CA2425569A1 - Methods of diagnosis of prostate cancer, compositions and methods of screening for modulators of prostate cancer - Google Patents

Abstract

Described herein are genes whose expression are up-regulated or down-regulat ed in prostate cancer. Also described are such genes whose expression is furthe r up-regulated or down-regulated in drug-resistant prostate cancer cells. Related methods and compositions that can be used for diagnosis and treatmen t of prostate cancer are disclosed. Also described herein are methods that can be used to identify modulators of prostate cancer.

Description

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METHODS OF DIAGNOSIS OF PROSTATE CANCER, COMPOSITIONS AND METHODS OF SCREENING FOR
MODULATORS OF PROSTATE CANCER
CROSS-REFERENCES TO RELATED APPLICATIONS
This application claims priority from the following applications: USSN
091687,576 filed October 13, 2000, USSN 60/276,791 filed March 16, 2001; USSN
60/288,589, filed May 4, 2001; USSN 09/733,742, filed December 8, 2000; USSN
09/733,288, filed December 8, 2000; USSN 09/847,046, filed April 30, 2001;
USSN
60/276,888, filed March 16, 2001; USSN 60/286,214, filed April 24, 2001; USSN
60/281,922, filed April 6, 2001; USSN 60/263,957, filed January 24, 2001, 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 prostate cancer; and to the use of such expression profiles and compositions in the diagnosis, prognosis and therapy of prostate cancer. The invention further relates to methods for identifying and using agents and/or targets that inhibit prostate cancer.
BACKGROUND OF THE INVENTION
Prostate cancer is the most commonly diagnosed internal malignancy and second most common cause of cancer death in men in the U.S., resulting in approximately 40,000 deaths each year ( Landis et al., CA Cancer J. Clin. 48:6-29 (1998);
Greenlee et al., CA Cancer J. Clin. 50(1):7-13 (2000)), and incidence of prostate cancer has been increasing rapidly over the past 20 years in many parts of the world (Nalcata et al., Int. J. Urol.
7(7):254-257 (2000); Majeed et al., BJU Int. 85(9):1058-1062 (2000)). It develops as the result of a pathologic transformation of normal prostate cells. In tumorigenesis, the cancer cell undergoes initiation, proliferation and loss of contact inhibition, culminating in invasion of surrounding tissue and, ultimately, metastasis.
Deaths from prostate cancer are a result of metastasis of a prostate tumor.
Therefore, early detection of the development of prostate cancer is critical in reducing mortality from this disease. Measuring levels of prostate-specific antigen (PSA) has become a very common method for early detection and screening, and may have contributed to the slight 'decrease in the mortality rate from prostate cancer in recent years (Nowroozi et al., Cancer Control 5(6):522-531 (1998)). However, many cases are not diagnosed until the disease has progressed to an advanced stage.
Treatments such as surgery (prostatectomy) , radiation therapy, and cryotherapy are potentially curative when the cancer remains localized to the prostate.
Therefore, early detection of prostate cancer is important for a positive prognosis for treatment. Systemic treatment for metastatic prostate cancer is limited to hormone therapy and chemotherapy. Chemical or surgical castration has been the primary treatment for symptomatic metastatic prostate cancer for over 50 years. This testicular androgen deprivation therapy usually results in stabilization or regression of the disease (in 80% of patients), but progression of metastatic prostate cancer eventually develops (Panvichian et al., Cancer Control 3(6):493-500 (1996)). Metastatic disease is currently considered incurable, and the primary goals of treatment are to prolong survival and improve quality of life (Rago, Cancer Control 5(6):SI3-52I (1998)).
Thus, methods that can be used for diagnosis and prognosis of prostate cancer and effective treatment of prostate cancer, and including particularly metastatic prostate cancer, would be desirable. Accordingly, provided herein are methods that can be used in diagnosis and prognosis of prostate cancer. Further provided are methods that can be used to screen candidate bioactive agents for the ability to modulate, e.g., treat, prostate cancer.
Additionally, provided herein are molecular targets and compositions for therapeutic intervention in prostate cancer and other cancers.

SUMMARY OF THE INVENTION
The present invention therefore provides nucleotide sequences of genes that are up- and down-regulated in prostate cancer cells. Such genes are useful for diagnostic purposes, and also as targets for screening for therapeutic compounds that modulate prostate 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 prostate 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 1-16.
In one embodiment, the present invention provides a method of determining the level of a prostate cancer associated transcript in a cell from a patient.
In one embodiment, the present invention provides a method of detecting a prostate 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 1-16.
In one embodiment, the polynucleotide selectively hybridizes to a sequence at least 95% identical to a sequence as shown in Tables 1-16. In another embodiment, the polynucleotide comprises a sequence as shown in Tables 1-16.
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 prostate cancer. In another embodiment, the patient is suspected of having metastatic prostate cancer.
In one embodiment, the patient is a human.
In one embodiment, the patient is suspected of having a taxol-resistant cancer.
In one embodiment, the prostate 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 prostate 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 prostate cancer-associated transcript in the biological sample by contacting the biological sample with a polynucleotide that selectively hybridizes to a sequence at least ~0% identical to a sequence as shown in Tables 1-16, thereby monitoring the efficacy of the therapy. In a further embodiment, the patient has metastatic prostate cancer. In a further embodiment, the patient has a drug resistant (e.g., taxol resistant) form of prostate cancer.
In one embodiment, the method further comprises the step of: (iii) comparing the level of the prostate cancer-associated transcript to a level of the prostate 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 prostate 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 1-16.
In one aspect, the present invention provides an isolated nucleic acid molecule consisting of a polynucleotide sequence as shown in Tables 1-16.
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 1-16.
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 1-16.

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 prostate 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 prostate 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 1-16.
In another aspect, the present invention provides a method for identifying a compound that modulates a prostate cancer-associated polypeptide, the method comprising the steps of: (i) contacting the compound with a prostate 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 1-16; 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 prostate cancer-associated cell to treat prostate 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 prostate 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 1-16 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 prostate cancer.
In one embodiment, the control is a mammal with prostate 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 1-16 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 prostate 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 prostate 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 prostate cancer. In one embodiment, a gene is selected from Tables 1-16. 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 prostate cancer drug comprising administering the drug to a transgenic animal expressing or over-expressing the prostate cancer modulatory protein, or an animal lacking the prostate 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 1-16, 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 prostate cancer is provided. The method comprises determining the expression of a gene of Tables 1-16, 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 prostate cancer.
In a further embodiment, the biochip also includes a polynucleotide sequence of a gene that is not up- and down-regulated in prostate cancer.
In one embodiment a method for screening for a bioactive agent capable of interfering with the binding of a prostate cancer modulating protein (prostate cancer modulatory protein) or a fragment thereof and an antibody which binds to said prostate cancer modulatory protein or fragment thereof. In a preferred embodiment, the method comprises combining a prostate cancer modulatory protein or fragment thereof, a candidate bioactive agent and an antibody which binds to said prostate cancer modulatory protein or fragment thereof. The method further includes determining the binding of said prostate 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 prostate 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 prostate cancer modulating protein, or a fragment thereof. In another embodiment, the protein is encoded by a nucleic acid selected from those of Tables 1-16.
Further provided herein are compositions capable of eliciting an immune response in an individual. In one embodiment, a composition provided herein comprises a prostate cancer modulating protein, preferably encoded by a nucleic acid of Tables 1-16, or a fragment thereof, and a pharmaceutically acceptable carrier. In another embodiment, said composition comprises a nucleic acid comprising a sequence encoding a prostate cancer modulating protein, preferably selected from the nucleic acids of Tables 1-16, and a pharmaceutically acceptable carrier.
Also provided are methods of neutralizing the effect of a prostate 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 1-16.
In another aspect of the invention, a method of treating an individual for prostate cancer is provided. In one embodiment, the method comprises administering to said individual an inhibitor of a prostate cancer modulating protein. In another embodiment, the method comprises administering to a patient having prostate cancer an antibody to a prostate 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 prostate cancer (PC), including metastatic prostate cancer, as well as methods for screening for compositions which modulate prostate cancer. Also provided are methods for treating prostate cancer.
In addition to the other nucleic acid and peptide sequences, the present invention also relates to the identification of PAA2 as a gene that is highly over expressed in prostate cancer patient tissues. PAA2 sequence is identical to the zinc transporter ZNT4.
Results presented herein demonstrate that PAA2/ZNT4 is highly expressed in prostate cancer cells. The prostate gland is unique in that it has the highest capacity of any organ in the body to accumulate zinc. Zinc uptake is regulated by prolactin and testosterone, which induce the expression of a member of the ZIP family of zinc transporters (Costello et al., 1999, J, Biol.
Chem. 274:17499-17504). Zinc accumulation in the prostate functions to inhibit citrate oxidation, which results in a decrease in cellular ATP production (Costello and Franklin, 1998, Prostate 35:285-296). Cancer cells are more sensitive to decreased ATP
production and have evolved to prevent zinc accumulation. Without wishing to be bound by theory, the up-regulation of ZNT4 in prostate cancer cells may result in protection of the cells from high zinc levels by its ability to pump accumulated zinc out of the cells.
The present invention also relates to nucleic acid sequencess encoding PBH1.
PBH1 is related to human TRPC7 (transient receptor potential-related channels, NP_003298), a putative calcium channel highly expressed in brain (Nagamine et al., Genomics 54:124-131 (1998)). Trp is related to melastatin, a gene down-regulated in metastatic melanomas (Duncan et al., Cancer Res. 58:1515-1520 (1998)), and MTRl, a gene locallized to within the Beckwith-Wiedemann syndrome/Wilm's tumor susceptability region (Prawitt et al., Hum.
Mol. Genet. 9:203-216 (2000)). Without wishing to be bound by theory, it is believed that PBHl functions as a calcium channel.
As a calcium channel, PBHl is an ideal target for a small molecule therapeutic, or a therapeutic antibody that disrupts channel function. CD20, the target of Rituximab in non-Hodgekin's lymphoma (Maloney et al., Blood 90:2188-2195 (1997); Leget and Czuczman, Curr. Opin. Oncol. 10:548-551 (1998)), is a plasma membrane calcium channel expressed in B cells (Tedder and Engel, Immunol. Today 15:450-454 (1994)).
Similarly, a small molecule, or antibody that inhibits or alters a calcium signal mediated by PBHl, will result in the death of prostate cancer cells.
PBHl, and other genes of the invention, are also be useful as targets for cytotoxic T-lymphocytes. Genes that are tumor specific, or that are expressed in immune-privileged organs, are currently being used as potential vaccine targets (Van den Eynde and Baon, Int. J. Clin. Lab. Res. 27:81-86 (1997)). The expression pattern of PBHl indicates that it is an ideal target for cytotoxic T-lymphocytes. Thus, therapies that utilize PBHl-specific cytotoxic T-lymphocytes to induce prostate cancer cell death are also provided by this invention. See, e.g., U.S. Patent No. 6,051,227 and WO 00/32231, the disclosures of which are herein incorporated by reference.

The present invention is also related to the identification of PAA3 as a gene that is important in the modulation of prostate cancer and or breast cancer.
Tables 1-16 provide unigene cluster identification numbers, exemplar accession numbers, or genomic nucleotide position numbers for the nucleotide sequence of genes that exhibit increased or decreased expression in prostate cancer samples.
Definitions The term "prostate cancer protein" or "prostate cancer polynucleotide" or "prostate cancer-associated transcript" refers to nucleic acid and polypeptide polymorphic 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 unigene cluster of Tables 1-16; (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 unigene cluster of Tables 1-16, and conservatively modified variants thereof; (3) specifically hybridize under stringent hybridization conditions to a nucleic acid sequence, or the complement thereof of Tables 1-16 arid 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 unigene cluster of Tables 1-I6. 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 "prostate cancer polypeptide" and a "prostate cancer polynucleotide,"
include both naturally occurring or recombinant forms.
A "full length" prostate cancer protein or nucleic acid refers to a prostate 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 prostate cancer polynucleotide or polypeptide sequences. For example, a full length prostate cancer nucleic acid will typically comprise all of the exons that encode for the full length, naturally ocurnng protein. 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 prostate 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 occurring, 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, W)7, or by manual alignment and visual inspection (see, e.g., Current Protocols in 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.nlm.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., supra).
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 BLOSUM62 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., Karlin & Altschul, PPoc. 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 expression vector and supports the replication or expression of the expression vector. Host cells may be cultured cells, explants, cells in 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 occurnng and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function similarly to the naturally occurring amino acids. Naturally occurring 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 occurnng 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-ICTB
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); 5) 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 (3rd 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, Carbolzydrate Modifications in Antiserzse 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 Jenkins et al., Chem. Soc. Rev. (1995) pp 169-176). Several nucleic acid analogs are described in Rawls, 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 (T~ for mismatched versus perfectly matched basepairs. DNA and RNA typically exhibit a 2-4°C drop in T~ 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 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 radioisotope may be, for example, 3H, 14C, 32P, 35S, or 125I. In some cases, particularly using antibodies against the proteins of the invention, the radioisotopes are used as toxic moieties, as described below.
The labels may be incorporated into the prostate 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 Cytochem., 30:407 (1982). The lifetime of radiolabeled peptides or radiolabeled antibody compositions may extended by the addition of substances that stablize the radiolabeled peptide or antibody and protect it from degradation. Any substance or combination of substances that stablize the radiolabeled peptide or antibody may be used including those substances disclosed in US Patent No. 5,961,955.
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 in 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 in 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 linked 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 that is determinative of the presence of the nucleotide sequence, in a heterogeneous population of nucleic acids and other biologics (e.g., total cellular or library DNA or RNA). Similarly, the phrase "specifically (or selectively) binds" to an antibody or "specifically (or selectively) immunoreactive with," when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein, in a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay or nucleic acid hybridization conditions, the specified antibodies or nucleic acid probes bind to a particular protein nucleotide sequences at least two times the background and more typically more than 10 to 100 times background.
Specific binding to an antibody under such conditions requires an antibody that is selected for its specificity for a particular protein. For example, polyclonal antibodies raised to a particular protein, polymorphic variants, alleles, orthologs, and conservatively modified variants, or splice variants, or portions thereof, can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with the desired prostact cancer protein and not with other proteins. This selection may be achieved by subtracting out antibodies that cross-react with other molecules. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow & Lane, Antibodies, A
Laboratory Manual (1988) for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity).
The phrase "stringent hybridization conditions" refers to conditions under which a probe will hybridize to its target 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 f Tijssen, Techniques in Biocherrlistry and 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 8.3 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, 5x SSC, and 1%
SDS, incubating at 42°C, or, 5x 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 48°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 sec - 2 min., an annealing phase lasting 30 sec. - 2 min., and an extension phase of about 72°C for 1 - 2 min. Protocols and guidelines for low and high stringency amplification 25 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 30 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%
formamide, 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 prostate cancer protein includes the determination of a parameter that is indirectly or directly under the influence of the prostate cancer protein or nucleic acid, e.g., a functional, physical, or chemical effect, such as the ability to decrease prostate 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 prostate 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 prostate 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 prostate 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 prostate cancer can also be performed using prostate cancer assays known to those of skill in the art such as an in vitro 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 in vivo; mRNA and protein expression in cells undergoing metastasis, and other characteristics of prostate 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 prostate 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 prostate cancer polynucleotide and polypeptide sequences are used to refer to activating, inhibitory, or modulating molecules IO or compounds identified using in vitro and in vivo assays of prostate 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 prostate 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 prostate cancer protein activity. Inhibitors, activators, or modulators also include genetically modified versions of prostate 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 prostate 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 prostate cancer can also be identified by incubating prostate cancer cells with the test compound and determining increases or decreases in the expression of 1 or more prostate cancer proteins, e.g., 1; 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50 or more prostate cancer proteins, such as prostate cancer proteins encoded by the sequences set out in Tables 1-16.
Samples or assays comprising prostate 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 prostate 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 ofAnimal 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, Fundamentallmmufzology.

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)'2, 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)'2 dimer into an Fab' monomer. The Fab' monomer is essentially Fab with part of the hinge region (see Fundamental 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., Immunology Today 4:72 (1983); Cole et al., pp.
77-96 in Monoclonal Antibodies and Cancer Therapy (i985); Coligan, Current Protocols in Immunology (1991); Harlow ~ Lane, Antibodies, A Laboratory Manual (1988); and Goding, Monoclonal 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 prostate 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 prostate or other tissue) may be distinguished from cancerous or metastatic cancerous tissue of the prostate, or prostate cancer tissue or metastatic prostate cancerous tissue can be compared with tissue samples of prostate and other tissues from surviving cancer patients. By comparing expression profiles of tissue in known different prostate 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 prostate cancer versus non-prostate 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 prostate 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 pxofiles. Metastatic tissue can also be analyzed to determine the stage of prostate 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 prostate cancer expression profile. This may be done by making biochips comprising sets of the important prostate 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 prostate cancer proteins can be evaluated for diagnostic purposes or to screen candidate agents. In addition, the prostate cancer nucleic acid sequences can be administered for gene therapy purposes, including the administration of antisense nucleic acids, or the prostate cancer proteins (including antibodies and other modulators thereof) administered as therapeutic drugs.
Thus the present invention provides nucleic acid and protein sequences that are differentially expressed in prostate cancer, herein termed "prostate cancer sequences." As outlined below, prostate cancer sequences include those that are up-regulated (i.e., expressed at a higher level) in prostate cancer, as well as those that are down-regulated (i.e., expressed at a lower level). In a preferred embodiment, the prostate cancer sequences are from humans;
however, as will be appreciated by those in the art, prostate cancer sequences from other organisms may be useful in animal models of disease and drug evaluation; thus, other prostate 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.). Prostate cancer sequences from other organisms may be obtained using the techniques outlined below.
Prostate 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, prostate cancer nucleic acid sequences are useful in a variety of applications, including diagnostic applications, which will detect naturally occnrnng nucleic acids, as well as screening applications; e.g., biochips comprising nucleic acid probes or PCR
microtiter plates with selected probes to the prostate cancer sequences can be generated.
A prostate cancer sequence can be initially identified by substantial nucleic acid and/or amino acid sequence homology to the prostate 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 prostate cancer-associated sequences, the prostate 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 prostate cancer samples with metastatic cancer samples from other cancers, such as lung, breast, gastrointestinal cancers, ovarian, etc. Samples of different stages of prostate 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 prostate, 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 prostate 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, prostate cancer sequences are those that are up-regulated in prostate cancer; that is, the expression of these genes is higher in the prostate 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 (1990 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).
In another preferred embodiment, prostate cancer sequences are those that are down-regulated in prostate cancer; that is, the expression of these genes is Lower in prostate cancer tissue as compared to non-cancerous tissue (see, e.g., Tables 8, 12 and 14). "Down-regulation" as used herein often means at least about a 1.5-fold change more preferrably a two-fold change, preferably at least about a three fold change, with at least about five-fold or higher being most preferred.
Informatics The ability to identify genes that are over or under expressed in prostate 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 prostate cancer.
Or as another example, subcellular toxicological information can be generated to better direct drug structure and activity correlation (see Anderson, Pharmaceutical 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 IJ.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 prostate cancer, i.e., the identification of prostate 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); Biological Sequence Analysis:
Probabilistic Models of Proteins and Nucleic Acids (Durbin et al., eds., 1999);
Bioiraformatics: A Practical Guide to the Analysis of Genes and Proteins (Baxevanis &
Oeullette eds., 1998)); Rashidi & Buehler, Bioinformatics: Basic Applications in Biological Science and Medicine (1999); Introduction to Computational Molecular Biology (Setubal et al., eds 1997); Bioinformatics: Methods and Protocols (Misener & Krawetz, eds, 2000);
Bioinformatics: Sequence, Structure, and Databanks: A Practical Approach (Higgins &
Taylor, eds., 2000); Brown, Bioinfor7natics: A Biologist's Guide to Biocomputing and the Internet (2001); Han & Kamber, Data Mining: Concepts and Techniques (2000);
and IO Waterman, Introduction to Computational 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 prostate 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 lOBaseT), 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., DRAM, 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 prostate cancer-associated proteins Prostate cancer proteins of the present invention may be classified as secreted proteins, transmembrane proteins or intracellular proteins. In one embodiment, the prostate 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. Sorne 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 Karolinska 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., Nuc. Acids Res.
26:320-322-(1998)).
In another embodiment, the prostate 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 molecule 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 I5 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 jpn.
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 extracellular domains of transmembrane proteins are diverse; however, conserved motifs are found repeatedly among various 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.
Prostate 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 in 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 prostate 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. Prostate 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 prostate cancer nucleic acids As described above, prostate cancer sequence is initially identified by substantial nucleic acid and/or amino acid sequence homology or linkage to the prostate 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. Typically, linked sequences on a mRNA are found on the same molecule.
The prostate cancer nucleic acid sequences of the invention, e.g., the sequences in Tables 1-16, 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 prostate 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., supra. 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/LTniGenen.
Once the prostate cancer nucleic acid is identified, it can be cloned and, if necessary, its constituent parts recombined to form the entire prostate 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 prostate cancer nucleic acid can be further-used as a probe to identify and isolate other prostate cancer nucleic acids, e.g., extended coding regions. It can also be used as a "precursor" nucleic acid to make modified or variant prostate cancer nucleic acids and proteins.
The prostate cancer nucleic acids of the present invention are used in several ways. In a first embodiment, nucleic acid probes to the prostate 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 prostate cancer nucleic acids that include coding regions of prostate cancer proteins can be put into expression vectors for the expression of prostate cancer proteins, again for screening purposes or for administration to a patient.
In a preferred embodiment, nucleic acid probes to prostate 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 prostate 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, washing, 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 S 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, IJ.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 are 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 prostate cancer-associated sequences. These assays are typically performed in conjunction with reverse transcription. In such assays, a prostate 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 prostate 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 arid 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 polymerise, 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-Elmer, 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., Proc. Natl. Acid. Sci. USA 86:1173 (1989)), self sustained sequence replication (Guatelli et al., Proc. Nat. Acid. Sci. USA 87:1874 (1990)), dot PCR, and linker adapter PCR, etc.
Expression of prostate cancer proteins from nucleic acids In a preferred embodiment, prostate cancer nucleic acids, e.g., encoding prostate cancer proteins are used to make a variety of expression vectors to express prostate 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 & Fioeffler, 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 prostate 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 prostate 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 44.

appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art (e.g., Fernandez & Hoeffler, supra).
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 prostate cancer proteins of the present invention are produced by culturing a host cell transformed with an expression vector containing nucleic acid encoding a prostate cancer protein, under the appropriate conditions to induce or cause expression of the prostate cancer protein. Conditions appropriate for prostate 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 Saecharomyces cerevisiae and other yeasts, E. coli, Bacillus subtilis, Sf9 cells, CI29 cells, 293 cells, Neurospora, BHK, CHO, COS, HeLa cells, IiLTVEC (human umbilical vein endothelial cells), THPl cells (a macrophage cell line) and various other human cells and cell lines.
In a preferred embodiment, the prostate 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 PCT/US97/01019 and PCT/US97/01048, 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, prostate 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 prostate 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 lividans, among others (e.g., Fernandez & Hoeffler, supra).
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, prostate 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, prostate cancer protein is produced in yeast cells.
Yeast expression systems are well known in the art, and include expression vectors for Saccharomyces cerevisiae, Candida albica~zs and C. maltosa, Hansenula polymorpha, Kluyveromyces fragilis and K. lactis, Pichia guillerimondii and P. pastoris, Schizosaccharomyces pombe, and Yarrowia lipolytica.
The prostate 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 prostate cancer protein may be fused to a Garner protein to form an immunogen. Alternatively, the prostate cancer protein may be made as a fusion protein to increase expression, or for other reasons. For example, when the prostate cancer protein is a prostate cancer peptide, the nucleic acid encoding the peptide may be linked to other nucleic acid for expression purposes.
In a preferred embodiment, the prostate cancer protein is purified or isolated after expression. Prostate 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 prostate cancer protein may be purified using a standard anti-prostate cancer protein antibody column.
Ultrafiltration and diafiltration techniques, in conjunction with protein concentration, are also useful. For general guidance in suitable purification techniques, see Scopes, Protein Purification (1982). The degree of purification necessary will vary depending on the use of the prostate cancer protein. In some instances no purification will be necessary.
Once expressed and purified if necessary, the prostate 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 prostate cancer proteins In one embodiment, the prostate cancer proteins are derivative or variant prostate cancer proteins as compared to the wild-type sequence. That is, as outlined more fully below, the derivative prostate 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 prostate cancer peptide.
Also included within one embodiment of prostate 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 prostate 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 prostate 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 prostate 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 prostate 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 prostate 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 arrive 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 prostate 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 prostate cancer proteins as needed. Alternatively, the variant may be designed such that the biological activity of the prostate 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 prostate cancer polypeptides are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a prostate 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 prostate cancer polypeptide. Derivatization with bifunctional agents is useful, for instance, for crosslinking prostate cancer polypeptides to a water-insoluble support matrix or surface for use in the method for purifying anti-prostate cancer polypeptide antibodies or screening assays, as is more fully described below. Commonly used crosslinking agents include, e.g., 1,1-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 Beryl, threonyl or tyrosyl residues, methylation of the amino groups of the lysine, arginine, and histidine side chains (Creighton, Proteins: Structure 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 prostate 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 prostate cancer polypeptide, and/or adding one or more glycosylation sites that are not present in the native sequence prostate cancer polypeptide. Glycosylation patterns can be altered in many ways. For example the use of different cell types to express prostate cancer-associated sequences can result in different glycosylation patterns.
Addition of glycosylation sites to prostate 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 prostate cancer polypeptide (for O-linked glycosylation sites). The prostate cancer amino acid sequence may optionally be altered through changes at the DNA
level, particularly by mutating the DNA encoding the prostate cancer polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids.
Another means of increasing the number of carbohydrate moieties on the prostate 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 prostate 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., Anal.
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.
Enzymol., 138:350 (1987).
Another type of covalent modification of prostate cancer comprises linking the prostate 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.
Prostate cancer polypeptides of the present invention may also be modified in a way to form chimeric molecules comprising a prostate cancer polypeptide fused to another, heterologous polypeptide or amino acid sequence. In one embodiment, such a chimeric molecule comprises a fusion of a prostate 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 prostate cancer polypeptide. The presence of such epitope-tagged forms of a prostate cancer polypeptide can be defected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the prostate 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 prostate 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 (Hope et al., BioTeclanology 6:1204-1210 (1988)); the KT3 epitope peptide (Martin et al., Scierace 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. USA 87:6393-6397 (1990)).
Also included are other prostate cancer proteins of the prostate cancer family, and prostate 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 prostate 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 prostate 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 prostate cancer proteins In a preferred embodiment, when the prostate cancer protein is to be used to generate antibodies, e.g., for immunotherapy or immunodiagnosis, the prostate 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 prostate 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 andlor 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 immunization 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 1-16 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 (Goding, Monoclonal Antibodies: Principles and 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 1-16 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 prostate cancer protein are capable of reducing or eliminating a biological function of a prostate cancer protein, as is described below. That is, the addition of anti-prostate cancer protein antibodies (either polyclonal or preferably monoclonal) to prostate cancer tissue (or cells containing prostate cancer) may reduce or eliminate the prostate cancer. Generally, at least a 25%
decrease in IO 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 prostate eancer 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., Nature 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., Nature 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 and Cancer Therapy, 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-I3 (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 prostate cancer with an antibody raised against prostate cancer proteins. As used herein,~mmunotherapy 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 expressing the antigen and under conditions for expression of the antigen, leading to an immune response.
In a preferred embodiment the prostate 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 prostate cancer protein.
In another preferred embodiment, the prostate 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 prostate 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 prostate 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 prostate cancer protein. The antibody is also an antagonist of the prostate cancer protein.
Further, the antibody prevents activation of the transmembrane prostate cancer protein. In one aspect, when the antibody prevents the binding of other molecules to the prostate 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-(3, IL-1, INF-y and IL,-2, or chemotherapeutic agents including SFLT, 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, prostate cancer is treated by administering to a patient antibodies directed against the transmembrane prostate 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 prostate cancer protein. In another aspect the therapeutic moiety modulates the activity of molecules associated with or in close proximity to the prostate cancer protein. The therapeutic moiety may inhibit enzymatic activity such as protease or collagenase or protein kinase activity associated with prostate cancer.
In a preferred embodiment, the therapeutic moiety can also be a cytotoxic agent. In this method, targeting the cytotoxic agent to prostate cancer tissue or cells, results in a reduction in the number of afflicted cells, thereby reducing symptoms associated with prostate 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 prostate 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 prostate cancer proteins not only serves to increase the local concentration of therapeutic moiety in the prostate cancer afflicted area, but also serves to reduce deleterious side effects that may be associated with the therapeutic moiety.
In another preferred embodiment, the prostate 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 prostate 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 prostate cancer antibodies of the invention specifically bind to prostate 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 p,M, 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 prostate cancer sequence for diagnostic and therapeutic applications In one aspect, the RNA expression levels of genes are determined for different cellular states in the prostate cancer phenotype. Expression levels of genes in normal tissue (i.e., not undergoing prostate cancer) and in prostate cancer tissue (and in some cases, for varying seventies of prostate 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 prostate 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 Biotechnology 14:1675-1680 (1996), hereby expressly incorporated by reference. Other techniques include, but are not limited to, quantitative reverse transcnptase 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 prostate cancer protein and standard immunoassays (ELISAs, etc.) or other techniques, including mass spectroscopy assays, 2D gel electrophoresis assays, etc. Proteins corresponding to prostate cancer genes, i.e., those identified as being important in a prostate cancer phenotype, can be evaluated in a prostate 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 prostate cancer nucleic acid probes are attached to biochips as outlined herein for the detection and quantification of prostate cancer sequences in 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 prostate cancer protein are detected. Although DNA or RNA encoding the prostate cancer protein may be detected, of particular interest are methods wherein an mRNA encoding a prostate 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 prostate 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 prostate cancer proteins, antibodies, nucleic acids, modified proteins and cells containing prostate 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, prostate cancer proteins, including intracellular, transmembrane or secreted proteins, find use as markers of prostate cancer.
Detection of these proteins in putative prostate cancer tissue allows for detection or diagnosis of prostate cancer. In one embodiment, antibodies are used to detect prostate 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 prostate cancer protein is detected, e.g., by immunoblotting with antibodies raised against the prostate cancer protein.
Methods of immunoblotting are well known to those of ordinary skill in the art.
In another preferred method, antibodies to the prostate cancer protein find use in in situ imaging techniques, e.g., in histology (e.g., Methods in Cell Biology: Antibodies in Cell Biology, volume 37 (Asai, ed. 1993)). In this method cells are contacted with from one to many antibodies to the prostate 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 prostate 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 prostate 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 prostate 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 prostate cancer proteins.
Antibodies can be used to detect a prostate 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 prostate cancer protein.
In a preferred embodiment, in situ hybridization of labeled prostate cancer nucleic acid probes to tissue arrays is done. For example, arrays of tissue samples, including prostate cancer tissue and/or normal tissue, are made. In situ hybridization (see, e.g., Ausubel, supra) 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 prostate cancer proteins, antibodies, nucleic acids, modified proteins and cells containing prostate cancer sequences are used in prognosis assays. As above, gene expression profiles can be generated that correlate to prostate 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, prostate cancer probes may be attached to biochips for the detection and quantification of prostate 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 prostate cancer proteins, antibodies, nucleic acids, modified proteins and cells containing prostate 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, Genome Res 6:986-94, 1996).
In a preferred embodiment, the prostate cancer proteins, antibodies, nucleic acids, modified proteins and cells containing the native or modified prostate cancer proteins are used in screening assays. That is, the present invention provides novel methods for screening for compositions which modulate the prostate cancer phenotype or an identified physiological function of a prostate 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 prostate cancer, test compounds can be screened for the ability to modulate gene expression or for binding to the prostate 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 prostate cancer, with changes of at least 10%, preferably 50%, more preferably 100-300%, and in some embodiments 1000% or greater. Thus, if a gene exhibits a 4-fold increase in prostate cancer tissue compared to normal tissue, a decrease of about four-fold is often desired;
similarly, a 10-fold decrease in prostate 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 prostate 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 prostate cancer nucleic acid probes are attached to biochips as outlined herein for the detection and quantification of prostate 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 prostate cancer-associated sequences, e.g., a polynucleotide sequence set out in Tables 1-16. 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 prostate cancer, modulate prostate cancer proteins, bind to a prostate cancer protein, or interfere with the binding of a prostate 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 prostate cancer phenotype or the expression of a prostate 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 prostate cancer phenotype, e.g. to a normal tissue fingerprint. In another embodiment, a modulator induced a prostate cancer phenotype.
Generally, a plurality of assay mixtures are 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 500 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 prostate 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 prostate 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., Nature, 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 IO hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc. Nat. Acad.
Sci. USA
90:6909-6913 (1993)), vinylogous polypeptides (Hagihara et al., J. Amer. Chem.
Soc.
l I4:6568 (1992)), nonpeptidal peptidomimetics with a Beta-D-Glucose scaffolding (Hirschmann et al., J. Amer. Chem. Soc. 114:9217-9218 (1992)), analogous organic syntheses of small compound libraries (Chen et al., J. Amer. Chem. Soc. 116:2661 (1994)), oligocarbamates (Cho, et al., Science 261:1303 (1993)), andlor peptidyl phosphonates (Campbell et al., J. Org. Chem. 59:658 (1994)). See, generally, 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):309-3I4 (1996), and PCT/LTS96/10287), 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 I8, 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 prostate 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 ligand/antibody 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 samlsle 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 occurring 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 prostate cancer can also be nucleic acids, as defined below. As described above generally for proteins, nucleic acid modulating agents may be naturally occurring 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 certain embodiments, the activity of a prostate 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 prostate cancer protein mRNA, or a subsequence thereof.
Binding of the antisense polynucleotide to the mRNA reduces the translation and/or stability of the mRNA.
In the context of this invention, antisense polynucleotides can comprise naturally-occurring nucleotides, or synthetic species formed from naturally-occurring 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 prostate cancer protein mRNA. See, e.g., Isis Pharmaceuticals, Carlsbad, CA; Sequitor, Inc., Natick, MA.
Such antisense polynucleotides can readily be synthesized using recombinant 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 prostate cancer molecules. Antisense or sense oligonucleotides, according to the present invention, comprise a fragment 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 (Cafzcer Res. 48:2659 (1988 and van der Krol et al.
(BioTechniques 6:958 (1988)).
In addition to antisense polynucleotides, ribozymes can be used to target and inhibit transcription of prostate 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 ribozymes, RNase P, and axhead ribozymes (see, e.g., Castanotto et al., Adv.
in Pharmacology 25: 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. USA 90:6340-6344 (1993);
Yamada et al., Human Gene Therapy 1:39-45 (1994); Leavitt et al., Proc. Natl. Acad. Sci.
USA 92:699 703 (1995); Leavitt et al., Human Gene Therapy 5:1151-120 (1994); and Yamada et al., Virology 205: 121-126 (1994)).
Polynucleotide modulators of prostate 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 prostate 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 90/10448. 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.
As noted above, gene expression monitoring is conveniently used to test candidate modultors (e.g., protein, nucleic acid or small molecule). 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 chemiluminescent, 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, allealine 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 prostate 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 prostate cancer expression pattern leading to a normal expression pattern, or to modulate a single prostate 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 prostate cancer tissue reveals genes that are not expressed in normal tissue or prostate cancer tissue, but are expressed in agent treated tissue. These agent-specific sequences can be identified and used by methods described herein for prostate 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 prostate cancer tissue sample.
Thus, in one embodiment, a test compound is administered to a population of prostate cancer cells, that have an associated prostate 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., PGT 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., prostate cancer tissue may be screened for agents that modulate, e.g., induce or suppress the prostate cancer phenotype. A change in at least one gene, preferably many, of the expression profile indicates that the agent has an effect on prostate cancer activity. By defining such a signature for the prostate 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 "prostate cancer proteins"
or a "prostate cancer modulatory protein". The prostate cancer modulatory protein may be a fragment, or alternatively, be the full length protein to the fragment encoded by the nucleic acids of Tables 1-16. Preferably, the prostate cancer modulatory protein is a fragment. In a preferred embodiment, the prostate cancer amino acid sequence which is used to determine sequence identity or similarity is encoded by a nucleic acid of Tables 1-16.
In another embodiment, the sequences are naturally occurring allelic variants of a protein encoded by a nucleic acid of Tables 1-16. In another embodiment, the sequences are sequence variants as further described herein.
Preferably, the prostate 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 prostate cancer proteins are conjugated to an immunogenic agent as discussed herein. In one embodiment the prostate cancer protein is conjugated to BSA.
Measurements of prostate cancer polypeptide activity, or of prostate cancer or the prostate cancer phenotype can be performed using a variety of assays. For example, the effects of the test compounds upon the function of the prostate 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 prostate 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 tire assays of the invention, mammalian prostate 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 prostate 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 prostate cancer polypeptide levels are determined in 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 prostate 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 prostate 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 "prostate cancer proteins."
The prostate 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 prostate cancer proteins can be used in the assays.
Thus, in a preferred embodiment, the methods comprise combining a prostate cancer protein and a candidate compound, and determining the binding of the compound to the prostate cancer protein. Preferred embodiments utilize the human prostate 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 prostate cancer proteins may be used.
Generally, in a preferred embodiment of the methods herein, the prostate 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 carried 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 prostate 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 prostate 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 prostate 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 prostate 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 prostate 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 competitar is added first, followed by the test compound. Displacement of the competitor is an indication that the test compound is binding to the prostate cancer protein and thus is capable of binding to, and potentially modulating, the activity of the prostate 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 prostate 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 prostate cancer protein.
In a preferred embodiment, the methods comprise differential screening to identity agents that are capable of modulating the activity of the prostate cancer proteins. In this embodiment, the methods comprise combining a prostate cancer protein and a competitor in a first sample. A second sample comprises a test compound, a prostate 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 prostate 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 prostate cancer protein.
Alternatively, differential screening is used to identify drug candidates that bind to the native prostate cancer protein, but cannot bind to modified prostate cancer proteins. The structure of the prostate 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 prostate 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 prostate cancer protein. The methods comprise adding a test compound, as defined above, to a cell comprising prostate cancer proteins. Preferred cell types include almost any cell. The cells contain a recombinant nucleic acid that encodes a prostate 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 prostate cancer agents are identified.
Compounds with pharmacological activity are able to enhance or interfere with the activity of the prostate cancer protein. Once identified, similar structures are evaluated to identify critical structural feature of the compound.
In one embodiment, a method of inhibiting prostate cancer cell division is provided. The method comprises administration of a prostate cancer inhibitor.
In another embodiment, a method of inhibiting prostate cancer is provided. The method comprises administration of a prostate cancer inhibitor. In a further embodiment, methods of treating cells or individuals with prostate cancer are provided. The method comprises administration of a prostate cancer inhibitor.
In one embodiment, a prostate cancer inhibitor is an antibody as discussed above. In another embodiment, the prostate 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 suspension 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, 7~

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 prostate 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 of Animal Cells a Manual of Basic Technique (3'd ed., 1994), herein incorporated by reference. See also, the methods section of Garkavtsev et al. (I996), supra, herein incorporated by reference.
Contact inhibition and density limitation of 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), 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 prostate 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, supra. 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 speci, fic naarkers 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, tumor vascularization, and potential interference with tumor growth.
in Biological Responses in Cancer, 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. Chem. 251:5694-5702 (1976); Whur et al., Br. J.
Cancer 42:305-312 (1980); Gullino, Angiogenesis, tumor vascularization, and potential interference with tumor growth. in Biological Responses in 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 prostate 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 lasI and counting the radioactivity on the distal side of the filter or bottom of the dish. See, e.g., Freshney (1984), supra.
Tumor growth in vivo Effects of prostate 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 prostate cancer gene is disrupted or in which a prostate cancer gene is inserted. Knock-out transgenic mice can be made by insertion of a marker gene or other heterologous gene into the endogenous prostate cancer gene site in the mouse genome via homologous recombination. Such mice can also be made by substituting the endogenous prostate cancer gene with a mutated version of the prostate cancer gene, or by mutating the endogenous prostate 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., Manipulating the Mouse Embryo: A Laboratory Manual, Cold Spring Harbor Laboratory (1988) and Teratocarcinomas and Embryonic Stem Cells: A
Practical Approach, 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 Inst. 52:921 (1974)), a SC)D 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 prostate 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.
Methods of identifying variant prostate cancer-associated sequences Without being bound by theory, expression of various prostate cancer sequences is correlated with prostate cancer. Accordingly, disorders based on mutant or variant prostate cancer genes may be determined. In one embodiment, the invention provides methods for identifying cells containing variant prostate cancer genes, e.g., determining all or part of the sequence of at least one endogenous prostate 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 prostate cancer genotype of an individual, e.g., determining all or part of the sequence of at least one prostate 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 prostate cancer gene to a known prostate cancer gene, i.e., a wild-type gene.
The sequence of all or part of the prostate cancer gene can then be compared to the sequence of a known prostate 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 prostate cancer gene of the patient and the known prostate cancer gene correlates with a disease state or a propensity for a disease state, as outlined herein.
In a preferred embodiment, the prostate cancer genes are used as probes to determine the number of copies of the prostate cancer gene in the genome.
In another preferred embodiment, the prostate cancer genes are used as probes to determine the chromosomal localization of the prostate 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 prostate cancer gene locus.

Administration of pharmaceutical and vaccine compositions In one embodiment, a therapeutically effective dose of a prostate 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 Pharmaceutical Compounding (1999); and Pickar, Dosage Calculations (I999)). As is known in the art, adjustments for prostate 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 prostate 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 prostate 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 prostate cancer proteins and modulators may be directly applied as a solution or spray.
The pharmaceutical compositions of the present invention comprise a prostate 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 prostate 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 Iiposome or a protection barrier. Means of protecting agents from digestion are well known in the art.
The compositions for administration will commonly comprise a prostate cancer protein modulator dissolved in a pharmaceutically acceptable carrier, preferably an aqueous carrier. A variety of aqueous Garners 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, The 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 Pharmaeologial Basis of Therapeutics, supra.
The compositions containing modulators of prostate 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 prostate cancer protein-modulating compounds can be administered alone or in combination with additional prostate 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 1-16, such as antisense polynucleotides or ribozymes, will be introduced into cells, in vitro or in vivo. The present invention provides methods, reagents, vectors, and cells useful for expression of prostate cancer-associated polypeptides and nucleic acids using ifa 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, Iiposomes, 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 En.zymology 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, prostate cancer proteins and modulators are administered as therapeutic agents, and can be formulated as outlined above.
Similarly, prostate cancer genes (including both the full-length sequence, partial sequences, or regulatory sequences of the prostate cancer coding regions) can be administered in a gene therapy application. These prostate 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.
Prostate 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., Vaccine 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 Imnzunol. 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. Imnzunol. Methods 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 (Kaufmann, ed., p. 379, 1996);
Chakrabarti, et al., Nature 320:535 (1986); Hu et al., Nature 320:537 (I986);
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., Sem. Hematol. 30:16 (1993);
Falo et al., Nature Med. 7:649 (1995)), adjuvants (Warren et al., Annu. Rev. Immunol. 4:369 (1986);
Gupta et al., Vaccine 11:293 (1993)), liposomes (Reddy et al., J. Immunol.
148:1585 (1992);
Rock, Immunol. Today 17:131 (1996)), or, naked or particle absorbed cDNA
(Ulmer, et al., Science 259:1745 (1993); Robinson et al., Vaccine 11:957 (1993); Shiver et al., In: Concepts in vaccine development (Kaufmann, ed., p. 423, 1996); Cease & Berzofsky, Annu.
Rev.
Immunol. 12:923 (1994) and Eldridge et al., Sem. 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;
WO 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 prostate 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., J Leukoc Biol 68:793-806 (2000); Hipp et al., In Vivo 14:571-85 (2000)).
Methods for the use of genes as DNA vaccines are well known, and include placing a prostate cancer gene or portion of a prostate cancer gene under the control of a regulatable promoter or a tissue-specific promoter for expression in a prostate cancer patient.
The prostate cancer gene used for DNA vaccines can encode full-length prostate cancer proteins, but more preferably encodes portions of the prostate cancer proteins including peptides derived from the prostate cancer protein. In one embodiment, a patient is immunized with a DNA vaccine comprising a plurality of nucleotide sequences derived from a prostate cancer gene. For example, prostate cancer-associated genes or sequence encoding subfragments of a prostate 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 prostate cancer polypeptide encoded by the DNA
vaccine. Additional or alternative adjuvants are available.
In another preferred embodiment prostate cancer genes find use in generating animal models of prostate cancer. When the prostate cancer gene identified is repressed or diminished in cancer tissue, gene therapy technology, e.g., wherein antisense RNA directed to the prostate cancer gene will also diminish or repress expression of the gene. Animal models of prostate cancer find use in screening for modulators of a prostate cancer-associated sequence or modulators of prostate cancer. Similarly, transgenic animal technology including gene knockout technology, e.g. as a result of homologous recombination with an appropriate gene targeting vector, will result in the absence or increased expression of the prostate cancer protein. When desired, tissue-specific expression or knockout of the prostate cancer protein may be necessary.
It is also possible that the prostate cancer protein is overexpressed in prostate cancer. As such, transgenic animals can be generated that overexpress the prostate 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 prostate cancer and are additionally useful in screening for modulators to treat prostate 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, prostate cancer-specific nucleic acids or antibodies, hybridization probes and/or primers, antisense polynucleotides, ribozymes, dominant negative prostate cancer polypeptides or polynucleotides, small molecules inhibitors of prostate cancer-associated sequences ete. 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 prostate 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 prostate cancer-associated polypeptide or polynucleotide, reaction tubes, and instructions fox testing prostate cancer-associated activity. Optionally, the kit contains biologically active prostate 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 TRIzol 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 I5 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 TRIzoI reagent is added to the homogenization mixture. The tubes are securely capped and shaken vigorously by hand (do not vortex) for I5 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 lml of TRIzol 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 4°C.

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 37°C and mixing prior to adding to RNA.
The Elution Buffer is incubated at 70°C. If there is precipitate in the buffer, warm up the 2 x Binding Buffer at 65°C. 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 u1 of preheated (70°C) 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 ~0%
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 Ha0 at lug/ul concentration.
Alternatively the RNA may be purified usin~other methods (e.~., Qia~en's RNeasy kit).
No more than 100 ug is added to the RNeasy column. The sample volume is adjusted to 100 u1 with RNase-free water. 350 u1 Buffer RLT and then 250 u1 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 u1 Buffer RPE and centrifuge for 15 sec at >10,000 rpm. The flowthrough is discarded.
500 u1 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 u1 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 2.5X 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 u1 of Superscript RT is used; for polyA+ mRNA, 1 u1 of Superscript RT is used. The final volume of first strand synthesis mix is 20 u1. The RNA
should be in a volume no greater than 10 u1. The RNA is incubated with 1 u1 of 100 pmol T7-T24 oligo for 10 min at 70°C followed by addition on ice of 7 u1 of:
4u15X 1st Strand Buffer, 2 u1 of O.1M DTT, and 1 u1 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:

u1 DEPC HaO; 30 u1 5X 2nd Strand Buffer; 3 u1 lOmM dNTP mix; 1 u1 10 U/ul E.coli DNA
Ligase; 4 u1 10 U/ul E.coli DNA Polymerase; and 1 u1 2 U/ul RNase H. Mix and incubate 2 hours at 16°C. Add 2 u1 T4 DNA Polymerase. Incubate 5 min at 16°C. Add 10 u1 of 0.5M
EDTA.
Cleaning ~ 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 7.5X 5M NH40Ac and 2.5X
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 80% ethanol. As much ethanol wash as possible should be removed before air drying the pellet; and resuspending it in 3 u1 RNase-free water.

In vitro Transcription ~IVT) and labeling with biotin In vitro Transcription (IVT) and labeling with biotin is performed as follows:
Pipet 1.5 u1 of cDNA into a thin-wall PCR tube. Make NTP labeling mix by combining 2 u1 T7 lOxATP (75 mM) (Ambion); 2 u1 T7 lOxGTP (75 mM) (Ambion); 1.5 u1 T7 lOxCTP
(75 mM) (Ambion); 1.5 u1 T7 lOxUTP (75 mM) (Ambion); 3.75 u1 10 mM Bio-11-UTP
(Boehringer-Mannheim/Roche or Enzo); 3.75 u1 10 mM Bio-16-CTP (Enzo); 2 u1 lOx transcription buffer (Ambion); and 2 u1 lOx T7 enzyme mix (Ambion). The final volume is 20 u1. 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 u1 volume is recommended but 20 u1 is all right. Do not go higher than 20 u1 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 KOAc; 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 uI (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 u1 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 herring sperm DNA;
0.5 mg/ml acetylated BSA; and 300 u1 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: ~.l Random Hexamers (1 ~.g/~,1): 4 ~.1 H20: u~l 14 ~,1 Incubate the above 14 ~.1 mixture at 70°C for 10 min.; then put on ice.
The Reverse transcription procedure uses the following mixture:
0. I M DTT: 3 ~,I
50X dNTP mix: 0.6 w1 H20: 2.4 ~.1 Cy3 or Cy5 dUTP (1mM): 3 ~.1 SS RT II (BRL): 1 ~l 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 50X dNTP mix contains 25mM of cold dATP, dCTP, and dGTP, lOmM
of dTTP and is made by adding 25 ~l each of 100mM dATP, dCTP, and dGTP; 10 p1 of 100mM dTTP to 15 p1 HaO. ]
RNA degradation is performed as follows. Add 86 ~,1 H20, 1.5 ~1 1M NaOH/
2 mM EDTA and incubate at 65°C, 10 min.. For U-Con 30, 500 p1 TE/sample spin at 7000 g for 10 min, save flow through for purification. For Qiagen purification, suspend u-con recovered material in 500 p1 buffer PB and proceed using Qiagen protocol. For DNAse digestion, add 1 u1 of 1/100 dilution of DNAse/30 uI Rx and incubate at 37°C for 15 min.
Incubate at 5 min 95°C to denature the DNAse.
Sample preparation For sample preparation, add Cot-1 DNA, 10 ~.1; 50X dNTPs, 1 ~1; 20X SSC, 2.3 ~.1; Na pyro phosphate, 7.5 ~1; 10 mg/ml Herring sperm DNA; 1 u1 of 1/10 dilution to 21.8 final vol. Dry in speed vac. Resuspend in 15 ~,1 H20. Add 0.38 ~1 10%
SDS. Heat 95°C, 2 min and slow 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+0.75m1 10% SDS in 250m1 H20; 1X SSC: 5 min., I2.5 ml 20X SSC in 250mI HaO;
0.2X SSC: 5 min., 2.5 ml 20X SSC in 250m1 HaO. Dry slides and scan at appropiate PMT's and channels.
Example 2: Taxol resistant Xenograft Model of Human Prostate Cancer Treatment regimens that include paclitaxel (Taxol; Bristol-Myers Squibb IO Company, Princeton, NJ) have been particularly successful in treating hormone-refractory prostate cancer in the phase II setting (Smith et al., Semin. Oncol. 26(1 Suppl 2):109-11 (1999)). However, many patients develop tumors which are initially, or later become, resistant to taxol. To identify genes that may be involved with resistance to taxol, or are regulated in response to taxol resistance, and therefore may be used to treat, or identify, taxol resistance in patients, the following experiments were carried out.
The androgen-independent human cell line CWR22R was grown as a xenograft in nude mice (Nagabhushan et al., Cancer Res. 56(13):3042-3046 (1996); Agus et al., J. Natl. Cancer Inst.91(21):1869-1876 (1999); Bubendorf et al., J. Natl.
Cancer Inst.
91(20):1758-1764 (1999)). Initially, these xenograft tumors were sensitive to therapeutic doses of taxol. The mice were treated continuously with sub-therapeutic doses, and the tumors were allowed to grow for 3-4 weeks, before surgical removal of the tumors. The tumor from an individual mouse was then minced, and a small portion was then injected into a healthy nude mouse, establishing a second passage of the tumor. This mouse was then treated continuously with the same sub-therapeutic dose of taxol. This process was repeated 14 times, and a portion of each generation of xenograft tumor was collected. There was increasing resistance to therapeutic doses of taxol with each generation. Bythe end of the process, the tumors were fully resistant to therapeutic doses of taxol. RNA from each generation of tumor was then isolated, and individual mRNA species were quantified using a custom Affymetrix GeneChip~ oligonucleotide microarray, with probes to interrogate approximately 35,000 unique mRNA transcripts. Genes were selected that showed a statistically significant up-regulation, or down-regulation, during the subsequent generations of increasingly taxol-resistant tumors. Only one gene was significantly up-regulated, whereas 24 genes were down-regulated; these are presented in Table 10.

The gene sequences identified to be overexpressed in prostate cancer may be used to identify coding regions from the public DNA database. The sequences may be used to either identify genes that encode known proteins, or they may be used to predict the coding regions from genomic DNA using exon prediction algorithms, such as FGENESH
(Salamov and Solovyev, 2000, Genome Res. 10:516-522). In addition, one of ordinary skill in the art would understand how to obtain the unigene cluster identification and sequence information according to the exemplar accession numbers provided in Tables 1-16. (see, http://www.ncbi.nlm.nih.gov/LTniGene/).

TABLE1: shows genes, including expression sequence tags, differentially expressed in prostate tumor tissue compared to normal tissue as analyzed using the Affymetrix/Eos Hu01 GeneChip array. Shown are the relative amounts of each gene expressed in prostate tumor samples and various normal tissue samples showing the highest expression of the gene.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title Ri: Ratio of tumor to normal body tissue Pkey UnigenelD Uningene Title R1 ExAccn 131919 Hs.272458ESTs 372 120328 Hs.290905ESTs; Weakly similar 32.6 AA196979 to (def!ine not ava 105201 Hs.31412 ESTs 30.1 101486 Hs.1852 acid phosphatase; prostate252 119073 Hs.279477ESTs 24.8 133428 Hs.183752microseminoprotein; 23.8 M34376 beta-128180 Hs.171995kallikrein 3; (prostate21.4 AA595348 specific antigen 104080 Hs.57771 Homo sapiens mRNA for 18.9 AA402971 serine protease (T

127537 Hs.162859ESTs 18.6 131665 Hs.30343 ESTs 17.4 101050 Hs.1832 neuropeptide Y 17.3 130771 Hs.1915 folate hydrolase (prostate-specific17 N48056 memb 108153 Hs.40808 ESTs 16.9 AA05d237 107485 Hs.262476S-adenosylmethionine 16.7 W63793 decarboxylase 1 106155 Hs.33287 ESTs 16.5 129534 Hs.11260 ESTs 16.4 100569 Hs.171995 16 Antigen, Prostate Specific, Alt.
Splice 35 101889 Hs.181350kallikrein 2; prostatic15.4 135389 Hs.99872 fetal Alzheimer antigen15 101506 Hs.62192 coagulaCbn factor III 13.9 M27436 (thromboplastin;

134374 Hs.8236 ESTs 12.7 133944 Hs.7780 ESTs 12.5 109141 Hs.193380ESTs 12.3 130974 Hs2178 H28 histone family; 11.8 X57985 member Q

114768 Hs.182339ESTs 11.8 104394 Hs.172i29ypl9hi.r1 Soares breast11.8 H46617 3NbHBst Homo sap 125299 Hs.102720ESTs 11.6 4$ 104660 Hs.14846 ESTs 11.4 100116 Hs.78045 actin; gamma 2; smooth11 D00654 muscle; enteric 131061 Hs.268744ESTs; Moderately similar10.9 N64328 to KIAA0273 [H.

126645 126645 Homo sapiens BAC clone10.7 AI167942 RG041D11 from 7q2 135153 Hs.95420 Homo Sapiens mRNA for 10.6 N40141 JM27 protein; comp 107033 Hs.113314ESTs -AA599629 10.6 118417 N66048 ESTs; Weakly similar 10.5 to polymerase [H.sa 126758 Hs.293960ESTs 102 115674 Hs.8364 ESTs 10.1 134989 Hs.92381 ESTs; Weakly similar 10.1 AA236324 to !!!! ALU CLASS
A

$5 107102 Hs.30652 ESTs 10.1 116787 Hs.15641 ESTs 10.1 115719 Hs.59622 ESTs 10 123209 Hs.203270ESTs 9.9 101664 Hs.121017H2A histone family; 9.8 M60752 member A

112971 Hs.83883 ESTs 9.7 102519 Hs.80296 Purkinje cell protein 9.7 117984 Hs.106778ESTs 9.7 105840 Hs.22209 ESTs 9.4 129523 Hs274509 T-cell receptor; gamma9.4 M30894 cluster 65 132964 Hs.167133ESTs 92 121853 Hs.98502 ESTs 9 115764 Hs.91011 anterior gradient 2 8.9 AA421562 (Xenopus Iaevis; sec 119617 Hs.55999 ESTs 8.9 100552 Hs.301946 8.9 Protein Kinase Ht3l, Camp-Dependent 105627 Hs.23317 ESTs 8.8 101461 Hs.76422 phospholipase A2; group8.7 M22430 IIA (platelets;

131725 Hs.31146 ESTs; Highly similar 8.5 AA456264 to (defline not ava 124526 Hs.293185yz61c5.s1 Soares_multiple-sclerosis-2NbH8.5 118528 Hs.49397 ESTs 8.2 133845 Hs.76704 ESTs 8.2 133354 Hs.334762ESTs; Weakly similar 8.1 AA055552 to KIAA0319 [H.sapi 105912 Hs.20415 ESTs; Weakly similar 8 AA402000 to GS3786 [H.sapien 119018 Hs.278695ESTs 8 100394 Hs.66052 CD38 antigen (p45) 8 114132 Hs.24192 ESTs 7.9 116786 Hs.301527tumor necrosis factor 7.7 H25836 (ligand) superfami 106579 Hs.23023 ESTs 7.6 128790 Hs.105700secreted frfzzled-related7.5 AA291725 protein 4 114965 Hs.72472 ESTs 7.4 112033 Hs.22627 ESTs 7.1 102398 U42359 Human N33 protein form7 1 (N33) gene, exo 101201 Hs2256 matrix metalloproteinase6.9 L22524 7 (matrilysin;

109272 Hs.288462ESTs 6.9 103145 Hs.169849myosin-binding protein6.9 X66276 C; slow-type 101803 Hs.155691pre-B-cell leukemia 6.8 M86546 transcription factor 120562 Hs.302267ESTs; Weakly similar 6.8 AA280036 to WOlA6.c [C.elega 109112 Hs.257924ESTs 6.8 109795 Hs.326416ESTs 6.7 107532 Hs.173684ESTs; Weakly similar 6.7 219643 to (defline not ava 130336 Hs.171995kallikrein 3; (prostate6.6 X07730 specific antigen 131425 Hs.26691 ESTs 6.6 120588 Hs.16193 Homo sapiens mRNA; 6.6 AA281591 cDNA DKFZp586B211 (fr 132902 Hs.59838 ESTs 6.6 125674 Hs.323378H.sapiensmRNAfortransmembraneprotein6.6 133724 Hs.75746 aldehyde dehydrogenase6.5 130343 Hs.278628ESTs; Moderately similar6.5 AA490262 to APXL gene pr 120215 Hs.108787Homo sapiens Mcd4p 6.5 241050 homolog mRNA; complet 129215 Hs.126085ESTs 6.5 131881 Hs.3383 upstream regulatory 6.5 AAOf 0163 element binding prot 133376 Hs.7232 ESTs 6.4 105376 Hs.8768 ESTs; Weakly similar 6.4 AA236559 to neuronal thread 104674 Hs.26289 ESTs 6.4 100727 Hs.334786Human HF.12 gene mRNA 6.3 130150 Hs.15113 homogentisate 1;2-dioxygenase6.3 AF000573 (homogenti 121770 Hs278428 Homo sapiens mRNA for 6.3 AA421714 KIAA0896 protein;

123475 Hs250528 ESTs; Weakly similar 6.3 AA599267 to ANKYRIN; BRAIN
V

133061 Hs.296638prostate differentiation6.3 A8000584 factor 116429 Hs279923 ESTs; Weakly similar 6.2 AA609710 to similar to GTP-b 101233 Hs.878 sorbitol dehydrogenase6.2 104691 Hs.37744 ESTs 6.2 127248 AA325029 EST27953 Cerebellum 6.2 II Homo sapiens cDNA

127775 Hs.179902ESTs; Weakly similar 6.2 H04106 to (defline not ava 105500 Hs.222399ESTs 6.1 131463 Hs.2714 forkhead (Drosophila)-like-X74142 1 6.1 132116 Hs.40289 ESTs 6 130828 Hs.203213ESTs 5.9 115357 Hs.72988 ESTs 5.8 105496 Hs.301997ESTs 5.7 116334 Hs.48948 ESTs 5.7 107968 Hs.61539 ESTs 5.7 120132 Hs.125019ESTs; Weakly similar 5.6 238839 to !Ill ALU SUBFAMI

106375 Hs.289072ESTs 5.6 132550 Hs.170195bone morphogenetic 5.6 AA029597 protein 7 (osteogenic 124777 Hs.id0237ESTs; Weakly similar 5.6 841933 to neuronal thread 100311 Hs.337616phosphodiesterase 3B; 5.6 D50640 cGMP-inhibited 101791 Hs.62354 Human beige-like protein5.5 M83822 (BGL) mRNA; par 117698 Hs.45107 ESTs 5.5 N4f002 132387 Hs.281434heat shock 70kD protein5.5 122041 Hs.98732 Homo sapiens Chromosome5.5 AA431407 16 BAC clone CIT

133723 Hs262476 S-adenosylmelhionine 5.5 AA088851 decarboxylase 1 1 13938 W81598 ESTs 5.4 133015 Hs.246315 ESTs 5.4 125745 Hs.75722 ribophorin II 5.4 107295 Hs.80120 UDP-N-acetyl-alpha-D-galactosamine:polyp5.4 $ 108186 Hs.7780 ESTs 5.3 100184 Hs.21223 calponin 1; basic; 5.3 D17408 smooth muscle 104466 Hs.326392 Human guanine nucleotide5.3 N25110 exchange factor 104033 Hs.98944 ESTs 5.3 110844 Hs.i6753i ESTs;Weaklysimilarto(defl!nenotava5.3 1 129056 Hs.108336 ESTs; Weakly s!m!lar 5.3 ~ H70627 to !!!! ALU SUBFAMI

102805 Hs.25351 Iroquois-class homeodomain5.3 090304 protein 133493 Hs.194369 Homo sapiens chromosome5.3 AA284143 1 atrophin-1 rel 129184 Hs.109201 ESTs; Highly similar 5.2 W26769 to (defline not ava 134158 Hs.79428 BCL2/adenovirus E18 5.2 015174 l9kD-interacting pro 1$ 107240 Hs.159872 ESTs 5.2 104787 AA027317 ESTs; Weakly similar 5.2 to !!!! ALU SUBFAMI

123527 Hs.108327 damage-specific DNA 5.2 AA608679 binding protein 1 (1 116646 Hs.194228 ESTs; Moderately similar5.2 F03048 to 1!!! ALU SUB

101448 Hs.195850 keratin 5 (epidermolysis5.1 M21389 bullosa simplex 20 116188 Hs.184598 ESTs; Weakly similar 5.1 AA464728 to !!!! ALU SUBFAMI

126259 Hs.281428 ESTs; Moderately similar5.1 221472 to !!!! ALU SUB

105921 Hs.169119 ESTs 5.1 103375 Hs.54416 sine oculis homeobox 5.1 X91868 (Drosophila) homolo 128871 Hs.106778 ESTs; Highly similar 5.1 AA400271 to (defline not ava 2$ 112681 Hs.148932 ESTs; Moderately similar5.1 887331 to semaphorin V

105784 Hs.226434 ESTs 5.1 116238 Hs.47144 ESTs 5 102913 Hs.80342 keratin 15 5 103011 Hs.326035 early growth response5 126023 H58881 yr36d09.r1 Soares 5 fetal fNer spleen 103709 Hs.13804 ESTs 5 118981 Hs.39288 ESTs; Weakly sim!lar 5 N93839 to !!!! ALU SUBFAMI

134807 Hs.89732 zinc finger protein 5 100079 Hs.23311 Human mRNA for KIAA03674.9 AB002365 gene; partial cd 3$ 132047 Hs.3796 Eph86 4.9 132880 Hs.177537 ESTs 4.9 124049 Hs.74519 primase; polypeptide 4.8 F10523 2A (58kD) 133330 Hs.71119 Human N33 mRNA; complete4.8 042360 cds 104776 AA026349 ESTs 4.8 40 122593 Hs.128749 Homo Sapiens alpha-methylacyl-CoA4.8 AA453310 raceme 103912 Hs.143087 ESTs 4.8 113961 Hs.26009 Homo Sapiens mRNA 4.8 W86307 for KIAA0860 protein;

105288 Hs.3585 ESTs; Weakly similar 4.8 AA233168 to coded for by C.

135035 Hs.284186 ESTs 4.8 45 104144 Hs.183390 ESTs; Weakly similar 4.8 AA447439 to ZINC FINGER PROT

129389 Hs.288126 ESTs 4.8 125982 898091 RAE1 (RNA export 1; 4.8 S.pombe) homolog 125162 Hs.26243 ESTs 4.8 103023 Hs.117950 multifunctional polypeptide4.7 X53793 similar to S

$0 129735 W80701 ESTs; Weakly similar 4.7 to HERV-E envelope 104479 Hs.106390 ESTs 4.7 103731 AA070545 zm7c3.r1 Stratagene 4.7 neuroepithelium (#93 126575 Hs.127602 ESTs -W72416 4.7 124578 Hs.231500 Human glucose transporter-like4.7 N68321 protein-!

$$ 130617 Hs.1674 glutamine-fructose-6-phosphate4.7 M90516 transamin 116752 Hs.91622 Homo sapiens clone 4.7 H06373 24456 mRNA sequence 100279 Hs.82007 Human mRNA for KIAA00944.7 D42084 gene; partial cd 126288 Hs.89576 ESTs 4.7 131836 Hs.32990 ESTs 4.7 AA6i0086 106717 Hs.239489 TIA1 cytotox!c granule-associated4.7 AA465093 RNA-bi 114542 Hs.91011 ESTs 4.6 103806 AA130614 zoif2.r1 Stratagene 4.6 neuroepithelium NT2R

130529 AA173238 small inducible cytokine4.6 A5 (RANTES) 115675 Hs.82065 ESTs 4.6 6$ 111386 Hs.293798 ESTs 4.6 106503 Hs.29679 ESTs 4.6 119943 Hs.14158 copine III 4.6 104459 Hs.100070 EST 4.6 100774 Hs.89603 Muan 1, Epithelial, 4.6 HG371-HT1063 Alt. Splice 6 100652 Hs.142653 4.6 RetTransfortning Gene 132015 Hs.3731 ESTs 4.6 126086 H70975 yr73g01.r1 Soares fetal4.6 liver spleen 1NF

130888 Hs.173094ESTs 4.6 106390 Hs.20166 Prostate stem cell 4.6 AA446964 antigen 126959 AA199853 ESTs; Moderately similar4.5 to !!!! ALU SUB

131584 Hs.29117 H.sapiens mRNA for 4.5 X91648 pur alpha extended 3' 104838 Hs.20953 ESTs 4.5 125661 850319 ESTs 4.5 103171 Hs.234726alpha-1-antichymotrypsin4.5 103928 Hs.199160ESTs 4.5 102899 Hs.75730 signal recognition 4.5 X06272 particle receptor ('d 100892 Hs.18078962 Small Nuclear Ribonucleoprotein4.5 HG4557-HT49 Ui, isnr 106167 Hs.7956 ESTs 4.5 129404 Hs.317584ESTs 4.5 106990 Hs.24758 ESTs 4.5 132316 Hs.44566 Human protein immuno-reactive4.4 028831 with anti-132056 Hs.38176 Homo sapiens mRNA for 4.4 T89386 KIAA0606 protein;

133718 Hs.198760neurofilament; heavy 4.4 X15306 polypeptide (200kD) 101470 Hs.1846 tumor protein p53 (Li-Fraumeni4.4 M22898 syndrome) 131904 Hs.284296ESTs; Highly s!milar 4.4 AA143019 to surface 4 integr 105804 Hs.22514 ESTs 4.4 122861 Hs.119394ESTs 4.4 111336 Hs.29894 ESTs 4.4 121944 Hs.98518 ESTs 4.4 134401 Hs.211577ESTs; Highly similar 4.4 AA243746 to CGi protein [H.s 126458 Hs.288969ESTs; Weakly similar 4.4 AA815252 to !!!! ALU SUBFAMI

133435 Hs.323966ESTs; Moderately similar4.4 T23983 to !!!! ALU SU8 105178 Hs21941 ESTs 4.3 127315 AA640834 nr27b06.r1 NCI_CGAP_Pr34.3 Homo sapiens cDN

132645 Hs.54424 H.sapiens mRNA for 4.3 X87870 hepatocyte nuclear fa 116162 Hs.282990ESTs; Wealdy similar 4.3 AA461487 to F52C12.2 [C.eleg 118040 Hs.47567 EST 4.3 130008 Hs.278427cerebellar degeneration-related4.3 M31423 protein 126607 Hs.114688ESTs 4.3 123061 Hs.105130EST 4.3 109391 Hs.184245ESTs 4.3 109175 AA180496 ESTs 4.3 127003 Hs.173540ESTs; Weakly similar 4.3 AA550806 to (defline not ava 102547 Hs.46638 chromosome 11 open 4.3 057911 reading frame 8 134208 Hs.79993 peroxisomal biogenesis4.3 088871 factor 7 104258 Hs.5462 solute tamer family 4.3 AF007216 4; sodium bicarbon 130759 Hs.18946 ESTs; Weakly similar 4.3 AA094720 to (defline not ava 132160 Hs.295923seven in absentia (Drosophila)4.3 AA281770 homolog 1 135062 Hs.93872 ESTs 4.3 126510 Hs.334762ESTs; Wealdy similar 4.2 849702 to KIAA0319 [H.sapi 122055 Hs.98747 EST 4.2 133136 Hs.6574 suppressin (nuclear 4.2 AF007165 deformed epidermal a 109890 Hs.20843 ESTs 4.2 $0 133294 Hs.69997 H.sapiens mRNA for 4.2 879723 translin associated z 134436 Hs.83190 fatty aad synthase 4.2 S80437 {3' region} [human, 107375 Hs.251064NBR2 4.2 122223 Hs.27413 ESTs -AA436158 4.2 103044 Hs.248210H.sapiens Mahlavu hepatocellular4.2 X55777 carcino 55 120125 Hs.59815 EST 4.2 128969 Hs.283978ESTs; Highly similar 4.2 T65327 to (defline not ava 129637 Hs.1179 TATA box binding protein4.2 D90359 (TBP)-assoaate 106566 AA455921 ESTs; Weakly similar 4.2 to !!!! ALU SUBFAMI

