038_s ESTs 2.8 4.8 6o Y00503 keratin 3.1 1.1 RC_R27006 ESTs 1.6 3.7 f RC_AA416886ESTs; 3.1 3.1 Weakly similar to predicted using RC_AA460450fibroblast 1.5 3.7 growth factor receptor (bacteria-RC_AA488433ESTs; 1.1 4 Weakly similar to deduced amino acid ()$RC_AA278400_f Homoapiens mRNA;
partial cds 1.5 3.6 U28831 Human 0.6 protein immuno-reactive with anti-PTH4.4 RC_AA199588Homo 1.8 4.7 Sapiens actin-related protein Arp3 (ARP3) igg AF006082 Homo Sapiens actin-related1.6 10.9 protein Arp2 (ARP2) RC_H90899 desmoplakin (DPI; DPII) 5.5 5.4 RC_W95070 desmoplakin (DPI; DPII) 2.6 RC_T90946 f Human mRNA far KIAA263 1,1 3,9 gene; complete cds D87258 protease; sedne;11 (IGF 3.5 binding) 2.4 AA313414 s ESTs; Weakly similar 1.5 5.3 to cDNA EST EMBL:T1157 RC_H73484 s ESTs; Weakly similar 6.3 to similar to Yeast 1.3 AFFX-HUMISGF3AIM97935_3 2.3 13.5 AFFX-HUMRGElM10098_5 7.9 1.1 1 ~ AFFX-M27830 0.5 7.4 AFFX-M27830 5 0.6 5.4 RC_AA063431 f ESTs 0.8 4.1 RC_T63769_f ferritin; light polypeptide3.7 1.1 1~9 Table 8A shows the accession numbers for those pkeys lacking unigeneID's for Table ~. For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oaklaald California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT number Accessions 125076 190299_1 AA973971 T88817 AA253263 114636 109698_1 AA075488 AA129081 AA074851 AA082852 AA074732 AA084908 AA084751 123526 genbank_AA608657 AA608657 2$ 123533 genbank_AA608751 AA608751 125090 genbank_T91518 T91518 125154 genbank_W38419 W38419 118475 genbank_N66845 N66845 118505 genbank_N67343 N67343 101046 entrez_K01160K01160 $0 AF017458 AJ008207 AJ008183 AJ008196 AJ008241 AJ008208 AF103210 AF068668 AW351514 D78345 T29140 J00231 NM_002179 AW405146 AA301091 X04646 H64660 $5 108470 genbank_AA079500 AA079500 101447 entrez_M21305 M21305 124447 genbank_N48000 N48000 101624 entrez_M55998 M55998 (0 X69861 AW402964 M90808 298735 298734 298736 AF035018 X79161 000545 AF174046 124842 217726_1 856485 837248 859992 103758 AA084874 f at AA084874 f 1 ~ AW407182 L03632 AW405058 L03627 AW407470 872738 L21959 AW375738 X87888 1$ 038589 218332 AF060122 AF194807 AF060135 AF064506 AF064504 AF063773 L26540 ~$ W26785 AW384496 AW407708 AA541663 AA911602 AI821461 AA588300 AA327050 109097 genbanILAA167512 AA167512 TABLE 9: Figure 9 from BRCA 001-2 US
$ Table 9 depicts a preferred group of genes upregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number 1 ~ ExAccn: ExempIarAccession number, Genbank accession number UnigenelD; Unigene number Unigene Title: Unigene gene title 1$ Pkey ExAccn UnigenelD UnigeneTitle 100690 AA383256estrogen receptor 1 Hs.1657 102211 BE314524putative transmembrane protein Hs.78776 103587 BE2702665T4 oncofetal trophoblast Hs.82128 glycoprotein 20 104115 AF183810opposite strand to trichorhinophalangeal Hs.26102 syndrome I

105038 AW503733KIAA1488 protein Hs.9414 105500 AW602166CEGP1 protein Hs.222399 105990 A1690586hypothetical protein FLJ22060 Hs.29403 106155 AA425414nuclear factor I/B
Hs.33287 2$ 106373 AW503807histone acetyltransferase Hs.21907 106414 BE568205mitogen-activated protein Hs.28827 kinase kinase kinase 2 110009 BE075297ESTs, Weakly similar to Hs.6614 A43932 mucin 2 precursor, intestinal 111900 AF131784Homo sapiens clone 25194 Hs.25318 mRNA sequence 114540 AI904232prohibitin Hs.75323 116470 AI2721415RY (sex determining region Hs.83484 Y)-box 4 117280 M18217 Homo Sapiens cDNA: FLJ21409 Hs.172129 fis, clone COL03924 Hs.2533 121723 AA243499hypothetical protein FLJ10134 Hs.104800 124059 BE387335ESTs, Weakly similar to Hs.283713 S64054 hypothetical protein YGL050w 3 131148 AW953575p53-induced protein PIGPC1 $ Hs.303125 132371 AA235448PR02000 protein Hs.46677 134169 AI690916transducer of ERBB2,1 Hs.178137 302235 AL049987Homo Sapiens mRNA; cDNA
Hs.166361 DKFZp564F112 452410 AL133619Homo Sapiens mRNA; cDNA
Hs.29383 DKFZp434 TABLE 10: Figure 10 from BRCA 001-3 PCT
Table 10 depicts a preferred group of genes upregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplaron number, Genbank Accessi accession number UnigenelD: Unigene number Unigene Title:
Unigene gene title R1: Ratio of tumor to normal body tissue R2: Ratio of percenfife tumor 90~" to body 1$ R3: Ratio of percentile body 75~" to tumor R4: Ratio of tumor to normal breast tissue Pkey ExAccn UnigenelDUnigene Title R1 R2 R3 R4 100082 AA130080 proteasome (prosome,4.2 15236 12.2 Hs.4295 macropain) 268 subu 100103 AA380887 dolichyl-phosphate 9.8 12313 5 Hs.5085 mannosyltransferase p 100131 D12485 ectonucleotide pyrophosphataselphosphodi13.224419 9.9 Hs.11951 100147 D13666 osteoblast specific15.7103066 5 Hs.136348 factor 2 (fasciclin 2S 100154 H60720 KIAA0101 gene product4.1 32078 10.6 Hs.81892 100157 D14661 Wilms'tumourl-associating4.7 11926 3 Hs.119 protein 100169 AL037228 D123 gene product 5.1 10621 9.2 Hs.82043 100203 .BE242284adenylate cyclase 4.7 47 1 4.3 Hs.172199 7 100210 D26361 KIAA0042 gene product4.7 47 4 0.7 Hs.3104 100219 AW972300 bone marrow stromal3.8 35093 1.9 Hs.118110 cell antigen 2 100234 D29677 KIAA0054 gene product;4.1 64 16 3 Hs.3085 Helicase 100248 NM_015156Hs.78398KIAA0071 protein 3.4 77 23 5.9 100252 NM 006207Hs.170040platelet-derived 4.5 45 4 4 growth factor receptor-100260 D38491 KIAA0117 protein 5.9 59 1 2.6 Hs.322478 3$ 100279 D42084 KIAA0094protein 3.5 96 28 1.3 Hs.82007 100286 BE247550 growth factor receptor-bound3.1 30698 1.5 Hs.86859 protein 7 100294 AA331881 peroxiredoxin 3 12.81281 11.7 Hs.75454 100335 AW247529 platelet-activating4.2 18744 5.4 Hs.6793 factor acetylhydrola 100365 AI878927 mesoderm specific 4.5 12929 3.1 Hs.79284 transcript (mouse) hom 100375 D80004 KIAA0182 protein 3.5 78 23 4.8 Hs.75909 100409 D86957 KIAA0202 protein 10.21021 4.8 Hs.80712 100410 D86961 lipoma HMGIC fusion4 40 1 3.8 Hs.79299 partner-like 2 100414 NM_014735Hs.82292KfAA0215 gene product3.2 32 2 2.9 100418 D86978 KIAA0225 protein 3.6 36 7 3.2 Hs.84790 100438 AA013051 topoisomerase (DNA)5.6 76 14 2 Hs.91417 II binding protein 100439 AA347720 KIAA0264 protein 3.5 35 9 3.1 Hs.122669 100448 AF234887 cadherin, EGF LAG 5.5 14527 2.2 Hs.57652 seven-pass G-type rece 100449 D87470 KIAA0280 protein 3.4 34 1 1.2 Hs.75400 100522 X51501 prolactin-induced 22.776034 1.4 Hs.99949 protein S0 100552 AA019521 lysosomal 14.41449 4.7 Hs.301946 100643 NM_005032Hs.4114plastin 3 (T isoform)4.1 25963 1.9 100661 BE623001 Homo Sapiens ribosomal3.3 11636 2.2 Hs.132748 protein L39 mRNA, 100666 L05424 CD44 antigen (homing8.5 85 1 3.2 Hs.169610 function and Indian 100667 L05424 CD44 antigen (homing3 594201 2.3 Hs.169610 function and Indian S 100745 BE207168 nuclear receptor 5 82 17 0.9 S Hs.144630 subfamily 2, group F, m 100774 J05581 mucin 1, transmembrane3.5 37 11 2.8 Hs.89603 100783 AF078847 general transcription9.7 97 10 7.2 Hs.191356 factor IIH, polype 100821 M26460 gb:Homo sapiens 3.3 33 1 0.8 (clone 104) retinoblasto 100864 BE563957 activated RNA polymerase3.7 477130 3.1 Hs.74861 II transcriptio 60 100877 X80821 KIAA0874 protein 6.3 63 4 5.7 Hs.27973 100892 BE245294 S164 protein 4.7 47 1 4.2 Hs.180789 101038 BE297139 replication protein3.8 11530 7.1 Hs.79411 A2 (32kD) 101046 K01160 NM_002122:Homo Sapiens3.9 390100 11.1 major histocompat 101079 BE264901 carbonic anhydrase 3.9 39 8 3.6 Hs.250502 VIII

101084 AW409934 nucleolar GTPase 4.1 53 13 4 Hs.75528 101104 AW862258 neuropeptide Y receptor15.3153 1 14.1 Hs.169266 Y1 101185 NM_001621Hs.170087aryl hydrocarbon 11.3113 8 3.9 receptor 101188 L20320 cyclin-dependent 3.1 118 38 2 Hs.184298 kinase 7 (homolog of Xe $ 101201 L22524 matrix metalloproteinase8.2 396 48 0.9 Hs.2256 7 (MMP7; uterin 101232 AU077288 ADP-ribosylaGon 4 110 28 10.7 Hs.242894 factor-like 1 101275 BE545277 Ts translation elongation4.2 50 12 4.4 Hs.3273 factor, mitoch 101300 BE535511 transmembrane trafficking6.6 135 21 13.1 Hs.74137 protein 101396 BE267931 proliferating cell 6.4 249 39 22.4 Hs.78996 nuclear antigen 1 101447 M21305 gb:Human alpha satellite6.5 878 135 0.8 ~ and satellite 3 101448 NM_000424Hs.195850keratin 5 (epidermolysis4.8 622 130 0.7 bullosa simplex 141470 NM 000546Hs.1846tumor protein p53 5.1 97 19 9.3 (Li-Fraumeni syndrome) 101478 NM.-002890Hs.758RAS p21 protein 9.6 96 1 8.5 activator (GTPase activa 101484 AA053486 interferon-induced 11.2112 8 5.9 Hs.20315 protein with tetratri 1$ 101507 X16896 interleukin 1 receptor,3.9 39 2 3.5 Hs.82112 type I

101621 BE391804 guanylate binding 3.6 36 1 2,6 Hs.62661 protein 1, interferon-101624 M55998 gb:Human alpha-1 3.1 2898923 2.2 collagen type I
gene, 3 101664 AA436989 H2A histone family,6.9 103 15 8.4 Hs.121017 memberA

101684 M63256 cerebellar degeneration-related6.4 64 2 4.9 Hs.75124 protein 101724 L11690 bullous pemphigoid 9.4 94 1 0.3 Hs.620 antigen 1 (2301240kD) 101754 570114 TIA1 cytotoxic granule-associated8.9 89 5 8 Hs.239489 RNA-bi 101767 M81057 carboxypeptidase 3.6 824 227 1.4 Hs.180884 B1 (tissue) 101791 M83822 cell division cycle9 144 16 13 Hs.62354 4-like 101794 M84605 putative opioid 3.3 36 11 2.4 Hs.957 receptor, neuromedin K ( 2$ 101803 AW024390 pre-B-cell leukemia5.4 180 34 15.9 Hs.155691 transcription factor 101809 M86849 gap junction protein,12 120 8 9 Hs.323733 beta 2, 26kD (coon 101839 AA446644 GA733-2 antigen; 3.1 353 116 2.8 Hs.692 epithelial glycoprotein 101888 AL049610 transcription elongation7.3 73 1 5,3 Hs.95243 factorA (SII)-101960 AL036287 calponin 3, acidic 3.8 399 105 3.3 Hs.194662 102009 BE245149 protein tyrosine 4.6 148 32 11.3 Hs.82643 kinase 9 102095 011313 sterol carrier protein9.5 95 4 8.8 Hs.75760 2 102123 NM 001809Hs.1594centromere protein 4.2 42 7 3,4 A (17kD) 102125 NM_006456Hs.288215sialyltransferase 9.3 93 4 3 102139 NM_004419Hs.2128dual specificity 5.4 137 26 2.5 phosphatase 5 3 102162 AA450274 CDC16 (cell division4.6 151 33 2 $ Hs.1592 cycle 16, S. cerevi 102165 BE313280 death associated 9.3 93 5 8 Hs.159627 protein 3 102193 AL036335 secreted phosphoprotein45.7457 1 39.7 Hs.313 1 (osteopontin, 102211 BE314524 putative transmembrane3.9 442 114 1.3 Hs.78776 protein 102221 NM_006769Hs.3844LIM domain only 4.9 49 1 3.6 4~ 102242 027185 retinoic acid receptor3.1 31 1 1.3 Hs.82547 responder (tazaro 102258 NM 001546Hs.34853inhibitor of DNA 3.8 163 43 0.5 binding 4, dominant neg 102302 AA306342 protein kinase C-like4.5 45 1 3.6 Hs.69171 2 102304 AF015224 mammaglobin 1 8.5 2058243 1.4 Hs.46452 102348 037519 aldehyde dehydrogenase6.4 428 67 2.3 Hs.87539 3 family, member 4$ 102369 039840 hepatocyte nuclear 6.7 67 9 6.3 Hs.299867 factor 3, alpha 102407 AW602154 E74-like factor 5.3 53 1 4.8 Hs.82143 2 (ets domain transcript 102409 BE300330 selenophosphate 3.3 111 34 7.5 Hs.118725 synthetase 2 102457 NM_001394Hs.2359dual specificity 20.2202 5 1.3 phosphatase 4 102544 NM_003937Hs.169139kynureninase (L-kynurenine3.8 38 1 1.5 hydrolase) $0 102567 063830 TRAF family member-associated8.2 82 1 6.8 Hs.146847 NFKB activ 102580 060808 CDP-diacylglycerol 4.1 41 1 3.3 Hs.152981 synthase (phosphatida 102618 AL037672 extracellular matrix10.2628 62 17.2 Hs.81071 protein 1 102638 067319 caspase 7, apoptosis-related5 66 13 5.3 Hs.9216 cysteine pr 102663 NIvU.002270Hs.168075karyopherin (importin)6.1 126 21 2.4 beta 2 $$ 102669 071207 eyes absent (Drosophila)4.5 45 1 2.8 Hs.29279 homolog 2 102742 079293 Human clone 23948 4.1 41 1 2.4 Hs.159264 mRNA sequence 102784 085658 transcription factorAP-24.4 255 58 1.6 Hs.61796 gamma (activat 102805 090304 Iroquois homeobox 3.6 142 39 1.6 Hs.25351 protein 5 102813 BE242035 embryonic ectoderm 3.5 35 1 2.7 Hs.151461 development 102823 D85390 carboxypeptidase 5.6 56 1 5.3 Hs.5057 D

102825 BE262386 clones 23667 and 4.2 42 7 3.7 Hs.7137 23775 zinc finger prote 102899 AI815559 signal recognition 3.2 58 18 5 Hs.75730 particle receptor ('d 102913 NM_002275Hs.80342keratin 15 . 5.8 753 131 0.4 102927 BE512730 keratin 18 3.1 815 266 1.7 Hs.65114 6$ 102961 AL119505 activating transcription3.2 32 4 2.6 Hs.198166 factor2 102968 AU076611 methylene tetrahydrofolate5.7 251 44 6.6 Hs.154672 dehydrogenase 103003 AI910275 trefoil factor 1 5.6 1346239 5.4 Hs.1406 (p52) 103023 AW500470 multifunctional polypeptide5.8218 38 13 Hs.117950 similar to S

103024 NM 002343Hs.105938lactotransfemn 3.71421388 1.9 103036 M13509 matrix metalloproteinase3.194 30 5.8 Hs.83169 1 (MMP1; inters 103038 AA926960 CDC28 protein kinase3.5332 94 3.1 Hs.334883 1 $ 103119 X63629 cadherin 3, type 4.8312 65 30.9 Hs.2877 1, P-cadherin (placenta 103134 X65724 Nome disease (pseudoglioma)5.2331 64 1.5 Hs.2839 103134 X65724 Nome disease (pseudoglioma)4.949 5 3.8 Hs.2839 103171 AW583058 serine (or cysteine)3.31497458 2.1 Hs.234726 proteinase inhibito 103206 X72755 monokine induced 3.5796 228 3.2 Hs.77367 by gamma interferon 1 103208 AW411340 retinoblastoma-binding5.6191 34 3.5 ~ Hs.31314 protein 7 103226 X75042 v-rel avian reticuloendotheliosis4.153 13 4.9 Hs.44313 viral 103333 AA206186 monocyte to macrophage3.434 8 2.3 Hs.79889 differentiation-a 103346 X87613 thyroid hormone receptor3.943 11 1 Hs.5464 coactivating pr 103352 H09366 uracil-DNA glycosylase9.393 8 8.2 Hs.78853 1 103375 NM 005982Hs.54416sine oculis homeobox9.797 1 9.3 S (Drosophila) homolo 103376 AL036166 coated vesicle membrane6.398 16 9.1 Hs.323378 protein 103391 X94453 pyrroline~-carboxylate4.377 18 7.2 Hs.114366 synthetase (glut 103438 AW175781 M-phase phosphoprotein4.9153 31 2.4 Hs.152720 6 103453 AI878922 SMT3 (suppressor 4.9261 53 3.7 Hs.180139 of mif two 3, yeast) ho 2~ 103471 Y00815 protein tyrosine 3.5564 162 1.7 Hs.75216 phosphatase, receptor t 103500 AW408009 alkylglycerone phosphate3.949 13 2.5 Hs.22580 synthase 103557 AL133415 vimentin 7.5136 18 3.4 Hs.297753 103587 BE270266 5T4 oncofetal trophoblast7.979 2 6.9 Hs.82128 glycoprotein 103605 BE409838 cadherin 1, type 3.3745 229 1.8 Hs.194657 1, E-cadherfn (epitheli 2$ 103606 AW403814 BCL2-associated athanogene3.241 13 2.8 Hs.41714 103613 NM_000346Hs.2316SRY (sex determining7.373 1 5.2 region Y)-box 9 (ca 103658 NN~000088Hs.172928collagen, type I, 3.81612429 3.1 alpha 1 103666 NM_003528Hs.2178H2B histone family, 3.232 5 2.8 member Q

103988 AA314389 ADP-ribosylation 3.232 9 2.7 Hs.42500 factor-like 5 30 103990 AB033112 bromodomain and PHD 4.949 1 4.2 Hs.42179 finger containing, 104052 NM-,002407Hs.97644mammaglobin 2 7.2498 69 9.3 104115 AF183810 opposite strand to 29 290 1 26.8 Hs.26102 trichorhinophalangeal 104129 H63349 hypothetical protein3.737 7 2.1 Hs.98806 104146 AW880614 RNA binding motif 5.252 1 4.3 Hs.146381 protein, X chromosome 3S 104147 BE081342 HSPC039 protein 8 84 11 6.3 Hs.283037 104209 AB012113 small inducible cytokine5.858 1 3.2 Hs.16530 subfamily A (Cy 104239 AB002367 doublecortin and 6.464 8 3 Hs.21355 CaM kinase-like 104278 AW583693 N-terminal acetyltransferase4.7229 49 7.9 Hs.109253 complex and 104309 AI337300 hypothetical protein3.232 7 2.4 Hs.284123 MGC4604 104394 AA129551 Homo Sapiens cDNA: 5.3144 27 13.1 Hs.172129 FLJ21409 fis, clone C

104432 X51501 prolactin-induced 6.91494218 1.3 Hs.99949 protein 104558 856678 hypothetical protein7.777 8 6.9 Hs.88959 MGC4816 104567 AA040620 hypothetical protein3.737 5 2.5 Hs.5672 AF140225 104590 AW373062 nuclear receptor 6.1493 81 0.7 Hs.83623 subfamily 1, group I, m 45 104602 H47610 gb:yp75f03.s1 Soaresfetal3.838 4 1.2 liver spleen 104613 AF123303 hypothetical protein4.8231 49 7.3 Hs.24713 104633 H00820 ESTs, Weakly similar3.4154 46 3 Hs.30977 to 834087 hypotheti 104636 882252 protein kinase (CAMP-dependent,5 468 94 4.7 Hs.106106 catalyti 104660 BE298665 Homo Sapiens mRNA; 82 22 3.1 Hs.14846 cDNA DKFZp564D016 (fr 3.8 S~ 104667 AI239923 ESTs 14.9149 1 6.4 Hs.30098 104766 BE244072 macrophage erythroblast6.3165 26 3.2 Hs.20815 attacher 104787 AA027317 gb:ze97d11.s1 Soares3.840 11 3.8 fetal hear~NbHH19W

104804 AI858702 ESTs, Weakly similar7.777 1 5.1 Hs.31803 to N-WASP [H.sapien 104807 AI139058 leucine-rich repeat-containing7 70 1 6.5 Hs.125790 2 $$ 104846 AI250789 ESTs 4.7201 43 4.5 Hs.32478 104896 AW015318 ESTs 7.474 1 6 Hs.23165 104919 AA026880 prolactin receptor 3.9280 72 3.3 Hs.25252 104926 BE298808 DKFZP434N093 protein4.2135 32 4 Hs.33363 104943 AF072873 frizzled (Drosophila)16.2162 1 4.2 Hs.114218 homolog 6 104968 AI249502 ESTs 3.838 1 2.4 Hs.29669 104977 AI392640 amino acid transporter3.2522 165 1.9 Hs.18272 system A1 104997 AA121686 ESTs 3.232 4 2.9 Hs.10592 105029 AI122691 ESTs 3.7157 43 3.6 Hs.13268 105038 AW503733 KIAA1488 protein 5.555 1 5.2 Hs.9414 6S 105041 AB037716 KIAA1295 protein 10.3103 . 3.9 Hs.26204 1 105086 AA148710 lumican 6.666 1 5.4 Hs.79914 105088 H58589 Homo Sapiens cDNA 3.131 1 2.5 Hs.35156 FLJ11027 fis, clone PL

105091 AA148859hypothetical protein 3.232 1 3 Hs.179909 FLJ22995 105143 AI368836ESTs, Weakly similar 7.373 1 3.8 Hs.24808 to 138022 hypotheti 105154 AA307279methyl-CpG binding 4.290 22 2.8 Hs.35947 domain protein 4 105162 AL133033KIAA1025 protein 6 60 6 4.6 Hs.4084 105167 AW612147Homo sapiens C1orf19 3.838 2 3.2 Hs.32058 mRNA, partial cds 105178 AA313825AD036 protein 9.343647 5.8 Hs.21941 105195 AA975096hypothetical protein 5.757 8 5.3 Hs.19522 PR02849 105200 AA328102cytoskeleton associated4.545 1 3.6 Hs.24641 protein 2 105248 AW952479tropomodulin 3 (ubiquitous)4.343 1 3.9 Hs.22826 1~ 105252 AB039670ALEX1 protein 8 80 6 7.3 Hs.9728 105253 AW997484KIAA0456 protein 3.939 6 3.2 Hs.5003 105280 AA894638ESTs 3.535 7 2.7 Hs.14600 105288 N99673 ESTs, Weakly similar 4.545 10 0.5 Hs.3585 to AF1267431 DNAJ

105309 AK000796hypothetical protein 3.893 25 7.5 Hs.4104 1 105329 AA234561ESTs 2.813147 3.9 S Hs.22862 105344 AF151073hypothetical protein 3.979 20 6.5 Hs.8645 105376 AW994032hypothetical protein 5.118136 15.8 Hs.8768 FLJ10849 105386 AW500718Homo sapiens, clone 4.141 2 3.3 Hs.8115 MGC:16169, mRNA, com 105400 AF198620RNA binding motif 6.262 6 5.6 Hs.65648 protein 8A , 105426 W20027 ESTs 3.320663 2.2 Hs.23439 105483 AL137257Homo Sapiens cDNA: 3.2466146 8.4 Hs.23458 FLJ23015 fis, clone L

105496 AL117441hypothetical protein 16.61668 12.7 Hs.301997 FLJ13033 105500 AW602166CEGP1 protein 25.450820 3 Hs.222399 105508 AA173942Homo sapiens mRNA; 11713 10.6 Hs.326416 cDNA DKFZp564H1916 (f 9 25 105511 AB037829regulator of nonsense3.232 6 1.5 Hs.3862 transcripts 2; DKF

105516 AK001269hypothetical protein 8.383 3 1.8 Hs.30738 FLJ10407 105539 AB040884KIAA1451 protein 3.573 21 1.6 Hs.109694 105564 BE616694hypothetical protein 5.833658 2 Hs.288042 FLJ14299 105610 AA280072fetal Alzheimer antigen3.232 1 1 Hs.99872 105616 835343 Human DNA sequence 4.879 17 5.2 Hs.24968 from clone RP1-233616 105627 AA281279hypothetical protein 4 75 19 1.7 Hs.23317 FLJ14681 105640 AA001021thyroid hormone receptor4.545 1 3.7 Hs.6685 interactor 8 105645 AW294631ESTs 3.636 1 0.1 Hs.11325 105674 AI609530histone deacetylase 6.464 8 6 Hs.279789 3 3S 105687 NM_014517Hs.28423upstream binding protein4.715233 5.3 1 (LBP-1a) 105691 AI680737Homo Sapiens cDNA 5.757 8 4.1 Hs.289068 FLJ11918 fis, clone HE

105730 AW377314DKFZP5641052 protein 6.969 1 4.4 Hs.5364 105731 AA834664nuclear receptor coactivator3.434 1 3.1 Hs.29131 2 105743 BE246502sema domain, immunoglobulin3 30 10 0.9 Hs.9598 domain (Ig), 105759 AI123118chemokine-like factor,5.454 1 4.4 Hs.15159 alternatively spl 105772 H57111 ESTs 5.367 13 5.3 Hs.221132 105774 AW369278hypothetical protein 4.949 1 4.5 Hs.23412 FLJ20160 105784 W84446 hypothetical protein 3.398 30 4.7 Hs.226434 MGC4643 105795 AA878183Homo Sapiens cDNA 3.214346 3.6 Hs.17448 FLJ13618 fis, clone PL

45 105806 AF206019REV1 (yeasthomolog)-like4 40 3 3.2 Hs.110347 105807 AA788946ESTs, Moderately similar4.7747158 5.7 Hs.16869 to CA1C RAT COL

105823 AI559444ESTs 3.937194 4.6 Hs.293960 105832 AW802282pyruvate dehydrogenase3.668 19 6 Hs.22265 phosphatase 105840 AA601518secreted modular calcium-binding4.813428 3.2 Hs.22209 protein 5~ 105851 AI827976hypothetical protein 4.3772179 1.7 Hs.24391 FLJ13612 ' 105864 AI640775Homo Sapiens cDNA: 4.343 1 3.7 Hs.28332 FLJ21560 fis, clone C

105870 AW021691GCN5 (general control3.636 7 3.1 Hs.101067 of amino-acid synt 105875 AK001708hypothetical protein 3.434 8 2.9 Hs.32271 FLJ10846 105886 AK001735UDP-glucose:glycoprotein3.645 13 1.3 Hs.22983 glucosyltransfe S$ 105906 N25986 ESTs 3.434 1 1.5 Hs.22380 106012 AI240665ESTs 21.22126 17.4 Hs.8895 106020 AA043039hypothetical protein 3.947 12 4.4 Hs.7870 106024 AL122072heterogeneous nuclear4.417440 1.6 Hs.103804 ribonucleoprofein 106034 AW952005hypothetical protein 4.747 1 4 Hs.14928 FLJ12903 60 106036 AA382267ESTs 3.449 15 4.4 Hs.10653 106055 AA417034gb:zu04f10.s15oares_testis_NHT3.553 15 1.2 Homo sap 106057 BE614474F-box only protein 3.411635 2.2 Hs.289074 22 106060 NM_001329Hs.171391C-terminal bindingprotein3.6444125 4.6 106070 T74445 Homo sapiens clone 3.6365103 6.9 Hs.5957 24416 mRNA sequence 65 106095 AF115402E74-like factor 5 26.335614 1 Hs.11713 lets domain transcript 106096 AW379378protein tyrosine phosphatase,3.226783 2.3 Hs.170121 receptor t 106126 AA576953hypothetical protein 3.838 1 3.3 Hs.22972 FLJ13352 106155 AA425414nuclear factorI/B 9.9 48349 1.8 Hs.33287 106157 W37943 KIAA1323 protein 6.7 94 14 8 Hs,34892 106198 AI244563Homo Sapiens clone 3.3 95 29 4.4 Hs.325531 015h12 My015 protein 106236 AB040896KIAA1463 protein 3.8 83 22 7.5 Hs.21104 $ 106286 AI765107hypothetical protein3.3 97 30 6.4 Hs.274422 FLJ20550 106290 AW961393hypothetical protein4.5 11626 4.5 Hs.16364 FLJ10955 106310 898185 ESTs 7 70 3 1.3 Hs.17240 106323 A8007866KIAA0406 gene product3,2 37 12 2.6 Hs.158249 106330 AW977397ESTs 3.8 38 1 1.9 Hs.35580 1 106383 AA447453Homo sapiens mRNA; (f 25516 6.6 ~ Hs.27860 cDNA DKFZp586M0723 16 106389 AW748420Homo sapiens cDNA: 4.9 33770 2.7 Hs.6236 FLJ21487 fis, clone C

106394 242993 Homo sapiens clone 3.1 72 23 5 Hs.25320 25142 mRNA sequence 106432 AK000310hypothetical protein3.1 16554 1.6 Hs.17138 FLJ20303 106459 AA789081glioma-amplified 3.1 31 1 2.6 Hs.4029 sequence-41 15 106503 A8033042cofactor required 5.5 14727 4.4 Hs.29679 for Sp1 transcriptiona 106508 AI205785ESTs 4.4 22251 1.8 Hs.30348 106565 NIvL014892Hs.227602KIAA1116 protein 7.4 74 3 1.7 106586 AA243837ESTs 15.21521 12.6 Hs.57787 106589 AK000933Homo Sapiens cDNA 3.8 26369 3.9 Hs.28661 FLJ10071 fis, clone HE