112605 Hs.29852 ESTs 4.2 103364 Hs.279929H.sapiens mRNA for 4.2 X90872 gp25L2 protein 132811 Hs.57419 transcriptional repressor4.2 126570 Hs.326292ESTs 4.2 116298 Hs.94109 ESTs 4.2 103024 Hs.105938lactotransferrin 4.1 65 129133 Hs.108850yg95cfi.r1 Soares infant4.1 856728 brain iNIB Homo 133167 Hs.6641 kinesin family member 4.1 126871 Hs.14051 ESTs 4.1 132333 Hs.45032 ESTs 4.1 107376 Hs.327179solute carver family 4.1 090545 17 (sodium phospha 128517 Hs.100861ESTs; Weakly similar 4.1 AA280617 to p60 katanin [H.s 130555 Hs.116774ESTs 4.1 105765 Hs.24183 ESTs 4.1 126529 Hs.26369 ESTs 4.1 125928 Hs.181889ESTs 4.1 117280 Hs.172129ESTs; Moderately similar4.1 N22f 07 to !!!! ALU SUB

100234 Hs.3085 KIAA0054 gene product 4.1 100959 Hs.118127actin; alpha; cardiac 4.1 J00073 muscle 107130 Hs.12913 ESTs; Weakly similar 4.1 AA620582 to (defline not ava 105035 Hs.8859 ESTs 4.1 126735 Hs.226795glutathione S-transferase4.1 AA808949 pi 113D56 Hs.8036 ESTs; Moderately similar4 T26471 to !!!! ALU SUB

102460 Hs,211582Homo sapiens myos!n 4 048959 light chain kinase ( 106968 Hs,26813 ESTs; Weakly similar 4 AA504631 to (defline not ava 123107 Hs.104207ESTs 4 127256 Hs,267967ESTs; Weakly similar 4 AA327550 to !!!! ALU SUBFAMI

105329 Hs,22862 ESTs 4 115504 Hs.42736 ESTs 4 120726 Hs.97293 ESTs 4 103576 Hs.94560 desmoglein 2 4 127889 Hs.144941ESTs 4 106394 Hs25320 ESTs 4 128046 AA873285 ESTs 4 103391 Hs.114366pyrroline-5-carboxylate4 X94453 synthetase (glut 106448 Hs.27004 ESTs 4 126513 Hs.86276 ESTs; Moderately similar4 W27601 to (degine not 129593 Hs.98314 ESTs; Weakly similar 3.9 AA487015 to !!!! ALU SUBFAMI

110151 Hs.31608 ESTs 3.9 105344 Hs.8645 ESTs 3.9 104791 Hs.301871ESTs 3.9 123442 Hs.111496ESTs 3.9 127800 Hs.79428 BCl-2/adenovirus E1 3.9 AA521047 B l9kD-interacting pro 114555 Hs.167904ESTs 3.9 122138 Hs.163960ESTs 3.9 129565 Hs.198726vasoactive intestinal 3.9 X77777 peptide receptor 1 103471 Hs.75216 protein tyrosine phosphatase;3.9 Y00815 receptor t 133908 Hs.325474caldesmon 1 3.9 105635 Hs.301985ESTs 3.9 134285 Hs.81086 solute tamer family 3.9 AA460012 22 (organic ration 4Q 134125 Hs.50421 KIAA0203 gene product 3.9 125628 Hs.241493natural killer-tumor 3.9 AA418069 recognition sequenc 103695 Hs.186600ESTs 3.9 100642 Hs.182183 3.9 Caklesmon 1, Alt. Splice 6, Non-Muscle 104334 Hs.78771 ESTs 3.9 110242 Hs.19978 ESTs 3.9 125298 Hs289008 ESTs 3.9 104060 Hs.303193zt87a9.r1 Soares testis_NHT3.9 AA397968 Homo sapiens 105823 Hs.293960ESTs 3.9 126499 Hs.110445ESTs; Moderately s!milar3.9 AA315671 to unknown (M.m 130752 Hs.18895 KIAA0137 gene product 3.8 123494 Hs.112110ESTs 3.8 104846 Hs.32478 ESTs 3.8 108921 Hs.71721 ESTs -AA142913 3.8 115506 Hs.45207 ESTs 3.8 100452 Hs.241552Human mRNA for KIAA02683.8 D87742 gene; partial rd 104454 Hs.129228galactokinase 2 3,8 108730 Hs.102859ESTs 3.8 131223 Hs.24427 ESTs; Highly similar 3.8 AA247788 to (defline not ava 104784 Hs.269228ESTs 3.8 104946 Hs.73848 ESTs 3.8 106932 Hs.9394 ESTs 3.8 101724 Hs.620 bullous pemphigoid 3.8 M69225 antigen 1 (230/240kD) 106140 Hs.14912 Homo sapiens mRNA for 3.8 AA424524 KIAA0286 gene; par 128135 Hs.269721ESTs 3.8 120030 Hs.58694 ESTs 3.8 126457 Hs.50382 zh98g04.r1 Soares_fetal_liver_spleen_1NF3.8 123917 Hs.112969EST 3.7 110714 Hs.f7752 Homo sap!ans phosphatidylserine-speafic3.7 130577 Hs.162 insulin-like growth 3.7 M35410 factor binding prote 117667 Hs.44708 ser-Thr protein kinase 3.7 N39214 related to the my 126104 Hs.39712 ESTs; Weakly similar 3.7 N77278 to BONE/CARTILAGE P

100379 Hs.278721Homo sap!ens mRNA for 3.7 D82060 membrane protein w 115646 Hs.305971ESTs 3.7 125792 Hs.193700ESTs; Moderately similar3.7 A1005388 to Ill! ALU SUB

102162 Hs.1592 CDC16 (cell division 3.7 018291 cycle 16; S, cerevi 128530 Hs.183475ESTs; Moderately similar3.7 AA504343 to !!!! ALU SUB

119940 Hs.272531EST 3.7 110769 Hs.23837 yw34b06.s1 Morton Fetal3.7 N22222 Cochlea Homo sap 132914 Hs.60293 ESTs 3.7 113594 Hs.15683 ESTs 3.7 103702 Hs.279952ESTs; Highly similar 3.7 AA027793 to (defline not ava 130780 Hs.19347 ESTs 3.7 123288 Hs.291025EST 3.7 120691 Hs.22380 ESTs 3.7 103153 Hs.75295 guanylate cyclase 1; 3.7 X66534 soluble; alpha 3 129201 Hs.109390ESTs 3.7 114798 Hs.54900 ESTs 3.7 126801 Hs.7337 ESTs 3.7 105503 Hs.31707 ESTs 3.7 104260 Hs.194283Homo sapiens putative 3.7 AF008192 GR6 protein (G86) 125980 Hs.35699 ESTs 3.7 123255 Hs.105273ESTs 3.6 103862 Hs.6363 ESTs 3.6 100696 Hs.121686 3.6 Transcription Factor lia 134917 Hs.166994FAT tumor suppresser 3.6 X87241 (Drosophila) homolo 103520 Y10511 H.sap!ens mRNA for CD1763.6 protein 113778 Hs.302738ESTs 3.6 101838 Hs.75511 connective tissue growth3.6 M92934 factor 30 113702 T97307 ESTs; Moderately s!milar3,6 to !!!! ALU SUB

118201 Hs.48428 EST 3.6 116519 Hs.68554 EST 3.6 105886 Hs.22983 ESTs; Moderately similar3.6 AA400517 to UDP-GLUCOSE:

106709 Hs.170291ESTs 3.6 35 127858 Hs.27973 oc26h07.s1 NCI-CGAP-GCB13.6 AA806365 Homo sapiens cD

101964 S81578 dioxin-responsive gene 3.6 {putative polyade 105508 Hs.326416ESTs 3.6 116844 Hs.337434ESTs 3.6 105372 Hs.142296ESTs 3.6 40 100745 Hs.id4630 3.6 V-Erba Related Ear-3 Protein 127521 Hs.164018ESTs ~ 3.6 110758 Hs.274265talin 3.6 107307 Hs.44155 creative kinase; mitochondrial3.6 T52099 2 (sarcom 133200 Hs.i83639ESTs 3.6 45 114774 Hs.184325ESTs 3.6 120265 Hs.270696ESTs; Moderately similar3.6 AA173759 to !!!! ALU SUB

134359 Hs.199067v-erb-b2 avian erythroblastic3.6 M34309 leukemia v 116250 Hs.44829 ESTs; Moderately similar3.6 AA480975 to !11! ALU SUB

106313 Hs.35841 nuclear factor uX (CCAAT-binding3.6 AA436459 Uansc 50 131898 Hs.279780ESTs 3.6 133444 Hs.73793 vascular endothelia! 3.6 M27281 growth factor 128232 Hs.33d641ESTs 3.6 135357 Hs.79572 ESTs - 3.5 457951 AI369384 arylsulfatase D 3.5 55 108407 AA075519 zm87h9.s1 Stratagene 3.5 ovarian cancer (#93 126659 T16245 a disintegrin and metalloproteinase3.5 doma 104189 Hs.301804ESTs 3.5 125956 Hs.129014ESTs 3.5 103026 Hs.79386 Human mRNA for a 64 3.5 X54162 Kd autoantigen expre 60 133011 Hs.171921sema domain; !mmunoglobulin3.5 AA042990 domain (Ig);

131379 Hs.26176 ESTs 3.5 1267d2 Hs.169359yr57e06.r1 Soares fetal3.5 H&4106 liver spleen 1 NF

105560 Hs.306915ESTs 3.5 118472 Hs.42179 ESTs 3.5 65 105623 Hs.30127 ESTs; Highly similar 3.5 AA280895 to !!!! ALU SUBFAMI

120262 Hs.145807ESTs; Moderately similar3.5 AA172076 to !!!! ALU SUB

105027 Hs.26771 ESTs 3.5 130760 Hs.18953 phosphodiesterase 9A 3.5 117473 Hs.155560ESTs 3.5 102663 Hs.168075karyopherin (importinj 3.5 070322 beta 2 126349 Hs.13531 ESTs; Weakly similar 3.5 AA442868 to (defiine not ava 132154 Hs.41119 ESTs 3.5 N67f79 131689 Hs.30696 transcription factor-like3.5 AA599653 5 (basic helix 127862 Hs.i63191EST 3.5 126995 Hs.189810Human DNA sequence from3.5 W26950 PAC 388M5 on chr 119071 831180 ESTs 3.5 103941 Hs.96593 ESTs 3.5 110721 Hs.31319 ESTs 3.5 ' 126586 Hs.43086ESTs 3.5 AAOii247 103106 Hs.1857 phosphodiesterase 6G; 3.5 X62025 cGMP-spedfic; rod 116357 Hs.90797 Homo sap!ens clone 236203.5 AA50d806 mRNA sequence 105309 Hs.4i04 ESTs 3.5 130796 Hs.19525 ESTs 3.5 109101 Hs.52184 ESTs 3.5 103134 Hs.2839 Norrie disease (pseudoglioma)3.5 131798 Hs.301449adenovirus 5 E1A binding3.5 X86098 protein 118535 Hs.49418 ESTs 3.5 102592 Hs.11223 Human putative cytosolic3.4 062389 NADP-dependent 125905 Hs.6456 chaperon!n containing 3.4 T69868 TCP1; subunit 2 (b 109160 Hs.301997ESTs 3.4 105327 Hs.211593ESTs 3.4 106586 Hs.57787 ESTs 3.4 122635 AA454085 EST 3.4 132413 Hs.260116metalloprotease 1 (p!trilysin3.4 AA132969 family) 131938 Hs.34956 ESTs 3.4 133871 Hs.182793ESTs 3.4 107175 Hs.292503ESTs; Weakly similar 3.4 AA621751 to KIAA0601 prote!n 101188 Hs.184298cyclin-dependent kinase3.4 (20320 7 (homolog of Xe 126422 Hs.237658ESTs; Highly similar 3.4 H48518 to apolipoprotein A

118475 N66845 ESTs; Weakly similar 3.4 to !!!! ALU CLASS B

104558 Hs.88959 ESTs; Weakly similar 3.4 856678 to !!!! ALU SUBFAMI

128307 Hs.132005ESTs 3.4 112254 Hs.25829 ESTs 3.4 125408 Hs.89578 yv37e12.r1 Soares fetal3.4 N72353 liver spleen 1NF

109834 Hs.175955ESTs 3.4 130844 Hs20191 seven in absentia (Drosophila)3.4 D12122 homolog 2 127143 Hs.20843 nj68h04.s1 NCI-CGAP-PrlO3.4 AA533553 Homo Sapiens cD

135309 Hs.42500 ESTs 3.4 125724 Hs295978 stimulated traps-acting3.4 AA083407 factor (50 kDaj 127692 Hs.187983ESTs 3.4 116674 Hs.92127 ESTs 3.4 134700 Hs.8868 golgi SNAP receptor 3.4 AA481414 complex member 1 114846 Hs.166196ESTs 3.4 103649 Hs.155983H.sapiens mRNA for 5'0T83.4 270219 for unknown pro 134835 Hs.89925 caldum channel; voltage-dependent;3.4 L04569 L ty 130568 Hs.16085 ESTs; Highly similar 3.4 AA232535 to (decline not ava 111331 Hs.15978 ESTs 3.4 106036 Hs.10653 ESTs 3.4 130987 Hs.21893 ESTs 3.4 112814 Hs.35828 ESTs 3.4 127815 Hs.255015ob93c10.s1 NCI-CGAP-GCBs3.4 AA876009 Homo Sapiens cD

100144 Hs.75616 KIAA0018 gene product 3.4 101129 Hs.247992Homo Sapiens DNA binding3.4 L10405 protein for sur 130874 Hs.20621 ESTs 3.4 106882 Hs.26994 ESTs 3.4 103855 Hs.302267ESTs 3.4 125957 H45213 yo03b08.r1 Soares adult3.3 bran N2b5H855Y

114048 Hs.146085ESTs 3.3 109826 Hs.75354 ESTs 3.3 125355 Hs.170098ESTs; Highly similar 3.3 845630 to KIAA0372 [H.sapi 104182 Hs.143792ESTs; Weakly similar 3.3 AA479990 to glioma amplified 100294 Hs.75454 Human mRNA for Apoi 3.3 D49396 Human (MER5(Aopi-Mou 131688 Hs.30692 p21 (CDKN1A)-activated 3.3 024153 kinase 2 116256 Hs.88201 ESTs; Weakly similar 3.3 AA481256 to (defline not ava 102034 Hs.230 fibromadulin 3.3 130072 Hs.14658 Human chromosome 5q13.13.3 899606 done 5G8 mRNA

114615 Hs.159456ESTs; Highly similar 3.3 AA083812 to (defline not ava 128707 Hs.104105Meis (mouse) homolog 3.3 115048 Hs.190057ESTs 3.3 125862 Hs.31110 ESTs 3.3 135142 Hs.24192 ESTs 3.3 103119 Hs.2877 cadherin 3; P-cadherin 3.3 X63629 (placental) 104460 Hs.62604 ESTs 3.3 100365 Hs.79284 mesoderm specific transcript3.3 D78611 (mouse) hom 131524 Hs.30i804ESTs 3.3 102165 Hs.159627Death associated protein3.3 126966 Hs.182575solute carrier family 3.3 838438 15 (H+/peptide tra l~ 124839 Hs.140942ESTs 3.3 100709 Hs.100469 3.3 Af-6 (Gb:U02478) 132967 Hs.61635 Homo sap!ens BAC clone 3.3 AA032221 RG041 D11 from 7q2 102927 Hs.65114 keratin 18 3.3 132616 Hs.283558ESTs 3.3 15 125132 Hs.129781ESTs 3.3 111225 Hs.31652 ESTs 3.3 114956 Hs.87113 ESTs 3.3 122235 Hs.112227ESTs 3.3 112325 Hs.12315 ESTs 3.3 123360 Hs.178604ESTs 3.3 105150 Hs.155995Homo Sapiens mRNA for 3.3 AA169640 KIAA0643 protein;

107391 Hs.284294ESTs 3.3 113058 Hs.7569 EST 3.3 134371 Hs.82318 Brush-1 3.3 2$ 125669 Hs.333256ESTs; Moderately similar3.3 851308 to !!!! ALU SUB

111506 Hs.294105ESTs 3.3 122974 Hs.194215ESTs 3.3 102369 Hs.299867hepatocyte nuclear factor3.3 U39840 3; alpha 120408 HS.190151ESTs 3.3 117993 Hs.47402 ESTs; Weakly similar 3.3 N52039 to !!!! ALU SUBFAMI

129586 HS.11500 ESTs 3.3 128138 HS.126494ESTs 3.3 127265 AA332751 EST37214 Embryo, 8 week3.3 I Homo Sapiens c 107674 Hs.41143 Homo sapiens mRNA for 3.2 AAOf 1027 KIAA0581 protein;

35 104866 Hs.293691ESTs 3.2 103427 Hs.250655H.sapiens mRNA for Ptg-123.2 X97303 protein 132990 Hs.334334ESTs 32 127017 Hs.251946ESTs 32 132313 Hs.44481 forkhead (Drosophila)-like3.2 106880 Hs.32425 ESTs 3.2 107039 Hs.169780homologous to yeast 32 AA599751 nitrogen permease (c 120870 Hs.292581ESTs 3.2 107920 Hs.284207ESTs 3.2 104165 Hs.105116EST 32 45 107012 Hs.63908 ESTs 32 103605 Hs.194657H.sap!ens gene encoding32 235402 E-cadherin, exon 124006 Hs.270016ESTs 3.2 101300 Hs.74137 Homo Sapiens (clone 3.2 L40391 s153) mRNA fragment 101183 Hs.795 H2A histone family; 3.2 L19779 member 0 125596 825698 yg44h11.r2 Soares infant32 brain 1 NIB Homo 127261 AA661567 nu86b02.s1 NCI_CGAP 3.2 Alvi Homo sapiens cD

120090 Hs.59554 ESTs 3.2 129393 Hs.166982phosphatidylinositol 3.2 D13435 glycan; class F -120923 Hs.97129 ESTs 3.2 5$ 118907 Hs.274256ESTs 3.2 111552 Hs.191185ESTs 3.2 104431 Hs.99913 adrenergic; beta-1-; 3.2 J03019 receptor 133551 Hs.278634Human mRNA for KIAA01463.2 D63480 gene; partial cd 131615 Hs.192803xeroderma pigmentosum; 3.2 D14533 complementation g 60 126547 Hs.84072 transmembrane 4 superfamily3.2 U47732 member 3 103172 Hs.116774integrin; alpha 1 3.2 113867 Hs.24095 ESTs 32 133323 Hs.70937 H3 histone family; member3.2 111597 Hs.189716ESTs 3.2 65 121515 Hs.104696ESTs 3.2 107445 Hs.6639 ESTs 3.2 106887 Hs.334335ESTs 3.2 123052 Hs.185766ESTs 3.2 107072 Hs.130760Homo Sapiens mRNA; cDNA32 AA609113 DKFZp586N0318 (f 1~7 102214 Hs.32964 SRY (sex-determining 3.2 023752 region Y)-box 11 123147 AA487961 ab11h6.s1 Stratagene 3.2 lung (#93721) Homo 125435 Hs272138 ye87g03.r1 Soares fetal3.2 800940 liver spleen iNF

1 16246 Hs.250646ESTs; Highly similar 3.2 AA479961 to ubiquitin-conjug $ 105169 Hs.180789Homo sapiens (clone 3.2 AA180321 S164) mRNA; 3' end o 134001 Hs.78344 myosin; heavy polypeptide3.2 AF001548 11; smooth mus 124866 Hs.304389ESTs 3.2 133205 Hs.67619 Homo sapiens mRNA; 3.2 AA089559 chromosome f specific 102986 Hs.182378colony stimulating 3.2 X17648 factor 1 (macrophage) 1~ 101232 Hs.242894ADP-ribosylation factor-like3.1 132906 Hs.234896ESTs; Highly similar 3.1 AA142857 to geminin [H.sapie 104281 Hs.5669 ESTs 3.1 123926 Hs.227933ESTs; Highly similar 3.1 AA621348 to (defline not ava 134464 Hs.239720ESTs; Weakly similar 3.1 N79354 to Rga [D.melanogas 1$ 105322 Hs.i6346 ESTs 3.1 100631 Hs.48332 3.1 Serine/Threonine Kinase (Gb:725431) 130791 Hs.199263ESTs; Highly similar 3.1 AA259102 to (defline not ava 131220 Hs.300855ESTs 3.1 113237 Hs.123642ESTs 3.1 125562 Hs.98968 ESTs 3.1 134110 Hs.79136 Human breast cancer; 3.1 041060 estrogen regulated 132393 Hs.47334 ESTs; Moderately similar3.1 W85888 to !!!! ALU SUB

107439 Hs.296842ESTs; Moderately similar3.1 W27995 to non-muscle m 125863 Hs.40719 Homo sapiens mRNA; 3.1 AA299096 cDNA DKFZp564M0916 (f 25 105811 Hs.286192ESTs 3.1 129284 Hs.296141ESTs 3.t 125321 Hs.178294ESTs 3.1 107332 Hs.183297ESTs 3.1 123570 Hs.109653ESTs 3.1 100384 Hs.90800 matrix metalloproteinase3.1 D83646 16 (membrane-in 109063 Hs.38972 tetraspan 1 3.1 133284 Hs.182828zinc finger protein 3.1 009367 136 (clone pHZ-20) 131839 Hs.33010 Homo sapiens mRNA for 3.1 H80622 KIAA0633 protein;

117606 Hs.44698 ESTs 3.1 3$ 418998 Hs.287849ESTs 3.1 125180 Hs.103120ESTs 3.1 100789 HG3893-HT4163 Phosphoglucomutase 3.1 1, Alt. Splice 126017 Hs.159440ESTs 3.1 132452 Hs.247324Homo sapiens DNA sequence3.1 AA005262 from PAC 262D1 129077 Hs.108479ESTs 3.1 126563 Hs.181368U5 snRNP-specific protein3.1 W26247 (220 kD); orth 129650 Hs.118258ESTs 3.1 123465 AA599033 ESTs 3.1 126486 Hs.i52316EST51345 Gall bladder 3.1 AA345339 II Homo sapiens cD

4$ 126460 Hs.167031za36d05.r1 Soaresfetal3.1 W01616 liver spleen iNF

118697 Hs.43234 ESTs 3.1 103860 Hs.38057 ESTs 3.1 127968 Hs.124347ESTs 3.1 124984 Hs.223241yb15c11.s1 Stratagene 3.1 T47566 placenta (#937225) $~ 103903 Hs.15220 j312.seq.F Human fetal3.1 AA249334 heart, Lambda ZAP

106697 Hs.22242 ESTs 3.1 130892 Hs.20993 ESTs; Weakly similar 3 AA442604 to Ydr374cp [S.cere 114032 Hs.35014 ESTs -128835 Hs.106390ESTs 3 $$ 103667 Hs.247815H.sapiens H4A gene 3 126264 Hs2506t4 yy13h06.r1 Soares melanocyte3 N42897 2NbHM Homo 132626 Hs21275 ESTs 3 131107 Hs.75354 ESTs 3 126780 Hs.5811 ESTs 3 60 127363 Hs.22i Homo sapiens Cdc14i31 3 t6 AA307744 phosphatase mRNA;
c 103690 Hs.84063 ESTs 3 102589 Hs.8867 Homo sapiens Cy~fii 3 062015 mRNA, complete cds 125144 Hs24336 ESTs 3 132977 Hs.30t404RNA binding motif protein3 6$ 120714 Hs.146170ESTs 3 101038 Hs.79411 replication protein 3 J05249 A2 (32kD) 102856 Hs.248177Human histone H3 gene 3 105516 Hs.30738 ESTs 3 131137 Hs.33287 nuclear factor U8 3 1~~

127221 Hs.241551 ESTs 3 411888 Hs.24104 ESTs 3 131684 Hs.3066 granryme K (serine 3 026174 protease; granzyme 3;

100629 Hs.21291 3 SerinelThreon!ne Kinase (Gb:Z25428) 119944 Hs.58915 EST 3 113801 Hs.118281 zinc finger protein 3 133780 Hs.76152 decorin 3 104690 Hs.14449 ESTs 3 126371 Hs.304139 EST 3 127635 Hs.116346 ESTs 3 128434 Hs.143880 ESTs 3 435761 Hs.187555 ESTs 3 125025 Hs.50748 ESTs 3 124940 Hs.103804 heterogeneous nuclear3 899599 ribonucleoprotein 128742 Hs.25153i proteasome (prosome; 3 D00763 macropain) subunit;

107147 Hs.10450 Homo sapiens chromosome3 AA621125 2;10 repeat reg 112068 Hs.22545 ESTs 3 105346 Hs.263727 ESTs; Moderately similar3 AA235465 to !!!! ALU SUB

130972 Hs.21739 Homo sapiens mRNA; 3 AA370302 cDNA DKFZp58611518 (f 131230 Hs.274407 thymus specific ser!ne3 AA149987 peptidase 133743 Hs.75847 ESTs 3 127402 Hs.227949 ESTs; Highly similar 3 AA358869 to SEC13-RELATED
PR

117483 Hs.44189 ESTs 3 123659 Hs.112699 ESTs 3 2$ 103963 Hs.63290 EST114219 HSC172 cells3 AA298588 II Homo sapiens c 103795 Hs.7367 ESTs; Moderately similar3 AA112222 to (defline not 115092 Hs.80975 CD39-like 4 2.9 134831 Hs.89B90 pyruvate carboxylase 2.9 128579 Hs.101810 ESTs; Weakly similar 2.9 AA093378 to !!!! ALU SUBFAMI

134193 Hs.7980 ESTs 2.9 123522 Hs.112575 ESTs 2.9 107109 Hs.32793 ESTs 2.9 134694 Hs.88556 histone deacetylase 2.9 134399 Hs.82689 tumor rejection antigen2.9 H99801 (gp96) 1 35 134632 Hs.174139 H. sap!ens RNA for 2.9 106683 Hs.14512 ESTs 2.9 108555 AA084963 zn13e12.s1 Stratagene2.9 hNT neuron (#93723 100953 Hs.2110 Nucleic Acid-Binding 2.9 HG945-HT945 Protein (Gb:L12693) 130597 Hs.16492 ESTs; Wealdy similar 2.9 AA173998 to weakly similar t 40 101813 Hs.139226 replication factor 2.9 M87338 C (activator 1 ) 2 (40 106636 Hs286 AA459950ESTs 2.9 129109 Hs.108708 calcium/calmodulin-dependent2.9 AA491295 protein kin 125819 Hs.251871 stromal cell-demred 2.9 AA044840 factor 1 106282 Hs.9857 ESTs; Weakly similar 2.9 AA433946 to (defline not ava 45 100386 Hs.301636 peroxisomal biogenesis2.9 D83703 factor 6 114546 Hs.98074 ESTs; Moderately similar2.9 AA056263 to !!!! ALU SUB

105914 Hs.9701 Homo Sapiens growth 2.9 AA402224 arrest and DNA-damag 108552 AA084912 zn11c7.s1 Stratagene 2.9 hNT neuron (#937233 126505 Hs.190057 16a11 Human reUna 2.9 W26894 cDNA randomly primed 50 134098 Hs.79086 Human MRL3 mRNA for 2.9 X06323 ribosomal protein 129721 Hs.211539 eukaryotic translation2.9 L19161 initiation factor 100076 Hs.277422 Homo sapiens mRNA 2.9 AB000897 for cadherin FI83, par 117466 Hs.44104 ESTs -N29862 2.9 106335 Hs.36688 ESTs; Moderately similar2.9 AA437258 to WAP four-dis $S 134510 Hs250870 protein k!nase; mitogen-activated;2.9 025265 kinas 105835 Hs.32995 ESTs 2.9 106611 Hs.26267 ESTs; Weakly similar 2.9 AA458904 to torsinA [H.sapie 134087 Hs.173824 thymine-DNA glycosylase2.9 100641 Hs.182183 2.9 Caldesmon 1, Alt. Splice 4, Non-Muscle 60 f 04602 886920 ESTs 2.9 117203 Hs.42738 ESTs 2.9 131889 Hs.34073 BH-protocadherin (brain-heart)2.9 AA40t912 101707 Hs.155212 methyimalonyl Coenzyme2.9 M65131 A mutase 115271 Hs.5724 ESTs 2.9 65 125812 Hs.287912 lectin; mannose-b!nding;12.9 110740 Hs.19762 ESTs 2.9 103406 Hs.285728 H.sapiens mRNA for 2.9 X95677 ArgBPIB protein 104577 Hs.132390 ESTs 2.9 102772 Hs.161002 absent in melanoma 2.9 131710 Hs.30985 ESTs; Highly similar 2.9 AA233225 to (defline not ava 125231 Hs.268903ESTs 2.9 127380 Hs.15535 Homo Sapiens clone 245822.9 AI417137 mRNA sequence 104229 Hs.61289 inosltol phosphate 5'-phosphatase2.9 A8002346 2 (syn 126600 Hs.191385ESTs 2.9 125175 Hs.303030EST 2.9 103849 Hs.34578 ESTs; Weakly similar 2.9 AA187045 to !!!! ALU SUBFAMI

102126 Hs.78961 protein phosphatase 2.9 014575 1; regulatory (inhlb 124906 Hs.107815ESTs 2.9 131148 Hs.303125ESTs 2.9 123158 Hs.218329heat shock 70kD protein2.9 133667 Hs.75462 Human BTG2 (BTG2) mRNA;2.9 072649 complete cds 105182 Hs.18271 ESTs; Weakly similar 2.9 AA191014 to Ydr372cp [S.cere 133968 Hs232068 Human mRNA for transcription2.9 D15050 factor AREB

117425 Hs.336901ESTs 2.9 111087 Hs.37637 ESTs 2.9 129641 Hs.11805 ESTs 2.9 128639 Hs.102897ESTs 2.9 133209 Hs.79265 ESTs; Moderately similar2.9 AA114183 to glutamate py 135154 Hs.267812sorting nexin 4 2.9 126838 Hs.279609pigment epithelium-derived2.9 AA858097 factor 103803 Hs.106149ESTs 2.9 102139 Hs.2128 dual specificity phosphatase2.9 128104 AA971000 op67g11.s1 Soares-NFL-T-GBC2.8 Si Homo sapi 127834 Hs.337631nz22dO8.s1 NCI-CGAP-GCBs2.8 AA761415 Homo Sapiens cD

133101 Hs.180952ESTs 2.8 127250 Hs.217916ESTs 2.8 135063 Hs.93883 myelin protein zero 2.8 D10537 (Charcot-Marie-Tooth 126323 Hs.68644 yy80gO6.r1 Soares_multiple-sclerosis-2Nb2.8 121873 Hs.145696ESTs 2.8 122090 Hs.98684 ESTs 2.8 118728 Hs.322645ESTs 2.8 135400 Hs.99915 androgen receptor (dihydrotestosterone2.8 M23263 r 125278 Hs.129998ESTs 2.8 3$ 124387 Hs.109019ESTs 2.8 124803 Hs.12186 cyclin K 2.8 H45968 Hs.32149 ESTs 2.8 104261 Hs.5409 RNA polymerise I subunit2.8 105366 Hs.282093ESTs 2.8 106070 Hs.5957 Homo sapiens done 244162.6 AA417761 mRNA sequence 131356 Hs.25960 v-myc avian myelocytomatosis2.8 M13241 viral relat 112009 Hs.26255 EST 2.8 133199 Hs250175 Homo sapiens clone 239042.8 AA609773 mRNA sequence 110379 Hs.33130 ESTs 2.8 103890 Hs.72085 ESTs; Weakly similar 2.8 AA236843 to unknown [S.cerev 128152 820353 yg20fi0.rlSoaresinfantbrainiNlBHomo2.8 107008 Hs.23740 ESTs 2.8 135243 Hs.97101 ESTs 2.8 103058 Hs.184510stratifin 2.8 132020 Hs293845 ESTs 2.8 116354 Hs.292566ESTs 2.8 125867 Hs.12372 ESTs 2.8 120603 Hs.98541 ESTs; Highly similar 2.8 AA282787 to (defline not ava -115119 Hs.46847 Human DNA sequence from2.8 AA256524 clone 30M3 on ch 133865 Hs.170290discs; large (Drosophila)2.8 F09315 homolog 5 109415 Hs.110826Homo sapiens CAGF9 mRNA;2.8 AA227219 partial cds 128687 Hs.23767 ESTs 2.8 109984 Hs.10299 ESTs; Moderately similar2.8 H09594 to !!!! ALU SUB

133179 Hs.66731 homeo box 813 2.8 115998 Hs.336629ESTs; Weakly similar 2.8 AA448488 to zinc finger prot 112180 Hs.25067 EST 2.8 120428 Hs.173694ESTs; Moderately similar2.8 AA236822 to (defline not 106241 Hs.6019 ESTs 2.8 131060 Hs.22564 myosin VI 2.8 ()~111383 Hs.40919 ESTs 2.8 102123 Hs.1594 centromere protein A 2.8 014518 (l7kD) 102722 Hs.79981 Human done 23560 mRNA 2.8 079242 sequence 129887 Hs.274324PCAF associated factor 2.8 W92041 65 alpha 126663 Hs.181297ESTs 2.8 104367 Hs.134342ESTs; Weakly similar 2.8 H17438 to seventransmembra 107316 Hs.193700ESTs; Moderately similar2.8 T63174 to !!1! ALU SUB

128059 Hs.145096ESTs 2.8 124447 N48000 ESTs 2.8 $ 111398 Hs.125565deafness; X-linked 2.8 800086 1; progressive 134085 Hs.79018 chromatin assembly 2.8 020979 factor I (150 kDa) 124788 Hs.100912ESTs 2.8 112248 Hs.326416ESTS 2.8 121309 Hs.97312 ESTs 2.8 zO 103076 Hs.75319 ribonucleot!de reductase2.8 X59618 M2 polypeptide 107071 Hs.35198 ESTs 2.8 104425 Hs.35380 ESTs - 2.8 132991 Hs.62245 solute carrier family 2.8 AA446906 25 (mitochondrial 104968 Hs.29669 ESTs 2.8 z$ 121153 Hs.97694 ESTs 2.8 131216 Hs.243901ESTs 2.8 109682 Hs.22869 ESTs 2.8 131990 Hs.168818ESTs; Moderately similar2.8 H77734 to roundabout 1 132027 Hs.18144dESTs; Weakly similar 2.8 N78844 to R12C12.6 [C.eleg 127383 Hs.190478ESTs 2.8 132598 Hs.530 collagen; type IV; 2.8 M81379 alpha 3 (Goodpasture 101121 Hs.1313 tumor necrosis factor 2.8 L09753 (ligand) superfami 123000 Hs.105640ESTs 2.8 121329 Hs.1755 ESTs 2.8 2$ 100481 Hs.121489 2.7 Cystatin D

113803 Hs.283683ESTs 2.7 110934 Hs.169001ESTs; Weakly s!m!lar 2.7 Nd8708 to cytochrome P-450 432888 T86823 ESTs 2.7 121802 Hs.188898ESTs 2.7 3O 130396 Hs.155313Human mRNA for IfIAA03332.7 AB002331 gene; partial cd 121103 Hs.97697 ESTs; Weakly similar 2.7 AA398936 to (defline not ava 131129 Hs.23240 ESTs 2.7 130943 Hs.272429calcium-sensing receptor2.7 D50855 (hypocalciuric 134676 Hs.87819 ESTs; Weakly similar 2.7 W28051 to keratin 9; cytos 35 1 1 1900 Hs.25318ESTs 2.7 106025 Hs.173334ESTs 2.7 126144 Hs.40639 yx92a07.r1 Soaves melanocyte2.7 N39696 2NbHM Homo 103248 Hs.75262 cathepsin 0 2.7 127230 Hs.274170Homo Sapiens Opa-interacting2.7 H30501 protein OIP

101584 Hs.84072 transmembrane 4 superfamily2.7 M35252 member 3 124131 Hs.i67489ESTs 2.7 129689 Hs.77873 ESTs 2.7 132892 Hs.9973 ESTs 2.7 120827 Hs.132967ESTs . 2.7 4$ 134579 Hs.85963 ESTs; Moderately similar2.7 N23222 to !!!! ALU SUB

106149 Hs.256301ESTs 2.7 132037 Hs.332541ESTs; Weakly similar 2.7 AA203649 to HEM45 [H.sapiens 130542 Hs.179825Human sperm membrane 2.7 064675 prote!n BS-63 mRNA, 122851 Hs.99598 ESTs 2.7 $O 134983 Hs.196384prostaglandin-endoperoxide2.7 D28235 synthase 2 (p 120537 Hs.160422ESTs 2.7 131036 Hs.174140ATP citrate lyase 2.7 133889 Hs.211582ESTs ' AA099391 2.7 128847 Hs.106529zv81e01.r1 Soaves-total-fetus-Nb2HF8_9w2.7 $$ 112755 Hs.306044ESTs 2.7 423239 AA323591 EST26392 Cerebellum 2.7 II Homo sapiens cDNA

105031 Hs.12321 ESTs 2.7 126021 Hs.187516ESTs 2.7 102116 013706 Human ELAV-like neuronal2.7 protein 1 isofo 6O 133394 Hs.237225ESTs; Weakly similar 2.7 Ri 6759 to (defline not ava 104267 Hs.278439ESTs 2.7 107614 Hs.40241 ESTs; Highly similar 2.7 AA004878 to (defline not ava 129809 Hs.1259 asialoglycoproteinreceptor22.7 112109 Hs.283309ESTs; Weakly similar 2.7 845221 to t!!! ALU SUBFAMI

6$ 128422 T85681 yd60c06.r1 Soaresfetalliverspleen2.7 109494 Hs.43899 ESTs 2.7 118696 Hs.292284Homo Sapiens RNA polymerase2.7 N72086 III largest 106053 Hs.36727 ESTs; Highly similar 2.7 AA416963 to histone H2A [H.s 104440 Hs.284380gamma-glutamyltransferase2.7 zzz 129426 Hs.111323EST; Highly similar to AA412087 (defline not avai 2.7 123798 AA620411 small inducible cytokine A5 (RANTESj 2.7 106716 Hs.238928ESTs 2.7 103663 278291 278291 Homo sapiens brain fetus Homo sap 2.7 114162 Hs.22265 ESTs 2.7 113063 Hs.5027 ESTs 2.7 127897 AA773857 af80c09.r1 Soares NhHMPu-Si Homo sapiens 2.7 130621 Hs.16803 ESTs; Weakly similar to AA621718 (defline not ava 2.7 116245 Hs.42796 ESTs; Highly similar to AA479958 (defline not ava 2.7 125499 811878 yf49d11.r1 Soares infant brain 1 NIB Homo 2.7 133960 Hs.77899 tropomyosin 1 (alpha) M19267 2.7 104470 Hs.246358ESTs; Weakly similar to N28843 Similar to colla 2.7 134982 Hs.92308 ESTs 2.7 106803 Hs.284295ESTs 2.7 104899 Hs.285574ESTs 2.7 125401 Hs.337585ESTs; Moderately similar AI204637 to KIAA0350 [H. 2.7 111253 Hs.15768 ESTs; Moderately similar N70042 to !!!! ALU SUB 2.7 118449 Hs.i 64478ESTs; Weakly similar to N66413 (defline not ava 2.7 134507 Hs.84318 replication protein A1 M63488 (70kD) 2.7 2~ 121609 Hs.98185 EST 2.7 113835 Hs.27475 ESTs 2.7 113962 Hs.285290ESTs; Highly similar to W86375 (defline not ava 2.7 121913 Hs.98558 ESTs 2.7 108194 Hs.216717ESTs 2.7 2$ 130799 Hs.12696 ESTs 2.7 123184 Hs.18166 Homo sapiens mRNA for AA489072 KIAA0870 protein; 2.7 103420 Hs.173497SEC23-like protein B 2.7 106186 Hs.6315 acetylserotonin N-methyltransferase-like AA427398 2.7 101349 L77559 Homo sapiens DGS-B partial mRNA 2.7 3O 112954 Hs.6655 ESTs 2.7 133054 Hs.291079ESTs; Weakly similar to 807876 unknown [S.cerev 2.7 128131 Hs.25640 claudin 3 2.6 101864 Hs.75777 transgelin 2.6 111948 Hs.26303 ESTs 2.6 35 130145 Hs.151051protein kinase mitogen-activated U07620 10 (MAP 2.6 126507 Hs.23964 ESTs 2.6 117903 Hs.47111 ESTs 2.6 116345 Hs.199067ESTs 2.6 132227 Hs.4248 ESTs 2.6 4O 125746 Hs.274256y[42b06.r1 Soares placenta H03574 Nb2HP Homo sa 2.6 105073 Hs.89463 ESTs 2.6 102764 U82310 Homo saplens unknown protein mRNA, parti 2.6 131367 Hs.173933ESTs 2.6 130792 Hs.19500 nuclear localization signal AA307896 deleted in v 2.6 45 107427 Hs.46736 ESTs 2.6 117477 Hs.d4175 ESTs 2.6 106290 Hs.16364 ESTs 2.6 126829 Hs.7910 ESTs 2.6 118836 Hs.173001ESTs 2.6 100147 Hs.1363d8osteoblast specific factor D13666 2 (fasciclin 2.6 104278 Hs.109253ESTs; Highly similar to C02582 (defline not ava 2.6 135051 Hs.83484 ESTs 2.6 126081 Hs.227835collagen; type I; alpha AI346024 1 - 2.6 123579 AA608983 af5d4.s1 Soares testis_NHT
Homo sap!ens 2.6 55 130115 Hs.149923X-box binding protein M31627 1 2.6 101434 Hs.1430 coagulation factor XI
M20218 (plasma thrombopla 2.6 122962 Hs.104720ESTs; Moderately similar AA478429 to !!!! ALU SUB 2.6 126151 Hs.40808 ESTs 2.6 128925 Hs.21851 Homo sapiens mRNA~ cDNA
D61676 DKFZp586J2118 (f 2.6 128919 Hs.103391insulin-like growth factor L27559 binding prote 2.6 130296 Hs.154103LIM protein (similar to RQ9286 rat protein king 2.6 128402 Hs.191637ESTs 2.6 129273 Hs.109968ESTs 2.6 125483 Hs.7788 ESTs 2.6 65 132953 Hs.321264ESTs 2.6 130963 Hs.21639 nuclear protein; marker U57099 for different!at 2.6 120614 Hs.194154ESTs; Weakly similar to AA284281 !!!! ALU SUBFAMI 2.6 123251 Hs.103267ESTs; Moderately similar AA490858 to Rabln3 (R.no 2.6 121710 Hs.96744 ESTs 2.6 125428 Hs.851 ESTs; Highly similar 2.6 W74608 to (defiine not ava 115906 Hs.82302 ESTs 2.6 108432 AA076626 Homo Sapiens clone 238512.6 mRNA sequence 126191 Hs.191911ESTs 2.6 106164 Hs.281434ESTs 2.6 111519 Hs.268615ESTs 2.6 134590 Hs.173840ESTs 2.6 102565 059748 Human desert hedgehog 2.6 (hDHH) mRNA, parti 129879 Hs.13109 ESTs 2.6 114264 Hs.334609ESTs 2.6 106236 Hs.21104 ESTs 2.6 135192 Hs.321709purinergic receptor 2.6 AF000234 P2X; ligand-gated io 109833 Hs.29889 ESTs 2.6 105756 Hs.8535 ESTs; Weakly similar 2.6 AA303088 to transformation-r 1 121422 Hs.97967 ESTs 2.6 ~ AA406210 130417 Hs.155485Human huntingtin interacting2.6 058522 protein (HI

124312 Hs.102329ESTs 2.6 108998 Hs.97199 ESTs 2.6 127081 Hs.180591ESTs; Weakly similar 2.6 888362 to weak similarity 129574 Hs.11463 ESTs; Weakly similar 2.6 AA458603 to (defiine not ava 112410 Hs.26904 ESTs 2.6 123929 Hs.112981ESTs 2.6 122905 Hs.104835ESTs 2.6 116399 Hs.110637Homo Sapiens homeobox 2.6 AA599729 protein A10 (HOXA1 130279 Hs.153934core-binding factor; 2.6 AA424044 runt domain; alpha 130021 Hs.1435 guanosine monophosphate2.6 M24470 reductase 100585 Hs.199160 2.6 Trithorax Homok~g Hrx 104965 Hs.30177 ESTs 2.6 117711 Hs.46485 EST 2.6 3~ 124792 Hs.48712 ESTs 2.6 111299 Hs.74313 ESTs 2.6 103616 Hs.32971 ~phosphoinositide-3-kinase;2.6 246973 class 3 133629 Hs.195614IfIAA0017 gene product 2.6 Di3642 126484 Hs.169977ESTs 2.6 35 100858 HG4245-HT4515 2.6 Forkhead Family Afxi 133547 Hs.301927T-cell receptor; alpha 2.6 X02883 (V;D;J;C) 126680 Hs.133865ESTs 2.6 125739 Hs.92137 v-myc avian myelocytomatosis2.6 AA428557 viral oncog 102276 Hs.10247 Human (memc) mRNA, 3'0T82.6 105586 Hs.191538ESTs 2.6 103978 Hs.34136 ESTs 2.6 125054 Hs.268601ESTs; Weakly similar 2.6 T80622 to (detiine not ava 114212 Hs.21201 ESTs; Highly similar 2.6 239338 to (defline not ava 116959 Hs.40022 EST 2.6 45 109228 Hs.306995ESTs 2.6 133989 Hs.78202 SWIISNF related; matrix2.6 029175 associated; acti 100640 Hs.182183 2.6 Caldesmon 1, Aft. Splice 3, Non-Muscle 133093 Hs.285996ESTs 2.6 114306 Hs.6540 ESTs 2.6 106060 Hs.171391C-terminal binding protein2.5 107748 Hs.60772 EST 2.5 100134 Hs.49 macrophage scavenger 2.5 D13264 receptor 1 133969 Hs.78 GA-binding protein transcription2.5 013044 factor; -130992 Hs.74316 ESTs 2.5 55 127493 Hs.291701oc39a08.s1 NCI_CGAP_GCBi2.5 AA808081 Homo Sapiens cD

132869 Hs.203961ESTs 2.5 117570 Hs.44583 EST 2.5 124644 Hs.109654ESTs 2.5 103558 Hs.2785 keratin 17 2.5 132883 Hs.5897 ESTs 2.5 102009 Hs.82643 protein tyrosine kinase2.5 116058 Hs.20159 ESTs 2.5 121989 Hs.193784ESTs 2.5 131257 Hs.24908 ESTs 2.5 65 100320 Hs.75275 homolog of yeast (S. 2.5 D50916 cerevisiae) ufd2 102959 Hs.121524glutathione reductase 2.5 132969 Hs.6166 ESTs 2.5 130869 Hs.2057 uridine monophosphate 2.5 AA128100 synthetase (orotat 129645 Hs.1181315;10-methenyltetrahydrofolate2.5 L38928 syntheiase 126399 AA128075z116dO8.r1 Soares~regnant_uterus Hs.83883 NbHPU 2.5 134069 U29607 Homo sapiens eIF-2-associated Hs.78935 p67 homolo 2.5 109816 F11013 ESTs; Weakly similar to Hs.61960 KIAA0176 [H.sapi 2.5 134801 X02160 insulin receptor 2.5 Hs.89695 104232 AB002351Human mRNA for KIAA0353 Hs.10587 gene; partial cd 2.5 107361 U72513 Human RPL13-2 pseudogene Hs.159486 mRNA; complete 2.5 106057 AA417067ESTs 2.5 Hs.289074 134252 AA031782Homo sapiens mRNA; cDNA
Hs.80720 DKFZp586B1722 (f 2.5 128062 AA379500ESTs 2.5 Hs.105547 1~ 110009 H10933 ESTs 2.5 Hs.6614 111375 N93696 ESTs 2.5 Hs.20432 122642 AA454186ESTs 2.5 Hs.99361 127999 AA837495ESTs; Weakly similar to Hs.69851 Wiskott-Aldrich 2.5 105029 AA126855ESTs 2.5 Hs.13268 15 105082 AA143763ESTs; Weakly similar to Hs.26765 Similarity to S. 2.5 TABLE 1 A show the accession numbers for those primekeys lacking unigene)D'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 126086 1606216_1H7568f H70975 125596 1708455_1825698 856582 856018 25 118417 37186_1AF080229 AF080231 AF080230 AF080232 AF080233 AF080234 AA204833 AW003247 AW496808 A1080480 AI63f 7Q3 AI651023 AI867418 AW818140 AA502500 Ai206 f 99 AI67f282 127261 231687_1AA330501 AA661567 126659 1541209_1T16245 819694 F13545 H10299 T66048 T65279 H18006 127315 37938_1AFf 16622 A1114507 AA640834 AA377999 45 128422 1811283_1T77794 T85681 AI310815 AA484951 ' 50 129735 44573_2AI950087 N70208 897040 N36809 AI308119 AW967677 A1741346 AI689062 AA2829f 5 AW102898 AI872193 55 AA856975 AW5055f2 AI96f530 AW629970 BE612881 AW276997 AW513601 AW512843 AA0442Q9 AW85&538 AA780419 AA55fOQ5 W80701 AW613456 AI373032 AI564269 F0053f H83488 W37181 W78802 866056 A1002839 ()0123147 219802AA487961 130529 158447_1AA178953 AA192740 123579 genbank_AA608983 109175 genbanILAA180496 100789 tigr_HT4163S67998 65 100858 tigr_HT4515U10072 102116 entrez_U13706 U13706 102398 entrez_U42359 U42359 102764 entrez_U82310 U82310 118475 genbanILN66845 N66845 104776 genbank_AA026349 AA026349 104787 genbank-AA027317 AA027317 113702 genbanILT97307 T97307 113938 genbanILW81598 W81598 1 0 122635 genbank-AA454085 AA454085 108407 genbank-AA075519 AA075519 108432 genbank_AA076626 AA076626 108555 genbank_AA084963 AA084963 101349 entrez_L77559 L77559 1 $ 124447 genbank_N48000 N48000 119071 genbank_R31180 831180 103520 entrez_Y10511 Y10511 103663 genbank_Z78291 278291 ZO 126959 546044_1 AA199853 AA206355 123465 genbank_AA599033 AA599033 MISSING AT THE TIME OF PUBLICATION

TABLE 2: shows a preferred subset of the Accession numbers for genes found in Table 1 which are differentially expressed in prostate tumor tissue compared to normal prostate tissue.
Pkey: Unique Eos probeset idenflfier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number 1 ~ Unigene Unigene gene title Tifle:

Ri : Raflo of tumor to normal body tissue (Relaxed ratio (87170) Pkey ExAccnUnlgenelD UnigeneTitle R1 131919 Hs.272458 ESTs 372 120328 Hs.290905 ESTs; Weaklysimilarto32.6 AA196979 (defline notava 101486 Hs.1852 acid phosphatase;252 M24902 prostate 119073 Hs.279477 ESTs 24.8 133428 Hs.183752 miaoseminoprotein;23.8 M34376 beta-128180 Hs.171995 kallikrein 21.4 AA595348 3; (prostate specific antigen 104080 Hs.57771 Homo sapiens 18.9 AA402971 mRNA for serine protease (T

127537 Hs.i62859 ESTs 18.6 131665 Hs.30343 ESTs 17.4 ~5 101050 Hs.i832 neuropeptide 17.3 130771 Hs.1915 folate hydrolase17 N48056 (prostate-specific memb 107485 Hs.262476 S-adenosylmethionine16.7 W63793 decarboxylase 1 106155 Hs.33287 ESTs 16.5 129534 Hs.11260 ESTs 16.4 100569 Antigen, Prostate HG2261-HT2351 Specific, Alt.
Splice 16 101889 Hs.181350 kallikrein 15.4 S39329 2; prostaflc 135389 Hs.99872 fetal Alzheimer15 U05237 antigen 133944 Hs.7780 ESTs 12.5 130974 Hs.2178 H2B hisfone family;11.8 X57985 member Q

35 114768 Hs.182339 ESTs 11.8 104660 Hs.14846 ESTs 11.4 131061 Hs.268744 ESTs; Moderately10.9 N64328 similar to KIAA0273 [H.

126645 Hs.61635 Homo Sapiens A1167942 BAC done RG041 D11 from 7q2 10.7 135153 Hs.95420 Homo sapiens 10.6 N40141 mRNA for JM27protein;
comp 107033 Hs.113314 ESTs 10.6 118417 ESTs; Weakly similar 10.5 N66048 to polymerise [H.sa 126758 Hs293960 ESTs 102 107102 Hs.30652 ESTs 10.1 116787 Hs.15641 ESTs 10.1 45 115719 Hs.59622 ESTs 10 123209 Hs203270 ESTs 9.9 101664 Hs.121017 H2A histone 9.8 M60752 family; member A

112971 Hs.83883 ESTs 9.7 117984 Hs.106778 ESTs 9.7 5~ 129523 Hs274509 T-cell receptor,9.4 M30894 gamma cluster 132964 Hs.167133 ESTs 9.2 121853 Hs.98502 ESTs 9 119617 Hs.55999 ESTs 8.9 105627 Hs.23317 ESTs 8.8 55 101461 Hs.76422 phospholipase 8.7 M22430 A2; group IIA (platelets;

124526 Hs293185 yz61c5.s1 Soares_multip~8.5 N62096 sclerosis_2NbH

133845 Hs.76704 ESTs 8.2 133354 Hs.334762 ESTs; Weakly 8.1 AA055552 similar to KIAA0319 [H.sapi 119018 Hs.278695 ESTs 8 ()~100394 Hs.66052 CD38 antigen 8 D84276 (p45) 106579 Hs.23023 ESTs 7.6 114965 Hs.72472 ESTs 7.4 112033 Hs22627 ESTs 7.1 102398 Human N33 protein form 7 U42359 t (N33) gene, exo 65 101201 Hs2256 matrix metalloproteinase6.9 122524 7 (matrilysin;

101803 Hs.155691 pre-B-cell 6.8 M86546 leukemia Uansaiption factor 120562 Hs.302267 ESTs; Weakly 6.8 AA280036 similar to WOtA6.c [C.elega 109112 Hs.257924 ESTs 6.8 109795 Hs.326416 ESTs 6.7 130336 Hs.i71995 kallikrein 6.6 X07730 3; (prostate specific antigen 131425 Hs26691 ESTs 6.6 132902 Hs.59838 ESTs 6.6 133724 Hs.75746 aldehyde dehydrogenase6.5 120215 Hs.108787 Homo sapiens 241050 Mcd4p homolog mRNA;
complet 6.5 131881 Hs.3383 upstream regulatory6.5 AA010163 element b!nding prot 100727 Hs.334786 Human HF.12 6.3 X07290 gene mRNA

121770 Hs.278428 Homo sapiens 6.3 AA421714 mRNA for KIAA0896 protein;

123475 Hs.250528 ESTs; Weakly 6.3 AA599267 s!milar to ANKYRIN;
BRAIN V

133061 Hs296638 prostate differentiation6.3 AB000584 factor 116429 Hs.279923 ESTs; Weakly 6.2 AA609710 similar to similar to GTP-b 101233 Hs.878 sorbitol dehydrogenase6.2 104691 Hs.37744 ESTs 6.2 127248 EST27953 Cerebellum II
AA325029 Homo Sapiens cDNA6,2 105500 Hs222399 ESTs 6.1 130828 Hs203213 ESTs 5,9 115357 Hs.72988 ESTs 5.8 116334 Hs.48948 ESTs 5.7 120132 Hs.125019 ESTs; Weakly 5.6 238839 similar to !!!! ALU
SUBFAMI

106375 Hs.289072 ESTs 5.6 124777 Hs.140237 ESTs; Weakly 5.6 841933 similar to neuronal thread 101791 Hs.62354 Human beige-like5.5 M83822 protein (BGL) mRNA;
par 117698 Hs.45i07 ESTs 5.5 122041 Hs.98732 Homo Sapiens AA431407 Chromosome 16 BAC done CIT 5.5 133723 Hs.262476 S-adenosylmethionine5.5 AA088851 decarboxylase 1 113938 ESTs 5.4 133015 Hs.246315 ESTs - 5.4 3O 108186 Hs.7780 ESTs 5.3 104466 Hs.326392 Human guanine 5.3 N25110 nucleotide exchange factor 104033 Hs.98944 ESTs 5.3 ii0844 Hs.167531 ESTs; Weakly 5.3 N3i952 similar to (def!ine not ava 129056 Hs.10B336 ESTs; Weakly 5.3 H70627 similar to !!!! ALU
SUBFAMI

35 133493 Hs.194369 Homo Sapiens 5.3 AA284143 chromosome 1 atrophin-1 rel 129184 Hs.10920i ESTs; Highly 5.2 W26769 similar fo (defline not ava 101448 Hs.195850 keratin 5 (epidermolysis5.1 M21389 bullosa simplex 116188 Hs.184598 ESTs; Weakly 5.1 AA464728 similar to !!!! ALU
SUBFAMI

105921 Hs.169119 ESTs 5.1 40 103375 Hs.54416 sine oculis 5.1 X91868 homeobox (Drosophila) homolo 128871 Hs.106778 ESTs; Highly 5.1 AAd00271 similar to (defline not ava 116238 Hs.47144 ESTS 5 102913 Hs.80342 keratin 15 5 103011 Hs.326035 early growth 5 X52541 response 1 45 118981 Hs.39288 ESTs; Weakly 5 N93839 similar to !!!! ALU
SUBFAMI

TABLE 2A shows the accession numbers for those primekeys lacking unigene>D'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 Accession AI867418 AW818140 AA502500 AI206199 AI67i282 127248 227560_1AA364195 AA325029 AW962050 107033 235652_1 AI141999 AA730176 844544 841778 AW300793 AW966157 102398 entrez-042359042359 113938 genbank-W81598W81596 TABLE 3: shows genes, including expression sequence tags, differentially expressed in prostate tumor tissue compared to normal tissue as analyzed using the Affymetrix/Eos Hu02 GeneChip array. Shown are the relative amounts of each gene expressed in prostate tumor samples and various normal tissue samples showing the highest expression of the gene.
1 ~ Pkey: Unique Eos probeset identifier number ExAcar: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title Ri: Ratio of tumor to normal body tissue Pkey ExAccn UnigenelD Unigene Title R1 100131 Hs.t phosphodiesterase 6.3 D12485 1951 (/nucleotide pyrophosp 2~ 100235 Hs.13421KIAA0056 protein 5.1 100570 Hs.171995 Antigen, Prostate HG2261-HT2352 Spedfic, AIL
Splice 100819 Hs.2387 Transglutaminase HG4020-HT4290 10.5 101063 Hs.80247cholecystokinin 8.5 101247 Hs.78802glycogen synthase 4.7 L33801 kinase 3 beta 101416 Hs.279477v-ets avian erythroblastosis4.7 M17254 virus E26 0 101447 Human alpha satellite11 M21305 and satellite 3 ju 101485 Hs.89546seledin E (endothelia(9.8 M24736 adhesion molecul 101514 Hs.123072RA83B; member RAS 6.2 M28214 oncogene family 101626 Hs.44 pleiofrophin (heparin8.4 M57399 binding growth fac 101863 Hs.2178H28 histone family;4.9 M60750 member A

101758 Hs.79217pyrroline-5-carboxylate5.4 M77836 redudase 1 101768 Hs.78989 7.5 101817 Hs.152292SWIISNF related; 5.5 M88163 matrix assodated;
acti 101888 Hs.95243transcription elongation5.7 M99701 factor A (511)-102031 Hs.2156RAR-related orphan 132 004898 receptor A

102052 Hs.505iSLi transcription 8.9 007559 factor; LIMlhomeodoma 102221 Hs.3844LIM domain only 5.6 102233 Hs.79334nuclear factor; 7.4 026173 interleukin 3 regulated 102302 Hs.69171protein kinase C-like8.2 102348 Hs.87539aldehyde dehydrogenase5.9 102457 Hs2359dual spec~city phosphatase5.1 102473 Hs.180398LIM domain-containing5.7 049957 preferred transkx 102669 Hs29279eyes absent (Drosophila)9 071207 homolog 2 102698 Hs.t867progasfricsin (pepsinogen10.6 075272 C) 102751 Hs.68583mitochondrial intermediate15.6 080034 peptidase 102823 Hs.5057carboxypeptidase 4.9 102869 Hs.572orosomucoid 1 22.6 103031 Hs.123114cystatin S 4.7 103043 Hs.93379eukaryotic translation4.9 X55733 initiation factor 5~ 103093 Hs.44926dipeptidylpeptidase5.8 X60708 IV (CD26; adenosine 103376 Hs.323378coated vesicle membrane5.2 X92098 protein 103401 Hs.54431specific granule 7.4 X95240 protein (28 kDa);
cysts 103613 Hs.2316SRY (sex determining5.2 246629 region Y)-box 9 (ca 103677 H.sapiens mRNA for 4.9 283806 axonemal dynein heavy 103962 Hs.83243ESTs 6 104084 Hs.30732ESTs 6.4 104257 Hs.9222estrogen recepfor-binding6.8 AF006265 fragment-assoc 104301 Hs.6783ESTs 10.5 104769 Hs293943ESTs; Weakly similar6.3 AA025887 to !!!! ALU SUBFAMI

104851 Hs.10290U5 snRNP-spedfic 4.9 AA040882 40 kDa protein (hPrpB-104896 Hs23165ESTs 5.8 104956 Hs20509ESTs; Weakly similar6.4 AA074880 to hypothetical pro 104957 Hs.10026ESTs; Weakly similar4.8 AA074919 to ORF YJL063c [S,c 104967 Hs291000ESTs 6.5 f75105099 Hs23729Homo sapiens done 7 AA150776 24405 mRNA sequence 105298 Hs2&369ESTs 5.1 105304 Hs.190325 ESTs 4.7 105370 Hs.22791 ESTs; Weakly s!m!lar10.3 AA236476 to transmembrane pr 105427 Hs28248 ESTs 5 AA25i330 105542 Hs.266957 ESTs; Weakly 8.8 AA261858 similar to heat shock prote 105628 Hs.79828 ESTs; Weakly similar5.5 AA281251 to putative zinc ti 105640 Hs.6685 ESTs; Weakly similar8 AA281623 to KIAA0742 protein 105645 Hs.11325 ESTs 14 105691 Hs.289b68 transcription 6.3 AA287097 factor 4 105730 Hs.5364 DKFZP5641052 protein4.9 105808 Hs.286131 KIAA0438 gene 7 AA393808 product 105826 Ns.194477 ESTs; Moderately5 AA398243 similar to similar to N

105903 Hs.200016 ESTs; Weakly 9.9 AA401433 s!milar to diphosphoinosito 105906 Hs.22380 ESTs 11.5 106065 ~ Hs.25206 ESTs 5.1 1$ 106094 Hs.23317 ESTs 10.9 106157 Hs.34892 ESTs 6.6 106184 Hs.10762 ESTs 8.5 106211 Hs.126083 ESTs 8.4 106213 Hs.8769 Homo sapiens mRNA;
AA428258 d)NA DKFZp564E153 (fr 5.7 106272 Hs.323099 ESTs 5.8 106369 Hs.288856 ESTs 6.3 106400 Hs.94109 ESTs 5.4 106474 Hs.42484 Homo Sapiens mRNA;
AA4502i2 d)NA DKFZp564C053 (fr 9.2 106507 Hs.267819 .protein phosphatase5.6 AA452584 1; regulatory (inhib 106523 Hs.31511 ESTs 4.7 106532 Hs.37443 ESTs 4.7 106557 Hs.22247 ESTs 5.7 106575 Hs.105421 ESTs 7.2 106618 Hs.8715 ESTs; Weakly similar5.6 AA459249 to Similarity with 106820 Hs.12592 ESTs 5.4 106846 Hs.34892 ESTs 5.3 106973 Hs.11923 Human DNA sequence7.5 AA505141 from clone 167A19 on 107110 Hs.12784 KIAA0293 protein 6.1 107127 Hs.179898 ESTs 7.1 107159 Hs.10600 ESTs; Weakly similar5.2 AA621340 to ORF YKR081 c [S.c 107217 Hs.35861 DKFZP586E162i 15.1 D51095 protein 107365 Hs.i 11256 arachidonate 4.7 U78294 15-lipoxygenase; second typ 107630 Hs.60178 ESTs 5.3 107734 Hs.7517 ESTS 4.8 4~ 107760 Hs.252085 EST 7.6 107997 Hs.82223 Human DNA sequence10.5 AA037388 from clone 141 H5 on c 108012 Hs.173334 ESTs 6.5 106520 Hs.46786 ESTs 7.9 108583 Hs.68826 ESTs 5.6 108613 Hs.69165 ESTs 6 108664 Hs.69588 EST 6.3 108677 Hs.118531 ESTs 5.9 108807 Hs.49376 ESTs; Weakly similar5.8 AA129968 to PROTEIN PHOSPHAT

108910 ESTs 5 5O 108933 Hs.337232 ESTs 12.7 108948 Hs.118258 ESTs 6.8 109014 Hs.262036 ESTs 15.3 109124 Hs.183887 ESTs 6.1 109142 Hs.41295 ESTs 5.1 109277 Hs.86043 ESTs 5.5 t09342 Homo Sapiens mRNA; d7NA (f6 AA213620 DKFZp586M14i8 109562 Hs.187931 ESTs; Moderately10.8 F01811 similar to voltage-gate 109565 Hs23648 ESTs 7 109648 Hs.7154 ESTs 9.9 109799 Hs.180378 Homo Sapiens 6.4 F10770 done 669 unknown mRNA;
cam 109859 Hs.20792 ESTs 5.3 110181 Hs.31742 ESTs 16.8 110854 Hs.27931 ESTS 10 110924 Hs.12940 yy84a09.s1 Soares-multiple_sderosis_2Nb5.6 111046 Hs.318584 ESTs 6.9 111091 Hs.33032 Homo Sapiens mRNA;
N59858 cDNA DKFZp434N185 (fr 5.2 111157 Hs.99364 ESTs 5 111164 Hs.122489 ESTs; Weakly 5.6 N66857 similar to !!!! ALU CLASS
C

111221 Hs.15119 ESTs 6.2 111348 Hs.9585 ESTs 5.4 111353 Hs.6616 ESTs 5.3 111495 Hs.9683 ESTs 5.8 111540 Hs.9786 ESTs 6 111579 Hs.167115 KIAA0830 protein12.6 111581 Hs.5794 ESTs 7.1 111734 Hs.128749 ESTs 6.2 111861 Hs.25231 ESTs 9.4 111870 Hs.18685 ESTs; Weakly similar6.5 837778 to hypothetical pro 1O 111937 Hs.1d846 Homo Sapiens mRNA;
840431 cDNA DKFZp564D016 (fr 4.8 111987 Hs.6763 KIAA09d2 protein 6.4 112184 Hs.330242 ESTs 5.6 112286 Hs.158135 KIAA0981 protein9.3 112380 Hs.5740 ESTs 4.7 IS 112452 Hs.157461 ESTs 6 112601 Hs.78225 annexin A1 5.4 112753 Hs.169882 ESTs 5.8 112902 Hs.129190 ESTs 5.1 112984 Hs.289014 ESTs 4.9 113021 Hs.129836 KIAA1028 protein10.8 113083 Hs.266957 ESTs; Weakly 5.7 T40530 similar to heat shock prote 113200 Hs.10263 ESTs 7.3 113494 Hs.86538 ESTs 8.7 113849 Hs.8858 ESTs; Moderately 4.9 W60439 similar to cbp146 [M.mu ZJ~113883 Hs.11958 oxidative 3 alpha4.7 W72382 hydroxysteroid dehydro 113950 Hs.30504 Homo Sapiens mRNA;
W85765 d)NA DKFZp434E082 (fr 6.7 113986 Hs.21894 ESTs 5.9 113989 Hs.268828 ESTs 4.7 114124 Hs.125019 ESTs; Highly 21.3 238595 similar to KIAA0886 protein 114340 Hs.143611 ESTs 9.6 114346 Hs.130489 ESTs 5.2 114435 Hs.164975 Bicaudal D (Drosophila)7.4 AA018216 homolog 1 114463 Hs.40109 KIAA0872 protein 8.2 114652 Hs.107149 ESTs; Weakly 5.4 AA101416 similar to PTB-ASSOCIATED
S

35 114721 Hs.103822 ESTs 4.8 114730 Hs.331328 ESTs; Weakly 5.1 AA133527 similar to The KIAA0138 gen 114833 Hs.87159 ESTs; Moderately 5.5 AA234362 similar to CGI-66 prote 114860 Hs.42179 ESTs; Moderately 6.3 AA235112 similar to similar to m 114884 Hs293672 ESTs 5.2 4O i14895 Hs.76591 KIAA0887protein 4.7 114908 Hs.54973 ESTs 5.2 114932 Hs.16218 KIAA0903 protein 5.7 115084 Hs.42484 Homo Sapiens mRNA;
AA255566 cDNA DKFZp564C053 (fr 5.2 115140 Hs279938 ESTs; Weakly similar5.9 AA258030 to supported by GEN

45 115468 Hs.48499 ESTs; Highly similar4.7 AA287061 to Bdeight protein 115583 Hs.45231 LDOC1 protein 7.6 115709 Hs.58279 ESTs 4.8 115772 Hs.131740 ESTs 5 115774 Hs.288390 ESTs; Moderately5.4 AA424029 similar to dynamin; int 115776 Hs.81897 ESTs 5 115821 Hs.130965 ESTs; WeaWy similarto13.7 115955 Hs.44198 Homo sapiens BAC 10.6 AA446121 done RG054D04 from 7q3 116024 Hs.83883 Human DNA sequence6.8 AA451748 from done 718J7 on c 116108 Hs.28777 ESTs 6 55 116117 Hs.31575 SEC63; endoplasmic7.3 AA459117 reticulum translocon 116146 Hs.15423 ESTs 5.5 116296 Hs.62601 Homo Sapiens mRNA;
AA489033 d)NA DKFZp586K1318 (f 5.7 116379 Hs.71252 ESTs 5.9 116393 Hs.306051 protein phosphatase5.9 AA599463 2 (formerly 2A); reg 116401 Hs.59698 ESTs 7.9 116416 Hs.39982 ESTs 9.2 116587 Hs.121429 ESTs 5.2 116601 Hs.-05i40 ESTs 4.9 116684 Hs.66095 ESTs 7.2 65 116722 HSFIH32 Stratagene cat#9372125.5 F13654 (1992) Hom 116766 Hs.95097 ESTs 5.9 117453 Hs.108319 thyroid hormone 6.9 N29568 receptor-assodated prot 117557 Hs.44532 diubiquitin 4.8 117708 Hs.126280 ESTs 6.3 118001 Hs.47447 ESTs 11.4 118229 Hs.166254 heat shock 90kD 6.2 N62339 protein 1; alpha 118599 Hs.203697 ESTs 5.8 118645 Hs.125180 growth homwne 7.1 N70358 receptor 118873 Hs.44577 ESTs 6 118985 Hs.55028 ESTs 9.3 119107 Hs.63841 ESTs 6 119126 Hs.117183 ESTs 17.9 119271 Hs.65328 ESTs 6 1O 119367 Hs.250895 ESTs 5 119721 Hs.48376 ESTs 15.4 119741 Hs.43670 kinesin family 10.1 W70205 member 3A

119780 Hs.191381 ESTs; Weakly 5.3 W72967 similar to hypothetical pro 120217 Hs.66035 ESTs 4.8 1$ 120266 Hs.205442 ESTs; Weakly 8.8 AA173939 similar to inner centromere 120294 Hs.i5388i ESTs; Highly 4.9 AA190888 similar to NY-REN-62 antige 120418 Hs26613 Homo Sapiens mRNA;
AA236010 cDNA DKFZp586F1323 (f 4.7 120486 Hs.137569 tumor protein 5.6 AA253400 63 kDa with strong homolog 120524 Hs.192905 ESTs 4.9 2~ 120571 Hs.34892 ESTs 8.8 120596 Hs237323 ESTs 6.2 120713 Hs.96557 ESTs 9.9 120992 Hs.97594 ESTs 16.4 121429 Hs.41167 ESTs 6.9 25 121503 Hs290347 ESTs 7.6 121512 Hs.193736 ESTs 5.8 121816 Hs.48827 ESTs 4.6 122027 Hs.98721 EST; Weakly similar5.6 AA431302 to N-copine [H.sapie 122294 Hs.98927 ESTs 5.7 3O 122411 Hs,99083 ESTs 6.5 122791 Hs.129836 KIAA1028 protein12.4 122792 Hs,99519 ESTs 5.1 122969 Hs,104336 ESTs 4.9 123095 Hs.27413 ESTs 5.4 35 123100 Hs.306219 Homo Sapiens 5 AA485957 clone 25032 mRNA sequence 123295 Ns.250830 ESTs 4.7 123311 Hs.105069 ESTs 7.4 123583 Hs.iii240 ESTs 9.1 123619 ESTs 4.7 4~ 123645 Hs.i88691 ESTs 4.8 123709 Hs.112742 ESTs 7 123968 Hs.108327 damage-spedfic 5 C14333 DNA binding protein 1 (1 124178 Hs.97101 putative G protein-coupled6.8 H45996 receptor 124352 Hs.102406 ESTs 102 45 124357 yw37g07.s1 Morton Fetal 10.6 N22401 Cochlea Homo sap 124515 Hs.109370 ESTs 142 124911 Hs.174195 ESTs 4.8 125154 ESTs 4.7 125992 za36e07.r1 Soares fetal 5.1 W01626 liver spleen 1 NF

126802 Hs.97056 ESTs 5.1 126812 Hs.173933 ESTs; Weakly 4.6 236290 similarto NUCLEAR FACTOR

127080 Hs.190173 ESTs 5 127308 Hs.334390 ESTs 4.8 127370 Hs.70337 immunoglobulin 4.7 A1024352 superfamily; member4 55 127386 Hs.106728 ESTs 4.8 127965 HS292059 ESTs 4.8 128172 Hs265130 ESTs 5 128305 Hs279009 ESTs 5.8 128420 Hs.41296 ESTs; Weakly similarto17 A1088155 unknown [H.sapie 6O 128467 Hs.180428 ESTs; Weakly 4.8 AA176446 similar to hypothetical 43.

128610 Hs.10247 activated leucocyte7.9 L38608 cell adhesion molecu 128625 Hs.102652 ESTs; Weakly 8.1 AA242816 similar to KIAA0437 [H.sapi 128651 Hs.103135 ESTs 6.5 129088 Hs.194431 KIAA0992 protein5.2 f)5129136 Hs.250723 ESTs 5.1 129171 Hs.7753 calumenin 5.8 129229 Hs.109643 polyadenylate 5.8 AA211941 binding protein-intera~in 129386 Hs260024 Cdc42 effector 52 N27524 protein 3 129467 Hs.44208 ESTs 5.1 129564 H22136Hs.75295 guanylate cydase16.3 1; soluble; alpha 3 129699 AA458578Hs.12017 KIAA0439 protein;9.2 homok~g of yeast ubiqu 129821 F11019Hs.12696 cortadin SH3 8.6 domain-binding protein 129823 X00948Hs.1053f4 relaxin 2 (H2)9.1 129847 W46767Hs.296178 ESTs; Weakly 5.4 similar to RNA POLYMERASE

129912 AA047344Hs.107213 ESTs; Highly 6.5 similar to NY-REN-6 antigen 129958 L20591Hs.1378 annexin A3 5.1 129977 J04076Hs.1395 early growth 8.6 response 2 (Krox-20 (Drosop 130061 082256Hs.172851 arginase; type7.4 II

1~ 130241 078313Hs.153203 MyoD family 4.9 inhibitor 130466 N21679Hs.180059 ESTs 5.8 130541 X05608Hs.211584 neurofilament;6.7 light polypeptide (68kD) 130619 AA477739Hs.12532 ESTs 6.4 130925 N71935Hs.169378 multiple PDZ 7.9 domain protein 130938 AA013250Hs.2i398 ESTs; Moderately6.2 similar to PUTATIVE
GLU

130971 H20332Hs.301444 signal sequence6.4 receptor, gamma (translo 131066 F09006Hs.22588 ESTs 5 131126 F09012Hs.181326 myotubularin 6.4 related protein 2 131310 J02960Hs.2551 adrenergic; beta-2-;7.9 receptor, surface 2~ 131487 AA253220Hs.27373 Homo sapiens mRNA; d)NA DKFZp56401763 (f5.9 131561 X59841Hs.294101 pre-B-cell 7.6 leukemia transcription factor 131562 090551Hs28777 H2A histone family;5.1 member L

131579 N62922Hs.29088 ESTs 11 131629 AA442119Hs238809 ESTs 4.9 131682 AA428368Hs.30654 ESTs 4.8 131699 868657Hs.90421 ESTs; Moderately6.5 similar to I!!! ALU
SUB

131795 N32724Hs.32317 Sox-like transcriptional5.6 factor 132053 H9338fHs.38085 ESTs; Weakly 7.2 similar to putative glycine 132122 065092Hs.40403 Cbp/p300-interacting5.6 iransactivator; wit 132191 AA449431Hs.288361 KIAA0741 gene 8 product 132256 AA608856Hs.431 murine leukemia 5.5 viral (bmi-1) oncogene h 132482 AA429478Hs.238126 ESTs; Highly 6.6 similar to CGI-49 protein [

132533 AA021608Hs.172510 ESTs 5.8 132572 AA448297Hs237825 signal recognition6.2 particle 72kD

132581 842266Hs.52256 ESTs; Weakly 16 similar to beta-TrCP
protei 132700 N47109Hs.5521 ESTs 6.8 132701 AA279359Hs.55220 BCL2-assodated 5.3 athanogene 2 132725 L41887Hs.184167 splidng factor;7.8 arginine/serine-rich 132783 N74897Hs278894 DEADIH (Asp-Glu-Ala-Asp/His)5.9 box polypep 132790 X75535Hs.168670 peroxisomal 8 famesylated protein 132939 076189Hs.61152 exostoses (multiple)-like52 133142 F03321Hs.65874 ESTs 5.2 133342 029589Hs.7138 cholinergic receptor,10.3 muscarinic 3 133434 AA278852Hs.30212 ESTs 5.8 133453 M68941Hs.73826 protein tyrosine4.9 phosphatase; non-recept 133520 X74331Hs.74519 primase; polypeptide13.1 2A (58kD) 133544 T33873Hs.74624 protein tyrosine4.6 phosphatase; receptort 133608 013315Hs.75207 glyoxalase I 4.8 133626 H75939Hs.75277 Homo sapiens mRNA; d)NA DKFZp586M141 (fr 5 5~ 133633 D21262Hs.75337 nudeolar phosphoprotein6.3 p130 133797 S66431Hs.76272 retinoblastoma-binding6 protein 2 133928 N34096Hs.7766 ubiquitin-conjugating5.4 enzyme E2E 1 (homo 134095 047414Hs.79069 cydin G2 5.2 134249 N89827Hs.80667 RALBPi associated6.5 Eps domain containing 134321 AA418230Hs.8172 ESTs 7 134453 X70683Hs.83484 SRY (sex determining4.7 region Y)-box 4 134542 X57025Hs.85112 insulin-like 7.7 growth factor 1 (somatomedi 134570 066615Hs.172280 SWUSNF related;6.4 matrix associated; adi 134592 082613Hs.289104 Alu-binding 5.4 protein with zinc finger dom 134654 W23625Hs.8739 ESTs; Weakly 5 similar to ORF YGR200c [S.c 134666 AA482319Hs.8752 putative type 5.4 II membrane protein 134806 249099Hs.89718 spermine synthase6.7 134951 AA431480Hs.169358 ESTs 9.8 135066 X04602Hs.939f3 interieukin 5.7 6 (interferon; beta 2) ()$135155 AA358268Hs.i66556 ESTs;Moderatelysimilartotranscriptio4.9 135411 L10333Hs.99947 reticulon 1 5.3 300023 M10098AFFX control:18S ribosomal4.6 RNA

300254 AW079607Hs.55610 ESTs; Weakly 7.8 similar to ZnT-3 [H.sapiens 300273 AW013907Hs.167531 ESTs; Moderately11.5 similar to predicted us 300319 AW157646 Hs.153506 ESTs; Weakly similar to miaotubule-acti 8.5 300566 Hs.326392 son of sevenless5.8 H86709 (Drosophila) homolog 300578 Hs.134289 ESTs 4.4 300671 Hs.938i0 ESTs 7.9 $ 300675 Hs.1251)34 ESTs; Weakly 4.5 AA039352 similar to ORF YDL040c [S.c 300680 Hs.24817 ESTs; Weakly 5.2 AW468066 similar to KIAA0986 protein 300762 Hs.20509 ESTs 6.4 300810 Hs.146847 ESTs 5.8 300813 Hs208341 ESTs; Weakly 10.6 AA406411 similar to KIAA0989 protein l~ 300823 Hs.106823 ESTs; Weakly 5.6 AI863068 similar to putative zinc fi 300834 Hs.147924 ESTs 6.7 300923 Hs.i852 ESTs 7.6 300962 Hs293744 ESTs 5.5 301015 Hs.20252 ESTs; Weakly 7 AA947682 similar to Chain A; Cdc42hs 1$ 301042 Hs.197733 ESTs 24.9 301242 Hs23782 ESTs 11.8 301254 Hs.283390 EST cluster 4.3 A1049624 (not in UniGene) with axon h 301262 Hs.7130 ESTs; Moderately 4.3 H29500 similar to N-copine [H.

301388 Hs.262036 ESTs; Weakly 6.6 AA156879 similar to ZINC FINGER
PROT

20 301563 Hs.44208 ESTs; Weakly 5.7 AI802946 similar to match to ESTs AA

301656 Hs.151258 EST duster (not6.8 AW008475 in UniGene) with axon h 301689 Hs.301789 ESTs; Weakly 6.3 244810 similar to similar to C.ele 301783 Hs.83937 Homo sapiens 6.2 AL046347 PAC done DJ1159004 from 7p 301805 Hs.142846 ESTs; Weakly 8.5 AI800004 similar to MesPi [M.musculu 2$ 301846 Hs.6823 ESTs; Weakly similar4.6 820002 to intrinsic factor 301891 Hs.279591 Homo sapiens 6.3 AF131855 done 25056 mRNA sequence 302005 Hs.123119 ESTs 36.8 302056 Hs.30488 ESTs; Moderately9.5 AI457532 similar to ROSA26AS [M.

302067 Hs.222399 ESTs; Weakly 5.8 H05698 similar to protein-tyrosine 302099 Hs.137576 ribosomal protein8.8 AL021397 L34 pseudogene 1 302147 Hs.151717 KIAA0437 protein5.9 302214 Hs.159425 Homo sapiens 4.3 AJ001454 mRNA for testican-3 302236 Hs.6557 zinc finger protein4.3 302358 Hs.322848 EST duster (not5.5 D81150 in UniGene) with axon h 3$ 302410 Hs.218366 EST duster (not26.8 NM-004917 in UniGene) with axon h 302486 Hs.183512 multiple UniGene8.2 AC003682 matches 302582 Hs.249195 EST duster (not6.4 NM_000522 in UniGene) with axon h 302785 Hs.11065 EST duster (not 5 AA425562 in UniGene) with axon h 302792 Hs.46821 ESTs; Weakly 4.8 AA343696 similar to putative [H.sapi 302881 Hs.105314 relaxin 1 (H1) 78.8 302892 Hs.42346 histone deacetylase8.5 302970 Hs.312679 EST duster (not7.4 AW118352 in UniGene) with axon h 302977 Hs.315111 EST duster (not5.5 AW263124 in UniGene) with axon h 303029 EST duster (not in UniGene)4.6 AFi99613 with axon h 4$ 303125 Hs.111782 EST duster (not5.8 AF161352 in UniGene) with axon h 303280 Hs.170307 ESTs 4.3 303306 Hs.61441 EST duster (not 6.4 AA215297 in UniGene) with axon h 303309 Hs.145416 ESTs 6.6 303344 Hs250646 ESTs; Highly 19.5 AA255977 similar to ubiquitin-conjug $~ 303360 Hs.326567 EST duster (not6.6 AA298471 in UniGene) with axon h 303401 Hs.309497 ESTs 6.8 303525 Hs.273294 ESTs 4.8 303526 Hs.96900 ESTs 12.1 303540 Hs.309490 ESTs; Weakly 8.2 AA355607 similar to MMSET type I [H.

$$ 303572 Hs.242540 ESTs 8.4 303685 Hs.23643 EST duster (not 4.9 AW500106 in UniGene) with axon h 303699 Hs.19525 EST duster (not 15.7 D30891 in UniGene) with axon h 303702 Hs.224961 ESTs; Weakly 6.3 AW500748 similar to 73 kDA subunit o 303718 Hs.114658 ESTs 4.6 6O 303722 Hs.145010 ESTs 12.5 303732 Hs.125759 ESTs; Weakly 4.3 AW502405 similar to tumor suppressor 303735 Hs.169055 ESTs; Weakly 5.4 AA707750 similar to ds-Golgi matrix 303752 Hs.5957 EST duster (not 5.3 A1017286 in UniGene) with axon h 303753 Hs.9414 ESTs 13 6$ 303813 Hs.i 14658 EST duster 7.8 AI275850 (not in UniGene) with axon h 304053 Hs.125565 translocase 4.8 800493 of inner mitochondrial membr 304218 Hs27973 ESTs; Weakly similar6 N66373 to ZK354.7 [C.elega 305200 Hs.45207 EST singleton 5.7 AA668128 (not in UniGene) with axon 306716 Hs25i354 ESTs 5.7 307848 AI364186EST singleton (not in 7.3 UniGene) with axon 307871 AI368665Hs.31476 EST singleton 5.4 (not in UniGene) with axon 308050 AI460004Hs.31608 EST singleton 8.1 (not in UniGene) with axon 308362 AI613519Hs.105749 EST singleton 5.5 (not in UniGene) with axon 308923 AI863051Hs.279815 ESTs 4.4 309116 AI927149Hs29797 ribosomal protein4.5 309375 AW075342Hs.9271 EST singleton 7.4 (not in UniGene) with axon 309674 AW205604Hs.266009 ESTs; Weakly 5 similar to !!!! ALU
SUBFAMI

310095 AI921750Hs.144871 ESTs 5 1~ 310098 AI685841Hs.161354 ESTs 11.6 310250 AI478629Hs.158465 ESTs 5.8 310365 AI262148Hs.145569 ESTs 9.7 310382 AI734009Hs.127699 EST duster 10.4 (not in UniGene) 310409 AI612775Hs.145710 ESTs . 4.6 15 310431 AI420227Hs.149358 ESTs 72.9 310573 AW292180Hs.156142 ESTs 7.6 310598 AI338013Hs.140546 ESTs 9.2 310639 AW269082Hs.175162 ESTs 4.5 310787 AW262580Hs.147674 ESTs 4.9 2~ 310816 AI973051Hs.224965 ESTs 7.6 311251 AI655662Hs.197698 ESTs 41.3 311280 AI767957Hs.198248 ESTs; Weakly 4.5 similar to Y38A8.1 gene pro 311330 AI679524Hs.201629 ESTs; Moderately4.6 similar to !!!! ALU
SUB

311515 AWi367i3Hs23862 ESTs 5.9 25 311574 AI824863Hs211420 ESTs 4.8 311587 AI828254Hs.271019 ESTs 5.8 311596 AI682088Hs.79375 ESTs 26.4 311631 AI8095i9_ Hs.27133 ESTs 6.4 311688 AW025661Hs.240090 ESTs 7.4 311783 AI682478Hs.13528 EST 4.6 311826 AA765470Hs.85092 ESTs 6.7 311853 AW014013Hs.107056 ESTs 5.3 311901 816890Hs.137135 ESTs 5.6 311932 AW451654Hs257482 ESTs 4.3 35 312153 AA759250Hs.118625 cytochrome 11 b~561 312182 AA834800Hs.326263 EST duster 16.9 (not in Un!Gene) 312242 AI380207Hs.125276 ESTs 4.7 312296 C01367Hs.127128 ESTs 5.3 312407 846180Hs.153485 ESTs 6.2 312424 AA847398Hs291997 ESTs 4.8 312425 849353Hs293892 ESTs 52 312480 868651Hs.144997 ESTs 9.5 312518 C17785Hs.182738 ESTs 6.3 312521 AA033609Hs.239884 ESTs 112 312527 AI695522Hs.191271 ESTs 4.7 312539 A1004377Hs200360 ESTs 7 312546 AI623511Hs.118567 ESTs 5.1 312563 AA976064Hs.180842 ESTs 6.5 312623 AA694607Ns.176956 EST cluster 10.8 (not in UniGene) 312857 AA772279Hs.126914 ESTs 5 312890 AI813654Hs.5957 ESTs 5.8 312903 AA939266Hs.278626 ESTs 7.7 312905 H92571Hs.234478 ESTs 6.5 312976 AA836271Hs.i25830 ESTs 4.6 312983 A1079278Hs269899 ESTs 5.1 312996 AA249018Hs.154331 EST duster 7 (not in Un!Gene) 313035 N36417Hs.144928 ESTs 6.3 313166 AI801098Hs.151500 ESTs 4.3 313188 A1039702Hs.179573 collagen; type4.8 I; alpha 2 ()~313218 AA827805Hs.124296 ESTs 5 313226 AI200281Hs.123910 ESTs 5.9 313325 AI420611Hs.127832 ESTs 4.6 313326 A1088120Hs.122329 ESTs 7.4 313425 AA745689Hs.186838 ESTs; Weakly 6.3 similar to similar to zinc 65 313499 AI261390Hs.146085 ESTs 5.6 313540 AI797301Hs.5740 ESTs 5.9 313568 AW467376Hs.129640 ESTs 4.3 313569 AI273419Hs.135146 ESTs; Weakly 4.6 similar to ZK1058.5 (C.e!eg 313603 AW468119Hs287631 EST duster (not6.8 in UniGene) 313615 AW295194Hs.301997 DKFZP434N126 5.2 protein 313625 AW468402Hs.25d020 ESTs 7.8 313634 AA688292Hs.337786 ESTs 4.4 313635 AA507227Hs.6390 ESTs 8.1 $ 313638 AI753075Hs.104627 ESTs 6.7 313670 C16690Hs.23767 EST duster (not4.4 in UniGenej 313671 W49823Hs.1046i3 ESTs 4.4 313676 AA861697Hs.120591 EST duster 13.4 (not in UniGene) 313703 A1161293Hs.280380 ESTs; Weakly 10 similar to KIAA0525 protein 1O 313712 AA768553Hs.74170 ESTs 5.2 313800 AW296132Hs.55098 ESTs 5.4 313979 A1535895Hs.221024 ESTs 4.3 314121 AI732100Hs.187619 ESTs 13.6 314123 AW245993Hs.223394 ESTs 6.4 1$ 314171 AI821895Hs.193481 ESTs 29.4 314188 AL138431Hs.164243 ESTs 4.6 314219 AL036001Hs.48376 ESTs 5.7 314236 AA743396Hs.189023 ESTs 4.9 314237 AA732359Hs.96264 ESTs 4.4 2~ 314284 AA731431Hs.293464 EST duster 6.4 (not in UniGene) 314305 A1280112Hs.125232 ESTs 5.3 314343 AI754701Hs.328476 ESTs; Weakly 62 similar to alternatively sp 314530 A1052358Hs.193726 ESTs 4.5 314691 AW207206Hs.136319 ESTs 17 2$ 314695 AW5Q2698Hs.118152 ESTs 8.9 314785 AI538226Hs.32976 ESTs ~ 9.4 314801 AA481027Hs.109045 ESTs; Weakly 8 similar to ORF YGR245c (S.c 314864 AA493811Hs294068 ESTs 6 314807 A1872225Hs.222886 ESTs 19.3 30 314916 AA548906Hs.122244 ESTs 4.5 314954 AA521381Hs.187726 ESTs 5.3 31'4981 Hs.293334 ESTs 4.6 315021 AA533447Hs.312989 EST duster 5.1 (not in UniGene) 315051 AW292425Hs.t63484 EST 15.5 35 315052 AA876910Hs.134427 ESTs 20 315073 AW452948Hs.257631 ESTs 5.3 315084 AI82i085ESTs 8.2 315214 A1915927Hs.34771 ESTs 5.4 315220 A1420753Hs.66731 ESTs 5.1 4O 315278 AI985544Hs.12450 ESTs 5.8 315282 AI222165Hs.144923 ESTs 4.5 315368 AW291563Hs.104696 ESTs B

315369 AA764918Hs.256531 ESTs 4.8 315378 AI263393Hs.145008 ESTs 6.2 4$ 315379 A1378329Hs.126629 ESTs 5.4 315402 AW293424Hs.75354 ESTs 5.1 315442 AA977935Hs.127274 ESTs 6.6 315443 AW003416Hs.160604 ESTs 5.5 315528 837257Hs.184780 ESTs 8.1 $~ 315593 AW198103Hs.158154 ESTs 9.9 315634 AA837085Hs.220585 ESTs 7.8 315705 AW4492&5Hs.313636 ESTs 8.9 315707 A1418055Hs.181160 ESTs 5.1 -315714 AA744015Hs.298138 EST duster 6.1 (not in UniGene) $$ 315740 TQ5558Hs.i56880 EST duster 6.8 (not in UniGene) 315762 AI391470Hs.158618 ESTs 5.3 315769 AA744875Hs.189413 ESTs 5 315843 AA679430Ns.i91897 ESTs 5.7 315990 AI800041Hs.190555 ESTs 9.2 6O 316012 AA764950Hs.119898 ESTs 4.3 316036 AA7080i6Hs.190389 ESTs 5.9 316055 AA693880Hs.6947 EST duster (not 6.7 in UniGenej 316074 AW517542Hs293273 ESTs 5.5 316100 AW203986Hs.213003 ESTs 5.1 65 316169 AI127483Hs.120451 ESTs 82 316442 AA760894Hs.153023 ESTs 17.1 316491 AA766025Hs.186854 EST 4.6 316504 AW135854Hs.132458 ESTs 4.3 316667 AW015940Hs.232234 ESTs 7.6 316854 AA83f215Hs.159066 ESTs; Weakly 5.1 similar to predicted using 316905 AW138241Hs210846 ESTs 6.4 317008 AW051597Hs.143707 ESTs 4.4 317019 AA864968Hs.127699 ESTs 11 $ 317194 AW445167Hs.126036 ESTs 13.5 317224 D56760Hs.93029 ESTs 8.7 317404 AI806867Hs.126594 ESTs 8.7 317501 AA931245Hs.137097 ESTs 11.1 317548 AI654187Ns.f95704 ESTs 142 1O 317651 AW292779Hs.i69799 ESTs 5.8 317758 AI733277Hs.128321 ESTs 5.4 317850 N29974Hs.152982 EST cluster 11.4 (not in UniGene) 317869 AW295184Hs.i29142 ESTs; Weakly similar to DEOXYRIBONUCLEAS
13.8 317902 AI828602Hs211265 ESTs 5.3 1$ 317916 AI56507iHs.159983 ESTs 7.7 318239 A1085198Hs.164226 ESTs 13.1 318268 AI817736Hs.i82490 ESTs 6.2 318327 AW294013Hs.200942 ESTs 4.6 318363 845530Hs.1440 gamma-aminobutyric6 acid (GABA) A recepto 2~ 318428 AI949409Hs.194591 ESTs 12.3 318464 AI15i010Hs.157774 ESTs 4.3 318524 AW291511Hs.159066 ESTs 25.9 318540 T30280Hs.274803 EST cluster 7 (not in UniGene) 318591 AW206806Hs.i 15325 ESTs 4.8 2$ 318615 Ai133617Hs.10177 ESTs 5.5 318646 AW175665Hs278695 ESTs 5.7 318667 AI493742Hs.165210 ESTs 11 318668 W26276Hs.136075 ESTs 5.9 318753 AA578265Hs.7130 copine IV 5.5 319080 245131Hs.23023 ESTs 16.9 319181 F06504Hs.27384 EST cluster 4.6 (not in UniGene) 319191 AF07f538Hs.79414 prostate epithelium-spedfic6.6 Ets transcr 319233 821054Hs.180532 ESTs 4.9 319586 D78808Hs.283683 ESTs 8.2 35 319750 AA621606Hs.117956 ESTs 9.3 319763 AA460775Hs.6295 ESTs 14.3 319824 AA424266Hs.123642 EST cluster 12.8 (not in UniGene) 319838 AA337642Hs.95262 nuclear factor 5.i related to kappa B bindin 319913 AA179304Hs.271586 ESTs; Moderately4.3 similar to !!!! ALU
SUB

4O 319964 T80579Hs290270 ESTs 5.8 320076 AI653733Hs271593 ESTs 8.5 320102 AW296219Ns.115325 FiAB7; member 9.8 RAS oncogene family-like 320187 T99949Hs.303428 EST duster 9.8 (not in UniGene) 32021 1 Hs.i25783 DEME-6 protein7.9 4$ 320324 AF071202Hs.139336 ATP-binding 562 cassette; sub-family C (CFTR

320455 849889Hs.24144 EST duster (not8.3 in UniGene) 320464 A1089817Hs.237146 ESTs 5.4 320561 NM_006953Hs.159330 EST duster 7 (not in UniGene) 320574 AL049443Hs.161283 Homo sap!ens mRNA; d)NA DKFZp586N2020 (f 4.4 $0 320576 AL049977Hs.162209 Homo sapiens mRNA; d7NA DKFZp564C122 (fr 6.7 320654 AW263086Hs.118112 ESTs 6 320796 AF038966Hs.31218 seaetory carrier13.5 membrane protein 1 320800 AI681006Hs.71721 ESTs 6.2 320813 AW360847Hs.16578 ESTs 9.3 $$ 320853 A1473796Hs.135904 ESTs 8.1 320856 D59945Hs.65366 EST duster (not6 in UniGene) 320899 AA633772Hs.116796 ESTs 9.2 320918 AW195012Hs.293970 ESTs 5 320973 H19732Hs.247917 ESTs 5.9 321099 AA018386Hs.64341 ESTs 4.6 321190 H52d62Hs.163872 EST duster 5.8 (not in UniGene) 321318 A8033041Hs.137507 EST duster 8.4 (not in UniGene) 321382 AW372449Hs.175982 EST duster 7.3 (not in UniGenej 321441 AW297633Hs.118498 ESTs 14.7 6$ 321538 H80483Hs.469D3 EST duster (not9.2 in UniGen~) 321609 H86021Hs.182538 ESTs; Weakly 4.8 similar to hMmTRAIb [H.sapi 321636 A1791838Hs.193465 ESTs 5.5 321638 AI356352Hs.f08932 ESTs 4.6 321644 AI204177Hs237396 ESTs 6.6 321681 Hs.190173 EST duster 4.6 AA233821 (not in UniGene) 321726 Hs.144465 EST duster 5 X91221 (not in UniGene) 321758 Hs.196151 EST duster 6.2 U29112 (not in UniGene) 321877 Hs.189222 EST duster 4.6 AL109784 (not in UniGene) 321899 Hs.29468 ESTs 4.6 321902 Hs.145010 ESTs 8.2 322007 Hs.i64649 ESTs 5.1 322055 Hs.146001 EST duster 4.3 AL137646 (not in UniGene) 322092 Hs.135624 EST duster) 4.3 AF085833 (not in UniGene 322221 Hs.179662 nudeosomen 1-like4.4 AI890619 assembly protei 1 322278 EST duster (not 5.8 AF086283 in UniGene) 322303 Hs.157601 EST duster 22 W07459 (not in UniGene) 322437 Hs.170253 ESTs; 4.4 AW393804 Weakly similar to rabaptin-4 [H.sa 322493 Hs.279819 EST duster 7.2 AF143235 (not in UniGene) 1$ 322782 Hs.202577 EST duster 18.4 AA056060 (not in UniGene) 322811 Hs.105872 ESTs 6.9 322818 Hs.293616 ESTs 10.7 322826 Hs.t80059 ESTs 5 322887 Hs.86149 ESTs; 11.9 A1986306 Weakly similar to KIAA0969 protein a.0322889 Hs.124918 ESTs 7.1 322924 Hs.136075 ESTs 4.5 322982 Hs.128430 ESTs 6.6 322994 Hs.i91461 ESTs 4.7 AA422i f6 323040 Hs.10862 ESTs 6.9 25 323041 Hs.26691 EST duster 8.3 AL118747 (not in UniGene) 323045 Hs.188836 ESTs 4.6 323048 Hs.175110 EST duster 7.5 AL118923 (not in UniGene) 323070 Hs.264330 ESTs 7.5 323071 Hs.5722 ESTs 4.7 30 323097 Hs.296261 guanine 4.9 244354 nudeotide binding protein (G pr 323131 Hs.270124 EST duster 6.1 AA176982 (not in UniGene) 323136 Hs.30177 EST duster 4.3 AL120351 (not in UniGene) 323175 Hs.336454 ESTs 6.2 323218 Hs.13396 Homo sapiens 6.3 AFt31846 clone 25028 mRNA
sequence 35 323226 Hs.21906 Homo sapiens 12.6 AF055019 done 24670 mRNA
sequence 323236 Hs293960 ESTs 10.9 323262 Hs.190642 ESTs 7.6 323276 Hs.323822 ESTs 7.6 323287 Hs.1042t5 ESTs 24.7 40 323335 Hs.i6t712 ESTs 14.1 323341 Hs.108646 ESTs 5.3 323362 Hs.117182 ESTs 6.1 323486 Hs299221 ESTs; 8.5 C05278 Moderately similarto [PYRUVATE DE

323496 Hs.300700 ESTs 4.5 4$ 323507 Hs.128387 ESTs 4.4 323545 Hs.224569 ESTs 5.8 323623 Hs.146589 EST duster 5 AA314280 (not in UniGene) 323663 Hs243023 ESTs 7.7 323691 Hs.145599 EST duster 5.9 AA317561 (not in UniGene) $0 323810 Hs.108806 ESTs 6.2 323846 Hs.137635 ESTs 6 323929 Hs.145958 ESTs 10.7 323959 Hs.6831 ESTs 5.4 323996 Hs217882 ESTs 5.8 55 323997 Hs.274454 EST duster 4.4 AA844907 (not in UniGene) 324019 EST duster (not 4.6 AW177009 in UniGene) 324130 Hs.130198 ESTs 11 324295 Hs.143691 ESTs 13.7 324296 Hs.192524 ESTs 6.8 60 324307 Hs.4994 transducer 4.9 AA627642 of ERBB2; 2 (TOB2) 324330 EST duster (not 4.3 AA884766 in UniGene) 324385 Hs.284247 EST duster 4.7 F28212 (not in UniGene) 324430 Hs.184598 EST duster 13.6 AA464018 (not in UniGene) 324452 Hs.170953 ESTs 7.6 65 324547 Hs.74170 ESTs 5.6 324603 Hs.292934 ESTs 242 324617 Hs.195839 ESTs 54 324618 Hs.87159 ESTs 4.6 324620 Hs.94109 EST duster 5.7 AA448021 (not in UniGene) 324626 ESTs 9 324658 Hs.129179 22 AI694767 ESTs 324676 Hs.112451 4.9 AW503943 ESTs 324691 Hs.293341 i0.6 AI217963 ESTs; Weakly similar to Pro-a2(XI) [H.sa 324696 Hs.257339 102 AA641092 ESTs 324713 Hs.163440 5.5 AW340249 ESTs 324715 Hs.131798 7.2 AI739168 EST cluster (not in UniGene) 324718 Hs.116467 34.4 AI557019 ESTs 324720 Hs.292437 4.8 AA578904 ESTs 1 324752 Hs.272072 7.9 O AI279919 ESTs; Moderately similar to !!!!
ALU SUB

324753 Hs.144871 52 AA612626 EST cluster (not in UniGene) 324790 Hs.159337 7.6 AI334367 ESTs 324801 Hs.14553 12.6 AI819924 ESTs 324804 ESTs 6.5 1$ 324845 Hs.337533 4.5 AA361016 ESTs .

324888 Hs.136102 4.4 protein 324929 Hs.125350 6.5 AI741633 ESTs 324961 EST cluster 5.1 AA613792 (not in UniGene) 325108 Hs.22380 7.1 AA401863 ESTs 326816 CH20_hs 6552458 9.6 gi~

326997 CH21 hs 5667660 4.8 gi~

327098 CH21 hs 6682516 4.3 gi~

328492 CH.07-hs 5868455 5.8 gi~

329362 CH.X-hs 4.3 gi~5868837 329929 GH.16,~2 ~6165201 5.5 gi 329960 CH.16~2 ~5091594 7.6 gi 330020 CH.16~2 ~6671887 6 gi 330211 CH.05~2 ~6013592 12.6 gi 330384 androgen 9 M23263 receptor (dihydrotestosterone r 3O 330430 Antigen, Prostate Specific, HG2261-HT2352 Alt. Splice 13.8 Hs.321110 330546 Hs.299867 6 U31382 guanine nucleotide binding protein 330551 hepatocyte 4.9 U39840 nuclear factor 3; alpha 330658 Hs.30732 6 AA319514 ESTs 330700 Hs.20999 5.5 AA037415 ESTs 35 330704 Hs.6759 5.1 AA056557 ESTs 330705 Hs.157078 11.7 AA102571 ESTs 330706 Hs.177576 14.5 AA121140 ESTs; Moderately sim!larto kynurenine a 330712 Hs.52620 5 AA167269 ESTs 330725 Hs.24052 7.2 AA252033 ESTs; Weakly similar to !!1!
ALU SUBFAMI

40 330732 Hs.35254 4.9 AA281092 ESTs 330762 Hs.15251 18.5 AA449677 Human DNA
sequence from clone on 330763 Hs.143187 4.3 AA450200 FK506-binding protein 3 (25kD) 330772 Hs.11356 5.8 AA479114 ESTs 330786 EST 4.6 45 330892 Hs.91202 15.3 AA149579 ESTs 330949 Hs.142896 10.3 H01458 ESTs 330977 Hs.315181 4.4 H20826 ESTs 331017 Hs.108920 11.8 N24619 ESTs 331099 Hs.14846 11.6 836671 ESTs 50 331128 Hs268714 4.8 851361 ESTs 331151 Hs.268838 13 882331 ESTs 331195 Hs.168439 4.9 T64447 ESTs 331320 Hs.300141 4.8 -AA262999 ESTs 331321 Hs.87929 6.1 AA278355 ESTs 55 331337 Hs.118630 9.2 AA287662 ESTs 331348 Hs.88143 9.9 AA400596 ESTs 331359 Hs.81897 4.3 AA416979 ESTs 331383 Hs.43543 4.6 AA454543 ESTs 331422 Hs.237339 4.9 F10802 ESTs; Moderately similar to !!!!
ALU SUB

6O 331442 Hs.41223 7.5 H77381 ESTs 331466 Hs.43455 5.4 N21680 ESTs 331479 Hs.44076 6.5 N27154 ESTs 331490 Hs291039 12.5 N32912 ESTs; Weakly similar to hypothetical 43.

331493 Hs.93817 4.6 N34357 ESTs 65 331561 Hs.48703 9.2 N62780 ESTs 331615 Hs.5472 4.6 N92352 ESTs 331659 Hs.334305 8.7 W48868 ESTs 331696 Hs.65949 10.3 protein 331811 Hs.187958 4.8 AA404500 ESTs 331848 Hs.98268 signal recognition7.5 AA417039 particle 72kD

331873 Hs.98640 ESTs 6.5 331889 Hs.98802 Homo sapiens Chromosome33.6 AA431407 16 BAC clone CIT

331967 Hs.99589 KIAA1028 protein 6.8 331974 Hs.105322 ESTs 5.3 AA46d518 332043 Hs.201591 ESTs 10.8 332076 Hs.291156 ESTs 4.4 332173 Hs.100725 ESTs 5.5 332247 ESTs 142 1O 332249 Hs.194140 ESTs 72 332325 Hs.339667 ESTs 5.6 332396 ESTs; Weakly similar to 212 AA340504 similarto human 332434 Hs.237731 transcription 15.3 N75542 factor 4 332493 Hs.56729 ESTs; Highly similar7.1 N95495 to GTP-binding prot 15 332522 Hs.178357 glutathione S-Uansferase6.6 L38503 theta 2 332526 Hs.17731 inosftol 1;4;5-triphosphate5.8 AA281753 receptor; ty 332530 Hs.19280 inhibin; beta 5.5 M31682 B (adivin AB beta polypep 332533 Hs.325825 folate hydrolase38.1 M99487 (prostate-specific memb 332538 Hs.20991 ESTs 6.5 332546 Hs.22587 solute carrier 4.8 D84454 family 35 (UDP-galactose 332594 Hs.32951 methyl CpG binding5.6 AA279313 protein 2 332610 Hs.40513 ESTs; Weakly similar5.6 AA412405 to BETA GALACTOSIDA

332661 Hs.6390 ESTs 6.9 332697 Hs.75725 carboxypeptidase 24.3 25 332712 Hs.79306 inositol 1;4;5-triphosphate9.9 D26070 receptor, iy 332716 Hs.79630 v-myc avian myelocytomatosis5.6 L00058 viral oncog 332726 Hs.83428 synaptophysin-like5 872029 protein 332781 ESTs; Weakly similar to 4.5 AA233258 D1007.5 [C.elega 332797 CH22-FGENES.6-2 30.8 3O 332798 CH22 FGENES.6 5 66.8 332799 CH22_FGENES.6 8 19.8 332933 CH22-FGENES.38 7 5.6 332980 CH22_FGENES.54-1 5.5 332984 CH22_FGENES.54-6 4.9 3$ 333168 CH22_FGENES.94-1 4.7 333169 CH22_FGENES.94-2 4.4 333452 CH22 FGENES.157_1 4.8 333456 CH22_FGENES.157 5 4.3 333458 CH22_FGENES.157 7 4.6 40 333611 CH22-FGENES217_6 4.7 333621 CH22-FGENES.219 5 5.5 333814 CH22-FGENES.282 2 7.1 333849 CH22_FGENES.290 S 62 333949 CH22_FGENES.303_5 4.3 45 333951 CH22_FGENES.303 7 4.9 333955 CH22-FGENES.303_11 5.6 334150 CH22_FGENES.339-1 5.1 334223 CH22_FGENES.360 4 20.3 334297 CH22_FGENES.372 3 9.4 334443 CH22_FGENES.387 2 4.6 334444 CH22-FGENES.387 4 5.6 334447 CH22_FGENES.387 7 13.1 334570 CH22 FGENES.405 11 5.4 334749 CH22-FGENES.427_1 5.3 334777 CH22_FGENES.430 9 4.7 ~

334960 CH22-FGENES.465 29 5.2 335179 CH22_FGENES.504_9 8.8 335293 CH22_FGENES.527 6 4.7 335550 CH22-FGENES.576_11 5.1 335581 CH22 FGENES.581 19 5.7 335586 CH22_FGENES.581 25 4.3 335809 CH22_FGENES.617_6 62 335810 CH22_FGENES.617-7 5.8 335822 CH22 FGENES.619 7 7.1 65 335824 CH22_FGENES.619-11 8.5 335853 CH22_FGENES.626-5 4.3 335886 CH22 FGENES.632 4 4.3 336034 CH22_FGENES.678 5 6.8 336441 CH22_FGENES.827_7 7.6 336624 CH22-FGENES.6-3 43.3 336625 CH22 FGENES.6-4 37.9 336679 CH22 FGENES.43-7 5.3 337577 CH22_C65E1.GENSCAN.B-1 4.9 338255 CH22 EM:AC005500.GENSCAN.276-313.4 338260 CH22 EM:AC005500.GENSCAN.279-104.6 338561 CH22 EM:AC005500.GENSCAN.421-54.6 338562 CH22 EM:AC005500.GENSCAN.421-64.3 338759 CH22 EM:AC005500.GENSCAN.517-65.1 1~ 338763 CH22 EM:AC005500.GENSCAN.517-165.5 338764 CH22-EM:AC005500.GENSCAN.517-177.1 TABLE 3A shows the accession numbers for those primekeys lacking unigenelD'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 (DbubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
1O Pkey: Unique Eos probeset identifier number CAT number: Gene duster number Accession: Genbank accession numbers 1S Pkey CAT number Accession 109342 genbank-AA213620AA213620 125154 genbank_W38419W38419 101447 entrez M21305M21305 124357 genbanl~N22401N22401 ZS 108910 genbanI~AA136590AA136590 322278 47271 1 W69304 AF086283 ta69200 324330 300543_1 AA884766 AW974271 AA592975 AA447312 303029 37699_1 AF199613 AF108756 324961 376239_1 AA613792 AW182329 T05304 AW858385 329362 c_~hs 6 3_ 336625 CH22 4072FG_6_4_ 338255 CH22_6856FG
LINK_EM:AC00 LINK_EM:AC00 4O 329929 c16~2 329960 c16~2 338561 CH22 7294FG~LINK_EM:AC00 336562 CH22 7295FG-LINK_EM:AC00 338759 CH22_7581FG
LINK_EM:AC00 4S 338763 CH22 7585FG~LINK_EM:AC00 338764 CH22 7586FG-LINK_EM:AC00 94_1 LINK_EMA

333169 CH22_401FG
94 2 LINK EM:A

333452 CH22 702FG_157-1 LINK-EM:

157 5_LINK-EM:

333458 CH22 708FG_157 7 LINK_EM:

217_6_LINK_EM:

333621 CH22_882FG
219_5_LINK_EM:

333814 CH22 1083FG_282 2 LINK_EM

SS 333849 CH22_1118FG_290 ~ 8 LINK_EM

335179 CH22_2515FG
504 9 LINK_EM

333949 CH22 1225FG_303 5 LINK_EM

303 7 LINK_EM

333955 CH22 1231FG_303_11 LINK E

6O 335293 CH22 2635FG_527 6 LINK_EM

326816 c20_hs 326997 c21 hs 576_11 LINK E

335561 CH22_2938FG_581 6S 335586 CH22_2944FG_581 25 LINK_E

328492 c_7-hs 335809 CH22_3181FG_617-6-LINfLEM
335810 CH22_3182FG_617 7 LINI<_EM
335822 CH22_3195FG 619 7 LiNK_EM
335824 CH22_3197FG 619_11 LINI~E

330020 c16~2 330211 c-5~2 1O 337577 CH22-5864FG LINK_C65E1.G

332797 CH22 13FG_6_2 LINK-C4G1.G
332798 CH22 14FG-6-5_LINK-C4G1.G
332799 CH22-15FG_6_6-LINK C4G1.G
15 334150 CH22 1429FG-339-1 LINK_EM

332980 CH22 204FG 54_1 LINK-EMJ~
332984 CH22 208FG_54_6 LINK_EM:A
334223 CH22_1507FG-360_4-LINItEM
ZO 334297 CH22 1588FG 372 3 LINK_EM
327098 c21 hs 334443 CH22_1742FG387 2 LINK_EM
334444 CH22_1743FG_387_4_LINK-EM
334447 CH22 1746FG_387 7-LINK-EM
334570 CH22 1875FG_405 11 LINK-E
334749 CH22_2061FG 427_1 LINK-EM

334960 CH22-2281FG 465 29-LINI~E
3~ 336441 CH22_3861FG-827 7 LINK-DJ

332247 372969_1 AA669Q97 AA513815 AA026798 AA676526 AA704429 AA704269 AW118292 4O 332396 20265_1 AW579842 BE156562 BE156690 BE156489 BE081033 AK001559 853463 Hi 1063 332781 32044-1 AK001764 BE313896 AA380199 AA38015t AAt94996 AWi 18089 AA495B71 AI378909 AW992310 AW992409 AI911857 AA657643 AI804471 Ai242589 AI623968 809556 TABLE 3B shows the genomic positioning for those primekeys lacking unigene iD's and accession numbers in Table 3. For each predicted axon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted axon are also listed.
Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al." refers to the publication entitled 'The DNA sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402:489-495.
1~ Strand: Indicates DNA strand from which axons were predicted.
Nt_position: Indicates nucleotide positions of predicted axons.
Pkey Ref StrandNt position 333611 Dunham,Plus6548368-6548507 I. et.al.

333621 Dunham,Plus8597414-8597560 I. et.al.

333814 Dunham,Plus7894165-7894252 I. etal.

333849 Dunham,Plus8018323-8018472 I. et.ai.

333949 Dunham,Plus8589634-8589791 I. et.al.

333951 Dunham,Plus8592501-8592637 I. et.al.

333955 Dunham,Plus8597414-8597560 I. etal.

334150 Dunham,Plus10529221-10529854 I. etal.

334297 Dunham,Plus13420934-13421058 I. et.al.

334443 Dunham,Plus14298981-14299056 t. et.al.

334444 Dunham,Plus14306433-14306492 I. et.al.

334447 Dunham,Plus14308764-14308824 I. et.al.

334570 Dunham,Plus14994868-14994943 I. etal.

334777 Dunham,l.etal.Plus16259586-16260166 3~ 335179 Dunham,Plus21634405-21634526 I. etal.

335581 Dunham,Plus24976198-24976334 I. et.al.

335586 Dunham,Plus24990333-24990497 I. et.ai.

335809 Dunham,Plus26310772-26310909 I. et.al.

335810 Dunham,Plus26314767-26314849 I. et.al.

335822 Dunham,Plus26364087-26364196 t. et.al.

335824 Dunham,Plus26376860-26376942 I. et.al.

335886 Dunham,Plus26934235-26934364 I. etal.

336034 Dunham,Plus29014404-29014590 I. et.al.

336441 Dunham,l.et.al.Plus34187606-34187663 337577 Dunham,Plus595377-595678 I. et.al.

338260 Dunham,Plus15458919-15459257 I. etai.

332797 Dunham,Minus216964-216798 I. etal.

332798 Dunham,Minus232147-231974 1. etal.

332799 Dunham,l.etal.Minus232421-232307 4$ 332933 Dunham,Minus2035790-2035681 I. et.al.

332980 Dunham,Minus5136165-5136019 I. etal.

332984 Dunham,Minus2632606-2632457 I. etal.

333168 Dunham,Minus3729896-3729788 1. et.al.

333169 Dunham,Minus3730664-3730767 I. et.al.

5~ 333452 Dunham,Minus5136165-5136019 I. et.al.

333456 Dunham,Minus2631933-2631797 I. et.al.

333458 Dunham,Minus5143942-5143806 I. et.al.

334223 Dunham,Minus12734365-12734269 I. et.al.

334749 Dunham,Minus16090666-16090106 I. et.al.

55 334960 Dunham,Minus20160968-20160795 I. et.al.

335293 Ounham,Minus22316408-22316275 I. et.al.

335550 Dunham,l.etal.Minus24666714-24668658 335853 Dunham,l.et.al.Minus26614629-26614506 336624 Dunham,Minus227714-227577 I. et.al.

336625 Dunham,Minus229124-229024 I. et.al.

336679 Dunham,Minus2035790-2035681 I. etal.

338255 Dunham,Minus15242294-15242231 I. et.al.

338561 Dunham,Minus22311966-22311856 I. et.al.

338562 Dunham,Minus22312594-22312465 I. etal.

65 338759 Dunham,l.etal.Minus26582475-26582199 338763 Dunham,Minus26628148-26628009 I. et.al.

338764 Dunham,Minus26641232-26641101 I. et.al.

3299605091594Minus1031-1162 3299296165201Minus156410-156553 3300206671887Plus 172397-172491 3268166552458Plus 198354-198436 3269975867660Minus71389-72147 3270986682516Minus1061684-1062361 3302116013592Plus 59158-59215 3284925868455Minus46094-46241 3293625868837Minus65688-68173 TABLE 4: shows a preferred subset of the Accession numbers for genes found in Table 3 which are differentially expressed in prostate tumor tissue compared to normal prostate tissue.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD:Unigene number 1~ Unigene Unigene gene title Title:

Ri: Ratio of tumor to normal body tissue Pkey ExAccnUntgenelD Unigene Title Ri IS

100819 10.5 HG4020-HT4290Hs2387 Transglutaminase 102698 Hs.1867 progastricsin 10.6 U75272 (pepsinogen C) 102869 Hs.572 orosomucoid 1 22.6 105370 Hs22791 ESTs; Wealdy 10.3 AA236476 similar to transmembrane pr 20 105645 Hs.11325 ESTs 14 106094 Hs.23317 ESTs 10.9 109014 Hs.262036 ESTs 15.3 109562 Hs.187931 ESTs; Moderately10.8 F01811 similar to voltage-gate 113021 Hs.129836 KIAA1028 protein10.8 2$ 114124 Hs.125019 ESTs; Highly 21.3 238595 similar to KIAA0886 protein 122791 Hs.129836 KIAA1028 protein12.4 124352 Hs.102406 ESTs 102 301042 Hs.197733 ESTs 24.9 302005 Hs.123119 ESTs 36.8 3~ 302410 Hs218366 EST duster (not26.8 NM_004917 in UniGene) with exon h 302881 Hs.105314 relaxin 1 (H1)78.8 303344 Hs.250646 ESTs; Highly 19.5 AA255977 similar to ubiquitin-conjug 303753 Hs.9414 ESTs 13 310431 Hs.149358 ESTs 72.9 35 311251 Hs.197698 ESTs 41.3 311596 Hs.79375 ESTs 26.4 312153 Hs.118625 cytochrome 11 AA759250 b-561 312521 Hs239884 ESTs 112 313676 Hs.120591 EST duster 13.4 AA861697 (not in UniGene) 314171 Hs.193481 ESTs 29.4 314907 Hs222886 ESTs 19.3 315051 Hs.163484 EST 15.5 315052 Hs.134427 ESTs 20 317548 Hs.195704 ESTs 142 45 317869 Hs.129142 ESTs; Weakly AW295184 similar to DEOXYRIBONUCLEAS
13.8 318428 Hs.194591 ESTs 12.3 318524 Hs.159066 ESTs 25.9 319080 Hs23023 ESTs 16.9 319763 Hs.6295 ESTs 14.3 320324 Hs.139336 ATP-binding 562 AF071202 cassette; sub-family C (CFTR

321441 Hs.118498 ESTs 14.7 322303 Hs.157601 EST duster 22 W07459 (not in UniGene) 322782 Hs.202577 EST duster 18.4 AA056060 (not in UniGene) 322818 Hs.293616 ESTs 10.7 55 323287 Hs.104215 ESTs 24.7 324603 Hs292934 ESTs 242 324617 Hs.195839 ESTs 54 324658 Hs.129179 ESTs 22 324691 Hs.293341 ESTs; Weakly 10.6 A1217963 similar to Pro-a2(XI) [H.sa 324696 Hs.257339 ESTs 102 324718 Hs.116467 ESTs 34.4 330211 CH.05~2 gi~6013592 12.6 330430 13.8 Hs.321110 Antigen, Prostate Spedfic, Alt. Splice 330706 Hs.177576 ESTs; Moderately14.5 AA121140 similar to kynurenine a 65 330762 Hs.15251 Human DNA sequence AA449677 from done 437M21 on 18.5 330892 Hs.91202 ESTs 15.3 330949 Hs.142896 ESTs 10.3 331099 836671Hs.14846 ESTs 11.6 331151 882331Hs.268838 ESTs 13 331889 AA431407Hs.98802 Homo sapiens CIT
Chromosome 16 BAC clone 33.6 332247 N58172ESTs 142 332396 AA340504ESTs; Weakly similar 212 to similarto human 332533 M99487Hs.325825 folate hydrolase38.1 (prostate-specific memb 332697 T94885Hs.75725 carboxypeptidase24.3 E

332797 CH22 FGENES.6 2 30.8 332798 CH22 66.8 FGENES.6 b 1O 332799 _ 19.8 CH22 FGENES.6-6 334223 CH22 FGENES.360_4 20.3 336624 CH22 FGENES.6-3 43.3 336625 CH22_FGENES.6-4 37.9 TABLE 4A shows the accession numbers for those primekeys lacking unigene11.7'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: Genbankaccessionnumbers Pkey CAT number Accession 336624 CH22_4071FG-_6_3-336625 CH22 4072FG_6_4_ 330211 c_5.~2 332797 CH22-13FG_6_2_LINfC_C4G1.G

332798 CH22_14FG-6-5_LINK_C4G1.G

332799 CH22 15FG-6-6-LINI~C4G1.G

334223 CH22 1507FG_360-4-LINK_EM

332247 372969_1 AA669097 AA513815 AA026798 AA676526 AA704429 332396 20265_1 AW579842 BE156562 BE156690 BE156489 BE081033 AIf001559 BE149402 M85387 AW367811 TI4B~E 4B shows the genomic positioning for those primekeys lacking unigene )D's and accession numbers in Table 4. For each predicted exon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted exon are also listed.
Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al' refers to the publication entilled'The 1~ DNA sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402:489-495.
Strand: Indicates DNA strand from which axons were predicted.
Nt~osition: Indicates nucleotide positions of predicted axons.
15 Pkey fief Strand N~position 332797 Dunham, Minus216964-216798 1. et.al.

332798 Dunham, Minus232147-231974 I. et.al.

332799 Dunham, Minus232421-232307 I. et.al.

334223 Dunham, Minus12734365-12734269 1. etal.

336624 Dunham, Minus227714-227577 1. et.al.

336625 Dunham, Minus229124-229024 I. et.al.

330211 6013592 Plus59158-59215 TABLE 5:1170 GENES UP-REGULATED IN PROSTATE CANCER COMPARED TO
NORMAL ADULT TISSUES
Table 5 shows 1170 genes up-regulated in prostate cancer compared to normal adult tissues.
These were selected from 59680 probesets on the Affymetrix/Eos Hu03 GeneChip array such that the ratio of "average" prostate cancer to "average" normal adult tissues was greater than or equal to 3.44. The "average" prostate cancer level was set to the 85t'' percentile amongst 73 prostate cancers. The "average" normal adult tissue level was set to the 85a' percentile amongst 162 non-malignant tissues. In order to remove gene-specific background levels of non-specific hybridization, the 7.5'~ percentile value amongst the 162 non-malignant tissues was subtracted from both the numerator and the denominator before the ratio was evaluated.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene titte R1: Ratio of tumor to normal tissue Pkey ExAccn UnigenelDUnigene Title . 8i 446057AI420227Hs.149358ESTs, Weakly similar 86.42 to A46010 X-linked 400302N48056 Hs.1915folate hydrolase (prostate-specific66.46 memb 414569AF109298Hs.t prostate cancer assodated58.36 18258 protein 1 417407AA923278Hs290905ESTs, Weakly similar 56.16 to protease [H.sapi 431579AW971082Hs222886ESTs, Weakly similar 53.38 to TRHY_HUMAN TRICH

409361NM_005982Hs.54416sine oculis homeobox 4828 (Drosophila) homolo 409731AA125985Hs.56145thymosin, beta, identified4524 in neuroblast 400298AA032279Hs.61635six transmembrane 43.48 epithelial antigen of 420154A1093t55Hs.95420JM27protein 41.12 433466AA508353Hs.105314relaxin 1 (H1) 39.88 400296AA305627Hs.139336ATP-binding cassette,38.42 sub-family C (CFTR

400292AA250737Hs.72472ESTs 38.00 432887AI926047Hs.i62859ESTs 36.48 439176AI446444Hs.190394ESTs, Weakly similar 36.45 to 828096 line-1 pr 430722AW968543Hs203270ESTs, Weakly similar 3320 to ALU1 HUMAN ALU
S

437052AA861697Hs.120591ESTs 33.02 418396A1765805Hs26691ESTs 32.68 434036At65913tHs.197733hypothetical protein 32.44 407709AA456135Hs23023ESTs 32.10 426747AA535210Hs.171995kallikrein 3, (prostate31.80 speafic antigen 407168845175 ESTs 31.72 440260AI972867Hs.7130copine IV 30.52 421513X00949 Hs.105314relaxin 1 (H1) 30.10 416370N90470 Hs203697ESTs, Weakly similar 29.68 to 138022 hypotheU

407122H20276 Hs.31742ESTs - 2924 400287S39329 Hs.181350kallikrein 2, prostafic28.90 432244AI669973Hs.200574ESTs 28.74 451939080456 Hs27311single-minded (Drosophila)28.74 homolog 2 415989AI267700Hs.111128ESTs 28.34 418961AW967646Hs.23023ESTs 27.34 425628NM_004476Hs.1915folate hydrolase (prostate-specific27.32 memb 458509AA654650Hs282906ESTs 2724 448290AK002107Hs20843Homo sapiens cDNA 27.16 FLJ11245 fis, clone PL

428336AA503115Hs.183752microseminoprotein, 26.17 beta-450096AI682088Hs223368holocarboxylase synthetase25.60 (biotin-[prop 400299X07730 Hs.171995kallikrein 3, (prostate24.91 specific antigen 437571AA760894Hs.153023ESTs 24.74 453160AI263307Hs.146228H2B histone family, 24.66 member L

453096AW294631Hs.1t325ESTs 24.46 425075AA506324Hs.1852add phosphatase, prostate2423 407202N58172 Hs.109370ESTs 24.18 424846AU077324Hs.1832neuropeptide Y 23.57 453370AI47g523Hs.182356ATP-binding cassette, 23.16 sub-family C (CFTR

422805AA436989Hs.121017H2A histone family, 22.52 member A

444917868651Hs.144997ESTs 2226 $ 408826AF216077Hs.48376Homo Sapiens done HB-222.02 mRNA sequence 413597AW302885Hs.117183ESTs 21.76 426429X73114Hs.169849myosin-binding protein21.32 C, slow-type 435981H74319Hs.188620ESTs 21.12 432966AA650114 ESTs 21.07 1O 418848A1820961Hs.193465ESTs 21.06 405685 20.90 443271BE568568Hs.195704ESTs 19.98 478819AA228776Hs.i9i721ESTs 19.94 420757X78592Hs.99915androgen receptor (dihydrotestosterone19.72 r 1$ 418994AA296520Hs.89546selectin E (endothelial19.56 adhesion molecul 429918AW873986Hs.119383ESTs 19.04 415539AI733881Hs.72472ESTs 18.43 450382AA397658Hs.60257Homo sapiens d)NA FLJ1359818.34 fis, done PL

418829AA516531Hs.55999NK homeobox (Drosophila),i family 3, A 828 429984AL050102Hs.227209hypothetical protein 17.82 443822A1087412Hs.143611ESTs, Weakly similar 17.66 to 2004399A chromos 431676AI685464Hs292638gba88f04.x1 NCI_CGAP-PflB17.64 Homo Sapiens 410330AW023630Hs.46786ESTs 17.52 432441AW292425Hs.i63484ESTs 17.41 2$ 452792A8037765Hs.30652KIAA1344 protein 17.39 445472AB006631Hs.12784Homo Sapiens mRNA for 17.00 KIAA0293 gene, par 414565AA502972Hs.183390hypothetical protein 16.82 430487D87742Hs.241552KIAA0268 protein 16.72 431716D89053Hs.268012fatty-add-Coenzyme 16.60 A ligase, long-chain 3~ 419536AA603305 gb:np12d11.s1 NCI-CGAP-Pr316.50 Homo sapiens 439677882331Hs.164599ESTs 16.46 449625NM Hs.23796odz (odd Oz/ten-m, 16.32 014253 Drosophila) homolog 408430S79876Hs.44926dipeptidylpeptidase 1628 IV (CD26, adenosine 447033AI357412Hs.157601ESTs 16.02 3$ 453006A1362575Hs.f67133ESTs 15.74 431474AL133990Hs.190642ESTs 15.70 420218AW958037Hs.22437ribosomal protein L4 15.64 408000L11690Hs.620bullous pemphigoid 15.54 antigen 1 (2301240kD) 416208AW291168Hs.41295ESTs, Wealdy similar 15.48 to MUC2_HUMAN MUCIN

40 430226BE245562Hs.255fadrenergic, beta-2-, 75.40 receptor, surface 415263AA948033Hs.130853ESTs 15.38 432437W07088Hs293685ESTs 1526 428398A1249368Hs.98558ESTs 1521 429900AA460421Hs.30875ESTs 14.90 4$ 449156AF103907Hs.171353prostate cancer antigen14.89 411096080034Hs.68583mitochondria) intermediate14.81 peptidase 435974029690Hs.37744Homo Sapiens beta-1 14.76 adrenergic receptor 444484AK002126Hs.11260hypothe8cal protein 14.76 422728AW937826Hs.103262ESTs, Weakly similar 14.60 to ZN91 HUMAN ZINC

418601AA279490Hs.86368calmegin 14.56 448999AF179274Hs22791transmembrane protein 14.55 with EGF-like and 445885AI734009Hs.127699KIAA1603 protein 14.44 452712AW838616 gb:RCS-LT0054-140200-013-D011422 LT0054 Homo' 432189AA527941 gb:nh30c04.s1 NCI-CGAP_Pr314.12 Homo sapiens $$ 424565AW102723Hs.75295guanylate cydase 1, 13.78 soluble, alpha 3 429290AF203032Hs.198760neurofilament, heavy 13.57 polypeptide (200kD) 419264AA877104Hs.293672ESTs, Weakly similar 13.40 to ALUB HUMAN !!!!