106596 AA452379ESTs, Moderately 4.9 49 1 4.1 Hs.293552 similar to ALU7_HUMAN
A

106611 849131 ATP-dependant interferon5.8 58 5 3.1 Hs.26267 response protei 106628 AW188205Homo sapiens clone 5.3 16632 14.9 Hs.12311 23570 mRNA sequence 106650 AL049951Homo Sapiens mRNA; 75 14 0.8 Hs.22370 cDNA DKFZp56400122 (f5.4 106683 BE296396DIPB protein 3.6 21058 4.7 Hs.14512 2$ 106698 N28524 hypothetical protein5.7 57 10 4.8 Hs.29403 FLJ22060 106710 N38902 hypothetical protein4.4 37184 3.2 Hs.334437 MGC4248 106717 AA600357TIA1 cytotoxic granule-associated4.3 10124 1.6 Hs.239489 RNA-bi 106747 NM_007118Hs.171957triple functional 4.6 46 1 4.
domain (PTPRF interact 106834 AL044182KIAA0753 gene product3.5 58 17 1.6 Hs.28070 106846 AB037744KIAA1323 protein 5.4 19236 4.4 Hs.34892 106868 BE185536molecule possessing 3.3 696214 1.8 Hs.301183 ankydn repeats indu 106882 AA149537hypothetical protein3.8 38 1 1.6 Hs.26994 FLJ20477 106893 AAS35868mannosidase, alpha, 4.3 43 10 2.2 Hs.25253 class 1A, member 106895 AK001826hypothetical protein3.6 36 1 1.2 Hs,25245 FLJ11269 35 106897 AF039023RAN binding protein 4.5 45 1 3.8 Hs.167496 6 106916 AA134329Homo Sapiens, clone 5.7 94 17 7.3 Hs,24170 IMAGE:3685398, mRNA, 106962 AI868648ESTs 3.5 18052 2.3 Hs.22315 106968 AF216751CDA14 5.5 13024 12.5 Hs.26813 106990 AA280722ESTs, Weakly similar3.2 26683 1.8 Hs.24758 to 138022 hypotheti 107008 AL157479KIAA1598 protein 5.1 29859 4.4 Hs,23740 107014 AA598820gb:ae36h12.s1 Gessler3.3 22869 2.8 Wilms tumor Homo s 107032 AV650537succinate-CoA ligase,3.1 55 18 3.8 Hs.247309 GDP-forming, beta 107056 AW401864programmed cell death3.1 75 24 2.2 Hs.18720 8 (apoptosis-induc 107071 AW385224ectonucleotide pyrophosphatase/phosphodi3.1 367119 2.3 Hs.35198 4$ 107080 AL122043hypothetical protein3.9 98 25 8.6 Hs.19221 DKFZp566G1424 107102 AB037765KIAA1344 protein 6.3 63 1 5.4 Hs.30652 107109 AA249096ESTs 4.6 71 16 3.6 Hs.32793 107136 AV661958GK001 protein 2.5 392155 4.3 Hs.8207 107151 AW378065ESTs 15.61567 10.8 Hs.8687 $~ 107217 AL080235DKFZP586E1621 protein4.8 48 8 3.1 Hs.35861 107222 BE172058tumor rejection antigen3.4 25174 23.7 Hs.82689 (gp96) 1 107240 AI290284ESTs 3.6 36 6 0.5 Hs.159872 107248 AW263124nuclear receptor 5.4 48390 4 Hs,315111 co-repressor/HDAC3 comp 107295 AA186629UDP-N-acetyl-alpha-D-galactosamine:polyp4.6 19944 19.2 Hs.80120 $$ 107299 BE277457hypothetical protein12.515613 2.9 Hs,30661 MGC4606 107316 T63174 Homo Sapiens mRNA; 11035 9,6 Hs.193700 cDNA DKFZp58610324 (f 3.2 107318 T74445 Homo sapiens clone 3,5 35 1 2.6 Hs.5957 24416 mRNA sequence 107485 AL042613S-adenosylmethionine5.8 15126 11.4 Hs.262476 decarboxylase 1 107612 AI498986Homo Sapiens cDNA 3.2 32 5 2.1 Hs.60090 FLJ13595 fis, clone PL

60 107638 A1580492hypothetical protein4.4 73 17 6.2 Hs.42743 107727 AA149707ubiquitin-like 3 3.5 28280 3.7 Hs.173091 107859 AW732573potassium voltage-gated5.7 85 15 7.8 Hs.47584 channel, delayed 107876 AW372451CGI-79 protein 3.5 35 1 1 Hs.61184 107884 AA054949ESTs 4.3 43 10 2.7 Hs.61307 6$ 107886 AA025782ESTs 3.1 31 9 2.2 Hs,61284 107908 AF087999ESTs 4.7 47 4 4.3 Hs.42826 107922 BE153855Ig superfamily receptor9 90 1 5.5 Hs.61460 LNIR

107994 AA036811 LIM domains containing4.545 1 3.8 Hs.48469 1 108040 AL121031 SWIISNF related, 6.565 2 6 Hs.159971 matrix associated, acti 108055 AJ404672 hypothetical protein7.474 8 6 Hs.334483 FLJ23571 108063 BE548479 hypothetical protein3.434 1 2.3 Hs.14838 FLJ10773 108339 AW151340 ESTs, Weakly similar18.7187 1 17 Hs.51615 to ALU7_HUMAN ALU
S

108467 AI478658 brefeldin A-inhibited3.838 1 3.2 Hs.94631 guanine nucleotide 108539 AA084677 hypothetical protein5.757 1 4.9 Hs.54558 FLJ22222 108634 AW022410 ESTs 3.232 5 1.7 Hs.69507 108647 BE546947 homeo box C10 8.7247 29 5.7 Hs.44276 1 108695 AB029000 KIAA1077 protein 3.7625 168 3.8 ~ Hs.70823 108778 AF133123 general transcription3.737 1 3.2 Hs.90847 factor IIIC, polyp 108806 AF070578 Homo sapiens clone 3.434 1 2.8 Hs.71168 24674 mRNA sequence 108807 A1652236 hypothetical protein3.535 1 3.2 Hs.49376 FLJ20644 108810 AW295647 hypothetical protein5.353 1 2.8 Hs.71331 MGC5350 108846 AL117452 DKFZP586G1517 protein4.896 20 6.5 Hs.44155 108857 AK001468 anillin (Drosophila 5.454 1 4 Hs.62180 Scraps homology, act 108893 BE276891 retinoic acid induced3.1529 170 4.1 Hs.194691 3 108917 AI380268 ESTs, Weakly similar3.333 5 1.7 Hs.173648 to Zinc-finger prot 109010 NM_007240Hs.44229dull specificity 3.434 1 2.6 phosphatase 12 109060 BE062109 chloride channel, 3.131 8 2 Hs.241551 calcium activated, fam 109101 AW608930 hypothetical protein3.471 21 2.4 Hs.52184 FLJ20618 109112 AW419196 hypothetical protein4.1334 82 3.4 Hs.257924 FLJ13782 109124 AK000684 hypothetical protein3.333 1 2.9 Hs.183887 FLJ22104 109128 H89083 ESTs 4 40 7 1.1 Hs.181915 109160 BE220601 hypothetical protein3.8233 62 3.8 Hs.301997 FLJ13033 109166 AA219691 RA86 interacting, 8.8199 23 16.1 Hs.73625 kinesin-like (rabkines 109173 AA179962 EST 3.232 1 2.2 Hs.73643 109178 AW976516 Homo sapiens cDNA: 3.232 10 2.9 Hs.283707 FLJ21354 fis, clone C

109235 AI381800 calcitonin gene-related4.9121 25 10.4 Hs.300684 peptide-receptor 109273 AA375752 Homo sapiens mRNA; 114 39 9.9 Hs.82719 cDNA DKFZp586F1822 (f 2.9 109292 AW975746 KIAA1702 protein 7.171 1 6.5 Hs.188662 109391 AL096858 KIAA0929 protein 6.969 5 6.2 Hs.184245 Msx2 interacting nuclea 109411 898881 sex comb on midleg 3.339 12 1.5 Hs.109655 (Drosophila)-like 109412 BE543313 hypothetical protein4.256 14 2.2 Hs.209473 FLJ10520 3 109415 U80736 trinucleotide repeat12.3123 1 11.3 $ Hs.110826 containing 9 109481 AA878923 hypothetical protein3.2286 91 5.7 Hs.289069 FLJ21016 109517 AI631874 casein kinase 2, 8.383 8 1.9 Hs.155140 alpha 1 polypeptide 109597 AA989362 ESTs 5.959 10 4.2 Hs.293780 109729 F10024 ESTs 3.241 13 3.3 Hs.268740 109795 AA173942 Homo sapiens mRNA; 208 36 1.8 Hs.326416 cDNA DKFZp564H1916 (f 5.9 109799 AW965076 hypothetical protein5 50 5 4.1 Hs.180378 669 109883 868827 syntrophin, beta 3.737 4 2 Hs.95011 1 (dystrophin-associate 109912 AW390822 L-kynureninelalpha-aminoadipate14.2142 1 9.5 Hs.301528 aminotra 109937 A1084066 myosin regulatory 4.141 7 1.7 Hs.20072 light chain interactin 45 109958 AA001266 ESTs 4.258 14 0.8 Hs.133521 109984 AI796320 Homo Sapiens cDNA 3.2136 43 3.6 Hs.10299 FLJ13545 fis, clone PL

110009 BE075297 ESTs, Weakly similar6.3693 110 7.2 Hs.6614 to A43932 mucin 2 p 110240 AI668594 ESTs, Weakly similar4.6913 199 2.9 Hs.176588 to CP4Y_HUMAN CYTOC

110369 AK000768 hypothetical protein3.838 7 2.8 Hs:107872 FLJ20761 110426 AI610702 ESTs, Weakly similar6.778 12 3 Hs.28212 to TRHY_HUMAN TRICH

110478 H11236 peroxisomal biogenesis3.737 1 2.1 Hs.31034 factor 11A

110481 AF075089 ESTs 3.636 10 2.5 Hs.36823 110581 H61560 gb:yr22g03.s1 Soaresfetalliverspleen3.333 1 1.8 110674 AA071276 KIAA0859 protein 3.535 8 1.9 Hs.19469 $ 110705 AB007902 KIAA0442 protein 3.6282 79 1.7 $ Hs.32168 110721 H97678 ESTs 4.4103 24 3.8 Hs.31319 110731 NM 014899Hs.188006KIAA0878 protein 3.3138 42 3.6 110769 BE000831 Homo sapiens cDNA 13.5135 1 5.1 Hs.23837 FLJ11812 fis, clone HE

110775 N22414 gb:yw39a07.s1 Weizmann5.454 1 3.7 Olfactory Epithet 110787 AA831267 hypothetical protein4.747 4 4.2 Hs.12244 FLJ20097 110799 A1089660 dpy-30-like protein 5 50 1 4.3 Hs.323401 110818 AL157503 Homo sapiens mRNA; 31 1 2.7 Hs.27552 cDNA DKFZp586N2424 (f 3.1 110839 AF153330 solute tamer family 8.484 1 5.3 Hs.30246 19 (thiamine traps 110844 AI740792 methylcrotonoyl-Ccenzyme10.5105 4 7.1 Hs.167531 A carboxylase 2 6$ 110854 BE612992 hypothetical protein7.979 1 6.2 Hs.27931 FLJ10607 similar to 110882 AW963705 molecule possessing 3.9353 90 1.2 Hs.301183 ankydn repeats indu 110908 AI433165 ESTs 3.131 1 1.3 Hs.9856 110915 BE092285hypothetical protein20.92091 19.5 Hs.29724 FLJ13187 110930 BE242691ESTs 3.4 11534 2.4 Hs.14947 110970 Y19062 staufen (Drosophila,3.5 35 9 3.2 Hs.96870 RNA-binding protein 111084 H44186 PDZ domain containing4.3 43 1 2 Hs.15456 1 $ 111125 N63823 ESTs, Moderately 5.4 54 1 4.3 Hs.269115 similar to Z195_HUMAN
Z

111132 A8037807hypothetical protein7.2 72 10 6.1 Hs.83293 111164 N46180 Homo Sapiens cDNA 7.7 77 1 5 Hs.122489 FLJ13289 fis, clone OV

111179 AK000136asporin (LRR class 25.128812 6.7 Hs.10760 1) 111184 AI815486Homo sapiens cDNA 3.9 14637 9.8 Hs.243901 FLJ20738 fis, clone HE

1 111190 AK002055hypothetical protein6.3 63 1 5.8 ~ Hs.151046 FLJ11193 111221 AB037782KIAA1361 protein 3.7 11933 6.7 Hs.15119 111223 AA852773KIAA1866 protein 3.6 402112 4.9 Hs.334838 111229 AW389845ESTs 4.3 43 1 1 Hs.110855 111234 AA902656NIF3 (Ngg1 interacting3.3 33 1 1.1 Hs.21943 factor 3, S.pombe 1$ 111241 AA345644PAN2 protein 4.8 61 13 5.6 Hs.288880 111345 AW263155hypothetical protein4.3 43 5 2.2 Hs.14559 FLJ10540 111353 W20090 ESTs 4.1 41 1 2.6 Hs.6616 111357 BE314949hypothetical protein3.8 425111 4 Hs.87128 FLJ23309 111378 AW160993hypothetical gene 4.3 65 15 5.7 Hs.326292 DKFZp434A1114 20 111389 AK000987oxidation resistance3.4 31491 2.4 Hs.169111 1 111540 U82670 zinc finger protein 3.5 35 1 2.1 Hs.9786 275 111806 BE071382hypothetical protein3.5 10530 9.6 Hs.279008 FLJ20170 111884 AW502285hypothetical protein3.2 37 12 3.5 Hs.127236 FLJ12879 111923 BE383234Homo Sapiens, clone 6.2 62 2 5.9 Hs.25925 MGC:15393, mRNA, com 2$ 111929 AF027208prominin (mouse)-like8.1 32841 1.7 Hs.112360 1 111942 840576 hypothetical protein4.2 12530 7.4 Hs.21590 DKFZp56400523 111987 NM_015310Hs.6763KIAA0942 protein 6.5 65 10 1.5 112092 844538 gb:yg29c02.s1 Soares3.3 33 10 2.3 infant brain 1NI8 H

112134 841823 ESTs; calsyntenin-2 6.1 18531 6.6 Hs.7413 112197 NM_003655Hs.5637ESTs 3.5 507145 3.3 112198 AI432672hypothetical protein3.5 40 12 2.5 Hs.288539 FLJ22191 112244 AB029000KIAA1077 protein 5.7 567100 6.7 Hs.70823 112253 851818 gb:yg77h12.s1 Soares4 70 18 6.8 infant brain 1NIB
H

112269 853734 ESTs, Weakly similar3.7 37 1 3 Hs.25978 to 2109260A B cell 3$ 112275 AW972635hypothetical protein4.3 45 11 4.4 Hs.301904 FLJ12671 112280 AA863360ESTs, Weakly similar2.8 751270 1.3 Hs.26040 to fatty acid omega 112305 AK000914hypothetical protein3.5 41 12 3.7 Hs.26244 FLJ10052 112483 AW969785Homo Sapiens cDNA 4.2 42 6 3.6 Hs.285885 FLJ11321 fis, clone PL

112513 868425 hypothetical protein4.7 54 12 4.5 Hs.13809 FLJ10648 112571 AA412205ESTs 4'.848 2 3.4 Hs.140996 112971 242387 transmembrane, prostate4.5 39087 5.3 Hs.83883 androgen induced 113023 AL134324ESTs 3.2 99 31 3.1 Hs.7312 113047 AI571940ESTs 9.6 12413 9 Hs.7549 113073 N39342 microtubule-associated9.1 91 6 8.3 Hs.103042 protein 18 4$ 113083 AA283057hypothetical protein6.5 65 6 4.8 Hs.266957 FLJ14281 ' 113287 T66847 ESTs, Weakly similar3.5 35 1 1.4 Hs.194040 to 138022 hypotheti 113296 AW449560inner mitochondria) 3.5 35 4 3.3 Hs.89576 membrane peptidase 113523 AI791905hypothetical protein7.6 76 1 4.2 Hs.95549 113604 A1075407ESTs, Moderately 3.1 453148 7 Hs.296083 similar to 154374 gene 113617 AI869372Homo Sapiens cDNA 3.6 36 4 2.6 Hs.17207 FLJ11922 fis, clone HE

113702 T97307 gb:ye53h05.s1 Soares12.312911 11.7 fetal liverspleen 113783 AL359588hypothettcal protein4.6 46 4 4.3 Hs.7041 DKFZp762B226 113791 AI269096chitobiase, di-N-acetyl-3.6 36 1 1.2 Hs,135578 113794 T62849 membrane-spanning 3.3 744227 2.5 Hs.11090 4-domains, subfamily A

$ 113804 BE247683dual specificity 3.3 18054 2.1 $ Hs.14611 phosphatase 11 (RNAIRNP

113808 W44735 Homo sapiens cDNA: 5.1 51 5 4.5 Hs.9286 FLJ21278 fis, clone C

113847 NM_005032Hs.4114plastin 3 (T isoform)3.2 23875 2.1 113849 AA457211bromodomain adjacent4.3 43 8 3.6 Hs.8858 to zinc finger doma 113867 AW002834ESTs 6.1 11018 10.2 Hs.24095 113886 W76027 hypothetical protein4 48 12 4 Hs.23920 FLJ11105 113923 AW953484hypothetical protein3.7 23965 3.6 Hs.3849 FLJ22041 similar to 113936 W17056 nuclear receptor 4.3 819191 1.2 Hs.83623 subfamily 1, group I, m 113950 AI267652Homo sapiens mRNA; 12312 7 Hs.30504 cDNA DKFZp434E082 (fr 10.7 114030 AI825386hypothetical protein4.4 44 6 2.3 Hs.164478 FLJ21939 similar to 6$ 114051 AB026436dual specificity 4.5 45 4 2.6 Hs.177534 phosphatase 10 114057 AF116653Homo Sapiens PR008233.5 35 6 3.2 Hs.34192 mRNA, complete cds 114082 AK001612Homo sapiens cDNA 3.1 31 5 1.5 Hs.26962 FLJ10750 fis, clone NT

114124 W57554 lymphoid nuclear 24.2242 10 5.6 Hs.125019 protein (LAF-4) mRNA

114138 AW384793 Homo Sapiens mRNA; 67 1 6.3 Hs.15740 cDNA DKFZp434E033 (fr 6.7 114162 AF155661 pyruvate dehydrogenase3.873 19 1.8 Hs.22265 phosphatase 114196 AF017445 fucose-1-phosphate 4.4104 24 5.1 Hs.150926 guanylyltransferase 114208 AL049466 ESTs 5.757 1 4.9 Hs.7859 114239 AL137667 Homo Sapiens mRNA; 33 1 2.4 Hs.267445 cDNA DKFZp434B231 (fr 3.3 114251 H15261 ESTs 4.246 11 1.4 Hs.21948 114306 AF100143 fibroblastgrowth 4.545 2 3 Hs.6540 factor 13 114460 AF183810 trichorhinophalangeal4.444 1 3 Hs.26102 syndrome I

1 114542 AW970128 anterior gradient 4.7770 166 5.8 O Hs.91011 2 (Xenepus laevis) hom 114652 AI521936 novel protein similar5.252 3 2.3 Hs.107149 to archaeal, yeast 114767 AI859865 minichromosome maintenance4.6196 43 10 Hs.154443 deficient (S.

114768 AF212848 ets homologous factor13.7137 1 8.9 Hs.182339 114774 AV656017 CGI-76 protein 3.3168 51 7.3 Hs.184325 1 114798 AA159181 serologically defined7.4137 19 1.8 S Hs.54900 colon cancer antig 114821 AI648602 ESTs 4.757 12 4.7 Hs.55468 114860 AL157545 bromodomain and PHD 9.191 1 7.6 Hs.42179 finger containing, 114918 BE165762 hypothetical protein10.1111 11 10.2 Hs.23518 from BCRA2 region 114940 BE092696 ESTs 6.467 11 5 Hs.75928 20 114965 AI733881 BMP-R1B 35.9359 10 29.7 Hs.72472 114969 AW162998 KIAA1376 protein 9.494 8 7.3 Hs.24684 114988 AA251089 gb:zs04f05.s1 NCI_CGAP_GCB1 115 1 6.9 Homo Sapiens 11.5 115004 AA329340 mannosyl (alpha-1,3-)-glycoprotein4.242 9 1.1 Hs.4867 beta-115054 AW265668 hypothetical protein5.151 1 4.2 Hs.87729 FLJ12428 25 115061 AI751438 Homo Sapiens mRNA 4.5290 65 3.7 Hs.41271 full length insert cDN

115140 NM_014158Hs.279938HSPC067 protein 4.848 1 4.4 115142 AI623693 ESTs 3.249 16 4.2 Hs.191533 115188 AK000219 hypothetical protein3.333 1 3 Hs.88367 FLJ20212 115206 AW183695 ESTs 5.858 1 5 Hs.186572 115221 AW365434 hypothetical protein5.5343 62 2.5 Hs.79741 FLJ10116 115282 AI422867 ESTs 11.2112 1 10.3 Hs.88594 115291 BE545072 hypothetical protein4.596 21 7.8 Hs.122579 FLJ10461 115536 AK001468 anillin (Drosophila 5.959 1 4.2 Hs.62180 Scraps homology, act 115583 NM_012317Hs.45231leucine zipper, down-regulated9.898 1 8.8 in cancer 35 115600 AA081395 Homo Sapiens cDNA 4.646 2 1.8 Hs.42173 FLJ10366 fis, clone NT

115622 A1088691 Homo Sapiens mRNA; 44 7 1.1 Hs.208414 cDNA DKFZp564D0472 (f 4.4 115646 N36110 solute carrier family3.2372 115 2.1 Hs.305971 2 (facilitated glu 115674 AW992356 Homo Sapiens pyruvate10.2506 50 2.8 Hs.8364 dehydrogenase kina 115675 W87707 interieukin 6 signal5.2405 78 10.1 Hs.82065 transducer (gp130, 4~ 115719 AW992405 Homo Sapiens, clone 7.6144 19 13.9 Hs.59622 IMAGE:3507281, mRNA, 115725 AW899053 F-box only protein 3.158 19 2.5 Hs.76917 8 115764 AW582256 anterior gradient 5.7368 65 28.5 Hs.91011 2 (Xenepus laevis) hom 115821 AW338063 zinc-finger protein 3.939 8 2.2 Hs.130965 ZBRK1 115825 850956 gycosyltransferase 4.279 19 1.9 Hs.159993 4$ 115839 BE300266 transducin-like enhancer5.858 1 4.4 Hs.28935 of split 1, hom 115844 AI373062 hypothetical protein6.262 1 5.4 Hs.332938 MGC5370 115892 AA291377 ESTs 3.240 13 0.7 Hs.50831 115967 AI745379 ESTs 8.4101 12 8.7 Hs.42911 116093 AW673312 hypothetical protein3.636 1 2 Hs.50848 FLJ20331 $0 116097 AI198719 ESTs 5.151 1 2 Hs.176376 116107 AL133916 hypothetical protein3.434 8 1 Hs.172572 FLJ20093 116127 AF126743 DNAJ domain-containing3.535 8 3.3 Hs.279884 116129 AF189011 putative ribonuclease4.545 9 3.4 Hs.49163 III

116204 AW861622 Homo Sapiens cDNA 5.252 4 3.9 Hs.108646 FLJ14934 fis, clone PL

S$ 116226 AW976438 RBP1-like protein 3.838 7 2.1 Hs.17428 116238 AV660717 DKFZP586N0819 profein5.1198 39 17.9 Hs.47144 116250 N76712 ESTs, Weakly similar13.3133 8 3.2 Hs.44829 to 138022 hypotheti 116256 AA328153 ESTs, Weakly similar3.3106 33 9.8 Hs.88201 to A Chain A, Cryst 116298 AI955411 Homo sapiens cDNA 4.8179 38 2.8 Hs.94109 FLJ13634 fis, clone PL

116336 AL133033 KIAA1025 protein 3.2173 55 3 Hs.4084 116351 AL133623 similar to mouse 3.737 1 1.8 Hs.82501 Xm1 / Dhm2 protein 116365 N50174 ESTs 3.939 10 0.6 Hs.46765 116379 AA448588 hypothetical protein5.6106 19 9 Hs.71252 DKFZp761C169 116429 AF191018 putative nucleotide 3.6256 72 3.7 Hs.279923 binding protein, est 6$ 116450 AI654450 Homo sapiens mRNA; 119 39 2 Hs.47274 cDNA DKFZp564B176 (fr 3.1 116461 AA313607 Homo Sapiens cDNA: 5.5315 58 3.1 Hs.58633 FLJ22145 fis, clone H

116470 AI272141 SRY (sex determining3.4496 144 1.6 Hs.83484 region Y)-box 4 2~~

116507 AI418366ESTs 3.131 4 1.9 Hs.68501 116579 AW888411leukemia-associated 3.3931 279 5.6 Hs.81915 phosphoprotein p18 ( 116625 F01601 RNA binding motif, 3.636 1 1.9 Hs.241567 single stranded inter 116674 AI768015ESTs 4.596 22 6.9 Hs.92127 116680 AW902848ESTs 4.242 1 2.7 Hs.273829 116710 F10577 v-crk avian sarcoma 7.171 9 6.9 Hs.306088 virus CT10 oncogene 116724 AA741307hypothetical protein4.3190 44 5.4 Hs.65641 FLJ20073 116786 H25836 ESTs, Moderately 22.8228 9 12.4 Hs.301527 similar to unknown [H.s 116787 AW362955Homo Sapiens cDNA 4.9108 22 9 Hs.15641 FLJ14415 fis, clone HE

116790 AW161357microtubule-associated4.6163 35 7.3 Hs.101174 protein tau 116844 H64938 ESTs, Weakly similar6.969 10 2.4 Hs.337434 to A46010 X-linked 117027 AW085208ESTs 4.848 1 2.5 Hs.130093 117067 H91164 ESTs 3.333 1 2.3 Hs.335797 117129 H95785 ESTs, Highly similar3.138 13 1.7 Hs.167652 to 1819485A CENP-E

1$ 117147 AW901347hypothetical protein4.848 1 0.9 Hs.38592 FLJ23342 117170 N25929 ADP-ribosylation 3.1295 96 27.9 Hs.42500 factor-like 5 117209 W03011 MSTP043 protein 3.641 12 2.8 Hs.306881 117280 M18217 Homo Sapiens cDNA: 3.9322 83 4.4 Hs.172129 FLJ21409 fis, clone C

117367 A1041793ESTs 3.572 21 1.3 Hs.42502 117412 N32536 solute carver family17.4174 9 6.9 Hs.42645 16 (monocarboxylic 117475 N30205 ESTs, Weakly similar3.235 11 0.7 Hs.93740 to 138022 hypotheti 117634 AW341639hypothetical protein5 50 1 4.7 Hs.13323 FLJ22059 117667 U59305 Ser-Thr protein kinase4.5211 47 5 Hs.44708 related to the my , 117852 AW877787KIAA0853 protein 4.646 1 3.8 Hs.136102 2$ 117873 N49967 HSPC043 protein 3.131 1 2.7 Hs.46624 117924 AI521436ESTs 4.949 1 4.4 Hs.38891 118138 AA374756Homo sapiens mRNA 5 50 2 3.1 Hs.93560 for KIAA1771 protein, 118449 A1813865hypothetical protein3.689 25 0.9 Hs.164478 FLJ21939 similar to 118467 AF091434platelet derived 3.2378 117 2.8 Hs.43080 growth factor C

118472 AL157545bromodomain and PHD 14.5145 1 2.4 Hs.42179 finger containing, 118475 N66845 gb:za46c11.s1 Soaresfetal3.1199 64 1 liver spleen 118509 N22617 Homo Sapiens cDNA 6 60 5 3.7 Hs.43228 FLJ11835 fis, clone HE

118528 AI949952ESTs 3.381 25 1.5 Hs.49397 118828 N79496 EST, Moderately similar3.4740 217 2.8 Hs.50824 to 154374 gene N

3 118836 AW134482hypothetical protein4.3162 38 12.1 $ Hs.173001 FLJ13964 118854 T58283 Homo Sapiens cDNA: 3.4118 35 2.3 Hs.10450 FLJ22063 fis, clone H

118873 AI824009ESTs 3.535 1 2.9 Hs.44577 118888 AI191811ESTs 8.484 10 0.8 Hs.54629 118901 AW292577ESTs 7.373 3 5.4 Hs.94445 118981 N29309 ESTs 5 50 5 4.7 Hs.39288 118991 NM_016657Hs.250696KDEL (Lys-Asp-Glu-Leu)3.737 6 0.5 endoplasmic retic 119023 N98488 gb:zb82h01.s1 Soares3.336 11 0.6 senescent fibroblas 119088 839261 Homo Sapiens cDNA: 3,3167 51 2.6 Hs.90790 FLJ22930 fis, clone K

119126 845175 ESTs 5.353 6 2.3 Hs.117183 4$ 119128 H09334 ESTs 3.737 4 3 Hs.92482 119271 A1061118Fanconi anemia, complementation8.282 1 6.4 Hs.65328 group F

119298 Nfvi_001241Hs.155478cyclin TZ 4 40 4 1.2 119307 BE048061ephrin-A3 3.3571 171 2 Hs.37054 119367 T78324 ribosomal protein 3.434 3 2.4 Hs.250895 L34 $0 119427 AW474547Homo sapiens PIG-M 4.660 13 4.8 Hs.53565 mRNA for mannosyltran 119580 AL079310high-mobility group 8.194 12 6.5 Hs.92260 protein 2-like 1 119586 AF088033ESTs 3.333 8 0.9 Hs.159225 119638 NM_016122Hs.56148NY-REN-58 antigen 3.333 10 0.5 119676 AA243837ESTs 5.454 1 4.1 Hs.57787 55 119717 AA918317B-cell CLLllymphoma 4.646 7 0.8 Hs.57987 11B (zinc finger pro 119771 AI905687EST 3.52073595 2.1 Hs.2533 119780 NM_016625Hs.191381hypothetical protein4.444 1 3.1 119786 AL133396prion protein 2 (dublet)3.434 1 2.5 Hs.121281 119805 AJ223810ESTs, Weakly similar3.636 1 2.9 Hs.43213 to IEFS HUMAN TRANS

119859 AW245741ESTs, Weakly similar5.252 6 1.8 Hs.58461 to A35659 krueppel-119899 A1057404ESTs 3.737 4 1.9 Hs.58698 119940 AL050097DKFZP586B0319 protein6.9162 24 2.6 Hs.272531 119943 BE565849copine III 3.7590 159 3.8 Hs.14158 120132 W57554 lymphoid nuclear 6.9319 47 2.1 Hs.125019 protein (LAF-4) mRNA

6$ 120150 BE005771hypothetical protein5.353 5 0.9 Hs.153746 FLJ22490 120215 AF109219phosphatidylinositol3.2106 34 3.3 Hs.108787 glycan, class N

120260 AK000061hypothetical protein3.434 1 1.7 Hs.101590 120296 AW995911hypothetical protein4.2 12430 1.8 Hs.299883 FLJ23399 120352 806859 ESTs, Weakly similar7.5 11215 2.5 Hs.193172 to 138022 hypothe6 120378 AA223249abl-interactor 12 3.3 33 10 2.8 Hs.285728 (SH3-containing protei 120418 AW966893Homo Sapiens mRNA; 48 1 0.5 Hs.26613 cDNA DKFZp586F1323 (f 4.8 120473 AA251973ESTs 3.4 34 4 0.1 Hs.269988 120493 AW968080Homo Sapiens clone 3.9 16142 2 Hs.152939 24630 mRNA sequence 120524 AA261852ESTs 6.8 68 1 0.2 Hs.192905 120554 AA284447ESTs 3.2 32 5 0.6 Hs.271887 120562 BE244580hypothetical protein8.5 12715 1.6 Hs.302267 FLJ10330 120571 AB037744KIAA1323 protein 3.7 37 1 0.5 Hs.34892 120572 H39599 ESTs 3.6 36 8 0.2 Hs.294008 120588 AA703226Homo sapiens mRNA; 10118 1.6 Hs.16193 cDNA DKFZp586B211 (fr 5.6 120649 AA687322leucine zipper protein5.4 54 10 2.5 Hs.192843 FKSG14 120658 AI952639ESTs 3.2 32 8 3 Hs.98267 120713 AW449855Homo sapiens cDNA 5.3 58 11 3.3 Hs.96557 FLJ12727 fis, clone NT

120821 Y19062 staufen (Drosophila,3.3 33 3 0.2 Hs.96870 RNA-binding protein 120822 AA347422EST, Weakly similar 3.8 38 7 0.2 Hs.238040 to 834087 hypothetic 120915 AL135556ESTs 3.5 37 11 0.1 Hs.97104 120922 AA481003ESTs 3.1 31 1 0.4 Hs.97128 12D977 AA398155ESTs 7.9 79 1 2.7 Hs.97600 120999 AI972375hypothetical brain 5.1 51 1 2.4 Hs.29626 protein my038 121125 AL042981KIAA1201 protein 3.7 37 10 1 Hs.251278 121176 AL121523ESTs 7 70 1 0.9 Hs.97774 121202 AA970946ESTs 3.9 39 1 0.2 Hs.97794 2S 121429 AA406293ESTs 3.4 34 1 0.8 Hs.41167 121448 AF044197B-cell attracting 3.5 35 1 2.6 Hs.100431 chemokine 1 (CXCL13;