416445AL043004Hs.300678KIAA0135 protein 13.32 407275AI364186 gb:qw34h07.x1 NCI-CGAP_Ut41324 Homo Sapiens 408369838438Hs.182575solute carrier family 1321 15 (H+/peptide tra 446720AI439136Hs.140546ESTs 13.06 434988A1418055Hs.161160ESTs 13.02 448172N75276Hs.135904ESTs 12.98 416182NM-004354Hs.79069cydin G2 12.94 65 420544AA677577Hs.98732Homo Sapiens Chromosome12.79 16 BAC clone CIT

445413AA151342Hs.12677CGI-147 protein 12.64 452588AA889120Hs.110637homeo box A10 12.62 407819842185Hs274803ESTs 12.60 433444AW975324Hs.129816ESTs 12.60 421059AI654133Hs.30212thyroid receptor interacting12.30 protein 15 420077AW512260Hs.87767ESTs 1224 453930AA419466Hs.36727hypothetical protein 1222 441610AW576148Hs.148376ESTs 1220 451009AA013140Hs.115707ESTs 12.18 433764AW753676Hs.39982ESTs 12.16 440286U29589 Hs.7138cholinergic receptor, 12.04 muscadnic 3 443912837257 Hs.184780ESTs 11.92 419526AI821895Hs.193481ESTs 11.91 d23073BE252922Hs.123119MAD (mothers against 11.87 decapentaplegic, Dr 452784BE463857Hs.151258hypothetical protein 11.86 414422AA147224Hs.71814ESTs 11.76 450203AF097994Hs.301528L-kynurenine/alpha-aminoadipate11.68 aminotra 436679AI127d83Hs.120451ESTs, Weakly similar 11.60 to unnamed protein 1~ 440901AA909358Hs.128612ESTs 11.60 448045AJ297436Hs20166prostate stem cell 11.51 antigen 433887AW204232Hs.279522ESTs 11.50 434980AW770553Hs293640sterol 0-acyltransferase11.38 (acyl-Coenzyme 425905AB032959Hs.161700novel C3HC4 type Zinc 11.33 finger (ring finge 434680T11738 Hs.127574ESTs 11.32 449650AF055575Hs.297647calaum channel, voltage-dependent,11.18 L ty 431173AW971198Hs294068ESTs 11.16 434539AW748078Hs.214410ESTs, Weakly similar 11.16 to MUC2_HUMAN MUCIN

410037AB020725Hs.58009KIAA0918 protein 11.14 25 417708N74392 Hs.50495ESTs 11.14 458332A1000341Hs220491ESTs 11.12 420381D50640 Hs.301782phosphodiesterase 3B, 11.10 cGMP-inhibited 425665AK001050Hs.159066hypothetical protein 11.08 425710AF030880Hs.159275solute carrier family,member411.08 3O 428728NM U16625Hs.191381hypothetical protein 11.04 407021U52077 gb:Human mariners transposase11.02 gene, comp 410733D84284 Hs.66052CD38 antigen (045) 11.02 401714 10.90 434485AI623511Hs.118567ESTs 10.89 35 415786AW419196Hs257924hypothetical protein 10.87 452340NM_002202Hs.505ISL1 transcription 10.85 factor, LIMlhomeodoma 453628AW243307Hs.170187hypothetical protein 10.72 408063BE086548Hs.42346calaneurin-binding 10.67 protein calsarcin-1 417687AI828596Hs250691ESTs 10.64 434666AF151103Hs.112259T cell receptor gamma 10.53 locus 432374W68815 Hs.301885Homo sapiens cDNA FLJ1134610.50 fis, clone PL

428819AL135623Hs.193914KIAA0575 gene product 10.48 413409AI638418Hs.21745DEADM (Asp-Glu-Ala-AspIHis)10.44 box polypep 428775AA434579Hs.143691ESTs 1021 45 436556AI364997Hs.7572ESTs 1020 441690881733 Hs.33106ESTs 10.14 419852AW503756Hs.286184hypothetical protein 10.10 dJ551 D2.5 421991NM_014918Hs.110488KIAA0990 protein 10.04 423698AA329796Hs.1098DKFZp434J1813 protein 10.02 452039A1922988Hs.172510ESTs 10.00 433043W57554 Hs.125019ESTs 9.98 433927AI557019Hs.116467small nuclear protein 9.97 PRAC

445424AB028945Hs.12696cortactin SH3 domain-binding9.96 protein ' 432240AI694767Hs.129179Homo sapiens cDNA FLJ135819.88 fis, clone PL

5J 433104AL043002Hs.128246ESTs, Moderately similar9.84 to unnamed prot 452744AI267652Hs.30504Homo sapiens mRNA; 9.82 cDNA DKFZp434E082 (fr 431217NM_013427Hs250830Rho GTPase activating 9.75 protein 6 427398AW390020Hs.20415chromosome 21 open 9.70 reading frame 11 446896T15767 Hs22452Homo sapiens mRNA for 9.70 KIAA1737 protein, 421470827496 Hs.1378annexin A3 9.64 4065,54 9.60 40142d 9.58 407902AL117474Hs.41181Homo sapiens mRNA; 9.56 cDNA DKFZp727C191 (fr 423545AP000692Hs.129781chromosome 21 open 9.54 reading frame 5 f)5439024896696 Hs.35598ESTs 9.51 431548AI834273Hs.9711novel protein 9.48 409262AK000631Hs.52256hypothetical protein 9.45 446271D82484 Hs.100469ESTs 9.42 448692AW013907Hs224276methylaotonoyl-Coenzyme926 A carboxylase 2 1~

414140AA281279Hs23317hypothetical protein 9.24 435980AF274571Hs.129142deoxyribonuclease II 9.24 beta 421246AW582962Hs.300961CGI-47 protein 9.20 427304AA761526Hs.163853ESTs 9.16 442914AW188551Hs.99519hypothetical protein 9.16 413627BE182082Hs.246973ESTs 9.14 439699AF086534Hs.187561ESTs, Moderately similar9.10 to ALUi HUMAN A

437718AI927288Hs.196779ESTs 9.07 439820AL360204Hs283853Homo sapiens mRNA full9.06 length insert cDN

1 447342A1199268Hs.19322Homo Sapiens, Similar 9.05 O to RIKEN cDNA 2010 446223BE300091Hs.119699hypothetical protein 9.04 410001AB041036Hs.57771kallikrein 11 9.03 424012AW368377Hs.137569tumor protein 63 kDa 9.03 with strong homolog 441791AW372449Hs.175982hypothetical protein 9.02 448206BE622585Hs.3731ESTs, Moderatelysimilarto9.02 138022 hypot 414269AA298489 olfactory receptor, 8.99 family 51, subfamily 442061AA401863Hs.22380ESTs 8.98 420092AA814043Hs.88045ESTs 8.85 411630U42349 Hs.71119Putative prostate cancer8.80 tumor suppresso 20 421863AI952677Hs.108972Homo Sapiens mRNA; 8.80 cDNA DKFZp434P228 (fr 454141AW138413Hs.182356ATP-binding cassette, 8.80 sub-family C (CFTR

418278A1088489Hs.83937hypothetical protein 8.78 428330L22524 Hs2256matrix metalloproteinase8.76 7 (maUilysin, 432415T16971 Hs.289014ESTs, Weakly similar 8.75 to A43932 mucin 2 p 424906AI566086Hs.153716Homo sapiens mRNA for 8.74 Hmob33 protein, 3' 415245N59650 Hs.27252ESTs 8.72 442409BE208843Hs.129544hypothetical protein 8.70 404571 8.66 418033W68180 Hs.259855elongation factor-2 8.64 kinase 3O 456497AW967956Hs.123648ESTs, Weakly similar 8.56 to AF1084601 ubinu 405876 8.54 448807AI571940Hs.7549ESTs 8.52 445372N36417 Hs.144928ESTs 8.48 425171AW732240Hs.300615ESTs 8.44 35 419968X04430 Hs.93913interleukin 6 (interferon,8.36 beta 2) 407385AA610150Hs272072ESTs, Weakly similar 8.31 to 138022 hypotheG

433172AB037841Hs.102&52hypothetical protein 8.30 422631BE218919Hs.118793hypothetical protein 8.27 412719AW016610Hs.129911ESTs 8.24 4O 418849AW474547Hs.53565Homo sapiens PIG-M 8.22 mRNA for mannosyltran 444922AI921750Hs.144871Homo Sapiens cDNA FLJ137528.22 fis, done PL

427674NI~003528Hs.2178H2B histone family, 8.20 member Q

432101AI918950Hs.11092EphA3 8.17 416288H51299 gb:yp07c06.s1 Soares 8.15 breast 3NbHBst Homo 45 404915 8.08 440106AA864968Hs.127699KIAA1603 protein 8.07 442861AA243837Hs.57787ESTs 8.06 452259AA317439Hs.28707signal sequence receptor,8.06 gamma (translo 443250A1041530Hs.132107ESTs 8.06 SO 437267AW511443Hs.258110ESTs 8.04 452891N75582 Hs212875ESTs, Weakly similar 8.02 to DYH9-HUMAN CILI

422219AW978073 regulator of mitotic 8.00 spindle assembly 1 453049BE537217Hs.30343ESTs - 8.00 439731AI953135Hs.45140hypothetical protein 7.98 55 408554AA836381Hs.7323nuclear receptor co-repressor/HDAC37.94 comp 421154AA284333Hs287631Homo sapiens cDNA FLJ142697.94 fis, clone PL

430107AA465293Hs.105069ESTs 7.94 433404T32982 Hs.102720ESTs 7.93 450813AI739625Hs.203376ESTs 7.90 416239AL038450Hs.48948ESTs 7.85 448212AI475858 gbac87d07.x1 NCI_CGAP-CLLi7.82 Homo sapiens 449532W74653 Hs.271593ESTs, Moderately similar7.82 to A47582 B-cel 413930M86153 Hs.75618RAB11A, member RAS 7.80 oncogene family 458191AI420611Hs.127832ESTs 7.80 65 444858A1199738Hs208275ESTs, Weakly similar 7.78 to ALUA_HUMAN !Ill 457498AI732230Hs.191737ESTs 7.78 407235D20569 Hs.169407SAC2 (suppressor of 7.76 actin mutations 2, y 433759AA680003Hs.109363Homo Sapiens cDNA: 7.74 FLJ23603 fis, clone L

433805AA706910Hs.112742ESTs 7.74 426485NM-006207Hs.170040platelet-derived growth7.72 factor receptor-446028844714 Hs.106795Homo Sapiens d)NA FLJ131367.72 fis, done NT

418555AI417215Hs.87159hypothetical protein 7.70 447499AW262580Hs.147674protocadherin beta 7.70 419839024577 Hs.93304phospholipase A2, group7.68 VII (platelet-ac 416857AA188775Hs.292453ESTs 7.68 413801M62246 Hs.35406ESTs, Highly similar 7.66 to unnamed protein 425480AB023198Hs.158135KIAA0981 protein 7.66 420120AL049610Hs.95243transcription elongation7.64 factor A (S11)-424099AF071202Hs.139336ATP-binding cassette, 7.64 sub-family C (CFTR

446307T50083 Hs.9094ESTs 7.63 429220AW207206Hs.136319ESTs 7.59 420345AW295230Hs.25231ESTs 7.54 429208AA447990Hs.190478ESTs 7.54 447247AW369351Hs.287955Homo sapiens cDNA FW130907.53 fis, clone NT

440995T57773 Hs.10263ESTs 7.53 448706AW291095Hs21814interleukin 20 receptor,7.52 alpha 410227AB009284Hs.61152exostoses (multiple)-like7.49 431616AA508552Hs.195839ESTs, Weakly similar 7.46 to 138022 hypotheG

434217AW014795Hs.23349ESTs 7.44 431467N71831 Hs256398Homo Sapiens mRNA; 7.42 cDNA DKFZp434E0528 (f 448519AW175665Hs.244334Homo Sapiens prostein 7.42 mRNA, complete cds 446791AI632278Hs.34981ESTs 7.40 419743AW408762Hs.127478Homo Sapiens done 244167.39 mRNA sequence 445855BE247129Hs.145569ESTs 7.36 425211M18667 Hs.1867progastricsin (pepsinogen7.35 C) 419131AA406293Hs.301622ESTs 7.34 400294N95796 Hs.179809Homo sapiens prostein 7.33 mRNA, complete cds 441736AW292779Hs.169799ESTs 7.28 427701AA411101Hs.221750nuclear autoantigenic 7.24 sperm protein (his 457733AW974812Hs.291971ESTs 7.24 418432M14156 Hs.85112insulin-like growth 7.22 factor 1 (somatomedi 441201AW118822Hs.128757ESTs 7.21 419953BE267154Hs.125752ESTs 7.20 35 419991AJ000098Hs.94210eyes absent (Drosophila)720 homolog 1 425018BE245277Hs.154196E4F transcription factor720 424560AA158727Hs.150555protein predicted by 7.18 done 23733 435380AA679001Hs.192221ESTs 7.14 420658AW965215Hs.130707ESTs 7.12 4O 408291A8023191Hs.44131KIAA0974 protein 7.10 409110AA191493Hs.48778niban protein 7.10 414485W27026 Hs.182625VAMP (vesicle-assoclated7.10 membrane protei 430039BE253012Hs.153400ESTs, Weakly similar 7.10 to ALUi HUMAN ALU
S

450832AW970602Hs.105421ESTs ~ 7.10 45 417153X57010 Hs.81343collagen, type II, 7.08 alpha 1 (primary oste 412446A1768015Hs.92127ESTs 7.07 412953245794 Hs.238809ESTs 7.06 418051AW192535Hs.19479ESTs 7 421566NM_000399Hs.1395early growth response 7.04 2 (Krox-20 (Drosop 5O 446999AA151520Hs279525hypothetical protein 7.04 440529AW207640Hs.16478Homo sapiens d)NA: 7.04 FLJ21718 fis, clone C

441111A1806867Hs.126594ESTs 7.01 451027AW519204Hs.40808ESTs ' 7.00 408432AW195262 gb:xn67b05.x1 NCI-CGAP7.00 CMLi Homo Sapiens 55 432223AA333283Hs.285336Homo Sapiens, done 7.00 IMAGE:3460280, mRNA

444805AB007899Hs.12017homolog of yeast ubiquitin-protein6.99 ligas 414212AA136569Hs295940KIAA0187 gene product 6.98 431725X65724 Hs2839Norrie disease (pseudoglioma)6.98 449685AW296669Hs.66095ESTs 6.97 6O 447313092981 Hs.18081Homo Sapiens clone 6.96 DTIPiB6 mRNA, CAG
rep 424590AW966399Hs.46821hypothetical protein 6.94 449655A1021987Hs.59970ESTs 6.92 419563AA526235Hs.193162Homo Sapiens d)NA FLJ119836.90 fis, clone HE

434163AW974720Hs25206group XII secreted 6.89 phospholipase A2 65 415809232789 Hs.46601ESTs 6.86 425782066468 Hs.159525cell growth regulatory6.85 with EF-hand doma 417958AA767382Hs.193417ESTs 6.84 427408AA583206Hs2156RAR-related orphan 6.79 receptor A

445873AA250970Hs251946poly(Arbinding protein,6.74 cytoplasmic 1-I

410718AI920783Hs.191435ESTs 6.74 432363AA534489 gb:nf76g1 1.s1 NCI_CGAP-Co36.74 Homo Sapiens 436521AW203986Hs.213003ESTs 6.73 435604AA625279Hs.26892uncharacterfzed bone 6.73 marrow protein BM04 $ 419083AI479560Hs.98613Homo Sapiens cDNA FLJ122926.72 fis, clone MA

418245AA088767Hs.83883transmembrane, prostate6.70 androgen induced 420714BE172704Hs.222746KIAA1610 protein 6.70 412707AW206373Hs.16443Homo sapiens cDNA: FLJ217216.67 fis, clone C

421896N62293Hs.45107ESTs 6.66 1~ 411078A1222020Hs.182364CocoaCrisp 6.66 452465AA610211Hs.34244ESTs 6.66 422763AA033699Hs.83938ESTs, Moderately similar6.66 to MAS2 HUMAN M

444618AV653785Hs.300171ELL-RELATED RNA POLYMERASE6.64 II, ELONGATIO

450164AI239923Hs.30098ESTs 6.63 1$ 431060AF039307Hs.249171homeo box A11 6.62 408031AA081395Hs.42173Homo sapiens cDNA FLJ103666.62 fis, clone NT

420285AA258124Hs.293878ESTs, Moderately similar6.62 to ZN91 HUMAN Z

444670H58373Hs.37494hypothetical protein 6.62 444489A1151010Hs.157774ESTs 6.60 ZO 445685AW779829Hs.263436gb:hn88a05.x1 NCI-CGAP 6.60 Kidi 1 Homo sapien 435677AA694142Hs.293726ESTs, Weakly similar 6.59 to TSGA RAT TESTIS

452221C21322Hs.11577hypothetical protein 6.59 431510AA580082Hs.112264ESTs 6.56 415874AF091622Hs.78893KIAA0244 protein 6.54 2$ 418405A1868282Hs.11898ESTs, Highly similar 6.54 to KIAA1370 protein 452768AW069459Hs.61539ESTs 6.54 401451 6.52 416289W26333 ESTs 6.52 431778AL080276Hs268562regulator of G-protein 6.51 signalling 17 409089NM Hs.50421KIAA0203 gene product 6.50 442833AA328153Hs.88201ESTs, Weakly similar 6.50 to A Chain A, Cryst 431992NM_002742Hs.2891protein kinase C, mu 6.49 418833AW974899Hs.292776ESTs 6.48 429163AA884766 gb:am20a10.s1 Soares-NFL-T-GBC-Si6.46 Homo s 3$ 430403AF039390Hs.241382tumor necrosis factor 6.46 (ligand) superfami 443058AW451642Hs.i6732ESTs 6.46 418564AA631143Hs.179809Homo sapiens prostein 6.44 mRNA, complete cds 432674AA641092Hs257339ESTs, Weakly similar 6.44 to 138022 hypotheti 423600AI633559Hs.29076ESTs 6.44 4~ 404253 6.42 433610AA806822Hs.112547ESTs 6.42 421552AF026692Hs.105700seaeted frfzzled-related6.41 protein 4 407118AA156790Hs262036ESTs, Weakly similar 6.40 to Z223_HUMAN ZINC

408608N79738Hs.136102KIAA0853 protein 6.40 45 421452AI925946Hs.104530fetal hypothetical protein6.40 433285AW975944Hs.237396ESTs 6.40 434926BE543269Hs.50252mitochondrfal ribosomal6.40 protein L32 446189H85224Hs.214013ESTs 6.40 416806NM_000288Hs.79993peroxisomal biogenesis 6.38 factor 7 416467H57585Hs.37467ESTs 6.36 453403BE466639Hs.61779Homo Sapiens cDNA FLJ135916.34 fis, clone PL

429769NM_004917Hs.218366kallikrein 4 (prostase,6.34 enamel matrfx, p 423642AW452650Hs.157148hypothetical protein 6.32 MGC13204 ' 425843BE313280Hs.159627death assodated protein6.32 55 439221AA737106Hs.32250ESTs, Moderately similar6.32 to 178885 serfn 428194.AA765603Hs.180877H3 histone, family 3B 6.30 (H3.3B) 431958X63629Hs.2877cadherfn 3, type 1, 6.30 P-cadherin (placenta 439366AF100143Hs.6540fibroblast growth factor6.30 452789AW081626Hs.242561ESTs 6.30 416836D54745Hs.80247cholecystokinin 6.30 436962AW377314Hs.5364DKFZP5641052 protein 6.29 433383AF034837Hs.192731double-stranded RNA 6.29 specific adenosine d 418636AW749855 gb:OV4-BT0534-281299-053-c05626 BT0534 Homo 450728AW162923Hs.25363presenilin 2 (Alzheimer625 disease 4) 65 440293A1004193Hs.22123ESTs 624 453745AA952989Hs.63908hypothetical protein 624 426595AW971980Hs.62402p21/Cdc42/Rac1-activated624 kinase 1 (yeast 444412AI147652Hs.216381Homo sapiens clone HH409624 unknown mRNA

413384NM-000401Hs.75334exostoses (multiple) 6.22 426320W47595Hs.169300transforming growth 6.22 factor, beta 2 423349AF010258Hs.127428homeo box A9 6.20 429165AW009886Hs.118258prostate cancer associated6.18 protein 1 424800AL035588Hs.153203MyoD family inhibitor 6.18 409564AA045857Hs.54943fracture callus 1 (rat)6.16 homolog 438796W67821Hs.109590genethonin 1 6.16 425451AF242769Hs.157461mesenchymal stem cell 6.14 protein DSC54 451663AI872360Hs.209293ESTs 6.14 413623AA825721Hs.246973ESTs 6.12 1~ 452232AW020603Hs.271698radial spoke protein 6.12 453390AA862496Hs.28482ESTs 6.12 435542AA687376Hs269533ESTs 6.12 420424AB033036Hs.97594KIAA1210 protein 6.11 407103AA424881Hs.256301hypothetical protein 6.10 15 409734BE161664Hs.56155hypothetical protein 6.10 432686BE223007Hs.152460Homo sapiens cDNA FLJ129096.10 fis, clone NT

438361AA805666Hs.146217Homo Sapiens cDNA: 6.i0 FLJ23077 Cps, clone L

411479AW848047 gb:IL3-CT0214-291299-052-A126.10 CT0214 Homo 438849W28948Hs.10762ESTs 6.08 452726AF188527Hs.61661ESTs, Weakly similar 6.08 to AF1746051 F-box 445895D29954Hs.13421KIAA0056 protein 6.08 440774AI420611Hs.127832ESTs 6.07 422583AA410506Hs.118578KIAA0874 protein 6.06 427500AW970017Hs.293948ESTs, Weakly similar 6.04 to S65657 alpha-iC-443646A1085198Hs298699ESTs 6.04 410566AA373210Hs.43047Homo Sapiens cDNA FLJ135856.02 fis, clone PL

417845AL117461Hs.82719Homo sapiens mRNA; 6.02 cDNA DKFZp586F1822 (f 430273AI311127Hs.125522ESTs 6.02 434792AA649253Hs.132458ESTs 6.01 3O 442490AW965078Hs.30212thyroid receptor interacting6.01 protein 15 420026AI831190Hs.166676ESTs 6.00 437782AI370876Hs.123163exportin 1 (CRM1, yeast,6.00 homology 447359NM_012093Hs.18268adenylate kinase 5 6.00 447713AI420733Hs.207083ESTs 6.00 35 451073AI758905Hs206063ESTs 6.00 451640AA195601Hs26771Human DNA sequence 6.00 from clone 747H23 on 410889X91662Hs.66744twist (Drosophila) 5.97 homolog (acrocephalos 441222AI277237Hs.44208hypothetical protein 5.96 447732AI758398Hs.161318ESTs 5.96 4O 437756AA767537Hs.197096ESTs 5.95 408829NM_006042Hs.48384heparan sulfate (glucosamine)5.94 3-0-sulfot 453911AW503857Hs.4007Sarcolemmal-associated5.94 protein 414065AA114016Hs.75746aldehyde dehydrogenase5.93 1 family, member 408875NM_015434Hs.48604DKFZP434B168 protein 5.92 45 439451AF086270Hs278554heterochromatin-like 5.92 protein 1 423853AB011537Hs.i33466slit (Drosophila) homolog5.91 453060AW294092Hs21594hypothetical protein 5.91 420407AA814732Hs.145010IipopolysaGCaride-specific5.91 response 5-li 450480X82125Hs25040zinc finger protein 5.90 408446AW450669Hs.45068hypothetical protein 5.88 DKFZp4341143 421039NM-003478Hs.101299cullin 5 5.88 451684AF216751Hs26813CDA14 5.88 436063AK000028Hs.250867ribosomal protein S24 5.86 -410507AA355288Hs271408transitional epithelia5.86 response protein 55 420179N74530Hs21168ESTs 5.84 453878AW964440Hs.19025DC32 5.84 452270AW975014Hs.26 terrochelatase (protoporphyria)5.83 435867AA954229Hs.114052ESTs 5.82 417683AW566008Hs.239154ankyrin repeat, family5.82 A (RFXANK-like), 6O 432005AA524190Hs.120777ESTs, Weakly similar 5.81 to ELL2 HUMAN RNA
P

406815AA833930Hs.288t>36tRNA isopentenylpyrophosphate5.80 transferas 437980850393Hs.278436KIAA1474 protein 5.80 425856AA364908Hs.98927hypothetical protein 5.79 400301X03635Hs.1657estrogen receptor 1 5.78 65 446261AA313893Hs.13399hypothetical protein 5.78 FLJ12615 similar to 410141807775Hs.287657Homo Sapiens cDNA: 5.77 FLJ21291 fis, clone C

427258AA400091Hs.39421ESTs 5.76 419108AA389724Hs.191264ESTs, Weakly similar 5.78 to ALU7_HUMAN ALU
S

442029AW956698Hs.14456neural precursor cell 5.76 expressed, develop 407783AW996872Hs.172028a disintegrin and metalloproteinase5.75 doma 434408A1031771Hs.132586ESTs 5.74 415077L41607 Hs.934glucosaminyl (N-acetyl)5.74 transferase 2, I

432435BE218886Hs.282070ESTs 5.74 433313W20128 Hs.296039ESTs 5.73 431740N75450 Hs.183412ESTs, Moderately similar5.73 to AF11672167 412991AW949013 gb:OV4-FT0005-110500-201-e125.72 FT0005 Homo 418852BE537037Hs.273294hypothetical protein 5.72 418882004996 Hs.89433ATP-binding cassette, 5.72 NM sub-family C (CFTR

1O 446867- Hs.16349KIAA0431 protein 5.72 437866AA156781Hs.83992metallothionein 1 E 5.72 (functional) 410232AW372451Hs.61184CGI-79 protein 5.70 414452AA454038Hs.29032ESTs 5.70 422762AL031320Hs.119976Human DNA sequence 5.70 from clone RP1-20N2 15 428730AA625947Hs25750ESTs 5.70 431571AW500486Hs.180610splicing factor prolinelglutamine5.70 rich ( 433393AF038564Hs.98074itchy (mouse homology 5.70 E3 ubiquitin prote 450616AL133067Hs25214hypothetical protein 5.70 443774AL117428Hs.9740DKFZP434A236 protein 5.69 20 446100AW967109Hs.13804hypothetical protein 5.69 dJ4620232 419168AI336132Hs.33718Homo sapiens cDNA FLJ126415.68 fis, clone NT

416653AA768553Hs.77496metallothionein 1 E 5.67 (functional) 452679242387 Hs.4299transmembrane, prostate5.66 androgen induced 450244AA007534Hs.125062ESTs 5.66 25 408621AI970672Hs.46638chromosome 11 open 5.65 reading frame 8 450325AI935962Hs.26289ESTs 5.65 439671AW162840Hs.6641kinesin family member 5.64 452387AI680772Hs.4316trinucleotide repeat 5.64 containing 12 413992W26276 Hs.136075RNA, U2 small nuclear 5.63 30 444151AW972917Hs.128749alpha-methylacyl-CoA 5.63 racemase 417791AW965339Hs.111471ESTs 5.62 410196AI9364d2Hs.59838hypothetical protein 5.60 415123D60925 ESTs 5.60 429170NM-001394Hs.2359dual specificity phosphatase5.60 35 434415BE177494 gb:RC6-HT0596-270300-011-C055.60 HT0596 Homo 440738A1004650Hs.225674WD repeat domain 9 5.60 443830A1142095Hs.143273ESTs 5.60 449603AI655662Hs.197698ESTs 5.60 414342AA742181Hs.75912KIAA0257 protein 5.59 4O 422634NM_016010Hs.118821CGI-62 protein 5.56 435047AA454985Hs.54973cadherin-like protein 5.55 400268 5.55 452055AI377431Hs293772hypothetical protein 5.54 437073AI885608Hs.94122ESTs 5.54 45 434072H70854 Hs283059Homo sapiens PR01082 5.53 mRNA, complete cds 418339AA639902Hs.104215ESTs, Moderately similar5.52 to SPCN-HUMAN S

434551BE387162Hs280858ESTs, Highly similar 5.52 to A35661 DNA excis 439569AW602166Hs222399CEGP1 protein 5.51 441102AA973905Hs.16003intermediate filament 5.50 protein syncoilin $O 448310AI480316 gbam26h09.x1 Soares_NFILT_GBC_Si5.50 Homo s 413173BE076928Hs.70980ESTs 5.48 436246AW450963Hs.119991ESTs 5.48 449300AI656959Hs.222165ESTs - 5.48 452823A8012124Hs.30696transcription factor-like5.48 5 (basic helix 5$ 451403AA885569Hs.15727Homo sapiens cDNA FLJ145115.46 fis, clone NT

417061AI675944Hs.188691Homo Sapiens cDNA FLJ120335.44 fis, clone HE

429126AW172356Hs.99083ESTs 5.44 431316AA502663HS.145037ESTs 5.44 439192AW970536Hs.105413ESTs 5.44 431938AA938471Hs.115242specific granule protein5.44 (28 kDa); cyste 451552AA047233Hs.33810ESTs 5.43 416991N36389 Hs295091KIAA0226 gene product 5.42 427638AA406411Hs.208341ESTs, Weakly similar 5.42 to KIAA0989 protein 427718AI798680Hs.25933ESTs 5.42 65 438710AA833907Hs.178724ESTs, Weakly similar 5.42 to ALU1 HUMAN ALU
S

406076AL390179Hs.137011Homo Sapiens mRNA; 5.40 cDNA DKFZp547P134 (fr 431263AW129203Hs.13743ESTs 5.40 421264AL039123Hs.103042microtubule-associated5.38 protein 18 421685AF189723Hs.106778ATPase, Ca++transporting,5.37 type 2C, memb 408460AA054726Hs.285574ESTs 5.36 d09091AW970386Hs.269423ESTs 5.36 421987A1133161Hs286131CGI-101 protein 5.36 428002AA418703 NhHMPu-Si Homo sapi 5.36 gb:zv98c03.s1 Soares 441217AI922183Hs2132d6_ 5.36 ESTs 426006849031 Hs.22627ESTs 5.35 422806BE314767Hs.1581glutathione S-transferase5.34 theta 2 432281AK001239Hs274263hypothetical protein 5.32 451982F13036 Hs.27373Homo saplens mRNA; 5.32 cDNA DKFZp56401763 (f 421129BE439899Hs.89271ESTs 5.31 444042NM_004915Hs.10237ATP-binding cassette, 5.31 sub-family G (WHIT

410150AW382942Hs.6774ESTS 5.30 423952AW877787Hs.136102KIAA0853 protein 5.30 452822X85689 Hs.288617hypothetical protein 5.30 447752M73700 Hs.347lactotransferrin 5.29 441766853790 Hs.23294hypothetical protein 529 431359AW993522Hs292934ESTs 5.27 427212AW293849Hs.58279ESTs, Weakly similar 527 to ALU7_HUMAN ALU
S

449916T60525 Hs299221pyruvate dehydrogenase5.27 kinase, isoenryme 454014AW016670Hs233275ESTs 527 419714AA758751Hs.98216ESTs 5.26 428845AL157579Hs.153610KlAA0751 gene product 5.26 417333AL157545Hs.42179bromodomain and PHD 5.24 finger containing, 419986AI345455Hs.78915GA-binding protein 5.24 transcription factor, ~5 407182AA312551Hs.230157ESTs 5.22 420111AA255652 gb:zs21h11.r1 NCI-CGAP_GCBi5.22 Homosapiens 428058AI821625Hs.191602ESTs 5.22 459551AI472808 gbaj70e07.x1 Soares_NSF-FS_9W-OT-PA_P-S5.22 432524AI458020Hs293287ESTs 5.22 436207AA334774Hs.12845hypothetical protein 5.22 410870U81599 Hs.66731homeo box 813 5.22 451418BE387790Hs.26369hypothetical protein 5.22 409757NM-001898Hs.123114cystatin SN 521 441124T97717 Hs.119563ESTs 5.21 428593AW207440Hs.185973degenerative spermatocyte5.21 (homolog Droso 436401A1087958Hs29088ESTs 5.20 437113AA744693 gb:ny26c10.si NCI_CGAP-GCBs5.20 Homo Sapiens 450947AI745400Hs204662ESTs 5.20 453279AW893940Hs.59698ESTs 5.20 445467AI239832Hs.15617ESTs, Weakly similar 5.19 to ALU4_HUMAN ALU
S

448944AB014605Hs22599atrophin-1 interacting5.19 protein 1; act'rvi 412198AA937111Hs.69165ESTs 5.18 422646H87863 Hs.151380ESTs, Weakly similar 5.18 to T16584 hypotheti 438986AF085888Hs269307ESTs 5.18 453954AW118336Hs.75251DEAD/H (Asp-Glu-Ala-AspMis)5.18 box binding 447541AK000288Hs.18800hypothetical protein 5.18 434029AA621763Hs.170434Homo Sapiens cDNA FLJ142425.16 fis, clone OV

459294AW977286Hs.169531RBPi-like protein 5.16 429441AJ224172Hs204096lipophilin B (uteroglobin5.16 family member) 424692AA429834Hs.151791KIAA0092 gene product 5.15 427359AW020782Hs.79881Homo sapiens cDNA: 5.15 FW23006 fis, done L

419872AI422951Hs.146162ESTs 5.15 429422AK001494Hs202596Homo sapiens cDNA FLJ106325.14 fis, clon8 NT ' 448902245998 Hs22543Homo Sapiens mRNA; 5.14 cDNA DKFZp76111912 (f 459055N23235 Hs.30567ESTs, Weakly similar 5.14 to 834087 hypotheti 431318AA502700Hs293147ESTs, Moderately similar5.14 to A46010 X-lin 452953AI932884Hs271741ESTs, Weakly similar 5.13 to A46010 X-linked 428372AK000684Hs.183887hypothetical protein 5.f2 434401AI864131Hs.71119Putative prostate cancer5.12 tumor suppresso 416434AW163045Hs.79334nuclear factor, intedeukin5.11 3 regulated 410268AA316181Hs.61635six transmembrane epithelial5.10 antigen of 417517AF001176Hs.82238POP4 (processing of 5.10 precursor , S. cerev 453616NM_003462Hs.33846dynein, axonemal, light5.10 intermediate pol 427958AA418000Hs.98280potassium intermediatelsmall5.09 conductance 407945X69208 Hs.606ATPase, Cu++Uansporting,5.08 alpha polypep 425154NM_001851Hs.154850collagen, type IX, 5.08 alpha 1 412863AA121673Hs.59757zinc finger protein 5.06 420807AA280627Hs.57846ESTs 5.06 430568AA769221Hs270847delta-tubulin 5.06 433687AA743991 gb:ny57g01.s1 NCI-CGAP_PrIB5.06 Homo sapiens 438375AW0159d0Hs.232234ESTs 5.06 418092845154 Hs.106604ESTs 5.06 418576AW968159Hs.289104Alu-binding protein 5.05 with zinc finger dom 413328Y15723 Hs.75295guanylate cyclase 1, 5.04 soluble, alpha 3 414271AK000275Hs.75871protein kinase C binding5.04 protein 1 432729AK000292Hs.278732hypothetical protein 5.04 433433AI692623Hs.121513Homo Sapiens clone 5.04 T3-1 placenta expres 439662H97552 Hs269060ESTs 5.04 1~ 439743AL389956Hs.283858Homo sapiens mRNA full5.04 length insert cDN

417511AL049176Hs.82223chordin-like 5.02 437814A1088192Hs.135474ESTs, Weakly similar 5.02 to DDX9-HUMAN ATP-D

426342AF093419Hs.169378multiple PDZ domain 5.02 protein 429782NM_005754Hs220689Ras-GTPase-activating 5.02 protein SH3-domain 15 429975AI167145Hs.i65538ESTs 5.02 436209AW850417Hs.254020ESTs, Moderately similar5.02 to unnamed prot 438571AW020775Hs.56022ESTs 5.02 450223AA418204Hs241493natural killer-tumor 5.02 recognition sequenc 408267AW380525Hs267705tubulin-speafic chaperone5.01 a 417730244761 gb:HSC28F061 normalized5.00 infant brain cDN

425465L18964 Hs.190dprotein kinase C, iota5.00 430599NM_004855Hs.247118phosphatidylinositol 5.00 glycan, lass B

450961AW978813Hs.250867metallothionein 1E 5.00 (functional) 451386AB029006Hs.26334spastic paraplegia 5.00 4 (autosomal dominant 25 420380AA640891Hs.102406ESTs 4.99 424947877952 Hs.239625ESTs, Weakly similar 4.99 to alternatively sp 442653BE269247Hs.170226gb:601185486F1 NIH 4.98 MGC-8 Homo Sapiens cD

457211AW972565Hs.32399ESTs, Weakly similar 4.97 to S51797 vasodilat 425851NM-001490Hs.159642glucosaminyl (N-acetyl)4.97 transferase 1, c 3O 446279AA490770Hs.182382ESTs 4.96 433377AI752713Hs.43845ESTs 4.96 450218802018 Hs.168640ankylosis, progressive4.96 (mcuse) homolog 412715NM-000947Hs.74519primase, polypeptide 4.94 2A (58kD) 448164861680 Hs.26904ESTs, Moderately similar4.94 to 2195-HUMAN Z

35 420121AW968271Hs.191534ESTs, Weakly similar 4.94 to ALUi HUMAN ALU
S

421689N87820 Hs.106826KIAA1696 protein 4.93 445808AV655234Hs298083ESTs, Moderately similar4.92 to PC4259 fern 416533BE244053Hs.79362retinoblastoma-like 4.92 2 (p130) 418049AA211467Hs.190488Homo Sapiens, Similar 4.92 to nuclear localiz 4O 436039AW023323Hs.121070ESTs 4.92 432653N62096 Hs293185ESTs, Weakly similar 4.91 to JC7328 amino as 420324AF163474Hs.96744prostate androgen-regulated4.91 transcript 1 403047 4.91 436899AA764852Hs291567ESTs 4.90 45 431117AF003522Hs250500delta (Drosophila)-like4.90 427617D42063 Hs.179825RAN binding protein 4.88 428804AK0007i3Hs.193736hypothetical proteinFLJ207064.88 433050A1093930Hs.163440Homo sapiens cDNA: 4.88 FLJ21000 fis, clone C

418575AA225313Hs.222886ESTs, Weakly similar 4.86 to TRHY_HUMAN TRICH

432615AA557191Hs.55028ESTs, Weakly similar 4.86 to 154374 gene NF2 412652AI801777Hs.6774ESTs 4.86 432473AI202703Hs.152414ESTs 4.86 449071NM-005872Hs.22960breast caranoma amplified4.86 sequence 2 -450654AJ245587Hs.25275Kruppel-type zinc finger4.85 protein 55 418866T65754 Hs.100489gb:yc11c07.s1 Stratagene4.85 lung (937210) H

407596886913 gb:yq30f05.r1 Soares 4.84 fetal liver spleen 456516BE172704Hs.222746KIAA1610 protein 4.84 426501AW043782Hs.293616ESTs 4.84 448730AB032983Hs21894KIAA1157 protein 4.84 458339AW976853Hs.172843ESTs 4.83 422083NM-001141Hs.111256arachidonate 15-lipoxygenase,4.82 second typ 420159AI572490Hs.99785Homo sapiens cDNA: 4.82 FLJ21245 fis, clone C

424103NM_001918Hs.139410dihydrolipoamide branched4.82 chain transact' 449535W15267 Hs.23672low density lipoprotein4.82 receptor-related 65 422048NM 012445Hs288126spondin 2, extracellular4.82 matrix protein 416737AF154335Hs.79691LtM domain protein 4.82 419972AL041465Hs.294038golgin-67 4.81 420235AA256756Hs.31178ESTs 4.81 423412AF109300Hs.147924prostate cancer assoaated.
protein 5 4.80 429598AA811257Hs.269710ESTs 4.80 457114AI821625Hs.191602ESTs 4.80 421828AW891965Hs.289109histone deaceiylase 4.79 424602AK002055Hs.30fhypothetical protein 4.78 428364AA426565Hs.160541ESTs, Moderately similar4.78 to ALUi HUMAN A

452335AW188944Hs.61272ESTs 4.78 410765AI694972Hs.66180nucleosome assembly 4.77 protein 1-like 2 421040AA715026Hs.135280ESTs 4.76 421518A1056392Hs.208819ESTs 4.76 452560BE077084 ESTs 4.76 409752AW963990 gb:EST376063 MAGE resequences,4.75 MAGH Homo 439703AF086538Hs.196245ESTs 4.75 418836A1655499Hs.161712ESTs 4.74 450642839773 Hs.7130copine IV 4.74 419879217805 Hs.93564Homer, neuronal immediate4.74 early gene, 2 411440AW749402 gb:QV4-BT0383-281299-061-c064.74 BT0383 Homo 450649NM_001429Hs297722E1A binding protein 4.74 p300 408738NM 014785Hs.47313KIAA0258 gene product 4.73 435020AW505076Hs.301855DiGeorge syndrome critical4.72 region gene 8 2~ 411624BE145964 KIAA0594 protein 4.72 439360AA448488Hs.55346ribosomal protein L44 4.72 440491835252 Hs.24944ESTs, Wealdy similar 4.72 to 2109260A B cell 442611BE077155Hs.177537hypothetical protein 4.72 DKFZp761B1514 443555N71710 Hs.21398ESTs, Moderately similar4.72 to A Chain A, H

453800BE300741Hs.288416hypothetical protein 4.72 457528AW973791Hs.292784ESTs 4.72 416795AI497778Hs.168053HBV pX associated protein-84.71 407302874206 Hs.268755ESTs, Weakly similar 4.71 to 178885 serine/th 404721 4.70 426261AW242243Hs.168670peroxisomal famesylated4.70 protein 431924AK000850Hs272203Homo sapiens cDNA FLJ208434.70 fis, clone AD

435256AF193766Hs.13872cytokine-like protein 4.70 438295AI394151Hs.37932ESTs 4.70 442655AW027457Hs.30323ESTs, Weakly similar 4.70 to 834087 hypotheti 415788AW628686Hs.78851KIAA0217 protein 4.69 442760BE075297Hs.10067ESTs, Weakly similar 4.69 to A43932 mudn 2 p 432432AA541323Hs.115831ESTs 4.68 454398AA463437Hs.11556Homo sapiens d)NA FLJ125664.68 fis, clone NT

452741BE392914Hs.30503Homo sapiens cDNA FLJ113444.67 fis, clone PL

424853BE549737Hs.132967Human EST done 122887 4.67 mariner transposo 419706C04649 Hs.77899tropomyosin 1 (alpha) 4.66 412088AI689496Hs.108932ESTs 4.65 416276041060 Hs.79136LIV-1 protein, estrogen4.64 regulated 429281AA830856Hs2980BHomo sapiens d)NA: 4.64 FLJ21122 fis, done C

448207AI475490Hs.170577ESTs 4.64 408374AW025430Hs.155591forkhead box F1 4.64 447162BE328091Hs.157396ESTs, Weakly similar 4.6d to A46010 X-linked 451900AB023199Hs.27207KIAA0982 protein 4.63 421437AW821252Hs.104336hypothetical protein 4.63 5~ 418624AI734080Hs.104211ESTs 4.63 426172AA371307Hs.125056ESTs 4.62 439831AW136488Hs25545ESTs 4.61 452994AW962597Hs.31305KIAA1547 protein - 4.61 457726AI217477Hs.194591ESTs 4.60 434629AA789081Hs.4029glioma-amplified sequence-414.60 403764 4.58 410659A1080175Hs.68826ESTs 4.58 432383AK000144Hs.274449Homo sapiens d)NA FLJ201374.58 tis, done CO

451246AW189232Hs.39140cutaneous T-cell lymphoma4.58 tumor antigen 6O 433234AB040928Hs.65366KIAA1495 protein 4.57 424983A1742434Hs.169911ESTs 4.56 437812AI582291Hs.16846ESTs, Weakly similar 4.56 to 04HUD1 debrisoqu 438447A1082883Hs.167593hypothetical protein 4.55 FLJ13409; KIAA1711 434715BE005346Hs.116410ESTs 4.55 447673AI823987Hs.182285ESTs 4.54 408897N50204 Hs283709lipopolysaccharide 4.54 spedfic response-7 p 436645AW023424Hs.156520ESTs 4.54 421247BE391727Hs.1029fgeneral transcription 4.53 0 factor IIH, polyps 450377AB033091Hs24936KIAA1265 protein 4.53 433644AW342028Hs256112gb:h675d03.x1 NCI-CGAP_Ut24.53 Homo sapiens 408321AW405882Hs.44205cortistatin 4.53 439225AA192669Hs,45032ESTs 4.52 440348AW015802Hs.47023ESTs 4.52 $ 446351AWd44551Hs.258532x 001 protein 4.52 451212AW902672Hs.287334ESTs 4.52 430294AI538226Hs.135184guanine nucleotide 4.52 binding protein 4 435005080743Hs.4316trinucleoC~de repeat 4.52 containing 12 448072AId59306Hs.24908ESTs 4.50 1 403721 4.50 ~

451018AW965599Hs.247324mitochondria) ribosomal4.50 protein S14 453070AK001465Hs.31575SEC63, endoplasmic 4.49 reticulum translocon 417412X16896Hs.82112interleukin 1 receptor,4.48 type I

439735A1635386Hs.142846hypothetical protein 4.48 15 435663A1023707Hs.134273ESTs 4.48 424036AA770688Hs.81946H2A histone family, 4.48 member L

426386AA748850Hs.174877bladder cancerovere~ressedprotein4.48 408622AA056060Hs202577Homo sapiens cDNA FLJ121664.47 fls, done MA

444269A1590346Hs.146220ESTs 4.47 ZO 430187A1799909Hs.158989ESTs 4.46 427761AA412205Hs.140996ESTs 4.46 430261AA305127Hs237225hypothetical protein 4.46 444169AV648170Hs.58756ESTs 4.44 430598AK001764Hs247112hypothetical protein 4.44 412903BE007967Hs.155795ESTs 4.44 417048A1088775Hs.55498geranylgerany) diphosphate4.44 synthase 1 442710A1015631Hs23210ESTs 4.44 457413AA743462Hs.165337ESTs 4.44 400303AA242758Hs.79136LIV-1 protein, estrogen4.42 regulated 3O 443268AI800271Hs.129445hypothetical protein 4.42 438209AL120659Hs.6111aryl-hydrocarbon receptor4.42 nuclear transl 431724AA514535Hs283704ESTs 4.4i 412280AW205116Hs.272814hypothetical protein 4.40 DKFZp434E1723 440801AA906366Hs.190535ESTs 4.40 35 452959AI933416Hs.189674ESTs 4.40 453861A1026838Hs.30120ESTs, Weakly similar 4.40 to NUCL HUMAN NUCLE

417421A4138201Hs.82120nuclear receptor subfamily4.40 4, group A, m 447270AC002551Hs.331general transcription 4.38 factor IIIC, polyp 433641AF080229 gb:Human endogenous 4.38 retrovirus K clone 4O 447078AW885727Hs.301570ESTs 4.38 424242AA337476 hypothetical protein 4.37 408170AW204516Hs.31835ESTs 4.36 448757AI366784Hs.48820TATA box binding protein4.36 (TBP)-associate , 420021AA252848Hs293557ESTs 4.36 4$ 449694AI659790Hs.253302ESTs 4.36 453867AI929383Hs.108196hypothetical protein 4.36 DKFZp434N185 458712AI347502Hs.173066hypothetical protein 4.36 417251AW015242Hs.99488ESTs, Weakly similar 4.35 to YK54 YEAST HYPOT

434423NM_006769Hs.3844LIM domain only 4 4.35 423427AL137612Hs.285848KIAA1454 protein 4.34 415715F30364 ESTs 4.33 404561 4.32 422969AA782536Hs.122647N-myristoyitransferase4.32 423685BE350494Hs.49753uveal autoantigen with4.32 coiled coil domai 55 443977AL120986Hs.150627ESTs, Weakly similar 4.32 to 138022 hypotheti 425071NM Hs.154424deiodinase, iodothyronine,4.32 013989 type II

431583AL042613Hs262476S-adenosylmethionine 4.31 decarboxylase 1 411379AI816344Hs.12554ESTs, Weakly similar 4.30 to NPL4_HUMAN NUCLE

421476AW953805Hs21887ESTs 4.30 6O 425178H16097Hs.161027ESTs 4.30 439262AA832333Hs.124399ESTs 4.30 442818AK001741Hs.8739hypothetical protein 4.30 421977W94197Hs.110165ribosomal protein L26 4.29 homolog 437114AA836641Hs.163085ESTs 4.28 65 420195N44348Hs.300794Homo sapiens cDNA FLJ11177428 ts, clone PL

418330BE409405Hs.94722ESTs 4.27 419750AL079741Hs.i83114Homo Sapiens cDNA FLJ142364.26 fis, clone NT

437065AL036450Hs.103238ESTs 4.26 455276BE176479 gb:RC3-HT0585-160300-022-b09424 HT0585 Homo 416292AA179233Hs.42390nasopharyngeal carcinoma4.24 susceptibility 423740Y07701 Hs.132243aminopeptidase puromycin4.24 sensitive 442023AI187878Hs.144549ESTs 4.24 426764AA732524Hs.151464ESTs, Weakly similar 423 to ALUC-HUMAN !!i!

454058AI273419Hs.135146hypothetical protein 4.23 456511AA282330Hs.145668ESTs 4.22 448330AL036449Hs207163ESTs 4.22 424701NM-005923Hs.151988mitogen-activated protein421 kinase kinase 432621AI298501Hs.12807ESTs, Weakly similar 420 to T46428 hypotheti I~ 445707AI248720Hs.114390ESTs 420 419910AA662913Hs.190173ESTs, Weakly similar 420 to A46010 X-linked 424065NM-002914Hs.139226replication factor 4.20 C (activator 1 ) 2 (40 440749W22335 Hs.7392hypothetical protein 4.20 442787W93048 Hs.227203hypothetical protein 420 I5 443414854594 Hs25209ESTs 420 443556AA256769Hs.94949methylmalonyl-CoA epimerase4.20 444170AW613879Hs.102408ESTs 420 446751AA766998Hs.85874Human DNA sequence 420 from clone RP11-16L21 421041N36914 Hs.14691ESTs, Moderately similar4.19 to 138022 hypot 447476BE293466Hs20880ESTs, Weakly similar 4.19 to 138022 hypotheti 448543AW897741Hs21380Homo sapiens mRNA; 4.18 cDNA DKFZp586P1124 (f 410294A8014515Hs288891KIAA0615 gene product 4.18 433607AA602004Hs23260ESTs 4.18 435552AI668636Hs.193480ESTs, Moderately similar4.18 to ALU6 HUMAN A

25 447124AW976438Hs.1742$- 4.18 RBP1-like protein 453308AW959731Hs.32538ESTs 4.17 439328W07411 Hs.118212ESTs, Moderately similar4.16 to ALU3_HUMAN A

430473AW130690Hs299842ESTs 4.16 437257AI283085Hs290931ESTs, Weakly similar 4.16 to YFJ7 YEAST HYPOT

438018AK001160Hs.5999hypothetical protein 4.16 443857A1089292Hs287621hypothetical protein 4.15 446711AF169692Hs.12450protocadherin 9 4.15 419103240229 Hs.96423hypothetical protein 4.14 405403 4.14 35 407378AA299264 ESTs, Moderately similar4.14 to 138022 hypot 408986AW298&02Hs.197687ESTs 4.14 418727AA227609Hs.94834ESTs 4.14 434400AI478211Hs.186896Homo sapiens cDNA FLJ114174.14 fis, done HE

438578AA811244Hs.164168ESTs 4.14 4~ 450459AI697193Hs299254Homo sapiens cDNA: 4.14 FLJ23597 fis, done L

429887AW366286Hs.145696splicing factor (CC1.3)4.13 448148NM_016578Hs20509HBV pX assoaated protein-84.13 450316W84446 Hs.17850hypothetical protein 4.12 417531NM_003157Hs.1087serine/threonine kinase4.12 45 431592869016 Hs293871hypothetical protein 4.12 MGC10895s 432463AA548518Hs.186733ESTs 4.12 433613AA836126Hs.5869ESTs 4.12 434739AA804487Hs.144130ESTs 4.12 438259AW205969Hs.131808ESTs 4.12 5~ 425810AI923627Hs.31903ESTs 4.10 432672AW973775Hs.130760myosin phosphatase, 4.10 target subunit 2 433345AI681545Hs.152982hypothetical protein 4.10 432712AB016247Hs288031sterol-C5-desaturase 4.09 (fungal ERG3, delta -453020AL162039Hs.3i422Homo sapiens mRNA; 4.09 cDNA DKfZp434M229 (fr 55 412045AA099802Hs.4299transmembrane, prostate4.09 androgen induced 435114AA775483Hs288936mitochondrial ribosomal4.08 protein L9 443204AW205878Hs29643Homo sapiens cDNA FLJ131034.08 fis, clone NT

445459AI478629Hs.158465likely ortholog of 4.08 mouse putative IKK
re 438938H46212 Hs.137221ESTs 4.07 4541 BE549773Hs.40510uncoupling protein 4.06 i9 4 411000N40449 Hs201619ESTs, Weakly similar 4.06 to S38383 SEB48 pro 418926AA232658Hs.87070UDP-glucose:glycoprotein4.06 glucosyltransfe 424432A8037821Hs.146858protocadherin 10 4.06 449673AA002064Hs.18920ESTs 4.06 65 429299AI620463Hs.99197hypothetical protein 4.06 422174AL049325Hs.112493Homo Sapiens mRNA; 4.05 cDNA DKFZp564D036 (fr 455497AA112573Hs285691Homo sapiens prostein 4.05 mRNA, complete cds 415138C18356 Hs.78045tissue factor pathway 4.04 inhibitor 2 402791 4.04 426792AL044854Hs.172329KIAA0576 protein 4.04 438660U95740Hs.6349Homo sapiens, done 4.04 IMAGE:3010666, mRNA, 442768AL048534Hs.48458ESTs, Weakly similar 4.04 to ALUB_HUMAN ALU
S

447568AF155655Hs.18885CGI-116 protein 4.04 428342AI739i68Hs.l3iHomo sapiens d)NA FLJ134584.04 798 fis, done PL

453439AI572438Hs.32976guanine nucleotide 4.02 binding protein 4 453857AL080235Hs.35861DKFZP586E1621 protein 4.02 428249AA130914Hs.183291zinc finger protein 4.02 432015AL157504Hs.159115Homo sapiens mRNA; 4.02 d)NA DKFZp58600724 (f 1~ 445495BE622641Hs.38489ESTs, Weakly similar 4.02 to 138022 hypotheti 451746M86178 ESTs 4.02 452211A1985513Hs.233420ESTs 4.02 453046AA284040Hs2i944iESTs, Highly similar 4.02 fo CA5B_HUMAN CAR80 456038AA203285Hs.294141ESTs, Weakly similar 4.02 to altematNely sp 15 452449AW068658Hs20943ESTs 4.02 407204841933Hs.140237ESTs, Weakly similar 4.01 to ALUi HUMAN ALU
S

428046AW812795Hs.155381ESTs, Moderately similar4.01 to 138022 hypot 438520AA706319Hs.98416ESTs 4.01 443292AK000213Hs.9196hypothetical protein 4.01 432715AA247152Hs.200483ESTs, Weakly similar 4.00 to KIAA1074 protein 403797 4.00 418347AA216419Hs.269295gb:nc16e03.s1 NCI_CGAP-Pr14.00 Homo Sapiens 419459AW291128Hs.278422DKFZP586G1122 protein 4.00 420911U77413Hs.1002930-linked N-acetylgiucosamine4.00 (GIcNAc) tr 2$ 425176AW015644Hs.301430TEA domain family member4.00 1 (SV40 transcr 447505AL049266Hs.18724Homo sapiens mRNA; 4.00 d)NA DKFZp564F093 (fr 453773AL133761 gb:DKFZp761C1413-r17614.00 (synonym: hamy2) 434384AA631910Hs.162849ESTs 3.99 422471AA311027Hs.271894ESTs, Weakly similar 3.99 to 138022 hypotheti 427386AW836261Hs.177486ESTs 3.98 433394AI907753Hs.93810cerebral cavernous 3.98 malformations 1 441269AW015206Hs.178784ESTs 3.97 419629AB020695Hs.91662KIAA0888 protein 3.96 435008AF150262Hs.162898ESTs 3.98 35 456649874441Hs.117176poly(A)-binding protein,3.96 nuclear 1 418723AA504428Hs.10487Homo Sapiens, done 3.96 IMAGE:3954132, mRNA, 428738NM-000380Hs.192803xeroderma pigmentosum,3.95 complementation g 430456AA314998Hs.241503hypothetical protein 3.95 422017NM_003877Hs.110776STAT induced STAT inhibitor-23.95 409960BE261944Hs.153028hexokinase l 3.95 455309AW894017 gb:RC4-NN0027-150400-012-g043.95 NN0027 Homo 450295AI766732Hs.201194ESTs 3.94 456660AA909249Hs.112282solute carrier family 3.94 30 (zinc transport 410908AA121686Hs.10592ESTs ~ 3.94 45 447145AA761073Hs.192943TRAF family member-assodated3.94 NFKB activ 449318AW236021Hs.108788Homo sapiens, Similar 3.94 to RIKEN d)NA 5730 449869W57990Hs.60059Homo Sapiens cDNA FLJ114783.94 fis, done HE

411887AWi82924Hs.128790ESTs 3.93 437531AI400752Hs.112259T cell receptor gamma 3.93 locus 452238F01811Hs.187931ESTS 3.93 410486AW235094Hs.193424zinc finger protein 3.92 424882AI379461Hs.153636far upstream element 3.92 (FUSE) binding prot 426269H15302Hs.168950Homo sapiens mRNA; 3.92 d)NA DKFZp566A1046 (P

427043AA397679Hs.298460ESTs 3.92 $5 440404A1015881Hs.125616mitochondrial ribosomal3.92 protein S5 452762AW501435Hs.f71409v-akt murine thymoma 3.92 viral oncogene homo 453058AW612293Hs.288684Homo sapiens cDNA FLJ117503.92 fis, clone HE

423583AL122055Hs.129836KIAA1028 protein 3.92 d08001AA046458Hs.95296ESTs 3.92 419197N48921Hs.27441KIAA1615 protein 3.91 428695AI355647Hs.189999purinergic receptor 3.91 (family A group 5) 401747 3.91 410011AB020641Hs.57856PFTAIRE protein kinase3.91 432205AI806583Hs.125291ESTs 3.91 65 447857AA081218Hs.58608Homo Sapiens d)NA FLJ142063.91 fis, done NT

446494AA463276Hs.288906WW Domain-Containing 3.91 Gene 409928AL137163Hs.57549hypothetical protein 3.90 dJ473B4 411598BE336654Hs.70937H3 histone family, 3.90 member A

424790AL119344Hs.13326ESTs, Weakly similar 3.90 to 2004399A chromos 1s$

425707AF115402Hs.11713E74-like factor 5 (ets3.90 domain transcript 431325AW026751Hs.5794ESTs, Weakly similar 3.89 to 2109260A B cell 451806NM_003729Hs.27076RNA 3'-terminal phosphate3.89 cyclase 401045 3.89 433023AW864793Hs.34161thrombospondin 1 3.89 452160BE378541Hs.279815cysteine sulfinic acid3.89 decarboxylase-rei 437372AA323968Hs.283631hypothetical protein 3.89 DKFZp547G183 417067AJ001417Hs.81086solute carrier family 3.88 22 (extraneuronal 410467AF102546Hs.63931dachshund (Drosophila)3.88 homolog 1~ 422660AW297582Hs.237062hypothetical protein 3.88 FLJ22548 similar to 431930A8035301Hs.272211cadherin 7, type 2 3.88 453047AW023798Hs.286025ESTs 3.88 433891AA613792 gb:no97h03.s1 NCI-CGAP-Pit3.88 Homo Sapiens 401785 3.88 431088AA491824Hs.196881ESTs 3.88 451952AL120173Hs.301663ESTs 3.87 422089AA523172Hs.103135ESTs, Weakly similar 3.87 to SFR4_HUMAN SPLIC

452277AL049013Hs.28783KIAA1223 protein 3.87 438279AA805166Hs.165165HIV-1 rev binding protein3.86 458229AI929602Hs.177phosphatidylinositol 3.86 glycan, class H

406414 3.86 417193AI922189Hs.288390hypothetical protein 3.85 413174AA723564Hs.191343ESTs 3.85 433332AI367347Hs.127809Homo sapiens clone 3.85 TCCCTA00151 mRNA sequ 411089AA456454Hs.118637cell division cycle 3.85 2-like 1 (PITSLRE
pr 412494AL133900Hs.792ADP-ribosylaGon factor3.84 domain protein 1 413530AA130158Hs.19977ESTs, Moderately similar3.84 to ALU8 HUMAN A

459592AL037421Hs208746ESTs, Moderately similar3.84 to pot. ORF I [

418329AW247430Hs.84152cystathionine-beta-synthase3.83 451468AW503398Hs210047ESTs, Moderately similar3.83 to 138022 hypot 434804AA649530 gb:ns44f05.s1 NCI-CGAP-AIv13.83 Homo sapiens 401819 3.82 424179F30712 Homo Sapiens, clone 3.82 IMAGE:4285740, mRNA

424850AA151057Hs.153498chromosome 18 open 3.82 reading frame 1 426472BE246138Hs.30853ESTs 3.82 426625T78300 Hs.171409serologically defined 3.82 colon cancer antig 427585D31152 Hs.179729collagen, type X, alpha3.82 1 (Schmid metaph 427756AI376540Hs.15574ESTs 3.82 444701AI916512HS.198394ESTs 3.82 4O 423052M28214 Hs.123072RAB3B, member RAS oncogene3.82 family 429259AA420450Hs292911ESTs, Highly similar 3.82 to S60712 band-6-pr 416111AA033813Hs.79018chromatin assembly 3.82 factor 1, subunit A ( 433586T85301 gb:yd78d06.s1 Soares 3.81 fetal liver spleen 438527AI969251Hs.143237RAB7, member RAS oncogene3.81 family-like 1 410297AA148710Hs.159441lum~can 3.81 429898AW117322Hs.42366ESTs 3.81 409079W87707 Hs.82065interleukin 6 signal 3.80 transducer (gp130, 419423D26488 Hs.90315KIAA0007 protein 3.80 429643AA455889Hs.187548FYVE-finger containing3.80 RabS effector pro 5O 431499NN~,001514Hs258561general transcription 3.80 factor IIB

445060AA830811Hs.88808ESTs 3.80 449419834910 Hs.119172ESTs 3.80 450584AA040403Hs.60371ESTs - 3.80 426137AL040683Hs.167031DKFZP566D133 protein 3.79 420185AL044056Hs.158047ESTs 3.79 410076T05387 Hs.7991ESTs 3.78 444078BE246919Hs.10290U5 snRNP-specific 40 3.78 kDa protein (hPrp8-417318AW953937Hs.12891ESTs 3.78 414664AA587775Hs.66295multi-PDZ-domain-containing3.78 protein 410275085658 Hs.61796transcription factor 3.77 AP-2 gamma (activat 410503AW975746Hs.188662KIAA1702 protein 3.77 434170AA626509Hs.122329ESTs 3.77 421838AW881089Hs.108806Homo Sapiens mRNA; 3.77 cDNA DKFZp566M0947 (f 425268AI807883Hs.156932Homo Sapiens cDNA FLJ206533.76 fis, clone KA

431696AA259068Hs267819protein phosphatase 3.76 1, regulatory (inhib 411990AW963624Hs.31707ESTs, Weakly similar 3.76 to YEW4-YEAST HYPOT

430291AV660345Hs238126CGI-49 protein 3.76 448779BE042877Hs.177135ESTs 3.76 452682AA456193Hs.155606progesterone membrane 3.75 binding protein 452598AI831594Hs.68647ESTs, Weakly similar 3.75 to ALU7_HUMAN ALU
S

439498AA908731Hs.58297CLLLB protein 3.75 440258AI741633Hs.125350ESTs 3.74 456848AL121087Hs.296406KIAA0685 gene product 3.74 415082AA160000Hs.137396ESTs, Weakly similar 3.74 to JC5238 galactosy 420653AI224532Hs.88550ESTs 3.74 431637AI879330Hs.265960hypothetical protein 3.74 440411N30256 Hs.156971hypothetical protein 3.74 DKFZp434G1415 405917 3.74 l0 419440AB020689Hs.90419KIAA0882 protein 3.74 451230BE546208Hs.26090hypothetical protein 3.73 429597NM_003816Hs.2442a disintegrin and metalloproteinase3.73 doma 430144AI732722Hs.187694ERGL protein; ERGIC-53-like3.72 protein 438394BE379623Hs27693peptidylprolyl isomerase3.72 (cyclophilin)-I

440527AV657117Hs.184164ESTs, Moderately similar3.72 to S65657 alpha 449433AI672096Hs.9012ESTs, Weakly similar 3.72 to S26650 DNA-bindi 456228BE503227Hs.134759ESTs 3.72 448663BE614599Hs.106823hypothetical protein 3.72 415075L27479 Hs.77889Friedreich ataxia region3.72 gene X123 433544AI793211Hs.165372ESTs, Moderately similar3.71 to ALU1 HUMAN A

418293AI22d483Hs.16063hypothetical protein 3.71 449897AW819642Hs.24135transmembrane protein 3.71 vezatin; hypotheti 420297AI628272Hs.88323ESTs, Weakly similar 3.70 to ALU1 HUMAN ALU
S

423065896158 Hs.194606Homo sapiens, clone 3.70 MGC:5406, mRNA, comp 429340N35938 Hs.199429Homo Sapiens mRNA; 3.70 cDNA DKFZp434M2216 (f 437777AA768098Hs.189079ESTs 3.70 440351AF030933Hs.7179RAD1 (S. pombe) homolog3.70 443603BE502601Hs.134289ESTs, Weakly similar 3.70 to KIAA1063 protein 446965BE242873Hs.16677WD repeat domain 15 3.70 412350AI659306Hs.73826protein tyrosine phosphatase,3.70 non-recept 433852AI378329Hs.126629ESTs 3.70 433142AL120697Hs.110640ESTs 3.69 419994AA282881Hs.190057ESTs 3.69 412628A1972402Hs.173902hypothetical protein 3:69 431416AA532718Hs.178604ESTs 3.69 439444AI277652Hs.54578ESTs, Weakly similar 3.68 to 138022 hypotheti 414709AA704703Hs.77031Sp2 transcription factor3.68 447397BE247676Hs.18442E-1 enryme 3.68 405718 3.68 4O 425217AU076696Hs.155174ClxS (cell division 3.68 cycle 5, S. pombe, h 442242AV647908Hs.90424Homo sapiens cDNA: 3.68 FLJ23285 fis, clone H

424690BE538356Hs.i51777eukaryotic translation3.68 initiation factor 421734AI318624Hs.107444Homo Sapiens cDNA FLJ205623.67 fis, done KA

427221L15409 Hs.174007von Hippel-Lindau syndrome3.67 ~5 439864A1720078Hs291997ESTs, Weakly similar 3.66 to A47582 8-cell gr 402408 3.66 426327W03242 Hs.44898Homo Sapiens done TCCCTA001513.66 mRNA sequ 427119AW880562Hs.114574ESTs 3.66 427356AW023482Hs.97849ESTs 3.66 5~ 452946X95425 Hs.31092EphA5 3.66 419078M93119 Hs.89584insulinoma-associated 3.66 416295A1064824Hs.193385ESTs 3.65 427144X95097 Hs.2126vasoactive intestinal 3.65 peptide receptor 2 -447500AI381900Hs.159212ESTs 3.65 55 453127AI696671Hs.294110ESTs 3.65 423396AI382555Hs.127950bromodomain-containing3.65 419346AI830417 polybromo 1 3.64 441540C01367 Hs.127128ESTs 3.64 446501A1302616Hs.150819ESTs 3.64 459527AW977556Hs.291735ESTs, Weakly similar 3.63 to 178885 serine/th 44&320AF126245Hs.14791aryl-Coenryme A dehydrogenase3.63 family, me 435706W31254 Hs.7045GL004 protein 3.63 400110 3.62 410313810305 Hs.1856B3ESTs 3.62 65 4147138E465243Hs.12664ESTs 3.62 436279AW900372Hs.180793ESTs, Weakly similar 3.62 to S65657 alpha-1C-439818AL360137Hs.19934Homo Sapiens mRNA full3.62 length insert cDN

451797AW663858Hs.56120small indudble cytokine3.62 subfamily E, me 451294AI457338Hs29894ESTs 3.62 434194AF119847Hs.283940Homo Sapiens PR01550 3.62 mRNA, partial cds 404939 3.62 408101AW968504Hs.123073CDC2-related protein 3.62 kinase 7 435846AA700870Hs.14304ESTs 3.61 432833N51075 Hs.47191ESTs 3.61 427276AA400269Hs.49598ESTs 3.61 433495AW373784Hs.71 alpha-2-glycoprotein 3.60 1, zinc 403137 3.60 404165 3.60 T 409571AA504249Hs.187585ESTs 3.60 1~

410561BE540255Hs.6994Homo sapiens cDNA: 3.60 FLJ22044 fis, clone H

412924BE018422Hs.75258H2A histone family, 3.60 member Y

434228242047 Hs283978Homo Sapiens PR02751 3.60 mRNA, complete als 436797AA731491Hs.178518hypothetical protein 3.60 437162, AW005505Hs.5464thyrcid hormone receptor3.60 coactivating pr d37444H46008 Hs.31518ESTs 3.60 404210 3.59 446157BE270828Hs.131740Homo Sapiens cDNA: 3.59 FLJ22562 fis, clone H

437587AI591222Hs.122421Human DNA sequence 3.58 from clone RPi-187J11 423147AA987927Hs.131740Homo Sapiens cDNA: 3.57 FLJ22562 fis, done H

452226AA024898Hs.296002ESTs 3.56 443775AF291664Hs204732matrix metalloproteinase3.56 452501AB037791Hs.29716hypothetical protein 3.56 428647AA830050Hs.124344ESTs 3.56 ~5 422443NM 014707Hs.116753histone deacetylase 3.55 447966AA340605Hs.105887ESTs, Weakly similar 3.55 to Homolog of rat Z

420892AW975076Hs.172589nuclear phosphoprotein3.55 similar to S. cer 420230AL0343d4Hs.298020forkhead box C1 3.55 418428Y12490 Hs.85092thyroid hormone receptor3.54 interactor 11 428949AA442153Hs.104744hypothetical protein 3.54 DKFZp434J0617 444929A1685841Hs.161354ESTs 3.54 433339AF019226Hs.8036glioblastoma overexpressed3.54 424369887622 Hs.26714KIAA1831 protein 3.54 433002AF048730Hs279906cyclin Ti 3.53 435425Hi6263 Hs.31416ESTs 3.53 415621AI648602Hs.131189ESTs 3.53 416974AF010233Hs.80667RALBP1 associated Eps 3.53 domain containing 405793 3.52 409770AW499536 gb:Ul-HF-BROp-aji-o-12-0-ULr13.52 NIH MGC_5 425305AA363025Hs.155572Human done 23801 mRNA 3.52 sequence 428939AW236550Hs.131914ESTs 3.52 438388AA806349Hs.44698ESTs 3.52 443703AV646177Hs213021ESTs ~ 3.52 457940AL360159Hs.30445Homo Sapiens TRIpartite3.52 motif protein ps 402444 3.52 409643AW450866Hs257359ESTs 3.51 418250U29926 Hs.83918adenosine monophosphate3.51 deaminase (isofo 432745AI821926Hs269507gb:nt78f05.x5 NCI_CGAP_Pr33.51 Homo Sapiens 414222AL135173Hs.878sorbitol dehydrogenase3.51 5O 430061A8037817Hs230188KIAA1396 protein 3.51 421491H99999 Hs.42736ESTs 3.50 422384AA224077Hs.42438Sm protein F 3.50 434565T52172 ESTs ' 3.50 438379N23018 Hs.171391C-terminal binding 3.50 protein 2 439741BE379646Hs.6904Homo Sapiens mRNA full3.50 length insert cDN

447311837010 Hs.33417Homo Sapiens cDNA: 3.50 FW22806 fis, clone K

447805AW627932Hs.19614gemin4 3.50 454265H03556 Hs.300949ESTs, Weakly similar 3.50 to thyroid hormone 418838AW385224Hs.35198ectonucleotide pyrophosphatase/phosphodi3.50 l7O448804AW512213Hs.42500ADP-ribosylation factor-like3.50 409617BE003760Hs.55209Homo Sapiens mRNA; 3.49 cDNA DKFZp434K0514 (f 434075AW003416Hs.160604ESTs 3.49 444190AI878918Hs.10526cysteine and glyane-rich3.49 protein 2 435017AA336522Hs.12854angiotensin II, type 3.48 I receptor-associat 6$ 423445NM_014324Hs.128749alpha-methylacyd-CoA 3.48 racemase 420271AI954365Hs.42892ESTs 3.48 443664AI681307Hs.166674ESTs 3.48 444168AW379879 gb:RC1-HT0256-081199-011-f013.48 HT0256 Homo 446074AA079799Hs29263hypothetical protein 3.48 452582AL137407Hs.29911Homo sapiens mRNA; 3.48 cDNA DKFZp434M232 (fr 431542H63010 Hs.5740ESTs 3.48 432697AW975050Hs.293892ESTs, Weakly similar 3.48 to ALU4_HUMAN ALU
S

435572AW975339Hs239828ESTs, Weakly similar 3.47 to GAG2 HUMAN RETRO

d07192AA609200 gb:af12e02.s1 Soares-testis-NHT3.47 Homo sap 413435X51405 Hs.75360catboxypeptidase E 3.46 447210AF035269Hs.17752phosphatidylserine-spedfic3.46 phospholipas 447958AW796524Hs.68644Homo Sapiens microsomal3.46 signal peptidase 425312AA354940Hs.145958ESTs 3.46 1~ 442007AA301116Hs.142838nudeolar phosphoprotein3.46 Nopp34 417455AW007066Hs.18949ESTs, Weakly similar 3.45 to CA2B HUMAN COLLA

426931NM 003416Hs.2076zinc finger protein 3.45 7 (KOX 4, clone HF.1 408739W01556 Hs.238797ESTs, Moderately similar3.45 to 138022 hypot 436024AI800041Hs.190555ESTs 3.45 408418AW963897Hs.44743KIAA1435 protein 3.45 409151AA306105Hs.50785SEC22, veside trafficking3.44 protein (S. c 418626AW299508Hs.135230ESTs 3.44 420560AW207748Hs.59115ESTs 3.44 420686AI950339Hs.40782ESTs 3.44 428870AA436831Hs.36049ESTs 3.44 436754A1061288Hs.133437ESTs 3.44 437960AI669586Hs.222194ESTs 3.44 452300AW628045Hs.28896Homo sapiens mRNA full3.44 length insert d7N

421887AW161450Hs.109201CGI-86 protein 3.44 TABLE 5A shows the accession numbers for those primekeys lacking a unigene>D
in Tables 5, 6, and 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 Gene cluster number number.

Accession: Genbank accession numbers Pkey CAT numberAccession 407596 1003489_1886913 886901 H25352 801370 H43764 AW044451 W21298 409770 1154048_1AW499536 AW499553 AW502138 AW499537 AW502i36 419346 184129_1 AI830417 AA236612 424179 236389_1 F30712 F35665 AW263888 AI904014 AI904018 AA336927 432363 345469_1 AA534489 AW970240 AW970323 433641 37186_1 AF080229 AF080231 AF080230 AF080232 AF0802,33 433687 373061_1 AA743991 AA604852 AW272737 433891 376239_1 AA613792 AW182329 T05304 AW858385 437113 _ AA744693 AW750059 433234_1 444168 593829_1 AW379879 AI126285 H12014 448310 757918_1 AI480316 AW847535 451746 883303_1 M86178 AI813822 D56993 452560 922216_1 BE077084 AWt39963 AW863127 AW806209 AW806204 AW806205 AW806206 452712 928309_1 AW838616 AW838660 BE144343 AI914520 AW888910 BE184854 BE184784 BE1766i5 BEi76555 BEt76489 BE1766i0 TABLE 5B shows the genomic positioning for those primekeys lacking unigene )D's and accession numbers in Tables ~, 6, and 7. For each predicted axon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted axon are also listed.
Pkey: Unique number corresponding to an Eos probeset 1~ Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham 1. et al." refers to the publication entitled "The DNA sequence of human chromosome 22 " Dunham I. et al., Nature (1999) 402:489-495.
Strand: Indicates DNA strand from which axons were predicted.
Nt~osition: indicates nucleotide positions of predicted axons.
Pkey Ref Strand_ Nt~osition 4010458117619Plus 90044-90184,91111-91345 2~ 4014248176894Plus 24223-24428 4014516634068Minus 119926-121272 4017146715702Plus 96484-96681 4017479789672Minus 118596-118816,119119-119244,119609-119761,120422-120990,130161-130381,130468-130593,131097-131258,131866-131932,132451-132575,133580-134011 4017857249190Minus 165776-165996,166189-166314,166408-166569,167112-167268,167387-167469,168634-168942 4018197467933Minus 28217-28486 4024089796239Minus ' 110326-110491 4024449796614Plus 28391-28517 4027916137008Minus 51036-51207 3fl4030473540153Minus 59793-59968 4031379211494Minus 92349-92572,92958-93084,93579-93712,93949-94072,94591-94748,95214-95337 4037217528046Minus 156647-157366 4037647717105Minus 118692-118853 4037978099896Minus 123065-125008 4041659926489Minus 69025-69128 4042105006246Plus 169926-170121 4042539367202Minus 55675-56055 4045619795980Minus 69039-70100 4045717249169Minus 112450-112648 4047219856648Minus 173763-174294 4049157341766Minus 100915-101087 4049396862697Plus 175318-175476 4054036850244Minus 37491-37670,40951-41031 4056854508129Minus 37956-38097 4057189795467Plus 113080-113266 4057931405887Minus 89197-89453 4058766758747Plus 39694-40031 4059177712162Minus 106829-107213 4064149256407Plus 49593-49850 4065547711566Plus 106956-107121 TABLE 6:286 GENES ENCODING EXTRACELLULAR OR CELL SURFACE
PROTEINS UP-REGULATED IN PROSTATE CANCER COMPARED TO
NORMAL ADULT TISSUES
Table 6 shows 286 genes up-regulated in prostate cancer compared to normal adult tissues that are likely to be extracellular or cell-surface proteins. These were selected as for Table 5 and the predicted protein contained a structural domain that is indicative of extracellular localization (e.g. egf, 7tm domains).
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title Ri: Ratio of tumor to normal tissue 1.0Pkey ExAccn UnigenelDUningene Title Ri 409361NM_005982Hs.54416sine oculis homeoboic 4828 (Drosophila) homolo 409731AA125985Hs.56145thymosin, beta, identified4524 in neuroblast 400298AA032279Hs.61635six transmembrane epithelial43.48 antigen of 420154A1093155Hs.95420JM27 protein 41.12 426747AA535210Hs.171995kailikrein 3, (prostate31.80 specific antigen 400299X07730 Hs.171995kallikrein 3, (prostate24.91 specific antigen 425075AA506324Hs.1852 acid phosphatase, prostate2423 424846AU077324Hs.1832 neuropeptide Y 23.57 4o5sa5 2o.so 420757X78592 Hs.99915androgen receptor (dihydrotestosterone19.72 r 418994AA296520Hs.89546selectin E (endothelial19.56 adhesion molecul 452792AB037765Hs.30652KIAA1344 protein 17.39 445472AB006631Hs.12784Homo sapiens mRNA for 17.00 KIAA0293 gene, par 414565AA502972Hs.183390hypothetical protein 16.82 431716D89053 Hs.268012fatty-acid-Coenryme 16.60 A ligase, long-chain 408430S79876 Hs.44926dipep6dylpep6dase IV 1628 (CD26, adenosine 408000L11690 Hs.620 bullous pemphigoid 15.54 antigen 1 (230/240kD) 430226BE245562Hs2551 adrenergic, beta-2-, 15.40 receptor, surface 444484AK002126Hs.11260hypothetical protein 14.76 418601AA279490Hs.86368calmegin 14.56 448999AF179274Hs22791 transmembrane protein 14.55 with EGF-like and 416182NM_004354Hs.79069cydin G2 12.94 420544AA677577Hs.98732Homo sapiens Chromosome12.79 16 BAC clone CIT

445413AA151342Hs.12677CGI-147 protein 12.64 453930AA419466Hs.36727hypothetical protein 1222 440286029589 Hs.7138 cholinergic receptor, 12.04 muscarinic 3 452784BE463857Hs.151258hypothetical protein 11.86 450203AF097994Hs.301528L-kynurenine/alpha-aminoadipate11.68 aminotra 448045AJ297436Hs.20166prostate stem cell 11.51 antigen 449650AF055575Hs.23838calcium channel, voltage-dependent,11.18 L ty 420381D50640 Hs.337616phosphodiesterase 3B, 11.10 cGMP-inhibited 425665AK001050Hs.159066hypothetical protein 11.08 425710AF030B80Hs.159275solute tamer family, 11.08 member 4 428728NM 016625Hs.191381hypothetical protein 11.04 407021052077 gb:Human mariners transposase11.02 gene, comp 410733D84284 Hs.66052CD38 antigen (p45) 11.02 452340NM-002202Hs.505 ISL1 transcription 10.85 factor, LIMlhomeodoma 428819AL135623Hs.193914KIAA0575 gene product 10.48 421991NM_014918Hs.110488KIAA0990 protein 10.04 431217NM 013427Hs.250830Rho GTPase activating 9.75 protein 6 421470827496 Hs.1378 annexin A3 9.64 409262AK000631Hs.52256hypothetical protein 9.45 435980AF274571Hs.129142deoxyribonuclease II 924 beta 421246AW582962Hs.102897CGI-47 protein 920 410001AB041036Hs.57771kallikrein 11 9.03 441791AW372449Hs.175982hypothetical protein 9.02 404571 8.66 456497AW967956Hs.1236A8ESTs, Weakly similar 8.56 to AF108A601 ubinu 419968X04430 Hs.93913interleukin 6 (interferon,8.36 beta 2) 433172A8037841Hs.102652hypothetical protein 8.30 422631BE218919Hs.118793hypothetical protein 8.27 427674NM-003528Hs.2178 H2B histone family, 820 member Q

404915 8~

452259AA317439Hs.28707signal sequence receptor,8.06 gamma (translo 452891N75582 Hs212875ESTs, Weakly similar 8.02 to DYH9 HUMAN CILIA

1O 439731AI953135Hs.45140hypothetical protein 7.98 419839U24577 Hs.93304phospholipase A2, group7.68 Vll (platelet-ac 420120AL049610Hs.95243transcription elongation7.64 factor A (S11)-424099AF071202Hs.139336ATP-binding cassette, 7.64 sub-family C (CFTR

448706AW291095Hs.21814interleukin 20 receptor,7.52 alpha 410227AB009284Hs.61152exostoses (multiple)-like7.49 425211M18667 Hs.1867 progastricsin (pepsinogen7.35 C) 441736AW292779Hs.i69799ESTs 7.28 419991AJ000098Hs.94210eyes absent (Drosophila)7.20 homolog 1 425018BE245277Hs.154196E4F transaipGan factor720 424560AA158727Hs.150555protein predicted by 7.18 clone 23733 409110AA191493Hs.48778niban protein 7.10 421566NM-000399Hs.1395 early growth response 7.QA
2 (Krox-20 (Drosop 431725X65724 Hs.2839 Nome disease (pseudoglioma)6.98 425782U66468 Hs.159525cell growth regulatory6.85 with EF-hand doma 427408AA583206Hs.2156 RAR-related orphan 6.79 receptor A
~

435604AA625279Hs26892 uncharacterized bone 6.73 marrow protein BM04 415874AF091622Hs.78893KIAA0244 protein 6.54 401451 6.52 431778AL080276Hs.268562regulator of G-protein6.51 signalling 17 409089NM 014781Hs.50421KIAA0203 gene product 6.50 431992NM_002742Hs.2891 protein leinase C, 6.49 mu 404253 6.42 421552AF026692Hs.105700secreted frizzled-related6.41 protein 4 416806NM_000288Hs.79993peroxisomal biogenesis6.38 factor 7 431958X63629 Hs.2877 cadherin 3, type 1, 6.30 P-cadherin (placenta 439366AF100143Hs.6540 fibroblast growth factor6.30 416836D54745 Hs.80247choleeystokinin 6.30 433383AF034837Hs.i92731double-stranded RNA 629 specific adenosine d 450728AW162923Hs25363 presenilin 2 (Alzheimer625 disease 4) 4O 413384NM_000401Hs.7533A.exostoses (multiple) 622 423349AF010258Hs.127428homeo box A9 620 424800AL035588Hs.153203MyoD family inhthitor 6.18 425451AF242769Hs.157461mesenchymal stem cell 6.14 protein DSC54 447359NM_012093Hs.18268adenylate kinase 5 6.00 410889X91662 Hs.66744twist (Drosophila) 5.97 homolog (aaocephalos 408829NM_006042Hs.48384heparan sulfate (glucosamine)5.94 3-0-sulfot 453911AW503857Hs.4007 Sarcolemmal-assoaated 5.94 protein 408875NM 015434Hs.48604DKFZP434B168 protein 5.92 450480X82125 Hs25040 zinc finger protein 5.90 5O 451684AF216751Hs26813 CDA14 5.88 400301X03635 Hs.1657 estrogen receptor 1 5.78 415077L41607 Hs.934 glucosaminyl (N-acetyl)5.74 transferase 2, I

418852BE537037Hs.273294hypothetical protein 5.72 446867AB007891Hs.i6349KIAA0431 protein 5.72 410232AW372451Hs.61184CGI-79 protein 5.70 422762AL031320Hs.119976Human DNA sequence 5.70 from clone RP1-20N2 450616AL133067Hs.302689hypothetical protein 5.70 408621AI970672Hs.46638chromosome 11 open 5.65 reading frame 8 439671AW162840Hs.6641 kinesin family member 5.64 6O 410196AI936442Hs.59838hypothetical protein 5.60 429170NM-001394Hs.2359 dual speaficity phosphatase5.60 440738A1004650Hs.225674WD repeat domain 9 5.60 414342AA742181Hs.75912KIAA0257 protein 5.59 422634NM_016010Hs.118821CGI-62 protein 5.56 400268 5'~'~

439569AW602166Hs.222399CEGP1 protein 5.51 452823AB012124Hs.30696transcription factor-like5.48 5 (basic helix 431938AA938471Hs.54431speafic granule protein5.44 (28 kDa); cysts 427638AA406411Hs.208341ESTs, Weakty s'smilar 5.42 to KIAA0989 protein 421264AL039123Hs.103042microtubule-associated5.38 protein 18 421685AF189723Hs.106778ATPase, Ca++transporting,5.37 type 2C, memb 421987A1133161Hs.286131CGI-101 protein 5.36 422806BE314767Hs.1581 glutathione S-transferase5.34 theta 2 432281AK001239Hs.274263hypothetical protein 5.32 451982F13036 Hs.27373Homo sapiens mRNA; 5.32 cDNA DKFZp56401763 (f 444042NM-004915Hs.10237ATP-binding cassette, 5.31 sub-family G (WHIT

447752M73700 Hs.105938ladotransferrin 5.29 451418BE387790Hs.26369hypothetical protein 5.22 IO 428593AW207440Hs.185973degeneratNe spermatocyte521 (homok>g Droso 447541AK000288Hs.18800hypothetical protein 5.18 459294AW977286Hs.17428RBPi-like protein 5.16 424692AA429834Hs.151791KIAA0092 gene product 5.15 416434AW163045Hs.79334nuclear factor, interleukin5.11 3 regulated 1$ 410268AA316181Hs.61635sixtransmembrane epithelial5.10 antigen of 417517AF001176Hs.82238POP4 (processing of 5.10 precursor , S. cerev 453616NM_003462Hs.33846dynein, axonemal, light5.10 intermediate pol 427958AA418000Hs.98280potassium intermediatelsmall5.09 conductance 407945X69208 Hs.606 ATPase, Cu++transporting,5.08 alpha polypep ZO 418576AW968159Hs289104Alu-binding protein 5.05 with zinc finger dom 413328Y15723 Hs.75295guanylate cydase 1, 5.04 soluble, alpha 3 432729AK000292Hs.278732hypothetical protein 5.Q4 426342AF093419Hs.169378multiple PDZ domain 5.02 protein 429782NM_005754Hs.220689Ras-GTPase-ad'rvating 5.02 protein SH3-domain ~$ 436209AW850417Hs.254020ESTs, Moderately similar5.02 to unnamed prot 430599NM-004855Hs.247118phosphatidylinositof 5.00 glycan, c4ass B

451386AB029006Hs.26334spastic paraplegia 5.00 4 (autosomal dominant 457211AW972565Hs.32399ESTs, Weakly similar 4.97 to S51797 vasodilat 425851NM-001490Hs.159642glucosaminyl (N-acetyl)4.97 transferase 1, c 421689N87820 Hs.106826KIAA1696 protein 4.93 416533BE244053Hs.79362retinoblastoma-like 4.92 2 (p130) 432653N62096 Hs.293185ESTs, Weakly similar 4.91 to JC7328 amino aci 403047 4.91 431117AF003522Hs.250500delta (Drosophila)-like4.90 35 427617D42063 Hs.199179RAN binding protein 4.88 428804AK000713Hs.193736hypothetical protein 4.88 449071NM-005872Hs.22960breast cardnoma amplified4.86 sequence 2 407596886913 gb:yq30f05.r1 Soares 4.84 fetal fryer spleen 456516BE172704Hs.222746KIAA1610 protein 4.84 4O 458339AW976853Hs.172843ESTs 4.83 422083NM_001141Hs.111256arachidonate 15-lipoxygenase,4.82 second typ 449535W15267 Hs.23672low density lipoprotein4.82 receptor-related 422048NM U12445Hs.288126spondin 2, extracellular4.82 matrix protein 424602AK002055Hs.151046hypothetical protein 4.78 45 410765AI694972Hs.66180nudeosome assembly 4.77 protein 1-like 2 419879217805 Hs.93564Homer, neuronal immediate4.74 early gene, 2 450649NM_001429Hs25272 E1A binding protein 4.74 p300 411624BE145964Hs.103283KIAA0594 protein 4.72 404721 4.70 5O 426261AW242243Hs.168670peroxisomal famesylated4.70 protein 416276U41060 Hs.79136LIV-1 protein, estrogen4.64 regulated 408374AW025430Hs.155591forkhead box F1 4.64 451900AB023199Hs.27207KIAA0982 protein ' 4.63 421437AW821252Hs.104336hypothetical protein 4.63 55 ~ 434629AA789081Hs.4029 glioma-ampliBed sequence-414.60 d03764 4~~

421247BE391727Hs.102910general transcription 4.53 factor IIH, polyps 403721 d~~

453070AK001465Hs.31575SEC63, endoplasmic 4.49 reticulum translocon ()O417412X16896 Hs.82112interleukin 1 receptor,4.48 type I

439735AI635386Hs.142846hypothetical protein 4.48 430261AA305127Hs.237225hypothetical protein 4.46 430598AK001764Hs.247112hypothetical protein 4.44 400303AA242758Hs.79136LIV-1 protein, estrogen4.42 regulated 65 438209AL120659Hs.6111 aryl-hydrocarbon receptor4.42 ~ nuclear transl 417421AL138201Hs.82120nuclear receptor subfamily4.40 4, group A, m 447270AC002551Hs.331 general transcription 4.38 factor IIIC, polyp 434423NM_006769Hs.3844 LIMdomainonly4 4.35 404561 4.32 422969AA782536Hs.122647N-myristoyitransferase4.32 423685BE350494Hs.49753uveal autoantigen with4.32 coiled coil domai 425071NM 013989Hs.154424deiodinase, iodothyronine,4.32 type II

431583AL042613Hs262476S-adenosylmethionine 4.31 decarboxylase 1 442618AK001741Hs.8739 hypothetical protein 4.30 423740Y07701 Hs.293007aminopeptidase puromycin4.24 sensitive 424701NM_005923Hs.151988mitogen-activated protein421 kinase kinase 424085NM_00291dHs.139226replication factorC 4.20 (activator 1) 2 (40 410294AB014515Hs.323712KIAA0615 gene product 4.18 447124AW976438Hs.17428RBP1-like protein 4.18 438018AK001160Hs.5999 hypothetical protein 4.16 443857A1089292Hs.287621hypothetical protein 4.15 446711AF169692Hs.12450protocadherin 9 4.15 405403 4.14 448148NM 016578Hs.20509HBV pX associated protein-84.13 417531NM_003157Hs.1087 serinelthreonine kinase4.12 433345AI681545Hs.152982hypothetical protein 4.10 432712A8016247Hs288031sterol-C5-desaturase 4.09 (fungal ERG3, delta 435114AA775483Hs.288936mitochondria) ribosomal4.08 protein L9 445459AI478629Hs.158465likely ortholog of 4.08 mouse putative IKK
re 402791 4~~

438660095740 Hs.6349 Homo sapiens, clone 4.04 IMAGE:3010666, mRNA, 447568AF155655Hs.18885CGI-116 protein 4.04 452211AI985513Hs233420ESTs 4.02 443292AK000213Hs.9196 hypothetical protein 4.01 420911077413 Hs.1002930-linked N-acetylglucosamine4.00 (GIcNAc) tr 428738NM-000380Hs.192803xeroderma pigmentosum,3.95 complementation g 430456AA314998Hs.241503hypothetical protein 3.95 437531AI400752Hs.112259T cell receptor gamma 3.93 locus 428695AI355647Hs.189999purinergic receptor 3.91 (family A group 5) 410011A802064iHs.57856PFTAIRE protein kinase3.91 446494AA463276Hs.288906WW Domain-Containing 3.91 Gene 409928AL137163Hs.57549hypothetical protein 3.90 dJ473B4 411598BE336654Hs.70937H3 histone family, 3.90 member A

425707AF115402Hs.11713E74-like factor 5 (ets3.90 domain transcript 451806NM_003729Hs.27076RNA 3'-terminal phosphate3.89 cyclase 401045 3.89 437372AA323968Hs283631hypothetical protein 3.89 DKFZp547G183 417067AJ001417Hs.81086solutecamerfamily22(extraneuronal3.88 4O 410467AF102546Hs.63931dachshund (Drosophila)3.88 homolog 431930A8035301Hs.272211cadherin 7, type 2 3.88 453047AW023798Hs.286025ESTs 3.88 401785 3~~

458229AI929602Hs.177 phosphatidylinositol 3.86 glycan, class H

4$ 406414 3.86 412494AL133900Hs.792 ADP-ribosylation factor3.84 domain protein 1 418329AW247430Hs.84152cystathionine-beta-synthase3.83 424850AA151057Hs.153498chromosome 18 open 3.82 reading frame 1 427585D31152 Hs.179729collagen, type X, alpha3.82 1 (Schmid metaph SO d23052M28214 Hs.123072RAB3B, member RAS oncogene3.82 family 416111AA033813Hs.79018chromatin assembly 3.82 factor 1, subunit A ( 419423D26488 Hs.90315KIAA0007 protein 3.80 429643AA455889Hs.167279FYVE-finger-containing3.80 Rab5 effector pro 431499NM_001514Hs.258561general Uansaip6on 3.80 factor IIB

55 444078BE246919Hs.10290U5 snRNP-specific 40 3.78 kDa protein (hPrpB-430291AV660345Hs238126CGI-49 protein 3.76 431637AI879330Hs.265960hypothetical protein 3.74 440411N30256 Hs.151093hypothetical protein 3.74 DKFZp434G1415 405917 3.74 451230BE546208Hs26090 hypothetical protein 3.73 429597NM_003816Hs.2442 a disintegrin and metalloproteinase3.73 doma 415075L27479 Hs.77889Friedreich ataxia region3.72 gene X123 440351AF030933Hs.7179 RADi (S. pombe) homolog3.70 443603BE502601Hs.134289ESTs, Weakly similar 3.70 to KIAA1063 protein 65 446965BE242873Hs.16677WD repeat domain 15 3.70 412350AI659306Hs.73826protein tyrosine phosphatase,3.70 non-recept 433852AI378329Hs.126629ESTs 3.70 447397BE247676Hs.i8442E-1 enryme 3.68 405718 3~~

425217AU076696Hs.155174CDCS (cell division 3.68 cycle 5, S. pombe, h 421734AI318624Hs.107444Homo sapiens cDNA FLJ205623.67 fis, clone KA

427221L15409 Hs.174007von Hippel-Lindau syndrome3.67 402408 3.66 $ 452946X95425 Hs.31092EphA5 3.66 419078M93119 Hs.89584insulinoma-associated 3.66 427144X95097 Hs.2126vasoactive intestinal 3.65 peptide receptor 2 423396AI382555Hs.127950bromodomain-containing3.65 446320AF126245Hs.14791aryl-Coenryme A dehydrogenase3.63 family, me 1O 404939 3.62 403137 3.60 437162AW005505Hs.5464thyroid hormone receptor3.60 coactivating pr 404210 3.59 443775AF291664Hs.204732matrix metalloproteinase3.56 15 452501A8037791Hs.29716hypothetical protein 3.56 422443NM_014707Hs.116753histone deacetylase 3.55 420230AL034344Hs.284186forkhead box C1 3.55 418428Y12490 Hs.85092thyroid hormone receptor3.54 interactor 11 433002AF048730Hs279906cyclin Ti 3.53 ZO 405793 3.52 457940AL360159Hs.306517Homo sapiens TRlpartite3.52 motif protein ps 402444 3.52 418250029926 Hs.83918adenosine monophosphate3.51 deaminase (isofo 414222AL135173Hs.878 sorbitol dehydrogenase3.51 25 422384AA2240T7Hs.42438Sm protein F 3.50 447805AW627932Hs.19614gemin4 3.50 454265H03556 Hs.300949ESTs, Weakly similar 3.50 to thyroid hormone 423445NM 014324Hs.128749alpha-methylacyl-CoA 3.48 racemase 413435X51405 Hs.75360carboxypeptidase E 3.46 447210AF035269Hs.17752phospha6dylserine-spedfic3.46 phospholipas 426931NM-003416Hs.2076zinc finger protein 3.45 7 (KOX 4, clone HF.1 408418AW963897Hs.44743KIAA1435 protein 3.45 421887AW161450Hs.109201CGI-86 protein 3.44 Table 7: 42 GENES ENCODING SMALL MOLECULE TARGETS UP-REGULATED IN
PROSTATE CANCER COMPARED TO NORMAL ADULT TISSUES
Table 7 shows 42 genes up-regulated in prostate cancer compared to normal adult tissues that are likely to be small molecule targets. These were selected as for Table 5 and the predicted protein contained a structural domain that is indicative of a drugable structure (e.g. protease, kinase, phosphatase, receptor). The functional domain is indicated for each gene.
Pkey: Unique Eos probeset identifier number ExAccn:
Exemplar Accession number, Genbank accession number UnigenelD: ene number Unig Unigene ene gene title Titte:
Unig PSDomain:
Protein Structural Domain 1$ Ri: Ratio of tumor vs. normal tissue Pkey ExAccnUnigenelD UnigeneTitle PSDomain R1 2~ 426747 AA535210Hs.171995 kallikrein trypsin 31.80 3, (prostate specific antigen 400299 X07730Hs.t71995 kallikrein trypsin 24.91 3, (prostate specific antigen 420757 X78592Hs.99915 androgen receptorAndrogen-recep,hormone19.72 (dihydrotestosterone rec,zf-C4 r 408430 S79876Hs.44926 dipepGdylpeptidaseDPPIV_N term,Peptidase_S91628 IV (CD26, adenosine 430226 BE245562Hs.2551 adrenergic, 7tm 1 15.40 beta-2-, receptor, surface 25 411096 U80034Hs.68583 mitochondrial Peptidase-M3 14.81 intermediate peptidase 440286 U29589Hs.7138 cholinergic 7tm-1 12.04 receptor, muscarfnic 420381 D50640Hs.337616 phosphodiesterasePDEase 11.10 38, cGMP-inhibited 407021 U52077gb:Human marinerl transposase 11.02 gene, comp SET,Transposase-1 401424 arginase 9.58 410001 AB041036Hs.57771 kallikrein trypsin 9.03 428330 L22524Hs.2256 matrix metalloproteinasePeptidase M10 8.76 7 (matrilysin, 424099 AF071202Hs.139336 ATP-binding ABC-tran,ABC_membrane7.64 cassette, sub-family C (CFTR

419991 AJ000098Hs.94210 eyes absent Hydrolase 7.20 (Drosophila) homolog 431992 NM-002742Hs2891 protein Itinase pkinase,DAG PE-bind,PH6.49 C, mu 35 447359 NM-012093Hs.18268 adenylate kinaseadenylatekinase 6.00 400301 X03635Hs.1657 estrogen receptorOest recep,zf-C4,hormone_rec5.78 421685 AF189723Hs.106778 ATPase, Ca++transporting,Ei-E2 ATPase,Hydrolase5.37 type 2C, memb 444042 NM_004915Hs.10237 ATP-binding ABC tran 5.31 cassette, sub-family G (WHIT

447752 M73700Hs.105938 lactotransferrfntransfemn,7tm-1 529 4~ 407945 X69208Hs.606 ATPase, Cu++transporfing,E1-E2 ATPase,Hydrolase,HMA5.06 alpha polypep 403047 trypsin 4.91 427617 D42063Hs.199179 RAN binding Ran BPi,zf-RanBP,TPR,pro-isomerase protein 2 4.88 422083 NM_001141Hs.111256 arachidonate Iipoxygenase,PLAT4.82 15-lipoxygenase, second iyp 449535 W15267Hs.23672 low density Idl-recept b,IdLrecept4.82 lipoprotein receptor-relateda,EGF

45 425071 NM-013989Hs.154424 deiodinase, T4_deiodinase 4.32 iodothyronine, type II

423740 Y07701Hs293007 aminopeptidasePeptidase Mi 424 puromyan sensitive 424701 NM-005923Hs.151988 mitogen-activatedpkinase 421 protein kinase kinase 424085 NM-002914Hs.139226 replication I-helicaset 420 factor C (activator AAA,Vira 1) 2 (40 417531 NM Hs.1087 serine/threonine_ 4.12 003157 kinase 2 pkinase 5~ - Hs.189999 pudnergic 7tm 1 3.91 428695 AI355647receptor (family A
group 5) 410011 AB020641Hs.57856 PFTAIRE proteinpkinase 3.91 kinase 1 424850 AA151057Hs.153498 chromosome Idl recept a 3.82 18 open reading frame 412350 AI659306Hs.73826 protein tyrosineY,~hosphatase,Band_41,PDZ3.70 phosphatase, non-recept 447397 BE247676Hs.18442 E-1 enryme Hydrolase 3.68 55 452946 X95425Hs.31092 EphAS EPH Ibd,fn3,pkinase,SAM3.66 427144 X95097Hs.2126 vasoactive intestinal7tm 2 3.65 peptide receptor 2 443775 AF291664Hs.204732 matrix metalloproteinasePeptidase M10 3.56 457940 AL360159Hs.306517 Homo sapiens SPRY,7tm 1 3.52 TRlpadite motif protein ps 418250 U29926Hs.83918 adenosine monophosphateA deaminase 3.51 deaminase (isofo 413435 X51405Hs.75360 carboxypeptidaseZn_carbOpept 3.46 E

447210 AF035269Hs.17752 phosphatidylserine-specificlipase 3.46 phospholipas 1~8 TABLE 8: 136 GENES SIGNIFICANTLY DOWN-REGULATED IN PROSTATE
CANCER COMPARED TO NORMAL PROSTATE
Table 8 shows 136 genes significantly down-regulated in prostate cancer compared to normal prostate . These were selected from 59680 probesets on the Affymetrix/Eos Hu03 GeneChip array such that the ratio of "average" normal prostate to "average" prostate cancer tissues was greater than or equal to 2. The "average" normal prostate level was set to the mean amongst 4 normal prostate tissues. The "average" prostate cancer level was set to the 85"' percentile amongst 73 tumor samples. In order to remove gene-specific background levels of non-specific hybridization, the 10'h percentile value amongst all the tissues was subtracted from both the numerator and the denominator before the ratio was evaluated.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title Ri: Ratio of normal prostate to prostate cancer Pkey ExAccn UnigenelD Unigene Title Ri 425932 M81650 Hs.1968 semenogelin I 57.69 425545 N98529 Hs.158295 Human mRNA for myosin19.70 light chain 3 (MLC

426752 X69490 Hs.172004 titin 1525 442082 841823 Hs.7413 ESTs; calsyntenin-2 10.05 407245 X90568 Hs.172004 titin 9.38 422711 D60641 Hs21739 Homo sapiens mRNA; 9.05 cDNA DKFZp58611518 (f 420813 X51501 Hs.99949 prolactin-induced 8.18 protein 411987 AA375975 Hs.183380 'ESTs,ModeratelysimilartoALU7-HUMAN7.45 5.62 416030 H15261 Hs.21948 ESTs 5.51 444892 AI620617 Hs.148565 ESTs 527 444573 AW043590 Hs225023 ESTs 520 428068 AW016437 Hs233462 ESTs 5.08 437440 AA846804 Hs.123694 ESTs 4.95 404113 4.75 452279 AA286844 Hs.61260 hypothetical protein4.75 421058 AW297967 Hs.188181 ESTs 4.63 445592 AV654382 Hs.17947 'ESTs, Weakly similar4.53 to K02F3.10 [C.ele 4.49 x05227 4.45 454059 NM_003i54Hs.37048 statherin 4.45 450152 A1138635 Hs22968 ESTs 4.40 407013 U35637 'gb:Human nebulin mRNA, partial4.03 cds' 403612 4.02 440089 AA864468 Hs.135646 ESTs 4.00 408988 AL119844 Hs.49476 Homo sapiens done 3.98 TUAS Cri-du-chat regi 436726 AA324975 Hs.128993 'ESTs, Weakly similar3.95 to KIAA0465 protei 459367 BE148877 'gb:CM4-HT0244-111199-040-h123.95 HT0244 Hom 427318 AF186081 Hs.175783 zinc transporter 3.92 411762 AW860972 "gb:QVO-CT0387-180300-167-h073.85 CT0387 Hom 418668 AW407987 Hs.87150 Human clone A9A28R113.75 (CAC)n!(GTG)n repea 458311 AF069478 'gb:AF069478 Homo sapiens 3.61 astrocytoma Ii 403649 3.60 419682 H13139 Hs.92282 paired-like homeodomain3.58 transcription fa 412519 AA196241 Hs.73980 'troponin T1, skeletal,3.51 slow"

414206 AW276887 Hs.46609 ESTs 3.45 427419 NM 000200Hs.177888 histatin 3 3.37 420777 AA280223 Hs.130865 ESTs 3.35 428134 AA421773 Hs.161008 ESTs 3.31 450218 802018 Hs.168640 'Ank, mouse, homotog3.30 oP

433474 A1192195 Hs.147174 'EST, Highly similar3.30 to ubiquitin-protei 418833 AW97d899 Hs.292776 ESTs 3.26 400440 X83957 Hs.83870 nebulin 3.16 413778 AA090235 Hs.75535 'myosin, light 3.06 polypeptide 2, regulatory 423151 AW838068 'gb:OV3-LT0048-010300-109-f023.05 LT0048 Hom 445060 AA830811 Hs.88808 ESTs 2.98 457065 AI476318 Hs.192480 ESTs 2.95 $ 432456 H00093 'gb:ph8fi2u-19/iTV Outward 2.92 Alu-primed fin 405678 2.85 406707 S73840 Hs.931 'myosin, heavy polypeptide2.81 2, skeletal m 444105 AW189097 Hs.166597 ESTs 2.78 433968 AL157518 Hs.90421 PR02463 protein 2.73 438522 AA809431 Hs.258886 ESTs 2.73 436562 H71937 Hs.169756 'complement component2.68 1, s subcomponent"

412417 AA102268 Hs.42175 ESTs 2.67 455590 BE072259 'gb:QV4-BT0536-271299-059-g042.65 BT0536 Hom 415380 F07953 Hs.16085 putative G-protein 2.65 coupled receptor 428729 AL162331 Hs.191436 hypothetical protein2.64 408537 AW207734 'gb:Ul-H-BI2-age-h-01-0-Ul.si2.63 NCI-CGAP_S

424706 AA741336 Hs.152108 iranscriptional 2.63 unit N143 413212 BE072092 'gb:PM4-BT0532-160200-003-bii2.63 BT0532 Hom 406704 M21665 Hs.929 'myosin, heavy polypeptide2.62 7, cardiac mu 437507 AA758538 Hs.246882 ESTs 2.60 410384 AI933794 Hs.42745 ESTs 2.5B

408074 820723 Hs.124764 ESTs 2.58 436653 AA829828 Hs.292402 ESTs 2.52 458090 AI282149 Hs.56213 'ESTs, Highly similar2.51 to FXD3_HUMAN FORK

432003 AI689154 Hs.122972 ESTs 2.50 436915 AA737400 Hs.142230 ESTs 2.50 410028 AW576454 Hs258553 ESTs 2.46 448920 AW408009 Hs.22580 alkylglycerone 2.45 phosphate synthase 422046 AI638562 'gb:ts50a10.x1 NCI_CGAP-Uti2.44 Homo sapiens 451122 AA015767 Hs.193587 ESTs 2.40 422646 H87863 Hs.151380 ESTs 2.36 451237 AW600293 "gb:EST00049 pGEM-T library2.36 Homo sapiens 400001 AFFX control: BioB-3 2.36 415835 245365 'gb:HSC2NF061 normalized infant2.36 brain cD

3$ 439706 AW872527 Hs.59761 ESTs 2.36 423341 AW242394 Hs.252495 ESTs 2.36 436486 AA742221 Hs.120633 ESTs 2.35 407449 AJ002784 gb:Homo sapiens mRNA; fetal2.33 brain cDNA 5 430573 AA744550 Hs.136345 ESTs 2.32 401974 2.31 443356 AL044498 Hs.133262 'ESTs, Weakly 2.31 similar to PH0217 reverse 430751 NM U12471 Hs247868 transient receptor2.25 potential channel 5 439128 AI949371 Hs.153089 ESTs 2.25 448765 815337 Hs.21958 'Homo sapiens cDNA 225 FLJ10532 fis, clone N

451130 AI762250 Hs211347 ESTs 2.24 405420 2.23 455029 AW851258 'gb:IL3-CT0220-160200-066-H062.23 CT0220 Hom 438224 AA933999 'gb:on91f04.s1 Soares-NFL-T_GBC_Si2.23 Homo 407764 BEOOB347 'gb:CMO-BN0154-080400-325-h042.23 BN0154 Hom 413549 BE252470 'gb:60i108292F1 N(H_MGC_16 2.23 Homo sapiens 437010 AA741368 Hs.291434 ESTs 2.23 435111 AI914279 Hs.213740 ESTs 2.22 403375 2.21 455060 AW853441 'gb:RCi-CT0252-030100-023-g092.21 CT0252 Hom 409792 AW854i53 'gb:RC3-CT0254-060400-029-d032.20 CT0254 Hom 421154 AA284333 Hs287631 'Homo sapiens cDNA2.19 FLJ14269 fis, clone P

401963 2.18 435034 AF168711 Hs.159397 x 010 protein 2.18 448996 AW998989 Hs.105749 KtAA0553 protein 2.18 436816 AW297599 Hs255667 ESTs 2.17 442252 AI733395 Hs.129124 ESTs 2.17 419310 AA236233 Hs.188716 ESTs 2.16 418579 H91800 Hs.124156 ESTs 2.16 423315 854109 Hs26096 ESTs 2.16 432744 AA988835 Hs.38664 ESTs 2.15 424492 A1133482 Hs.165210 ESTs 2.15 424770 AA425562 'gb:zw46e05.r1 Soares total-fetus_Nb2HF82.15 437101 AA744518 Hs.120610 ESTs 2.15 428793 AC004957 Hs298975 'ESTs, Highly similar2.15 to collapsin-2-lik 415708 H56475 "gb:yt87dii.rl Soares,~ineal~land-N3HPG2.13 459619 2.12 427506 AK000134 Hs.179100 hypothetical protein FLJ201272.12 452508 AA804174 Hs.184354 ESTs 2.10 410881 AW809157 "gb:RCO-ST0118-041099-031-c07_1 ST01182.10 Homo Sapiens cDNA, mRNA sequence"

403087 2.10 403869 2.10 445028 D81194 Hs.282499 ESTs 2.10 447884 H29505 "gb:ym60d10.r1 Soares infant brain 2.10 1NIB Homo Sapiens cDNA clone 5', mRNA sequence"

1O 414575 H11257 Hs.295233 ESTs 2.09 420351 BE218221 Hs.190044 ESTs 2.08 426998 BE274360 "gb:601121068F1 NIH_MGC 20 Homo sapiens2.08 cDNA clone 5', mRNA sequence"

405455 2.08 423843 AA332652 "gb:EST36627 Embryo, 8 week I Homo sapiens cDNA 5' end similar to similar to 15 monoamine oxidase B, mRNA sequence" 2.08 406135 2.07 427046 BE246180 Hs.121385 ESTs 2.07 403493 2.05 444514 A1682905 Hs.270431 "ESTs, Weakly similarto 2o CONTAMINATION WARNING ENTRY (H.sapiens]" 2.05 435884 AA701443 Hs.192868 ESTs 2.05 419629 AB020695 Hs.91662 KIAA0888 protein 2.03 405900 ' 2.03 457350 AW974438 Hs.194136 "ESTs, Moderately similar 2.02 to AF0914571 zinc finger protein RiN ZF (R.norvegicus]"

25 400007 AFFX contrcl: BioDn-5 2.01 406978 M64358 "gb:Human rhom-3 gene, exon." 2.00 TABLE 8A shows the accession numbers for those primekeys lacking a unigene)D
in Table 8. For each probeset we have listed the gene cluster number from which the oIigonucleotides 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: Genbankaccessionnumbers Pkey CAT number Accessions 409792 1154677_1AW854153 AW500210 BE145772 AW501310 2~ 410881 1225682AW809157 AW812181 AW812175 AW812172 AW812161 AW812165 411762 1256906_1AW860972 AW862598 AW862599 AW860988 AW860983 AW860B98 413212 1353792_1BE072092 BE072i06 BE072086 BE072098 BE072103 422046 210744_1A1638562 T16929 H13401 F07773 855836 438224 452656_1AA933999 AA781181 455029 1249374_1AW851258 AW851435 AW851106 AW851421 455060 1251259_1AW853441 BE145228 BE145218 BE145162 BE145283 458311 543550_1AF069478 AF069479 AF069480 TABLE 8B shows the genomic positioning for those primekeys lacking unigene ID's and accession numbers in table 8. For each predicted axon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted axon are also listed.
Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I.
et al." refers to the publication entitled "The DNA

1 sequence of human chromosome 22." Dunham I. et ~ al., Nature (1999) 402:489-495.

Strand: Indicates DNA strand from which axons were predicted.

Nt~osition: Indicates nucleotide positions of predicted axons.

Pkey Ref Strand N~position 4019633126783Plus 51382-51521 4019743126777Plus 85330-85683 4030878954241Plus 169511-169795 4033759255944Minus 92554-92795 4034937341425Plus 157568-159084 4036128469060Minus 94723-94859 4036498705159Minus 27141-27247 4038697280046Minus 34379-34583 4041139588571Minus 13446-13646 4045677249169Minus 101320-101501 4051639966267Minus 161171-161299 4052276731245Minus 22550-22802 4054207211837Minus 13428-13582 3~ 4054557656675Plus 134112-134671 4056784079670Plus 151821-152027 4059006758795Minus 71181-71535 4061359164918Minus 65489-65715 TABLE 9: 1001 GENES SIGNIFICANTLY UP-REGULATED IN NORMAL PROSTATE
COMPATED TO PROSTATE CANCER
Table 9 shows 1001 genes significantly up-regulated in prostate cancer compared to normal prostate. These were selected from 59680 probesets on the Affymetrix/Eos Hu03 GeneChip array such that the ratio of "average" normal prostate to "average" prostate cancer tissues was greater than or equal to 8.14. The "average" normal prostate level was set to the mean amongst 4 normal prostate tissues. The "average" prostate cancer level was set to the 85'~
percentile amongst 73 tumor samples. In order to remove gene-specific background levels of non-specific hybridization, the 10'x' percentile value amongst all the tissues was subtracted from both the numerator and the denominator before the ratio was evaluated.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Titte: Unigene gene title R1: Ratio of prostate cancer to normal prostate Pkey ExAccnUnigenelD Unfgene Title R1 451002 AA013299Hs.8018 ESTs, Wealdy similar1684.00 to ALU3-HUMAN ALU S

435596 AA689465Hs.188999 ESTs 738.00 443576 A1078027Hs.169338 ESTs 246.86 434247 AA928116Hs272065 ESTs 245.20 400452 AK000185gb:Homo sapiens cDNA FLJ20178222.00 fis, clone 405932 221.33 427906 AA864330Hs.166520 ESTs 212.00 443685 AI686550Hs.174481 ESTs 163.20 451554 AI474866Hs.193237 ESTs 149.45 418323 NM_002118Hs.1162 major histocompatibility126.11 complex, class 429480 M36860Hs.9295 elasGn (supravalvular123.27 aortic stenosis, 426025 AW138330Hs.233778 ESTs 120.00 418917 X02994Hs.1217 adenosine deaminase106.75 404407 105.71 442027 AI652926Hs.128395 ESTs 100.53 433704 AA608684Hs.121705 ESTs, Moderately 94.00 similar to ALUC HUMAN 1 453758 U83527gb:HSU83527 Human fetal 89.18 brain (M.Lovett) 415354 F06495gb:HSC1AB051 normalized 87.73 infant brain cDN

424239 M67439Hs.143526 dopamine receptor86.82 444143 AW747996Hs.160999 ESTs 86.43 401672 n.26 430590 AW383947Hs246381 CD68 antigen 68.47 411972 BE074959gb:PMO-BT0582-310100-001-f0868.00 BT0582 Homo 448992 AI766053Hs.188346 ESTs 6126 408828 BE540279gb:601059857F1 NIH-MGC-10 57.71 Homo sapiens c 409653 AW451693Hs220826 ESTs ' 56.40 402964 54.67 422673 N59027gb:yv59d11.r1 Soares fetal 54.00 liver spleen 422568 AA372275Hs.279800 Homo sapiens cDNA54.00 FW11383 fis, done HE

438907 832704Hs.301298 ESTs 52.96 405172 52.96 444897 AW137088Hs.144857 ESTs 52.32 458019 AW592931Hs256298 ESTs 51.63 405275 AB028989Hs.88500 mitogen-activated 50.98 protein kinase 8 inter 457815 AA703679Hs.106999 ESTs, Weakly similar49.60 to SYTS_HUMAN SYNAP

424385 AA339666gb:EST44776 Fetal brain 48.90 I Homo sapiens c 407172 T54095gb:ya92c05.s1 Stratagene 47.98 placenta (93722 428202 AA424163Hs.156895 ESTs 46.83 435672 AI700148Hs283626 ESTs 43.57 420283 AA485224Hs.57734 G protein-coupled 43.00 receptor kinase-intera 417016 AA837098Hs269933 ESTs 42.70 438854 AF074994Hs24240 ESTs 42.67 406134 42.43 457319 AA480895Hs.201552 ESTs, Weakly similar42.31 to T17288 hypotheti 409314 AA070266gb:zm69d04.r1 Stratagene 4225 neuroepithelium 401124 41.61 429316 AI371157Hs.178538 ESTs 40.00 420317 A8006628Hs.96485 KIAA0290 protein 39.64 457586 AW062439gb:MRO-CT0060-120899-001-f0839.60 CT0060 Homo 417407 AA923278Hs.290905 ESTs, Weakly similar38.73 to protease [H.sapi 430269 BE221682Hs.178364 ESTs 38.06 l~ 439602 W79114Hs.58558 ESTs 36.69 433686 AA604799Hs.136528 ESTs, Moderately 3629 similar to ALUi HUMAN A

417993 AW963705Hs.295806 ESTs, Weakly similar36.18 to ALU7-HUMAN ALU S

428214 AA936282Hs.120397 ESTs 36.10 416906 AA333990Hs.80424 coagulation factor36.08 XIII, A1 polypeptide 426264 BE314852Hs.168694 hypothetical protein36.00 415911 H08796Hs.124952 ESTs 36.00 457502 AA076049Hs274415 Homo sapiens cDNA 3523 FLJ10229 fis, done HE

421566 NM-000399Hs.1395 early growth response3520 2 (Krox-20 (Drosop 401468 34.89 458561 AI220150Hs.211195 ESTs 34.60 433601 BE350738Hs.123993 ESTs, Weakly similar3324 to T00366 hypotheti 454977 AW848032gb:IL3-CT0214-231299-053-Di32.96 1 CT0214 Homo 402828 32.93 414522 AW518944Hs.76325 Homo sapiens cDNA:31.76 FLJ23125 fis, done L

402842 31.68 421245 AA285363gb:HTH280 HTCDL1 Homo sapiens31.59 cDNA 5'I3' 401631 F05183Hs.1799 CD1D antigen, d 3126 polypeptide 408057 AW139565gb:Ul-H-811-aea-d-04-0-Ul.si3124 NCI-CGAP-Su 408069 H81795gb:ys68a10.r1 Soares retina3120 N2b4HR Homo 438694 T87479Hs.291797 ESTs 31.09 449156 AF103907Hs.171353 prostate cancer 29.78 antigen 3 428796 AU076734Hs.193665 solute carrier 29.76 family 28 (sodium-coupled 452549 AI907039gb:PM-BT134-020499-566 BT13429.59 Homo sapien 410129 BE244074Hs.285531 regulator of Fas-induced29.53 apoptosis 414464 AI870175Hs.13957 ESTs 29.47 412326 807566Hs.73817 Small inducible 2922 cytokine A3 (homologous 459081 W07808gb:zb03a12.r1 Soares-fetal-lung-NbHLI9W2920 448702 AW102670Hs.122464 ESTs 29.13 451939 080456Hs27311 single-minded (Drosophila)28.74 homolog 2 4O 443412 W84893Hs.9305 angiotensin receptor-like28.61 457324 AB028990Hs24390i KIAA1067 protein 2824 424247 X14008Hs.234734 lysozyme (renal 28.18 amyloidosis) 457140 AI279960Hs.178140 ESTs 28.12 444151 AW972917Hs.128749 alpha-methylacyl-CoA28.06 racemase 457669 AW104257Hs.123426 ESTs, Weakly similar27.61 to putative serine/

412429 AV650262Hs.75765 GR02 oncogene 27.36 405495 27.33 407997 AW135429Hs.243577 ESTs 26.96 5O 442115 AW452332Hs257554 ESTs 26.36 409038 T97490Hs.50002 small inducible 26.34 cytokine subfamily A (Cy 402838 26.32 449846 AI979284Hs200552 ESTs -417153 X57010Hs.81343 collagen, type 2620 II, alpha 1 (primary oste 439792 NM Hs.6684 KIAA0476 gene product25.91 450096 Ai682088Hs.223368 ESTs 25.60 424196 AL133660Hs.142926 Homo sapiens mRNA;25.57 cDNA DKFZp434M0927 (f 414246 BE391090Hs.280278 EST 25.57 420848 NM-005188Hs.99980 Cas-Br-M (marine) 25.48 ecotropic retroviral t 424778 AA251048Hs.153042 lymphocyte antigen25.42 409126 AA063426gb:zf70d)8.s1 Soares~ineal~land-N3HPG2525 443936 AW083491Hs.31196 ESTs 2522 419392 W28573gb:51f10 Human retina cDNA 25.01 randomly prim 411201 T74588Hs.8509 ESTs, Weakly similar24.85 to C03-HUMAN COMPLE

422940 BE077458gb:RC1-BT0606-090500-015-b0424.76 BT0606 Homo 437571 AA760894Hs.153023 ESTs 24.74 433973 A1014723Hs.131770 ESTs 24.57 422416 BE019557Hs.11900 Human DNA sequence24.53 from done RP4-583P15 421552 AF026692Hs.105700 secreted frizzled-related24.49 protein 4 443668 025758Hs.134584 24.49 ESTs 424800 AL035588Hs.153203MyoD family inhibitor 24.10 453633 AA357001Hs.34045hypothetical protein 24.04 430565 AL122081Hs.244343cadherin related 23 24.00 433694 AI208611Hs.12066Homo Sapiens cDNA FW1172023.89 fis, clone HE

451045 AA215672 gb:zr96e09.s1 NCI_CGAP_GCBi23.83 Homo Sapiens 408583 AW449674Hs.47359ESTs 23.73 444040 AF204231Hs.182982golgin-67 23.62 414182 AA136301 gb:zk93g04.s1 Soares~regnant-uterus-NbH23.39 1~ 418678 NM_001327Hs.167379cancerJtestisantigen 2320 408380 AF123050Hs.44532diubiquitin 22.68 456076 BE243877Hs.76941ATPase, Na+/K+transporting,22.65 beta 3 poly 418299 AA279530Hs.83968integrin, beta 2 (antigen22.38 CD18 (p95), 1y 444917 868651Hs.144997ESTs 2226 444381 BE387335Hs.283713ESTs 22.06 415788 AW628686Hs.78851KIAA0217 protein 22.04 410896 AW809637 gb:MR4-ST0124-261099-015-b0722.00 ST0124 Homo 412978 AI431708Hs.820homeo box C6 21.95 458418 AV653846Hs.126261Homo Sapiens Chromosome21.94 16 BAC done CIT

2O 454791 BE071874 gb:RC2-BT0522-120200-014-a0621.84 BT0522 Homo 408748 J05500Hs.47431spectrin, beta, erythrocytic2126 (includes s 416011 H14487 gb:ym18c10.r1 Soares 2124 infant brain 1N18 H

440474 AI207936Hs.7195gamma-aminobulyric 21.14 add (GABA) A recepto 447047 AI623698Hs.246306Homo Sapiens d)NA: 21.11 FW23529 fis, done L

426793 X89887Hs.172350HIR (histone cell cycle21.10 regulation defec 409841 AW502139 gb:Ul-HF-BROp-ajr-e-05-0-ULr121.07 NIH_MGC 5 405685 20.90 457359 AI983207Hs.192481ESTs, Weakly similar 20.84 to SYPH HUMAN SYNAP

423067 AA321355Hs.285401ESTs 20.74 422355 AW403724Hs.140immunoglobulin heavy 20.73 constant gamma 3 (G

401201 20.73 458278 W28912Hs.129019ESTs 20.68 439097 H66948 gb:yr86d10.r1 Soares 20.67 fetal liver spleen 414875 H42679Hs.77522major histocompatibility20.66 complex, class 4oos2s 2o.ss 451355 NM-004197Hs.444serine/threonine kinase20.64 446982 AW500221Hs.43616Homo sapiens mRNA for 20.61 FLJ00029 protein, 417105 X60992Hs.81226CD6 antigen 20.61 405777 20.51 424123 AW966158Hs.58582Homo sapiens d)NA FLJ127022020 fis, clone NT

425009 X58288Hs.154151protein tyrosine phosphatase,20.10 receptor t 443271 BE568568Hs.195704ESTs 19.98 421064 AI245432Hs.101382tumor necrosis factor,19.98 alpha-induced pro 418819 AA228776Hs.191721ESTs 19.94 457595 AA584854 gb:no09h11.s1 NCI_CGAP19.90 Phei Homo sapiens 404426 19.84 412571 043143Hs.74049fms-related tyrosine 19.79 kinase 4 431457 NM_012211Hs.256297integrin, alpha 11 19.62 414002 NM_006732Hs.75678FBJ mudne osteosarcoma19.57 viral oncogene h 5O 418994 AA296520Hs.89546Setedin E (endothelial19.56 adhesion molecul 437158 AW090198Hs.4779KIAA1150 protein 19.52 437866 AA156781Hs.83992ESTs 19.44 417421 AL138201Hs.82120nuclear receptor subfamily-4, group A, m 19.34 433057 X15675Hs.296832Human pTR7 mRNA for 1922 repetitive sequence 421730 AW449808Hs.164036glucosamine (N-acetyl)-6-sulfatase1921 (Sanf 456557 AA284477Hs.96618ESTs 18.77 440806 AI247422Hs.129966ESTs 18.76 439845 AL355743Hs.56663Homo sapiens EST from 18.65 done 41214, full 416155 AI807264Hs.205442ESTs, Weakly similar 18.64 to AF1176101 inner 437820 AA769062Hs.16029ESTs, Weakly similar 18.62 to alternatively sp 450923 AW043951Hs.38449ESTs 18.59 418329 AW247430Hs.84152cystathionine-beta-synthase18.58 424537 AI673027Hs.143271ESTs 18.55 447742 AF113925Hs.19405caspase recruitment 18.52 domain 4 415251842863Hs.7124ESTs 18.47 440770 AA912815Hs.222078ESTs 18.40 407711 A1085846Hs.25522ESTs 18.32 427157 051166Hs.173824thymine-DNA glycosylase1828 409647 AW501751Hs.279733ESTs 18.15 417240 N57568Hs.176028 EST 18.13 435732 AF229178Hs.123136 leudne rich repeat18.12 and death domain con 436896 AW977385Hs.278615 ESTs 18.12 432485 N90866Hs.276770 CDW52 antigen 17.90 (CAMPATH-1 antigen) 429490 AI971131Hs.293684 ESTs, Weakly similar17.82 to alternatively sp 429984 AL050102Hs.227209 DKFZP586F1019 17.82 protein 449214 AI889114Hs.195663 ESTs 17.75 433867 AK000596Hs.3618 hippocaldn-like 17.72 431735 AW977724Hs.75968 thymosin, beta 17.71 4, X chromosome 1~ 401515 17.67 444045 A1097439Hs.135548 ESTs 17.58 442754 AL045825Hs.210197 ESTs 17.55 426559 A8001914Hs.170414 paired basic amino17.54 acid leaving system 432415 Ti6971Hs.289014 ESTs 17.50 15 427829 AI188225Hs.127462 ESTs 17.50 432516 808003Hs.188013 ESTs 17.44 435259 AA152106Hs.4859 cydin L ania-6a 17.36 414989 T81668gb:yd29c04.r1 Soares fetal 17.31 fNer spleen 444880 AW118683Hs.154150 ESTs 17.30 417651 806874Hs.268628 ESTs 1727 453457 AL037103Hs270599 ESTs, Weakly similar1722 to unnamed protein 424246 AW452533Hs.143604 Kaiso 1722 419078 M93119Hs.89584 insulinoma-assodated17.18 417696 BE241624Hs.82401 CD69 antigen (p60,17.14 early T-cell act'rvati 25 431117 AF003522Hs250500 delta (Drosophila)-like17.14 455254 AW877015gb:QV2-PT0010-250300-096-f1217.14 PT0010 Homo 425782 U66468Hs.159525 cell growth regulatory17.12 with EF-hand doma 426678 H08170Hs.113755 ESTs 17.12 426403 NM-000361Hs.2030 thrombomodulin 17.01 425905 AB032959Hs.161700 KIAA1133 protein 17.00 438867 AW451157Hs.181157 ESTs 16.98 420940 AA830664Hs.143974 ESTs 16.94 459234 AI94Q425gb:CMO-CT0052-150799-024-d)416.92 CT0052 Homo 404756 16.91 422247 U18244Hs.113602 solute carrier 16.90 family 1 (high affinity a 420568 F09247Hs.167399 protocadherin 16.88 alpha 5 443559 A1076765Hs.269899 ESTs 16.80 438703 AI803373Hs.31599 ESTs 16.78 411424 AW845985gb:RC2-CT0163-200999-002-H0816.70 CT0163 Homo 402895 16.69 422538 NM_006441Hs.118131 5,10-methenyltetrahydrofolate16.68 synthetase 447108 AW449602Hs.217953 ESTs, Moderately 16.65 similar to NK TUMOR REC

448520 AB002367Hs21355 doubiecortin and 16.54 CaM kinase-like 1 438567 AW451955Hs.153065 ESTs 16.52 45 407811 AW190902Hs.40098 cysteine knot superfamily16.50 1, BMP antagon 410721 823534Hs2730 heterogeneous nuclear16.50 dbonudeoprotein 437133 A8018319Hs.5460 KIAA0776 protein 16.40 408182 AA047854gb:zf49gOd.r1 Soares retina16.32 N2b4HR Homo 417315 A1080042Hs.180450 rfbosomal protein16.30 SO 431840 AA5349Q8Hs.2860 POU domain, lass 1628 5, transcription facto 439882 AA847856Hs.124565 ESTs 1620 418277 AW135221Hs.130812 ESTs 16.09 410688 AW796342gb:PM2-UM0027-230200-002-h02' UM0027 Homo 16.04 420120 AL049610Hs.95243 transcription elongation16.04 factor A (S11)-$5 429597 NM_003816Hs.2442 a disintegrin and 16.02 metalloproteinase doma 447033 AI357412Hs.157601 EST - not in UniGene16.02 421684 BE281591Hs.106768 hypothetical protein15.94 408599 AA055800Hs222933 ESTs 15.93 446012 AV656098Hs.172382 hypothetical protein15.86 6O 409671 AA076769gb:7B02B10 Chromosome 7 15.85 Fetal Brain d)NA

405934 , 15.84 426108 AA622037Hs.166468 programmed cell 15.84 death 5 416208 AW291168Hs.41295 ESTs 15.48 410708 AA534370Hs.154088 Homo Sapiens d)NA:15.42 FLJ22756 fis, done K

65 447342 AI199268Hs.19322 ESTs; Weakly similar15.38 to !!!! ALU SUBFAMI

454563 AW807530gb:CMO-ST0081-130999-054-40215.37 ST0081 Homo 411507 AW850140gb:IL3-CT0219-261099-023-D1115.36 CT0219 Homo 438170 AI916685Hs.194601 ESTS 1529 416292 AA179233Hs.42390 nasopharyngeal 1526 cardnoma susceptibility 406638 M13861gb:Human T-cell receptor 1526 active beta-cha 446686 AW138043Hs.156307 ESTs 1525 434485 AI623511Hs.118567 ESTs 1524 441188 AW292830Hs255609 ESTs 1522 444172 BE147740Hs.104558 ESTs 1522 409521 BE244854Hs.159578 Homo Sapiens mRNA15.16 for FLJ00020 protein, 420748 AA279956Hs.88672 ESTs 15.14 422583 AA410506Hs.118578 H.sapiens mRNA 15.14 for ribosomal protein L18 424240 A8023185Hs.143535 caldum/calmodulin-dependent15.12 protein kin 451118 AI862096Hs.60640 ESTs 15.12 437495 BE177778gb:RCi-HT0598-310300-012-f0715.12 HT0598 Homo 445467 AI239832Hs.15617 ESTs, Weakly similar15.Q6 to ALU4-HUMAN ALU S

418305 AW006783Hs.6686 ESTs 15.03 402812 15.02 436851 AA732480Hs.293581 ESTs 15.00 400991 15.00 415752 BE314524Hs.78776 Human putative 14.96 transmembrane protein (nm 429900 AA460421Hs.30875 ESTs 14.90 403683 14.84 2O 430315 NM_004293Hs239147 guanine deaminase 14.80 451952 AL120173Hs.301663 ESTs 14.72 424687 J05070Hs.i51738 matrix metalloproteinase14.69 9 (gelatinase B

447229 BE617135gb:601441677F1 NIH_MGC-65 14.67 Homo sapiens c 425818 A8021225Hs.159581 matrix metalloproteinase14.65 17 (membrane-in 448553 A1638449Hs.173031 ESTs 14.63 431089 BE041395Hs283676 ESTs, Weakly similar14.60 to unknown protein 459145 AI903354gb:RC-BT029-100199-117 BT02914.55 Homo sapien 449650 AF055575Hs297647 ESTs, Moderately 14.54 similar to caldum than 400952 14.46 445685 AI734009Hs.127699 EST duster (not 14.44 in UniGene) 407938 AA905097Hs.85050 phospholamban 14.42 431676 AI685464Hs292638 ESTs 14.40 437210 AA311443Hs293563 Homo Sapiens mRNA;14.36 cDNA DKFZp586E2317 (f 451900 AB023199Hs27207 KiAA0982 protein 14.36 445600 AA126419Hs.301632 ESTs 14.32 412368 AW945992Hs.181125 immunoglobulin 14.31 lambda locus 409055 AW304028Hs.300578 ESTs 1423 408763 W57550Hs.301526 Homo Sapiens cDNA1422 FLJ13181 fis, done NT

446734 AL049278Hs.16074 Homo Sapiens mRNA;1422 d7NA DICFZp5641153 (fr 413551 BF242639Hs.75425 ubiquitin assodated1422 protein 421913 AI934365Hs.109439 osteoglydn (osteoinductive1422 factor, mime 452712 AW838616gb:RCS-LT0054-140200-013-DOt1422 LT0054 Homo 451468 AW503398Hs210047 ESTs 14.16 406038 Y14443Hs.88219 zinc finger protein14.14 424909 S78187Hs.153752 cell division 14.07 cycle 25B

434078 AW880709Hs283683 EST 14.07 415254 AI815831Hs.184378 ESTs 14.05 418196 AI745649Hs26549 ESTs, Weakly similar14.02 to T00066 hypotheti 410020 T86315Hs.728 ribonudease, RNase 13.98 A family, 2 (liver, 411352 NM-002890Hs.758 RAS p21 protein activator13.98 (GTPase active 429848 AF145439Hs225946 chemokine (C-C 13.95 motif) receptor 9 413729 BE159999gb:QV1-HT0412-270300-123-d1013.90 HT0412 Homo 13.88 420319 AW406289Hs.96593 hypothetical protein13.85 448272 AI479094Hs.170786 ESTs 13.80 422695 AA315158gb:EST186956 HCC cell line 13.80 (metastasis t 424565 AW102723Hs.75295 guanylate cydase 13.78 1, soluble, alpha 3 458048 H30340Hs.173705 Homo sapiens d7NA:13.78 FLJ22050 fis, clone H

408894 AI935400Hs217286 ESTs 13.76 6O 454093 AW860158gb:RCO-CT0379-290100-032-b0413.75 CT0379 Homo 410889 X91662Hs.66744 twist (Drosophila)13.74 homolog (acrocephalos 457751 AI908236gb:IL-BT166-180399-010 BTi6613.72 Homo sapien 455131 AW857913gb:RCO-CT0323-231199-031-b0513.69 CT0323 Homo 408364 AW015238Hs.128453 ESTs 13.67 425907 AA365752Hs.155965 ESTs 13.62 402359 13.60 401044 13.53 409877 AW502498Hs.157150 ESTs, Weakly similar13.53 to zinc finger prot 423690 AA329648Hs23804 ESTs 13.49 430685 AI690234Hs.191666 ESTs, Weakly similar13.47 to reverse transcri 414052 AW578849Hs.283552 ESTs, Weakly similar13.46 to unnamed protein 447858 AW080339Hs.211911 ESTs 13.44 435716 AI573283Hs.38458 ESTs 13.44 439120 H56389gb:yt87c03.r1 Soares~ineal,~land_N3HPG13.43 402788 13.40 451591 AA886446Hs.146278 ESTs 13.40 405411 13.38 426558 AW188574Hs.2d218 ESTs 13.34 1 453506 AA132818Hs.110407 ESTs, Weakly similar13.33 O to coded for by C.