121463 AK000282hypothetical protein10.31031 9.3 Hs.239681 FLJ20275 121517 A1002968ESTs, Weakly similar3.5 14341 2.6 Hs.235402 to T26525 hypotheti 121553 AA412488TATA box binding 4.6 46 3 0.8 Hs.48820 protein (TBP)-associate 121556 AA412494EST 4.2 77 19 1,.4 Hs.98152 121581 AA416568gb:zu05c10.s1 Soares3.2 32 1 0.8 testis_NHT Homo sap 121709 AI338247Homo Sapiens mRNA; 34 10 0.7 Hs.98314 cDNA DKFZp586L0120 (f 3.4 121723 AA243499hypothetical protein2.9 21474 3.7 Hs.104800 FLJ10134 121831 AA449644Homo sapiens cDNA 3.9 39 1 0.2 Hs.193063 FLJ14201 fis, clone NT

3$ 121853 AA425887hypothetical protein4.4 48 11 0.9 Hs.98502 FLJ14303 121873 AV650929splicing factor (CC1.3)3.6 15042 3.2 Hs.145696 121913 AI249368ESTs; protease inhibitor2.7 864321 0.6 Hs.98558 15 (PI15) 121916 AW117207ESTs 3.5 35 3 2.3 Hs.98523 122004 AI810721ESTs 4.9 49 7 3.7 Hs.95424 122063 AW794215KIAA1085 protein 3.2 88 28 1.2 Hs.301226 122223 AF169797adaptor protein containing12.61267 7.5 Hs.27413 pH domain, PT

122235 AA436475membrane-associated 4.1 43 11 1.6 Hs.112227 nucleic acid binding 122273 AI298368fucose-1-phosphate 3.1 31 1 1 Hs.150926 guanylyltransferase 122383 AA446189ESTs 3.3 53 16 4 Hs.99051 122507 BE567620ESTs 3.2 29191 4 Hs.99210 122524 AA449453ESTs, Weakly similar3.1 31 6 0.8 Hs.192915 to ALU1 HUMAN ALU
S

122636 AW651706hypothetical protein3.5 35 1 3 Hs.99519 FLJ14007 122637 AA454149EST 3.2 32 10 3.1 Hs.99357 122798 AW366286splicing factor (CC1.3)3.2 36 11 2.5 Hs.145696 $0 122861 AA335721ESTs 5.6 10820 1.8 Hs.119394 122873 AA749382ubiquitin-conjugating3.6 36 1 3.4 Hs.118797 enryme E2D 3 (homo 122946 A1718702major histocompa6bility3.7 16244 12.4 Hs.308026 complex, class 122963 AA478446KIAA1096 protein 7.2 72 1 5.7 Hs.69559 122974 AA447871ESTs, Weakly similar4.7 59 13 4.7 Hs.194215 fo 138022 hypotheti S 123016 AW338067Homo Sapiens cDNA 3.3 20763 3.5 5 Hs.323231 FLJi 1946 fis, clone HE

123090 AL135185niban protein 3.8 20755 5.5 Hs.48778 123137 A1073913ESTs, Weakly similar9.9 35136 13.9 Hs.100686 to JE0350 Anterior 123255 AA830335ESTs 4.1 72 18 1.5 Hs.105273 123284 AA488988ESTs 3.7 41 11 1.6 Hs.293796 60 123442 AA299652Homo Sapiens cDNA 6.7 67 2 2.1 Hs.111496 FLJ11643 fis, clone HE

123449 AL049325Homo sapiens mRNA; 34 1 2.6 Hs.112493 cDNA DKFZp564D036 (fr 3.4 123475 BE439553Homo Sapiens, clone 9.7 1D211 6 Hs.250528 IMAGE:4098694, mRNA, 123494 AW179019mitochonddal ribosomal4.2 42 7 2.9 Hs.112110 protein L42 123503 AW975051ESTs, Weakly similar3.9 39 1 3.2 Hs.293156 to 178885 serinelth 6$ 123516 AB037860nuclear factor IIA 4.3 43 1 3.5 Hs.173933 123518 AL035414hypothetical protein5.8 58 1 4.9 Hs.21068 123523 AA608588gb:ae54e06.s1 Stratagene3.1 927295 2,1 lung carcinoma 123527 AF150208damage-specific DNA 5 12125 5.9 Hs.108327 binding protein 1 (1 123570 AA608955ESTs 6.8 68 10 6.1 Hs.109653 123619 AA602964gb:no97c02.s1 NCI_CGAP_Pr28.5 85 1 4.3 Homo Sapiens 123673 BE550112ESTs, Weakiy similar3.9 39 5 3.7 Hs.158549 to T2D3_HUMAN TRANS

$ 123709 AA706910ESTs 3.9 60 16 4.8 Hs.112742 123926 AA425769AIg5, S. cerevisiae,3.4 80 24 3.8 Hs.227933 homolog of 123960 AW082862hypothetical protein4.5 45 2 3.6 Hs.287733 FLJ23189 124006 AI147155ESTs 5.8 32155 17 Hs.270016 124059 BE387335ESTs, Weakly similar10.488085 5.3 Hs.283713 to S64054 hypotheti 124287 H88296 inorganic pyrophosphatase3.1 41 14 2.7 Hs.5123 124292 H11341 Homo Sapiens cDNA: 3.2 32 1 1.5 Hs.13366 FLJ23567 fis, clone L

124308 AA249027ribosomal protein 10.51051 9.9 Hs.241507 S6 124315 NM_005402Hs.288757v-ral simian leukemia12.814111 12.2 viral oncogene hom 124461 AF283776Homo Sapiens mRNA; 31 1 1.8 Hs.80285 cDNA DKFZp586C1723 (f 3.1 1$ 124483 AI821780ESTs 3.3 33 1 1.7 Hs.179864 124677 801073 gb:ye84c03.s1 Soaresfetalliverspleen4.2 42 7 3 124777 841933 ESTs, Weakly similar3.4 21063 3.3 Hs.140237 to ALU1 HUMAN ALU
S

124940 AF068846heterogeneous nuclear6.5 16225 14.7 Hs.103804 ribonucleoprotein 125079 T90298 ESTs 3.1 31 6 2.4 Hs.271396 125091 T91518 gb:ye20f05.s1 Stratagene3.4 985286 2.8 lung (937210) H

125103 AA570056ESTs, Moderately 3.6 22463 4 Hs.122730 similar to KIAA1215 pro 125144 A8037742KIAA1321 protein 6.3 63 6 5 Hs.24336 125150 W38240 Empirically selected3.6 38 11 2.6 from AFFX single pr 125156 W93048 hypothetical protein3.1 31 1 2.8 Hs.250723 MGC2747 125226 AA782536N-myristoyltransferase3.2 37 12 3.6 Hs.122647 2 125279 AW401809KIAA1150 protein 13.11311 5.1 Hs.4779 125299 T32982 ESTs 7.7 81 11 7.6 Hs.102720 125303 AA173319hypothetical protein14.31439 13.1 Hs.288193 MGC12217 125377 W72949 UBX domain-containing3.3 34 11 3.2 Hs.77495 1 125390 AL038165translocase of outer8.2 12415 11.5 Hs.75187 mitochondria) membr 125471 AA421691UDP-glucose ceramide3.7 22461 21 Hs.152601 glucosyltransferase 125617 AA287921ESTs 6.7 67 1 6 Hs.164950 125621 T62641 acetyl-Coenryme A 5.5 55 10 4.2 Hs.278544 acetyltransferase 2 (a 125628 AA418069natural killer-tumor5.5 63 12 1 Hs.241493 recognition sequenc 3$ ~ 125660 AW292171scaffold attachmentfactorB4.3 68 16 2.8 Hs.23978 125698 AF078847general transcription4.8 48 5 4.1 Hs.191356 factor IIH, polype 125745 AI858032ribopharin II 6.8 22333 2.8 Hs.75722 125770 AA143045v-kit Hardy-Zuckerman8.3 87 11 0.4 Hs.81665 4 feline sarcoma v 125827 NM 003403Hs.97496YY1 transcription 11,312411 9.7 factor 125852 AW630088Homo Sapiens mRNA; 3064 26.5 Hs.76550 cDNA DKFZp564B1264 (f 30.6 126349 T30968 hypothetical protein4.9 68 14 1.4 Hs.13531 FLJ10971 126384 AW090198KIAA1150 protein 6.4 74 12 6.6 Hs.4779 126590 W78968 H3 histone, family 5 26453 3.4 Hs.181307 3A

126645 AA316181six transmembrane 3.8 38 1 2.7 Hs.61635 epithelial antigen of 126663 AW518478ESTs 3.6 36 6 2.9 Hs.181297 126695 AA643322a disinfegrin and 3.1 31 1 2.5 Hs.172028 metalloprofeinase doma 126764 AA036755syntaxin 16 4.4 76 18 1 Hs.102178 126801 AW663887hypothetical protein3.8 38 1 3 Hs.7337 FLJ10936 126813 AW163483double ring-finger 6.7 15523 1.4 Hs.48320 protein, Dorfin $ 126838 AL043489mitochondria) comer 8.8 11013 10.5 0 Hs.279609 homolog 2 126855 AA129640ESTs 3.6 36 10 1.9 Hs.128065 126971 T26989 aspartate beta-hydroxylase5.5 79 15 4.4 Hs.283664 127167 AA625690ESTs 3.1 33 11 2.3 Hs.190272 127251 AA936428ESTs 3.5 35 1 3.1 Hs.128638 5$ 127349 AA412108ESTs 4.8 10622 1 Hs.269350 127439 D60237 SH3 domain binding 7.5 75 1 6.5 Hs.14368 glutamic acid-rich pr 127537 AI926047ESTs 3.8 38 7 3.4 Hs.162859 127542 AA703684ESTs, Moderately 3.3 33 9 0.9 Hs.245474 similar to ALU5_HUMAN
A

127677 AF175265vacuolar protein 4.3 15235 12.5 Hs.264190 sorting 35 (yeast homol 60 127774 AA313639cystein-rich hydrophobic5.4 73 14 6.8 Hs.119488 domain 2 127999 AW978827nucleoiar protein 5.2 81 16 1.1 Hs.69851 family A, member 1 (H!

128218 AA186733stromal cell protein3.9 22057 2.5 Hs.292154 128305 AI954968matrix Gla protein 9.4 94 3 5.3 Hs.279009 128470 AL049974Homo Sapiens mRNA; 46 8 3.9 Hs.100261 cDNA DKFZp564B222 (fr 4.6 6S 128482 AI694143programmed cell death7.2 72 1 5.8 Hs.296251 4 128501 AL133572protein containing 3.8 38 1 0.9 Hs.199009 CXXC domain 2 128517 AW994403hypothe6cai protein 5.6 73 13 6.1 Hs.100861 FLJ14600 128530 AI932995 Homo Sapiens clone 4.2 10425 7.8 Hs.183475 25061 mRNA sequence 128579 N25956 Homo sapiens cDNA 3.1 17255 3.1 Hs.101810 FLJ14232 fis, clone NT

128595 031875 short-chain alcohol 3.3 10532 3 Hs.272499 dehydrogenase family 128610 N48373 activated leucocyte 7.3 10615 5 Hs.10247 cell adhesion molecu $ 128653 D87432 solute tamer family 3.1 31 1 2.2 Hs.10315 7 (cationic amino 128742 AA307211 proteasome (prosome,3.6 13036 3.5 Hs.251531 macropain) subunit, 128773 NM_004131Hs.1051granryme B (granzyme3.9 43 11 1.8 2, cytotoxicT-lymp 126790 AF026692 secreted frizzled-related17.440924 7.8 Hs.105700 protein 4 128793 AB011125 KIAA0553 protein 3.1 34 11 2.7 Hs.105749 10128794 NM_014720Hs.105751Ste20-related serinelthreonine3.6 36 5 1.5 kinase 128835 AK001731 Homo sapiens mRNA; (f 28887 7.9 Hs.106390 cDNA DKFZp586H0924 3.3 128906 857988 epithelial protein 11.31138 2.5 Hs.10706 lost in neoplasm beta 128925 867419 Homo Sapiens cDNA 7.1 39256 3.6 Hs.21851 FLJ 12900 fis, clone NT

128949 AA009647 a disintegrin and 4.6 13229 9.7 Hs.8850 metalloproteinase doma 1$129017 AA115333 ESTs 8.2 82 1 7.4 Hs.107968 129075 BE250162 dihydrofolate reductase5 50 1 3.3 Hs.83765 129095 L12350 thrombospondin 2 3.2 814257 2.4 Hs.108623 129151 N23018 C-terminal binding 4.4 44 1 3.8 Hs.171391 protein 2 129168 A1132988 chromosome 14 open 14.21426 9.4 Hs.109052 reading frame 2 20129229 AF013758 polyadenylate binding7.1 71 1 6.2 Hs.109643 protein-interactin 129243 BE169531 TAK1-binding protein5 64 13 6.3 Hs.109727 2; KIAA0733 protein 129259 AF220050 uncharacterized hematopoietic5.2 75 15 6.4 Hs.181385 stem/proge 129278 NM_015344Hs.11000leptin receptor overlapping3.7 39 11 3.2 transcript-I

129337 NM_014918Hs.110488KIAA0990 protein 9.5 95 1 8.5 2$129351 AL049538 ras association (RaIGDS/AF-6)7.6 92 12 1.4 Hs.62349 domain con 129366 BE220806 Homo sapiens clone 7.1 15021 14.5 Hs.184697 23785 mRNA sequence 129393 BE219987 phosphafidylinositol3.9 54 14 5.1 Hs.166982 glycan, class F

129457 X61959 aspartylglucosaminidase3.6 36 1 2.7 Hs.207776 129486 NM_005754Hs.220689Ras-GTPase-activating4 40 4 3.2 protein SH3-domain 30129586 AW964541 hypothetical protein4.6 19944 2.3 Hs.11500 FLJ21127 129598 N30436 Homo sapiens cDNA 4.2 42 1 3.8 Hs.11556 FLJ12566 fis, clone NT

129691 M26939 collagen, type III, 6.4 1111175 5 Hs.119571 alpha 1 (Ehlers-Danl 129698 BE242144 ATP-binding cassette,4.8 48 8 3.8 Hs.12013 sub-family E (OABP

129721 NM_001415Hs.211539eukaryotic translation5.8 17130 2.9 initiation factor 35129740 BE165866 nuclear receptor 4.5 45 1 2.4 Hs.83623 subfamily 1, group I, m 129755 842216 Homo sapiens clone 5.3 53 9 3.6 Hs.12342 24538 mRNA sequence 129801 839246 Homo Sapiens cDNA 3.1 31 2 2.5 Hs.239666 FLJ13495 fis, clone PL

129821 AB028945 cortactin SH3 domain-binding11.41141 10 Hs.12696 protein 129869 AI222069 hypothetical protein4.7 556119 4.5 Hs.13015 similar to mouse Dn 129965 T71333 ESTs 3.1 31 3 3 Hs.13854 129977 NM_000399Hs.1395early growth response3.2 32 1 0.2 2 (Krox-20 (Drosop 130036 BE061916 chromosome 8 open 6.7 67 1 5.7 Hs.125849 reading frame 2 130057 AF027153 solute carrier family1 1 1 1 Hs.324787 5 (inositol transp 130095 AK001635 hypothetical protein14.621915 7.6 Hs.14838 FLJ10773 4S130115 T47294 X-box binding protein3.1 1336434 1.4 Hs.149923 1 130170 AW977534 calciumlcalmodulin-dependent5.3 53 9 3.2 Hs.151469 sedne prot 130173 038847 TAR (HIV) RNA-binding4.2 46 11 1.1 Hs.151518 protein 1 130343 AB040914 KIAA1481 protein 13.233125 12.4 Hs.278628 130356 AF127577 nuclear receptor 3.3 354108 4 Hs.155017 interacting protein $0130367 AL135301 hypothetical protein8.1 81 9 5.5 Hs.8768 FLJ10849 130385 AW067800 stanniocalcin 2 72.27221 1.9 Hs.155223 130407 BE385099 hypothetical protein6.5 65 4 5.3 Hs.334727 MGC3017 130417 AW163518 hun6ngtin interacting3.5 79 23 2.5 Hs.155485 protein 2 130441 063630 protein kinase, DNA-activated,6.1 61 1 5.7 Hs.155637 catalytic 130455 D90041 N-acetyltransferase 10.870666 9.2 $ Hs.155956 1 (arylamine N-acety 130466 W19744 Homo Sapiens cDNA 3.9 39 1 1.9 Hs.180059 FLJ20653 fis, clone KA

130526 AW876523 hypothetical protein3.9 39 1 2.6 Hs.15929 FLJ12910 130567 AA383092 replication protein 4.4 44 1 4.1 Hs.1608 A3 (14kD) 130604 AA383256 estrogen receptor 32,23221 4,7 Hs.1657 1 60130614 AI354355 down-regulator of 5.2 25148 21 Hs.16697 transcription 1, TBP-b 130617 M90516 glutamine-fructose-6-phosphate10 1001 7.6 Hs.1674 transamin 130619 A1963376 chromosome 1 open 3.9 39 1 3.4 Hs.12532 reading frame 21 ,130625 AF176012J domain containing 10.51051 9 Hs.260720 protein 1 130677 AL161961 KIAA1554 protein 6.8 12919 12.1 Hs.17767 6S130681 862676 Rho-associated, coiled-coil4.1 41 1 3.6 Hs.17820 containing p 130693 868537 ESTs 9.2 23426 16.8 Hs.17962 130712 AJ271881 bromodomain-containing17.51752 12.8 Hs.279762 7 20.4 130723 BE247676E-1 enryme 8.1 81 3 2.8 Hs.18442 130751 AF052105chromosome 12 open 4.9 49 1 4.3 Hs.18879 reading frame 130780 AA197226hypothetical protein3.6 100 28 6.6 Hs.19347 MGC11321 130863 Y10805 HMT1 (hnRNP methyltransferase,3.4 525 1545.3 Hs.20521 S, cerevi $ 130871 AF080158inhibitor of kappa 10.5121 12 1.6 Hs.226573 light polypeptide gen 130888 AL044315Homo Sapiens mRNA 6 202 34 3.7 Hs.173094 for KIAA1750 protein, 130974 NM_003528Hs.2178H2B histone family, 7.1 100 14 7.5 member Q

130979 NM_012446Hs.169833single-stranded-DNA-binding3.2 87 27 1.7 protein 130987 BE613269hypothetical protein3.5 124 35 6.5 Hs.21893 DKFZp761N0624 1 130993 T97401 ESTs 4.5 45 1 2.5 ~ Hs.21929 131076 AA749230dolichyl-phosphate 3.2 210 66 3.8 Hs.26433 (UDP-N-acetylglucosam 131085 BE207357KIAA1821 protein 3.8 42 11 0.6 Hs.3454 131126 NM_016156Hs.181326KIAA1073 protein 6.7 67 6 1.9 131129 BE541042Homo sapiens cDNA: 5.8 115 20 2.5 Hs.23240 FLJ21848 fis, clone H

15 131148 AW953575p53-induced protein 3.8 585 1533.7 Hs.303125 PIGPC1 131164 AW013807keratin 19 5.2 13202563.2 Hs,182265 131176 AA465113ESTs, Weakly similar3.8 38 1 3.3 Hs.23853 to A34615 profilagg 131200 BE540516hypothetical protein4.8 48 1 4.1 Hs.293732 MGC3195 131216 AI815486Homo sapiens cDNA 6.1 343 56 16.4 Hs.243901 FLJ20738 fis, clone HE

20 131245 AL080080thioredoxin domain-containing8 100 13 2.9 Hs.24766 131248 A1038989Bardet-Biedl syndrome4 95 24 1.1 Hs.332633 2 131273 AW206008Homo sapiens cDNA: 4.6 239 53 3.5 Hs.283378 FLJ21778 fis, clone H

131319 NM_003155Hs.25590stanniocalcin 1 3.5 402 1142.1 131367 AI750575nuclear factorl/A 3.3 775 2332.4 Hs.173933 2$ 131375 AW293165ESTs 3.8 38 1 3 Hs.143134 131379 AK001123hypothetical protein3.9 116 30 0.5 Hs.26176 FLJ10261 131388 NM_014810Hs.92200KIAA0480 gene product7.6 76 1 5 131475 AA992841KIAA1458 protein 5.1 113 22 6.1 Hs.27263 131492 AI452601nuclear receptor 8.4 169 20 4.6 Hs.288869 subfamily 2, group F, m 131501 AV661958GK001 protein 3.1 197 63 18.7 Hs.8207 131535 N22120 hypothetical protein5.9 59 1 4.4 Hs.75277 FLJ 13910 131544 AL355715programmed cell death5.1 51 1 3.9 Hs.28555 9 (PDCD9) 131546 AA093668muscleblind (Drosophila)-like3.8 79 21 6.9 Hs.28578 131562 Ntv~003512Hs.28777H2A histone family, 4 350 88 3 member L

3 131564 T93500 Homo sapiens cDNA 4.7 381 81 6.4 $ Hs.28792 FLJ11041 fis, clone PL

131604 AA306477hypothetical protein4.6 46 7 3.8 Hs.29379 FLJ10687 131684 NM 002104Hs.3066granryme K (serine 3.2 82 26 6.6 protease, granryme 3;

131687 BE297635heat shock 70kD protein6.7 93 14 8.4 Hs.3069 9B (mortalin-2) 131689 AB012124transcription factor-like3.8 51 14 1.7 Hs.30696 5 (basic helix 40 131693 AW963776SAR1 protein 7.2 72 4 5.7 Hs.110796 131739 AF017986secreted frizzled-related2.1 15617571.7 Hs.31386 protein 2 131742 AA961420ESTs 11.7117 1 10.1 Hs.31433 131775 AB014548KIAA0648 protein 4.8 48 1 4.6 Hs.31921 131787 D87077 KlAA0240 protein 3.2 207 64 5,5 Hs.196275 4$ 131798 X86098 adenovirus 5 E1A 3.4 115 34 9.1 Hs.301449 binding protein 131836 W00712 DKFZP566F084 protein5.8 91 16 1.4 Hs.32990 131853 A1681917ESTs, Highly similarto4.9 632 1291.7 Hs.3321 IRX1 HUMAN IROQU

131877 J04088 topoisomerase (DNA) 6.8 68 1 5.6 Hs.156346 II alpha (170kD) 131881 AW361018upstream regulatory 4 140 35 1.8 Hs.3383 element binding prot $~ 131885 BE502341ESTs 5.7 57 1 4.5 Hs.3402 131904 AF078866Homo Sapiens cDNA: 5.5 90 17 2.9 Hs.284296 FLJ22993 fis, clone K

131919 T15803 protein phosphatase 5.6 95 17 9.1 Hs.272458 3 (formerly 2B), cat 131941 BE252983ubiquitin specific 7.4 103 14 6.5 Hs.35086 protease 1 002916Hs.35120 replication factor 3.7 37 1 3.4 131945 NM C (activator 1 ) 4 (37 $ _ hypothetical protein3.5 35 1 2.5 $ 131949 AK000010FLJ20003 Hs.258798 131965 W79283 ESTs 5.5 168 31 4.4 Hs.35962 131977 U90441 procollagen-proline,3.7 37 9 2.8 Hs.3622 2-oxoglutarate 4-di 131985 AA503020hypothetical protein40.2402 1 4 Hs.36563 FLJ22418 131993 AI878910cisplatin resistance-associated7.3 73 1 1.2 Hs.3688 overexpr 132064 AA121098serum-inducible kinase22,6226 10 0.9 Hs.3838 132094 NM_016045Hs.3945CGI-107 protein 3.1 227 73 16.8 132109 AW190902cysteine knot superfamily3.5 73 21 6.3 Hs.40098 1, BMP antagon 132116 AW960474ESTs 3.6 141 39 12.6 Hs.40289 132143 D52059 KIAA0871 protein 4.9 49 1 4.1 Hs.7972 65 132160 W26406 seven in absentia 4.4 53 12 2.1 Hs.295923 (Drosophila) homolog 132164 AI752235procollagen-lysine, 5 225 45 9.1 Hs.41270 2-oxoglutarate 5-dio 132180 NM_004460Hs.418fibroblast activation10.7433 41 7.2 protein, alpha 20$

132197 AI699482ESTs 3.4 58 17 4 Hs.42151 132256 A1078645murine leukemia viral4.2 42 1 2.2 Hs.431 (bmi-1) oncogene h 132298 NM_015986Hs.7120cytokine receptor-like3.4 34 2 3 molecule 9 132316 028831 KIAA1641 protein 18.618610 1.5 Hs.44566 132325 N37065 hypothetical protein5.5 32359 10.5 Hs.44856 FLJ12116 132358 NM_003542Hs.46423H4 histone family, 3.3 979298 2.2 member G

132384 AA312135HSPC034 protein 3.6 36 1 3.1 Hs.46967 132388 W32624 ArgIAbl-interacting 5.9 18632 3.7 Hs.278626 protein ArgBP2 132393 AL135094hypothetical protein4.2 15938 7.1 Hs.47334 FLJ14495 132407 BE613126B aggressive lymphoma4.6 46 1 4.3 Hs.47783 gene 132425 N87549 zinc finger protein 3.6 14641 1.1 Hs.125287 ZNF140-like protein 132440 AB020699KIAA0892 protein 3.3 33 4 2.9 Hs.112751 132465 AW169847KIAA1634 protein 8.3 14518 3.7 Hs.49169 132522 AB023164KIAA0947 protein 4.6 46 1 4.4 Hs.5070 ~ 132528 T78736 SMC4 (structural 9.3 93 1 8.4 $ Hs.50758 maintenance of chromoso 132530 AA306105SEC22, vesicle trafficking4.9 49 1 4.4 Hs.50785 protein (S. c 132543 BE568452protein regulator 11.820117 19.1 Hs.5101 of cytokinesis 1 132572 AI929659signal recognition 3.8 38 1 3 Hs.237825 particle 72kD

132592 AW803564Homo Sapiens cDNA: 4.8 93 20 3.1 Hs.288850 FLJ22528 fis, clone H

2~ 132602 AW606927hypothetical protein6.1 61 2 5.9 Hs.5306 DKFZp586F1122 simil 132616 BE262677hypothetical protein3.4 19358 12.3 Hs.283558 PR01855 132617 AF037335carbonic anhydrase 14.239028 22.5 Hs.5338 XII

132618 AL050025hypothetical protein3.3 909274 3.2 Hs.279916 FLJ20151 132632 AU076916guanine monphosphate5 50 1 4.1 Hs.5398 synthetase 25 132668 AB018319KIAA0776 protein 4.2 17141 12.6 Hs.5460 132742 AA025480ESTs, Weakly similar6.5 65 1 5.6 Hs.292812 to T33468 hypotheti 132790 AW242243peroxisomal famesylated3.7 37 1 2.2 Hs.168670 protein 132811. 025435 CCCTC-binding factor7 11517 5.4 Hs.57419 (zinc finger protei 132852 AL120050Homo Sapiens cDNA: 3.3 61 19 5.1 Hs.58220 FLJ23005 fis, clone L

30 132856 NM_001448Hs.58367glypican 4 4.8 48 1 3.6 132880 BE077155hypothetical protein12.61268 9.9 Hs.177537 DKFZp761B1514 132902 AI936442hypothetical protein11 18717 10.4 Hs.59838 FLJ10808 132906 BE613337geminin 3.3 10633 2.6 Hs.234896 132914 AL047045Homo Sapiens clone 3,5 11032 2.1 Hs.60293 122482 unknown mRNA

35 132968 AF234532myosinX 4.1 62 15 4.9 Hs.61638 132977 AA093322RNA binding motif 22.12219 17.8 Hs.301404 protein 3 132990 X77343 transcription factor12.731125 2.4 Hs.334334 AP-2 alpha (activat 132994 AA112748clone H00310 PR00310p13 380127 5.5 Hs.279905 133011 NM_006379Hs.171921sema domain, immunoglobulin7.3 27137 2.3 domain (Ig), 40 133015 AJ002744UDP-N-acetyl-alpha-D-galactosamine:polyp4.6 42793 10.4 Hs.246315 133070 092649 a disinfegrin and 3.6 36 1 3.1 Hs.64311 mefalloproteinase doma 133091 AK001628KIAA0483 protein 5.2 11723 5 Hs.64691 133192 AA218564vacuolar protein 3.1 359118 2.5 Hs.67052 sorting 26 (yeast homol 133197 AI275243hypothetical protein5.1 58 12 5.7 Hs.180201 FLJ20671 45 133199 AF231981homolog of yeast 3 816275 3.9 Hs.250175 long chain polyunsatura 133221 W32474 RAP2A, member of 3.1 23476 8.6 Hs.301746 RAS oncogene family 133240 AK001489ADP-tibosylation 8,1 81 1 4.6 Hs.242894 factor-like 1 133271 248633 H.sapiens mRNA for 12.41246 10.8 Hs.283742 retrotransposon 133291 BE297855NRAS-related gene 3.3 33 1 2.9 Hs.69855 $0 133294 AJ001388zinc finger protein 7.9 23430 18.9 Hs.69997 238 133350 AI499220hypothetical protein4.6 46 5 3.5 Hs.71573 FLJ10074 133362 AK001519CGI-74 protein 5 11022 9.7 Hs.7194 133370 AF245505DKFZP56411922 protein3.2 725227 3.2 Hs.72157 133407 AF017987secreted frizzled-related4.1 37491 1.1 Hs.7306 protein 1 SS 133422 AB033061KIAA1235 protein 4.3 43 1 3.9 Hs.73287 133435 AI929357Homo sapiens clone 5.5 18634 16.5 Hs.323966 H63 unknown mRNA

133479 W01556 ESTs, Moderately 3.5 35 7 2.1 Hs.238797 similar to 138022 hypot 133493 AW998046arginine-glutamic 3.6 39 11 0.4 Hs.194369 acid dipeptide (RE) re 133504 NM_004415Hs.74316desmoplakin (DPI, 4.1 640158 3 DPII) 60 133517 NM 000165Hs.74471gap junction protein,3.2 351111 5.2 alpha 1, 43kD (con 133536 W25797 amyloid beta (A4) 3.2 22671 2.8 Hs.177486 precursor protein (pro 133578 AU077050translin 3.4 17853 8.8 Hs.75066 133633 D21262 nucleolar and coiled-body4.7 47 1 4 Hs.75337 phosphprotein 133640 AW246428ubiquitin-conjugating8.5 85 1 7.2 Hs.75355 enzyme E2N (homolo 65 133669 NM_006925Hs.166975splicing factor, 3.6 36 1 0.4 argininelserine-rich 133681 AI352558tyrosine 3-monooxygenaseltryptophan3.4 23468 10.7 Hs.75544 5-mo 133746 AW410035MAD (mothers against9.3 93 1 7.8 Hs.75862 decapentaplegic, Dr 133765 M62194 cadherin 11, type 3.2 560174 2.6 Hs.75929 2, OB-cadherin (osteob 133780 AA557660decorin 5.4 14427 13.3 Hs.76152 133784 BE622743arfaptin 1 4.7 47 1 4.1 Hs.301064 133814 NM_002462Hs.76391myxovirus (influenza)3.3 380114 4.9 resistance 1, homo 133829 AW630088Homo sapiens mRNA; (f 30446 7.8 Hs.76550 cDNA DKFZp564B1264 6.7 133845 AA147026ESTs 6.2 60097 4.1 Hs.76704 133913 AU076964calumenin 3.3 889267 5 Hs.7753 133968 AA355986transcription factor83.7 91 25 2.6 Hs.232068 (represses interi 133990 848316 Homo sapiens mRNA; (f 91 27 8.5 Hs.7822 cDNA DKFZp564C1216 3.4 133999 AA535244RAB2, member RAS 7.8 78 1 5.6 Hs.78305 oncogene family 134032 NM_005025Hs.78589serine (or cysteine)5.9 59 1 3.3 proteinase inhibito 134064 AF091622KIAA0244 protein 5.8 58 1 4.9 Hs.78893 134087 051166 thymine-DNA glycosylase6.4 10016 4.4 Hs.173824 134089 851273 ESTs 5.1 51 9 3.8 Hs.79029 134095 NM_004354Hs.79069cyclin G2 5 50 1 3.2 134098 BE513171mitochondria) ribosomal4.8 24651 3.9 Hs.79086 protein L3 134110 041060 LIV-1 protein, estrogen4.5 1472330 2.1 Hs.79136 regulated 134125 NM 014781Hs.50421KIAA0203 gene product4.6 69 15 5.8 134246 D28459 ubiquitin-conjugating7 97 14 7.5 Hs.80612 enzyme E2A (RAD6 h 134257 C05768 Homo Sapiens clone 3.4 34 5 2.6 Hs.8078 FBD3 Cri-du-chat crit 134272 X76040 protease, serine,15 3.6 36 1 2.8 Hs.278614 134282 845621 hypothetical protein6.7 67 9 5.7 Hs.81057 MGC2718 134288 A1022650erbb2-interacting 4.5 13731 12 Hs.8117 protein ERBIN

134321 BE538082ESTs, Moderately 5.2 52 1 4.9 Hs.8172 similar to A46010 X-lin 2$ 134326 AW903838chondroitin sulfate 8.6 56866 22.4 Hs.81800 proteoglycan 2 (vers 134328 AW959281ESTs 4.8 53 11 3.7 Hs.8184 134348 AW291946interieukin 6 signal7.1 71 4 6.4 Hs.82065 transducer (gp130, 134359 NM 001982Hs.199067v-erb-b2 avian erythroblastic3 68 23 2.8 leukemia v 134367 AA339449phosphoribosylglycinamide4.4 44 1 4.1 Hs.82285 formyltransfer 134374 N22687 ESTs 13.344534 6 Hs.8236 134380 AU077143minichromosome maintenance4.5 45 2 3.4 Hs.179565 deficient (S.