416445 AL043004Hs.300678 Human serine/threonine13.32 kinase mRNA, part 457084 A1074149Hs.150905 ESTs, Weakly similar13.32 to chondroitin 4-su 403838 13.32 427337 246223Hs.176663 Fc fragment of 13.30 IgG, low affinity Illb, r 15 434318 AW207552Hs.116328 ESTs, Weakly similar1328 to dJ134E15.1 [H.sa 435193 N41359Hs.218107 ESTs 1328 414756 AW451101Hs.159489 ESTs, Moderately 1327 similar to hexokinase I

420626 AF043722Hs.99491 RAS guanyl releasing1326 protein 2 {caldum 420052 AA418850Hs.44410 ESTs 1325 414020 NM_002984Hs.75703 small inducible 1325 cytokine A4 (homologous 422647 W07492Hs.157101 ESTs 1321 433598 AI762836Hs.271433 ESTs, Moderately 1321 similar to ALU2-HUMAN A

409065 AB033113Hs.50187 KIAA1287 protein 1320 435063 821966Hs.57734 G protein-coupled 13.19 receptor kinase-intera 439367 BE386844Hs.248746 ESTs 13.17 451957 AI796320Hs.10299 Homo sapiens cDNA 13.16 FW13545 fis, clone PL

420569 AA278362Hs.289062 Homo Sapiens cDNA13.14 FLJ12334 fis, clone MA

447883 BE262802Hs.4909 dickkopf (Xenopus 13.07 laevis) homolog 3 3O 426490 NM_001621Hs.170087 aryl hydrocarbon 13.06 receptor 414789 AA155859Hs.79708 ESTs 13.05 451418 BE387790Hs.26369 ESTs 13.04 443494 T99719Hs270404 Homo Sapiens cDNA:13.03 FLJ22389 fis, clone H

425878 AW964806Hs.38085 ESTs, Weakly similar13.02 to putative glycine 35 431912 AI660552Hs.154903 ESTs, Weakly similar13.00 to A56154 Abl subst 407122 H20276Hs.31742 ESTs 13.00 456491 AL137466Hs.97277 Homo Sapiens mRNA;12.99 cDNA DKFZp434H1322 (f 448172 N75276Hs.135904 ESTs 12.98 452144 AA032197Hs.102558 ESTs 12.96 419953 BE267154Hs.125752 ESTs 12.96 416182 NM_004354Hs.79069 cydin G2 12.94 451154 AA015879Hs.33536 ESTs 12.93 412257 AW903830gb:CM4-NN1037-250400-155-h0412.93 NN1037 Homo 449784 AW16i319Hs.12915 ESTs 12.92 45 432695 D63480Hs.278634 KIAA01A6 protein 12.92 454105 NM_001259Hs.38481 cyclin-dependent 12.92 kinase 6 439093 AA534163Hs.5476 serine protease 12.90 inhibitor, Kazal type, 416098 H41324Hs.31581 ESTs, Moderately 12.88 similar to STi B-HUMAN
S

424897 D63216Hs.153684 tripled-related 12.88 protein $O 414604 AU076649Hs.76556 growth arrest and 12.88 DNA-damage-inducible 3 414664 AA587775Hs.66295 Homo Sapiens HSPC31112.84 mRNA, partial cds 452560 BE077084gb:RC5-BT0603-220200-013-C0712.84 BT0603 Homo 413869 NM_000878Hs.75596 interleukin 2 receptor,-beta 12.80 452359 BE167229Hs.29206 Homo sapiens clone12.80 24659 mRNA sequence 5$ 435886 BE265839Hs.12126 hepatocellular 12.78 caranoma-associated anti 445230 U97018Hs.12451 echinoderm miaotubule-associated12.78 protei 412226 W26786gb:15d7 Human retina cDNA 12.77 randomly prime 446619 AU076643Hs.313 seaeted phosphoprotein12.76 1 (osteopontin, 447769 AW873704Hs.48764 ESTs 12.76 414478 AI306389Hs.76240 adenylate kinase 12.76 425383 D83407Hs.156007 Down syndrome 12.68 aitical region gene 1-lik 450704 H85157Hs.40696 ESTs 12.66 405856 12.66 412935 BE267045Hs.75064 tubulin-specific 12.65 chaperone c 65 402802 12.62 452588 AA889120Hs.110637 Homeo box A10 12.62 419978 NM_001454Hs.93974 forkhead box J1 12.62 403137 12.60 430226 BE245562Hs.2551 adrenergic, beta-2-,12.57 receptor, surface 448076 Hs.20196 adenylate cydase 12.56 450462 Hs.300828 Homo sapiens mRNA 12.54 F07097 full length insert cDN

405236 12.52 409292 gb:zm58e05.s1 Stratagene 12.47 AA071051 fibroblast (937 421540 Hs.10242 ESTs 12.47 425840 Hs.301824 ESTs 12.44 443181 Hs.54548 ESTs 12.42 452436 Hs.31447 ESTs 12.42 455183 gb:RCO-HN0007-160300-011-f0912.40 AW984111 HN0007 Homo 1~ 432887 Hs.162859 ESTs 12.37 410494 Hs.64016 protein S (alpha) 12.36 439024 Hs.35598 ESTs 12.36 451246 Hs.39140 cutaneous T-cell 12.36 AW189232 lymphoma tumor antigen 432892 Hs.15995 ESTs 12.35 15 418982 Hs.13073 ESTs 12.35 414516 Hs279551 ESTs 12.34 440134 gb:601301619F1 NIH_MGC-21 1229 BE410734 Homo Sapiens c 443873 Hs.16291 ESTs 1228 454020 Hs256527 ESTs 1224 420077 Hs.87767 ESTs 1224 443837 Hs.9884 spindle pole body 1224 AI984625 protein 407519 gb:H.sapiens mRNA HTPCRX01 1223 X64979 for olfactory 435839 Hs25951 Rho guanine nucleotide1222 AF249744 exchange factor ( 25 448552 Hs.20104 hypothetical protein1220 451009 Hs.115707 ESTs 12.18 423066 Hs.120171 ESTs 12.17 439556 Hs.163603 ESTs 12.16 443062 Hs.8963 Homo Sapiens mRNA 12.15 N77999 full length insert d7N

445873 Hs.251946 Homo sapiens d7NA:12.14 AA250970 FLJ23107 fis, clone L

453542 Hs.33190 Homo sapiens mRNA 12.11 AW836724 expressed only in plac 440106 Hs.i27699 ESTs 12.10 417605 Hs.82294 regulator of G-protein12.10 AF006609 signalling 3 3$ 440286 Hs.7138 cholinergic receptor,12.04 U29589 muscarinic 3 420061 Hs.29410 ESTs 12.02 458727 Hs.92679 Homo sapiens done 11.96 A1022813 CDABP0014 mRNA sequen 445407 Hs221889 ESTs, Weakly similar11.95 AI222658 to la Costa [D.mela 418250 Hs.83918 adenosine monophosphate11.94 U29926 deaminase (isofo 4O 414129 Hs270798 ESTs 11.93 409799 Hs.76845 phosphoserine phosphatase-like11.92 438461 Hs.286049 phosphoserine aminotransferase11.92 443912 Hs.184780 ESTs 11.92 424606 gb:EST49786 Gall bladder 11.90 AA343936 I Hamo sapiens 45 434217 Hs23349 ESTs 11.90 451533 Hs.26530 serum deprivation 11.90 NM_004657 response (phosphatidyl 422423 Hs.116481 CD72 antigen 11.89 409398 gb:PM4-PT0019-121299-004-F0211.89 AW386461 PT0019 Homo 423853 Hs.133466 slit (Drosophila) 11.82 AB011537 homok~g 1 446180 Hs.14220 hypothetical protein11.80 414341 Hs.75909 KIAA0182 protein 11.80 406538 11.79 433253 Hs.24218 ESTs -AW450502 11.79 447397 Hs.18442 E-1 enzyme 11.78 55 451684 Hs.26813 CDA14 11.76 416862 Hs23575 ESTs 11.74 425770 Hs.159492 spastic ataxia 11.72 NM_014363 of Charlevoix-Saguenay (s 428826 Hs.194019 att<actin 11.72 433037 Hs.279938 HSPC067 protein 11.72 NM_014158 447476 Hs.20880 ESTs 11.72 452092 Hs27842 hypothetical protein11.72 412922 Hs.74870 H2.0 (Drosophila)-like11.72 M60721 homeo box 1 401680 Hs.180398 LIM domain-containing11.69 NM_005578 preferred transkx 422576 Hs.1i8554 CGI-83 protein 11.68 6$ 450203 Hs.301528 L-kynureninelalpha-aminoadipate11.68 AF097994 aminotra 410531 gb:QVO-CT0224-261099-035-g0211.67 AW752953 CT0224 Homo 425917 Hs.117167 Homo sapiens d)NA:11.66 W28517 FLJ23067 fis, done L

418693 Hs.87409 thrombospondin 1 11.64 400557 11.62 I8~

416188 BE157260Hs.79070 v-myc avian myelocytomatosis11.60 viral oncog 419047 AW952771Hs.90043 ESTs 11.59 420441 AI986160Hs.88446 ESTs 11.59 400885 11.57 409853 AW502327gb:Ul-HF-BROp-aka-a-07-0-ULr111.56 NIH_MGC 5 400802 11.56 434540 NM Hs.5184 TH1 drosophila homolog11.55 431449 M55994Hs.256278 tumor necrosis 11.55 factor receptor superfami 425928 S55736Hs238852 ESTs, Weakly similar11.54 to hypothetical pro IO 434701 AA460479Hs.4096 KIAA0742 protein 11.53 434228 242047Hs.283978 ESTs; KIAA0738 11.52 gene product 420729 AW964897Hs290825 ESTs -11.52 428328 AA426080Hs.98489 ESTs 11.50 433887 AW204232Hs279522 ESTs 11.50 15 414812 X72755Hs.77367 monokine induced 11.46 by gamma interferon 457718 F18572Hs22978 ESTs 11.44 452260 AA453208Hs.28726 RAB9, member RAS 11.42 oncogene family 459029 AA131376Hs285203 fibroblast growth 11.42 factor 12 456267 AI127958Hs.83393 cystatin ElM 11.39 433285 AW975944Hs.237396 ESTs 11.38 449186 AW291876Hs.196986 ESTs 11.37 447861 AI434593Hs.164294 ESTs 11.37 456023 800028gb:ye70a06.s1 Soares fetal 11.36 liver spleen 439444 A1277652Hs.54578 ESTS 11.31 25 401163 11.31 430886 L36149Hs.248116 chemokine (C motif)1128 XC receptor 1 450784 AW246803Hs.47289 ESTs 1128 452391 AL044829Hs.29331 carnitine palmitoylUansferase1127 I, muscle 449625 NM Hs.23796 odz (odd Ozften-m,1126 014253 Drosophila) homolog 1 3O 456827 AA075687Hs.147176 epidermal growth 1124 factor receptor substra 439328 W07411Hs.118212 ESTs, Moderately 1124 similar to ALU3-HUMAN A

432093 H28383gb:y152c03.r1 Soares breast1124 3NbHBst Homo 407335 AA631047Hs.158761 Homo Sapiens cDNA1123 FLJ13054 fis, clone NT

442501 AA315267Hs.23128 ESTs 1122 35 429746 AJ237672Hs.214142 5,10-methylenetetrahydrofolate1121 reductase 422858 835398gb:yg64g10.r1 Soares infant1120 brain 1 NIB H

415156 X84908Hs.78060 phosphorylase kinase,1120 beta 446713 AV660122Hs.282675 ESTs 1120 452221 C21322Hs.11577 ESTs 1120 4O 418261 W78902Hs293297 ESTs 11.17 433332 A1367347Hs.127809 ESTs 11.16 434539 AW748078Hs.214410 ESTs 11.16 413471 BE142098gb:CM4-HT0137-220999-017-d1111.14 HT0137 Homo 410037 AB020725Hs.58009 KIAA0918 protein 11.14 45 405601 11.13 458332 A1000341Hs.220491 ESTs 11.12 427654 AA410183Hs.137475 ESTs 11.12 427138 N77624Hs.173717 phosphafidic acid11.10 phosphatase type 2B

431475 AI567669Hs287316 ESTs 11.10 SO 425710 AF030880Hs.159275 solute tamer family,11.08 member 4 413748 AW104057Hs.19193 ESTs 11.07 409208 Y00093Hs.51077 integrin, alpha 11.07 X (antigen CD11C (p150), 457278 W92745Hs.193324 ESTs -11.03 407021 052077gb:Human marinerl transposase11.02 gene, comp $5 445701 AF055581Hs.13131 lymphocyte adaptor11.02 protein 408338 AW867079gb:MR1-SN0033-120400-002-c1010.95 SN0033 Homo 401030 BE382701Hs.25960 v-myc avian myelocytomatosis10.95 viral relat 437891 AW006969Hs.6311 hypothetical protein10.94 453874 AW591783Hs.36131 collagen, type 10.94 XIV, alpha 1 (undulin) f)O421562 AA530994Hs.105803 ghrelin precursor10.92 413431 AW246428Hs.75355 ubiquitin-conjugating10.92 enryme E2N (homolo 400132 10.92 436420 AA443966Hs.31595 ESTs 10.90 424880 NM-000328Hs.153614 retinitis pigmentosa10.88 GTPase regulator 65 433264 D85782Hs.3229 cysteine dioxygenase,10.88 type 1 429842 A1366213Hs.173422 KIAA1605 protein 10.87 412405 AW948126gb:RCO-MT0013-280300-031-a1210.85 MT0013 Homo 400615 10.80 425018 BF245277Hs.154196 E4F transcription10.80 factor 1 i81 456011 BE243628gb:TCBAP1D1053 Pediatric 10.79 pre-B cell acut 455982 BE176862gb:RC4-HT0587-170300-012-a0410.74 HT0587 Homo 450418 BE218418Hs.201802 ESTs 10.73 412490 AW803564Hs.288850 ESTs 10.72 $ 436962 AW377314Hs.5364 DKFZP5641052 protein10.70 437743 AI383497Hs.131811 ESTs, Weakly similar10.70 to ALUi HUMAN ALU S

449967 840978Hs.271498 ESTs, Moderately 10.70 similar to ALUi HUMAN A

449590 AA694070Hs.268835 ESTs 10.68 446035 NM Hs.13565 Sam68-like phosphotyrosine10.68 006558 protein, T-ST

1~ 426530 U24578Hs.170250 complement component10.66 dA

428600 AW863261Hs.15036 ESTs, Highly similar10.64 to AF1613581 HSPCO

420090 AA220238Hs.94986 ribonudease P (38kD)10.64 451593 AF151879Hs.26706 CGI-121 protein 10.62 438893 AF075031Hs29327 ESTs 10.62 15 459324 AW080953gb:xc28c12.x1 NCI-CGAP Cola10.61 Homo Sapiens 439883 AL359652Hs.171096 Homo Sapiens EST 10.58 from clone DKFZp43dA041 406513 AA715328Hs.291205 ESTs 10.57 407826 AA128423Hs.40300 calpain 3, (p94) 10.57 419550 D50918Hs.90998 KIAA0128 protein; 10.56 septin 2 20 428522 810184Hs.191987 ESTs, Weakly similar10.56 to ALU1 HUMAN ALU S

459526 AI142350Hs.146735 EST 10.55 411448 AA178955Hs.271439 ESTs 10.54 410102 AW248508Hs.279727 ESTs; 10.52 406577 10.52 2~ 408405 AK001332Hs.44672 hypothetical protein10.51 428966 AF059214Hs.194687 cholesterol25-hydroxylase10.50 400880 10.48 415875 AA894876Hs.5687 protein phosphatase10.48 1 B (formerly 2C), ma 434715 BE005346Hs.116410 ESTs 10.46 30 406851 AA609784Hs.180255 major histocompatibility10.44 complex, class 413409 AI638418Hs.21745 ESTs 10.44 418489 U76421Hs.85302 adenosine deaminase,10.44 RNA-specific, Bi (h 419465 AW500239Hs.21187 Homo Sapiens cDNA:10.44 FW23068 fis, clone L

419544 AI909154gb:OV-BT20Q-010499-007 BT20010.44 Homo sapien 35 432180 Y18418Hs.272822 RuvB (E cali homology-like10.44 413822 808950Hs.272044 ESTs, Weakly similar10.42 to ALUi IiUMAN ALU S

437446 AA788946Hs.i6869 ESTs, Moderately 10.41 similar to CA1C RAT COL

415701 NM-003878Hs.78619 gamma-glutamyl 10.41 hydrolase (conjugase, fol 443790 NM_003500Hs.9795 aryl-Coenryme A 10.40 oxidase 2, branched chaff 458873 AW150717Hs296176 STAT induced STAT 10.38 Inhibitor 3 415082 AA160000Hs.137396 ESTs 10.37 429124 AW505086Hs.196914 minor histocompaGbility10.36 antigen HA-1 417187 AB011151Hs.81505 KIAA0579 protein 10.34 426827 AW067805Hs.172665 methylenetetrahydrofolate10.34 dehydrogenase 4$ 424280 NM_000030Hs27i366 alanine-glyoxylate10.33 aminotransferase homo 446099 T93096Hs.17126 ESTs 10.32 423445 NM Hs.128749 alpha-methylacyl-CoA10.31 014324 racemase 409995 AW960597Hs.30164 ESTs 10.30 432242 AW022715Hs.162160 ESTs, Weakly similar10.30 to ALU4_HUMAN ALU S

50 406394 AA172106Hs.110950 Rag C protein 10.30 422283 AW411307Hs.114311 CDC45 (cell division1026 cycle 45, S.cerevis 401598 AA172106Hs.110950 Rag C protein -456995 T89832Hs.170278 ESTs 1026 5$ 416511 NM_006762Hs.79356 Lysosomal-associated1024 multispanning membr 427274 NM-005211Hs.174142 colony stimulating1024 factor 1 receptor, fo 456226 D13168Hs.82002 endothelin receptor1022 type B

426928 AF037062Hs.172914 reGnol dehydrogenase1021 5 (11-asand 9-cis 423032 AI684746Hs.119274 ESTs 1020 436556 AI364997Hs.7572 ESTs 1020 418400 BE243026Hs.301989 KIAA0246 protein 10.19 437401 AA757196Hs.121190 ESTs 10.19 403690 10.17 65 423790 BE152393gb:CM2-HT0323-171199-033-a0810.16 HT0323 Homo 434094 AA305599Hs238205 hypothetical protein10.16 434967 AW975009Hs292274 ESTs 10.16 432827 268128Hs.3109 Rho GTPase activating10.16 protein 4 432660 AI288430Hs.64004 ESTs 10.14 452234 AW084176Hs.223296 ESTs 10.14 445629 AI245701gb:qk31t05.x1 NCI_CGAP ICid310.13 Homo sapiens 457236 AA626142Hs.179991 ESTs, Weakly similar10.13 to KPCE_HUMAN PROTE

444605 A1174603Hs.254105 enolase 1, (alpha)10.12 450313 A1038989Hs.24809 hypothetical protein10.12 407482 NM 10.12 449971 AA807346Hs.288581 Homo Sapiens cDNA10.11 FLJ14296 fis, clone PL

441201 AW118822Hs.128757 ESTs 10.10 435157 AW014605Hs.179872 ESTs 10.10 1O 417308 H60720Hs.81892 KIAA0101 gene product10.09 442582 AI204266Hs.179303 ESTs 10.05 437252 AI433833Hs.i64159 ESTs, Weakly similar10.04 to ALUi HUMAN ALU S

448663 BE614599Hs.106823 H.sapiens gene 10.04 from PAC 42616, similar t 434467 BE552368Hs.231853 Homo sapiens cDNA10.04 FLJ13445 fis, clone PL

15 423698 AA329796Hs.1098 DKFZp434J1813 protein10.02 412707 AW206373Hs.16443 Homo Sapiens cDNA:10.00 FLJ21721 fis, clone C

414658 X58528Hs.76781 ATP-binding cassette,10.00 sub-family D (ALD) 421832 NM-016098Hs.108725 HSPC040 protein 10.00 423554 M90516Hs.i674 glutamine-fructose-6-phosphate10.00 transamin 452039 AI922988Hs.172510 ESTs 10.00 434673 AW137442Hs.136965 ESTs 10.00 427978 AA418280Hs.180040 Homo sapiens cDNA:10.00 FLJ22439 fis, clone H

457803 BE501815Hs.198011 ESTs 9.99 428279 AA425310Hs.155766 ESTs 9.98 444412 A1147652Hs.216381 Homo Sapiens done9.98 HH409 unknown mRNA

417049 N72394Hs.44862 ESTs 9.96 427509 M62505Hs.2161 complement component9.96 5 receptor 1 (C5a I

445424 AB028945Hs.12696 cortactin SH3 domain-binding9.96 protein 443678 AW009605Hs.231923 ESTs 9.96 3O 447567 AW474513Hs.224397 ESTs, Weakly similar9.94 to 848013 proline-r 414709 AA704703Hs.77031 Sp2 transcription 9.94 factor 434596 T59538gb:yb65g12.s1 Stratagene 9.94 ovary (937217) 427630 BE276115Hs.144980 ESTs, Weakly similar9.93 to CA13_HUMAN COLLA

416111 AA033813Hs.79018 chromatin assembly9.92 factor i, subunit A ( 35 423349 AF010258Hs.127428 homeo box A9 9.92 424308 AW975531Hs.154443 minichromosome 9.92 maintenance deficient (S.

416814 AW192307 Hs.80042 dolichyl-P-GIc:Man9GIcNAc2-PP-dolichylgl9.90 417986 AA481003Hs.97128 ESTs 9.90 425174 D87450Hs.154978 KIAA0261 protein 9.90 4O 438171 AW976507Hs.293515 ESTs 9.90 421984 AW972187Hs.110443 hypothetical protein9.89 408597 NM_005291Hs.46453 G protein-coupled 9.88 receptor 17 413907 A1097570Hs.71222 ESTs 9.87 451296 AW801383Hs.118578 H.sapiens mRNA 9.86 for ribosomal protein L18 45 433409 AI278802Hs25661 ESTs 9.85 450360 AW117416Hs.245484 ESTs 9.85 433104 AL043002Hs.128246 ESTs, Moderately 9.84 similar to unnamed prot 449824 AI962552Hs.226765 ESTs 9.84 452744 AI267652Hs.30504 Homo Sapiens mRNA;9.82 cDNA DKFZp434E082 (fr SO 431066 AF026273Hs.249175 intedeukin-1 receptor-associated9.82 kinase 426457 AW894667Hs.169965 chimerin (chimaerin)9.80 443371 AI792888Hs.145489 ESTs 9.80 437159 AL050072gb:Homo Sapiens mRNA; cDNA - 9.75 DKFZp566E1346 425242 D13635Hs.155287 KIAA0010 gene 9.74 product 55 447498 N67619Hs.43687 ESTs 9.74 426759 AI590401Hs.21213 ESTs 9.73 435129 AI381659Hs.267086 ESTs 9.72 437672 AW748265Hs.5741 ttavohemoprotein 9.72 b5+b5R

438209 AL120659Hs.6111 KIAA0307 gene product9.72 6O 438440 AA807228Hs.225161 ESTs 9.72 449720 AA311152Hs.288708 ESTs; Weakly similar9.72 to KIAA0226 (H.sapi 414291 AI289619Hs.13040 ESTs ~ 9.72 436206 AK001451Hs.265561 CD2-associated 9.70 protein 446896 T15767Hs22452 Homo Sapiens cDNA: 9.70 FLJ21084 fis, done C

65 412667 AW977540Hs.269254 ESTs 9.70 423301 S67580Hs.1645 cytochrome P450, 9.67 subfamily IVA, polypept 440757 AW118645Hs.160004 ESTs 9.67 441412 AI393657Hs.159750 ESTs 9.66 421044 AF061871Hs.101302 collagen, type 9.66 XII, alpha 1 414726 Hs.280099 ESTs 9.66 418485 Hs.124981 ESTs 9.66 433480 Hs.181125 immunoglobulin 9.65 X02422 lambda locus 441530 Hs.127112 ESTs 9.65 433533 Hs.65394 ESTs 9.65 421470 Hs.1378 annexin A3 9.64 438613 Hs.243122 hypothetical protein9.64 C05569 FW13057 similar to 429324 Hs.199245 inactivation escape9.62 450244 Hs.125062 ESTs 9.62 1~ 407660 Hs.279101 ESTs 9.61 406554 9.60 426404 Hs.273138 ESTs 9.58 447045 Hs.278569 KIAA0064 gene product9.58 449894 Hs.24129 hypothetical protein9.58 15 448376 Hs.196963 ESTs 9.56 407902 Hs.41181 Homo sapiens mRNA; 9.56 AL117474 cDNA DKFZp727C191 (fr 446572 Hs.282961 ESTs 9.56 459245 Hs.31939 manic frfnge (Drosophila)9.55 BE242623 homolog 423545 Hs.129781 chromosome 21 open9.54 AP000692 reading frame 5 414697 Hs.76927 translocase of outer9.54 BE266134 mitochondrial membr 410846 gb:MR4-ST0062-031199-018-b039.52 AW807057 ST0062 Homo 421181 Hs.184585 LIM domain only2 9.52 NM_005574 (rhombotin-like 1) 427308 Hs.174905 KIAA0033 protein 9.52 415995 Hs.994 phospholipase C, beta9.51 434846 Hs.119768 ESTs 9.51 414342 Hs.75912 Homo Sapiens d7NA: 9.50 AA742181 FLJ22199 fis, done H

416959 Hs.80612 ubiquitin-con]ugating9.50 D28459 enryme E2A (RAD6 h 443123 Hs.6588 ESTs 9.50 439312 Hs.270745 ESTs 9.48 3O 449375 Hs271224 ESTs 9.48 436357 gb:Homo Sapiens mRNA for 9.44 AJ132085 axonemal dynein 458723 Hs.244352 ESTs, Moderately 9.44 AW137726 similar to laminin alph 457526 Hs.192131 ESTs, Weakly similar9.43 AW450584 to RIBB [H.sapiens]

404741 9.43 3$ 422409 Hs.116237 vav 1 oncogene 9.43 NM_005428 403708 9.42 408806 Hs.289005 Homo Sapiens d)NA:9.42 AW847814 FLJ21532 fis, done C

417360 gb:EST04698 Fetal brain, 9.42 T06809 Stratagene (cat 422501 Hs.144967 ESTs 9.42 4O 426197 Hs.167835 aryl-Coenryme A 9.42 AA004410 oxidase 1, palmitoyl 452624 Hs.30054 coagulation factor 9.42 AU076606 V (proaccelerin, tabi 412110 gb:RCO-NN0021-040400-021-c109.41 AW893569 NN0021 Homo 414158 Hs288775 Homo Sapiens d7NA 9.41 AA361623 FLJ13900 fis, done TH

408101 Hs.123073 CDC2-related protein9.40 AW968504 kinase 7 45 414171 Hs.865 RAP1A, member of RAS 9.40 AA360328 onoogene family 415947 Hs.78934 mutS (E. coli) homolog9.40 U04045 2 (colon cancer, 426959 gb:601153869F1 NIH-MGC_19 9.39 BE262745 Homo sapiens c 417519 Hs.177669 ESTs, Weakly similar9.39 AI689987 to RMSi HUMAN REGUL

457181 Hs296422 FK506-binding protein9.39 BE514362 3 (25kD) SO 402835 9.38 404632 9.38 446566 Hs.17914 Homo sapiens cDNA: 9.37 H95741 FLJ22801 fis, clone K

455369 gb:CM1-NN1031-060400-178-d05' AW903533 NN1031 Homo 9.37 444001 Hs.152299 ESTs, Moderately 9.36 A1095087 similar to ALU5_HUMAN A

55 458191 Hs.127832 ESTs 9.36 431374 Hs.251871 CTP synthase 9.34 429327 Hs.199248 prostaglandin E 9.33 AA283981 receptor 4 (subtype EP4) 407061 gb:H.sapiens PTX3 gene promotor9.33 X97748 region.

416967 Hs.80645 interferon regulatory9.33 BE616731 factor 1 423013 Hs.22209 secreted modular 9.33 AW875443 caldum-binding protein 439461 Hs.103158 ESTs 9.33 418830 Hs.88959 Human DNA sequence 9.32 BE513731 from done 967N21 on 422763 Hs.83938 ESTs, Moderately,similar9.32 AA033699 to MASP-2 [H.sa 442739 Hs.8679 cytosolic acyl coenryme9.32 NM_007274 A thioester hydr 65 452859 Hs.288158 Homo Sapiens d7NA:9.32 AI300555 FW23591 fis, done L

403237 9.32 415000 Hs.239812 ESTs, Weakly similar9.31 AW025529 to CALM HUMAN CALMO

417951 Hs289069 Homo Sapiens d7NA: 9.30 AW976410 FLJ21016 fis, done C

419066 Hs.6975 PR01073 protein 9.30 448443 Hs.231934 ESTs 9.30 405125 9.30 409768 gb:Ul-HF-BROp-aji-h-03-0-ULr19.28 AW499566 NIH_MGC_5 453708 Hs.54629 ESTs 9.28 442271 Hs.8180 syndecan binding 9.27 AF000652 protein (syntenin) 410055 Hs.58241 gene for serine/threonine9.26 AJ250839 protein kinase 448692 Hs.224276 ESTs, Moderately 9.26 AW013907 similar to predicted us 417381 Hs.82042 solute carrier family9.25 AFi64142 23 (nucleobase tra 422497 Hs.1528 KIAA0053 gene product9.25 1~ 414140 Hs.23317 ESTs 9.24 435960 Hs.129142 ESTs; Weakiy similar9.24 AF274571 to DEOXYRIBONUCLEAS

458530 Hs.199889 ESTs, Weakly similar9.24 BE395035 to KIAA0874 protein 402585 9.24 420819 gb:zs95h11.s1 NCI_CGAP-GC81 9.23 AA280700 Homo sapiens 15 444755 Hs.183001 ESTs 9.22 4i 1630 Hs.71119 Putative prostate 9.22 U42349 cancer tumor suppresso 421246 Hs.300961 ESTs, Highly similar9.20 AW582962 toAF1518051 CGI-4 421924 Hs.109606 coronin, actin-binding9.19 BE514514 protein,1A

414888 Hs.77558 thyroid homwne receptor9.18 AL039185 interactor 7 434267 Hs.116243 ESTs 9.17 409213 Hs.51133 PTK6 protein tyrosine9.17 U61412 kinase 6 428242 Hs.2250 leukemia inhibitory 9.16 H55709 factor (cholinergic 451736 Hs.293684 ESTs, Weakly similar9.15 AW080356 to alternatively sp 413627 Hs.246973 ESTs 9.14 25 416134 Hs.74861 activated RNA polymerase9.14 AA528402 II transcriptic 449251 Hs.31444 ESTs 9.14 452813 Hs.191445 ESTs 9.14 443622 Hs.11805 ESTs 9.14 413260 gb:PM1-BT0585-290200-005-4079.12 BE075281 BT0585 Homo 413450 Hs.75372 N-acetylgalactosaminidase,9.12 299716 alpha-446442 Hs.257858 ESTs 9.12 438540 Hs.136906 ESTs 9.12 426251 Hs.i68383 Intercellular adhesion9.11 M24283 molecule 1 (CD54) 410290 Hs.73818 ubiquinol-cytochrome9.10 AA402307 c reductase hinge p 35 437398 Hs.126715 ESTs 9.10 421559 Hs.105751 Ste20-related serinelthreonine9.10 NM 014720 kinase 439699 Hs.187561 ESTs, Moderately 9.10 AF086534 similar to ALU1 HUMAN A

430799 Hs.164259 ESTs 9.09 424544 Hs.150403 dopa decarboxylase9.08 M88700 (aromatic L-amino aci 4O 453942 Hs.19928 ESTs 9.08 425844 Hs.159628 serine (or cysteine)9.08 T68073 proteinase inhibito 434658 Hs.194488 ESTs 9.07 453999 Hs.240087 ESTs 9.06 436490 Hs.18713 ESTs 9.05 45 409192 Hs233439 ESTs, Weakly similar9.05 AA065131 to ALU7 HUMAN ALU S

446223 Hs.119699 hypothetical protein9.04 447247 Hs.287955 Homo sapiens cDNA 9.04 AW369351 FLJ13090 fis, clone NT

450094 Hs295789 Homo sapiens mRNA; 9.04 A1174947 cDNA DKFZp564D1164 (f 432012 Hs.195969 ESTs 9.04 422520 Hs.117977 kinesin 2 (60-70kD)9.02 418650 Hs.86978 prolyl endopeptidase9.02 423008 Hs.123016 5-hydroxytryptamine9.02 M81590 (serotonin) receptor 436476 Hs.53631 ESTs -AA326108 9.02 448206 Hs.3731 ESTs 9.02 55 431574 Hs.261373 adenosine A2b receptor9.01 AW572659 pseudogene 443453 Hs.269882 ESTs 9.01 435472 Hs.283022 triggering receptor9.01 AW972330 expressed on myeloid 420337 Hs.14555 Homo sapiens cDNA: 9.00 AW295840 FLJ21513 fis, clone C

449810 Hs.23994 activin A receptor,9.00 AB008681 type IIB

406780 Hs.286 ribosomal protein 8.99 429169 Hs.197757 ESTs, Moderately 8.99 AW341130 similar to FGFE_HUMAN F

421326 Hs.103504 estrogen receptor 8.97 AF051428 2 (ER beta) 425491 Hs.255221 ESTs 8.96 425516 Hs.29567 ESTs 8.96 65 439773 Hs.143315 ESTs 8.96 443247 Hs.47378 ESTs 8.96 456623 Hs.108106 transcription factor8.95 438707 Hs.5326 poroupine 8.95 402240 8.95 ig~

444152 A1125694Hs.149305 Homo Sapiens cDNA8.95 FLJ14264 fis, clone PL

409842 AW501756gb:Ul-HF-BROp-ajm-o-09-0-ULr18.94 NIH_MGC 5 416277 W78765Hs.73580 ESTs 8.94 456697 AI908006Hs.i 11334 ferritin, light 8.94 polypeptide 410762 AF226053Hs.66170 HSKM-B protein 8.92 412942 AL120344Hs.75074 mitogen-activated 8.92 protein kinase-activat 442320 AI287817Hs.i29636 ESTs 8.92 449673 AA002064Hs.18920 ESTs 8.91 411486 N85785Hs.181165 eukaryotic translation8.90 elongation factor 437916 BE566249Hs.20999 Homo Sapiens cDNA:8.90 FLJ23142 fis, clone L

442732 AA257161Hs.8658 hypothetical protein8.89 DKFZp434E0321 419741 NM_007019Hs.93002 ubiquitin carrier 8.89 protein E2-C

411499 AW849292gb:IL3-CT0215-020300-090-E068.89 CT0215 Homo 431154 AW971228Hs.290259 ESTs 8.89 414922 D00723Hs.77631 glycine cleavage 8.88 system protein H (amino 418036 237976Hs.83337 latent transforming8.87 growth factor beta b 406422 8.87 422926 NM_016102Hs.121748 ring finger protein8.87 435220 D50030Hs.104 HGF activator 8.86 2O 418203 X54942Hs.83758 CDC28 protein kinase8.86 418613 AA744529Hs.86575 mitogen-activated 8.85 protein kinase kinase 439250 H66566Hs271711 ESTs 8.85 432359 AA076049Hs274415 Homo Sapiens cDNA 8.84 FLJ10229 fis, clone HE

450000 AI952797Hs.10888 .Homo sapiens cDNA:8.83 FLJ21559 fis, clone C

425657 T89839Hs.119471 ESTs 8.83 425694 U51333Hs.i59237 hexokinase 3 {white8.82 cell) 419972 AL041465Hs.294038 ESTs, Moderately 8.82 similar to ALU2 HUMAN A

436396 AI683487Hs299112 Homo Sapiens cDNA 8.82 FLJ11441 fis, clone HE

413413 D82520Hs.301834 Homo Sapiens cDNA8.82 FLJ10952 fis, clone PL

3O 428807 AA435997Hs.104930 ESTs 8.82 415839 840611Hs.137565 ESTs 8.81 419553 N34145Hs250614 ESTs 8.80 420309 AW043637Hs.21766 ESTs 8.80 421863 AI952677Hs.108972 Homo Sapiens mRNA;8.80 cDNA DKFZp434P228 (tr 447965 AW292577Hs.94445 ESTs 8.80 459172 BE063380gb:PMO-BT0275-291099-002-g108.80 BT0275 Homo 403259 8.78 411534 AW850473gb:IL3-CT0219-280100-061-Bii8.78 CT0219 Homo 456161 BE264645Hs.282093 Homo Sapiens cDNA:8.77 FLJ21918 fis, clone H

413654 AA331881Hs.75454 peroxiredoxin 3 8.76 401744 8.76 425348 AL137477Hs.155912 cadherin-like 8.76 423396 AI382555Hs.127950 bromodomain-containing8.75 450649 NM_001429Hs297722 Human DNA sequence8.75 from clone RPi-85F18 408331 NM-007240Hs.44229 dual specifiaty 8.74 phosphatase 12 423872 AB020316Hs.134015 uronyl2-sulfotransferase8.74 424906 AI566086Hs.153716 Homo Sapiens mRNA8.74 for Hmob33 protein, 3' 427596 AA449506Hs.179765 Homo Sapiens mRNA;8.73 cDNA DKFZp586H1921 (f 432488 AA551010Hs216640 ESTs 8.72 448980 AL137527Hs.22703 Homo sapiens mRNA;8.72 cDNA DKFZp434P1018 (f 429455 AI472111Hs292507 ESTs 8.71 429855 AW385597Hs.138902 ESTs, Weakly similar8.71 to 834087 hypotheti 441746 H59955Hs.127829 ESTs ' 8.70 411945 AL033527Hs.92137 v-myc avian myelocytomatosis8.70 viral oncog $5 413492 D87470Hs.75400 KIAA0280 protein 8.70 435706 W31254Hs.7045 GL004 protein 8.70 433741 AA609019Hs.159343 ESTs 8.70 426340 297989Hs.169370 FYN oncogene related8.69 to SRC, FGR, YES

422779 AA317036Hs.41989 ESTs 8.67 6O 449785 AI225235Hs288300 Homo sapiens cDNA:8.67 FLJ23231 fis, clone C

420144 AA811813Hs.119421 ESTs 8.66 420235 AA256756Hs.31178 ESTs 8.66 432606 NM_002104Hs.3066 granzyme K (serine 8.66 protease, granzyme 3;

425762 BE244076Hs.159578 Homo Sapiens mRNA8.65 for FLJ00020 protein, f)5427448 BE246449Hs.2157 Wiskott-Aldrich 8.64 syndrome (eczema-thrombo 418033 W68180Hs259855 Homo Sapiens cDNA 8.64 FLJ12507 fis, clone NT

429084 AJ001443Hs.195614 splicing factor 8.64 3b, subunit 3,130kD

417094 NM_006895Hs.81182 histamine N-methyltransferase8.64 457277 NM_004736Hs.227656 xenotropic and 8.63 polytropic retrovirus rec 422631 BE218919Hs.118793 hypothetical protein8.63 410679 AW795196Hs.215857 ring finger protein8.63 431585 BE242803Hs.262823 hypothetical protein8.62 40185 1 8.62 $ 401866 8.62 407783 AW996872Hs.172028 a disintegrin and 8.62 metalloproteinase dome 408242 AA251594Hs.43913 PIBF1 gene product 8.62 422250 AWd08530Hs.113823 CIpX (caseinolytic8.62 protease X, E. coli) 430259 BE550182Hs.127826 RaIGEF-like protein8.62 3, mouse homolog 1 452598 AI831594Hs.68647 ESTs, Weakly similar8.62 ~ to ALU7_HUMAN ALU S

419541 AW749617gb:RC3-BT0502-130100-012-g078.60 BT0502 Hamo 428839 AI767756Hs.82302 ESTs 8.60 429328 AA829402Hs.47939 ESTs 8.60 451491 AI972094Hs.286221 Homo sapiens cDNA 8.60 FLJ13741 fis, done PL

1$ 452561 AI692181Hs.49169 KIAA1634protein 8.60 420027 AF009746Hs.94395 ATP-binding cassette,8.60 sub-family D (ALD) 435205 X54136Hs.181125 immunoglobulin 8.60 lambda locus 430900 U91939Hs.248123 G protein-coupled 8.60 roceptor 25 405074 8.59 437991 A!479773Hs.181679 ESTs 8.59 436346 BE328882Hs.193096 ESTs, Moderately 8.58 similar to 0119 HUMAN U

411079 AA091228gb:cchn2152.seq.F Human fetal8.57 heart, Lam 418452 BE379749Hs.85201 C-type (calcium 8.56 dependent, carbohydrate-429109 AL008637Hs.196352 neutrophil cytosolic8.56 factor 4 (40kD) ~$ 448019 AW947164Hs.195641 ESTs 8.56 449865 AW204272Hs.199371 ESTs 8.55 431180 H55883gb:yq94h03.r1 Soares fetal 8.54 liver spleen 445988 BE007663Hs.13503 inactivation escape8.54 405676 8~'~

30 407235 D20569Hs.169407 SAC2 (suppressor 8.54 of actin mutations 2, y 414807 AI738616Hs.77348 hydroxyprostaglandin8.54 dehydrogenase 15-(N

425671 AF193612Hs.159142 lunatic fringe 8.54 (Drosophila) homolog 452413 AW082633Hs.212715 ESTs 8.54 421620 AA446183Hs.91885 ESTs 8.53 3$ 444539 AI955765Hs.146907 ESTs 8.52 415102 M31899Hs.77929 excision repair 8.51 cross-complementing rode 405552 8.51 418068 AW971155Hs.293902 ESTs, Weakly similar8.50 to prolyl 4-hydroxy 420133 AA426117Hs.14373 ESTs 8.50 438887 868857Hs.265499 ESTs 8.50 446468 A1765890Hs.16341 ESTs; Moderately 8.50 similar to !!!! ALU SUB

446585 AV659397Hs.282948 ESTs 8.50 441896 AW891873gb:CM3-NT0090-040500-173-b028.50 NT0090 Homo 437718 AI927288Hs.196779 ESTs 8.48 45 420656 AA279098Hs.187636 ESTs 8.48 429303 AW137635Hs.44238 ESTs 8.48 450624 AL043983Hs.125Q63 Homo Sapiens cDNA 8.48 FLJ13825 fis, clone TH

452573 AI907957Hs287622 Homo sapiens cDNA 8.48 FLJ14082 fis, clone HE

456341 AA229126Hs.122647 N-mydstoyltransferase8.48 $O 423024 AA593731Hs.75613 CD36 antigen (collagen8.47 type I receptor, 446985 AL038704Hs.156827 ESTs, Weakly similar8.46 to ALU1 HUMAN ALU S

431778 AL080276Hs.268562 regulator of G-protein8.46 signalling 17 400268 ' 8.46 421828 AW891965Hs289109 dimethylarginine 8.45 dimethylaminohydrolase $$ 417022 NM Hs.80905 Ras association 8.44 014737 (RaIGDS/AF-6) domain fam 421029 AW057782Hs.293053 ESTS 8.44 425171 AW732240Hs.300615 ESTs 8.44 459070 AI814302gb:wj71c12.x1 NCI_CGAP_Lul9 8.42 Homo Sapiens 8.42 ()~412643 AW971239Hs.293982 ESTs 8.42 424775 A8014540Hs.153026 SWAP-70 protein 8.42 446848 AW136083Hs.195266 ESTs; Weakly similar8.42 to S59501 interfero 448043 AI458653Hs.201881 ESTs 8.41 407183 AA358015gb:EST66864 Fetal lung III 8.40 Homo Sapiens 6$ 412324 AW978439Hs.6950d ESTs 8.40 419594 AA013051Hs.91417 topoisomerase (DNA)8.40 II binding protein 430968 AW972830gb:EST384925 MAGE resequences,8.40 MAGL Homo 431689 AA305688Hs267695 UDP-Gal:betaGIcNAc 8.40 beta 1,3-galactosyltr 438582 AI521310Hs.283365 ESTs, Weakly similar8.40 to ALUS_HUMAN ALU S

447685 AL122043Hs.19221 hypothetical protein8.40 DKFZp566G1424 459119 AW844498Hs.289052 Homo Sapiens LENG88.38 mRNA, variant C, part d00817 8.37 425265 BE245297gb:TCBAPi E2482 Pediatric 8.37 pre-B cell acct 409385 AA071267gb:zm61g01.r1 Stratagene 8.36 fibroblast (937 439121 BE047779Hs.44701 ESTs 8.36 419968 X04430Hs.93913 interleukin 6 (interferon,8.36 beta 2) 408327 AW182309Hs.249963 ESTs, Highly similar8.35 to dJ1170K4.4 [H.sa 403976 8.34 l~ 448064 AA379036gb:EST91809 Synovial sarcoma8.33 Homo sapien 442914 AW188551Hs.99519 Homo sapiens d)NA 8.33 FLJ14007 fis, clone Y7 428032 AW997704Hs.11493 Homo sapiens d)NA 8.32 FLJ13536 fits, done PL

434194 AF119847Hs.283940 Homo sapiens PR015508.32 mRNA, partial cds 458677 AW937670Hs.254379 ESTs 8.32 IS 420925 NM Hs.100391 T54protein 8.30 416475 T70298gb:yd26g02.s1 Soaves fetal 8.30 I'rver spleen 416852 AF283776Hs.80285 Homo Sapiens mRNA;8.30 d)NA DKFZp586C1723 (f 430676 AF084866gb:Homo Sapiens envelope 8.30 protein RIC-3 ( 428455 AI732694Hs.98520 ESTs 8.29 20 435343 AW194962Hs.199028 ESTs 8.29 450783 BE266695gb:601190242F1 NIH_MGC 7 8.29 Homo Sapiens cD

404846 8.28 422942 AF054839Hs.122540 tetraspan 2 8.28 453716 AA037675Hs.152675 ESTs 8.28 25 437098 AA744488Hs.132842 ESTs, Moderately 8.28 similar to ALU1 HUMAN A

443907 AU076484Hs.9963 TYRO protein tyrosine8.27 kinase binding pro 401930 AF106069Hs23168 ubiquitin spedfic 8.26 protease 15 446554 AA151730Hs.301789 ESTs, Weakly similar8.26 to similar to C.ele 426290 A8007918Hs.169182 KIAA0449 protein 8.25 419904 AA974411Hs.18672 ESTs 8.25 413886 AW958264Hs.103832 ESTs, Weakly similar8.24 to TRHY-HUMAN TRICH

424738 AI963740Hs.46826 ESTs 8.24 427359 AW020782Hs.79881 Hamo Sapiens d7NA:8.24 FLJ23006 fis, done L

424534 D87682Hs.150275 KIAA0241 protein 8.24 35 424429 063830Hs.146847 TRAF family member-assodated8.24 NFKB activ 442604 BE263710Hs.279904 ESTs 8.22 442992 AI914699Hs.13297 ESTs ~ 8.22 427210 BE396283Hs.173987 eukaryofic translation8.22 inifiation factor 457229 BE222450Hs.266390 ESTs 8.21 423730 AA330214gb:EST33935 Embryo,12 week 8.21 II Homo sapi 411928 AA888624Hs.19121 adaptor-related 820 protein complex 2, alpha 416051 AA835868Hs25253' Homo Sapiens d)NA:8.20 FLJ20935 fis, done A

417231 840739Hs21326 ESTs 8.20 422049 W25760Hs.77631 glydne deavage 8.20 system protein H (amino 45 427528 AU077143Hs.179565 minichromosome 820 maintenance defident (S.

458776 AV654978Hs.19904 cystathionase (cystathionine8.19 gamma-lyase 417687 AI828596Hs.250691 ESTs 8.18 423218 NM_015896Hs.167380 BLu protein 8.18 425397 J04088Hs.156346 topoisomerase 8.18 (DNA) II alpha (170kD) 406964 M21305Hs247946 Human alpha satellite8.18 and satellite 3 [u d02401 042349Hs.71119 Putafirve prostate8.18 cancer tumor suppresso 423397 NM_001838Hs.1652 chemokine (C-C motif)8.18 receptor 7 427857 AL133017Hs.2210 thyroid hormone -receptor interador 3 8.17 401519 8.17 55 447188 H65423Hs.17631 Homo Sapiens d7NA 8.16 FLJ20118 fis, done CO

424704 AI263293Hs.152096 cytochrome P450, 8.16 subfamily IIJ (arachido 435854 AJ278120Hs.4996 DKFZP564D166 protein8.14 448556 AW885606Hs.5064 ESTs 8.14 449217 AA278536Hs.23262 dbonudease, RNase 8.14 A family, k6 6O 453124 AI139058Hs23296 ESTs 8.14 442812 A1018406Hs.131284 ESTs 8.14 421129 BE439899Hs.89271 ESTs 8.14 I8g TABLE 9A shows the accession numbers for those primekeys lacking a unigene>D
in Table 9. 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 1$ Pkey CAT number Accession 1035720_-1 104479_1 108463_1 110159_1 AW753492 BE175371 AA311147 111586_1 ~$ 409385 AA071267 T65940 T64515 AA071334 1126716_1 AW386619 AW386289 AW876136 AW876203 AW876301 1156226_1 $ 1223902_1 AW807429 AW807364 AW807365 AW807078 AW807180 1248105_1 AW849424 AW849427 4$ 411972 BE074959 AW880160 1277844_1 1284289_1 412257 AW903830 BE0719i6 $0 _ AW948131 AW948158 AW948164 AW948151 $$ 414989 T81668 C19040 C17569 1596398_1 1843934_-1 200620_1 6$ 422673 N59027 AA314694 N53937 808100 219674_1 _ BE152393 AA330984 BE073904 424385 238731_1AA339666 AW952809 AA349119 430676 32168_1AF084866 AF084870 AF084864 AF084867 AF084869 AF084865 430968 326269_1AW972830 AA527647 AA489820 AA570362 432093 341283_1H28383 AW972670 H28359 AA525808 434596 38937_1T59538 T59589 T59598 T59542 AF147374 437159 43393_1AL050072 AW900148 437495 43765_1BE177778 BE177779 AL390180 AA359908 439120 46679_1H56389 AF085977 H56173 445629 645767_1AI245701 BE272724 2$ 447229 71288_1BE617135 AW504051 AW504283 448064. AA379036 AA150589 A1696854 BE621316 74761_1 451045 85673_1AA215672 AI696628 AA013335 H86334 AA017006 452560 922216_1BE0770B4 AW139963 AW863127 AW806209 AW806204 AW806205 454093 1007366-iAW860158 AW862385 AW860159 AW862386 AW862341 AW821869 3$ 454563 1224342AW807530 AW807540 AW807537 AW846086 BE141634 AW846089 454791 1234759_1BE071874 BE071882 AW820782 AW821007 455131 1254674_1AW857913 AW857916 AW857914 AW861627 AW861626 AW861624 455254 1266449_1AW877015 AW877133 AW876978 AW877071 AW876988 AW877069 455369 1285173_16AW903533 AW903516 AW903562 BE085202 BE085215 BE085214 455982 1396849_1BE176862 BE176876 BE176947 BE176878 456011 1410860_1BE243628 BE246081 BE247016 BE241984 BE241534 BE246091 456023 1416335_1800028 BE247630 457595 364225_AA584854 $0 457751 399422A1908236 AA663731 459070 883688_1AI814302 AI814428 459145 918957_1A1903354 A1903489 A1903488 459234 945240_AI940425 TABLE 9B shows the genomic positioning for those primekeys lacking unigene )D's and accession numbers in Table 9. For each predicted axon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted axon are also listed.
Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al." refers to the publication entitled 'The DNA sequence of human chromosome 22 " Dunham I. et al., Nature (1999) 402:489-495.
Strand: Indicates DNA strand from which axons were predicted.
1~ Nt~osition: Indicates nucleotide positions of predicted axons.
Pkey Ref Strand Nt~osition 1 400452 Minus90308-90505 400557 Plus208453-208528,209633-209813 400615 Plus118036-118166,118681-118807 400802 Minus174571-174856 400817 Plus170793-170948 ~ 400880 Plus29235-29336,36363-36580 400885 Minus58242-58733 400926 Minus52033-52158,53956-54120,54957-55052,55420-55480,56452-56666,57221-57718 400952 Plus192667-192826,194387-194876 400991 Plus159197-159320 ~5 401044 Plus73501-73674 401124 Minus124181-124391 401163 Plus5302-5545 401201 Minus138534-138629,139234-139294,140121-140335,142033-142479 401286 Minus147036-147318 ~ 401384 Minus58360-58545 401468 Plus13056-13482 401515 Plus29929-30126 401519 Plus157315-157950 401672 Plus128526-128704,130755-130860 35 401744 Plus14595-14751 401851 Minus146443-146664,147794-147971,148351-148480,148980-149111,149801-401866 Plus73126-73623 402240 Plus104382-104527,106136-106372 402359 Minus40403-41961 ~ 402585 Minus174893-175050,183210-183435 402788 Plus98273-101430 402802 Minus53242-53432 402812 Plus25026-25091,25844-25920 402828 Plus69071-69642 45 402835 Plus26961-27101 402838 Minus32589-32735,35478-35666 402842 Minus76355-76479 402895 Plus85537-85671,86379-86469 402964 Minus46624-46784 5~ 403137 Minus92349-92572,92958-93084,93579-93712,93949-94072,94591-94748,95214-95337 403237 Plus7271-7527 _ 403259 Plus4693-4857 403683 Plus217175-217446 403690 Minus78627-79583 55 403708 Minus134394-134812 403838 Plus19197-19502 403851 Plus22733-23007 403976 Plus24755-24969 404407 Minus48154-48499 60 404426 Plus77842-77954 404632 Plus45096-45229 404741 Plus143025-143467 404756 Plus82849-83627 404946 Plus134445-134750 65 405074 Plus44340-44559,44790-45059 405125 Plus137113-137814 405172 Plus153027-153262 405236 Minus151699-151915 405325 Minus25818-26380 405411 Minus17503-17778,18021-18290 405495 Minus72182-72373 405552 Plus 45199-45647 405601 Minus147835-147935,149220-149299 405685 Minus37956-38097 405777 Minus104773-105051 405856 Plus 101777-102043 1~ 405876 Plus 39694-40031 405932 Minus123525-123713 405934 Plus 159913-160605 406006 Minus42640-42776 406134 Plus 153291-153452 1 406189 Minus22007-22234 406422 Plus 163003-163311 406516 Minus128375-128449,128560-128784 406538 Plus 35196-35367,38229-38476,40080-40216,43522-43840 406554 Plus 106956-107121 2O 406577 Plus 11377-11509 TABLE 10: shows genes, including expression sequence tags differentially expressed in taxol resistant prostate tumor xenografts as compared to taxol sensitive prostate tumor xenografts. The genes are indicated as either being upregulated or downregulated during the induction of taxol resistance in sequential passages of the grafts.
Pkey: Unique Eos probeset identifier number 1~ ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title:Unigene gene title Eos: Internal Eos name F00-F14: passage number Pkey ExAccn UnigenelD UnigenTitle Eos fiesp.F00 F00 F02 F02 F05 F05 F07 F09 117921 Hs.47170 PM28UP 9 8 9 3220 3412216582 71111 N51002 LiprinA2 1 112971 Hs.4299 CNAldown2812673352702841501578389 4975 T17185 ESTs 290 126645 Hs.61635 PAA5down11110371 3467 3314 2 1 1 1 119018 Hs.179809 PAB2down841757909742704478426253175228238 N95796 ESTs 765 110844 Hs.167531 PAV7down1921471411231297365 5548 5484 N31952 ESTs 175 100654 Albumin, 605504728357445602187117127 HG2841-HT2969 A PMOi 117 Hs.75442 down 113 100655 Albumin, 65348668836838660617510195 115 HG284i-HT2970 A PM02down 97 Hs.75442 620 102076 Hs252437 PM03down941431901051078840 3431 4622 U09579 cydin-dep 101 102208 Hs.75442 PM04down424323518252296467188169143165t45 U22961 albumin 495 103739 -- mitochondrPM05down19060623037810621888 691926999 3~ 107036 Hs.15725 PM06down1241151881321116671 4970 3850 108242 - ESTs PMOldown2025213 2243 19310 101042118 108282 - solute PMOSdown5417873 10837 5324 1453 1534 AA065143 car 27 108679 - beta-1-gioPM09down8931292 8693891 74 118662359409 AA1i5963 680 656 108731 Hs.107476 1918525 601 323 7 14 1 1 AA126313 ATP syntha PMlOdown f0 110675 Hs.6598 PM11 3342372392312201191459364 56124 H89355 adrenergic down 115412 Hs.193552 PMl2down31628227134033411523810019683207 AA283804 ESTs 146 115844 Hs234607 PMl3down9394 15413291 2354 2376 1441 120588 Hs.16193 PMl4down15758 1411591273983 3537 i646 AA281591 ESTs 80 132349 Hs.181286 PMl5down21721415010612817785 5463 6656 Y00705 serine 146 pro 132888 Hs.5920 1501321781261395394 4867 4i80 AA490775 N-acetylma PMl6down 132967 Hs.61635 PMl7down20820321520518013265 6850 4863 133063 Hs.64065 PMiBdown148161150921084299 4265 29126 AA283085 ESTs 85 134374 Hs.8236 PMl9down2401942122311898912310795 6891 D62633 ESTs 230 135400 Hs.99915 PM20down16799 1781321012371 261221444 M23263 androgenr 36 4$

TABLE 11: shows genes, including expression sequence tags that are up-regulated in prostate tumor tissue compared to normal prostate tissue as analyzed using Affymetrix/Eos Hu01 GeneChip array. Shown are the ratios of "average" normal prostate to "average"
prostate cancer tissues.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title R1: Background subtracted normal prostate : prostate tumor tissue Pkey ExAccn Un'sgenelDUnigene Title Ri 101336L49169 Hs.75678 FBJ murine osteosarcoma viral 0.012 onoogene homolog B

1~ 130642M63438 Hs.156110Immunoglobulin kappavariabie iD-80.015 133512X01677 Hs.195188glyceraldehyde-3-phosphate dehydrogenase0.017 133436H44631 Hs.737 immediate early protein 0.017 129292X13810 Hs.1101 POU domain; class 2; transcription0.019 factor 2 100610HG2566-HT4792. Microtubule-Associated Protein 0.02 Tau, Alt. Splice, Exon 8 1$ 133448M34516 Hs.170116immunoglobulin lambda-like polypeptide0.021 125193W67577 Hs.84298 CD74 antigen (invariant polypeptide of major histocompatibility complex; class II antigen-associated)0.022 133456T49257 Hs.183704ubiquitin C . 0.022 134546AA459310 Hs.8518 Homo sapiens mRNA; cDNA DKFZp586L1722 (from clone DKFZp586L1722) 0.023 102131015085 Hs.1162 major histocompatibility complex;0.023 lass II; DM beta 101375M13560 Hs.84298 CD74 antigen (invariant polypeptide of major histocompatibiliiy complex; class II antigen-associated)0.023 100674HG3033-HT3194 Spliceosomal Protein Sap 62 0.024 2$ 134365832377 Hs.82240 syntaxin 3A 0.027 132335D60387 Hs.189885ESTs 0.027 110303H37901 Hs.32706 ESTs 0.028 131678N59162 Hs.30542 ESTs 0.028 116599D80046 Hs.250879ESTs 0.029 133769M17733 Hs.75968 thymosin; beta 4; X chromosome 0.029 107904AA026648 Hs.61389 ESTs 0.03 129427T80746 Hs.111334ferritin; light polypeptide 0.03 105987AA406631 Hs.110299mitogen-activated protein kinase 0.03 kinase 7 131466F03233 Hs.27189 ESTs 0.032 3$ 102859X00274 Hs.76807 Human HLA-DR alpha-chain mRNA 0.032 134626S82198 Hs.8709 caldecrin (serum calcium decreasing0.032 factor, elastase IV) 134170M63138 Hs.79572 cathepsin D (lysosomal aspartyl 0.033 protease) 131713X57809 Hs.181125immunoglobulin lambda gene cluster0.034 100748HG3517-HT3711 Alpha-1-Antitrypsin, 5' End 0.034 4~ 118769N74496 ESTs 0.034 111734825375 Hs.126916ESTs 0.036 109221AA192755 Hs.85840 ESTs; Weakly similar to stac [H.sapiens]0.036 133846AA480073 Hs.76719 U6 snRNA-associated Sm-like protein0.036 135281AA401575 Hs.97757 ESTs - 0.037 4$ 119073832894 Hs.45514 v-ets avian erythroblastosis virus0.037 E26 oncogene related 100760HG3576-HT3779 Major Histocompatibiliiy Complex,0.037 Class Ii Beta W52 101426M19483 Hs.25 ATP synthase; H+transprtng; mitochndrl0.038 F1 complex; beta polypept 129568AA428025 Hs.114360transforming growth factor beta-stimulated0.038 protein TSC-22 130900238468 Hs.21036 ESTs; Moderately similar to F259650.039 3 [H.sapiens]

133879M13829 Hs.77183 v-raf murine sarcoma 3611 viral 0.039 oncogene homolog 1 100627HG2702-HT2798 Serine/Threonine Kinase (Gb:125424)0.039 129424M55593 Hs.111301matrix metalloproteinase 2 (gelatinase A; 72kD gelatinase;

72kD type IV collagenase) 0.039 128652AA621245 Hs.103147ESTs; Weakly similar to similar 0.039 to SP:YR40_SACSU [C.elegans]

$$ 129979T72635 Hs.13956 ESTs 0.039 133468X03068 Hs.73931 major histocompaGbility complex; 0.04 lass It; DQ beta 1 102636067092 Human ataxia-telangiectasia locus protein (ATM) gene, axons 1a,1b, 2, 3 and 4, partial cds 0.04 129536M33493 Hs.184504tryptase; alpha 0.04 133599M64788 Hs.75151 RAP1; GTPase activating protein 0.041 102104012139 Human alphal (XI) collagen (COL11A1)0.041 gene, 5' region and axon 1 1313400Ø478305Hs.25817 Homo sapiens chromosome 19; cosmid 0.041 130446X79510 Hs.155693protein tyrosine phosphatase; non-receptor0.042 type 21 101352L77701 Hs.16297 COX17 (yeast) homolog; cytochrome 0.042 c oxidase assembly protein $ 1225930Ø453310Hs.128749alpha-methylacyl-CoA racemase 0.042 130181839552 Hs.151608Homo Sapiens done 23622 mRNA sequence0.042 134071114093 Hs.78950 branched chain keto acid dehydrogenase E1; alpha polypeptide (maple syrup urine disease) 0.442 1081290Ø053252Hs.185848ESTs; Weakly similar to !! ALU SUBFAMILY
J WARNING

1O ENTRY !! [H.sapiens] 0.00.3 130511L32137 Hs.1584 cartilage cligomeric matrix protein (pseudoachondroplasia;

epiphyseal dysplasia 1; multiple) 0.043 1333360Ø291456Hs.71190 ESTs 0.043 132982L02326 Hs.198118immunoglobulin lambda-Pike polypeptide0.044 15 1318800Ø047034Hs.33818 RecQ protein-like 5 0.044 130540035234 Hs.159534protein tyrosine phosphatase; receptor0.044 type; S

1334670Ø258595Hs.73931 major histocompatibility complex; 0.044 class II; DQ beta 1 101191L20688 Hs.83656 Rho GDP dissociation inhibitor (GDI)0.044 beta 101860M95610 Hs.37165 collagen; type IX; alpha 2 0.044 102799088898 Human endogenous retroviral H proteasefintegrase-derived mRNA, complete cds, and putative 0.044 envelope prot mRNA, partial cds 107200D20350 Hs.5628 ESTs 0.044 101166L14927 Hs2099 lipocalin 1 (protein migrating faster0.044 than albumin; tear prealbumin) 134289M54915 Hs.81170 pim-1 oncogene 0.044 25 1353290Ø436026Hs.98858 ESTs 0.044 124950T03786 Hs.15i531protein phosphatase 3 (tomverly 2B); catalytic subunit; beta isoform (calc!neurin A beta) 0.044 102919X12447 Hs.183760aldolase A; froctose-bisphosphate 0.044 100574HG2279-HT2375 Triosephosphate Isomerase 0.045 1312860Ø450092Hs.25300 Homo sap!ens Bones 24718 and 24825 0.045 mRNA sequence 102675072512 Human B-cell receptor assodated protein (hBAP) alternatively spliced mRNA, partial 3'0T8 0.045 131332850487 Hs.25717 ESTs 0.045 101634M57731 Hs.75765 GR02 oncogene 0.046 35 113118T47906 Hs.220512ESTs 0.046 124884877276 Hs.120911ESTs 0.046 130523W76097 Hs.214507ESTs 0.046 110244H26742 Hs.25367 ESTs; Weakly similar to ALR [H.sapiens]0.046 1319320Ø454980Hs.25601 chromodomain helicase DNA binding 0.046 protein 3 4O 132509H09751 Hs.5038 neuropathy target esterase 0.046 1333720Ø291139Hs.72242 ESTs 0.046 100817HG4011-HT4804 Dystrophin-Associated Glycoprotein,0.047 50 Kda, Alt. Splice 2 1067460Ø476436Hs.7991 ESTs 0.047 135401L14813 Hs.169271carboxyl ester lipase-like (bile 0.047 salt-stimulated lipase-like) 4$ 130479844163 Hs.12457 Homo Sapiens done 23770 mRNA sequence0.047 102589062015 Hs.8867 cysteine-rich; angiogenic inducer; 0.047 1215210Ø412165Hs.97358 EST 0.048 1353400Ø425137Hs.99093 Homo sapiens chromosome t9; cosmid 0.048 1323360Ø342422Hs.45073 ESTs 0.048 $O 1153680Ø282133Hs.88960 ESTs; Weakly similar to similar 0.048 to collagen [C.elegans]

101278L38487 Hs.110849estrogen-related receptor alpha 0.048 103284X80200 Hs.8375 TNF receptor-associated factor 4 0.048 100564HG2239-HT2324 Potassium Channel Protein.(Gb111585)0.048 133132240883 Hs.65588 ESTs; Weakly similar to dJ393P122 0.048 [H.sapiens]

55 1218110Ø424535Hs.98416 ESTs 0.048 1296130Ø279481Hs.238831ESTs; Weakly similar to collagen 0.049 alpha 1(XVIII) chain [M.musculus]

132468S79854 Hs.49322 deiodinase; iodothyronine; type 0.049 III

120111W95841 Hs.136031ESTs 0.049 103668283741 Hs.248174H2A histone family; member M 0.049 6O 130386F10874 Hs.234249mitogen-activated protein kinase 0.049 8 interacting protein 1 104275C02170 Hs.39387 ESTs; Weakly smlr to weak smlrity 0.049 to ribosomal prot L14 [C.elegans]

1063050Ø436146Hs.12828 ESTs 0.05 1164310Ø609878Hs.55289 ESTs; Weakly smir to 110 KD CELL 0.813 MEMBRANE GLYCOPROTEIN [H.sapiens]

1203390Ø206465Hs.256470EST 0.05 65 1144270Ø017063 ESTs; Highly similar to Mia-1 protein0.05 [H.sapiens]

118821N79070 Hs.94789 ESTs 0.05 118979N93798 Hs.43666 protein tyrosine phosphatase type 0.05 IVA; member 3 107495W78776 Hs.90375 ESTs 0.051 120240241732 Hs.66049 ESTs ~ 0.051 114331241309 Hs.12400 ESTs ' 0.051 130947840037 Hs.21506 ESTs 0.052 129242W81679 Hs.5174 ribosomal protein S17 0.052 131413AA482390 Hs.26510 ESTs; Modly smlr to vacuolar prot 0.052 sorting homolog r-vps33b [R.norvegicus]

112304854798 Hs.26239 ESTs 0.052 101416M17254 Hs.45514 v-ets avian erythroblastosis virus 0.052 E26 oncogene related 131201AA426304 Hs.24174 ESTs 0.052 101054K02405 Hs.73933 Human MHC lass II HLA-DO-beta mRNA 0.052 (D87 DOw2); complete cds 101306L41143 Hs.232069T-cell leukemia translocation altered0.053 gene 1O 129311T55087 yb45c08.r1 Stratagene fetal spleen (#937205) Homo sapiens cDNA

clone IMAGE:74126 5', mRNA sequenceØ053 129942095301 Hs.144442phospholipase A2; group X 0.053 119210893340 Hs.92995 ESTs 0.053 101046K01160 Accession not listed in Genbank 0.053 15 114086138266 Hs.12770 Homo sapiens PAC clone DJ0777023 0.053 from 7p14-p15 110171Hf9964 Hs.31709 ESTs 0.053 101004J04101 Hs.248109v-ets avian erylhroblastosis virus 0.053 E26 oncogene homolog 1 129715N58479 Hs.f 2126ESTs; Weakly similar to LRB [H.sapiens]0.053 101581M34996 Hs.198253major histocompaGbility complex; 0.053 class 1l; DO alpha 1 113285T66830 Hs.182712ESTs 0.053 127537AA569531 Hs.i62859ESTs 0.054 100813HG3995-HT4265 Cpg-Enriched Dna, Clone S19 0.054 101841M93107 Hs.76893 3-hydroxybutyrate dehydrogenase 0.054 (heart; mitocfrondrial) 135053877159 Hs.93678 ESTs 0.054 25 101419M17886 Hs.177592ribosomal protein; large; Pt 0.054 119724W69468 Hs.47622 ESTs 0.055 102673072509 Human alternatively spliced 88 (87)0.055 mRNA, partial sequence 129877AA248589 Hs.13094 ESTs; Weakly similar to ORF YGR101w0.055 [S.cerevisiae]

114788AA156737 Hs.103904EST 0.055 3O 123812AA620607 Hs.111591ESTs 0.055 117669N39237 Hs.44977 ESTs 0.055 123782AA610111 Hs.162695EST 0.055 102395041767 Hs.92208 a disintegrin and metalloproteinase0.055 domain 15 (metargidin) 133795M12529 Hs.f69401apolipoprotein E 0.055 123193AA489228 Hs.136956ESTs 0.056 ~

132595AA253369 Hs.f55742glyoxylate reductase/hydroxypyruvate0.056 reductase 104161AA456471 Hs.7724 KIAA0963 protein 0.056 115330AA281145 Hs.88827 ESTs 0.056 112893T08000 Hs.194684bassoon (presynapffc cytomatrix 0.056 protein) 4O 133475L29217 Hs.73987 CDC-like kinase 3 0.056 128699K03207 Hs.103972proline-rich protein BstNl subfamily0.056 102940X13956 Hs.24998 Hu 12S RNA induced by poly(rl); 0.056 poly(rC) and Newcastle disease virus 131299AA431464 Hs.25426 ESTs; Weakly similar to unknown 0.057 [H.sapiens]

102495051240 Hs.79356 Lysosomal-assoaated mulGspanning 0.057 membrane protein-5 45 129594870379 Hs.f 15396Human germline IgD chain gene; C-region;0.057 C-delta-1 domain 118593N69020 Hs.207689EST 0.057 126702054602 Hs2785 keratin 17 0.057 124386N27368 Hs.212414soma domain; immunoglobulin domain (1g); short basic domain;

seaeted; (semaphorin) 3E 0.057 130538M20786 Hs.159509alpha-2-plasmin inhibitor 0.057 114299240782 Hs.22920 similar to S68401 (cattle) glucose 0.057 induced gene 115604AA400378 Hs.49391 ESTs 0.057 106052AA416947 Hs.6382 ESTs; Highly similar to KIAA0612 0.057 protein [H.sapiens]

131730005681 Hs.31210 B-cell CLIJlymphoma 3 0.057 55 131285AA479498 Hs.25274 ESTs; Modly smlr to putative seven 0.058 pass Uansmembrane prot [H.sapiens]

129705X78706 Hs.12068 carnitine acetyltransferase 0.058 123175AA489010 Hs.178400ESTs 0.058 103592230644 Hs.123059chloride channel Kb 0.058 118196N59478 Hs.48396 ESTs; Moderately similar to tumor necrosis factor-alpha 6O -induced protein B12 [H.sapiens] 0.058 104886AA053348 Hs.144626growth differentiation factor 11 0.058 104250AF000575 Hs.105928leukocyte immunoglobulin-like receptor;
subfamily B (with TM

and ITIM domains); member 3 0.058 113301T67452 Hs.13104 EST 0.058 65 110441H50302 Hs.19845 ESTs; Highly smlr to prot phosphatase0.058 2A BR gamma subunit [H.sapiens]

125297239215 Hs.159409ESTs 0.058 135258AA292423 Hs.97272 ESTs; Weakly similar to dJ281 H8.2 0.058 [H.sapiens]

130633T92363 Hs.178703ESTs 0.058 112006842607 Hs.2224f hypothetical protein 0.058 130805012194 Hs.170238sodium channel; voltage-gated; type0.058 I; beta polypeptide 134907D80002 Hs.178292KIAA0180 protein 0.058 132619AA404565 Hs.53447 ESTs; Moderately similar to kinesin0.058 light chain 1 [M.musculus]

135115N35489 Hs.94653 neurochondrin 0.058 $ 100531HG1872-HT1907 Major Histocompatibility Complex, 0.058 Dg 124530N62256 Hs.102727EST 0.056 119960W87533 Hs.32699 ' ESTs; Moderately similar to LIV-10.058 protein [H.sapiens]

132793AA478999 Hs.56966 KIAA0906 protein 0.058 101076L04270 Hs.1116 (ymphotoxin beta receptor (TNFR 0.058 superfamily; member 3 1O 130655N92934 Hs.17409 cysteine-rich protein 1 (intestinal)0.058 134458AA192614 Hs.83577 cysteine and glydne-rich protein 0.058 3 (cardiac LIM protein) 105904AA401452 Hs.32060 ESTs 0.059 132878AA026793 Hs.58679 ESTs; Weakly similar to 4F2/CD98 0.059 light chain [M.musculus]

121828AA425166 Hs.98497 ESTs 0.059 15 133418076366 Hs.172727Treacher Collins-Franceschetti syndrome0.059 129317Nd6244 Hs.110373ESTs 0.059 130153D85815 Hs.15114 ras homolog gene family; member 0.059 D

124403N31745 Hs.102493ESTs 0.059 127683AA668123 Hs.134170ESTs 0.059 2O 129814W20070 Hs.168625KIAA0979 protein 0.059 131770D59682 Hs.31833 ESTs 0.06 117557N33920 Hs.44532 diubiquitin 0.06 103522Y105i4 H.sapiens mRNA for CD152 protein 0.06 ~

120029W91960 Hs.250640sequence-specific single-stranded-DNA-binding0.06 protein 25 102135015460 Hs.41691 activating transcription factor 0.06 B

123617AA609183 Hs.181131ESTs 0.06 112136846100 Hs.9739 ESTs 0.061 133725V00563 Hs.179543immunoglobulin mu 0.061 102069009196 Hs.82520 Hu 1.1 kb mRNA upregltd in reGnoic 0.061 add treated HL-60 neutrophilic cells 106555AA455000 Hs.16725 ESTs 0.061 123269AA491226 Hs.105280ESTs; Weakly similar to dJ963K232 0.061 [H.sapiens]

109088AAi66837 Hs.72620 DKFZP4341114protein 0.061 129399AA263028 Hs.111076malate dehydrogenase 2; NAD (mitochondrfal)0.061 129375W79850 Hs.11081 ESTs; Weakly similar to HPBRII-7 0.061 protein [H.sapiens]

35 135271AA397763 Hs.97562 ESTs 0.061 132958W90398 Hs.6147 KIAA1075 protein 0.061 129364AA477106 Hs.i 10757DNA segment on chromosome 21 (unique)0.061 2056 expressed sequence 123427AA598548 Hs.112471ESTs 0.061 105236AA219179 Hs.19105 translocase of inner mitochondrial 0.061 membrane 17 (yeast) homolog B

101012J04444 Hs.697 cytochrome o-1 0.062 134791L18983 Hs.89655 protein tyrosine phosphatase; receptor0.062 type; N

133700K01396 Hs.75621 protease inhibitor 1 (anti-elastase);0.062 alpha-1-antitrypsin 123887AA621065 Hs.112943ESTs 0.062 129363H05704 Hs.110746H sapiens HCR (a-helix coiled-coil 0.062 rod homologue) mRNA; complete cds 45 105719AA291644 Hs.36793 ESTs 0.062 124226H62396 Hs.190266ESTs 0.062 117437N27645 yw5e3.s1 Weizmann Olfactory Epithelium H sapiens d)NA done IMAGE:255676 3' smlr to contains 0.062 Ll.t3 Li repetitive element ;, mRNA seq 132741AA394133 Hs.55898 ESTs; Highly similar to OASIS protein0.062 [M.musculus]

50 134437M26041 Hs.198253major histocompaGbility complex; 0.062 doss II; DO alpha 1 107664AA010594 Hs.5326 ESTs; Moderately similar to pim-1 0.062 protein [H.sapiens]

120844AA349417 Hs.96917 ESTs 0.062 101574M34i82 Hs.158029protein kinase; cAMP-dependent; 0.062 catalytic; gamma 131219C00476 Hs.24395 small inducible cytokine subfamily 0.062 B (Cys-X-Cys); member 14 (BRAK) 55 103495Y09022 Hs.153591Not56 (D. melanogaster)-like protein0.062 129607AA404594 Hs.11607 ESTs 0.062 106467AA450040 Hs.154162ADP-ribosylation factor-like 2 0.062 128841T16358 Hs.106443ESTs 0.062 100515HGi723-HT1729 Macrophage Scavenger Receptor, AltØ062 Splice 2 119332T54095 ESTs; Weakly similar to !1 ALU SUBFAMILY0.062 J WARNING ENTRY!! [H.sapiens]

134516AA171939 Hs.23413 ESTs 0.062 135012X73608 Hs.93029 spardosteonectin; cwcv and kazal-like0.063 domains proteoglycan (testican) 103575226256 H.sapiens isoform 1 gene for L-type0.063 caldum channel, exon 1 115514AA297739 Hs.55609 ESTs; Weakly similar to ISOLEUCYL-TRNA
SYNTHETASE;

65 CYTOPLASMIC (H.sapiens] 0.063 103996AA321355 EST2393 Bone marrow Homo Sapiens 0.063 d)NA 5' end, mRNA sequence 110505H55992 Hs.20495 DKFZP434F011 protein 0.063 133912X62744 Hs.77522 major histocompaGbility complex; 0.063 doss II; DM alpha 129581M33600 Hs.180255major histocompatibility complex; 0.063 Bass II; DR beta 1 130139838280 Hs.150922 BCSi (yeast homology-like 0.064 105817AA397825 Hs.5307 synaptopodin 0.064 134658AA410617 Hs.178009 ESTs 0.064 100306D50495 Hs.80598 transcription elongation factor 0.064 A (S11); 2 100277D42053 Hs.75890 site-1 protease (subtilisin-like;
sterol-regulated; cleaves sterol regulatory element binding proteins) 0.064 133116D61259 Hs.6529 ESTs 0.064 134909AA521488 Hs.90998 KIAA0128 protein 0.064 130319X74794 Hs.154443 minichromosome maintenance deficient0.064 (S. cerevisiae) 4 1O 132057AA102489 Hs.173484 ESTs 0.064 108334AA070473 zm7c8.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA

clone IMAGE:5399 3', mRNA sequence 0.064 129763F10815 Hs.12373 KIAA0422 protein 0.064 135112T67464 Hs.94617 ESTs; Weakly similar to predicted 0.064 using Genefinder [C.elegans]

15 122269AA436856 Hs.98910 ESTs 0.064 133082AA457129 Hs.6455 RuvB (E coli homology-like 2 0.064 113213T58607 ya94a02.s1 Stratagene placenta (#937225) Homo sapiens cDNA clone IMAGE:69290 3', mRNA sequence. 0.065 106228AA429290 Hs.17719 ESTs 0.065 130192Y12661 Hs.i71014 VGF nerve growth factor inducibte 0.065 104894AA054087 Hs.18858 phospholipase A2; group IVC (cytosolic;0.065 calcium-independent) 103508Y10141 H.sapiens DATi gene, partial, VNTR 0.065 128474040671 Hs.100299 ligase III; DNA; ATP-dependent - 0.065 134012AA417821 Hs.237924 ESTs; Highly similar to CGI-69 protein0.065 [H.sapiens]

2$ 134536AA457735 Hs.850 IMP (inosine monophosphate) dehydrogenase0.065 111714823146 Hs.23466 ESTs 0.065 110521H57060 Hs.108268 ESTs 0,065 103282X80198 Hs.77628 steroidogenic acute regulatory protein0.065 related 113921W80730 Hs.28355 ESTs 0.065 129331N93465 Hs.110453 ESTs; Highly similar to CGI-38 protein0.065 [H.sapiens]

111316N74597 Hs.180535 ESTs; Weakly similar to mitogen 0.065 inducible gene mtg-2 [H.sapiens]

135138AA036794 Hs.95196 ESTs; Weakly similar to T20B12.3 0.065 [C.elegans]

107289T10792 Hs.172098 ESTs 0.065 121405AA406083 Hs.98007 ESTs 0.065 35 124965T16275 Hs.106359 ESTs 0.065 106595AA456933 Hs.174481 ESTs 0.066 100106AF015910 Homo sapiens unknown protein mRNA, 0.066 partial cds 134715AA282757 Hs.89040 prepronoaceptin 0.066 135367AA480109 Hs.9963 TYRO protein tyrosine kinase binding0.066 protein 111533808548 Hs.251651 EST 0.066 128509853109 Hs247362 dimethylarginine dimethylaminohydrolase0.066 101030J05037 Hs.76751 serine dehydratase 0.066 102753080226 Human gamma-aminobutyric add transaminase0.067 mRNA, partial cds 126991831652 Hs.821 biglycan 0.067 4-5109583F02322 Hs26135 ESTs 0.067 119241T12559 Hs.221382 ESTs 0.067 130569AA156597 Hs256441 EST; Moderately similar to CGI-136 0.067 protein [H.sapiens]

112926T10316 Hs.4302 ESTs 0.067 120495AA256073 Hs.190626 ESTs 0.067 130931AA278412 Hs21346 ESTs; Weakly similar to F42C5.7 0.067 gene product [C.elegans]

129982M87789 Hs.140 immunoglobulin gamma 3 (Gm marker) 0.067 133832H03387 Hs.241305 estrogen-responsive B box protein 0.067 110697H93721 Hs.20798 ESTs - 0.067 121183AA400138 Hs.97703 ESTs 0.067 $5 130953012707 Hs.2157 Wiskott-Aldrich syndrome (ecezema-thrombocytopenia)0.067 102218024183 Hs.75160 phosphofructokinase; muscle 0.067 114181239079 Hs.8021 KIAA1058 protein 0.067 116581D51287 Hs.82148 ribosomal protein S12 0.067 132498T87708 Hs.50098 ESTs 0.068 6O 103788AA096014 Hs.9527 ESTs; Highly similar to HSPC013 0.068 [H.sapiens]

102459048936 Human amiloride-sensitive epithelial sodium channel gamma subunit mRNA, 5' end, partial cds 0.068 100373D79999 Hs.77225 ADP-ribosyltransferase (NAD+; poly 0.068 (ADP-ribose) polymerase)-like 1 132717AA203321 Hs.151696 DKFZP727G051 protein 0.068 65 128863D87462 Hs.106674 BRCA1 associated protein-1 (ubiquitin0.068 carboxy-terminal hydrolase) 115193AA262029 Hs.88218 ESTs 0.068 124558N66046 Hs.141605 ESTs 0.069 117225N20392 Hs.42846 ESTs 0.069 110665H83380 Hs.32757 ESTs 0.069 132905070663 Hs.182965Kruppel-like factor 4 (gut) 0.069 105778AA348910 Hs.153299DOM-3 (C. elegans) homolog Z 0.069 134770872079 Hs.89575 CD79B antigen (immunoglobulin-associated0.069 beha) 123097AA485869 Hs.105671ESTs 0.069 100750HG3523-HT4899 Proto-Oncogene C-Myc, Alt. Splice 0.069 3, Orf 114 125091T91518 ye20f05.s1 Stratagene lung (#937210) H Sapiens cDNA clone IMAGE:

3' similar to contains Alu repetitive element;contains MER12 repetitNe element;

mRNA sequence. 0.069 100756HG3565-HT3768 Zinc Finger Protein (Gb:M88357) 0.069 113483T87768 Hs.16439 ESTs 0.069 101119L09708 Hs.2253 complementcomponent2 0.069 102286031628 Hs.12503 interleukin 15 receptor; alpha 0.07 135349D83174 Hs.9930 collagen-binding protein 2 (colligen0.07 2) 100991J03764 Hs.82085 plasminogen activator inhibitor, 0.07 type I

1 133675AA443720 Hs.7551 ESTs; Weakly similar to T25G3.1 0.07 J~ [C.elegans]

105422AA251014 Hs.12210 ESTs 0.07 102932X13334 Hs.75627 CD14 antigen 0.07 119147858878 Hs.65739 ESTs 0.07 104900AA055048 Hs.180481ESTs; Weakly similar to ACROSIN 0.07 PRECURSOR [H.sapiens]

ZO 133185AA481404 Hs.6686 ESTs 0.07 115496AA290674 Hs.71819 eukaryotic translation initiation 0.07 factor 4E binding protein 1 121005AA398332 Hs.97613 ESTs 0.07 124869869088 Hs.28728 ESTs; Weakly similar to F55A12.9 0.071 [C.elegans] -129154N23673 Hs.108969mannosidase; alpha; class 2B; mem!~er0.071 ZJ~112161848295 ESTs; Wkly smlr to !! ALU SUBFAMILY0.071 J WARNING ENTRY !! [H.sapiens]

125251W87486 Hs.14i464ESTs 0.071 134298J00116 Hs.81343 collagen; type II; alpha 1 (primary osteoarthmtis; spondyloepiphyseal dysplasia; congenital) 0.071 119745W70264 Hs.58093 ESTs 0.071 131306AA232686 Hs.25489 ESTs 0.071 107776AA018820 Hs.221147ESTs 0.071 134271AA199630 Hs.i84456ESTs; Wkly smlr to !! ALU SUBFAMILY0.071 SX WARNING ENTRY !! [H.sapiens]

101798M85220 Accession not listed in Genbank 0.071 135402S76942 Hs.99922 dopamine receptor D4 0.071 3$ 118742N74052 Hs.50424 EST 0.071 131867N64656 Hs.3353 Homo sapiens clone 24940 mRNA sequence0.071 102923X12517 Hs.1063 small nuclear ribonucleoprotein 0.072 polypeptide C

100775HG371-HT26388 Mucin 1, Epithelial, Alt. Splice 0.072 111020N54361 Hs.185726ESTs 0.072 134224X80822 Hs.163593ribosomal protein Ll8a 0.072 124059F13673 Hs.99769 ESTs 0.072 133972AA160743 Hs.78019 Homo sapiens clone 24432 mRNA sequence0.072 129681AA436009 Hs.178186ESTs; Weakly similar to WASP-family0.072 protein [H.sapiens]

103065X58399 Hs.8122i Human L2-9 transcript of unreacranged0.072 immunoglobulin V(H}5 pseudogene 4$ 124966T19271 Hs.155560calnexin 0.072 112270853021 Hs.203358ESTs 0.072 116704F10183 Hs.66140 EST 0.072 129890M13699 Hs.111461ceruloplasmin (ferroxidase) 0.072 127345AA972008 Hs.i66253ESTs; Highly similar to KIAA0476 0.072 protein [H.sapiens]

112436863090 Hs.28391 ESTs 0.072 114531AA053033 Hs.203330ESTs 0.072 135122H99080 Hs.94814 ESTs 0.072 103934AA281338 Hs.134200Homo Sapiens mRNA; cDNA DKFZp564C1860.072 (from clone DKFZp564C186) 109363AA215369 Hs.185764ESTs; Weakly similar to hypothetical0.072 protein [H.sapiens]

112647883329 Hs.33403 ESTs 0.073 127083244079 Hs.91608 otoferlin 0.073 133027AA402624 Hs.63236 synuclein; gamma (breast cancer-specific0.073 protein 1) .

122066AA432121 Hs.250986EST 0.073 110405H47542 Hs.33962 ESTs 0.073 128697A8002344 Hs.103915KIAA0346 protein 0.073 112221850380 Hs.25670 ESTs 0.073 100478HG1067-HT1067 Mucin (Gb:M22406) 0.073 115598AA400129 Hs.65735 ESTs 0.073 132491AA227137 Hs.4984 KIAA0828 protein 0.073 65 101655M60299 Human alpha-1 collagen type II gene,0.073 axons 1, 2 and 3 106018AA411887 Hs.34737 ESTs 0.073 129683W05348 Hs.158196DKFZPd348103 protein 0.073 134137F10045 Hs.79347 KIAA0211 gene product 0.073 114008W89i28 Hs.19872 ESTs 0.073 107653AA010210 Hs.47041 ESTs 0.073 104798AA029462 Hs.17235 ESTs 0.073 134082Li6991 Hs.79006 deoxythymidylate kinase 0.073 119180880413 Hs.92520 ESTs 0.073 107741AA016982 Hs.64341 ESTs 0.073 133683AA335223 Hs.75558 pepsinogen 5; group I (pepsinogen 0.073 A) 111694822035 Hs.23331 ESTs 0.073 120764AA338729 Hs.133096ESTs 0.073 119389T88826 Hs.90973 ESTs 0.074 100929HG688-HT688 Major Histocompatibility Complex, 0.074 Class Ii, Dr Beta 2 (Gb:X65561 ) 119388T88798 plasminogen activator inhibitor; 0.074 type I

133019AF009674 Hs.184d34.axin 0.074 105185AAi91495 Hs.189937ESTs 0.074 133413S72043 Hs.73133 metallothionein 3 (growth inhibitory0.074 factor (neurotrophic)) 101017J04599 Hs.821 biglycan 0.074 132865K02765 Hs.251972complementcamponent3 0.074 110882N36001 Hs.17348 ESTs; Wkly smlr to !! ALU SUBFAMILY0.074 SQ WARNING ENTRY !! [H.sapiens]

129197T90303 Hs.109308ESTs; Wkly smlr to leucine-rich 0.074 glioma-inactivated prot precursor [H.sapiens]

101184L19871 Hs.460 activating transcription factor 0.075 134910AA431320 Hs.9100 ESTs 0.075 119411T96621 Hs.203656EST 0.075 102000U01824 Hs.380 solute tamer family 1 (glial high 0.075 affinity glutamate transporter);
member 2 114691AA121893 Hs.103779ESTs; Weakly similar to envelope 0.075 protein [H.sapiens]

134179U53204 Hs.79706 plectin 1; intermediate filament 0.075 binding protein; 500kD

134503U34880 Hs.84183 diptheria toxin resistance protein required for diphthamide biosynthesis (Saccharomyces)-like 0.075 129719N66396 Hs.i67766ESTs; Moderately similar to Pro-a2(XI)0.075 [H.sap!ens]

113916W80464 Hs.31928 ESTs; Wkly smlr to alternatively 0.075 spliced product using exon 13A
[H.sapiens]

113897W73926 Hs.4947 ESTs 0.075 129697800841 Hs.172069DKFZP434C212 protein 0.075 112078844155 Hs.112218ESTs 0.075 121980AA429886 Hs.110407ESTs; Weakly similar to coded for 0.075 by C. elegans cDNA yk173c12.5 [C.elegans]

100898HG4638-HT5050 Spliceosomal Protein Sap 49 0.075 121626AA416974 Hs.98174 ESTs 0.075 3$ 133670AA243416 Hs.75470 hypothetical protein; expressed 0.075 in osteoblast 131879AA017t61 Hs.33792 ESTs 0.075 100254D38037 Hs.77643 FK506-binding protein 1B (12.6 kD) 0.075 133194AA291726 Hs.67201 ESTs 0.075 106081AA418394 Hs.25354 ESTs 0.075 115544AA351433 Hs.66187 Homo sapiens clone 23700 mRNA sequence0.076 119955W87460 Hs.58989 ESTs 0.076 104407H61361 Hs.102171immunoglobulin superfamily containing0.076 leucine-rich repeat 135019X58431 Hs.98428 Human Hox22 gene for a homeobox 0.076 protein 114815AA161488 Hs.103931DKFZP434B0335 protein 0.076 119471W31352 Hs.55445 ESTs 0.076 117788N48292 Hs.46849 ESTs 0.076 119406T95064 Hs.193771EST 0.076 130777861742 Hs256554 ESTs 0.076 130494L13197 Hs.75874 pregnancy-assoaated plasma protein 0.076 A

$0 104107AA424111 Hs.12598 T-cell lymphoma invasion and metastasis0.076 121483AA411981 Hs.25274 ESTs; Modly smlr to putative seven 0.076 pass transmembrane prot [H.sapiens]

104451M13299 Hs.102119blue cane pigment 0.076 118027N52770 Hs.75968 thymosin; beta 4; X chromosome 0.076 109419AA227560 Hs.86987 receptor-interacting swine-threonine0.076 kinase 3 55 115783AA424487 Hs.72289 ESTs; Weakly similar to LIV-1 protein0.076 [H.sapiens]

110585H62223 Hs.133526ESTs; Wkly smlr to 11!ALU SUBFAMILY0.076 SBi WARNING ENTRY !!![H.sap!ens]

123165AA488863 Hs.105216ESTs; Weakly smlr to !!ALU SUBFAMILY0.077 J WARNING ENTRY !! [H.sapiens]

103966AA303166 Hs.127270ESTs 0.077 109549F01528 Hs.21192 Homo sapiens clone 25155 mRNA sequence0.077 60 106730AA465520 Hs.22313 ESTs 0.077 120310AA193676 Hs.118926DKFZP586K0919 protein 0.077 104078AA402801 Hs.222010ESTs 0.077 117624N35978 Hs.82364 ESTs 0.077 112421862441 Hs.23127 ESTs 0.077 65 106958AA497026 Hs.22059 ESTs 0.077 129984W92811 Hs.183927ESTs; Weakly similar to !! ALU SUBFAMILY0.077 J WARNING ENTRY !! [H.sapiens]

122044AA431456 Hs.98736 EST 0.077 123280AA491285 Hs.17514dESTs 0.077 115710AA412535 Hs.55235 sphingomyelin phosphodiesterase 2; neutra I membrane (neutral sphingomyelinase)0.077 134129D87444 Hs.79305 KIAA0255 gene product 0.077 129321AA224502 Hs.206501Homo sapiens done 643 unknown mRNA; 0.078 complete sequence 130513AA460257 Hs.15866 ESTs 0.078 100996J03909 Hs.14623 interferon; gamma-inducible protein 0.078 128358A1095718 Hs.135015ESTs 0.078 128544859352 Hs.119273KIAA0296 gene product 0.078 106040AA412681 Hs.125139ESTs 0.078 106495AA452113 Hs.32454 ESTs; Moderately similar to KIAA05440.078 protein [H.sapiens]

1~ 131833840899 Hs.32973 glycine receptor; beta 0.078 119219897176 Hs.110783ESTs 0.078 135415X60655 Hs.99967 even-skipped homeo box 1 (homolog 0.078 of Drosophila) 109457AA232646 Hs.68061 ESTs; Weakly similar to sphingosine 0.078 k!nase [M.musculusj 117137H96670 Hs.42221 ESTs 0.078 15 107094AA609614 Hs.5241 ESTs 0.078 130165T90529 Hs.251613EST 0.078 124072H05252 Hs.101637EST; Weakly similar to hypothetical 0.078 protein [H.sapiensj 126151AA324743 Hs.40808 ESTs 0.078 119035801779 Hs.7740 ESTs ' 0.078 110157H18987 Hs.169731ESTs 0.078 128515AA149044 Hs.10086 ESTs; Highly similar to HYPOTHETICAL0.078 PROTEIN KIAA0195 [H.sapiensj 133069094836 Hs.6430 protein with polyglutamine repeat 0.078 112209849644 Hs.24865 ESTs ' 0.078 133361828279 Hs.71848 Human done 23548 mRNA sequence 0.078 25 134714089922 Hs.890 lymphotoxin beta (TNF superfamily; 0.078 member 3) 129905T8619fi Hs.132875ESTs; Weakly similar to predicted 0.079 using Genefinder [C.elegans]

120421AA236166 Hs.132957ESTs; Weakly similar to chondromodulin-I0.079 precursor [H.sapiens]

100885HG4490-HT4876 Proline-Rich Protein Prb4, Allele 0.079 102789086759 Hs.158336netrin 2 (chicken)-like ' 0.079 120139239273 Hs.77876 Human DNA from chromosome 19-spedfic0.079 cosmid 830923; genomic sequence 135238076343 Hs.96970 Human liver GABA transport protein 0.079 mRNA; 3' end 129618N54845 Hs.173030ESTs 0.079 132960AA609742 Hs.6150 KIAA0521 protein 0.079 108751AA127063 Hs.203717ESTs 0.079 35 134060D42039 Hs.78871 KIAA0081 protein 0.079 111338N79778 Hs.35094 extracellular matrix protein 2; female0.079 organ and adipocyte specific 112345856880 Hs.26563 ESTs 0.079 126456W00881 za56d02.r1 Soares fetal liver spleen 1 NFLS Homo sapiens d7NA clone IMAGE296547 5', mRNA sequence. 0.079 4O 128937239939 Hs.10726 ESTs 0.079 103485Y08409 Hs.248415thyroid hormone responsive SPOT14 0.079 (rat) homolog 111202N68280 Hs.107922ESTs 0.079 132625AA429890 Hs.166066dsplatin resistance associated 0.079 103434X98085 Hs.54433 tenasdn R (restrictin; janusin) 0.079 45 102616065581 Hs.159191rfbosomal protein L3-like 0.079 102667070867 Hs.83974 solute carrier family 21 (prostaglandin0.079 transporter); member 2 111422801127 Hs.19104 ESTs 0.079 101411M16938 Hs.820 homeo box C6 113267T65058 Hs.12725 ESTs; Weakly similar to !! ALU SUBFAMILY0.08 J WARNING ENTRY !1 [H.sapiens]

103559219585 Hs.75774 thrombospondin 4 131588AA258613 Hs.29189 KIAA1021 protein 107821AA020991 Hs.172856ESTs 134278H82839 Hs.81001 ESTs; Weakly similar to D113.6 [C.elegansj0.08 120893AA369800 Hs.97058 EST; Highly similar to CMP-N-acetydneuraminic0.08 add hydroxylase [H.sapiens]

55 108786AA128999 zo8f12.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens d)NA done IMAGE:567119 3', mRNA sequence0.08 106890AA489245 Hs.88500 KIAA1066 protein; JSAP1 homolog (mouse);0.08 JIP3 homolog (mouse) 119760W72267 Hs.58219 ESTs 132999Y00787 Hs.624 interleukin 8 129156AA028195 Hs.108973dolichyl-phosphate mannosyltransferase0.08 polypeptide 2; regulatory subunit 121171AA400008 Hs.i61814ESTs 103864AA207264 Hs.181077ESTs; Weakly similar to Miller-Dieker0.08 lissencephaly gene [H.sapiens]

128591AA255537 Hs.102057ESTs; Weakly similar to O-linked 0.08 GIcNAc transferase [H.sapiens]

122172AA435753 Hs.161854EST

65 112802897647 Hs.174855EST

107723AA015967 Hs.60680 EST

113011T23737 Hs.1600 chaperonin containing TCP1; subunit 0.081 5 (epsilon) 131279AA089853 Hs25197 STIP1 homology and U-Box containing 0.081 protein 1 103190X70083 Hs.58414 filamin C; gamma (actin-binding protein-280)0.081 103956AA292411 Hs.233348ESTs 0.081 112706889828 Hs.138493ESTs 0.081 126126M85370 EST01884 Fetal brain, Stratagene (cat#936206) Homo sapiens d)NA

done HFBCH10, mRNA sequence. 0.081 S 130094H43286 Hs.167017gamma-am!nobutyric add (GABA) B 0.081 receptor;1 100800HG39d5-HT4215 Phospholipid Transfer Protein 0.081 108675AA115240 Hs.61816 ESTs 0.081 129420AA234259 Hs.99816 ESTs 0.081 129666M77349 Hs.118787transforming growth factor; beta-induced;0.081 68kD

101645~M59807 Hs.943 natural killer cell transcript 4 0.081 130536T17045 Hs.159492spastic ataxia of Charlevoix-Saguenay0.081 (sacsin) 107732AA016181 Hs.59752 ESTs 0.081 123071AA482593 Hs.104285ESTs 0.081 113537T90457 Hs.191293ESTs 0.081 1S 101250L34060 Hs.79133 cadherin8 0.081 122521AA449433 Hs.149227ESTs; Weakly similar to PROLINE-RICH0.081 PROTEIN MP-3 [M.musculus]

133914N32811 Hs.77542 ESTs 0.061 102038005659 Hs.477 hydroxysteroid (17-beta) dehydrogenase0.081 110336H40338 Hs.174094ESTs; Weakly similarto !! ALU SUBFAMILY0.081 J WARNING ENTRY !! [H.sapiensj 118637N70274 Hs.49822 ESTs 0.081 117966N51589 Hs.94012 ESTs 0.082 104424H87671 Hs.182320ESTs; Weakly similar to Mouse 19.5 0.082 mRNA; complete cds [M.musculusj 100361D78361 Hs.125078Human mRNA for ornithine decarboxylase0.082 antizyme; ORF 1 and ORF 2 112974T17291 Hs.101174microtubule-associated protein tau 0.082 2S 132832D63482 Hs.57734 KIAA0148 gene product 0.082 132039239489 Hs.3781 Homo sapiens BAC clone RG118D07 0.082 from 7q31 113272T65383 Hs.12807 ESTs 0.082 104924AA058532 Hs.28774 ESTs . 0.082 111061N58054 Hs.36859 ESTs 0.082 129269845977 Hs.163593ribosomal protein Ll8a 0.082 102453048437 Hs.74565 amyloid beta (A4) precursor-like 0.082 protein 1 126204A1080388 Hs.134296ESTs 0.082 116615D80666 Hs.45203 ESTs 0.062 128856AA219552 Hs.204144ESTs; Modly smlr to tumor neaos!s 0.082 factor alpha-induced prot B12 [H.sapiens]

112776895850 Hs.34494 ESTs 0.082 105494AA256273 Hs.29288 Homo sapiens mRNA; d)NA DKFZp434P1740.082 (from done DKFZp434P174) 117000H84718 Hs.112236ESTs; Weakly similar to repressor 0.082 protein [H.sapiens]

112656885260 Hs.133151transient receptor potential channel0.082 128963J03890 Hs.1074 surfactant; pulmonary-assoctated 0.083 protein C

116957H79292 Hs.39960 ESTs 0.083 101057K03430 Human complement C1q B-chain gene, 0.083 axon A+1 121948AA429452 Hs.98582 ESTs 0.083 130822M80647 Hs2001 thromboxane A synthase 1 (platelet;0.083 cytochrome P450; subfamily ~

122743AAd58674 Hs.99478 EST 0.083 114569AA063316 zm2d1.s1 Stratagene corneal stroma (#937222) Homo Sapiens d)NA done !MAGE:5129473'similartoTR:E198281 REDUCTASE ;contains Alu repetitive 0.083 element;, mRNA sequence 132270070671 Hs.43509 ataxin 2 related protein 0.083 108126AA052951 Hs.47413 ESTs 0.083 SO 102880X04325 Hs.2679 gap junction protein; beta 1; 32kD
(connexin 32; Charcot-Marie-Tooth neuropathy; X-linked) 0.083 115365AA282089 Hs.88599 ESTs 0.083 114529AA052980 Hs.206704ESTs - 0.083 135017AA249586 Hs.9315 ESTs; Weakly similar to NEURONAL
OLFACTOMEDIN-RELATED

S ER LOCALIZED PROTEIN [H.sapiens] 0.083 S

123776AA610071 Hs.112813ESTs 0.083 114454AA021091 Hs.226208ESTs 0.083 101246L33799 Hs.202097procollagen C-endopeptidase enhancer0.083 107366078310 Hs.13501 pescadillo (zebrafish) homolog 1; 0.083 containing BRCT domain f)0132779T89601 Hs.95497 ESTs; Weakly similar to GLUCOSE
TRANSPORTER TYPE 5;

SMALL INTESTINE [H.sapiens] 0.083 129709AA112209 Hs.1209 aryl-Coenzyme A dehydrogenase; long0.083 chain 115244AA278767 Hs.914 Human mRNA for SB classll histocompatibility0.083 antigen alpha-chain 123253AA490878 Hs.111334ferritin; light polypeptide 0.083 6S 128469T23724 Hs.258677EST 0.083 132220AA431847 Hs.42409 ESTs; Highly similar to CGI-146 0.083 protein [H.sapiens]

111664Ri7939 Hs.22344 ESTs 0.083 102354038268 Human cytochrome b pseudogene, partial0.084 cds 112828898774 Hs.194338ESTs 0.084 110410H47868 Hs.34024 ESTs 0.084 102620066052 Human clone W2-6 mRNA from chromosome0.064 X

102550058087 Hs.14541 cullin 1 0.084 108417AA075716 zm89e5.s1 Stratagene ovarian cancer (#937219) H Sapiens cDNA clone $ IMAGE:54512 3' similar to gb:X14723 CLUSTERIN PRECURSOR

(HUMAN);, mRNA sequence 0.084 113299T67285 Hs.13089 ESTs 0.084 117869N49947 Hs.46990 ESTs 0.084 113734T98484 Hs.18377 EST 0.084 133325000424 Hs.7101 periodontal ligament fibroblast 0.064 protein 123368AA505022 Hs.124838ESTs 0.084 101615M55153 Hs.8265 transglutaminase 2 (C polypeptide;
protein-glutamine -gamma-glutamyltransferase) 0.064 119352T65972 Hs.193365ESTs; Moderately similar to altemat'rvely spliced product 1$ using exon 13A [H.sapiensj 0.084 123628AA620686 Hs.112884EST 0.084 103611238133 Hs.113973myosin; heavy polypeptide 8; skeletal0.064 muscle; perfnatal 131289AA485697 Hs.25334 ESTs; Weakly similar to ION CHANNEL
HOMOLOG RIC

PRECURSOR [M.musculus] 0.084 128678T15896 Hs.103535ESTs 0.084 130814AA256695 Hs.19813 ESTs 0.084 133391X57579 Hs.727 inhibin; beta A (activ!n A; activ!n0.064 AB alpha polypep6de) 129322AA437153 Hs.110407ESTs; Weakly similar to coded for 0.084 by C. elegans~cDNA yk173c12.5 [C.elegans]

109284AA196995 Hs.86092 ESTs 0.084 116689F09222 Hs.66099 ESTs 0.085 100545HG2147-HT2217 Mucin 3, Intestinal (Gb:M55405) 0.085 102634066711 Hs.77667 lymphocyte antigen 6 complex; locus0.085 E

111735825389 Hs.23856 ESTs; Weakly similar to FAST kinase0.085 [H.sapiens]

105181AA190676 Hs.10974 ESTs; Moderately similar to unknown0.085 [R.norvegicus]

122661AA455350 Hs.99401 EST 0.085 114543AA056121 Hs.158419ESTs 0.085 133597AA425908 Hs.75139 partner of RACi (arfaptin 2) 0.085 121064AA398647 Hs.97406 ESTs 0.065 122231AA436369 Hs.197728ESTs; Weakly similar to ZINC FINGER0.065 PROTEIN 135 [H.sapiensj 3$ 100309D50550 Hs.95659 lethal giant larvae (Drosophila) 0.085 homolog 1 101727M73481 Hs.73883 gastrin-releasing peptide receptor 0.085 131226AA165400 Hs.24476 ESTs 0.085 133580AA095041 Hs.181073ESTs 0.085 102792087964 Hs.227576GTP binding protein 1 0.085 104976AA086480 Hs.183669ESTs; Weakly similar to !! ALU SUBFAMILY0.065 J WARNING ENTRY !! [H.sapiens]

120865AA350631 Hs.96963 EST 0.065 106080AA418046 Hs.35124 ESTs 0.085 128571AA416619 Hs.101661ESTs 0.085 101838M92934 Hs.75511 connective tissue growth factor 0.085 4$ 128514H84261 Hs.1008d3ESTs; Wealdy similar to similar 0.065 to GTP-binding protein [C.elegans]

123099AA485931 Hs.79 aminoacylase 1 0.085 134067Y08200 Hs.78920 Rab geranylgeranyltransferase; alpha0.085 subunft 116967H80336 Hs.40124 EST 0.085 110053H12586 Hs.89563 nuclear cap binding protein 1; 80kD0.085 $0 114395AA007313 Hs.110155ESTs 0.085 107465W44681 Hs251385 marine retrovirus integration site 0.085 1 homolog 101963S85655 Hs.75323 prohibitin 0.085 112544870948 Hs.29153 ESTs - 0.086 111423801165 Hs.188507ESTs 0.086 $$ 127918AA806043 Hs.115396Human germline IgD chain gene; C-region;0.086 ' C-delta-1 domain 107300T40348 Hs.90488 ESTs 0.086 134947851194 yj71 a08.r1 Soares breast 2NbHBst Homo sap!ens cDNA clone IMAGE:154166 5' similar to gb:L11284 DUAL SPECIFICITY
MITOGEN-ACTIVATED PROTEIN

KINASE KINASE 1 (HUMAN);, mRNA sequenceØ066 60 124579N68345 Hs.127179ESTs; Weakly similar to TERATOCARCINOMA-DERIVED
GROWTH

FACTOR 1 [H.sapiens] 0.086 130471268280 Hs.183706adduan 1 (alpha) 0.086 116596D60755 Hs.92955 ESTs 0.086 105069AA136345 Hs.23617 ESTs; Weakly similar to ZFOC1 gene 0.086 product [H.sapiens]

f 102491051010 Human nicoGnamide N-methyltransferase0.086 $ gene, exon 1 and 5' franking region 130069AA055896 Hs.146428collagen; type V; alpha 1 0.066 130234AA280413 Hs.157441spleen focus forming virus (SFFV) 0.066 proviral integration oncogene spil 120540AA262992 Hs.96417 ESTs 0.086 122508AA449221 Hs.20432 ESTs 0.086 128054AI205718 Hs.i25416ESTs 0.086 133020AA053248 Hs.i85182ESTs; Highly similar to 40S RIBOSOMAL0.086 PROTEIN S10 [H.sapiens]

130056AA017356 Hs.171900armadillo repeat gene deletes in 0.086 velocardiofacial syndrome 130504048865 Hs.i58323CCAATIenhancerbinding protein (C/EBP);0.086 epsilon $ 133978W73859 Hs.78061 transcriptionfactor2l 0.086 105265AA227941 Hs.26088 ESTs 0.086 133035T15965 Hs.6333 ESTs 0.086 100768HG3636-HT3846 Myosin, Heavy Polypeptide 9, Non-Muscle0.086 129338T56800 Hs.47274 Homo sapiens mRNA; cDNA DKFZp564Bi760.086 (from clone DKFZp564B176) 132789W23761 Hs.56876 ESTs 0.086 116099AA456309 Hs.58831 regulator of Fas-induced apoptosis0.086 100721HG3355-HT3532 Peroxisome Proliferator Activated 0.087 Receptor (6b230972) 112569873150 Hs.75270 GTP-binding protein homologous 0.067 to Saccharomyces cerevisiae SEC4 130645AA020942 Hs.17200 STAM-like protein containing SH3 0.087 and ITAM domains 2 1$ 100751HG3527-HT3721 Luteinizing Hormone, Beta Subunit 0.087 134550M27161 Hs.85258 CD8 antigen; alpha polypepGde (p32)0.087 130885AA338646 Hs20912 adenomatous polyposis coli like 0.067 101446M21302 Hs.56306 small proline-rich protein 2A 0.087 116287AA487856 Hs.155829KIAA0676 protein 0.087 134034X89267 Hs.78601 uroporphyrinogen decarboxylase 0.087 130860066061 Hs241395 protease; serine;1 (trypsin 1) 0.087 109901H04992 Hs.30499 ESTs 0.087 107537220777 Hs.9857 ESTs; Weakly similar to peroxisomal short-chain alcohol dehydrogenase [H.sapiens] 0.087 2$ 133232AA496030 Hs.6845 ESTs 0.087 108559AA085161 zn12c5.s1 Stratagene hNT neuron (#937233) H Sapiens cDNA done IMAGE:54728 3' similar to TR:G11512280.087 61151228 LPGi P. " mRNA seq 121288AA40f735 Hs.97340 EST 0.087 108844AA1329i6 Hs.177961Human Chromosome i6 BAC clone CIT987SK-A-388D40.087 129874AA406488 Hs.181551ESTs 0.087 105139AA164543 Hs.110082ESTs 0.088 124789843803 Hs.78110 ESTs; Weakly similar to F17A92 0.088 [C.elegans]

115923AA441929 Hs.38205 ESTs 0.088 123640AAfi09292 Hs.11268iESTs 0.088 3$ 131607AA351409 Hs.172740microtubule-associated protein; 0.088 RP/EB family; member 3 130064T67053 Hs.181125immunoglobulin lambda gene cluster0.088 108752AA127070 Hs.71055 ESTs 0.088 124249H68077 Hs.108211ESTs 0.088 100109AJ000480 Hs.143513phosphoprotein regulated by mitogenic0.088 pathways 104642AAtX)d662 Hs.184245KIAA0929 protein Msx2 interacting 0.088 nuclear target (MINT) homolog ' 131752AA453311 Hs.31566 ESTs 0.088 114727AA132545 Hs.190202ESTs 0.088 120965AA398089 Hs.i79715ESTs 0.088 100396D84361 Hs.151123Human mRNA for p52 and p64 isoforms0.088 of N-Shc; complete cds 4$ 106218AA428451 Hs.91146 OKFZP586E0820 protein 0.088 111562809567 Hs.187569ESTs 0.088 121219AA400606 Hs.144344EST 0.088 101187L20316 Hs.208 glucagon receptor 0.088 101513M28210 Hs27744 RAB3A; member RAS oncogene family 0.088 $0 116454AA62i07i Hs.42034 ESTs; Moderately similar to T-complex0.088 protein 10A [H.sapiens]

116171AA463434 Hs.42658 ESTs 0.089 117500N31909 Hs.44278 ESTs 0.089 119978W88623 Hs.59190 EST _ 0.089 132005D58231 Hs.173091DKFZP434K151 protein 0.089 $$ 109914H05529 Hs.194704leucine-rich; glioma inactivated 0.089 130370M55265 Hs.155140casein kinase 2; alpha 1 polypeptide0.089 104262AF009801 Hs.105941bagpipe homeobox (Drosophila) homolog0.089 129706AA417181 Hs.120858ESTs 0.089 106398AA447545 Hs.18268 adenylate kinase 5 0.089 60 120884AA365356 Hs.97041 ESTs 0.089 130404X72012 Hs.76753 endoglin (Os4er-Rendu-Weber syndrome0.089 1) 114072238184 Hs.123633ESTs 0.089 131470X54938 Hs.2722 inositol 1;4;5-trisphosphate 3-kinase0.089 A

124573N67935 Hs.194703adaptor-related protein complex 0.089 4; mu 1 subunit 65 114717AA131240 Hs.252014EST 0.089 133806M12759 Hs.76325 Human 1g J chain gene 0.09 130470AA398552 Hs.15711 KIAA0639 protein 0.09 133182280787 Hs.240135H4 histone family; member J 0.09 116036AA452572 Hs.43866 ESTs 0.09 132404AA393903 Hs.4768 ESTs 0.09 122695AA456048 Hs.99403 ESTs; Moderately similar to undulin0.09 2 [H.sapiens]

125975AA495891 Hs.152290ESTs; Highly similar to PACAP type-3NIP0.09 type-2 receptor [H.sapiens]

110783N23669 Hs.26407 ESTs 0.09 $ 129860AA410343 Hs.129826tetraspan transmembrane 4 super 0.09 family 120740AA302650 Hs.96654 EST 0.09 119564W38206 Accession not listed in Genbank 0.09 134474AA054746 Hs.8379 ESTs 0.09 119014N95435 Hs.55144 ESTs 0.09 IO 109791F10669 Hs.13228 DRE-antagonist modulator; calsenilin0.09 117605N35073 Hs.44433 ESTs 0.09 121589AA416627 Hs.191598ESTs 0.09 104326D81655 Hs.143067ESTs 0.09 129861N69507 Hs.129849DKFZP564M182 protein 0.09 1$ 102795088667 Hs.198396ATP-binding cassette; sub-familyA 0.09 (ABC1); member4 119626W49499 Hs.184456ESTs; Wkly smlr to !! ALU SUBFAMILY0.09 SX WARNING ENTRY !! [H.sapiens]

110516H56894 Hs.37368 EST 0.09 105382AA236853 Hs.111801Homo Sapiens mRNA; cDNA DKFZp564H20230.09 (from done DKFZp564H2023) 123754AA609964 Hs.102021ESTs 0.09 108008AA039430 Hs.61920 ESTs 0.09 121057AA398619 Hs.142375ESTs; Moderately similar to putative0.091 envelope protein [H.sapiens]

123675AA609474 Hs.112713EST 0.091 135194C20975 Hs.9613 ESTs; Highly similar to angiopoietin-related0.091 protein [H.sapiens]

127070AA641812 Hs.190037ESTs 0.091 2$ 134051S67070 Hs.78846 heat shock 27kD protein 2 0.091 133382AA112532 Hs.7247 ESTs 0.091 103615246967 Hs.115460calicin 0.091 f 18457N66593 Hs.49230 EST 0.091 118504N67334 Hs.50158 ESTs 0.091 3O 112915T10176 Hs.4254 ESTs 0.091 132088AA470121 Hs.243960HLA-B assodated transcript-3 0.091 101504M27288 Hs.248156oncostatin M 0.091 112550871391 Hs.29074 ESTs 0.091 128551H09058 Hs.237323N-acetylglucosamine-phosphate mutase;0.091 DKFZP434B187 protein 35 112879T03541 Hs.115960ESTs 0.091 127079AI364691 Hs.128628ESTs; Moderately similar to CL3BC 0.091 [R.norvegicus]

101993001062 Hs.77515 inositol 1;4;5-triphosphate receptor;0.091 type 3 113020T23830 Hs.7303 ESTs; Weakly similar to PROHIBITIN 0.091 [H.sapiens]

120465AA251505 Hs.130861ESTs 0.091 4O 130152032645 Hs.151139E74-tike factor 4 (ets domain transcription0.091 factor) 104941AA065169 Hs.17805 ESTs 0.091 110090H16076 Hs.6915 ESTs 0.091 135375AA480888 Hs.99741 ESTs; Weakly similar to BRAIN PROTEIN0.091 H5 [H.sapiens]

123799AA620418 Hs.112861ESTs 0.092 4$ 118966N93438 Hs.76907 ESTs; Highly similar to HSPC002 0.092 (H.sapiens]

116969H80633 Hs.143038ESTs 0.092 125147W38150 Accession not listed in Genbank 0.092 100836HG4113-HT4383 Olfactory Receptor Orl7-201 0.092 114726AA132509 Hs.103827EST 0.092 $O 107311T57738 Hs.174112ESTs 0.092 112863T03148 Hs.4610 EST 0.092 129290AA521407 Hs.110095ESTs 0.092 103384X92762 Hs.79021 tafazz!n (cardiomyopathy; dilated 3A (X-linked); endocardial fibroelastosis 2; Barth syndrome) 0.092 55 112508868213 Hs.28847 ESTs O.Q92 111863837495 Hs23578 ESTs 0.092 131184AA452705 Hs.23954 ESTs; Weakly similar to KIAA0584 0.092 prote!n [H.sapiens]

107420W26567 Hs.4775 ESTs 0.092 111768827606 Hs.24185 ESTs 0.092 6O 112290853940 Hs.26016 ESTs 0.092 130581AA481982 Hs.16258 ESTs; Weakly similar to RAS-RELATED0.092 PROTEIN RAB-5A [H.sap!ens]

120744AA302772 Hs.228649EST 0.093 112226850761 Hs.25738 ESTs 0.093 116154AA460951 Hs.57100 ESTs 0.093 6$ 102640067674 Hs.194783solute carrier family 10 (sodium/bile0.093 add coUansporter family); member 129797X53595 Hs.1252 apolipoprote!n H (beta-2-glycoprotein0.093 I) 102705077180 Hs.50002 small Indudble cytokine subfamily 0.093 A (Cys-Cys); member 19 132408AA035547 Hs.47822 KIAA0380 gene product; RhoA-spedfic0.093 guanine nucleotide exchange factor 108441AA079079 zm97c9.si Stratagene colon HT29 (11937221) Homo sapiens d7NA done ~~$

IMAGE:545872 3' similar to contains element MER22 MER22 repetitive element ;, mRNA sequence 0.093 108145AA054133 Hs.63085 ESTs 0.093 106466AA449990 Hs.76057 lysophospholipase II ~ 0.093 $ 101697M64358 Human rhom-3 gene, axon 0.093 121294AA401958 Hs.240170 ESTs; Moderately similar to alternatively spliced product using exon 13A [H.sapiens] 0.093 117824N49065 Hs.125201 ESTs; Weakly similar to B7 [M.musculus]0.093 115771AA422049 Hs.40780 ESTs 0.093 102303033053 Hs.2499 protein kinase C-like 1 0.093 131405079255 Hs.26468 amyloid beta (A4) precursor protein-binding;0.093 family A; member 2 (X11-like) 112909T10069 Hs.101094 ESTs 0.093 124173H41281 Hs.107619 ESTs 0.093 112488866896 Hs.28788 ESTs 0.093 1$ 130554X59303 Hs.159637 valyl-tRNA synthetase 2 0.093 106413AA447964 Hs.6311 ESTs 0.093 111711822891 Hs.7093 ESTs 0.094 ' 117595N34933 Hs.44664 EST 0.094 113813W45174 Hs.31382 ESTs 0.094 107769AA018449 Hs.125220 Homo Sapiens DNA from chromosome 19-cosmids 830102:829350:827740 containing MEF2B; genomic sequence 0.094 114966AA250743 Hs.92198 ESTs; Highly similar to calcium-regulated heat sfable protein CRHSP-24 [H.sapiens] - 0.094 130297H94949 Hs.171955 trophinin-assisting protein (tastin)0.094 2$ 109589F02429 Hs.6581 ESTs 0.094 112592877631 Hs.29126 ESTs 0.094 102314034038 Hs.154299 coagulation factor II (thrombin) 0.094 receptor-like 1 116128AA459915 Hs.112193 mutS (E. coli) homolog 5 0.094 106809AA479704 Hs.220324 Human DNA sequence from clone 283E3 on chromosome 1p36.21-36.33.

Contains the alternatively spliced gene for Matrix Metalloproteinase in the Female Reproductive tract MIFR1;
-2; MMP21/22A; -B and -C; a novel gene;

the alternatively spliced CDC2L2 0.094 gene for 130607AA043894 Hs.16603 ESTs 0.094 120592AA281929 Hs.143974 ESTs 0.094 3$ 117230N20535 Hs.43265 melastatin 1 0.094 105948AA404597 Hs.7133 ESTs 0.094 101333L47738 Hs.80313 p53 inducible protein 0.094 101909S69265 Homo Sapiens mRNA for PLE21 protein;0.094 , complete cds 106959AA497031 Hs.8657 ESTs; Highly similar to CTG7a [H.sapiens]0.094 127034AA352389 ESTs; Wkly smlr to glucose-6-phosphatase0.095 catalytic subunit [R.norvegicus]

134430H52105 Hs.8309 KIAA0747 protein 0.095 120342AA207105 Hs.45068 Homo Sapiens mRNA; cDNA DKFZp43411430.095 (from clone DKFZp4341143) 104450L77564 Hs.103978 serine/threonine kinase 228 (spermiogenesis0.095 associated) 130902AA42d530 Hs21061 ESTs 0.095 ~$ 102708077594 Hs.37682 reGnoic add receptor responder (tazarotene0.095 induced) 2 107373085773 Hs.154695 phosphomannomutase 2 0.095 123569AA608952 Hs.195292 ESTs; Weakly similar to RNA helicase0.095 HDB/DICE1 [H.sapiens]

102687073379 Hs.93002 ubiquitin carrier protein E2-C 0.095 128888AA034951 Hs.106893 ESTs 0.095 $0 100283D43642 Hs.2430 transcription factor-like 1 0.095 102747079303 Hs.82482 protein predicted by done 23882 0.095 107798AA019346 Hs.60918 EST 0.095 123565AA608907 Hs.112614 EST - 0.095 116010AA449450 Hs.56421 ESTs; Weakly similar to Similarity 0.095 to H.infiuenza ribonuclease PH
[C.elegans]

$$ 117155H97536 Hs.42391 EST 0.095 133094AA115572 Hs.64746 chlorideintraceliularchannel3 0.095 113174T54659 Hs.9779 ESTs 0.095 102016003270 Hs.122511 centrin; EF-hand protein;1 0.095 130126A8002318 Hs.150443 KIAA0320 protein 0.095 60 134813X14767 Hs.89768 gamma-aminobutyric acid (GABA) A 0.095 receptor; beta 1 132055N69440 Hs.38132 ESTs 0.095 122229AA436198 Hs.103902 ESTs 0.096 127574AA907314 Hs.188905 ESTs 0.096 134432AA053022 Hs.8312 ESTs 0.096 65 128052AA878398 Hs.190491 ESTs 0.096 101637M58285 Hs.132834 hematopoietic protein 1 0.096 103386X92972 Hs.80324 protein phosphatase 6; catalytic 0.096 subunit 133079AA477561 Hs.6449 ESTs 0.096 120328AA196979 Hs.104129 ESTs; Weakly similar to protease 0.096 [H.sapiens]

107640AA009615 Hs.257808ESTs 0.096 123389AA521176 Hs.221231ESTs 0.096 103222' X74795 Hs.77171 minichromosome maintenance deficient0.096 (S. cerevisiae) 5 (cell division cycle 46) 111704822450 Hs.23396 ESTs; Highly similar to ZINC FINGER 0.096 PROTEIN 140 [H.sapiens]

126856AA306523 ESTi77475 Jurkat T-cells VI Homo 0.733 sapiens cDNA 5' end, mRNA sequence.

127071AA250806 ESTs 0.096 114550AA056755 Hs.151714ESTs 0.096 125955AI356943 Hs.143761ESTs 0.096 134363M37033 Hs.82212 CD53 antigen 0.096 1~ 128550W76492 Hs.170142ESTs O.Q96 122598AA453465 Hs.99329 ESTs 0.096 118898N90703 Hs.4236 KIAA0478 gene product 0.096 117661N39092 Hs.44940 ESTs 0.096 120996AA398281 Hs.143684ESTs 0.096 15 123388AA521172 Hs.i34417ESTs 0.096 106700AA463929 Hs.28701 ESTs 0.096 112962T16814 Hs.6828 ESTs 0.096 121262AA401372 Hs.97723 ESTs 0.096 134551844839 Hs.8526 i-beta-i;3-N-acetylglucosaminyltransferase0.096 112060843754 Hs.21164 ESTs 0.096 134678AA039935 Hs.182595dynein; axonemal; light polypeptide 0.096 100855HG4234-HT4504 Methylenetetrahydrofolate Reductase 0.097 132414N91193 Hs.48145 ESTs ' 0.097 112900T08758 Hs.3813 ESTs 0.097 25 115989AA447777 Hs.93135 ESTs 0.097 103561221488 Hs.143434contactin 1 0.097 131087AA009738 Hs.22824 ESTs; Weakly similar to p160 myb-binding0.097 protein [M.musculus]

120293AA190859 Hs.191428ESTs 0.097 111830836081 Hs.25085 EST 0.097 3O 113654T95770 Hs.17666 ESTs 0.097 132675AA179338 Hs.5476 serine proteinase inhibitor 0.097 120182240125 Hs.91968 ESTs 0.097 132879016282 Hs.5881 ELL gene (11-19 lysine-rich leukemia0.097 gene) 134211AA056681 Hs.8002t ESTs; Weakly similar to 62D9.p (D.melanogaster]0.097 35 115448AA284845 Hs.165051ESTs 0.097 118118N56901 Hs.47995 ESTs 0.097 107598AA004528 Hs.169444ESTs ~ 0.097 128933H01824 Hs.760 GATA-binding protein 2 0.097 114892AA235988 Hs.86024 ESTs 0.097 4O 101922575168 Hs.274 megakaryocyte-associated tyrosine 0.097 kinase 105444AA252374 Hs.19333 ESTs; Weakly similar to ATP(GTP)-binding0.097 protein [H.sapiens]

128155AA926843 Hs.143302ESTs 0.097 116276AA485870 Hs.44914 ESTs 0.097 111964841227 Hs.21860 ESTs 0.097 4$ 135100AA398926 Hs.251108Homo Sapiens mRNA; chromosome 1 speafic0.097 transcript KIAA0493 124872869251 Hs.101506EST 0.097 103084X59932 Hs.77793 o-src tyrosine kinase 0.097 124138H23i99 Hs.107010ESTs 0.098 130048831745 Hs.211612SEC24 (S. cerevisiae) related gene 0.098 family; member A

5O 100208D26129 Hs.78224 ribonudease; RNase A family;1 (pancreatic)0.098 123537AA608775 Hs.112589ESTs 0.098 118999N95019 Hs.55092 ESTs 0.098 119847W80384 Hs.9853 ESTs - 0.098 112819898618 Hs.35984 ESTs 0.098 5$ 131080J05008 Hs.2271 endothelin 1 0.098 127353AA190853 Hs.155360ESTs 0.098 132068X66365 Hs.38481 cyclin-dependent kinase 6 0.098 105744AA293436 Hs.12909 ESTs 0.098 133680M92357 Hs.101382tumor necrosis factor; alpha-induced0.098 protein 2 122899AA469960 Hs.178420ESTs; Highly similar to WASP interacting0.098 protein [H.sapiens]

128700059286 Hs.103982small inducible cytokine subfamily 0.098 B (Cys-X-Cys); member 11 104393H46486 Hs.226499nesca protein 0.098 123320AA496792 Hs.139572EST 0.098 129169N31641 Hs.109058ribosomal protein S6 kinase; 90kD; 0.098 polypeptide 5 65 135093051333 Hs.159237hexokinase 3 (white cell) 0.098 113269T65159 Hs.85044 ESTs 0.098 124283H86783 Hs.194136ESTs; Moderately similar to zinc 0.098 finger protein RIN ZF [R.norvegicus]

114376GMCSF Accession not listed in Genbank 0.099 100881HG4458-HT4727 Immunoglobulin Heavy Chain, Vdjc 0.099 Regions (Gb:123563) 116572D45654 Hs.65582DKFZP586C1324 protein 0.099 123956AA621747 Hs.112847EST 0.099 100818HG4018-HT4288 Opioid-Binding Cell Adhesion Molecule0.099 132754W47419 Hs.56007Human DNA from chromosome 19-specific0.099 cosmid F25965; genomic sequence $ 112741893080 Hs.35035ESTs 0.099 112748893299 Hs.166492ESTs , 0.099 130858S57235 Hs.246381CD68 antigen 0.099 124870869233 Hs.101504ESTs 0.099 125304239833 Hs.124940GTP-binding protein 0.099 121297AA401995 Hs.97860ESTs 0.099 128602AA046103 Hs.102367ESTs 0.099 124062H00440 Hs.144524ESTs; Weakly similar to signal transducer and activator of transcription 2 [M.musculus] 0.099 100547HG2149-HT2219 Mucin (Gb:M57417) 0.099 1$ 105652AA282505 Hs.19015ESTs 0.099 133390AA459945 Hs.72660KIAA0585 protein 0.099 133503M33195 Hs.743 Fc fragment of IgE; high affinity 0.099 I; receptor far; gamma polypeptide 109461AA232667 Hs.58210ESTs 0.099 102068009117 Hs.80776phospholipase C; delta 1 0.099 113464T86931 Hs.16295ESTs 0.099 104240A8002368 Hs.70500KIAA0370 protein 0.099 121113AA399109 Hs.161813ESTs 0.1 122896AA469952 Hs.97899ESTs; Weakly similar to dal2; len:343;
CAI: 0.17; ALC_YEAST P25335 ALLANTOICASE [S.cerevisiae] 0.1 2$ 102405043148 Hs.159526patched (Drosophila) homolog 0.1 103599233905 Hs.81218receptor-associated protein of the 0.1 synapse; 43kD

121079AA398719 Hs.14169ESTs; Weakly similar to CREB-binding0.1 protein [H.sapiens]

115820AA427487 Hs.39619ESTs; Weakly similar to RETICULOCALBIN0.781 1 PRECURSOR [H.sapiens]

125106T95766 Hs.189760ESTs 0.1 30 131373N68116 Hs.26146Down syndrome critical region gene 0.1 120224241239 Hs.106960ESTs 0.1 133090AA448228 Hs.6468 ESTs 0.1 132300AA133244 Hs.44234ESTs 0.1 113129T49384 Hs.8988 EST 0.1 3$ 110638H73197 Hs.17241ESTs 0.1 131364853255 Hs.26010ESTs 0.1 105370AA236476 Hs.22791ESTs; Weakly similar to transmembrane protein with EGF-like and iwo follistatin-like domains 1 [H.sapiens]0.238 1$

TABLE 11A shows the accession numbers for those primekeys 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 100610 19864_1AWi 61357 A1879062 AI928938 AW161097 AWi61167 BE314465 ~$ AI890696 AA308884 AA507078 841274 AI365507 T16348 100674 21517_2AW403342 AW248986 BE561709 AA357312 BE311834 BE389496 3$ M13930 AL047400 J00120 BE018476 AW675223 T26980 F06694 AA477850 AV653129 AI281360 AI274110 W8786i AA641366 AI538452 Ai538453 AI337957 AA477744 AA464600 AW950fi52 A1093842 AI474024 AA703369 811264 M13930 4$ 100751 24700_1N32759 N29730 N30831 N32604 N31955 AI206390 H87574 823494 AI186215 N30036 AI741512 J00117 NM_000737 AI130720 A1188454 AI188391 AI148857 Al 1 92447 AI209155 Ai148774 AI200658 W71989 AI207360 A1188824 AI200559 $0 AI200270 AA644163 AI199943 AI151301 A1189555 AI262724 AI148590 A1148695 AI126906 Ai149163 K03183 K03189 AI189842 AI221014 N30608 A1i86465 AI220865 AI188498 A1i38226 AI189968 AI221019 A1138197 A1i49426 A11489Q4 AI199951 X00264 NM_000894 AA371909 AA063496 100775 18179_3J05581 M61170 T27692 M34088 M34089 AW860335 AW579047 AA299158 AW3682d6 848123 850628 870441 H27245 N25459 AA464d36 AA297350 AA297466 881736 H02737 AW582505 A1089266 H68386 H41353 H28590 AW001860 A1i41623 AA250773 AI284778 AWSi 1412 AW083975 AA130377 AW026047 100817 19648_1 L34355 L46810 NM-000023 008895 AA424260 aA453282 837364 852832 AW298336 AA351391 NM_002545 L34774 100881 458_127BE561958 BE561728 BE397612 BE514391 BE269037 BE514207 100898 8542_1 BE387614 851501 AA199714 AW674779 F08178 BE269071 AW439312 AA292744 AW471d43 AI473989 AA593336 AA464070 102753 2226_1 L32961 NM 000663 080226 S75578 AA425061 AA429317 A1815143 5O 103522 21640_1Y10518 Y10514 283935 Y10508 AK000055 Y10519 AI742012 127071 188097_1AA250806 AA459220 119388 1762256_1T88798 892430 126856 20669_1A1084125 A1083773 A1479687 A1939609 A1968662 AF129507 103996 224545_1AA321355 AW964592 823284 H73883 823382 N47914 C01377 113213 23798-1NM_001395 Y08302 AI434619 AI470328 AI261807 AW024965 129311 16078_1AK000526 BE550084 W30689 AW271859 AA411456 A1341551 - AFOt5910 100106 15621_-5 100515 342_1 AA305746 D90187 T63943 AW951154 T29182 A1734941 AA2t4002 AW392865 N79454 AA19718t AI680371 1$ AI261656 AA730919 AI633441 AW195182 AI351622 AW243465 8E277647 AA599947 BE280735 BE390239 N74150 Tt2504 100627 tigr ZJ~_ M88357 100756 tigr_HT3768 100768 tigr_HT3846L29141 M69180 M81105 100813 figr_HT4265L33999 100836 tigr_HT4383004688 100855 tigr_HT4504009806 102104 entrez_U12139012139 125091 genbank_T91518T91518 100929 tigr_HT688X65561 125147 entrez-W38150W38150 102354 entrez_038268038268 35 102491 entrez_U51010051010 102636 entrez_067092067092 118769 genbank_N74496N74496 101046 entre~K01160K01160 101057 entrez-K03430K03430 108334 genbanl~AA070473 108441 genbank-AA079079 108786 genbank-AA128999 101655 entrez_M60299M60299 45 101697 entrea_M64358M64358 117437 genbank-N27645N27645 101798 entrez-M85220M85220 101909 entrez_S69265S69265 103508 entrez_Y10141Y10141 103575 entrez_126256226256 119332 genbank-T54095T54095 112161 genbanILR48295848295 119564 NOT_FOUND
entrez_W38206 114376 NOT_FOUND_entrez_GMCSF GMCSF

SS 100478 tigr_HT1067M22406 100547 tiger M57417 100564 tigr_HT2324211585 TABLE 12: shows genes, including expression sequence tags, that are down-regulated in prostate tumor tissue compared to normal prostate tissue as analyzed using Affymetrix/Eos Hu01 GeneChip array. Shown are the ratios of "average" normal prostate to "average"
prostate cancer tissues.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number 1~ UnigenelD: Unigene number Unigene Title: Unigene gene title Ri: Bad<ground subtracted normal prostate : prostate tumor tissue Pkey ExAccnUnigenelD Unigene Title Ri 100522 17.4 Prolactin-Induced Protein 130803 Hs.1968 semenogelin 1 16.785 118068 H5.13743 ESTs 13225 2~ 114251 _ 12.7 239898 Hs.21948 ESTs 112134 Hs.7413 ESTs ~
846025 8.735 101436 Hs.158295 Human alkali myosin light chain8.175 M20642 3 mRNA; complete cds 104028 Hs.221128 ESTs 8.15 108944 Hs.175783 ESTs; Highly similar to growth7.535 AA149204 arrest indudble gene product [H.sapiens]

103838 Hs.12622 ESTs 7.212 120489 Hs25882 DKFZP586M1824 protein 7.175 110279 Hs.27384 ESTs 6.701 127472 Hs.192013 ESTs 6.642 133301 Hs.7037 pallid (mouse) homolog; pallidin6.411 102457 Hs.2359 dual spedfidiy phosphatase 4 6.395 114011 Hs.15082 ESTs 6.15 101249 Hs.1904 protein kinase C; iota 6 123265 Hs.105265 ESTs; Wealdy similar to reverse6 AA491209 transcriptase [M.musculus]

119322 Hs.241569 ESTs; Modly smir to !! ALU 5.95 T49655 SUBFAMILY SQ WARNING ENTRY !! [H.sapiens]

101673 Hs.6241 phosphoinositide-3-kinase; regulatory5.925 M61906 subunit; polypept!de 1 (p85 alpha) 115586 Hs.92423 ESTs 5.7 120590 Hs.111441 ESTs; Weakly similar to similar5.7 AA281780 to Kruppel-like zinc finger protein [C.elegans]

109748 Hs.248323 Tubulin; alpha; brain-specific5.625 134727 Hs.8939 yes-assodated protein 65 kDa 5.5 129171 Hs.7753 calumenin 5.486 120390 Hs.111460 ESTs; Highly similar to multifunctional AA233122 calcium/calmodulin-dependent protein kinase II delta2 isofortn [H.sapiens] 5.4 131699 Hs.90421 ESTs; Modly smlr to !! ALU SUBFAMILY5.279 868657 SX WARNING ENTRY !! [H.sapiens]

104490 Hs.43087 ESTs; Weakly similar to dysferlin5266 N71503 [H.sapiens]

102124 Hs.29981 solute tamer family 26 (sulfate5.151 U14528 transporter); member 2 109280 Hs.86081 ESTs 5.134 109707 Hs.185701 Homo sapiens mRNA full length 5.075 F09739 insert d)NA done EUROIMAGE 21920 108067 Hs.40545 ESTs 5.075 135006 Hs.929 myosin; heavy polypep6de 7; cardiac5.055 M21665 muscle; beta 119182 Hs.77067 ESTs - 5.033 129806 Hs.173373 KIAA0931 protein 4.675 101435 Hs.1288 actin; alpha 1; skeletal muscle 4.626 125954 yt72c12.r1 Soares retina N2b4HR Homo 4.6 893943 Sapiens cDNA done IMAGE275735 5', 113989 Hs.221184 ESTs 4.559 104432 Hs.99949 prolactin-induced protein 4.451 112326 Hs.4268 ESTs 4.45 119063 Hs.53106 ESTs; Weakly similar to !! ALU 4.45 816833 SUBFAMILY J WARNING ENTRY !1 [H.sapiens]

130376 Hs.155174 KIAA0432 gene product 4.301 122484 Hs.98074 ESTs; Highly similar to aUophin-14.2 AA448286 interacting protein 4 [H.sapiens]

104142 ESTs; Moderately similar to !! ALU SUBFAMILY4.175 129413 Hs.11123 ESTs; Moderately similar to 4.1 N32787 hypothetical protein 2 [H.sapiens]

103678 Human DNA sequence from PAC 46H23, BRCA2 284483 gene region chromosome 13q12-134.05 114266 Hs.26d09 ESTs 4.05 115206 Hs.186572 ESTs 4.048 f)5123723 Hs.112759 ESTs; Highly similar to unknown4.041 AA609749 protein [R.norvegicus]

129130 Hs.172788 ESTs; Weakly similar to KIAA05124.028 H97993 protein [H.sapiens]

120217 241078Hs.66035 ESTs 4.028 108536 AA084524zn19d8.s1 Stratagene neuroepithelium 4.023 NT2RAM1937234 Homo Sapiens cDNA

134460 AA400030Hs.8360 ESTs; Weakly similar to 11 3.925 ALU CLASS B WARNING ENTRY 1! [H.sapiens]

120418 AA236010Hs.26613 Homo Sapiens mRNA; cDNA DKFZp586F13233.91 (from done DKFZp586F1323) 132783 N74897Hs.5683 DEADM (Asp-Glu-Ala-AspMis) 3.889 box polypept'~de 15 125052 T80174Hs.222779 ESTs; Moderately similar 3.85 to similar to NEDD-4 [H.sapiens]

108600 AA099585Hs.41175 ESTs 3.833 103099 X61100Hs.8248 NADH dehydrogenase (ubiquinone)3.818 Fe-S protein 1 (75kD) (NADH-coenryme 134948 H06773Hs.93850 protein kinase; AMP-activated;3.792 gamma 2 non-catalytic subunit 1O 120511 AA258144Hs.221576 ESTs 3.779 111861 837460Hs.25231 ESTs 3.768 113966 W86600Hs.9842 ESTs 3.75 131649 AA481254Hs.30120 ESTs 3.708 129775 894659Hs.12420 ESTs 3.707 1 110191 H20568Hs.27182 phospholipase A2-activating 3.7 ~ protein 112678 887160Hs.33665 ESTs 3.7 127115 AA375791Hs.131894 ESTs 3.674 132892 W92797Hs.59378 DKFZP434G162 protein 3.653 115023 AA252079Hs.63931 dachshund (Drosophila) homolog3.625 114932 AA242751Hs.16218 KIAA0903 protein 3.62 106865 AA487228Hs.19479 ESTs 3.614 134480 AA024664Hs.83916 NADH dehydrogenase (ubiquinone)3.613 1 alpha subcomplex; 5 (l3kD; B13) _ 124780 842493Hs.220839 ESTs 3.6 130631 AA025399Hs.169737 ESTs 3.592 25 134154 AA211320Hs.79404 neuron-specific protein 3.568 104160 AA455706Hs.99722 ESTs; Weakly similar to 78 KD GLUCOSE REGULATED PROTEIN

PRECURSOR 3.559 105524 AA258158Hs.22153 ESTs; Weakly similar to KIAA03523.542 [H.sapiens]

110168 H19673Hs.176586 ESTs 3.525 3O 109480 AA233299Hs.72158 ESTs 3.522 109585 F02367Hs.27252 ESTs 3.5 115134 AA257107Hs.194331 ESTs 3.5 116083 AA455653Hs.44581 ESTs; Weakly similar to HEAT 3.459 SHOCK 70 KD PROTEIN 6 [H.sapiens]

120524 AA261852Hs.192905 ESTs 3.45 35 116932 H74330Hs.150000 ESTs 3.425 130746 AA256976Hs.18800 ESTs; Weakly similar to KIAA05793.42 protein [H.sapiens]

107513 X05451Hs.158295 Human alkali myosin light 3.417 chain 3 mRNA; complete cds 118641 N70298Hs.49829 ESTs 3.407 126584 Ai028384Hs.127331 ESTs 3.399 4O 105134. Hs.22895 ESTs; Weakly similar to arylsulfatase3.325 AA159953 B precursor [H.sapiens]

123502 AA600116Hs.112526 ESTs 3.318 132389 N50866Hs.47135 ESTs 3.317 105691 AA287097Hs.75356 transaiptionfactor4 3.315 131505 H85897Hs27755 ESTs 3.309 4$ 120775 AA342104Hs.96777 EST 3.3 105579 AA278824Hs.19218 ESTs 3.295 128190 AA946876Hs.148376 ESTs 3.292 100819 HG4020-HT4290 3.288 Transglutaminase 130217 D29956Hs.152818 ubiquitin specific protease 3273 130068 AA608903Hs.106220 KIAA0336 gene product 3.269 134719 L07515Hs.89232 chromobox homolog 5 (Drosophila3.266 HP1 alpha) 110277 H29209Hs.151231 ESTs; Highly similar to FYVE
finger-containing phosphoinositide kinase [M.musculus] 3.26 127354 AA418880Hs.i85797 ESTs - 3212 129173 860523Hs.109087 ESTs 3.197 55 127464 AA970504Hs.146103 ESTs 3.179 124923 894500Hs.108046 ESTs 3.175 122465 AA448164Hs.99153 ESTs; Highly similar to CGI-733.151 protein [H.sapiens]

122027 AA431302Hs.98721 EST; Weakly similar to N-copine3.151 [H.sapiens]

103329 X85134.Hs.72984 retinoblastoma-binding protein3.15 129937 M95767Hs.135578 chitobiase; di-N-acetyl- 3.15 134197 AA057341Hs.87889 helicase-moi 3.15 107764 AA018219Hs.226923 ESTS 3.125 121775 AA421773Hs.161008 ESTs 3.125 114768 AA149007Hs.182339 Ets homologous factor 3.12 6$ 132381 N48818Hs.46884 ESTs 3.11 123105 AA485973Hs.143947 ESTs 3.104 121176 AA400080Hs.97774 ESTs 3.1 125053 T8Q620Hs,186473 ESTs 3.075 105909 AA401739Hs.5111 ESTs 3.066 119767 Hs.58119 ESTs 3.057 115776 Hs.58197 ESTs 3.056 111713 Hs.220950 ESTs 3.05 115301 Hs.d3948 ESTs 3.05 $ 118448 Hs.49189 ESTs 3 106586 Hs.256269 ESTs 2.995 110415 Hs29739 ESTs; Weakly similar to RAS-RELATED2.979 H48239 PROTEIN RAB-3A [H.sapiens]

105173 Hs.8364 ESTs 2.978 101102 Hs.79059 transforming growth factor; 2.976 L07594 beta receptor III (betaglycan; 300kD) l0 110543 Hs.258544 ESTs 2.976 125593 Hs.202949 KIAA1102 protein 2.964 100824 2.957 Oncogene Aml1-Evi-1, Fusion Activated 106822 Hs.31835 ESTs 2.95 131963 Hs.3592 ESTs 2.95 15 111221 Hs.15119 ESTs 2.936 113620 Hs.17252 EST 2.917 105220 Hs.17212 ESTs 2.917 123234 Hs.105252 ESTs 2.904 125250 Hs.222926 ESTs; Weakly similar to D209222.9 W87465 [C.elegans]

2O 116196 Hs.63386 ESTs 2.9 122100 Hs.41086 ESTs; Weakly similar to OXYSTEROL-BINDING2.896 AA432243 PROTEIN [H.sapiens]

111712 Hs.113716 ESTs 2.895 126589 Hs.187698 ESTs; Weakly similar to Yer140wp2.895 W78107 [S.cerevisiae] ' 111132 Hs.13149 ESTs; Highly similar to unknown2.894 N64378 function [H.sapiens]

25 115307 Hs.191346 ESTs 2.886 108989 Hs.18827 KIAA0849 protein 2.883 129486 Hs.220689 Ras-GTPase-activating protein2.879 H03686 SH3-domain-binding protein 119805 Hs.43213 ESTs 2.875 125721 Hs.7503 ESTs 2.871 103704 Hs.153688 ESTs 2.868 128420 Hs.14146 ESTs; Weakly similar to unknown2.866 A1088155 [H.sapiens]

120571 Hs.128679 ESTs 2.863 123059 Hs238202 EST 2.86 129462 Hs.111732 IgG Fc binding protein 2.856 35 125166 Hs.172609 nudeobindin 1 2.854 125992 za36e07.r1 Soares fetal liver spleen 2.852 W01626 1 NFLS Homo sapiens cDNA clone 109431 Hs.43635 ESTs 2.85 105077 Hs.5558 ESTs 2.847 131388 Hs.92200 KIAA04t30 gene product 2.846 4~ 121080 Hs.177953 ESTs 2.838 112575 Hs.17385 ESTs 2.836 130244 Hs.153293 KIAA0701 protein 2.825 134698 Hs.77910 3-hydroxy-3-methylglutaryl-Coenryme2.816 AA427783 A synthase 1 (soluble) 116355 Hs.88650 ESTs 2.813 45 115316 Hs.57846 ESTs 2.806 129677 Hs.198891 serine/threonine-protein 2.8 U48736 kinase PRPd homolog 130971 Hs.28707 signal sequence receptor, 2.799 H20332 gamma (translocon-associated protein gamma) 115054 Hs.87729 ESTs 2.795 130285 Hs202968 ESTs 2.792 $O 124308 Hs.227146 Homo Sapiens mRNA; cDNA DKFZp564J1422.783 H93575 (from done DKFZp564J142) 125502 Hs.191959 ESTs 2.778 114800 Hs.131887 ESTs; Weakly similar to ORF 2.768 AA159825 YNL227c [S.cerevisiae]