134395 AA456539lysosomal 6 60 5 5.9 Hs.8262 134401 AI916662kinectin 1 (kinesin 4.1 30173 6.1 Hs.211577 receptor) 134405 AW067903collagen, type XI, 4.6 1216267 4.4 Hs.82772 alpha 1 3 134415 AI750762protein tyrosine 4.9 16334 15.1 $ Hs.82911 phosphatase type IVA, m 134417 NM_006416Hs.82921solute tamer family 4.9 49 3 3.8 35 (CMP-sialic aci 134419 W95642 trefoil factor 3 3.2 1872592 3.3 Hs.82961 (intestinal) 134421 AUW7196 collagen, type V, 6.3 1075171 3.8 Hs.82985 alpha 2 134436 029344 fatty acid synthase 3.3 710217 2 Hs.83190 134485 X82153 cathepsin K (pycnodysostosis)34.341112 5.1 Hs.83942 134487 AF061739protein associated 4.8 15332 4.3 Hs.83954 with PRK1 134495 D63477 KIAA0143 protein 3.1 14748 12.7 Hs.84087 134520 BE091005activated RNA polymerise3.3 33 1 2 Hs.74861 li transcriptio 134542 M14156 insulin-like growth 4.2 42 5 2.6 Hs.85112 factor 1 (somatomedi 4S 134570 066615 SWIISNF related, 3.9 39 1 2.5 Hs.172280 matrix associated, acti 134590 AW903849HUEL (C4orf1)-interacting3.7 41 11 0.6 Hs.173840 protein 134604 NM_002884Hs.865RAP1A, member of 5.2 52 1 3 RAS oncogene family 134612 AW068223ubiquitin C-terminal4.9 49 1 3.7 Hs.171581 hydrolase UCH37 134643 AW299723bone morphogenefic 5.2 52 5 3.5 Hs.87223 profein receptor, typ 50 134654 AK001741hypothetical protein6.4 64 1 5.1 Hs.8739 FLJ10879 134656 AI750878thrombospondin 1 12.61261 10.8 Hs.87409 134672 AF271212disrupter of silencing5.4 81 15 2.6 Hs.322901 10 134700 AK000606golgi SNAP receptor 3.4 17952 1.5 Hs.8868 complex member 1 134711 X04011 cytochrome b-245, 3.2 14345 13.9 Hs.88974 beta polypeptide (chro S 134722 AF129536F-box only protein 7 70 6 6 $ Hs.284226 6 134856 8E281128TONDU 3.1 31 1 2.3 Hs.9030 134880 AI87919515 kDa selenoprotein5.7 57 1 5 Hs.90606 134917 X87241 FAT tumor suppressor3.2 15348 4.7 Hs,166994 (Drosophila) homolo 134921 AL137491Homo sapiens mRNA; (f 452114 2 Hs.125511 cDNA DKFZp434P1530 4 60 134982 AK002085Homo Sapiens cDNA 5.1 15030 7.2 Hs,92308 FLJ11223 fis, clone PL

134989 AW968058nudix (nucleoside 8.2 11414 9.9 Hs,92381 diphosphate linked moi 135029 H58818 hydroxysteroid (17-beta)11.51151 10 Hs.187579 dehydrogenase 7 135035 AL034344forkhead box C1 5.4 25948 1.4 Hs.284186 135051 AI272141SRY (sex determining3.3 1296394 2.2 Hs.83484 region Y)-box 4 6$ 135062 AK000967KIAA1682 protein 3.8 24064 3.2 Hs.93872 135073 W55956 Homo Sapiens mRNA; (f 10113 7.9 Hs.94030 cDNA DKFZp586E1624 8.1 135098 AW274526ovarian carcinoma 3.3 33 1 2.6 Hs.277721 antigen CA125 135117 W52493 Homo sapiens cDNA 5.353 1 4.1 Hs,94694 FLJ10561 fis, clone NT

'15144 NM 016255Hs.95260Autosomal Highly Conserved7.474 5 2.4 Protein 135154 AK001835sorting nexin 4 6.669 11 6.3 Hs.267812 135155 AI207958Homo sapiens, Similar6.161 1 5.1 Hs.166556 to TEA domain fami $ 135172 AB028956KIAA1033 protein 3.488 26 1.4 Hs.12144 135242 AI583187cyclin E1 3.131 1 2.3 Hs.9700 135243 BE463721putative G protein-coupled3.416950 9.1 Hs.97101 receptor 135269 NM_003403Hs.97496YY1 transcription 3.4475142 2.5 factor 135356 BE312948hypothetical protein 3.131 10 1.7 Hs.18104 FLJ11274 I 135357 AI565004cafhepsin D (lysosomal4.7710151 2.5 ~ Hs.79572 aspar<yl protease 135389 U05237 fetal Alzheimer antigen20.62064 19.1 Hs.99872 135397 L14922 replication factor 3.232 1 2.4 Hs.166563 C (activator 1 ) 1 (14 135400 X78592 androgen receptor 3.211737 9.4 Hs.99915 (dihydrotestosterone r AI471525 Hs.247486ESTs 3.858 16 5.5 1 X70683 Hs.93668ESTs 1.81047596 1.6 S

L14922 Hs.821285T4 oncofetal trophoblast5 28558 1.2 glycoprotein M23263 Hs.904 amylo-1;6-glucosidase; 3,131 1 2.6 4-alpha-glucanotransferas AI267886 Hs.148027polymerase (RNA) II 7.8137 18 11.9 (DNA directed) polypeptide B

AA044840 Hs.241676stromal cell-derived 4.711425 0.9 factor 1 2~ N90960 Hs.227459ESTs; Moderately similar 4.7151 32 9.3 to !!!! ALU SUBFAMILY

AA873285 Hs.137947ESTs 4.747 3 4.4 T56679 Hs.865 RAP1A; member of RAS 4 40 1 3.4 oncogene family AA305536 "EST176522 Colon carcinomaI 3.6121 34 11.8 (Caco-2) cell line I

AI369384 aryisulfafase D 3.511333 1.7 2$ AA219081 Hs.242396ESTs; Moderately similar] 3.4107 32 9.9 to Ill! ALU SUBFAMILY

TABLE l0A
Table 10 A shows the accession numbers for those pkeys lacking unigenelD's for Table 10.
For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers 1$
Pkey CAT number Accession 123619371681_1 AA602964 AA609200 121581283769_1 AA416568 AA442889 123523genbank_AA608588 AA608588 1008216gr_HT4306 M26460 U09116 125091genbank 2$ 125150_ NOT_FOUND_entrez_W38240 118475genbank_N66845 N66845 104787genbank_AA027317 AA027317 106055genbank_AA417034 AA417034 113702genbank_T97307 T97307 101046entrez_K01160 K01160 101447entrez_M21305 M21305 101624entrez_M55998 M55998 124677genbank_R01073 801073 110581genbanILH61560 H61560 3 119023genbank_N98488 N98488 $

110775genbank_N22414 N22414 112092genbank_R44538 844538 112253genbank_R51818 851818 107014genbank_AA598820 AA598820 40 114988genbank_AA251089 AA251089 TABLE 11: Figure 11 from BRCA 001-3 PCT
Table 11 depicts a preferred group of genes upregulated in tumor tissue compared to normal breast tissue. .
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title R1: Ratio of tumor to normal body tissue R2: Ratio of 90~ percentile tumor to normal body 1$ R3: Ratio of 75w percentile normal body to tumor R4: Ratio of tumor fo normal breast (issue Pkey ExAccn UnigenelD Unigene TitleR1 R2 R3 R4 ~

100131 D12485 Hs.11951 ectonucleotide13.224419 9.9 pyrophosphataselphosphodi 100147 D13666 Hs.136348 osteoblastspecificfactor2(fasciclin15.7103066 5 100522 X51501 Hs.99949 prolactin-induced22.776034 1.4 protein 100666 L05424 Hs.169610 CD44 antigen8.585 1 3.2 (homing function and Indian 2$ 101104 AW862258 Hs.169266 neuropepfide15.31531 14.1 Y receptor Y1 101478 NM 002890Hs.758 RAS p21 9.696 1 8.5 protein activator (GTPase activa 101724 L11690 Hs.620 bullous pemphigoid9.494 1 0.3 antigen 1 (2301240kD) 101754 S70114 Hs.239489 TIA1cytotoxicgranule-associated8.989 5 8 RNA-bi 101888 AL049610 Hs.95243 transcription7.373 1 5.3 elongation factor A (SII)-102165 BE313280 Hs.159627 death 9.393 5 8 associated protein 3 102304 AF015224 Hs.46452 mammaglobin8.520582431.4 102348 U37519 Hs.87539 aldehyde 6.442867 2.3 dehydrogenase 3 family, member 102457 NM_001394Hs.2359 dual specificity20.22025 1.3 phosphatase 4 102567 U63830 Hs.146847 TRAF family8.282 1 6.8 member-associated NFKB activ 3$ 102823 D85390 Hs.5057 carboxypeptidaseD5.656 1 5.3 103557 AL133415 Hs.297753 vimentin7.513618 3.4 103613 NM_000346Hs.2316 SRY (sex 7.373 1 5.2 determining region Y)-box 9 (ca 104115 AF183810 Hs.26102 opposite 29 2901 26.8 strand to trichorhinophalangeal 104667 A1239923 Hs.30098 ESTs 14.91491 6.4 104804 AI858702 Hs.31803 ESTs, 7.777 1 5.1 Weakly similar to N-WASP [H.sapien 104807 AI139058 Hs.125790 leucine-rich7 70 1 6.5 repeat-containing 2 104896 AW015318 Hs.23165 ESTs 7.474 1 6 104943 AF072873 Hs.114218 frizzled16.21621 4.2 (Drosophila) homolog 6 105038 AW503733 Hs.9414 KIAA1488 5.555 1 5.2 protein 4S 105329 AA234561 Hs.22862 ESTs 2.813147 3.9 105500 AW602166 Hs.222399 CEGP1 25.450820 3 protein 105516 AK001269 Hs.30738 hypothetical8.383 3 1.8 protein FLJ10407 105730 AW377314 Hs.5364 DKFZP56410526.969 1 4.4 protein 106012 AI240665 Hs.8895 ESTs 21.22126 17.4 106095 AF115402 Hs.11713 E74-like 26.335614 1 factor 5 (ets domain transcript 106155 AA425414 Hs.33287 nuclear 9.948349 1.8 factor 118 107102 AB037765 Hs.30652 KIAA1344 6.363 1 5.4 protein 107136 AV661958 Hs.8207 GK001 protein2.53921554.3 107151 AW378065 Hs.8687 ESTs 15.61567 10.8 $$ 107922 BE153855 Hs.61460 IgsuperfamilyreceptorLNIR9 90 1 5.5 108339 AW151340 Hs.51615 ESTs, 18.71871 17 Weakly similar to ALU7 HUMAN ALU
S

109112 AW419196 Hs.257924 hypothetical4.133482 3.4 protein FLJ13782 109292 AW975746 Hs.188662 KIAA17027.171 1 6.5 protein 109415 U80736 Hs.110826 trinucleotide12.31231 11.3 repeat containing 9 109912 AW390822 Hs.301528 L-kynureninelalpha-aminoadipate14.21421 9.5 aminotra 110009 BE075297 Hs.6614 ESTs, Weakly6.36931107.2 similar to A43932 mucin 2 p 110915 BE092285 Hs.29724 hypothetical20.92091 19.5 protein FLJ13187 111164 N46180 Hs.122489 Homo sapiens7.777 1 5 cDNA FLJ13289 fis, clone OV

111179 AK000136 Hs.10760 asporin 25.128812 6.7 (LRR class 1) 111190 AK002055 Hs.151046 hypothetical6.363 1 5.8 protein FLJ11193 111223 AA852773 Hs.334838 KIAA18663.64021124.9 protein 111357 BE314949 Hs.87128 hypothetical3.84251114 protein FLJ23309 112244 AB029000 Hs.70823 KIAA1077 5.75671006.7 protein 113047 AI571940 Hs.7549 ESTs 9.612413 9 113702 T97307 gb:ye53h05.s1 Soares12.312911 11.7 fetal liver spleen 114124 W57554 Hs.125019 lymphoid 24.224210 5.6 nuclear protein (LAF-4) mRNA

114138 AW384793 Hs.15740 Homo Sapiens 67 1 6.3 mRNA; cDNA DKFZp434E033 (fr 6.7 1 114768 AF212848 Hs.182339 ets homologous13.71371 8.9 ~ factor 114860 AL157545 Hs.42179 bromodomain9.191 1 7.6 and PHD finger containing, 3 114965 AI733881 Hs.72472 BMP-R1B 35.935910 29.7 114988 AA251089 gb:zs04f05.s1 NCI_CGAP_GCB1 1151 6.9 Homo Sapiens 11.5 115206 AW183695 Hs.186572 ESTs 5.858 1 5 15 115719 AW992405 Hs.59622 Homo Sapiens,7.614419 13.9 clone IMAGE:3507281, mRNA, 115844 AI373062 Hs.332938 hypothetical6.262 1 5.4 protein MGC5370 ~

116470 AI272141 Hs.83484 SRY (sex 1.810475961.6 determining regicn Y)-box 4 116786 H25836 Hs.301527 ESTs, Moderately22.82289 12.4 similarto unknown [H.s 117280 M18217 Hs.172129 Homo Sapiens3.932283 4.4 cDNA: FLJ21409 fis, clone C

2~ 117412 N32536 Hs.42645 solute carver17.41749 6.9 family 16 (monocarboxylic 118472 AL157545 Hs.42179 bromodomain14.51451 2.4 and PHD finger containing, 3 119271 A1061118 Hs.65328 Fanconi 8.282 1 6.4 anemia, complementation group F

119771 AI905687 Hs.2533 EST 3.520735952.1 120562 BE244580 Hs.302267 hypothetical8.512715 1.6 protein FLJ10330 25 121463 AK000282 Hs.239681 hypothetical10.31031 9.3 protein FLJ20275 121723 AA243499 Hs.104800 hypothetical2.921474 3.7 protein FLJ10134 122963 AA478446 Hs.69559 KIAA1096 7.272 1 5.7 protein 123137 A1073913 Hs.100686 ESTs, 9.935136 13.9 Weakly similar to JE0350 Anterior 123619 AA602964 gb:no97c02.s1 NCI_CGAP8.585 1 4.3 Pr2 Homo sapiens 123709 AA706910 Hs.112742 ESTs 3.960 16 4.8 124006 AI147155 Hs.270016 ESTs 5.832155 17 124059 BE387335 Hs.283713 ESTs, 10.488085 5.3 Weakly similar to S64054 hypotheti 124308 AA249027 Hs.241507 ribosomal10.51051 9.9 protein S6 125279 AW401809 Hs.4779 KIAA1150 13.11311 5.1 protein 3 125617 AA287921 Hs.164950 ESTs 6.767 1 6 $

127439 D60237 Hs.14368 SH3 domain 30.63064 26.5 binding glutamic acid-rich pr 128305 AI95496B Hs.279009 matrix 7.575 1 6.5 Gla protein 128482 AI694143 Hs.296251 programmed7.272 1 5.8 cell death 4 128790 AF026692 Hs.105700 secreted17.440924 7.8 frizzled-related protein 4 128925 867419 Hs.21851 Homo Sapiens7.139256 3.6 cDNA FLJ12900 fis, clone NT

129017 AA115333 Hs.107968 ESTs 8.282 1 7.4 129229 AF013758 Hs.109643 polyadenylate7.171 1 6.2 binding protein-interactin 129337 NM_014918Hs.110488 KIAA09909.595 1 8.5 protein 129366 BE220806 Hs.184697 Homo 7.115021 14.5 Sapiens clone 23785 mRNA sequence ~S 129821 AB028945 Hs.12696 cortactin11.41141 10 SH3 domain-binding protein 130036 BE061916 Hs.125849 chromosome6.767 1 5.7 8 open reading frame 2 130057 AF027153 Hs.324787 solute 1 1 1 1 carver family 5 (inositol transp 130095 AK001635 Hs.14838 hypothetical14.621915 7.6 protein FLJ10773 130343 AB040914 Hs.278628 KIAA148113.233125 12.4 protein S~ 130385 AW067800 Hs.155223 stanniocalcin72.27221 1.9 130407 BE385099 Hs.334727 hypothetical6.565 4 5.3 protein MGC3017 130441 U63630 Hs.155637 protein 6.161 1 5.7 kinase, DNA-activated, catalytic 130455 D90041 Hs.155956 N-acetyltransferase10.870666 9.2 1 (arylamine N-acety 130604 AA383256 Hs.1657 estrogen 32.23221 4.7 receptor 1 5$ 130617 M90516 Hs.1674 glutamine-fructose-6-phosphatetransamin10 1001 7.6 130712 AJ271881 Hs.279762 bromodomain-containing17.51752 12.8 131148 AW953575 Hs.303125 p53-induced3.85851533.7 protein PIGPC1 131388 NN~,014810Hs.92200 KIAA04807.676 1 5 gene product 131564 T93500 Hs.28792 Homo Sapiens4.738181 6.4 cDNA FLJ11041 fis, clone PL

131742 AA961420 Hs.31433 ESTs 11.71171 10.1 131877 J04088 Hs.156346 topoisomerase6.868 1 5.6 (DNA) II alpha (170kD) 131985 AA503020 Hs.36563 hypothetical40.24021 4 profein FLJ22418 132316 U28831 Hs.44566 KIAA1641 18.618610 1.5 protein 132528 T78736 Hs.50758 SMC4 (structural9.393 1 8.4 maintenance of chromoso 6$ 132742 AA025480 Hs.292812 ESTs, 6.565 1 5.6 Weakly similar to T33468 hypotheti 132990 X77343 Hs.334334 transcription12.731125 2.4 factorAP-2 alpha (activat 133015 AJ002744 Hs.246315 UDP-N-acetyl-alpha-D-galactosamine:polyp4.642793 10.4 133199 AF231981Hs.250175 homolog of 3 8162753.9 yeast long chain polyunsatura 133240 AK001489Hs.242894 ADP-ribosylation8.1 81 1 4.6 factor-like 1 133271 248633Hs.283742 H.sapiens mRNA12.41246 10.8 for retrotransposon 133640 AW246428Hs.75355 ubiquitin-conjugating8.5 85 1 7.2 enzyme E2N (homolo 133746 AW410035Hs.75862 MAD (mothers 9.3 93 1 7.8 against decapentaplegic, Dr 133999 AA535244Hs.78305 RAB2, member 7.8 78 1 5.6 RAS oncogene family 134110 041060Hs.79136 LIV-1 protein, 4.5 14723302.1 estrogen regulated 134485 X82153Hs.83942 cathepsin K 34.341112 5.1 (pycnodysostosis) 134654 AK001741Hs.8739 hypothetical 6.4 64 1 5.1 protein FLJ10879 1 ~ 134880 Hs.90606 15 kDa selenoprotein5.7 57 1 5 135029 H58818Hs.187579 hydroxysteroid11.51151 10 (17-beta) dehydrogenase 135389 005237Hs.99872 fetal Alzheimer20.62064 19.1 antigen 128305 AI954968Hs.279009 matrix Gla 9.4 94 3 5.3 protein Table 11A shows the accession numbers for those pkeys lacking unigenelD's for Table 11.
For each probeset, we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT number Accession 113702 genbank_T97307 T97307 114988 genbank_AA251089 AA251089 TABLE 12: Figure 12 from BRCA 001-3 PCT
Table 12 depicts a preferred group of genes upregulated in tumor tissue compared to normal breast tissue.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title R1: Ratio of tumor to normal body tissue R2: Ratio of 90~ percentile tumor to body 1 R3: Ratio of 75~ percentile body S to tumor R4: Ratio of tumor to normal breast tissue Pkey ExAccn UnigenelD UnigeneTitleR1 R2 R3 R4 2~ 100131 D12485 Hs.11951 phosphodiesterase13.2244 19 9.9 I (PC-1j 105500 AW602166 Hs.222399 ESTs 25.4508 20 3 112244 AB029000 Hs.70823 KIAA10775.7567 1006.7 protein 114124 W57554 Hs.125019 ESTs 24.2242 10 5.6 119771 AI905687 Hs.2533 ESTs 3.520735952.1 25 121723 AA243499 Hs.104800 ESTs 2.9214 74 3.7 128790 AF026692 Hs.105700 secreted17.4409 24 7.8 frizzled-related protein 4 131148 AW953575 Hs.303125 ESTs 3.8585 1533.7 131985 AA503020 Hs.36563 ESTs 40.2402 1 4 133199 AF231981 Hs.250175 Homo 816 2753.9 Sapiens clone 23904 mRNA sequence TABLE 13: Table 1 from BRCA 001-5 US
Table 13 depicts a preferred group of genes upregulated in breast cancer cells.
Pkey: Unique Eos probeset idenflfier number 1 ~ ExAccn: ExempIarAccession number, Genbank accession number UnigenelD: Unigene number Unigene Tifle: Unigene gene title R1: Ratio of tumor to normal body tissue Pkey ExAccn UniGene ID Unigene Title R1 100038 control 16.7 100039M97935 control 6.3 100040M97935 control 8.3 100041M97935 control 14.8 100082AB003103Hs.4295proteasome (prosome; 7.5 macropain) 26S sub 100091AF000177Hs.111783Lsm1 protein 4.9 100100AF006084Hs.11538actin related protein 4.7 213 complex; subunit ~S 100103AF007875Hs.5085dolichyi-phosphate mannosyltransferase13.4 p 100114D00596Hs.82962thymidylate synthetase 15.9 100121D10495Hs.155342protein kinase C; delta4.6 100123D10523Hs.168669oxoglutarate dehydrogenase7.5 (lipoamide) 100128D11094Hs.61153proteasome (prosome; 4.4 macropain) 26S sub 3~ 100131D12485Hs.11951phosphodiesterase Ilnucleotide8.7 pyrophosp 100137D13627Hs.15071chaperonin containing 9.5 TCP1; subunit 8 (t 100144D13643Hs.75616Human mRNA for KlAA00186 gene; comp 100147D13666Hs.136348osteoblast specific 8.5 factor 2 (fasciclin I-like 100154D14657Hs.81892KIAA0101 gene product 10.5 3 100164D14812Hs.173714MORF-relafed gene X 4.6 S

100169D14878Hs.82043D123 gene product 7.9 100190D21090Hs.178658RAD23 (S. cerevisiae) 5.6 homolog B

100203D25538Hs.172199adenylate cyclase 7 9.9 100209D26308Hs.76289biliverdin reductase 4.9 B (flavin reductase (N

100215D26598Hs.82793proteasome (prosome; 14.2 macropain) subunit 100216D26599Hs.1390proteasome (prosome; 11.3 macropain) subunit 100219D28137Hs.118110bone marrow stromal 5.7 cell anflgen 2 100227D28915Hs.82316interferon-induced; 5.7 hepatitis C-associated 100248D31888Hs.78398KIAA0071 protein 7.4 4S 100287D43950Hs.1600chaperonin containing 5.6 TCP1; subunit 5 (e 100294D49396Hs.75454antioxidant protein 12.9 100307D50525H's.699hypothetical protein 8.4 100335D63391Hs.6793platelet-activating 6.8 factoracetylhydrolase;

100340D63487Hs.82563KIAA0153 protein 4.4 S~ 100355D78129Hs.71465Homo Sapiens mRNA for 12.6 squalene epoxid 100363D78514Hs.78563ubiquitin-conjugating 4.6 enryme E2G 1 (hom 100368D79987Hs.153479extra spindle poles; 6.5 S. cerevisiae; homolo 100372D79997Hs.184339KIAA0175 gene product 8.4 100375D80004Hs.75909KIAA0182 protein 4.5 5 100379D82060Hs.278721Ke4 gene; mouse; human 8.1 S homolog of 100387D83777Hs.75137KIAA0193 gene product 10.7 100393D84145Hs.39913novel RGD-containing 7.2 profein 100398D84557Hs.155462minichromosome maintenance7.2 deficient (m 100405D86425Hs.82733nidogen 2 5.4 100406D86479Hs.118397AE-binding protein 1 4.3 100409D86957Hs.80712KIAA0202 protein ~ 11.9 100421D86985Hs.79276Human mRNA for KIAA02329.7 gene; comp 100446D87464Hs.10037KIAA0274 gene product 6.4 100447D87465Hs.74583KIAA0275 gene product 10 6S 100448D87469Hs.57652EGF-like-domain; multiple6.2 100467D89052Hs.7476ATPase; H+transporting;7.5 lysosomal (vacu 100468D89289Hs.118722fucosyltransferase 8 5 (alpha (1;6) fucosyltr 100486HT1112Hs.10842Ras-Like Protein Tc4 ' 16.9 100497HT1400Hs.79137Carboxyl Methyltransferase,5.6 Aspartate, A

$ 100618HT2710Hs.114599Cohagen, Type Viii, 7.5 Alpha 1 100661HT3018Hs.132748Ribosomal Protein L39 4.4 Homolog 100667HT3127Hs.169610Epican, Alt. Splice 4.6 100668HT3938Hs.169610Epican, Alt. Splice 4.4 100676HT3742Hs.287820Fibronectin, Alt. Splice9 1 100775HT26388Hs.89603Mucin 1, Epithelial, 4.7 Q Alt. Splice 9 100783HT4018Hs.191356Basic Transcription 13.7 Factor, 44 Kda Subun 100829HT4343Hs.278544Cytosoiic Acetoacetyl-Coenzyme10.6 A Thio 100830HT4344Hs.4756Rad2 5.5 100840HT4392Hs.183418Protein Kinase Pitslre,4.1 Alpha, Alt. Splice 15100850HT417Hs.297939Cathepsin B 4 100866HT4582Hs.75113TranscdptionFactorliia 4.9 100906HT5158Hs.5398Guanosine 5'-Monophosphate8.7 Synthase 100914HT511Hs.324178Ras Inhibitor Inf 7.2 100916HT544Hs.73946Endothelial Cell Growth5.9 Facfor 1 2~100945HT884Hs.180686Oncogene E6-Ap, Papillomavirus4.6 100975J02923Hs.76506lymphocyte cytosolic 30.1 protein 1 (L-plastin 100988J03589Hs.76480ubiquitin-tike 4 8.3 100996J03909Hs.14623interferon; gamma-inducible6.9 protein 30 100999J03934Hs.80706diaphorase (NADHINADPH)4.3 (cytochrom ~$101011J04430Hs.1211acid phosphatase 5; 5.9 tartrate resistant 101017J04599Hs.821biglycan 5.1 101031J05070Hs.151738matrix metalloproteinase37.2 9 (gelatinase B;

101038J05249Hs.79411replication protein 6.1 A2 (32kD) 101054K02405Hs.73931Human MHC class If HLA-DO-beta4.3 mRN

101061K03515Hs.180532glucose phosphate isomerase4.3 101091L06132Hs.149155voltage-dependent anion7.4 channel 1 101097L06797Hs.89414chemokine (C-X-C motif);4.6 receptor 4 (fus 101104L07615Hs.169266Human neuropeptide Y 18.3 receptor Y1 (NPY

101143L12723Hs.90093heat shock 70kD protein17.4 3 101152L13800Hs.9884Homo sapiens liver expressed7.6 S protein gen 101183L19779Hs.795H2A histone family; 10.9 member 0 101216L25876Hs.84113cyclin-dependent kinase7.4 inhibitor 3 (CDK

101233L29008Hs.878sorbitol dehydrogenase 14.6 1D1247L33801Hs.78802glycogen synthase kinase7.5 3 beta 101282L38810Hs.79387proteasome (prosome; 4.4 macropain) 26S sub 101326L42572Hs.78504inner membrane protein;5.8 mitochondrlal (m 101332L47276Hs.156346Homo sapiens (cell line18.9 HL-6) alpha topo 101348L77213Hs.30954phosphomevalonate kinase7.5 101352L77701Hs.16297COX17 (yeast) homolog; 9.3 cytochrome c ox 4$101378M13755Hs.833interferon-stimulated 18.1 protein;15 kDa 101396M15796Hs.78996proliferating cell nuclear8.6 antigen 101404M16342Hs.182447heterogeneous nuclear 4.5 ribonucleoprotein C

101439M20902Hs.268571apolipoprotein C-I 6.1 101464M22538Hs.51299NADH dehydrogenase (ubiquinone)8.7 ttavo $~101469M22877Hs.169248Human somatic cyfochrome4.2 c (HCS) gene 101472M22960Hs.118126protective protein for 6.5 ' beta-galactosidase ( 101478M23379Hs.758RAS p21 protein activator14 (GTPase activa 101484M24594Hs.20315interferon-induced protein9.2 101539M30818Hs.926myxovirus (influenza) 5.1 resistance 2; homol S$101540M30938Hs.84981X-ray repair complementing4.7 defective rep 101544M31169 Human propionyl-CoA 5.5 carboxylase beta-s 101552M31642Hs.82314hypoxanthine phosphoribosyltransferase8.5 101580M34677Hs.83363DNA segment on chromosome4.5 X (unique) 101600M37583Hs.119192H2A histone family; 5.7 member Z

101663M60750Hs.2178H2B histone family; 5.8 memberA

101664M60752Hs.121017H2A histone family; 13.5 member A

101667M60858Hs.79110nucleoiin 4 101684M63256Hs.75124cerebellar degeneration-related7.6 protein (62 101702M64929Hs.179574protein phosphatase 4.2 2 (formerly 2A); regu 6$101754M77142Hs.239489TIA1cytotoxicgranule-associated4.5 RNA-b 101758M77836Hs.79217pyrroline-5-carboxylate5.7 reductase 1 101767M81057Hs.180884carboxypeptidase B1 21.7 (tissue) 101770 Hs.78869transcription elongation4.6 M81601 factorA (SII);1 101791 Hs.62354cell division cycle 9.7 M83822 4-like 101803 Hs.155691pre-B-cell leukemia 5.5 M86546 transcription factor 101809 Hs.323733Homo Sapiens connexin 22.5 M86849 26 (GJB2) mRNA

101839 Hs.692membrane component; 4 M93036 chromosomal 4; su 101851 Hs.82045midkine (neurite growth-promoting7.6 M94250 factor 101888 Hs.95243transcription elongation11.4 M99701 factorA (Slfj-like 101973 Hs.80120UDP-N-acetyl-alpha-D~galactosamine:po4.6 101991 Hs.166Human SREBP-1 mRNA; 4.1 000968 complete cds 1 102009 Hs.82643protein tyrosine kinase4.4 ~ 002680 9 102025 Hs.78934mutS (E. colt) homolog 4 003911 2 (colon cancer; n 102047 Hs.83734syntaxin 4A (placental)6.1 102051 Hs.1197heat shock 10kD protein4.4 007550 1 (chaperonin 10 102083 Hs.75117interleukin enhancer 10.4 010323 binding factor 2; 45k 1$ 102095 Hs.75760sterol tamer protein 9.5 102130 Hs.1575small nuclear ribonucleoprotein6.6 015009 D3 polyp 102133 Hs.155596BCL2ladenovirus E1B 4.3 015173 19kD-interacting p 102148 Hs.75823ALL1-fused gene from 6.9 016954 chromosome 1q 102179 Hs.76364allograft inflammatory 4.8 019713 factor 1 ZQ 102180 Hs.83551microfibrillar associated7.2 019718 protein 2 102193 Hs.313secreted phosphoprotein7.2 020758 1 (osteopontin; b 102198 Hs.74598polymerase (DNA directed);4.3 021090 delta 2; regu 102202 Hs.574fructose-bisphosphatase4.5 102209 Hs.265827interferon; alpha-inducibie9.9 022970 protein (clone 102211 Hs.78776putative transmembrane 4.9 023070 protein 102220 Hs.65436lysyl oxidase-like 1 8.5 102224 Hs.148495proteasome (prosome; 5.4 024704 macropain) 26S sub 102234 Hs.278554chromobox homolog 3 7.7 026312 (Drosophfla HP1 g 102250 Hs.74122caspase 4; apoptosis-related5.4 028014 cysteine prot 102260 Hs.159557karyopherin alpha 2 6.3 028386 (RAG cohort 1; impo 102261 Hs.155935complement component 5.7 028488 3a receptor 1 102273 Hs.75981ubiquitin specific protease6.1 030888 14 (tRNA-guan 102298 Hs.54483N-myc (and STAT) interactor4.1 102302 Hs.69171protein kinase C-like 4.3 35 102305 Hs.90073chromosome segregation 5.4 033286 1 (yeast homolo 102320 Hs.82327glutathione synthetase 4.1 102330 Hs.77254chromobox homolog 1 4 035451 (Drosophila HP1 b 102348 Hs.87539aldehyde dehydrogenase 9.4 102361 Hs.75859chromosome 11 open reading5.2 039400 frame 4 102362 Hs.75932N-ethylmaleimide-sensitive9.3 039412 factor attachm 102369 Hs.299867hepatocyte nuclear factor7.7 039840 3; alpha 102395 Hs.92208a disintegrin and metalloproteinase10.4 041767 domai 102409 Hs.118725selenophosphate synthetase6.2 102418 Hs.79058suppressor of Ty (S.cerevisiae)4.1 043923 4 homolog 102425 Hs.3873palmitoyl-protein thieesterase4.8 044772 (ceroid-lipo 102457 Hs.2359dual specificity phosphatase6.3 102465 Hs.815482;4-dienoyl CoA reductase9.4 049352 1; mitochondri 102495 Hs.79356Lysosomal-associated 6.5 051240 multispanning mem 102534 Hs.198307von Hippel-Lindau binding8.6 056833 protein 1 102546 Hs.3577succinate dehydrogenase4.3 057877 complex; subuni 102549 Hs.198899eukaryotic translation 6.3 058046 initiation factor 3;
s 102557 Hs.264428tissue specific transplantation5 058766 antigen P35 102562 Hs.75653fumarate hydratase 6 102568 Hs.223025RAB31; member RAS oncogene9.1 059877 family $ 102580 Hs.152981CDP-diacylglycerol synthase7.9 S 060808 (phosphatid 102581 Hs.77256enhancer of zeste (Drosophila)7.6 061145 homolog 2 102590 Hs.79300Homo sapiens enterocyte7 062136 differentiation a 102591 Hs.324125amyloid beta (A4) precursor4 062325 protein-bindi 102592 Hs.11223Human putative cytosolic5 062389 NADP-depende 102617 Hs.198767Jun activation domain 6.1 065928 binding protein 102618 Hs.81071extracellular matrix 23.2 065932 protein 1 102638 Hs.9216caspase 7; apoptosis-related8.9 067319 cysteine prot 102663 Hs.168075karyopherin (importin) 7.1 070322 beta 2 102666 Hs.279910ATx1 (antioxidant protein4,7 070660 1; yeast) homo 65 102679 Hs.11342ninjurin 1; nerve injury-induced4.7 072661 protein-1 102687 Hs.93002ubiquitin Gamier protein7.7 102704 Hs.54089BRCA1 associated RING 5.6 076638 domain 1 ~1~

102705077180Hs.50002small inducible cytokine11.8 subfamily A (Cy 102721079241Hs.118666Human clone 23759 mRNA;15 partial cds 102729079254Hs.181311asparaginyl-tRNA synthetase5 102739079282Hs.155572Human clone 23801 mRNA6 sequence $ 102742079293Hs.159264Human clone 23948 mRNA13.1 sequence 102761082130Hs.118910tumor susceptibility 7 gene 101 102788086602Hs.74407nucleolar protein p40 4.1 102790087269Hs.154196E4F Transcription factor7.1 102801089606Hs.38041pyridoxal (pyridoxine;4.7 vitamin B6) kinase 1 102808090426Hs.179606nuclear RNA helicase; 7.5 ~ DECD variant of D

102817090904Hs.83724Human clone 23773 mRNA15.2 sequence 102823090914Hs.5057carboxypeptidase D 6.6 102827091327Hs.6456chaperonin containing 6 TCP1; subunit 2 (b 102838094592Hs.80658Human uncoupling protein6.1 homolog (UCP

1$ 102841095006Hs.37616Human D9 splice variant4.2 B mRNA; comp 102844096113Hs.324275Homo Sapiens Nedd-4-like6.8 ubiquitin-prot 102868X02419Hs.77274plasminogen activator;4 urokinase 102907X06985Hs.202833heme oxygenase (decycling)22.7 102919X12447 aldolase A; fructose-bisphosphate9.9 102929X13238Hs.74649cyfochrome c oxidase 5.4 subunit Vic 102973X16663Hs.14601hematopoietic cell-specific4.8 Lyn substrate 102983X17620Hs.118638non-metastatic cells 4.6 1; protein (NM23A) 102985X17644Hs.2707G1 to S phase transition20.6 103003X52003Hs.1406trefoil factor 1 (breast10.7 cancer; estrogen-ind 2$ 103018X53296Hs.81134interleukin 1 receptor5.8 antagonist 103023X53793Hs.117950multifunctional polypeptide4 similar to SA

103036X54925Hs.83169matrix metalloproteinase7.3 1 (interstitial col 103060X57766Hs.155324matrix metalloproteinase17.8 11 (stromelysin 103073X59417Hs.74077proteasome (prosome; 5.6 macropain) subunit 103075X59543Hs.2934ribonucleotide reductase4.2 M1 polypeptide 103080X59798Hs.82932cyclin D1 (PRAD1: parathyroid6.7 adenomat 103094X60787Hs.296281interieukin enhancer 5.7 binding factor 1 103105X61970Hs.76913proteasome (prosome; 5.8 macropain) subunit 103121X63679Hs.4147translocating chain-associating4.2 membrane 3$ 103149X66363Hs.171834PCTAIRE protein kinase12 103180X69433Hs.5337isocitrate dehydrogenase18.9 2 (NADP+); mit 103182X69819Hs.99995intercellular adhesion10.7 molecule 3 103188X70040Hs.2942macrophage stimulating4.1 1 receptor (c-met 103191X70218Hs.2903protein phosphatase 10.7 4 (formerly X); cataly 103193X70476Ns:75724coatomer protein complex;8.2 subunit beta 2 103194X70649Hs.78580DEADIH (Asp-Glu-Ala-AsplHis)13.7 box pol 103195X70940Hs.2642eukaryotic translation13.4 elongation factor 103206X72755Hs.77367monokine induced by 15.1 gamma interferon 103207X72790 Human endogenous retrovirus5.3 mRNA for 4$ 103208X72841Hs.31314retinoblastoma-binding12.3 protein 7 103216X74262Hs.16003retinoblastoma-binding4.1 protein 4 103226X75042Hs.44313v-rel avian reticuloendotheliosis6.9 viral onco 103230X75861Hs.74637testis enhanced gene 7.9 transcript 103262X78565Hs.289114hexabrachion (tenascin5 C; cytotactin) $.0103278X79882Hs.80680lung resistance-related5.7 protein 103297X81788Hs.9078immature colon carcinoma4.6 transcript 1 103302X82103Hs.3059coatomer protein complex;4.5 subunit beta 103316X83301Hs.324728SMA5 7.1 103330X85373Hs.77496small nuclear ribonucleoprotein4 polypepti $ 103349X89059 serinelthreonine kinase4.7 $ 9 103352X89398Hs.78853uracil-DNA glycosylase5.3 103364X90872Hs.279929SULT1C sulfotransferase4 103374X91788Hs.84974chloride channel; nucleotide-sensitive;1A4.2 103380X92396Hs.24167synaptobrevin-like 13.6 60 103395X94754Hs.279946methionine-tRNA synthetase14.2 103402X95404Hs.180370cofilin 1 (non-muscle)4.6 103410X96506Hs.295362DR1-associated protein8.3 1 (negative cofact 103420X97065Hs.173497Sec23 (S, cerevisiae) 4.9 homolog B

103421X97074Hs.119591adaptor related protein5 complex 2; sigma 6$ 103427X97303Hs.250655H.sapiens mRNA far 7 Ptg-12 protein 103430X97544Hs.20716translocase of inner 4.5 mitochondrial membr 103438X98263Hs.152720M-phase phosphoprotein4.5 103464 Hs.76473insulin-like growth 4.2 Y00285 factor 2 receptor 103470 Hs.174103integrin; alpha L (antigen4.5 Y00796 CD11A (p180);

103494 Hs.83050phospha6dylinositol 4.1 Y08991 3-kinase-associated p 103505 Hs.33102transcription factorAP-24.5 Y09912 beta (activating $ 103547 Hs.180062proteasome (prosome; 4.3 214982 macropain) subunit 103551 Hs.75248topoisomerase (DNA) 4 215115 II beta (180kD) 103565 Hs.146354thioredoxin-dependent 7.6 222548 peroxide reductase 103587 Hs.821285T4 oncofetal trophoblast14.6 229083 glycoprotein 103621 Hs.150675polymerase (RNA) II 6.3 247727 (DNA directed) pol 1 103622 Hs.278672membrane component; 4.4 ~ 248042 chromosome 11; s 103658 Hs.172928collagen; type h, alpha5.9 103680 Homo Sapiens DNA sequence4.4 293784 from PAC

103772 Hs.278554chromobox homolog 3 4.9 AA092473 (Drosophila HP1 g 103774 Hs.92918ESTs; Weakly similar 6.1 AA092898 to R07G3.8 [C.eleg 1$ 103821 Hs.198793KIAA0750 gene product 23.3 103835 Hs.93748ESTs;ModeratelysimilartoTRANSCRIP4 103886 Hs.105737ESTs; Weakly similar 4.9 AA236384 to gene 9306 protei 103890 Hs.72085ESTs; Weakly similar 7.8 AA236843 to unknown [S.cere 103892 Hs.239189ESTs 4.8 2Q 104054 Hs.7100hypothetical protein 5.3 104115 Hs.26102ESTs 28.7 104136 Hs.268371zv68f6.r1 Soares total_fetus_Nb2HF85.7 AA442669 9w 104147 Hs.283037ESTs; Highly similar 6.9 AA451992 to HSPC039 protein 104173 Hs.76561ESTs; Weakly similar 5.2 AA476564 to finger protein HZ

2$ 104181 Hs.283740ESTs 7.8 104183 Hs.114309ESTs 5,1 104192 Hs.21321Homo sapiens mRNA; cDNA4.3 AA486946 DKFZp564 104209 Hs.16530small inducible cytokine12.3 A8000221 subfamily A (Cy 104234 Hs.168212kinesin family member 6.2 104271 Hs.7381ATP synthase; H+transporting;4.2 C01687 mitochon 104278 Hs.109253ESTs; Highly similar 4.5 C02582 to N-terminal acetyl 104307 Hs.111680endosulfine alpha 4.7 104309 Hs.284123Homo Sapiens mRNA full 4.2 D55869 length insert cD

104370 Hs.21851Homo Sapiens mRNA; cDNA6.4 N19378 DKFZp586 3 104446 Hs.7351ESTs 4.9 $ L44497 104453 Hs.123114cystatin SN 11.6 104476 Hs.324275protease; serine;15 5.6 104558 Hs.88959Human DNA sequence from6.3 856678 clone 967N2 104592 Hs.325820serine protease; umbilical13.6 881003 endothelium 104634 Hs.19151ESTs 6.3 104636 Hs.106106ESTs 10.1 104658 Hs.27268Homo Sapiens mRNA; cDNA4.3 AA007145 DKFZp564 104667 Hs.30098ESTs 16.6 104675 Hs.301553ESTs; Moderately similar4.6 AA009596 to 1111 pLU SU

4$ 104767 Hs.8852ESTs 4.8 104785 Hs.7942ESTs 8.1 104791 Hs.301871ESTs; Moderately similar10.9 AA029046 to cAMP induc 104804 Hs.31803ESTs; Weakly similar 5.5 AA031357 to N-WASP [H.sap 104807 Hs.23296ESTs 10.4 104837 Hs.21126ESTs; Weakly similar 4.6 AA039469 to KIAA0299 [H.s 104849 Hs.241507Homo sapiens mRNA; cDNA4.3 AA040270 DKFZp564 104867 Hs.225979Human gene from PACs 4.5 AA045481 37M17 and 3058 104884 Hs.14511SCO (cytochrome oxidase4.7 AA053021 deficient; yeast 104906 Hs.26802ESTs; Weakly similar 8.8 AA055809 to phosphoprotein [

$ 104919 Hs.25252ESTs 5.5 $ AA057193 104921 Hs.1508ESTs 4.2 104926 Hs.33363DKFZP434N093 protein 7 104938 Hs.318725ESTs; Highly similar 7.1 AA064627 to CGI-72 protein [H

104943 Hs.114218ESTs 5.7 104957 Hs.10026ESTs; Weakly similar 4.7 AA074919 to ORF YJL063c [S

104961 Hs.33905ESTs 5.5 104968 Hs.29669ESTs 4.3 104975 Hs.50758chromosome-associated 8.3 AA086071 polypeptide C

104977 Hs.18272ESTs 6.2 6$ 104978 Hs.19322ESTs 6.7 104987 Hs.11861ESTs 9.2 105002 Hs.182704ESTs; Moderately similar6.9 AA113266 to alternatively 105012 AA116036chromosome 20 open 10.7 Hs.9329 reading frame 1 105019 AA121879proteasome (prosome; 5.7 Hs.9280 macropain) subunit 105029 AA126855ESTs 4.4 Hs.13268 105033 AA127964TP53 target gene 1 6.3 Hs.274329 105035 AA128486ESTs 6.5 Hs.8859 105039 AA130349ESTs 4 Hs.36475 105062 AA134968ESTs 4.3 Hs.36529 105076 AA142858ESTs 6.4 Hs.37810 105087 AA147884ESTs 9.2 Hs.9812 1 105091 AA148859ESTs; Weakly similar 5.7 ~ Hs.179909 to !!!! ALU SUBFA

105093 AA149051ESTs 6.3 Hs.32405 105107 AA152302DKFZP566G223 protein 6.2 Hs.25035 105127 AA158132ESTs; Weakly similar 5.7 Hs.301957 to contains similari 105132 AA159501HBV associated factor 4.2 Hs.247280 1$ 105143 AA165333ESTs 4.7 Hs.24808 105154 AA171736methyl-CpG binding 9 Hs.35947 domain protein 4 105162 AA176690KIAA1025 protein 9.1 Hs.4084 105186 AA191512Homo Sapiens mRNA; 19.3 Hs.28005 cDNA DKFZp564 105209 AA205072KIAA0980 protein 7.4 Hs.227743 105223 AA211388ESTs 5.1 Hs.7750 105252 AA227428ESTs; Weakly similar 11.1 Hs.9728 to KIAA0512 prote 105253 AA227448KIAA0456 protein 6.4 Hs.5003 105261 AA227871MEK partner 1 9.1 Hs.6361 105263 AA227926ESTs 6.7 Hs.6682 2S 105274 AA228122ATPase; H+transporting;5.3 Hs.281866 lysosomal (vacu 105297 AA233451transcriptional intermediary8.7 Hs.183858 factor 1 105309 AA233790ESTs; Weakly similar 7.4 Hs.4104 to cDNA EST yk38 105312 AA233854S-phase kinase-associated5.8 Hs.23348 protein 2 (p45) 105342 AA235286ESTs 4.5 Hs.157078 3 105376 AA236559ESTs; Weakly similar 5.8 ~ Hs.8768 to !!!! ALU SUBFA

105386 AA236950ESTs 5.5 Hs.8115 105397 AA242868ESTs; Weakly similar 7.7 Hs.7395 to house-keeping p 105399 AA243007ESTs; Highly similar 5.6 Hs.16420 to SH3 domain-bind 105400 AA243052RNA binding motif protein5.8 Hs.65648 8 3 105404 AA243303ESTs 9.1 S Hs.21187 105409 AA243562ESTs 4.4 Hs.301855 105436 AA252172ESTs; Moderately similar5.1 Hs.237856 to cAMP induc 105483 AA255874ESTs 4.9 Hs.23458 105493 AA256268ESTs 6 Hs.10283 105495 AA256317Homo Sapiens mRNA; 5.2 Hs.28785 cDNA DKFZp586 105496 AA256323DKFZP434N126 protein 8.7 Hs.301997 105500 AA256485CGI-96 protein 9.5 Hs.222399 105507 AA256678ESTs; Moderately similar4.1 Hs.226318 to CCR4-associ 105538 AA258860ring finger protein 4.1 Hs.32597 (C3H2C3 type) 6 4$ 105544 AA261954ESTs 8 Hs.24678 105546 AA262032ESTs; Weakly similar 8.1 Hs.268281 to 62D9.a [D.melan 105549 AA262417ESTs 4.6 Hs.5415 105551 AA262477ribonuclease HI; large9.1 Hs.25292 subunit 105560 AA262783ESTs 4.5 Hs.306915 50 105565 AA278302ESTs; Weakly similar 4.2 Hs.18349 to partial CDS [C.e 105566 AA278323Homo sapiens clone 11.9 Hs.17481 24606 mRNA sequen 105575 AA278717ESTs 5.9 Hs.12772 105584 AA279012ESTs; Weakty similar 4.4 Hs.3454 to KIAA0665 prote 105596 AA279418ESTs 4 Hs.18490 SS 105604 AA279787ESTs;Moderatelysimilartoputativepho5.6 Hs.15467 105610 AA279991ESTs; Weakly similar 5.3 Hs.99872 to trithorax homolo 105621 AA280865Homo Sapiens mRNA; 4.8 Hs.6375 cDNA DKFZp564 105627 AA281245ESTs 7.5 Hs.23317 105638 AA281599Homo sapiens mRNA for 5.9 Hs.247817 for histone H2B

105645 AA282138ESTs 6.4 Hs.11325 105650 AA282347ESTs; Highly similar 11.3 Hs.25635 to HSPC003 [H.sap 105666 AA283930ESTs 4.7 Hs.34906 105674 AA284755CDW52 antigen (CAMPATH-18 Hs.279789 antigen) 105687 AA286809ESTs 7.1 Hs.28423 65 105700 AA287643ESTs; Weakly similar 4.9 Hs.35254 to hypothetical pro 105705 AA290767Homo Sapiens mRNA; 8 Hs.101282 cDNA DKFZp434 105709 AA291268DKFZP586L0724 protein 6.8 Hs.26761 105731 Hs.29131ESTs 6.4 105753 Hs,110857ESTs 7 105774 Hs.23412ESTs 7.1 105784 Hs.17850ESTs 13.4 $ 105791 Hs.14368SH3-binding domain glutamic4.3 AA358038 acid-rich p 105807 Hs.16869ESTs; Moderately similar5.3 AA393803 to COLLAGEN

105808 Hs.286131KIAA0438 gene product 4.1 105812 Hs.20814ESTs; Highly similar 14.6 AA394126 to CGI-27 protein [H

105813 Hs.18585ESTs 4.9 1 105819 Hs.28783Homo Sapiens mRNA; cDNA4.9 ~ AA397920 DKFZp564 105870 Hs.101067ESTs 4.8 105874 Hs.171118ESTs 4 105896 Hs.7838Human ring zino-finger 4.8 AA400999 protein (ZNF127-105934 Hs.16577ESTs 5.2 1$ 105935 Hs.263727ESTs; Weakly similar 4 AA404277 to bisphosphate 3'-105966 Hs.5344adaptor-related protein8.3 AA406105 complex 1; gamma 105974 Hs.6224KIAA0895 protein 4.6 105990 Hs.29403ESTs; Weakly similar 4.5 AA410336 to PROBABLE AT

105995 Hs.5345ESTs 4.9 2~ 106000 Hs.20726ESTs 5.8 106007 Hs.11042ESTs; Weakly similar 6.9 AA411462 to veli 1 [H.sapiens 106016 Hs.8164KIAA0898 protein 5 106034 Hs.14928ESTs 6.6 106042 Hs.169895ubiquitin-conjugating 4.6 AA412700 enzyme E2L 6 2$ 106057 Hs.289074ESTs 4.5 106065 Hs.25206ESTs 12.3 106070 Hs.5957Homo sapiens clone 244165 AA417761 mRNA sequen 106103 Hs.12094ESTs 15.4 106126 Hs.22972ESTs; Moderately similar6.4 AA424006 fo HSAR [M.m 106154 Hs.6994ESTs 5.1 106157 Hs.34892ESTs 11.1 106166 Hs.19561NADH dehydrogenase (ubiquinone)19.3 AA425872 1 alp 106204 Hs.21479ESTs 4.7 106210 Hs.10338ESTs 5.7 3$ 106220 Hs.32196ESTs; Moderately similar7.7 AA428582 to metargidin p 106236 Hs.21104ESTs 8 106240 Hs.18552ESTs; Weakly similar 4.4 AA430074 to YIr218cp [S.cere 106263 Hs.28329ESTs 4.9 106288 Hs.24336ESTs 8.8 106293 Hs.301444signal sequence receptor;8.7 AA435591 gamma (transloc 106310 Hs.17240ESTs 4.5 106317 Hs.108124ESTs 4 106328 Hs.28020KIAA0766 gene product 4.4 106341 Hs.5243ESTs; Moderately similar23.7 AA441798 to pIL2 hypoth 4$ 106348 Hs.10702ESTs 4.7 106350 Hs.194698cyclin 82 6.1 106371 Hs.170310ESTs 6.8 106389 Hs.6236ESTs 4.7 106394 Hs.25320Homo sapiens clone 251424.4 AA447223 mRNA sequen $~ 106426 Hs.16206ESTs; Weakly similar 4.5 AA448282 to F55C12.5 [C.ele 106459 Hs.4029glioma-amplified sequence-414.8 106462 Hs.30532ESTs; Highly similar 5.2 AA449912 to CGI-77 protein [H

106468 Hs.14770ESTs 6.8 106479 Hs.75251ESTs 12.4 $$ 106494 Hs.18387transcription factorAP-24.5 AA452108 alpha (activating 106503 Hs.29679ESTs; Highly similar 5.1 AA452411 to mediator [H.sapie 106507 Hs.267819protein phosphatase 4.9 AA452584 1; regulatory (inhibito 106533 Hs.145998ESTs 8.3 106568 Hs.28285patched related protein7.6 AA455970 translocated in ren 106586 Hs.57787ESTs 8.2 106589 Hs.28661ESTs 4.8 106606 Hs.283437Homo Sapiens clone 238514.4 AA457730 mRNA sequen 106611 Hs.26267ESTs; Weakly similar 7 AA458904 to torsinA [H.sapie 106614 Hs.256150ESTs 4.5 6$ 106628 Hs.12311Homo Sapiens clone 235706.5 AA459657 mRNA sequen 106637 Hs.250824ESTs 5.5 106644 Hs.12680ESTs 4.4 106664 AA460969mitogen-activated protein8.4 Hs.7510 kinase kinase ki 106698 AA463745ESTs; Weakly similar 5.3 Hs.29403 to PROBABLE AT

106719 AA465171ESTs 5.6 Hs.236844 106726 AA465339ESTs 10.1 Hs.3886 $ 106747 AA476473triple functional domain10.4 Hs.171957 (PTPRF interacts 106759 AA477263ESTs 4.2 Hs.25584 106765 AA477717interleukin 13 receptor;6.9 Hs.306117 alpha 1 106784 AA478558APIS-like 1 5.1 Hs.227913 106831 AA482014centrin; EF-hand protein;5.1 Hs.29463 3 (CDC31 yeast 1 106836 AA482112ESTs 4.8 ~ Hs.238707 106840 AA482548ESTs 10.3 Hs.5534 106856 AA486183ESTs; Weakly similar 6.2 Hs.285123 to similar to oxyste 106865 AA487228ESTs 4.5 Hs.19479 106878 AA488872Homo Sapiens mRNA; cDNA7.9 Hs.12314 DKFZp586 1$ 106888 AA489101oxysterol binding protein6.4 Hs.24734 106895 AA489665ESTs 4.6 Hs.25245 106909 AA490323SUMO-1 activating enzyme4.2 Hs.250747 subunit 1 106919 AA490885ESTs 12.3 Hs.21766 106920 AA490899ESTs 6.2 Hs.296323 2~ 106941 AA496204ESTs 4 Hs.237971 106942 AA496347retinoblastoma-binding 4.8 Hs.31314 protein 7 106948 AA496788KIAA0532 protein 4 Hs.21077 106968 AA504631ESTs; Weakly similar 4.4 Hs.26813 to hypothetical 43.2 106973 AA505141Human DNA sequence from5.4 Hs.11923 clone 167A1 2$ 106980 AA521121bromodomain adjacent 4.1 Hs.8858 to zinc finger dom 106981 AA521157ESTs 5.7 Hs.74101 106998 AA598461insulin-like growth 18.7 Hs.195464 factor binding protein 107008 AA598710ESTs 6.2 Hs.23740 107028 AA599214ESTs 4.1 Hs.24143 107032 AA599472succinate-CoA ligase; 5.3 Hs.247309 GDP-forming; beta 107052 AA600134giyceronephosphate O-acyltransferase4.8 Hs.12482 107053 AA600147ESTs; Weakly similar 5.8 Hs.5741 to NADH-cytochro 107056 AA600310programmed cell death 4.9 Hs.18720 8 (apoptosis-induc 107080 AA609210ESTs 8.4 Hs.19221 3$ 107102 AA609723ESTs 8 Hs.30652 107109 AA609943ESTs 9.5 Hs.32793 107129 AA620553flap structure-specific4.9 Hs.4756 endonuclease 1 107132 AA620598ESTs 5.3 Hs.9052 107136 AA620795ESTs 4 Hs.8207 40 107140 AA620889ESTs 6.7 Hs.170088 107151 AA621169ESTs 19 Hs.8687 107159 AA621340ESTs; Weakly similar 8.1 Hs.10600 to ORF YKR081 c [

107174 AA621714ESTs 8.5 Hs.25338 107217 D51095 DKFZP586E1621 protein 7.2 Hs.35861 4$ 107252 D59971 ESTs 7.9 Hs.25925 107295 T34527 UDP-N-acetyl-alpha-D-galactosamine:po5.6 Hs.80120 107299 T40327 lung resistance-related8.4 Hs.30661 protein 107324 T81665 DKFZP586G1122 protein 7.5 Hs.278422 107372 U85625 ribonuclease 6 precursor4.7 Hs.8297 $0 107373 U85773 phosphomannomutase2 4.8 Hs.154695 107481 W58247 Homo sapiens kinesin 6.3 Hs.279766 superfamily motor 107531 Y13936 protein phosphatase 8.3 Hs.17883 1G (formerly 2C); ma 107859 AA024835potassium voltage~ated 7.3 Hs.47584 channel; delayed 107890 AA026030ESTs; Weakly similar 7.3 Hs.61311 to CALPAIN 2; LA

$$ 107908 AA026894ESTs 4.9 Hs.42826 108039 AA041341ESTs 5.4 Hs.46670 108040 AA041551ESTs 8.4 Hs.159971 108102 AA046424ESTs; Weakly similar 6.6 Hs.49433 to HYPOTHETICA

108217 AA058686ESTs 7.7 Hs.62588 ()0108255 AA063157ESTs 4 Hs.172608 108358 AA071514ESTs 4 Hs.1634 108609 AA100694Human DNA sequence from5.5 Hs.69499 BAC 15E10 108647 AA112396ESTs; Moderately similar14.3 Hs.44276 to HOMEOBO

108676 AA115562Homo Sapiens mRNA; cDNA5.2 Hs.274417 DKFZp564 6$ 108687 AA120785ESTs 5.6 Hs.54347 108695 AA121315KIAA1077 protein 10.5 Hs.70823 108733 AA126422zn84f1.s1 Stratagene 4.4 lung carcinoma 9372 108774 AA128125ESTs; Moderately similar4.6 Hs.71040 to CELL GROW

108828 AA131584DKFZP56400463 protein 5.5 Hs.273344 108872 AA134063ESTs 7.2 Hs.111680 108884 AA134958ESTs 11.3 Hs.293591 $ 108893 AA135894retino!c acid induced 8.9 Hs.194691 3 109008 AA156360ESTs 14.7 Hs.87128 109010 AA156460dual specificity phosphatase4.9 Hs.44229 12 109011 AA156542ESTs 4.6 Hs.72127 109042 AA159525Homo Sapiens DNA from 7.2 Hs.71779 chromosome 19 1 109086 AA166695tumor necrosis factor 4 ~ Hs.270737 (ligand) superfamily 109090 AA167006ESTs 5.9 Hs.70499 109101 AA167708ESTs 4.2 Hs.52184 109112 AA169379ESTs 4 Hs.257924 109160 AA179387DKFZP434N126 protein 4 Hs.301997 1$ 109166 AA179845RAB6 interacting; kines!n-like13.6 Hs.73625 (rabkinesin 109178 AA181600ESTs 11.8 Hs.283707 109179 AA181902ESTs; Weakly similar 5.4 Hs.192789 to !!!! ALU SUBFA

109261 AA195255ESTs 6.7 Hs.61779 109270 AA195515ESTs; Weakly similar 4.9 Hs.3585 to alternatively spli 20 109277 AA196332ESTs 5.4 Hs.86043 109313 AA206800ESTs; Moderately s!milar5.5 Hs.86276 to zinc finger p 109415 AA227219trfnucleotide repeat 20.1 Hs.110826 containing 9 109454 AA232255ESTs 4.7 Hs.295232 109467 AA232904ESTs 6.8 Hs.63187 2$ 109481 AA233342ESTs; Weakly similar 10.6 Hs.289069 to WD40 protein C

109508 AA233892ESTs; Weakly similar 8 Hs.55902 to !!!! ALU SUBFA

109514 AA234087ESTs; Weakly similar 8.2 Hs.262346 to ORF2: function 109572 F02027 ESTs 4.8 Hs.171937 109632 F04165 ESTs; Weakly similar 5.2 Hs.235873 to K11C4.2 [C.eleg 3~ 109644. F04477 ESTs; Moderatelysim!larto6.6 Hs.291531 GLYCERAL

109703 F09684 ESTs; Weakly similar 7.1 Hs.24792 to ORF YOR283w 109726 F10009 ESTs 5 Hs.9196 109747 F10161 ESTs 4.7 Hs.22969 109799 F10770 Homo Sapiens clone 669 4.5 Hs.180378 unknown mRNA

3 109814 F10979 Homo sapiens clone 237288.7 $ Hs.153106 mRNA sequen 110189 N20543 DKFZP586B1621 protein 16.6 Hs.6278 110240 H25577 ESTs; Weakly similar 6.2 Hs.176588 to CYTOCHROME

110280 H29285 ESTs 4.5 Hs.32468 110520 H56965 yr09f06.s1 Soares fetal5.7 Hs.4082 liver spleen 1NFL

40 110561 H59617 ESTs; Weakly s!milarto 19.5 Hs.5199 UBIQUITIN-CO

110707 H95079 ESTs; Weakly similar 6.2 Hs.15617 to !!!! ALU SUBFA

110734 H98714 ESTs 30.2 Hs.24131 110770 N22262 ESTs 5.8 Hs.131705 110780 N23174 solute tamer family 8.2 Hs.22891 7 (cationic am!no aci 4$ 110787 N24716 ESTs; Weakly similar 6.7 Hs.12244 to C44B9.1 [C.eleg 110794 N25262 ESTs 5.9 Hs.27931 110799 N26101 Human ring zinc-finger 4 Hs.323401 protein (ZNF127-110818 N29454 ESTs; Weakly similar 4.3 Hs.27552 to putative p150 [H

110839 N30856 solute tamer family 12.8 Hs.30246 19 (th!amine transpo 110844 N31952 Homo sap!ens mRNA full 10.1 Hs.167531 length insert cD

110854 N32919 ESTs 4.7 Hs.27931 110856 N33063 ESTs; Weakly similar 4.2 to S164 [H.sapiens 110860 N33438 ESTs 12.5 Hs.170065 110897 N39148 DKFZP434D156 prote!n 4 Hs.6880 $ 110915 N46252 ESTs 23.2 $ Hs.29724 110935 N48787 protease inhibitor 1 4.8 Hs.305979 (anti-elastase); alpha-110970 N51374 Homo Sapiens mRNA full 5.4 Hs.96870 length !nserf cD

111006 N53375 Homer; neuronal immediate4.7 Hs.166146 early gene; 3 111008 N53388 ESTs 13.3 Hs.7222 111018 N54067 mitogen-activated protein5.7 Hs.3628 k!nase kinase k!

111084 N59543 PDZ domain containing 8.3 Hs.15456 1 111100 N62522 ESTs 14.3 Hs.20450 111125 N63823 ESTs 7.9 Hs.269115 111132 N64378 ESTs; Highly sim!larto 4.4 Hs.83293 unknown function 6$ 111139 N64683 ESTs 6 Hs.290943 111164 N66857 ESTs; Weakly similar 4.1 Hs.14808 to !!!! ALU CLASS

111172 N67102 Homo sap!ens mRNA; cDNA5.5 Hs.21851 DKFZp586 111178 Hs.24633ESTs 5.7 111179 Hs.10760ESTs 37 111181 Hs.171802ESTs; Weakly similar 5.6 N67278 to hypothetical pro 111184 Hs.243901Homo Sapiens mRNA; cDNA8.7 N67437 DKFZp564 $ 111221 Hs.15119ESTs 7.3 111223 Hs.297939ESTs; Weakly similar 9 N68921 to neogenin [H.sap 111229 Hs.110855ESTs 8.9 111241 Hs.288880ESTs; Weakly similar 6.9 N69514 to CGI-82 protein [

111268 Hs.26118Homo Sapiens clone 247664.5 N70481 mRNA sequen 1 111295 Hs.21275ESTs; Weakly similar 5.6 ~ N73275 to ubiquitin-conjug 111299 Hs.24936ESTs 8.5 111336 Hs.29894ESTs 6.7 111357 Hs.87128ESTs 15 111370 Hs.94631brefeldin A-inhibited 5.2 N92915 guanine nucleotide-a 1 111806 Hs.279008ESTs 10 $ 833468 1 i 1825 Hs.286148stromal antigen 1 4.5 111836 Hs.25119ESTs 7.2 111890 Hs.12365ESTs 17.3 111923 Hs.25925Homo Sapiens clone 238607.3 839995 mRNA sequen 2~ 111942 Hs.21590ESTs 9.2 111987 Hs.6763KIAA0942 protein 10.6 112101 Hs.296341adenylyl cyclase-associated5.3 844793 protein 2 112134 Hs.7413ESTs 17.4 112197 Hs.5637ESTs 4.4 25 112244 Hs.70823KIAA1077 protein 11 112253 Homo Sapiens mRNA; cDNA9.3 851818 DKFZp566 112305 Hs.26244ESTs 4.4 112449 Hs.124186ring finger protein 6.3 112483 Hs.285885ESTs 4.9 112519 Hs.11861ESTs 14.3 112610 Hs.23643ESTs 5.2 112693 Hs.91065ESTs; Moderately similar4.6 888741 to proliferation 112751 Hs.8207ESTs 5.6 112801 Hs.157160protein kinase; DNA-activated;8.7 897486 catalytic p 35 112869 Hs.4747dyskeratosis congenita 5.9 T03313 1; dyskerin 112871 Hs.12285ESTs 5.8 112908 Hs.3530TLS-associated serine-arginine4.1 T10065 protein 112966 Hs.102548glucocor8coid receptor 5.7 T17119 DNA binding fact 112971 Hs.83883ESTs 6.4 4~ 112995 Hs.7155ESTs; Weakly similar 9.1 T23528 to TYKi protein [M

113047 Hs.7549ESTs 5.4 113075 Hs.6986ESTs; Weakly similar 5.7 T34660 to !lll ALU SUBFA

113117 Hs.159153ESTs 5.8 113206 Hs.241471ESTs; Moderately similar6.4 T58044 to !!!! ALU SU

4$ 113248 yc16e1.s1 Stratagene 4.6 T63857 lung (#93721) Homo 113260 Hs.287420ESTs 6.9 113277 Hs.11774protein (peptidyi-prolyl5.6 T65797 cisltrans isomeras 113278 Hs.11135yc11h10.s1 Stratagene 4.5 T65802 lung (#937210) Ho 113440 Hs.191445ESTs 6.4 113523 Hs.95549ESTs 6.4 113604 Hs.296083ESTs 8.7 113702 ESTs; Moderately similar9.5 T97307 to Illl ALU SU

113783 Hs.7041ESTs; Weakly similar 5.2 W19222 to 1111 ALU SUBFA

113794 Hs.11090ESTs 11.9 55 113808 Hs.9286ESTs 16.7 113811 Hs.6994ESTs 4 113822 Hs.17466retinoic acid receptor 4.8 W47350 responder (tazaroten 113823 Hs.55099rab6 GTPase activating 4 W47388 protein (GAP and 113836 Hs.12040ESTs; Weaklysimilarto 4.1 W56792 KIAA0881 prate 113857 Hs.5297Homo Sapiens mRNA; cDNA4.3 W65477 DKFZp564 113886 Hs.23920ESTs 4.6 113895 Hs.12921ESTs 7.1 113923 Hs.3849ESTs; Weakly similar 6.8 W80763 to FK506-binding p 113931 Hs.3496ESTs 6.1 6$ 113950 Hs.30504Homo sapiens mRNA; cDNA14 W85765 DKFZp434 113970 Hs.8109ESTs 15 114051 Hs.177534dual specificity phosphatase5.4 114057 W96222 ESTs 4.8 Hs.34192 114086 238266 Homo Sapiens PAC clone 5.1 Hs.288649 DJ0777023 fro 114098 238347 ESTs; Weakly similar 6.2 Hs.118338 to similar fo S. cere 114109 238435 ribosomal protein L21 4.6 Hs.184108 $ 114124 238595 ESTs; Highly similar 22 Hs.125019 to KIAA0886 prote 114138 238763 amyloid beta (A4) precursor8.8 Hs.15740 protein-bindi 114149 238814 ESTs 4 Hs.27196 114162 238909 ESTs 7.2 Hs.22265 114177 239062 ESTs 5.3 Hs.23740 1 114196 239211 fucose-1-phosphate guanylyltransferase4.4 ~ Hs.150926 114208 239301 ESTs 5.1 Hs.7859 114250 239897 ESTs 7.2 Hs.13297 114251 239898 ESTs 14.7 Hs.21948 114292 240715 delta-6 fatty acid desaturase19.4 Hs.184641 1$ 114297 240758 DKFZP434K151 protein 8.9 Hs.173091 114334 241342 ESTs 13.7 Hs.22941 114460 AA024604ESTs 10.1 Hs.26102 114471 AA028074ESTs 5.7 Hs.104613 114480 AA032243UDP-N-acetyl-alpha-D~alactosamine:po7.3 Hs.151678 20 114518 AA046407suppressor of varl (S.cerevisiae)4.3 Hs.106469 3-like 1 114542 AA055768ESTs 11.7 Hs.293380 114549 AA056484ESTs 7.3 Hs.292833 114652 AA101416ESTs; Weaklysimilarto 6.1 Hs.107149 PTB-ASSOCIAT

114673 AA113303transmembrane 4 superfamily4.3 Hs.95583 member (te 2$ 114698 AA126951ESTs; Highly similar 7.1 his.110857 to putative DNA-dir 114767 AA148885minichromosome maintenance5.3 Hs.154443 deficient (S

114799 AA159323ESTs 4.2 Hs.109929 114804 AA16D363ESTs 4.8 Hs.269956 114811 AA161161multiple inositol polyphosphate7.1 Hs.95907 phosphate 3 114821 AA165313ESTs 4.4 0 Hs.55468 114852 AA235035ESTs; Moderately similar5 Hs.38260 to ubiquitin spe 114901 AA236276ESTs; Weakly similar 16.9 Hs.196437 to 826660_1; parti 114902 AA236359ESTs 5.1 Hs.39504 114940 AA243012ESTs 8.5 Hs.75928 3$ 114965 AA250737ESTs 35.1 Hs.72472 115047 AA252627homeo box B5 5.7 Hs.82916 115054 AA252863ESTs 6.2 Hs.87729 115061 AA253217ESTs 13 Hs.41271 115082 AA255557NADH dehydrogenase (ubiquinone)28.2 Hs.198269 1 alp 115116 AA256486ESTs 8.8 Hs.62275 115140 AA258030ESTs; Weakly similar 4.1 Hs.279938 to supported by GE

115205 AA262470ESTs 8.3 Hs.284216 115206 AA262491ESTs 5.1 Hs.186572 115239 AA278650ESTs; Weakly similar 4.6 Hs.73291 to similar to the bet 4$ 115242 AA278755ESTs 8.3 Hs.283732 115249 AA278961ESTs 10.1 Hs.71124 115259 AA279071splicing factor 3b; 9.5 Hs.13453 subunit 1;155kD

115285 AA279799ESTs 5.8 Hs.293736 115291 AA279943ESTs 5.1 Hs.122579 $~ 115357 AA281793ESTs 5 Hs.72988 115377 AA282247ESTs 6.1 Hs.193063 11540D AA283198ESTs 4.9 Hs.89113 115439 AA284561ESTs 5.8 Hs.193090 115471 AA287138ESTs; Weakly similar 11.7 Hs.59346 to ASPARTYL-TR

$ 115506 AA292537Human DNA sequence from6.8 $ Hs.45207 clone 620E1 115522 AA331393ESTs 5.8 Hs.47378 115572 AA398392ESTs; Weakly similar 9.7 Hs.59594 to F33G12.3 gene p 115587 AA399264ESTs; Highly similar 8.7 Hs.283037 to HSPC039 protein 115600 AA400247ESTs 4 Hs.42173 115612 AA400948ESTs; Weakly similar 8.4 Hs.71243 to zinc finger prote 115646 AA404352ESTs 5.3 Hs.305971 115652 AA405098ESTs 16.1 Hs.38178 115657 AA405620ESTs; Weakly similar 4.7 Hs.55158 to weak similarity t 115658 AA405625Human DNA sequence from5.1 Hs.183056 clone 34821 6$ 115675 AA406546Homo sapiens mRNA; cDNA20.5 Hs.82065 DKFZp564 115721 AA417102ESTs 4.8 Hs.90960 115763 AA421560ESTs 7 ~~$

115764 AA421562anterior gradient 2 41.6 Hs.91011 (Xenepus laevis) homo 115835 AA428576ESTs 4.2 Hs.41371 115844 AA430124ESTs 11.9 Hs.7773 115875 AA433943ESTs; Weakly similar 33.5 Hs.43946 to Weak similarity $ 115888 AA435839KIAA0887 protein 7.2 Hs.76591 115922 AA441911ESTs; Weakly similar 5.1 Hs.71869 to KIAA0926 prote 115941 AA443602ESTs 4.8 Hs.46679 115947 AA443793ESTs 8.3 Hs.94761 115948 AA443798poly(A)-specific ribonuclease13.5 Hs.43445 (deadenylat 1 115951 AA443918cofilin 1 (non-muscle)7.5 ~ Hs.301048 115967 AA446887ESTs 8.8 Hs.42911 115984 AA447687ESTs 13.1 Hs.91109 116009 AA449448ESTs 5.5 Hs.44238 116024 AA451748Human DNA sequence 7.5 Hs.83883 from clone 718J7 1$ 116028 AA452112thioredoxin-like 12.7 Hs.42644 116050 AA453656ESTs 7.2 Hs.88417 116097 AA456099ESTs 11.8 Hs.176376 116108 AA457566ESTs 4.5 Hs.28777 116121 AA459254ESTs 4.5 Hs.48855 2~ 116127 AA459703v-mycavian myelocytomatosis4.3 Hs.279884 viral onto 116129 AA459956ESTs; Highly similar 7.6 Hs.49163 to putative ribonucle 116142 AA460649ESTs 4.8 Hs.39457 116204 AA465701ESTs 6.8 Hs.108646 116221 AA478397ESTs 4.9 Hs.50180 2$ 116222 AA478415ESTs 4 Hs.89986 116238 AA479362DKFZP586N0819 protein 4.6 Hs.47144 116246 AA479961ESTs; Highly similar 4 Hs.250646 to ubiquitin-conjuga 116249 AA480886ESTs 18.5 Hs.86693 116250 AA480975ESTs 10.8 Hs.44829 116254 AA481146ESTs; Weakly similar 9.1 Hs.41086 to OXYSTEROL-B

116256 AA481256ESTs; Weakly similar 8.4 Hs.88201 to lysophospholipa 116264 AA482594Homo Sapiens mRNA; 7.2 Hs.272239 cDNA DKFZp586 116265 AA482595ESTs; Weakly similar 11.1 Hs.55189 to F25B5.3 [C.eleg 116282 AA486550ESTs; Weakly similar 6.2 Hs.204501 to Wiskott-Aldrich 3$ 116298 AA489046ESTs 4.9 Hs.94109 116300 AA489194ESTs; Weakly similar 4.6 Hs.159471 to snRNP protein B
~

116327 AA490959Homo Sapiens mRNA; 5.8 Hs.28005 cDNA DKFZp564 116334 AA491457ESTs 4.3 Hs.48948 116337 AA496127ESTs 8.4 Hs.44070 4Q 116351 AA504116Homo Sapiens mRNA; 5.3 Hs.82501 cDNA DKFZp434 116357 AA504806Homo Sapiens clone 5.2 Hs.90797 23620 mRNA sequen 116415 AA609204KIAA0874 protein 6.6 Hs.27973 116443 AA620313ESTs; Weakly similar 4.5 Hs.190488 to KERATIN; TYP

116470 C13992 ESTs 4.5 Hs.83484 4$ 116480 C14088 glyceraldehyde-3-phosphate5.6 dehydrogena 116578 D51272 nucleolarphosphoproteinp1304.1 Hs.75337 116579 D51276 leukemia-associated 5.8 Hs.81915 phosphoprotein p18 116626 F02028 ESTs 4.9 Hs.81907 116647 F03069 ESTs; Weakly similar 6.1 Hs.15395 to ARGINYL-TRN

$~ 116674 F04816 ESTs 10.6 Hs.92127 116680 F08813 LINE retrotransposable4.2 Hs.273829 element 1 116700 F09983 ESTs 13 Hs.317589 116724 F13665 ESTs 8.5 Hs.65641 116726 F13681 ESTs 5.6 Hs.53913 $$ 116732 F13779 ESTs 11.6 Hs.165909 116734 F13789 DKFZP586D2223 protein 5.4 Hs.93796 116760 H11054 protein kinase C; delta4.3 Hs.155342 116780 H22566 ESTs 5.7 Hs.30098 116786 H25836 tumor necrosis factor 8.8 Hs.301527 (ligand) superfamily 116787 H28581 ESTs 8.6 Hs.15641 116790 H29532 microtubule-associated22.2 Hs.101174 protein tau 116803 H47357 ESTs; Moderately similar6.7 Hs.109701 to weak similar 116877 H68116 ESTs 6.5 Hs.168732 116921 H72948 biglycan 20.7 Hs.821 6$ 117216 N20083 ESTs 4.4 Hs.42792 117232 N20579 ESTs 7.4 Hs.61153 117284 N22162 ESTs; Weakly similar 4.1 Hs.183779 to cDNA EST yk33 117344 Hs.210706ESTs 7.4 117367 Hs.42502ESTs 10.5 117392 Hs.93405ESTs 5.8 117394 Hs.39871KIAA0727 protein 8.4 $ 117412 Hs.42645ESTs 18.1 117498 Hs.44268ESTs; Highly similar 5.8 N31726 to myelin gene expr 117557 Hs.44532diubiquitin 12.3 117634 Hs.13323ESTs; Weakly similar 4.4 N36421 to SODIUM-AND

117639 Hs.44833ESTs 6 1 117754 Hs.59757ESTs 7.6 ~ N47469 117852 Hs.136102KIAA0853 protein 5.9 117879 Hs.303025ESTs; Weakly similar 7.9 N50050 to keratin; 67K typ 117924 Hs.38891ESTs 7.9 117950 Hs.75478KIAA0956 protein 5 1$ 117992 Hs.172089Homo sapiens mRNA; 7 N52000 cDNA DKFZp586 118138 Hs.93560ESTs; Weakly similar 4.8 N57773 to frg [R.norvegicu 118215 Hs.779103-hydroxy-3-methylglutaryl-Coenryme13.4 118229 Hs.166254heat shock 90kD protein5.4 N62339 1; alpha 118265 Hs.48645EST 4.2 20 118336 Hs.47166ESTs 7.2 118363 Hs.48938ESTs 6 118429 Hs.74649ESTs 4.1 118470 Hs.291033ESTs 5.4 118472 Hs.42179ESTs 10.8 25 118475 ESTs; Weakly similar 4.5 N66845 to l!!! ALU CLASS

118493 Hs.50115ESTs 5.3 118528 Hs.49397ESTs 10.4 118542 Hs.49427ESTs 7.9 118600 ESTs 9.2 118695 Hs.50081Homo sapiens mRNA full9.8 N71781 length insert cD

118698 Hs.50187ESTs 4.3 118901 Hs.94445ESTs 8.1 118952 ESTs; Highly similar 12.5 N92966 to CGI-90 protein [H

118976 Hs.93391ESTs 5 3 118986 Hs.125830ESTs 7.3 $ N94362 118989 Hs.45105ESTs 8.2 119027 Hs.114611ESTs 5 119042 Hs.5472ESTs 4 119075 Hs.287820fibronectin 1 6 119260 Hs.102950ESTs; Highly similar 4.1 T15916 to coat protein gamm 119271 Hs.65328ESTs 12.1 119298 Hs.155478cyclin T2 5.6 119302 ESTs 14.3 119341 Hs.146388microtubule-associated4 T62571 protein 7 4$ 119495 Hs.55533ESTs 5.3 119580 Hs.92260high-mobility group 5.6 W42451 profein 2-like 1 119602 Hs.233694ESTs; Weakly similar 6.5 W46286 to ZK1058,5 [C.ele 119620 Hs.560092'-5'oligoadenylate 8.1 W47620 synthetase 3 119676 Hs.57787ESTs 5.5 $~ 119717 Hs.57987ESTs 4.6 119729 Hs.94806KIAA1062 protein 4 119805 Hs.43213ESTs 4 119859 Hs.58461ESTs 4.8 119867 Hs.250696KDEL (Lys-Asp-Glu-Leu)4.2 W80852 endoplasmic re $ 119873 Hs.44865Homo sapiens mRNA; 4.8 $ W81129 cDNA DKFZp586 119899 Hs.58698ESTs 5.9 119940 Hs.272531DKFZP58680319 profein 9 119943 Hs.14158copine III 4.8 119970 Hs.93581Homo sapiens mRNA; 4 W87812 cDNA DKFZp586 120131 Hs.75887coatomer protein complex;4.2 238656 subunit alpha 120150 Hs.153746ESTs 11 120206 Hs.91668ESTs 8.2 120241 Hs.65946ESTs 15.6 120255 Hs.5672ESTs; Weakly similar 4.2 AA169752 to Similarity to Yea 6$ 120314 Hs.221040KIAA1038 protein 6.8 120325 Hs.104106ESTs . 15.2 120352 Hs.193172ESTs 6.8 120428 AA236822KIAA1097 protein 5.6 Hs.173694 120524 AA261852ESTs 5.6 Hs.192905 120528 AA262107ESTs 4.5 Hs.104413 120571 AA280738ESTs 4.9 Hs.34892 $ 120649 AA287115ESTs 4.5 Hs.192843 120655 AA287347ESTs 6.7 Hs.238205 120668 AA287833ESTs 8.3 Hs.292913 120712 AA292654eukaryotic translation 4.6 Hs.102506 initiation factor 2 al 120713 AA292655ESTs 10.6 Hs.96557 1 120724 AA293470ESTs 5.4 ~ Hs.100747 120873 AA358015EST 7.1 120885 AA365515ESTs; Moderately similar4.6 Hs.301872 to !!!! ALU SU

120919 AA381125ESTs 8.2 Hs.301444 120948 AA397822ESTs; Highly similar 8.6 Hs.104650 to similar to mago n 1$ 120969 AA398116casein kinase 1; gamma 10.5 Hs.129206 3 120977 AA398155ESTs 10.9 Hs.97600 121103 AA398936EST 7.4 Hs.97697 121291 AA401753lung cancer candidate 5.3 Hs.8186 121320 AA403008T-cell receptor; alpha 13.5 Hs.301927 (V;D;J;C) 2~ 121463 AA411745ESTs; Weakly similar 8.9 Hs.239681 to KIAA0554 prote 121596 AA416740ESTs 22.6 Hs.174104 121723 AA419622ESTs; Weakly similar 8 Hs.104800 to Mouse 19.5 mRN

121748 AA421171ESTs 5.6 Hs.234545 122125 AA434411ESTs 5.3 Hs.98806 25 122522 AA449444ESTs 4 Hs.98969 122655 AA454756ESTs 4 Hs.97837 122704 AA456326ESTs 6.2 Hs.99445 122782 AA459894ESTs 5.3 Hs.99472 122856 AA463740Sro-like-adapter 13.1 Hs.75367 30 122882 AA465381ESTs; Weakly similar 5.5 Hs.108812 to 80041.5 [C.eleg 122928 AA476578ESTs 6.3 Hs.101840 122974 AA478625ESTs 6 Hs.194215 122997 AA479295Kelch motif containing 12.5 Hs.106290 protein 123016 AA480103ESTs; Weakly similar 4.4 Hs.323231 to alternatively spli 3S 123107 AA486071ESTs 8.3 Hs.104207 123111 AA486273ESTs 4.2 Hs.191721 123114 AA486407ESTs; Moderately similar5.2 Hs.129928 to KIAA0454 p 123136 AA487449ESTs 4.2 Hs.194024 123137 AA487468ESTs; Weakly similar 14.6 Hs.100686 to secreted cement 123169 AA488892ESTs; Weakly similar 4.5 to Gag-Pol polypro 123176 AA489020ESTs 5.2 Hs.69233 123338 AA504249ESTs 4 Hs.187585 123436 AA598714protease; serine;15 7.3 Hs.223014 123442 AA598803ESTs 5.9 Hs.111496 4$ 123449 AA598899Homo sapiens mRNA; cDNA4.1 Hs.112493 DKFZp564 123494 AA599786ESTs 4 Hs.112110 123503 AA600121ESTs 12.8 Hs.293156 123533 AA608751ESTs; Weakly similar 7.9 to 1111 ALU SUBFA

123619 AA609200ESTs 23.1 50 123673 AA609471ESTs 6.6 Hs.158549 123729 AA609778membrane component; 4.7 Hs.278672 chromosome 11; s 123819 AA620636ESTs 4 Hs.112264 123960 AA621785methylmalonate-semialdehyde7.6 Hs.287733 dehydroge 124000 D57317 activated RNA polymerise4.4 Hs.74861 II transcription $S 124006 D60302 ESTs 20.6 Hs.270016 124012 D80240 HUM5G11A Human fetal 6.7 Hs.241471 brain (TFujiwa 124021 F02859 ESTs 4.7 Hs.13974 124049 F10523 primase; polypeptide 4.7 Hs.74519 2A (58kD) 124059 F13673 ESTs 7.7 Hs.283713 124243 H66710 ESTs 5.5 Hs.133525 124308. H93575 Homo Sapiens mRNA; cDNA11.4 Hs.241507 DKFZp564 124314 H94877 GTP-binding protein 13.7 Hs.215766 124315 H94892 v-ral simian leukemia 14 Hs.288757 viral oncogene hom 124350 N21359 Homo sapiens mRNA; cDNA8.6 Hs.101282 DKFZp434 65 124352 N21626 ESTs 7.2 Hs.102406 124357 N22401 yw37g07.s1 Morton Fetal5.2 Cochlea Homo 124390 N29325 ESTs; Highly similar 7.9 Hs.7535 to COBW-like place 124438 N40188 ESTs 9.5 Hs.11090 124447 N48000 Homo Sapiens mRNA; 4.8 cDNA DKFZp586 124457 N50114 ESTs 6.1 Hs.266175 124539 N63172 cell division cycle 5.6 Hs.146409 42 (GTP-binding prote $ 124626 N74604 ESTs 12.8 Hs.11090 124632 N79515 interleukin 13 receptor;6.4 Hs.306117 alpha 1 124644 N91279 ESTs; Moderately similar8.3 Hs.109654 to outer membr 124676 801037 phosphoglycerate mutase12.3 Hs.181013 1 (brain) 124677 801073 ESTs; Weakly similar 5.4 to !!!! ALU CLASS

1 124724 812405 Homo Sapiens mRNA; 6.6 ~ Hs.112423 cDNA DKFZp586 124773 840923 ESTs 4.9 Hs.106604 124777 841933 ESTs 7.2 124792 844357 ESTs; Weakly similar 8.6 Hs.48712 to cDNA EST EMB

124857 863652 ESTs 4.9 Hs.137190 15124911 888992 ESTs 4.7 Hs.180612 124955 T10598 ESTs; Weakly similar 4.4 Hs.324841 to 1111 ALU SUBFA

124958 T11134 murine leukemia viral 12.6 Hs.431 (bmi-1) oncogene h 125038 T78089 ESTs 4.1 Hs.270134 125092 T92544 CD84 antigen (leukocyte14.8 Hs.137548 antigen) 2~125132 W15495 chromosome 21 open 6.7 Hs.129781 reading frame 5 125144 W37999 ESTs 4.8 Hs.24336 125154 W38419 ESTs 5.3 125243 W86423 ESTs 6.6 Hs.105413 125279 W93640 ESTs; Moderately similar5.8 Hs.4779 to similar to AD

2$125299 239436 ESTs 12.2 Hs.102720 125303 239821 ESTs 10.2 Hs.288193 125304 239833 GTP-binding protein 6.8 Hs.124940 125474 AA151216 tyrosine 3-monooxygenaseltryptophan8 Hs.75103 5-m 125509 AA044232 ESTs 5.4 Hs.288967 125580 AA126504 sorting nexin 4 4.1 Hs.267812 125582 AA507383 cytochrome c oxidase 11.5 Hs.74649 subunit Vlc 125670 AI432621 CD47 antigen (Rh-related4 Hs.82685 antigen; integri 125698 AA748483 general transcription 9.4 Hs.191356 factor IIH; polypepti 125745 AI283493 ribophorin II 6.2 Hs.75722 3 125852 H09290 Homo sapiens mRNA; 25.9 $ Hs.76550 cDNA DKFZp564 125972 AA434562 ESTs 4.1 Hs.35406 126160 N90960 ESTs; Weakly similar 16.4 Hs.265398 to transformation-r 126257 N99638 tumor necrosis factor 9.5 Hs.124084 receptor superfamily 126337 A1066486 similar to S. cerevisiae5.6 Hs.40500 RER1 126405 046278 ESTs 7.5 Hs.122489 126537 W40262 ESTs; Weakly similar 4.1 Hs.146310 to putative p150 [H

126590 W78968 H3 histone; family 4.5 Hs.181307 3A

126712 AA205862 ESTs 5.2 Hs.7942 126721 T72569 Thy-1 cell surface 4.4 Hs.125359 antigen 45126764 AI334393 ESTs 4.6 Hs.102178 126804 AI203334 ESTs 11.7 Hs.160628 126819 AA305536 ESTs 4 Hs.279607 126877 A1052047 ESTs 7 Hs.26102 126991 831652 biglycan 5.6 Hs.821 127479 AA513722 collagen; type X; alpha14.3 Hs.179729 1 (Schmid metaph 127514 AA826926 ESTs 4.5 Hs.204214 127663 W07286 ESTs; Weakly similar 5.1 Hs.10340 to weak similarity t 127677 AA916752 ESTs; Highly similar 17.3 Hs.264190 to MEM3 [M.muscu 127814 AA761755 ESTs; Weakly similar 4.1 ~ Hs.136713 to V4-1 [H.sapiens SS127997 AI281549 ESTs 5.5 Hs.311054 128092 AA904617 ESTs 5.8 Hs.166229 128218 H02682 ESTs; Moderately similar5.8 Hs.292154 to recombipatio 128466 D59653 EST 7.4 Hs.241471 128482 083908 programmed cell death 5.8 Hs.296251 4 128517 AA280617 ESTs; Weakly similar 8.3 Hs.100861 to p60 katanin [H.s 128530 AA504343 Homo Sapiens clone 6.6 Hs.183475 25061 mRNA sequen 128559 AA226801 metastasis associated 5.2 Hs.101448 1 128574 AA412048 keratin 8 5.1 Hs.38260 128595 031875 short-chain alcohol 27.1 Hs.152677 dehydrogenase family 65128610 L38608 activated leucocyte 13.2 Hs.10247 cell adhesion molecule 128629 AA399187 DKFZP434A043 protein 6.7 Hs.102708 128649 AA142853 Homo Sapiens mRNA for 4.5 Hs.103106 G7b protein (G

128651 AA446990 ESTs 6.1 Hs.103135 128653 848943 solute carver family 4,4 Hs.10315 7 (cationic amino aci 128656 AA458542 coatomer protein complex;14.3 Hs.10326 subunit epsilon 128717 T30617 Homo Sapiens mRNA; 24.5 Hs.104222 cDNA DKFZp566 $ 128727 M64174 Janus kinase 1 (a protein7.3 Hs.50651 tyrosine kinase) 128764 N49308 ESTs; Weakly similar 9.2 Hs.104938 to alpha 1 (XVIII) c 128781 X85372 small nuclear ribonucleoprotein5,4 Hs.105465 polypepti 128793 W93562 KIAA0553 protein 4.6 Hs.105749 128835 W15528 Homo sapiens mRNA; 4 Hs.106390 cDNA DKFZp586 10128845 AA455658 basement membrane-induced6.9 Hs.10649 gene 128871 AA400271 Homo Sapiens mRNA for 4.5 Hs.106778 putative Ca2~-t 128922 AA252023 ESTs; Weakly similar 6.4 Hs.9589 to HRIHFB2157 [H

128925 D61676 Homo sapiens mRNA; 6.4 Hs.21851 cDNA DKFZp586 128938 AA410325 ESTs 7 Hs.107260 1$128946 N29353 kynurenine 3-monooxygenase5.2 Hs.107318 (kynurenin 128948 AA485655 proteasome (prosome; 13.1 Hs.223025 macropain) subunit 128955 F10290 Homo Sapiens clone 5.8 Hs.185807 24758 mRNA sequen 129005 AA460049 ESTs; Weakly similar 12.6 Hs.13323 to SODIUM-AND

129009 AA131421 ESTs 9.8 Hs.75607 20129017 H13108 ESTs 13.9 Hs.107968 129057 X62466 CDW52 antigen (CAMPATH-110.7 Hs.276770 antigen) 129075 AA129465 ESTs 4.7 Hs.83765 129095 L12350 thrombospondin 2 4.4 Hs.108623 129124 AA234530 N-ethylmaleimide-sensitive20.7 Hs.108802 factor 2$129160 AA131252 ESTs 5.9 Hs.109007 129164 AA282183 ESTs 5.8 Hs.109045 129180 840556 ESTs; Highly similar 7.6 Hs.318401 to HSPC039 protein 129224 X89109 coronin; actin-binding12 Hs.109606 protein;1A

129229 AA211941 polyadenylate binding 7.9 Hs.109643 protein-interacting 30129240 W24360 interleukin 7 receptor5.3 Hs.237868 129241 AA435665 ESTs; Moderately similar8.4 Hs.109706 to HN1 [M.mus 129243 H88033 KIAA0733 protein 7.8 Hs.109727 129247 AA151574 pilin-like transcription6.4 Hs.109733 factor 129259 AA090695 ESTs 6.2 Hs.181385 3$129270 235227 ras homolog gene family;5.4 Hs.109918 member H

129281 AA026318 glucose regulated protein;4.4 Hs.289101 58kD

129300 C20976 ESTs; Highly similar 5.7 Hs.110165 to ribosomal protein 129318 N93155 ca(modulin 1 (phosphorylase7.7 Hs.285976 kinase; delta 129319 AA037467 ESTs 6 Hs.30340 40129351 AA167268 Human ras inhibitor 9.3 Hs.62349 mRNA; 3' end 129366 H18027 plexin C1 18.2 Hs.184697 129383 W92984 ESTs 5.9 Hs.288224 129388 AA151621 ESTs 4.1 Hs.110964 129391 T80814 discs; large (Drosophila)10.9 Hs.11101 homolog 3 (neur 4$129404 AA172056 ESTs 5.3 Hs.317584 129406 N23707 KIAA0712 gene product 4 Hs.111138 129426 AA412087 EST; Highly similar 8 Hs.111323 to protein inhibitor o 129453 AA421213 Lsm3 protein 5.5 Hs.111632 129513 C00225 ESTs; Weakly similar 5.5 Hs.306163 to fos39554_1 [H.s $0129519 AA298786 ESTs 6.8 Hs.112242 129606 821443 heatshock90kD protein 5 Hs.166254 1; alpha 129622 AA278243 ESTs 6.8 Hs.323949 129626 AA447410 ESTs; Weakiy similar 5.1 Hs.111334 to !!!! ALU SUBFA

129627 AA258308 Homo sapiens mRNA; 5.3 Hs.71968 cDNA DKFZp564 $ 129628 U26727 cyclin-dependent kinase8.2 $ Hs.1174 inhibitor 2A (mel 129642 850008 7-dehydrocholesterol 4.3 Hs.11806 reductase 129663 AA442768 translocase of inner 4.4 Hs.11866 mitochondrial membr 129665 M88458 KDEL (Lys-Asp-Glu-Leu)4 Hs.118778 endoplasmic re 129691 X06700 collagen; type III; 6 Hs.119571 alpha 1 (Ehlers-Danlos 60129783 AA454618 associated molecule 6.4 Hs.12479 with the SH3 domain 129800 AA252436 lysophospholipase I 7.7 Hs.12540 129836 AA452161 YME1 (S.cerevisiae)-like5 Hs.206521 1 129850 N20593 GDP dissociation inhibitor6.9 Hs.288932 2 129869 AA102520 ESTs; Weakly similar 5 Hs.13015 to heat shock prote 6$129896 AA043021 UDP-Gal:betaGIcNAcbeta1;4-galactosy6.6 Hs.13225 129982 M87789 immunoglobulin gamma 4 3 (Gm marker) 129985 AA450045 cargo selection protein5.8 Hs.140452 (mannose 6 phosp 130029 AA236412ESTs; Moderately similar5.6 Hs.236510 to PFT27 [M.m 130033 M90696 cathepsin S 5.4 Hs.181301 130036 AA195260ESTs; Moderately similar7.4 Hs.125849 to Illl ALU SU

130069 AA055896collagen; type V; alpha7.6 Hs.146428 1 $ 130077 T24055 ribosomal protein L26 4 Hs.91379 130080 X14850 H2A histone family; 12.1 Hs.147097 member X

130096 AA223874KIAA0704 protein 5 Hs.197955 130114 AA234717ESTs 7.8 Hs.14992 130125 M36803 hemopexin 7.2 Hs.1504 1 130135 M61764 tubulin; gamma 1 5.6 ~ Hs.21635 130170 AA610070calciumlcalmodulin-dependentserinepro7.5 Hs.151469 130189 043947 KIAA0100 gene product 6.4 Hs.151761 130208 AA620556peroxisomal D3;D2-enoyl-CoA6.4 Hs.15250 isomerase 130211 050840 UDP-glucose ceramide 4.5 Hs.23703 glucosyltransferas 1$ 130235 X14046 CD37 antigen 9.1 Hs.153053 130276 S75295 karyopherin alpha 1 8.6 Hs.169149 (importin alpha 5) 130280 L13738 activated p21cdc42Hs 5 Hs.153937 kinase 130313 AA620323ubiquitin-activating 6.1 Hs.154320 enryme E1C (homolo 130314 086967 KIAA0212 gene product 10 Hs.154332 20 130328 AA135673KIAA0391 gene product 6.1 Hs.154668 130356 X84373 nuclear receptor interacting10.6 Hs.155017 protein 1 130367 238501 ESTs; Weakly similar 8.3 Hs.8768 to !I!! ALU SUBFA

130378 T47333 TATA box binding protein7.1 Hs.155188 (TBP)-associa 130384 X66364 cyclin-dependent kinase5.6 Hs.166071 5 2$ 130393 013630 KIAA0005 gene product 4.1 Hs.155291 130399 AA449417Homo Sapiens mRNA for 4.6 Hs.155356 putative glucosy 130407 N29888 ESTs 7 Hs.155410 130414 M21121 small inducible cytokine4.1 Hs.241392 A5 (RANTES) 130417 U58522 huntingtin-interacting7.9 Hs.155485 protein 2 3~ 130421 021260 clathrin; heavy polypeptide-like4 Hs.178710 2 130441 U35835 protein kinase; DNA-activated;6.8 Hs.155637 catalytic p 130455 X17059 N-acetyltransferase 26.4 Hs.155956 1 (arylamine N-acetyl 130498 L38951 karyopherin (importin)4.8 Hs.180446 beta 1 130499 AA416723Homo Sapiens mRNA for 6.1 Hs.158286 KIAA0446 prot 3 130511 L32137 cartilage oligomeric 8.3 $ Hs.1584 matrix protein (pseud 130553 AA430032pituitary tumor-transforming7.5 Hs.252587 1 130558 H96654 ESTs; Weakly similar 5.6 Hs.15984 to gene pp21 protei 130568 AA232535ESTs; Highly similar 4 Hs.16085 to CGI-13 protein [H

130583 W24957 ESTs;ModeratelysimilartosimilartoC.e13.3 Hs.293907 130585 H66211 ESTs 10.1 Hs.16331 130604 X03635 estrogen receptor 1 39.9 Hs.1657 130614 AA132007ESTs 5.1 Hs.16697 130619 AA477739ESTs 5.9 Hs.12532 130622 AA235247ESTs; Weakly similar 4.1 Hs.16846 to cytochrome P45 4$ 130625 F03969 matrix metalloproteinase8.3 Hs.260720 2 (gelatinase A;

130627 L23808 matrix metalloprofeinase10.3 Hs.1695 12 (macrophage 130629 M60346 ATPase; H+transporting;7 Hs.1697 lysosomal (vacu 130635 M87503 interferon-stimulated 5.5 Hs.1706 transcription factor 130639 059711 ESTs 7.2 Hs.17132 $~ 130677 H17861 ESTs 13.5 Hs.17767 130681 082808 Rho-associated; coiled-coil6 Hs.17820 containing pro 130693 AA487202ESTs 6.1 Hs.17962 130703 N63295 ESTs 4.3 Hs.18103 130706 AA488843comichon-like 4 Hs.201673 $ 130712 AA292066adenylate cyclase 7 5.1 $ Hs.279762 130714 X92896 DNA segment on chromosome8.4 Hs.18212 X (unique) 130715 T98227 occludin 5.7 Hs.171952 130744 AA203527POP7 (processing of 6.2 Hs.18747 precursor; S. cerevis 130747 AA471293ESTs 8.2 Hs.6879 130751 AA435633Homo Sapiens clone 8.3 Hs.18879 23965 mRNA sequen 130796 839390 ESTs 4.5 Hs.19525 130800 AA223386ESTs; Weakly similar 7.7 Hs.19574 to katanin p80 subu 130855 AA425439putative DNAlchromatin4.3 Hs.143323 binding motif 130859 AA287327ceroid-lipofuscinosis;9.8 Hs.20478 neuronal 2; late info 6$ 130866 M58028 ubiquitin-activating 4.3 Hs.2055 enryme E1 (A1S9T a 130880 014678 kinesin-like 2 4.5 Hs.20830 130891 031891 SET domain; bifurcated;14 Hs.20991 130905 AA056489ESTs 8.7 Hs.129998 130913 W03592 translocase of outer 20.9 Hs.21198 mitochondrial membr 130919 AA291710collagen; type IV; alpha9 Hs.21276 3 (Goodpasture a 130921 AA074596bromodomain adjacent 5.3 Hs.194688 to zinc finger dom $ 130944 M97935 signal transducer and 18.8 Hs.21486 activator of transcrip 130974 X57985 H2B histone family; 13.4 Hs.2178 member Q

130987 845698 ESTs; Weakly similar 8.5 Hs.21893 to cAMP inducible 130999 N48963 KIAA0689 protein 7.2 Hs.21992 131010 AA435748ESTs; Weakly similar 5.2 Hs.169341 to phosphatidic acid 1 131046 X02530 small inducible cytokine10.1 ~ Hs.2248 subfamily B (Cy 131091 T35341 ESTs; Highly similar 6.3 Hs.22880 to dipeptidyl peptid 131153 H11760 ESTs 7.3 Hs.23606 131185 M25753 cyclin B1 6.2 Hs.23960 131200 AA609427ESTs; Moderately similar4.3 Hs.293732 to !!!! ALU SU

1$ 131206 AA044078ESTs 5.5 Hs.24210 131210 AA430047ESTs 7.1 Hs.95549 131227 AA429472DKFZP434P106 protein 5.6 Hs.236522 131244 D38076 RAN binding protein 5.5 Hs.24763 1 131245 AA620599DKFZP564E1962 protein 6.7 Hs.24766 2~ 131257 AA256042ESTs 5.8 Hs.24908 131319 U25997 stanniocalcin 8.9 Hs.25590 131339 'AA463450Nijmegen breakage syndrome6.5 Hs.25812 1 (nibrin) 131388 834531 KIAA0480 gene product 9.2 Hs.92200 131410 H84658 ESTs 12.1 Hs.279836 2$ 131472 AA608962calcyclin binding protein18.1 Hs.27258 131475 239053 ESTs 7.5 Hs.27263 131501 AA121127H3 histone; family 3A 5.5 Hs.8207 131514 X02152 lactate dehydrogenase 5.1 Hs.2795 A

131524 N39152 ESTs 4.3 Hs.301804 3~ 131528 D60856 UDP~lucosedehydrogenase8.4 Hs.28309 131544 N33236 ESTs; Weakly similar 5.6 Hs.28555 to 80511.8 [C.eleg 131557 D30946 signal sequence receptor;8.7 Hs.28707 gamma (transloc 131562 U90551 H2A histone family; 18.8 Hs.28777 member L

131564 AA491465ESTs 11.8 Hs.28792 3 131586 AA235385ESTs; Moderately similar4.7 $ Hs.26966 to alternatively 131587 M15182 glucuronidase; beta 5,2 Hs.183868 131589 U52100 epithelial membrane 4.4 Hs.29191 protein 2 131615 D14533 xeroderma pigmentosum; 4,6 Hs.192803 complementatio 131664 AA136126mitogen-activated protein4.3 Hs.30327 kinase-activated 131679 AA136660ESTs 9.4 Hs.30579 131684 U26174 granzyme K (serine protease;9.7 Hs.3066 granzyme 3 131687 L11066 heat shock 70kD protein6.2 Hs.3069 9B (mortalin-2) 131689 AA599653transcription factor-like8.3 Hs.30696 5 (basic helix-!oo 131693 W60913 ESTs; Weakly similar 9 Hs.110796 to cDNA EST yk45 4$ 131710 AA233225MR51 protein 5.2 Hs.30985 131716 D49738 cytoskeleton-associated6.6 Hs.31053 protein 1 131742 D31352 ESTs 11 Hs.31433 131762 H46831 ESTs; Moderately similar4.9 Hs.107767 to CaM-KII inh 131781 AA460450DKFZP586G1722 protein 9.2 Hs.31989 $0 131795 N32724 Sox-like transcriptional4.5 Hs.32317 factor 131809 L76517 presenilin 1 (Alzheimerdisease3)5.4 Hs.3260 131814 AA437226interleukin 10 receptor;4 Hs.157 alpha 131838 AA091932dynamin-like protein 6.7 Hs.180628 131877 J04088 topoisomerase (DNA) 5 Hs.156346 II alpha (170kD) $ 131885 AA044095ESTs 11.1 $ Hs.3402 131891 AA158258heterogeneous nuclear 5.6 Hs.30376 protein similar to r 131925 AA248470ESTs; Weakly similar 4.5 Hs.183180 to RING finger pro 131930 AA205460ESTs 14.3 Hs.69476 131941 D62657 ubiqui6n-specific protease6.2 Hs.35086 1 131965 W90146 ESTs 6.3 Hs.35962 131970 D86960 KIAA0205 gene product 4.2 Hs.3610 131971 870167 ESTs 4.3 Hs.154938 131974 AA410424Homo sapiens mRNA; cDNA4.6 Hs.268122 DKFZp586 131977 F09788 procollagen-proline; 6.4 Hs.3622 2~xoglutarate 4-diox f>$131994 AA479515Human DNA sequence from12 Hs.279882 clone 703H1 131997 D82399 Homo sapiens clone 2371410 Hs.136644 mRNA sequen 132017 W67251 Homo sapiens vav 3 oncogene4.7 Hs.267659 (VAV3) m 132021 T68246 chaperonin containing 5.2 Hs.306079 TCP1; subunit 5 (e 132065 D82226 proteasome (prosome; 8.5 Hs.211594 macropain) 268 sub 132085 D44466 proteasome (prosome; 13.5 Hs.3887 macropain) 26S sub 132089 AA131971ESTs 4.8 Hs.39122 $ 132109 AA599801ESTs 6.2 Hs.40098 132143 AA257056KIAA0871 protein 14.6 Hs.7972 132149 T10822 ESTs 5.3 Hs.324743 132153 N90141 ESTs; Moderately similar9.2 Hs.41066 to ELONGATI

132160 AA281770seven in absentia (Drosophila)5.5 Hs.295923 homolog 1 132164 084573 procollagen-lysine; 8.1 Hs.41270 2-oxoglutarate 5-dioxy 132180 AA405569fibroblast activation 15.4 Hs.418 protein; alpha; sepras 132183 L19183 hypotheficai protein 12.2 Hs.199695 132225 AA128980ESTs 5.6 132227 AA412620ESTs 6.7 Hs.4248 1 132235 F09058 ESTs 6.2 S Hs.42656 132256 AA608856murine leukemia viral 6 Hs.431 (bmi-1) oncogene h 132298 N41849 Homo Sapiens cytokine 5.6 Hs.7120 receptor related p 132314 AA285290small EDRK-rich factor 6.8 Hs.44499 2 132325 N37065 ESTs 4.7 Hs.44856 2~ 132384 AA479933Human DNA sequence from4.2 Hs.46967 clone 167A1 132387 870914 heat shock 70kD protein9.1 Hs.281434 1 132393 W85888 ESTs; Moderately similar4 Hs.47334 to !!!! ALU SU

132406 F09979 ESTs 15 Hs.4774 132407 AA431459ESTs 8 Hs.47783 2S 132413 AA132969KIAA1104 protein 4 Hs.260116 132446 AA426218ESTs 5.3 Hs.48764 132465 AA047896ESTs 15.4 Hs.49169 132482 AA429478ESTs; Highly similar 9 Hs.238126 to CGI-49 protein [H

132492 T03749 KIAA1089 protein 8.5 Hs.4990 30 132528 AA283006chromosome-associated 4.3 Hs.50758 polypeptide C

132540 AA488987synaptogyrin 2 9.8 Hs.5097 132543 AA417152protein regulator of 10.1 Hs.5101 cytokinesis 1 132580 L37042 casein kinase 1; alpha 5.9 Hs.283738 1 132586 AA412452DKFZP434N024 protein 4.2 Hs.52515 3 132608 AA199588ARP3 (actin-related 4.2 $ Hs.5321 protein 3; yeast) hom 132616 AA386264isocitrate dehydrogenase5.2 Hs.283558 2 (NADP+); mit 132617 AA171913carbonic anhydrase XII 10.1 Hs.5338 132618 AA253330adaptor-related protein4.8 Hs.279916 complex 1; gamma 132640 033821 Tax1 (human T-cell leukemia5.7 Hs.5437 virus type I

4O 132668 AA453614KIAA0776 protein 4.4 Hs.5460 132694 M60830 ecotropic viral integration15.6 Hs.5509 site 2B

132700 N47109 ES1's 7 Hs.5521 132724 AA417962geranylgeranyl diphosphate5.6 Hs.55498 synthase 1 132738 W42674 ESTs; Moderately similar4.9 Hs.264636 to neuronal thre 45 132742 AA490862ESTs; Weakly similar 7.9 Hs.292812 to C43H8.1 [C.eleg 132744 X54326 glutamyl-prolyl-tRNA 4.1 Hs.55921 synthetase 132795 H99152 ESTs 8 Hs.57079 132807 AA331777mutt (E. coli) homolog 8 Hs.57301 1 (colon cancer; n 132811 025435 transcriptional repressor4 Hs.57419 5~ 132817 AB004884tousled-like kinase 6.5 Hs.57553 2 132840 N23817 Homo sapiens clone 236755.6 Hs.5807 mRNA sequen 132845 D62588 ESTs 12.4 Hs.5813 132847 T48195 eukaryotic translation 7 Hs.58189 initiation factor 3;
s 132856 W79865 glypican 4 6.2 Hs.58367 55 132869 N26855 ESTs 6.5 Hs.203961 132874 AA425776ESTs 5.6 Hs.58609 132880 AA444369ESTs 7.2 Hs.177537 132894 D82422 ESTs 7.5 Hs.5944 132900 N56451 LIM domain only 7 4.4 Hs.5978 132903 AA235404Homo Sapiens clone 251869.1 Hs.5985 mRNA sequen 132904 X83618 3-hydroxy-3-methylglutaryl-CoenrymeA10.7 Hs.59889 132906 AA142857ESTs; Highly similar 10.2 Hs.234896 to geminin [H.sapie 132914 AA496037ESTs 4.7 Hs.60293 132918 AA252605KIAA0616 protein 7.1 Hs.6051 6$ 132936 AB002305KIAA0307 gene product 8.3 Hs.6111 132951 004209 microfibrillar-associated4.3 Hs.61418 protein 1 132957 AA234791Human gene from PAC 13.2 Hs.61469 753P9; chromoso 132959 AA028103ESTs; Weakly similar 18.9 Hs.61472 to unknown [S.cere 132968 N77151 myosin X 5.8 Hs.61638 132984 H80409 zinc finger protein 4.3 Hs.62112 207 132990 AA458761transcription factorAP-24.2 Hs.18387 alpha (activating $ 132994 AA505133solute carrter family 26.4 Hs.279905 2 (facilitated glucose 132998 Y00062 protein tyrosine phosphatase;4.4 Hs.170121 receptor typ 133002 AF006082ARP2 (actin-related 4.7 Hs.42915 protein 2; yeast) hom 133005 C21400 KIAA0970 protein 6.6 Hs.278605 133015 AA047036ESTs 7.9 Hs.246315 1 133016 W81298 growth factor receptor-bound5.2 ~ Hs.6289 protein 2 133039 X62055 protein tyrosine phosphatase;4 Hs.63489 non-recepto 133050 S67325 propionyl Ceenzyme A 5.2 Hs.63788 carboxylase; beta 133056 AA071387jumping translocation 5 Hs.6396 breakpoint 133062 833663 ESTs 5.4 Hs.64056 1$ 133083 N70633 chaperonin containing 6 Hs.6456 TCP1; subunit 2 (b 133091 AA122147KIAA0483 protein 5 Hs.64691 133093 AA598749ESTs 5.6 Hs.285996 133124 AA156049ESTs 4.1 Hs.267923 133126 D16469 ATPase; H+transporting;6.2 Hs.6551 lysosomal (vacu 2~ 133196 837367 Ras-GTPase activating 5.1 Hs.6727 protein SH3 doma 133214 Y10659 interleukin 13 receptor,6.2 Hs.285115 alpha 1 133225 241415 ESTs; Weakly similar 8.3 Hs.6823 to intrinsic factor-B

133228 N90029 Homo Sapiens clone 14004.7 Hs.6831 unknown prote 133239 AA059405Homo sapiens clone 246555.5 Hs.179882 mRNA sequen ~$ 133240 D31161 ESTs 9 Hs.242894 133257 AF006086actin related protein 7.7 Hs.6895 213 complex; subunit 133264 W72187 ESTs; Weakly similar 6.7 Hs.69192 to cDNA EST yk37 133274 AA488886ESTs 4.2 Hs.6949 133281 AA421079ESTs; Weakly similarto 4.9 Hs.69594 Sox-like transcri 3~ 133283 AA410507ESTs 4.3 Hs.&968 133287 L15702 B-factor; properdin 9.3 Hs.69771 133294 879723 zinc finger protein 30.4 Hs.69997 238 133297 AA600057KIAA0905 protein 10.4 Hs.70266 133318 AA256168ESTs 8.5 Hs.152316 3$ 133362 H06195 ESTs; Highly similar 14 Hs.7194 to CGI-59 profein [H

133370 AA156897DKFZP56411922 protein 5 Hs.72157 133391 X57579 inhibin; beta A (activin13.9 Hs.727 A; activin AB alp 133395 AA491296ESTs 4.3 Hs.72805 133422 N79516 ESTs; Weakly similar 4.5 Hs.73287 to eyelid [D.melano 4~ 133431 AA255438Homo Sapiens mRNA; cDNA8 Hs.7358 DKFZp566 133435 T23983 ESTs 5 Hs.323966 133449 AA094989voltage-dependent anionchannel38.7 Hs.7381 133468 X03068 major histocompa6bility5 Hs.73931 complex; class II

133484 X78710 metal-regulatory transcription5.3 Hs.211581 factor 1 4$ 133506 AA316868ESTs; Weakly similarto 6.8 Hs.74346 140G11.h [D.me 133517 X52947 gap junction profein; 5.7 Hs.74471 alpha 1; 43kD (conn 133551 D63480 KIAA0146 protein 4.8 Hs.278634 133569 AA313977transcription elongation9.5 Hs.172772 factor B (SIII); po 133572 W94333 translocase of inner 5 Hs.279915 mitochondrial membr $~ 133577 F03717 human immunodeficiency 7.4 Hs.75063 virus type I enh 133589 L37368 RNA-binding protein 5 Hs.75104 S1; serine-rich dom 133608 D13315 glyoxalase I 4.2 Hs.75207 133617 AA148318KIAA0069 protein 4.5 Hs.75249 133627 009587 glycyl-tRNA synthetase 10 Hs.75280 $$ 133633 D21262 nucleolar phosphoprotein4.5 Hs.75337 p130 133634 024166 microtubule-associated 15.2 Hs.234279 protein; RPIEB fa 133640 D83004 ubiquitin-conjugating 9.1 Hs.75355 enzyme E2N (homo 133644 D89077 Sro-like-adapter 6.4 Hs.75367 133649 AA479139acid phosphatase 1; 4.8 Hs.75393 soluble t7o133652 AA287383ESTs 4.2 Hs.7540 133674 AA458946ESTs 4.3 Hs.75497 133700 K01396 protease inhibitor 1 8.3 Hs.297681 (anti-elastase); alpha-133705 N21648 MpV17 transgene; murine4.6 Hs.75659 homolog; glom 133716 Y00282 ribophorin II 7.5 Hs.75722 ($ 133720 L27841 pericen~io(ar material 9.4 Hs.75737 1 133752 049278 ubiquitin-conjugating 4.5 Hs.75875 enzyme E2 variant 133765 D21255 cadherin 11 (OB-cadherin;6.4 Hs.75929 osteoblast) 133772 Hs,76038isopentenyl-diphosphate7.9 W73693 delta isomerase 133774 Hs.76067heat shock 27kD protein4.1 133776 Hs.177766ADP-ribosyltransferase 13 J03473 (NAD+; poly (AD

133784 Hs.301064ESTs 5.2 $ 133814 Hs.76391myxovirus (influenza) 11.7 M33882 resistance 1; homol 133829 Hs.76550Homo Sapiens mRNA; cDNA9.4 AA453783 DKFZp564 133834 Hs,288660serine protease; umbilical4.8 AA147510 endothelium 133839 Hs.170250complement component 6.7 133842 Hs.285013putative human HLA class7.1 073477 II associated p 133845 Hs.76704ESTs 6.3 133859 Hs.17876126S proteasome-associated13.7 086782 pad1 homolog 133867 Hs,76989KIAA0097 gene product 4.1 133868 Hs.183874cullin 4A 4 133871 Hs.182793ESTs 4.7 ~ 133893 Hs.77356transferrin receptor 8.3 $ X01060 (p90; CD71) 133914 Hs.77542ESTs 5 133918 Hs.58382ESTs; Weakly similar 4.5 W72783 to C13F10.5 [C.ele 133944 Hs.7780Homo sapiens mRNA; cDNA6.3 AA045870 DKFZp564 133946 Hs.1738784-nitrophenylphosphatase6.4 AA156565 domain and non 2~ 133963 Hs.184693transcription elongation6.3 L34587 factor B (SIII); po 133980 Hs.250811proteasome (prosome; 11.9 D00760 macropain) subunit 133990 Hs.7822Homo sapiens mRNA; cDNA8.2 C02374 DKFZp564 133999 Hs.78305RAB2; member RAS oncogene5,2 M28213 family 134030 Hs.78575prosaposin (variant 4.6 J03077 Gaucher disease and v 25 134032 Hs.78589protease inhibitor 12 6.5 281326 (neuroserpin) 134045 Hs.78768BB1 11.9 134046 Hs.172801isoleucine-tRNA synthetase5.2 134064 Hs.78893KIAA0244 protein 7.3 134070 Hs.78946cullin 3 4.7 3~ 134087 Hs.173824thymine-DNA glycosylase7 134090 Hs.79037heat shock 60kD protein4.5 M22382 1 (chaperonin) 134098 Hs.79086ribosomal protein; mitochondrial;9.4 134110 Hs.79136LIV-1 protein; estrogen4.4 041060 regulated 134132 Hs.220689Ras-GTPase-activating 6.6 032519 protein SH3-doma 3 134168 Human Chromosome 16 8.6 $ AA398908 BAC clone CIT9 Hs.181634 134170 Hs.79572cathepsin D (lysosomal 9.3 M63138 asparlyl protease) 134208 Hs.79993peroxisomal biogenesis 6.3 088871 factor 7 134258 Hs.808heterogeneous nuclear 4.3 L28010 ribonucleoprotein F

134288 ESTs 6.9 Hs.8117 134310 Homo sapiens clone 248567.4 AA313414 mRNA sequen Hs.8148 134326 Hs.81800chondroifln sulfate 6.1 016306 proteoglycan 2 (versic 134329 Hs.81848RAD21 (S. pombe) homolog8.6 D38551 ~

134331 ESTs; Weakly similar 6.1 AA452020 to CGI-128 protein Hs.111222 134351 Hs.82109syndecan 1 4.4 4$ 134357 Hs,82171Human clone 19187 placenta6.6 L43575 expressed m 134363 Hs.82212CD53 anflgen 5.3 134367 Hs.82285phosphoribosylglycinamide4.8 X54199 formyltransfe 134374 Hs.8236ESTs 15.2 134375 ESTs; Highly similar 7.2 AA412720 to CGI-118 protein Hs.82389 $0 134376 Hs.823962;5'-oligoadenylatesynthetasel6.4 134381 Hs.184270capping protein (acfln 4 056637 filament) muscle Z-134388 Hs.82575small nuclear ribonucleoprotein5.7 ~M15841 polypepti 134395 Hs,8262lysosomal-associated 6.9 L09717 membrane protein 2 134399 Hs.82689tumor rejection antigen4.5 H99801 (gp96) 1 $$ 134401 kinectin 1 (kinesin 11.2 AA243746 receptor) Hs.211577 134405 Hs.82772collagen; type XI; alpha15.3 134415 protein tyrosine phosphatase4.1 AA329274 type IVA; m Hs.82911 134417 Hs.82921solute tamer family 4.2 D87969 35 (CMP-sialic acid t 134419 Hs.82961trefoil factor 3 (intestinal)5.9 134421 collagen; type V; alpha5.8 Hs.82985 134423 Hs.83006ESTs; Highly similar 4.4 W96151 to CGI-139 protein 134438 ESTs; Highly similar 7 AA449984 to proteine kinase Hs.246857 JN

134446 Hs.83419KIAA0252 protein 4.6 134453 Hs.83484SRY (sex determining 5.1 X70683 region Y)-box 4 6$ 134470 Hs.83758CDC28 protein kinase 20.3 134487 Hs.83954Homo Sapiens unknown 5 838185 mRNA

134495 Hs.84087KIAA0143 protein 16.1 23$

134498 M63180 threonyl-tRNA synthetase6.1 Hs,84131 134506 045328 ubiquitin-conjugating 4.6 Hs.84285 enzyme E21 (homol 134529 H24460 FK506-binding protein 6.2 Hs.848 4 (59kD) 134570 066615 SWIISNF related; matrix4.8 Hs,172280 associated; actin $ 134582 AA234966 CGG triplet repeat 4.7 Hs.86041 binding protein 1 134600 868884 ESTs; Weakly similar 5.8 Hs.86347 to predicted using G

134623 X74496 prolyl endopeptidase 4.5 Hs.86978 134654 W23625 ESTs; Weakly similar 13.7 Hs.8739 to ORF YGR200c [

134655 AA454070 ESTs 5.8 Hs.123090 1 134675 AA250745 protein kinase; cAMP-dependent;8.9 ~ Hs.87773 catalyti 134711 X04011 cytochrome b-245; beta6.8 Hs,88974 polypeptide (chro 134714 089922 lymphotoxin beta (TNF 35.7 Hs.890 superfamily; mem 134722 W47183 ESTs; Weakly similar 8.1 Hs.284226 to neural F box pro 134776 J05582 mucin 1; transmembrane6.2 Hs.89603 l 134806 249099 spermine synthase 4.2 $ Hs.89718 134810 M27394 membrane-spanning 4-domains;7 Hs.89751 subfamily 134840 051477 diacylglycerol kinase;4.1 Hs.89981 zeta (104kD) 134843 H60595 progesterone binding 4.7 Hs.90061 protein 134853 D82348 5-aminoimidazole-4-carboxamide10.2 Hs.90280 ribonuc 20134866 084011 amylo-1;6-glucosidase;12.1 Hs.904 4-alpha-glucanotr 134868 239762 KIAA0882 protein 6 Hs.90419 134885 N27670 progesterone membrane 5 Hs.9071 binding protein 134982 N46086 ESTs 4.1 Hs.92308 134989 AA236324 Homo Sapiens mRNA; 16,8 Hs.92381 chromosome 1 spe 2$134992 H05625 ESTs 4 Hs.5831 134993 AA282343 purine-rich element 4.4 Hs.301005 binding protein B

135010 D59675 ESTs 7 Hs.92927 135015 054999 LGN profein 4.8 Hs.278338 135029 AA224180 ESTs; Moderately similarto13.6 17-beta-hydr 3 135032 AA243497 Human DNA sequence 4 ~ Hs.173685 from clone 30M3 135037 077948 general transcription 8 Hs.278589 factor II; i 135059 AA598449 Homo Sapiens clone 5.4 Hs.93832 24483 unknown mRN

135071 L08069 heat shock protein; 9.3 Hs.94 DNAJ-like 2 135083 AA495950 ESTs 6.7 Hs.94262 3 135117 W52493 Homo Sapiens clone 10.2 $ Hs.94694 24837 mRNA sequen 135144 AA044842 Homo sapiens mRNA; 6.6 Hs.95260 cDNA DKFZp586 135154 AA126433 sorting nexin 4 7.4 Hs.267812 135218 D31157 ESTs; Weakly similar 6.2 Hs.324277 to growth factor-res 135237 AA454930 ESTs 19.5 Hs.9691 135243 AA215333 putative G protein-coupled8.8 Hs.97101 receptor 135335 H20989 pyruvate kinase; muscle12.4 Hs.198281 135349 D83174 collagen-binding protein5.5 Hs.9930 2 (colligen 2) 135367 AA480109 TYRO protein tyrosine 5.4 Hs.9963 kinase binding pro 135389 005237 fetal Alzheimer antigen7.8 Hs.99872 4$135400 M23263 androgen receptor(dihydrotestosterone9.1 Hs.99915 re 135411 L10333 reticulon 1 5.3 Hs.99947 300019 M97935 AFFX control: STAT1 8.3 300021 M97935 AFFX control: STAT1 7 300022 M97935 AFFX control: STAT1 14 300089 AI199738 ESTs; Weakly similar 9.1 ~ Hs.208275 to 1111 ALU CLASS

300107 AI694585 ESTs; Weakly similar 7.4 Hs.270464 to 1!!! ALU CLASS

300254 AW079607 ESTs; Weakly similar 30.1 Hs.188417 to ZnT-3 [H.sapien 300328 AW015860 ESTs 11.9 Hs.224623 300549 AA699328 ESTs 5.5 Hs.298119 $ 300711 AI492179 ESTs; Weakly similar 11 $ Hs.166244 to cDNA EST yk40 300921 AW293224 ESTs 11 Hs.232165 301124 T79326 ESTs; Weakly similar 8.8 Hs.298262 to dJ88J8.1 [H.sapi 301165 N85789 ESTs; Weakly similar 6 Hs.150186 to PTERIN-4-ALP

301576 AI682905 ESTs; Weakly similar 4.7 Hs.270431 to 1111 ALU SUBFA

301604 AA373124 ESTs;WeaklysimilartoC17G10.1[C.ele8 Hs.24809 301704 AA526313 ESTs 4.2 Hs.293691 301782 N99399 EST cluster (not in 18 Hs.143046 UniGene) with exon h 301884 AA312082 GDNF family receptor 20.7 Hs.105445 alpha 1 301936 NM_004694Hs.114924EST cluster (not in 11.6 UniGene) with exon h 6$302002 AF013956 chromobox homolog 4 9.2 Hs.5637 (Drosophila Pc cla 302032 NM_001992Hs.1280B7EST cluster (not in 4.3 UniGene) with exon h 302067 H05698 ESTs; Weakly similar 7.8 Hs.222399 to protein-tyrosine 302145 NM_003613Hs.151407EST cluster (not in 15.1 UniGene) with axon h 302236 AI128606zinc finger protein 25.8 Ns.6557 161 302276 NM_004448Hs.323910EST cluster (not in 21.6 UniGene) with axon h 302290 AL117607Homo sapiens mRNA; 41.4 Hs.175563 cDNA DKFZp564 $ 302326 NM_004271EST cluster (not in 8.9 Hs.184018 UniGene) with axon h 302342 AB023141KIAA0924 protein 5.4 Hs.190386 302372 AL117406Homo sapiens mRNA; 8.9 Hs.200102 cDNA DKFZp434 302422 AB021227ma~ix metalloproteinase5.2 Hs.3743 24 (membrane-in 302431 AF129530EST cluster (not in 5.3 Hs.226434 UniGene) with axon h 1 302501 AF022726EST cluster (not in 9.9 ~ Hs.251446 UniGene) with axon h 302505 AL049650multiple UniGene matches4.3 Hs.247874 302533 L36149 chemokine (C motif 4.9 Hs.248116 XC receptor 1 302638 AA463798ESTs; Weakly similar 5.3 Hs.102696 to C11D2.4 [C.eleg 302656 AW293005ESTs 8.4 Hs.70704 1$ 302792 AA343696ESTs; Weakly similar 4.5 Hs.46821 to putative [H.sapie 302820 X04588 EST cluster (not in 6.8 Hs.85844 UniGene) with axon h 302838 U66049 EST cluster (not in 8.4 Hs.82171 UniGene) with axon h 302892 N58545 histone deacetylase 22.8 Hs.42346 3 302977 AW263124EST cluster (not in 6.8 Hs.315111 UniGene) with axon h 20 302989 N46406 EST cluster (not in 8.9 Hs.84700 UniGene) with axon h 303007 AA478876pallid (mouse) homolog;10.1 Hs.317714 pallidin 303052 AF140242EST cluster (not in 24.4 Hs.279926 UniGene) with axon h 303131 AW081061actin-like 6 6.3 Hs.103180 303132 Ai929819ESTs 17.7 Hs.4055 2$ 303153 U09759 mitogen-activated protein11.4 Hs.246857 kinase 9 303387 AA908797ESTs 15.8 Hs.180799 303499 AI815990ESTs 7.2 Hs.293515 303502 AA488528EST cluster (not in 5.3 UniGene) with axon h 303576 T07216 EST cluster (not in 16.2 Hs.301226 UniGene) with axon h 30 303620 AA397546ESTs 8.9 Hs.119151 303634 AI953377ESTs; Weakly similar 12 Hs.28444 to predicted using G

303642 AW299459EST cluster (not in 4.2 Hs.111977 UniGene) with axon h 303654 AA436942ESTs 8.4 Hs.288529 303733 AW502498ESTs; Weakly similar 5.2 Hs.15220 to zinc finger prote 3 303780 AI424014ESTs; Moderately similar28.4 $ Hs.18995 to KIAA0456 p 303792 C75094 ESTs; Highly similar 4.4 Hs.199839 to NG22 [H.sapiens 303842 AI337304ESTs; Weakly similar 8.1 Hs.126268 to similar to PDZ
d 303951 AW475081collagen; type I; alpha7.5 Hs.172928 1 304465 AA421948EST singleton (not 6.5 in UniGene) with axon 304507 AA456426EST 5.4 304591 AA505702EST singleton (not 9.8 in UniGene) with axon 304601 AA507875EST singleton (not 7.5 in UniGene) with axon 304659 AA533185EST singleton (not 7 in UniGene) with axon 305040 AA630582glyceraldehyde-3-phosphate12.4 Hs.169476 dehydrogena 4$ 305134 AA653159EST singleton (not 8.7 Hs.179661 in UniGene) with axon 305415 AA725116EST singleton (not 5.3 Hs.78465 in UniGene) with axon 305453 AA738110EST singleton (not 4.1 in UniGene) with axon 305898 AA872838keratin 8 7.7 305913 AA876109EST singleton (not 6.3 in UniGene) with axon $~ 305950 AA884479EST singleton (not 5.6 in UniGene) with axon 306004 AA889992EST singleton (not 13.2 Hs.2186 in UniGene) with axon 306009 AA894560EST singleton (not 4.4 Hs.283370 in UniGene) with axon 306060 AA906161EST singleton (not 4.6 Hs.76277 in UniGene) with axon 306398 AA970548EST singleton (not 7.6 Hs.297681 in UniGene) with axon S 306505 AA987722EST singleton (not 19.7 $ Hs.172928 in UniGene) with axon 306576 AA995761EST singleton (not 5.5 Hs.276092 in UniGene) with axon 307117 AI184111heat shock 27kD protein7.7 Hs.76067 1 307138 AI185516collagen; type I; alpha8.8 Hs.172928 1 307187 AI190870EST singleton (not 4.1 Hs.276417 in UniGene) with axon 307542 AI280859EST singleton (not 6 Hs.62954 in UniGene) with axon 307554 AI281603EST singleton (not 10.8 Hs.172928 in UniGene) with axon 307806 AI351739EST singleton (not 4.7 Hs.276726 in UniGene) with axon 308079 AI472733ESTs 4.2 Hs.270208 308307 A1581398collagen; type h alpha5.4 Hs.172928 1 6$ 308511 AI687580EST singleton (not 10.1 Hs.169476 in UniGene) with axon 308615 AI738593EST singleton (not 15.1 Hs.101774 in UniGene) with axon 308677 AI761173EST singleton (not 4.6 in UniGene) with axon 308852 AI829848 peptidylprolyl isomerase5.9 Hs.182937 A (cyclophilin A

308974 AI872290 immunoglobulin gamma 4.5 Hs.300697 3 (Gm marker) 308981 AI873242 EST singleton (not 7.6 in UniGene) with exon 308995 AI880172 EST singleton (not 6.6 in UniGene) with exon $ 309177 AI951118 EST singleton (not 24.3 in UniGene) with exon 309186 AI952723 EST singleton (not 6.1 Hs.90207 in UniGene) with exon 309198 AI955915 major histocompatibility5.6 complex; class I;

309226 AI969897 EST singleton (not 6.2 in UniGene) with exon 309279 AI990102 EST singleton (not 7.9 in UniGene) with exon 1 309583 AW170035 EST 64.5 ~

309624 AW191929 EST 5.3 Hs.252989 309629 AW192764 collagen; type I; alpha6.9 Hs.172928 1 309641 AW194230 EST 11.4 Hs.253100 309698 AW238461 ribosomal protein; 4.3 Hs.73742 large; PO

1$309700 AW241170 Homo sapiens clone 11.9 Hs.179661 24703 beta-tubulin m 310073 AI335004 ESTs 4.2 Hs.148558 310094 AW450967 ESTs 5.7 Hs.235240 310373 AW080778 ESTs 4.8 Hs.145582 310438 AW022192 ESTs 39.1 Hs.200197 2d310470 AI281848 ESTs 4.9 Hs.194691 310583 AW205632 ESTs 7 Hs.211198 310877 T47784 ESTs 4.1 Hs.188955 311067 AI587332 ESTs 11.2 Hs.209115 311166 AI821294 ESTs 24.1 Hs.118599 2$311199 T57896 EST cluster (not in 5.7 Hs.191095 UniGene) 311465 AI758660 ESTs 15.7 Hs.206132 311587 AI828254 ESTs 6.4 Hs.271019 311774 AA700870 ESTs 6.2 Hs.14304 311785 A1056769 ESTs 5 Hs.133512 30311923 T60843 ESTs 5.9 Hs.189679 311935 AA216387 EST cluster (not in 5.5 UniGene) 311972 N51511 ESTs 5.2 Hs.188449 312014 Ai435650 ESTs 4.3 Hs.128778 312047 AA588275 ESTs 14.7 Hs.180669 3$312147 T89855 EST cluster (not in 9,8 Hs.195648 UniGene) 312153 AA759250 cytochrome b-561 27.1 Hs.153028 312168 T92251 ESTs 4.2 Hs.198882 312172 AI222168 ESTs 6.1 Hs.191168 312226 AI796815 ESTs; Weakly similar 5.5 Hs.199993 to ubiquitous TPR

312292 AW451893 ESTs 18.4 Hs.151124 312312 A1080505 ESTs 11.9 Hs.134529 312369 AA582039 Homo sapiens mRNA; 4 Hs.173884 chromosome 1 spe 312407 846180 ESTs 13.6 Hs.153485 312430 AW139117 ESTs 4.1 Hs.117494 4$312470 AW451347 ESTs 4.6 Hs.175862 312483 AI417526 ESTs 15.3 Hs.7753 312521 AA033609 ESTs 12.5 Hs.319093 312544 AI498371 ESTs 14.6 Hs.183526 312638 AW439195 ESTs 5.3 Hs.256880 $0312754 899834 ESTs 8.4 Hs.250383 312772 H63791 EST cluster (not in 4.3 UniGene) 312821 AA699325 ESTs 8.3 Hs.269880 312837 AW292286 ESTs 7.1 Hs.255058 312849 AA846353 ESTs 5.9 Hs.194054 $$312854 AA828713 EST cluster (not in 4.1 Hs.321058 UniGene) 312992 AA088446 ESTs 7.3 Hs.170298 313096 AI422367 ESTs 6.1 Hs.163533 313112 AA732534 ESTs 4.2 Hs.269099 313126 AA720887 EST cluster (not in 18.1 Hs.283313 UniGene) 313136 N59284 ESTs 17 Hs.288010 313197 AI738851 ESTs 12.9 Hs.222487 313219 N74924 ESTs 7.1 Hs.182099 313258 AW068358 ESTs 13.7 Hs.183918 313328 AW449211 ESTs 27.9 Hs.105445 6$313352 AW292127 ESTs 9.8 Hs.144758 313417 AA741151 ESTs 8.2 Hs.137323 313455 AW081702 ESTs 6.9 Hs.98571 313590 AA804410EST cluster (not in 5.3 Hs.291677 UniGene) 313663 AI953261ESTs 7.6 Hs.169813 313667 069201 ESTs; Weakly similar 12.5 Hs.13684 to choline kinase is 313749 AW450376ESTs 5.5 Hs.119004 $ 313832 AW271022ESTs 4.3 Hs.133294 313881 AA535580ESTs 7.7 Hs.16331 313915 A1969390ESTs 27.1 Hs.163443 313955 AI858884ESTs 5.7 Hs.270647 313974 A1310151ESTs 4.3 Hs.173524 1 314097 AA648744ESTs 14.5 ~ Hs.269493 314129 AA228366ESTs 9.5 Hs.115122 314359 AA205569ESTs 5.4 Hs.194193 314384 AA535840ESTs; Weakly similar 5.3 Hs.162203 to alternatively spli 314394 AI380563ESTs 13.2 Hs.130816 314462 AA347951ESTs 6.2 Hs.326413 314465 AA602917ESTs 18.1 Hs.156974 314470 AI934422ESTs ' 4.2 Hs.30661 314488 AA358265ESTs 6.1 Hs.182890 314506 AA833655ESTs 27.8 Hs.206868 2O 314510 A1204418ESTs 9.5 Hs.190080 314558 A1873274ESTs 22.5 Hs.190721 314661 AA436432EST cluster (not in 13.3 Hs.324239 UniGene) 314691 AW207206ESTs 21.4 Hs.136319 314754 AW026761ESTs 4.4 Hs.134374 2$ 314775 AN49880 ESTs 4.4 Hs.188809 314943 AI476797cell division cycle 18.4 Hs.184572 2; G1 to S and G2 to M

314961 AW008061ESTs 10.2 Hs.231994 314963 AI689617ESTs 5.3 Hs.200934 315006 A1538613ESTs 20.7 Hs.298241 30 315010 AA531082ESTs 5 Hs.240049 315019 AA532807ESTs 6.1 Hs.105822 315033 AI493046ESTs 12 Hs.146133 315036 AA534953ESTs 8.3 Hs.163297 315037 AW205863ESTs; Weakly similar 6.1 Hs.133988 to gene MAC25 pr 3S 315051 AW292425EST 12.7 Hs.163484 315054 AI968598ESTs 7.6 Hs.78768 315073 AW452948ESTs 13.9 Hs.257631 315080 AA744550ESTs 4.4 Hs.136345 315083 AI221325ESTs 5.1 Hs.205442 315088 AA557351ESTs; Moderately similar4.7 Hs.152448 to MULTIFUN

315175 A1025842ESTs 11.9 Hs.152530 315196 AA972756ESTs 28.8 Hs.44898 315296 AA876905ESTs 16.1 Hs.125286 315303 AW194364ESTs; Weakly similar 25.7 Hs.128022 to FIG-1 PROTEIN

45 315352 AA604799ESTs; Moderately similar12.3 Hs.136528 to !!!! ALU SU

315364 AA643602ESTs; Highly similar 4.6 Hs.155485 to serine protease [H

315368 AW291563ESTs 4.8 Hs.104696 315390 AI801565ESTs; Weakly similar 4.4 Hs.200113 to alternatively spli 315408 AW273261ESTs 5 Hs.216292 315458 AA872000ESTs 7.6 Hs.116104 315472 AA828850ESTs 4.9 Hs.165469 315478 AA665612ESTs 5.2 Hs.120874 315498 AA628539ESTs; Moderately s!milar4.8 Hs.116252 to !!!! ALU SU

315527 AI791138ESTs 4.4 Hs.116768 SJ 315530 AI200852ESTs 22.4 Hs.127780 315562 AA737415ESTs 5.9 Hs.152826 315634 AA837085ESTs 8.8 Hs.220585 315647 AA648983ESTs 15 Hs.212911 315652 AI521489ESTs 6.3 Hs.3053 315676 AW002565ESTs 9.2 Hs.124660 315680 AA814309ESTs 8.1 Hs.123583 315735 A1831760ESTs 13.4 Hs.155111 315741 AA812168ESTs 5.4 Hs.122559 315769 AA744875ESTs 4.4 Hs.189413 65 315978 AA830893ESTs 10.4 Hs.119769 315984 A1015862ESTs 5 Hs.131793 316042 AW297979ESTs 14.7 Hs.170698 316136 AA830808 ESTs 4 Hs.124366 316177 A1908272 EST cluster (not in 32.6 Hs.293102 UniGene) 316313 AA741300 ESTs 4.8 Hs.202599 316405 AA757900 ESTs 4.8 Hs.270823 $ 316480 A1749921 ESTs 12.9 Hs.205377 316564 AI743571 ESTs; Weakly similar 8.1 Hs.168799 to 1111 ALU SUBFA

316714 AA809792 ESTs 5 Hs.123307 316715 A1440266 ESTs 4.2 Hs.170673 316828 AA828116 ESTs 5.2 Hs.173076 10316869 A1954880 ESTs 13.3 Hs.134604 316905 AW138241 ESTs 6.2 Hs.210846 316943 AW014875 ESTs 5.3 Hs.137007 316949 AA856749 ESTs 7.2 Hs.124620 317008 AW051597 ESTs 4.1 Hs.143707 1$317028 AA962623 ESTs; Weakly similar 4.2 Hs.189144 to RENAL SODIU

317067 AI805392 ESTs 4.5 Hs.325335 317069 AI732892 ESTs 6.4 Hs.190489 317210 AA490718 EST cluster (not in 4.4 UniGene) 317298 AI922374 ESTs 5.9 Hs.158549 20317658 AW139077 ESTs 4.6 Hs.202217 317674 AW294909 ESTs 5.2 Hs.132208 317685 AI798630 ESTs 4.3 Hs.149997 317836 AA983913 ESTs 12.4 Hs.128929 317881 AI827248 ESTs 12.1 Hs.224398 2$317902 AI828602 ESTs 8.8 Hs.211265 317916 A1565071 ESTs 12.6 Hs.159983 318042 AW294522 ESTs 5.6 Hs.149991 318053 A1074465 ESTs 4 Hs.133469 318064 AW296888 ESTs 5.2 Hs.170939 30318070 A1024594 ESTs 4.7 Hs.248942 318073 AW167087 ESTs 15.7 Hs.131562 318146 A1040125 ESTs 5.9 Hs.150521 318186 AW016773 ESTs 5.3 Hs.3709 318481 AI291584 ESTs; Weakly similar 7.6 Hs.145921 to HYPOTHETICA

3 318566 AI335361 ESTs 5.8 $ Hs.226376 318617 AW247252 nucleoside phosphorylase11.1 Hs.75514 318662 AI285898 ESTs 16.3 Hs.294014 318691 AW192139 H3 histone; family 4 Hs.181307 3A

318740 NM_002543Hs.77729EST cluster (not in 21.3 Uni6ene) 40318744 AI793124 ESTs 35 Hs.144479 318948 AA317274 ESTs 11.7 Hs.13996 319163 F15257 glycine dehydrogenase 7 Hs.27 (decarboxylating;

319478 806841 EST cluster (not in 8.9 Hs.270307 UniGene) 319545 883716 ESTs 8.2 Hs.14355 4$319668 NM 002731EST cluster (not in 25.4 Hs.87773 UniGene) 319763 AA460775 ESTs 7 Hs.6295 319913 AA179304 ESTs; Moderately similar8.7 Hs.271586 to !lll pLU SU

319936 W22152 EST cluster (not in 5.6 Hs.282929 UniGene) 319951 AA307665 ESTs 4.9 Hs.14559 $0319962 H06350 ESTs 9.2 Hs.135056 319977 AA632632 EST cluster (not in 4.6 UniGene) 320074 AA321166 EST cluster (not in 16.7 Hs.278233 UniGene) 320092 AF022799 calpain 9 (nCL-4) 5.4 Hs.113292 320107 AA836461 EST cluster (not in 5.3 Hs.291712 UniGene) $ 320133 D63271 EST cluster (not in 5.5 $ UniGene) 320167 AA984373 EST cluster (not in 15 Hs.90790 UniGene) 320187 T99949 EST cluster (not in 6.7 Hs.303428 UniGene) 320211 AL039402 DEME-6 protein 24.3 Hs.125783 320401 090449 nucleoside diphosphate10 Hs.152717 kinase type 6 (inh ()0320458 AI884396 ESTs 5.4 Hs.24131 320488 831386 EST cluster (not in 4.9 Hs.191791 UniGene) 320521 N31464 ESTs 9.5 Hs.24743 320661 AA864846 EST cluster (not in 6.6 Hs.115175 UniGene) 320691 861576 hypothetical protein 5.9 Hs.313951 6$320699 863161 EST cluster (not in 4 Hs.118249 UniGene) 320727 096044 EST cluster (not in 15.3 Hs.181125 UniGene) 320993 AL050145 Homo Sapiens mRNA; 7.2 Hs.225986 cDNA DKFZp586 321012 AA737314 EST cluster (not in 6,1 Hs.194324 UniGene) 321050 AW393497 EST cluster (not in 5 Un!Genej 321051 AF134149 EST cluster (not!n 11.4 Hs.240395 UniGene) 321171 AI769410 ESTs 7.7 Hs.221461 $ 321192 AA295304 ESTs; Weakly similar 5.5 Hs.297939 to neogen!n jH.sap 321354 AA078493 EST cluster (not!n 16.9 UniGene) 321387 H68014 ESTs; Weakly similar 4.2 Hs.141278 to !!!! ALU SUBFA

321412 AW366305 EST cluster (not!n 6.3 Hs.22891 UniGene) 321489 AW392474 ESTs; Moderately s!milar9 Hs.172759 to !!!! ALU SU

1 321539 N98619 ARP2 (actin-related 11.3 ~ Hs.42915 protein 2; yeast) hom 321593 H84762 ESTs 10.4 Hs.253197 321666 D28390 EST cluster (not in 19.9 Hs.272897 UniGenej 321891 AW157424 ESTs 5.6 Hs.165954 321910 H67065 ESTs; Weakly similar 5.4 Hs.271530 to !!!! ALU SUBFA

15321953 AW068268 ESTs; Weaklys!milarto!!!!6.5 Hs.292833 ALU CLASS

321978 N77342 EST cluster (not in 10.2 Hs.21851 Un!Gene) 322017 AA310039 ESTs 9.8 Hs.9192 322026 AA233527 low density lipoprotein27.8 Hs.283675 receptor (fam!lial 322035 AL137517 EST cluster (not in 40.2 Hs.306201 Un!Gene) 322171 AF085968 EST cluster (not in 5.7 Hs.48474 Un!Gene) 322175 AF085975 EST cluster (not!n 7.7 UniGene) 322236 AL134970 fo!lisfatin-like 1 14.4 Hs.104222 322303 W07459 EST cluster (not in 13.4 Hs.157601 UniGene) 322735 AA086123 EST cluster (not in 7.6 Hs.297856 UniGene) 2S322777 AA679082 ESTs 4.4 Hs.269947 322818 AW043782 ESTs 21 Hs.293616 322882 AW248508 D!George syndrome critical15.3 Hs.279727 region gene 2 322975 C16391 EST cluster (not in 21.3 UniGene) 322991 C18965 ESTs 11.7 Hs.159473 3 323011 AA580288 EST cluster (not in 8.9 0 UniGene) 323091 AW014094 ESTs 10.8 Hs.210761 323107 AI301107 ESTs 6.5 Hs.150790 323136 AL120351 EST cluster (not in 5.5 Hs.30177 UniGenej 323168 AL120862 ESTs 17.9 Hs.124165 3 323195 A1064982 multifunctional polypeptide5.8 $ Hs.117950 similar to SA

323201 AL049370 Homo Sapiens mRNA; 11.6 Hs.13350 cDNA DKFZp586 323203 AA203135 ESTs 6.4 Hs.130186 323243 W44372 EST cluster(not!nUn!Genej7.3 Hs.110771 323244 T70731 EST cluster (not in 15.8 Hs.193620 Un!Gene) 40323328 AA228078 EST cluster (not in 4.8 Hs.255096 UniGene) 323332 AI829520 ESTs 20.2 Hs.227513 323333 AA228883 EST cluster (not in 8.8 Hs,208558 UniGene) 323570 AL038623 ESTs; Weakly similar 5 Hs,208752 to !!!! ALU SUBFA

323604 A1151438 ESTs; Weakly similar 6.5 Hs,41271 to !!!! ALU SUBFA

4S323685 AA344205 EST cluster (not in 7.1 Hs.289088 UniGene) 323753 AA327102 EST cluster (not in 6.1 Hs.70266 UniGene) 323817 AA410943 EST cluster (not in 16.8 Un!Gene) 323845 AI684674 ESTs; Weakly similarto10.1 Hs.41127 waclaw (D.melan 323930 AA570698 ESTs 6.4 Hs.8173 323997 AA844907 EST cluster (not in 8 Hs.274454 UniGene) 324047 AA378201 EST cluster (not !n 6.3 Hs.271340 UniGene) 324261 AL044891 EST cluster (not in 50.1 Hs.269350 UniGene) 324302 AA543008 ESTs; Weakly similar 5.7 Hs.292471 to i!!! ALU SUBFA

324338 AL138357 ESTs 9.5 Hs.145078 324344 AW502000 EST cluster (not in 4.4 5 Hs.46677 Un!Gene) 324432 AA464510 EST cluster (not in 16.7 Hs.152812 UniGenej 324495 AW501411 ESTs; Weakly similar 5.5 Hs.122489 to !!!! ALU CLASS

324497 AW152624 ESTs 5.4 Hs.136340 324598 AA502659 ESTs 8.8 Hs.163986 324603 AW016378 ESTs 23.1 Hs.292934 324620 AA448021 EST cluster (not in 21.2 Hs.94109 Un!Gene) 324727 AI610425 ESTs 5 Hs.19597 324774 A1031771 ESTs 5 Hs.132586 324783 AA640770 EST cluster (not in 4.1 Hs.200994 UniGene) 65324824 AI826999 ESTs 6.3 Hs.224624 324826 AA704806 ESTs 11.7 Hs.143842 324902 D31323 ESTs 4.8 Hs.271492 324961 AA613792EST 13.3 cluster (not in UniGene) 324987 T06882 ESTs 19.6 Hs.172634 324988 T06997 EST 24.5 Hs.121028 cluster (not in Un!Gene) 325146 A1064690ESTs 4.6 Hs.171176 $ 325622 CH.14_hs 5.2 gi[5867000 326213 CH.17_hs5867224 8.1 g![

326474 CH.19_hs5867405 12.7 gi[

326816 CH.20 9.4 hs gi[6552458 326817 CH.20_hs 11.7 gi[6552458 1 327110 CH.21 6117842 14.7 ~ hs gi[

327196 CH.01_hs5867446 5.1 g![

327283 CH.01_hs 4.3 g![5867478 327313 CH.01 4.8 hs gi[5867501 327450 CH.02_hs5867766 4.1 gi[

1 328059 CH.06 6117819 6.2 S hs gi[

328304 CH.07_hs 5.4 gi[6004478 328492 CH.07_hs 7 gi[5868455 328857 CH.07 5.2 hs g![6381927 329367 CH.X_hs 7.6 gi[5868842 2~ 329373 CH.X_hs 12 gi[6682537 329655 CH.14_p2 4 gi[6448516 329899 CH.15_p2 4 gi[6563505 329960 CH,16_p2 7.6 g![5091594 330084 CH.19_p2 4 gi[6015302 2$ 330384 M23263 androgen 5.8 receptor (dihydrotestosterone re 330385 AA449749ESTs; 10.2 Highly s!milar to secreted apoptosi 330387 H14624 ESTs; 4.4 Highly similar to secreted apoptosi 330388 X03363 HER2 17.7 receptor tyrosine kinase (c-erbB-2;

330409 D50692 c-myc 10.1 Hs.78221 binding protein 30 330460 TIGR:HT544Hs.73946 Endothelial Cell Growth Factor 1 5.5 330486 M13755 interferon-stimulated 67 Hs.833 protein;15 kDa 330494 M29696 interleukin 6 Hs.237868 7 receptor 330500 M34423 galactosidase; 13.1 Hs.79222 beta 330510 M75099 FK506-binding 29 Hs.227729 prote!n (13kD) 35 330513 M81057 carboxypeptidase 38.5 Hs.180884 B1 (tissue) 330541 U22970 mu!tip(e 7.4 Hs.265827 UniGene matches 330542 U23942 cytochrome 15 Hs.226213 P450;

(lanosterol 14-alpha 330547 U32989 tryptophan 11 Hs.183671 2;3-dioxygenase 330551 U39840 hepatocyte 6.5 Hs,299867 nuclear factor3;
alpha 4~ 330562 U49082 transporter 7.7 Hs.76460 prote!n 330573 U62800 cystatin 4 Hs.83393 ElM

330673 D57823 Sec23 10.5 Hs.3214D3 (S, cerevisiae) homolog A

330711 AA164687mannosyl 24.3 Hs.177576 (alpha-1;3-)-glycoprotein beta-1 330814 AA015730ESTs; 44.1 Hs.265398 Weakly similar to transformation-r 4$ 330850 AA075298ESTs 4.4 Hs.322710 330874 AA127474ESTs; 8.1 Hs,191157 Weakly similar to !!!!
ALU
SUBFA

330884 AA133457ESTs 5.2 Hs.102548 330912 AA195936general 5 Hs.82719 transcription factor IIA;1 (37kD
a 330924 AA232136Homo 9.1 Hs.159737 Sapiens mRNA;
cDNA
DKFZp434 330997 H55762 ESTs 7.6 Hs,9302 331014 H98597 ESTs 13.5 Hs.30340 331024 N32919 ESTs 9.1 Hs,27931 331046 N66563 ESTs 10.5 Hs.191358 331135 861398 ESTs 7.4 Hs.4197 55 331145 872427 ESTs; 41.9 Hs.129873 Weakly similar to CYTOCHROME

331148 873816 ESTs 4.7 Hs.17385 331222 T98531 ESTs 4.1 Hs.173904 331230 W69807 hypothetical 4.9 Hs.16537 protein;
sim!lar to (U06944) 331306 AA252079dachshund 15.1 Hs.63931 (Drosophila) homolog 331327 AA281076ESTs 4.8 Hs.109221 331337 AA287662ESTs 7.6 Hs.50495 331341 AA303125ESTs; 13 Hs.23240 Weakly sim!lar to !!!!
ALU
SUBFA

331344 AA357927ESTs 12.4 Hs.126550 331362 AA417956ESTs 6.5 Hs.40782 65 331363 AA421562anterior 28.2 Hs,91011 gradient (Xenepus laevis) homo 331376 AA443802ESTs; 15.1 Hs.41007 Weakly similar to cDNA
EST
yk47 331384 AA456001ESTs 7.9 Hs.93847 DEMANDE OU BREVET VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVET COMPREND
PLUS D'UN TOME.

NOTE : Pour les tomes additionels, veuillez contacter le Bureau canadien des brevets JUMBO APPLICATIONS/PATENTS
THIS SECTION OF THE APPLICATION/PATENT CONTAINS MORE THAN ONE
VOLUME

NOTE: For additional volumes, please contact the Canadian Patent Office NOM DU FICHIER / FILE NAME
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Claims (24)

WHAT IS CLAIMED IS:

1. A method of detecting a breast cancer-associated transcript in a cell from a patient, the method comprising contacting a biological sample from the patient with a polynucleotide that selectively hybridizes to a sequence at least 80%
identical to a sequence as shown in Tables 1-25.

2. The method of claim 1, wherein the biological sample comprises isolated nucleic acids.

3. The method of claim 2, wherein the nucleic acids are mRNA.

4. The method of claim 2, further comprising the step of amplifying nucleic acids before the step of contacting the biological sample with the polynucleotide.

5. The method of claim 1, wherein the polynucleotide comprises a sequence as shown in Tables 1-25.

6. The method of claim 1, wherein the polynucleotide is immobilized on a solid surface.

7. The method of claim 1, wherein the patient is undergoing a therapeutic regimen to treat breast cancer.

8. The method of claim 1, wherein the patient is suspected of having breast cancer.

9. An isolated nucleic acid molecule consisting of a polynucleotide sequence as shown in Tables 1-25.

10. The nucleic acid molecule of claim 9, which is labeled.

11. An expression vector comprising the nucleic acid of claim 9.

12. A host cell comprising the expression vector of claim 11.

13. An isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1-25.

14. An antibody that specifically binds a polypeptide of claim 13.

15. The antibody of claim 14, further conjugated to an effector component.

16. The antibody of claim 15, wherein the effector component is a fluorescent label.

17. The antibody of claim 15, wherein the effector component is a radioisotope or a cytotoxic chemical.

18. The antibody of claim 15, which is an antibody fragment.

19. The antibody of claim 15, which is a humanized antibody

20. A method of detecting a breast cancer cell in a biological sample from a patient, the method comprising contacting the biological sample with an antibody of claim 14.

21. The method of claim 20, wherein the antibody is further conjugated to an effector component.

22. The method of claim 21, wherein the effector component is a fluorescent label.

23. A method for identifying a compound that modulates a breast cancer-associated polypeptide, the method comprising the steps of:
(i) contacting the compound with a breast cancer-associated polypeptide, the polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1-25; and (ii) determining the functional effect of the compound upon the polypeptide.

24. A drug screening assay comprising the steps of (i) administering a test compound to a mammal having breast cancer or a cell isolated therefrom;

(ii) comparing the level of gene expression of a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1-25 in a treated cell or mammal with the level of gene expression of the polynucleotide in a control cell or mammal, wherein a test compound that modulates the level of expression of the polynucleotide is a candidate for the treatment of breast cancer.