128625 Hs.102652 ESTs; Weakly similar to KIAA04372.766 AA242816 [H.sapiens] -130159 Hs.151310 PDZ domain protein (Drosophila2.75 H51098 inaD-like) 55 107127 Hs.22119 ESTs 2.742 113547 Hs.15233 ESTs 2.734 104639 Hs.18214 ESTs 2.727 127609 Hs.150318 ESTs 2.726 106922 Hs.10056 ESTs 2.725 124825 yg85c3.s1 Soares infant brain 1 NIB 2.725 852088 Homo sapiens cDNA clone 124333 Hs.154054 ESTs 2.708 117634 Hs.107854 ESTs; Weakly similar to SODIUM-TRANSP 2.706 101609 Hs.1787 proteolipid protein 1 (Pelizaeus-Merzbacher M54927 disease; spastic paraplegia 2;

65 uncomplicated) .
2.704 117142 Hs.42251 ESTs 2.7 112602 Hs203365 ESTs 2.695 106828 Hs.13797 ESTs 2.68 124377 Hs.179833 ESTs 2.675 101026 carboxypeptidase M 2.675 124560 ~ Hs.102754 ESTs ~ 2.675 124066 Hs.101615 ESTs 2.671 130281 Hs.15395 ESTs; Weakly similar to ARGINYL-TRNA2.66 812777. SYNTHETASE [H.sapiens]

110949 Hs.13308 ESTs 2.65 111031 Hs.221085 ESTs; Highly similar to mediator2.633 N54839 (H.sapiens]

121770 Hs.i 1469 KIAA0896 protein 2.63 134132 Hs.220689 Ras-GTPase-activating protein2.626 032519 SH3-domain-binding protein 112424 Hs.191265 ESTs 2.625 1O 122544 Hs.194410 ESTs 2.625 134425 Hs.172004 titin 2.624 111114 Hs.9238 ESTs 2.619 116119 Hs.44445 ESTs; Weakly similar to Kelch 2.615 AA459242 motif containing protein (H.sapiensJ

112079 Hs.23014 ESTs 2.6 123033 Hs.193945 ESTs 2.591 124196 Hs.144167 ESTs 2.586 125873 y125a04.r1 Soares breast 3NbHBst Homo 2.58 H14437 Sapiens d)NA done 117684 Hs.45050 ESTs 2.575 134938 Hs.168326 phosphoGdylinositol transfer 2.575 D30037 protein; beta 2~ 131822 Hs.200332 ESTs 2.568 135185 Hs.96038 Ric (Drosophila)-like; expressed2.564 071203 in many tissues 117690 Hs.93834 ESTs 2.557 N40467 ~

118807 Hs.50732 protein kinase; AMP-activated;2.552 N78582 beta 2 non-catalytic subunit 121369 Hs.128791 Human DNA sequence from clone2.55 AA405657 967N21 on chromosome 20p12.3-13. Contains 114860 Hs.106227 ESTs; Moderately similar to 2.549 AA235112 similar to murine RNA-binding protein [H.sapiensJ

121857 Hs.62694 ESTs; Highly s!milar to DNA-REPAIR2.548 110190 Hs.244624 ESTs 2.548 132573 Hs.51743 ESTs; Weakly similar to !!
AA045333 ALU SUBFAMILY SB2 WARNING ENTRY !!
[H.sapiensJ 2.542 109706 Hs.12780 ESTs 2.537 3O 135109 Hs.94592 klotho 2.525 132810 Hs.5737 KIAA0475 gene product 2.525 124879 Hs.101533 ESTs 2.525 103840 Hs.50932 ESTs 2.525 119066 Hs.34492 ESTs 2.519 114833 Hs.87310 ESTs; Moderately similar to 2.507 AA234362 CGI-66 protein [H.sapiensJ

112998 Hs.103288 ESTs 2.5 123312 Hs.99601 ESTs 2.499 121873 Hs.145696 splicing factor (CC1.3) 2.491 123321 Hs.23972 ESTs 2.491 107760 Hs.95078 EST 2.483 102580 Hs.152981 CDP-diacylglycero! synthase 2.481 060808 (phosphatidate cytidylyltransferase) 103053 Hs.5947 mel transforming oncogene (derived2.475 X56741 from cell line NK14)- RA88 homolog 124756 Hs.106294 ESTs 2.475 1 12936 Hs.6185 ESTs; Weakly similar to BcDNA.GH121742.475 T15665 [D.melanogasterJ

125178 Hs.125731 ESTs 2.475 112423 Hs.22123 ESTs 2.471 123515 Hs.112535 EST 2.462 102842 Hs21903 caldum channel; voltage-dependent;2.457 095020 beta 4 subunit 102400 Hs.171957 hiple functional domain (PTPRF2.455 042390 interacting) 5O 113187 Hs.9992 ESTs 2.452 131687 Hs.3069 heat shock 70kD protein 9B (mortalin-2)2.448 115314 Hs256501 ESTs 2.437 128211 Hs.166707 ESTs; Highly similar to Ran-binding2.43 A1206427 protein 2 [H.sapiens]

134281 Hs.81047 aldehyde oxidase 1 2.425 115985 Hs.132094 ESTs; Moderately similar to 2.425 AA447709 putative transcription factor CA150 [H.sapiensJ

111348 Hs.9585 ESTs 2.418 129430 Hs.197877 Homo Sapiens clone 23777 putative2.418 AA258842 transmembrane GTPase mRNA; partial cds 133863 Hs.76930 synuclein; alpha (non A4 component2.417 C13990 of amyloid precursor) 111164 Hs.14808 ESTs; Weakly similar to !! 2.416 N66857 ALU CLASS C WARNING ENTRY !! [H.sapiens]

132143 Hs.7972 KIAA0871 protein 2.412 130330 Hs.154679 synaptotagmin 1 2.408 114219 Hs.27389 ESTs 2.406 117101 Hs.24341 DKFZP58611419 protein 2.403 125433 Hs.54320 ESTs 2.4 111099 Hs.21958 ESTs 2.4 120323 Hs.110347 Homo Sapiens mRNA for alpha 2.397 AA195405 integrin binding protein 80; partial 118624 Hs.21801 ESTs 2.394 123570 Hs.109653 ESTs 2.389 123562 Hs.190065 ESTs 2.388 131546 Hs.28578 muscleblind (Drosophila)-like 2.385 103143 Hs.75535 myosin; light polypepC~ie 2; 2.384 X66141 regulatory; cardiac; slow 123645 Hs.188691 ESTs 2.383 130123 Hs.150390 zinc finger protein 262 2.379 $ 131682 Hs.30654 ESTs 2.378 115909 Hs.59761 ESTs 2.375 125168 Hs.252497 ESTs 2.372 123973 Hs.182151 ESTs 2.361 135197 Homo sapiens tissue inhibitor of metalloproteinase2.357 076456 4 mRNA, complete cds 1~ 118689 Hs.184544 ESTs 2.357 107734 Hs.93386 ESTs 2.354 124590 Hs.4138i ESTs; Weakly similar to ub!quitin2.35 N69220 hydrolyzing enryme I [H.sapiens]

111163 Hs.17606 ESTs 2.348 112349 Hs.22665 ESTs; Moderately similar to 2.345 858877 dJ83L6.1 [H.sapiens]

1$ 129076 Hs.169343 ESTs 2.345 134238 Hs.184571 splidng factor, arginine/serine-rich2.341 116766 Hs.95097 ESTs 2.336 106331 Hs.34795 ESTs 2.333 129003 Hs.10784 ESTs 2.332 20 132368 Hs.46637 ESTs; Weakly similar to cDNA 2.332 AA599814 EST yk289g5.5 comes from this gene [C.elegans]

124697 Hs.186467 ESTs; Modiy smlr to !! ALU 2.322 806273 SUBFAMILY J WARNING ENTRY !! [H.sapiens]

120273 Hs.221139 ESTs 2.313 127110 Hs.100861 ESTs; Weakly s!m!lar to p60 2.307 AA304993 katanin [H.sapiens] ' 105450 Hs.93842 ESTs 2.301 119819 Hs.58383 ESTs 2.297 102302 Hs.69171 protein kinase C-like 2 2.288 130596 Hs.16475 ESTs 2.282 114161 Hs.22385 ESTs; Weakly similar to KIAA09702.278 238904 protein [H.sapiens]

130542 Human sperm membrane protein BS-63 mRNA,2.277 064675 complete cds 104491 Hs.39328 ESTs 2275 116988 ys69e12.s1 Soares retina N2b4HR Homo 2.275 H82527 Sapiens cDNA clone 126823 Hs.7870 ESTs; Weakly similar to YIr350wp2.273 AA370120 [S.cerevis!ae]

108800 Hs.90424 ESTs 2.273 101310 Hs.934 glucosaminyl (N-acetyl) transferase2.269 L4i607 2; !-branching enzyme 3$ 126842 Hs.21085 ESTs 2.255 127251 Hs.128638 ESTs 2.251 124647 Hs.125033 ESTs 2.249 127112 Hs.125103 ESTs 2247 101973 Hs.80120 UDP-N-acetyl-alpha-D-galactosamine:polypeptide2.246 120999 Hs.127437 ESTs 2.245 130225 Hs.15299 HMBA-indudble 2.243 119980 Hs249247 heterogeneous nuclear protein 2.243 W88678 similar to rat helix destabilizing protein 124222 Hs222844 ESTs 224 129199 Hs.128629 ESTs 2236 4$ 106802 Hs.16570 ESTs; Weakly similar to !! 2231 AA479101 ALU SUBFAMILY SO WARNING ENTRY !! [H.sapiens]

126160 Hs247277 ESTs; Weakly similar to transformation-related2.229 N90960 protein [H.sapiens]

104627 Hs.19603 ESTs 2.228 106474 Hs.42484 Homo sapiens mRNA; cDNA DKFZp564C0532.226 AA450212 (from clone DKFZp564C053) 113096 Hs.8345 ESTs 2.225 $~ 135336 Hs.99027 ESTs 2.225 135344 Hs.i68491 ESTs; Moderately s!milar to 2.225 862976 TRF1-interacting ankyrin-related 126156 Hs.118448 ESTs; Moderately similar to 2.222 AA508354 AKT3 protein kinase (H.sapiens]

128885 Hs.180141 cofilin 2 (muscle) . - 2.218 107900 Hs.176600 ESTs; Moderately similar to 2217 AA026385 !! ALU SUBFAMILY SB2 WARNING

$$ 114481 Hs.151572 ESTs 2212 109292 Hs.188662 ESTs 2.212 104257 Hs.9222 estrogen receptor-binding fragment-assodated2.209 AF006265 gene 9 132932 Hs.6093 ESTs 2.204 127392 Hs.14896 Homo Sapiens done 24590 mRNA 2.204 AA262728 sequence 60 104641 Hs.18564 ESTs 22 122529 Hs.99229 ESTs 2.195 124307 Hs.162395 proline synthetase co-transcribed2.193 H93562 (bacterial homology 133601 Hs.75155 transferdn 2.193 119904 Hs.128927 ESTs; Weakly similar to !! 2.192 W85709 ALU SUBFAMILY SP WARNING ENTRY !! [H.sapiens]

6$ 100348 Hs.4994 transducer of ER882; 2 (TOB2) 2.185 126871 Hs200334 ESTs 2.18 127793 Hs.30445 ESTs; Weakly similar to transcription2.178 A1298835 regulator Staf-50 (H.sapiens]

105149 Hs.8958 ESTs 2.177 121367 zw39g8.s1 Soares_total_fetus-Nb2HF8 AA405648 9w H Sapiens d7NA clone IMAGE:772478 2.177 111836 836228Hs.25119 ESTs 2.175 133394 816759Hs.237225 ribosomal protein S5 pseudogene2.175 123207 AA489697Hs.145053 ESTs 2.175 129801 F11087Hs.239666 ESTs 2.175 103393 X94612Hs.41749 protein kinase; cGMP-dependent;2.161 type II

132415 AA043223Hs.4815 nudix (nucleoside diphosphate 2.157 linked moiety X)-type motif 3 106369 AA443828Hs.25324 ESTs 2.157 122963 AA4784d6Hs.69559 KIAA1096 protein 2.156 133473 M19309Hs.73980 troponin T1; skeletal; slow 2.155 lO 134257 C06270Hs.8078 Homo Sapiens mRNA; cDNA DKFZp586L0812.155 (from done DKFZp586L081) 135156 AA056012Hs.9552 binder of Arl Two 2.151 104055 AA393755Hs.117211 ESTs; Highly similar to CGI-622.15 protein [H.sapiens]

102313 U33921HSU33921 Clontech adult lung cDNA library2.15 (HL1158a) Homo Sapiens d)NA

109788 F10638Hs.12432 Homo Sapiens clone 24407 mRNA2.15 sequence 15 103507 Y10032Hs.159640 serum/glucocorticoid regulated2.15 kinase 116000 AA448710Hs.41327 ESTs 2.t5 105856 AA399164Hs.227676 ESTs; Moderately similar 2.137 to !! ALU SUBFAMILY SQ

103153 X66534Hs.75295 guanylate cyclase 1; soluble;2.137 alpha 3 .

126202 AA652238Hs.199726 ESTs 2.135 20 115955 AA446121Hs.44198 Homo sapiens BAC done RG054D042.134 from 7q31 104164 AA458770Hs27023 KIAA0917 protein 2.132 108692 AA121270Hs.82960 ESTs ~ 2.128 122878 AA465341Hs.99640 ESTs 2.126 134771 L13939Hs.89576 adaptor-related protein complex2.125 1; beta 1 subunit 25 104298 D31120Hs.40368 adaptor-related protein complex2.125 1; sigma 2 subunit 104840 AA039595Hs.42458 Homo sapiens mRNA; d)NA DKFZp586C18172.125 (from done DKFZp586C1817) 122180 AA435798Hs.98835 ESTs; Moderately similar to 2.125 putative ring zinc finger protein 131012 H01992Hs.202949 KIAA1102 protein 2.125 134092 H17490Hs.7905 ESTs; Highly similar to sorting2.123 nexin 9 [H.sapiens]

30 118617 N69666Hs.183413 ESTs; Modtly smlr to !! ALU 2.123 SUBFAMILY J WARNING ENTRY !! [H.sapiens]

107155 AA621202Hs.7946 DKFZP586D1519 protein 2.12 130925 N71935Hs.169378 multiple PDZ domain protein 2.12 -135167 U63717Hs.95821 osteoclast stimulating factor2.118 105952 AA405263Hs.181400 ESTs 2.109 35 110308 H38148Hs.32775 ESTs 2.108 116368 AA521186Hs.94217 ESTs 2.107 132939 U76189Hs.61152 exostoses (multiple)-like 2.102 117881 N50073Hs.84926 ESTs; Highly similar to B-INDi2.1 protein [M.musculus]

121723 AA419622Hs.104800 ESTs; Weakly similar to Mouse2.096 19.5 mRNA; complete cds [M.musculus]

40 103500 Y09443Hs22580 alkylglycerone phosphate synthase2.094 121429 AA406293Hs.193498 ESTs 2.093 134632 AA398710Hs.174139 chloride channel 3 2.091 129785 F10980Hs.184780 ESTs 2.~

1 1 1065 Hs.18740 ESTs; Weakly similar to 1-evidence2.089 45 114710 AA129931Hs.79081 protein phosphatase 1; catalytic2.083 subunit; gamma isoform 132711 N73702Hs.238927 ESTs 2.083 133377 80549011s.7239 SEC24 (S. cerevisiae) related2.079 gene family; member B

124773 840923Hs.106604 ESTs 2.078 117759 N47587Hs.97345 ESTs; Weakly similar to TROPOMODULIN2.076 (H.sapiens]

127386 AI457411Hs.106728 ESTs 2.076 101167 L15309Hs.193677 zinc finger protein 141 (clone2.075 pHZ-44) 109597 F02582Hs.14474 ESTs 2.074 124390 N29325Hs.7535 ESTs; Highly similar to COBW-like2.07 placental protein [Haapiens]

116225 AA478609Hs.47278 Human Chromosome 16 BAC done 2.07 55 131243 816667Hs24752 spectrin SH3 domain binding 2.069 protein 1 130557 T90830Hs.15981 ESTs; Weakly similar to line-12.067 protein ORF2 [H.sapiens]

134103 D14826Hs.155924 CAMP responsive element modulator2.064 108833 AAi31866Hs.61661 ESTs; Weakly similar to DY3.62.063 [C.elegans]

112286 853765Hs.158135 KIAA0981 protein 2.063 125624 AA165411zq49a01.r1 Stratagene hNT neuron (#937233)2.061 Homo Sapiens cDNA clone 124612 N72200Hs.13913 ESTs 2.058 116335 AA495830Hs.87013 ESTs 2.~7 112248 851361Hs23423 ESTs 2.056 115789 AA424754Hs.43149 ESTs 2.056 107029 AA599219Hs.187492 ESTs; Weakly similar to ALR 2.056 [H.sapiens]

110294 H30270Hs.165062 ESTs 2.054 120532 AA262354Hs.186648 ESTs 2.054 118180 N59249Hs.48349 ESTs 2.~2 132018 AA293194Hs.3737 ESTs 2.052 132617 AA171913Hs.5338 carbonic anhydrase XII 2.05 131526 N36167Hs.28274 ESTs 2.05 113254 T64438Hs.11449 DKFZP5640123 protein 2.05 122785 AA459978Hs.99508 ESTs 2.05 107203 D20426Hs.5656 EST 2.05 105713 AA291321Hs.184319 ESTs; Moderately similar 2.046 to KIAA1006 protein [H.sapiens]

129385 D82675Hs.110950 Homo Sapiens clone 25007 2.042 mRNA sequence 119116 843845Hs.64595 DKFZP566E2346 protein 2.04 116405 AA600253Hs.55601 ESTs; Highly similar to host2.04 cell factor 2 [H.sapiens]

1~ 125924 AA526849Hs.82109 syndecan 1 2.039 105599 AA279442Hs.143460 protein kinase C; nu 2.037 119741 W70205Hs.43670 kinesin family member 3A 2.037 101449 M21494Hs.118843 creative kinase; muscle 2.036 107109 AA609943Hs.32793 ESTs 2.034 15 117040 H89112yw25e5.s1 Morton Fetal Cochlea Homo 2.034 sapiens cDNA clone IMAGE:25328 132906 AA142857Hs.234896 ESTs; Highly similar to 2.031 geminin [H.sapiens]

105479 AA255546Hs23467 ESTs 2.027 102031 U04898Hs2156 RAR-related orphan receptor 2.027 A

119846 W80363Hs.58446 ESTs 2.024 2O 124809 846482Hs.106875 ESTs 2.024 130286 AA041548Hs.154023 KIAA0573 protein 2.023 124457 N50114Hs.128704 ESTs 2.017 125144 W37999Hs.24336 ESTs 2.017 120581 AA281257Hs.125868 ESTs 2.014 25 104931 AA062731Hs.108319 thyroid hormone receptor-associated2.012 protein;150 kDa subunit 120548 AA278846Hs.187634 ESTs 2.011 113933 W81362Hs.30567 ESTs 2.011 123072 AA485041Hs.104308 ESTs 2.009 123648 AA609323Hs.112689 ESTs 2.008 116875 H67749Hs.161022 EST 2.003 103179 X69398Hs.82685 CD47 antigen (Rh-related 1.995 antigen; integrin-associated signal transducer) 103478 Y07755Hs.38991 S100 calcium-binding protein1.995 111007 N53378Hs22543 ESTs 1.995 120470 AA251797zsll f3.s1 NCI-CGAP_GCBi Homo Sapiens1.989 cDNA clone 35 112280 853457Hs26040 ESTs; Weakly similar to fatty1.989 acid omega-hydroxylase [H.sapiens]

114127 238652Hs.106961 ESTs; Weakly similar to 1.988 TYL [H.sapiens]

129863 AA151005Hs.129872 sperm surface protein 1.988 106320 AA436608ESTs 1.988 108933 AA147224Hs.71814 ESTs 1.986 4~ 105906 AA401633Hs22380 ESTs 1.982 109029 AA157911Hs.72200 ESTs 1.982 118470 N66769Hs.82781 ESTs 1.975 115358 AA281886Hs.88923 ESTs 1.975 115257 AA279060Hs.193516 B-cell CLL/lymphoma 10 1.974 126879 AA719776. zh38g04.s1 Soares-pineal~land_N3HPG
Homo Sapiens cDNA clone IMAGE:4143901.974 109547 F01479Hs26966 ESTs 1.973 127111 AA805726Hs.220509 ESTs 1.969 101266 L36645Hs.73964 EphA4 1.966 129319 AA037467Hs.30340 ESTs 1.965 106211 AA428240Hs.126083 ESTs 1.962 112753 893696Hs.169882 ESTs 1.961 120489 AA255538Hs.190504 ESTs 1.959 129699 AA458578Hs.12017 KIAA0439 protein; homolog 1.956 of yeast ubiquitin-protein ligase Rsp5 105425 AA251129Hs24416 ESTs 1.953 55 134740 L37362Hs.89455 opioid receptor; kappa 1 1.95 109324 AA210700Hs.86405 Homo sapiens mRNA; cDNA DKFZp564P0561.95 (from clone DKFZp564P056) 124303 H93043Hs.107070 ESTs 1.95 102337 U36922Human fork head domain protein (FKHR)1.948 mRNA, 3' end 109441 AA228100Hs.86998 nuclear factor of activated 1.946 T-cells 5 6O 127364 AA179573Hs.90061 progesterone binding protein1.942 105255 AA227498Hs.3623 ESTs 1.942 130672 L19783Hs.177 phosphatidylinositol glycan; 1.942 class H

104301 D45332Hs.6783 ESTs 1.94 132442 862589Hs.167419 ESTs 1.939 65 105519 AA258063Hs23438 ESTs 1.937 132902 AA490969Hs.168147 ESTs 1.936 118873 N89881Hs.44577 ESTs 1.936 114124 238595Hs.125019 ESTs; Highly similar to 1.934 KIAA0886 protein [H.sapiens]

115075 AA255486Hs.88045 ESTs 1.933 110695 Hs.124777 ESTs 1.931 105360 Hs.187626 ESTs 1.931 124998 Hs.77910 3-hydroxy-3-methylglutaryl-Coenryme1.929 T56013 A synthase 1 (soluble) 121816 Hs.187509 ESTs 1.927 $ 111717 Hs.110776 STAT induced STAT inhibitor-21.925 128874 Hs.106801 ESTs 1.925 109391 Hs.184245 KIAA0929 protein Msx2 interacting1.913 AA219699 nuclear target (MINT) homolog 126129 Hs.40334 ESTs 1.911 115553 Hs.71414 ESTs 1.905 1O 113811 Hs.4878 ESTs 1.905 108345 zm66di.s1 Stratagene neuroepithelium 1.904 AA070906 (#937231) Homo sapiens cDNA clone 120472 Hs.104472 ESTs; Weakly similar to Gag-Pol1.903 AA251875 polyprotein [M.musculus]

116602 Hs.241673 EST 1.901 121121 Hs.189095 ESTs; Weakly similar to zinc 1.9 AA399371 finger protein SALL1 [H.sapiens]

I 125330 Hs.114574 ESTs 1.896 130095 Hs.14838 ESTs 1.894 119782 Hs.58262 ESTs 1.894 104115 Hs.26102 ESTs 1.893 131313 Hs.22370 Homo sapiens mRNA; cDNA DKFZp564001221.891 C17938 (from clone DKFZp56400122) 20 105583 Hs24549 ESTs 1.891 122825 Hs.99580 ESTs 1.887 119495 Hs.55533 ESTs 1.886 130309 Hs.15423 Homo sapiens BAC clone RGi 1.886 AA134289 14B19 from 7q31.1 125628 Hs.241493 natural killer-tumor recognition1.886 AA418069 sequence 25 110611 Hs.14671 ESTs; Highly similar to gene 1.885 H66947 ERCC5 protein [H.sapiens]

117301 Hs.43215 ESTs 1.884 131406 Hs.26471 Wnt inhibitory factor-1 1.881 126428 Hs.64988 ESTs ' 1.881 120285 Hs.111110 titin-cap (telethonin) 1.878 112724 Hs.17757 ESTs 1.878 103121 Hs.4147 translocating chain-associating1.875 X63679 membrane protein 124381 Hs.109008 ESTs 1.875 117226 Hs.177322 ESTs; Weakly similar to putative1.875 N20468 p150 [H.sapiens]

105610 Hs.124691 ESTs; Weakly similar to trithorax1.875 AA279991 homologue 2 [H.sapiens]

3$ 111229 Hs.110855 ESTs 1.875 120627 Hs.190474 ESTs 1.873 107048 Hs.i0669 ESTs; Moderately similar to 1.872 AA6000i2 KIAAtk00 [H.sapiens]

104041 Hs.197114 RNA binding protein 1.872 115162 Hs.227806 ras GTPase activating protein-like1.872 4O 102239 Hs.1376 hydroxysteroid (1 1-beta) dehydrogenase1.87 100043 AFFX control:18S ribosomal RNA 1.868 120296 Hs.22385 ESTs; Weakly similar to KIAA09701.867 AA191353 protein [H.sapiens]

129011 Hs.107932 DNA segment; single copy; 1.867 S72869 probe pH4 (transforming sequence; thyroid-1;

134851 Hs.90232 KIAA0552 gene product 1.866 45 117392 Hs.93405 ESTs 1.864 114530 Hs.191797 ESTs 1.863 123541 Hs.112592 ESTs 1.863 124890 Hs.34145 ESTs; Weakly similar to RAS-RELATED1.862 878618 PROTEIN RAB-8 (H.sapiens]

105299 Hs.194720 ATP-binding cassette; sub-family1.861 AA233511 G (WHITE); member 2 103560 Hs.182787 myosin; heavy polypept 6; 1.861 220656 cardiac muscle; alpha (cardiomyopathy;
hypertrophic 1) 113073 Hs.6841 ESTs 1.86 120407 Hs.107283 ESTs 1.859 103892 Hs.17155 ESTs - 1.858 123795 Hs.70488 ESTs 1.857 AA62038i $$ 108524 Hs.68138 ESTs 1.857 113953 Hs.187554 ESTs 1.856 110721 Hs.31319 ESTs 1.856 129426 Hs.168272 EST; Highly smlr to prot inhibitor1.853 AA412087 of activated STAT prot PIASx-alpha [H.sapiens]

112102 Hs.21303 ESTs 1.852 118502 Hs.50150 ESTs 1.852 107619 Hs.60015 ESTs 1.851 100436 Hs.75912 KIAA0257 protein 1.85 120652 Hs.191648 ESTs 1.85 121643 Hs.193767 ESTs 1.843 f)$117387 Hs.53810 ESTs 1.843 1321)84 Hs.3886 karyopherin alpha 3 (importin 1.843 Y12394 alpha 4) 124449 Hs.t21820 ESTs 1.841 120263 Hs.193919 ESTs 1.838 127226 Hs.3463 ribosomal protein S23 1.838 111837 Hs.24453 ESTs 1.835 128727 Hs.50651 Janus kinase 1 (a protein tyrosine1.834 M64174 kinase) 114439 Hs.128629 ESTs 1.833 102332 Human nebulin mRNA, partial cds 1.83 126579 Hs.146082 ESTs 1.83 102341 Hs.8110 adducin 3 (gamma) 1.83 114246 Hs.12079 ESTs 1.828 131757 Hs.316 DEAD/H (Asp-Glu-Ala-Asp/His) 1.823 D17532 box polypepfide 6 (RNA helicase; 54kD) 108904 Hs.711 d8 ESTs; Weakly similar to putative1.823 AA136521 p150 [H.sapiens]

1~ 115084 Hs.42484 Homo sapiens mRNA; cDNA DKFZp564C0531.823 AA255566 ((rom clone DKFZp564C053) 131957 Hs.183232 ESTs 1.822 100131 Hs.11951 phosphodiesterase (/nucleotide D12485 pyrophosphatase 1 (homologous to mouse Ly-41 antigen) 1.822 124163 Hs.189838 ESTs 1.821 15 1113204 Hs.48443 ESTs 1.821 107727 Hs.173091 DKFZP434K151 protein 1.82 100357 Hs.241548 RAS p21 protein activator 1.82 116295 Hs.91216 ESTs; Highly similar to partial1.82 AA489016 CDS; human putative tumor suppressor [H.sapiens]

124833 Hs.128697 ESTs 1.817 122587 Hs.6968 ESTs 1.817 114359 Hs.153483 ESTs; Moderately similar to 1.815 241589 H1 chloride channel [H.sapiens]

111289 Hs.238246 ESTs 1.813 110826 Hs.15347 ESTs 1.812 104106 Hs.42457 ESTs 1.811 130043 Hs.193953 ESTs; Weakly similar to 1! 1.253 AA055404 ALU SUBFAMILY J WARNING ENTRY !! [H.sapiens]

115864 Hs.81200 ESTs 1.81 129737 Hs.122684 ESTs 1.81 124477 Hs.102682 ESTs 1.809 100782 1.806 Basic Transcription Factor 2, 34 Kda Subunit 106101 Hs.34395 ESTs 1.806 115479 zs52h09.s1 NCI_CGAP-GCBs H sapiens cDNA1.804 AA287596 clone IMAGE:701153 116104 Hs.78524 ESTs 1.804 114173 Hs.21963 ESTs 1.804 132632 Hs.5398 guanine-monophosphate synthetase1.803 35 119135 Hs.169681 death effector domain-containing1.802 131559 Hs.28728 ESTs; Weakly similar to F55A12.91.801 N91087 [C.elegans]

126922 Hs.i61671 ESTs 1.8 117375 Hs.108812 ESTs 1.8 103571 Hs211608 nucleoporin 153kD 1.8 40 105978 Hs.15973 ESTs 1.8 125904 Hs.163586 ESTs 1.799 133883 Hs.77221 choline kinase 1.798 105777 Hs23096 ESTs 1.797 110166 Hs.174309 ESTs 1.796 45 105038 Hs.7584 ESTs; Weakly similar to hypothetical1.796 AA130273 protein; similar to [H.sapiens]

105427 Hs28248 ESTs 1.795 115278 Hs.67466 ESTs; Weakly similar to BACN32Gt1.794 AA279757 i.d [D.melanogaster]

133104 Hs.65029 growth arrest-specific 1 . 1.794 131170 Hs.23796 Human DNA sequence from clone 1.792 N48674 1052M9 on chromosome Xq25. Contains the 5O 100136 Hs.22868 protein tyrosine phosphatase; 1.791 D13540 non-receptor type 11 127263 EST35035 Embryo, 6 week, subtracted 1.79 AA331157 (total cDNA) I Homo sapiens cDNA

114157 Hs.24979 ESTs 1.79 125601 Hs.247043 KIAA0525 protein - 1.788 118472 Hs.42179 ESTs 1.787 $5 112456 Hs.28464 ESTs 1.787 130236 Hs.51957 SC35-interacting protein 1 1.786 133297 Hs.70266 KIAA0905 protein 1.784 125650 Hs.176578 ESTs 1.784 132056 Hs.38176 KIAA0606 protein; SCN Circadian1.783 T89386 Oscillatory Protein (SCOP) ()~129093 Hs.108614 KIAA0627 protein 1.783 123176 Hs.193424 ESTs 1.782 106340 Hs.22857 chord domain-containing protein1.781 100598 1.779 Guanine Nucleotide-Binding Protein G25k 104038 EST86676 HSC172 cells I Homo sapiens 1.778 AA374532 cDNA 5' end, mRNA sequence 65 122235 Hs.190104 ESTs 1.777 105104 Hs.76941 ATPase; Na+IK+ transporting; 1.776 AA151771 beta 3 polypeptide 107601 Hs.50223 ESTs 1.776 131467 Hs27194 DKFZP434K171 protein 1.776 118449 Hs.172466 ESTs; Weakly similar to KIAA07751.776 N66413 protein [H.sapiens]

107969 AA034030Hs.155212 methylmalonyl Coenryme A mutase1.775 115527 AA342079Hs252055 ESTs 1.775 132471 T16305Hs.49349 beta-site APP-cleaving enryme 1.775 105966 AA406105Hs.5344 adaptor-related protein complex1.774 1; gamma 1 subunit 127548 AA373091Hs.93832 Homo saplens clone 24483 unknown1.774 mRNA; parital cds 106217 AA428379Hs.24870 ESTs 1.773 131214 N26777Hs.172635 ESTs 1.773 106295 AA435664Hs.8583 s!milartoAPCBEC1 1.773 106328 AA436705Hs.28020 KIAA0766 gene product 1.772 1~ 124661 N93797Hs.3090 Eph81 1.772 122988 AA479166Hs.105633 ESTs 1.772 115504 AA291946Hs.42736 ESTs 1.771 105168 AA180208Hs.16606 ESTs; Highly similar to CGI-321.767 protein [H.sap!ens]

129153 AA188618Hs.181461 ariadne; Drosophila; homolog 1.766 of 15 105829 AA398290Hs.21965 ESTs 1.764 101811 M86917Hs.24734 oxysterol binding protein 1.764 100138 D13628Hs.2463 angiopoietin 1 1.764 124704 807335ye96ct.s1 Soares fetal liver spleen 1.763 1 NFLS Homo sapiens cDNA clone 122314 AA442257Hs.192076 ESTs 1.762 2O 109865 H02566Hs.191268 Homo Sapiens mRNA; cDNA DKFZp434N1741.761 (from done DKFZp434N174) 106206 AA428069Hs.89519 KIAA1046 protein 1.758 107135 AA620782Hs.23247 ESTs 1.757 105760 AA338960Hs.28170 ESTs 1.756 106288 AA435536Hs.24336 ESTs 1.756 25 103968 AA304566Hs.3542 ESTs 1.756 129559 AA234945Hs.11360 ESTs 1.756 117885 N50112Hs.47023 ESTs 1.754 107032 AA599472Hs.247309 succinate-CoA ligase; GDP-forming;1.754 beta subunit 124807 845963Hs.233811 ESTs; Weakly similar to ORF2 1.753 [M.musculus]

3O 100276 D42047Hs.82432 KIAA0089 protein 1.753 110924 N47938yy84a09.s1 Soares_multiple-sclerosis-2NbHMSP1.751 Homo sapiens cDNA clone 133002 AF006082Hs.62461 ARP2 (actin-related protein 1.751 2; yeast) homolog 132530 AA455917Hs.50785 SEC22; vesicle trafficking 1.75 protein (S. cerevisiae)-like 1 110759 N21671Hs.19025 ESTs 1.75 35 106138 AA424515Hs.33264 ESTs 1.75 107348 U43701Hs.184776 ribosomal protein L23a 1.75 115867 AA432162Hs.i65986 DKFZP586B2022 protein 1.749 135398 AA194075Hs.99908 nuclear receptor coactivator 1.747 113783 W19222Hs.7041 ESTs; Weakly similar to !! ALU 1.747 SUBFAMILY SQ WARNING ENTRY !! [H.sapiens]

4O 134898 X98330Hs.90821 ryanodine receptor 2 (cardiac) 1.745 132215 T10132Hs.4236 K!AA0478 gene product 1.744 104229 AB002346Hs.61289 synaptojanin 2 1.743 116166 AA461556Hs202949 KIAA1102 protein 1.743 115433 AA284252Hs.58372 ESTs 1.743 45 114908 AA236545Hs.54973 ESTs 1.742 127425 AA470941Hs.143162 ESTs 1.741 131089 238807Hs.22870 ESTs 1.739 113498 T88908Hs.189746 ESTs 1.738 116710 F10577Hs.70312 ESTs 1.735 127210 851476yg76f04.r1 Soares infant brain 1 NIB 1.733 Homo Sapiens cDNA clone 120554 AA279654Hs.194524 ESTs 1.733 129940 U18242Hs.13572 caldum modulating ligand 1.732 117023 H88157Hs.41105 ESTs - 1.731 111700 822212Hs.23361 ESTs 1.731 $$ 116911 H72240Hs.39292 ESTs; Moderately similar to 1.731 KIAA0745 protein [H.sapiens]

106025 AA412063Hs.6065 ESTs 1.728 108626 AA101984Hs.61697 G-protein coupled receptor 1.726 111614 812561Hs.191146 ESTs 1.726 134134 L76703Hs.i73328 protein phosphatase 2; regulatory1.725 subunit B (856); epsilon isoform 6O 106886 AA489086Hs.36545 ESTs 1.725 117998 N52136Hs.93828 ESTs 1.725 121204 AA400422Hs.55896 ESTs 1.725 121342 AA404995Hs.192480 ESTs 1.725 131129 827296Hs.23240 ESTs 1.725 65 116235 AA479181Hs.186726 ESTs 1.725 102423 U44754Hs.179312 small nuclear RNA activating 1.724 complex; polypeptide 1; 43kD

110273 H29050Hs.24096 ESTs 1.722 108758 AA127395Hs.222414 ESTs 1.722 110672 H88477Hs.19i178 ESTs 1.721 120271 AA176404Hs.111092 ESTs; Weakly sim!lar to ZINC 1.72 FINGER PROTEIN 136 [H.sapiens]

100227 D28915Hs.82316 interferon-induced; hepatitis 1.719 C-associated miaotubular aggregate prot (44kD) 129232 W69459Hs.109655 sex comb on midleg (Drosophila)-like1.719 134663 W73367Hs.8750 ESTs 1.717 104902 AA055475Hs.104143 dathrin; light polypeptide 1.717 (Lca) 120582 AA281290Hs.125287 ESTs; Weakly similar to BC3311911.717 1 [H.sapiens]

134891 F03517Hs.90787 ESTs 1.716 106219 AA428567Hs266i3 Homo sapiens mRNA; cDNA DKFZp586F13231.715 (from clone DKFZp586F1323) 116372 AA521311Hs.13854 ESTs 1.713 1~ 107570 AA001870Hs.237323 N-acetylglucosam!ne-phosphate1.713 mutase; DKFZP434B187 protein 106198 AA427816Hs.11803 ESTs 1.712 125136 W31479Hs.129051 ESTs 1.712 104973 AA085676Hs.6763 KIAA0942 protein 1.712 128710 J04813Hs.104117 cytochroma P450; subfamily 1.711 IIIA (niphedipine oxidase); polypept!de 15 123994 D20899Hs.107127 Homo sapiens mRNA; cDNA DKFZp564G0221.711 (from done DKFZp564G022) 127871 AA766511Hs.128848 ESTs 1.71 116089 AA455933Hs.41324 ESTs 1.709 123337 AA504153Hs.132797 ESTs; Weakly similar to ORF 1.708 YGL050w [S.cerevisiae]

123619 AA609200Hs.162686 ESTs 1.708 104781 AA026617Hs.2i6i0 ESTs; Highly similar to BAIT-assodated1.707 protein 1 [H.sapiens]

115114 AA256d68Hs.88148 ESTs 1.705 117852 N49408Hs.136102 KIAA0853 protein 1.705 127644 T57570Hs.77039 ribosomal protein S3A 1.704 111359 N91273Hs.27179 ESTs 1.702 25 131721 L36644Hs.31092 EphA5 1.7 132438 F08925Hs.48610 ESTs 1.7 132476 N67192Hs.49476 Homo sapiens done TUAS Cri-du-chat1.7 region mRNA

130990 F02488Hs.21917 KIAA0768 protein 1.7 128499 AA487503Hs.100636 ESTs 1.698 120780 AA342337Hs.241569 ESTs; Modtly smlr to !! ALU 1.697 SUBFAMILY SO WARNING ENTRY !! [H.sapiens]

132920 L06133Hs.606 ATPase; Cu++hansporting; alpha 1.696 polypeptide (Menkes syndrome) 135037 077948Hs.184122 general transcription factor 1.696 II; 1 110024 H11297Hs.31050 ESTs 1.695 134415 AA329274Hs.82911 protein tyrosine phosphatase 1.694 type IVA; member 2 3$ 102223 024685Hs.148226 Human anti-B cell autoantibody IgM heavy chain variable V-D-J region (VH4) gene; done Ei t; VH4-63 non-productive 1.694 rearrangement 126712 AA205862Hs.7942 ESTs 1.694 101507 M27492Hs.82112 intedeukin 1 receptor; type 1.692 I

106291 AA435551Hs.30824 ESTs 1.691 4~ 116826 H58691Hs.8215 ESTs; Weakly sim!larto double-stranded RNA-binding nuclear protein DRSBP76 [H.sapiens] 1.69 135339 D59269Hs.127842 Homo sapiens mRNA full length1.69 insert cDNA done EUROIMAGE 783648 118250 N62602yz75b6.s1 Soares_multip~ sclerosis-2NbHMSP
Homo sapiens cDNA done IMAGE:2888513' similar to contains Alu 1.689 repetitive element;, mRNA sequence 45 106470 AA450116Hs.186180 ESTs 1.688 108203 AA057678Hs.63408 ESTs 1.687 119748 W70313Hs.126906 ESTs 1.686 116576 D51228Hs.79404 neuron-spedfic protein 1.683 123035 AA481392Hs.105166 ESTs 1.683 126668 AA011616Hs.184086 ESTs 1.681 101512 M28209Hs.250716 RAB1; member RAS oncogene 1.678 family 102704 076638Hs.54089 BRCA1 associated RING domain 1.677 126218 AA256386Hs.13649 Novel human gene mapping to 1.676 chomosome 13; similarto rat RhoGAP

111180 N67277Hs.9403 ESTs 1.676 55 105937 AA404342Hs.173531 ESTs 1.675 114118 238520Hs.175930 ESTs 1.675 109203 AA190634Hs.108787 endoplasmic reticulum membrane1.675 protein 125245 W86608Hs.7243 ubiquitin spedfic protease 24 1.675 102906 X06956Hs.75318 tubulin; alpha 1 (testis spedfic)1.675 (~ 125914 AA262925Hs.180034 cleavage stimulation factor, 1.674 3' pre-RNA; subunit 3; 77kD

134294 063289Hs.81248 CUG triplet repeat; RNA-binding1.674 protein 1 109742 F10108Hs.183333 ESTs 1.673 134674 D63876Hs.87726 KIAA0154 protein 1.673 104079 AA402937Hs.103238 ESTs 1.671 65 107554 AA001386Hs.59844 ESTs 1.671 132439 AA243139Hs.4863 Homo sapiens done 25088 mRNA 1.669 sequence 124515 N58172Hs.109370 ESTs 1.668 124300 H92575Hs.105959 ESTs; Weakly similar to !! 1.668 ALU SUBFAMILY SO WARNING ENTRY !! [H.sap!ens]

126809 AA743475Hs.171693 ESTs 1.667 106095 AA419547Hs.11713 ESTs 1,664 101754 M77142Hs.239489 TIAi cytotoxic granule-associated1.663 RNA-binding protein 105188 AA192306Hs.23926 ESTs 1.663 113582 T91371Hs.16824 EST 1.661 119559 W38197Accession not listed in Genbank 1.661 119961 W87535Hs.59015 ring finger protein 9 1.657 123255 AA490890Hs.105273 ESTs 1,g,57 111078 N59230Hs.186574 ESTs 1,g,55 113082 T40528Hs.8246 ESTs 1 6,54 IO 119589 W44692Hs.124177 ESTs , 1,g,52 104308 D53639Hs.77904 ribosomal protein S26 1,g,5 103073 X59417Hs.74077 proteasome (prosome; macropa!n)1.65 subunit; alpha type; 6 124424 N35314Hs.107265 ESTs i,6,5 128890 AA096157Hs.182364 ESTs; Weakly similar to 25 1.65 kDa trypsin inhibitor [H.sapiens]

15 119400 T92767ye27d06.s1 Stratagene lung (#937210) Homo Sapiens cDNA clone IMAGE:118955 3', mRNA sequence. 1.65 131631 AA486868Hs.29802 slit (Drosophila) homolog 2 1,6,5 118229 N62339Hs.180532 heat shock 90kD protein 1; 1.649 alpha 118533 N67954Hs.49413 ESTs 1 130666 AA476307Hs.194035 KIAA0737 gene product , 1,647 103093 X60708Hs.44926 dipeptidylpeptidase IV (CD26; 1.647 adenosine deaminase complexing protein 2) 128667 069140Hs.103419 fasdculation and elongation 1.646 protein zeta 2 (zygin II) 112933 T15530Hs221439 ESTs 1.646 114546 AA056263Hs.132747 ESTs 1 25 126705 AA579377Hs.180532 heat shock 90kD protein 1; , alpha 1.644 114399 AA007595Hs.220937 ESTs 1,~2 118836 N79820Hs.50854 ESTs 1,~

100401 D85423Homo sapiens mRNA for Cdc5, partial 1.64 cds 105681 AA284865Hs.171228 KIAA1040 protein 1.639 132526 AA460128Hs.5074 similar to S. pombe diml+ 1.639 133809 AA034002Hs.76359 catalase 1,638 115968 AA447083Hs.134522 ESTs 1,637 116370 AA521256Hs.236204 ESTs; Moderately sim!lar to NUCLEAR PORE COMPLEX

PROTEIN NUP107 [R.norvegicus] 1.631 35 109644 F04477Hs.204802 ESTs; Moderately similar to DEHYDROGENASE; LIVER [H.sapiens] 1.627 103427 X97303H.sapiens mRNA for Ptg-12 protein 1.627 132186 T33888Hs.221040 KIAA1038 protein 1.626 131428 017838Hs.26719 PR domain containing 2; with 1.626 ZNF domain 4O 126638 AA649257Hs.188602 ESTs 1.625 114503 AA039568Hs.188083 ESTs 1.625 121242 AA400857Hs.97509 EST 1.625 122414 AA446885Hs.99087 ESTs; Moderately s!milar to 1.625 ZINC FINGER PROTEIN 141 [H.sapiens]

110632 H72344Hs.171635 ESTs 1 45 i 11389 Hs.169111 ESTs; Weakly similar to L82A .
N95837 [D.melanogaster] 1.624 112449 863802Hs.124186 ring finger protein 2 1.623 113070 T33464Hs.6298 ESTs 1.622 107229 D59284Hs.34&44 ESTs 1.618 132710 W93726Hs.55279 protease inhibitor 5 (maspin) 1.617 $O 124664 N9d814Hs.33540 ESTs; Weakly similar to KIAA07651.617 protein [H.sapiens]

130166 AA350690Hs.151411 KIAA0916 protein 1.616 125040 T78451Hs.199961 ESTs 1.615 132972 H39627Hs.164967 ESTs; Weakly similar to !! 1.615 ALU SUBFAMILY SB WARNING ENTRY !! [H.sapiens]

115873 AA433916Hs.90093 heat shock 70kD protein 4 1.611 5$ 120408 AA235045Hs.190151 ESTs 1.61 120934 AA383773Hs.191500 ESTs 1.61 115259 AA279071Hs.13453 splicing factor 3b; subunit 1.609 1;155kD

134330 D20113Hs.8185 ESTs; Highly similar to CGI-44 1.607 protein [H.sapiens]

115117 AA256492Hs.49007 poly(A) polymerase 1,806 125162 W44682Hs.109896 ESTs 1.605 103946 AA285246Hs.111650 ESTs; Weakly similar to Prt1 1.604 homolog [H.sapiens]

133389 AA166917Hs.72639 ESTs ~ 1.603 115528 AA342301Hs.53929 ESTs; Weakly similar to !! 1.602 ALU CLASS B WARNING ENTRY !! [H.sapiens]

129704 W81301Hs.12064 ubiquitin specific protease 1.602 65 109313 AA206800Hs.86276 ESTs; Moderately similar to 1.601 zinc finger protein dp [H.sapiens]

130457 058091Hs.155976 cullin 48 1.6 123076 AA485211Hs.190046 ESTs 1,6 115153 AA256460Hs.44610 ESTs 1,6 117731 N46433Hs.46609 ESTs 1,6 123344 AA504338Hs.171857 ESTs 1.599 131798 X86098Hs.3238 adenov!rus 5 E1A binding protein1.597 125370 AA256743Hs.151791 KIAA0092 gene product 1.596 114918 AA236813Hs.72324 ESTs; Highly similar to unknown1.596 (H.sapiens]

114807 AA160805Hs.199832 ESTs 1.596 105103 AA151593Hs.10130 ESTs 1.594 125004 T60120yb68f02.s1 Stratagene ovary (#937217) Homo Sapiens cDNA clone IMAGE:76347 3', mRNA sequence. 1.592 105658 AA282914Hs.10176 ESTs 1.589 110455 H52172yt85e8.s1 Soares~inea~gland-N3HPG Homo sapiens cDNA clone IMAGE:231113' similar to contains Alu 1.589 repetitive element;, mRNA sequence 119780 W72967Hs.191381 ESTs; Weakly similar to hypothetical1.587 protein [H.sapiens]

126983 AA211537zn55d01.r1 Stratagene muscle 937209 Homo sap!ens cDNA clone IMAGE:5620815', mRNA sequence. 1.586 IS 134675 AA250745Hs.87773 protein kinase; CAMP-dependent;1.584 catalytic; beta 105431 AA252033Hs.15036 ESTs; Weakly similar to !! 1.584 ALU SUBFAMILY J WARNING ENTRY !! (H.sapiens]

120187 240251Hs.56974 ESTs 1.584 115830 AA428137Hs.86434 ESTs 1.581 135069 AA456311Hs.93961 ESTs; Weakly similar to !! 1.581 ALU CLASS A WARNING ENTRY !! [H.sapiensJ

2~ 122997 AA479295Hs.106290 Kelch motif containing protein1.581 119707 W67569Hs.44143 ESTs; Weakly similar to SNF2alpha1.58 protein [H.sapiens]

131934 D80948Hs.34922 ESTs 1.58 106141 AA424558Hs.9302 phosducin-like 1.58 115271 AA279422Hs.5724 ESTs 1.579 25 131468 827598Hs.27197 KIAA0797 protein 1.577 131165 898173Hs23763 Max-interacting protein 1.575 117273 N21680Hs.43047 ESTs 1.575 101569 M33772Hs.182421 troponin C2; fast 1.575 116127 AA459703Hs.79070 v-myc avian myelocytomatosis 1.575 viral oncogene homolog 3O 120022 W90625Hs.58432 ESTs 1.575 117512 N32157Hs.82207 ESTs 1.574 106511 AA452865Hs.206713 UDP-Gal:betaGIcNAc beta 1;4-1.573 galactosyltransferase; polypeptide 116415 AA609204Hs.27973 KIAA0874 protein 1.573 127879 AA810215Hs.189079 ESTs 1.571 35 125211 W72798Hs.103177 ESTs; Wkly smir to cDNA EST 1.571 EMBL:D32579 comes from this gene [C.elegans]

114746 AA135638Hs.223756 ESTs 1.571 122698 AA456112Hs.99410 ESTs 1.57 116765 H12fi36Hs.121585 ESTs; Weakly similar to reverse1.568 transcriptase [H.sapiens]

130895 AA609828Hs21015 ESTs; Highly similar to tetracycline1.568 transporter-like protein [M.musculus]

40 114338 241366Hs.40109 KIAA0872 protein 1.567 111005 N53076Hs.5996 ESTs 1.567 128135 AA913491Hs.189143 ESTs; Modrdy smlr to !! ALU 1.567 SUBFAMILY J WARNING ENTRY !! [H.sapiens]

112046 843365Hs.22273 ESTs 1.566 132160 AA281770Hs.1840B1 seven in absentia (Drosophila)1.566 homolog 1 45 111568 810153Hs.20561 ESTs 1.566 127775 H04106Hs.179902 ESTs; Weakly similar to NG221.566 [H.sapiens]

115359 AA281936Hs.88914 ESTs 1.566 121845 AA425734Hs.165066 ESTs; Weakly similar to hypothetical1.565 protein (H.sapiens]

127854 AA769520ESTs; Weakly similar to REGULATOR OF
MITOTIC SPINDLE

$O ASSEMBLY 1 (H.sapiens] 1.564 120287 AA187679Hs.111114 ESTs 1.563 114940 AA243012Hs.75928 ESTs 1.562 126716 AA031700Hs251962 ESTs - 1.562 134161 097188Hs.79440 IGF-II mRNA-binding protein 1.561 $5 125390 H9509dHs.75187 translocase of outer mitochondrial1.561 membrane 20 (yeast) homolog 115334 AA281244Hs.65300 ESTs 1.559 113721 T97931Hs.18190 EST 1.558 114895 AA236177Hs.76591 KIAA0887 protein 1.558 119341 T62571Hs.146388 microtubule-associated protein1.558 6O 108012 AA039616Hs.61933 ESTs 1.558 130335 AA156499Hs.8454 protein kinase; CAMP-dependent;1.557 regulatory; type II; alpha 134351 882074Hs.82109 syndecan 1 1.557 133300 D51401Hs.70333 ESTs 1.553 106920 AA490899Hs24462 ESTs 1.553 65 118744 N74075Hs.94293 EST 1.552 126489 W20016Hs.144228 ESTs; Weakly similar to ZINC1.55 FINGER PROTEIN 83 [H.sapiens]

115913 AAd36720Hs.65487 ESTs 1.55 107868 AA025234Hs.61260 ESTs 1.55 134520 N21d07Hs.257325 ESTs 1.55 109703 Hs.24792 ESTs; Weakly similar to ORF 1.55 F09684 YOR283w [S.cerevisiae]

120288 Hs.55189 ESTs; Weakly similar to F25B5.31.548 AA187938 [C.elegans]

106356 Hs.31034 peroxisomal biogenesis factor 1.548 129460 Hs.11171 APG5 (autophagy 5; S. cerevisiae)-like1.547 133950 Hs.77823 ESTs 1.546 128172 Hs.142607 ESTs 1.546 114162 Hs.22265 ESTs 1.545 101803 Hs.155691 pre-B-cell leukemia transcription1.544 M86546 factor 1 113617 Hs.17207 ESTs 1.542 1~ 104896 Hs.23165 ESTs 1.541 114477 Hs.144260 EST 1.54 110731 Hs.188006 KIAA0878 protein 1.54 130367 Hs.8768 ESTs; Wkly smlr to !! ALU SUBFAMILY1.538 238501 SO WARNING ENTRY !! [H.sapiens]

130539 Hs.250857 Homo Sapiens calcium/calmodulin-dependent1.538 L07044 protein kinase II mRNA; partial cds 15 134921 Hs.169487 Kreisler (mouse) maf-related 1.537 W60186 leudne zipper homolog 130583 Hs.16281 ESTs; Moderately similar to W24957 similar to C.elegans protein encoded in cosmid T20D3 [H.sapiensj 1.537 133723 Hs.75744 S-adenosylmethionine decarboxylase1.537 106450 Hs.11859 ESTs 1.536 2~ 104120 Hs.89519 KIAA1046 protein 1.536 100533 1.535 Ras-Like Protein TclO

130664 Hs.17625 ESTs 1.535 127122 Hs.190049 ESTs 1.535 134264 Hs.8087 ESTs 1.535 2$ 132319 Hs.44625 ESTs 1.535 115465 Hs.43691 ESTs 1.533 125003 Hs.100445 ESTs 1.532 102273 Hs.75981 ubiquiGn spedfic protease 14 1.532 030888 (tRNA-guanine transglycosylase) 121875 Hs.98510 ESTs 1.532 3O 114366 Hs.469 succinate dehydrogenase complex;1.531 241747 subunit A; flavoprotein (Fp) 132944 Hs.6127 ESTs; Weakly similar to prostate-specific1.53 AA054515 transglutaminase [H.sapiens]

111199 Hs.29822 ESTs 1.53 113494 Hs.258738 ESTs 1.529 129515 Hs.112227 ESTs 1.528 133124 Hs.65490 ESTs 1.528 104785 Hs.7942 ESTs 1.526 105595 Hs.25866 ESTs 1.526 130198 Hs.151988 mitogen-activated protein 1.526 067156 kinase kinase kinase 5 114297 Hs.173091 DKFZP434K151 protein 1.525 4O 112876 Hs.4842 ESTs 1.525 127500 Hs.162115 ESTs 1.525 120519 Hs.129887 cadherin 19 (NOTE: redefinition1.525 AA258585 of symbol) 119859 Hs.58461 ESTs 1.525 129944 Hs.1361 cytochrome P450; subfamily I 1.524 L00389 (aromatic compound-indudble); polypeptide 45 118864 Hs.42148 ESTs; Weakly similar to Su(P) 1.523 N89670 [D.melanogasterj 123964 Hs.210115 EST 1.523 111676 Hs.166459 ESTs 1.522 128332 Hs.134173 ESTs 1.522 130455 Hs.155956 N-acetyltransferase 1 (arylamine1.521 X17059 N-acetyltransferase) SO 125181 Hs.12396 ESTs 1.521 127093 oa72d02.s1 NCI-CGAP_GCBi Homo sapiens AA768241 cDNA done IMAGE:1317795 3', mRNA sequence. 1.521 132156 Hs.4113 S-adenosylhomocysteine hydrolase-like1.521 125303 Hs.107295 ESTs 1.52 $5 132697 Hs.5518 Homo Sapiens mRNA; d7NA DKFZp566J21461.52 AA281951 (from done DKFZp566J2146) 117086 Hs.41840 ESTs 1.519 113355 Hs.14480 ESTs 1.518 108621 Hs.69506 ESTs 1.518 109384 Hs.86849 EST 1.518 128510 Hs.100816 RAB2B; member RAS oncogene 1.517 X94703 family 132968 Hs.61638 myosin X 1.515 117035 Hs.41182 ESTs 1.515 116781 Hs.52132 ESTs 1.513 108677 Hs.118531 ESTs 1.513 6$ 130214 Hs.15266 ESTs t.513 134700 Hs.8868 golgi SNAP receptor complex 1.512 AA481414 member 1 116618 Hs.45224 ESTs 1.508 126257 tumor neaosis factor receptor superfamily;1.508 N99638 member 10b 125859 Hs.118797 ubiquitin-conjugating enryme 1.508 AA806808 E2D 3 (homologous to yeast UBC4/5) 113837 W57698Hs.8888 ESTs 1.507 114317 241038Hs.469 succinate dehydrogenase complex;1.507 subunit A; flavoprotein (Fp) 100311 D50640Hs.184653 phosphodiesterase 3B; cGMP-inhibited1.507 126802 AA947601Hs.97056 ESTs 1.506 128661 882837Hs.103329 KIAA0970 protein 1.506 134194 AA233231Hs.79828 ESTs . 1.506 108953 AA149652Hs.d2128 ESTs 1.504 133240 D31161Hs.68613 ESTs 1.502 132671 X76302Hs.54649 putative nucleic acid binding1.501 protein RY-1 l~ 132609 248923Hs.53250 bone morphogenetic protein 1.501 receptor; type II (sedne/threonine kinase) 105574 AA278678Hs.258567 ESTs 1.5 113718 T97782Hs.256268 ESTs 1.5 127824 AI208365Hs.127811 ESTs 1.5 130132 U55936Hs.184376 synaptosomal-associated protein'1.5 23kD

15 127394 AA453224ESTs; Weakly similar to !! ALU SUBFAMILY1.5 J WARNING ENTRY !! [H.sapiens]

100485 HG1111-HT1111 Ras-Like Protein Tc21 1.5 101078 L04510Hs.792 ADP-ribosylation factor domain 1.5 protein 1; 64kD

128611 AA456845Hs.102471 KIAA0680 gene product 1.5 TABLE 12A shows the accession numbers for those primekeys lacking unigeneTD's for Table 12. 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 duster number Accession: Genbank accession numbers Pkey CAT number Accession 117040 46956-1AW970600 AA503323 H892i8 AFQ86031 H89112 100819 3022-1 L34840 NM_003241 031905 AI546931 AI791616 AI973065 100824 5_36 AI393237 AI521317 AI761348 AF025841 D43968 AW994987 AW467960 BE158135 BE158126 BEi58f45 N92860 AA847246 102313 27608_1033921 AI190489 AA573311 102337 553-1 AI8i4663 AA806761 AA76524i AA019317 AA092255 AA035405 AI24&476 AA345406 AI277554 AA134749 AA856624 8E613247 AI468977 AI192079 AI468976 AA044272 AWOi 5701 AW3i 6979 AA933042 AA6090i7 AI318393 AI424571 AI934945 AI804396 AI382221 AI813640 AI439635 AI52390i AW517242 124704 292319_1807335 807640 116988 185904_1AW953679 AW953680 AA244436 H82527 AA361046 AA244483 _ H52576 AF085971 H52172 126257 182217_1N99638 AW973750 AA328271 H90994 AA558020 AA234435 125624 154135_1AW968363 AA465492 834539 AA165411 104038 264235_1AA374532 AA421255 103427 43892_1BE514383 AA071273 AW247987 AW673286 BE312102 AW749824 104142 113242_1AA074713 AA447006 125873 10492_1 AW271838 AL133605 C01646 H29959 AA999896 D60676 AW999454 125954 4457 NM_016353 A8023584 W44753 809585 AA382865 823772 _ AA777386 AA806969 AI554876 AI584006 AI688556 AI688634 AI683152 A1096458 A1123822 AW170802 Ci6447 AI337674 127210 15307_6 AA305278 AA223833 2~ 135197 29440_1076456 NM-003256 AF057532 AA193414 AW293304 AW963378 121367 280429_1AA432071 AA405648 AW000908 Ti 6347 106320 6~ 1 AB028957 AL120001 AI267678 H10928 819844 AW970334 A1018713 AW972d50 AW972645 AA514964 T66172 F09785 101026 11075_1 NM_001874 J04970 T91426 AW205201 T84979 AA255727 AW752452 BE2d3244 AA843664 AI300080 BE169032 AW189979 AW974864 BE6i7311 BE243328 8E168049 100485 30576_2 A1207768 M31468 NM-012250 W01322 AA253280 AA253233 100522 19669_1 X51501 NM_002652 Y10179 J03460 A1791618 AI821473 100533 32905_1 NM-012249 M31470 AL043108 AA262561 AA178883 T29433 100598 23902 ALi21734 D54896 AA424269 BE242906 AA362118 BE018454 2 AI280348 AL048769 M35543 AA757734 A1i28865 H20289 118250 genbank_N62602 103678 entre~Z84483284483 119400 genbank_T92767 119559 entre~W38197W38197 MISSING AT THE TIME OF PUBLICATION

TABLE 13: shows genes, including expression sequence tags; up-regulated in prostate tumor tissue compared to normal prostate tissue as analyzed using Affymetrix/Eos Hu02 GeneChip array. Shown are the ratios of "average" normal prostate to "average" prostate cancer tissues.
Pkey: Unique Eos probeset identifier number ExAccn: Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title: Unigene gene title R1: Background subtracted normal prostate : prostate tumor tissue Pkey ExAccn UnigenelD Unigene Title R1 333516 CH22_FGENES.173-1 0.028 337954 CH22 EM:AC005500.GENSCAN.96-30.029 332496 Hs.204354 ras homolog gene 0.03 873299 family; member B

337944 CH22_EM:AC005500.GENSCAN.89-70.033 334111 CH22 FGENES.330_10 0.033 333657 CH22 FGENES.241 2 0.034 327718 CH.04_hs gi~6525284 0.034 336355 CH22 FGENES.817 5 0.035 322011 EST cluster (not in UniGene) 0.035 336377 CH22 FGENES.821 5 0.036 300254 Hs.188417 ESTs; Weakly similar0.037 AW079607 to ZnT-3 [H.sapiens]

330096 CH.19~2 gi~6015278 0.037 335191 CH22-FGENES.507_6 0.038 334040 CH22 FGENES.322 8 0.039 333586 CH22_FGENES.204_2 0.04 333295 CH22_FGENES.132 2 0.042 313326 Hs.122329 ESTs 0.043 329517 CH.10~2 gi~3983513 0.043 333403 CH22 FGENES.144 21 0.043 335226 CH22-FGENES.513 11 0.044 335976 CH22_FGENES.652-11 0.045 333637 CH22-FGENES.229-2 0.046 334582 CH22_FGENES.407 5 0.046 336437 CH22_FGENES.826 4 0.047 337461 CH22_FGENES.782-1 0.047 302892 Hs.6975 histone deacetylase 0.049 338689 CH22_EM:AC005500.GENSCAN.475-30.049 334721 CH22_FGENES.421 32 0.049 305867 EST singleton (not in UniGene)0.049 AA864572 with exon hit 335498 FGENES.571 7 0.05 311596 _ 0.05 AI682088 Hs.223368 ESTs 326959 CH21 hs gi~6469836 0.051 311688 Hs240090 ESTs 0.052 317298 Hs.158549 ESTs 0.052 332984 CH22_FGENES.54_6 0.052 321039 EST cluster (not in UniGene) 0.053 AW247083 _ 335844 CH22_FGENES.623 4 0.053 325371 CH.12_hs gi~5866920 0.054 335667 CH22_FGENES.590_18 0.054 333635 CH22 FGENES.228-2 0.054 336736 CH22_FGENES.110-2 0.055 335893 CH22-FGENES.635 1 0.055 333170 CH22_FGENES.94-5 0.055 329768 CH.14~2 gi~6015501 . 0.055 334030 CH22_FGENES.320-2 0.055 323359 Hs.137418 ESTs 0.055 300453 Hs.113029 ribosomal protein 0.055 334262 CH22_FGENES.367-12 0.055 306590 EST singleton (not in UniGene)0.055 A1000246 with exon hit 331087 Hs23398 ESTs 0.055 338620 CH22 EM:AC005500.GENSCAN.450-180.056 339045 CH22 DA59H18.GENSCAN28-5 0.056 308023 EST singleton (not in UniGene)0.057 AI452732 with axon hit 339067 CH22 DA59H18.GENSCAN.33-3 0.057 335689 CH22 FGENES.596 4 0.057 339069 CH22 DA59Hi8.GENSCAN.33-5 0.057 338176 CH22 EM:AC005500.GENSCAN.219-40.057 328159 CH.06-hs gi~5868065 0.058 335655 CH22 FGENES.590_6 0.058 336371 CH22 FGENES.820_1 0.058 336558 CH22 FGENES.842 3 0.059 337738 CH22 EM:AC000097.GENSCAN.100-40.059 1~ 334273 CH22_FGENES.369-2 0.059 335889 CH22 FGENES.633 3 0.059 327807 CH.05-hs gi~5867968 0.059 333315 CH22-FGENES.138 7 0.059 338825 CH22 DJ246D7.GENSCAN.4-6 0.06 1$ 337612 CH22-C20H12.GENSCAN.22-5 0.06 333897 CH22 FGENES.293-4 0.06 335990 CH22 FGENES.655 4 0.06 334264 CH22 FGENES.367 15 0.06 338653 CH22 EM:AC005500.GENSCAN.460-390.061 2O 322303 W07459EST cluster (not in UniGene) 0.061 333498 CH22_FGENES.168 8 0.061 336522 CH22 FGENES.839-3 0.061 301357 AW295677Hs.137840 ESTs; Moderately similar to HOMEOBOX

PROTEIN SIXi [H.sapiens] 0.062 25 305917 AA876469Hs.181357 laminin receptor 0.062 1 (67kD; ribosomal protein SA) 336143 CH22-FGENES.705-5 0.063 333493 CH22 FGENES.168 2 0.063 332533 M99487Hs.1915 folate hydrolase (prostate-speafic0.063 membrane antigen) 1 325844 CH.16 hs gi~6552453 0.063 336402 CH22 FGENES.823 17 0.063 335767 CH22 FGENES.607_1 0.064 301893 T80334EST cluster (not in UniGene) 0.064 with axon hit 324019 AW177009EST cluster (not in UniGene) 0.064 305801 AA845997EST singleton (not in UniGene)0.064 with axon hit 35 335188 CH22 FGENES.507 3 0.065 337533 CH22-FGENES.828-2 0.065 333311 CH22 FGENES.138 3 0.065 335668 CH22 FGENES.590_19 0.065 306786 A1041589EST singleton (not in UniGene)0.066 with axon hit 4O 306365 AA962086EST singleton (not in UniGene)0.066 with axon hit 306249 AA933840EST singleton (not in UniGene)0.066 with axon hit 335018 CH22 FGENES.474 6 0.066 333594 CH22 FGENES.210 3 0.066 333900 CH22_FGENES.293 7 0.066 325207 CH.10_hs gi~6552430 0.067 329888 CH.15~2 gi~6067149 0.067 326238 CH.17 hs gi~5867260 0.067 333658 CH22_FGENES.241 4 0.067 335809 CH22 FGENES.617 6 0.068 307427 AI243437EST singleton (not in UniGene)0.068 with axon hit 318428 AI949409Hs.224583 ESTs 0.069 327005 CH.21 hs gi~5867664 0.069 330463 HG998-HT998Sulfotransferase, Phenol-Preferring0.069 -333318 CH22-FGENES.138 10 0.07 55 333313 CH22 FGENES.138 5 0.07 325937 CH.16_hs gi~5867132 0.07 335663 CH22 FGENES.590 14 0.07 335349 CH22_FGENES.539 2 0.07 303396 AA224470Hs.25426 ESTs; Weakly similar 0.07 to unknown [H.sapiens]

332603 N66681Hs.33470 ESTs 0.07 333310 CH22 FGENES.138 2 0.071 309924 AW340812EST singleton (not in UniGene)0.071 with axon hit 336340 CH22_FGENES.814 15 0.071 308025 AI453365Hs.172928 collagen; type I; 0.071 alpha 1 65 306805 A1055966EST singleton (not in UniGene)0.071 with axon hit 335499 CH22-FGENES.571 8 0.071 329669 CH.14~2 gi~6272129 0.071 321666 D28390EST cluster (not in UniGene) 0.071 338174 CH22_EM:AC005500.GENSCAN.219-20.072 336556 CH22-FGENES.842_1 0.072 305451 Hs.140 immunoglobulin gamma 3 0.072 AA738105 (Gm marker) 336684 CH22-FGENES.46-1 0.072 326943 CH.21 hs gi~6004446 0.073 333947 CH22 FGENES.303 1 0.074 333214 CH22 FGENES.104_5 0.074 331917 Hs.174007 ESTs; Moderately s!milar0.074 AA446572 to !!!! ALU SUBFAMILY J WARNING

339102 CH22_DA59H18.GENSCAN.44-9 0.074 328122 CH.O6_hs gi~5668031 0.075 332250 Hs.226223 KIAA0618 gene product 0.075 32850fi CH.07 hs gi~5868471 0.075 331756 Hs.98504 ESTs 0.075 335193 CH22-FGENES.507_8 0.076 317729 Hs.128141 ESTs 0 304515 Hs.251577 hemoglobin; alpha 2 .
AA458708 0.076 313644 Hs.124960 ESTs 0.076 326145 CH.17 hs gi~5867204 0.076 336394 CH22_FGENES.823-6 0.077 306516 EST singleton (not in UniGene) 0.077 AA989542 with axon hit 2~ 300629 Hs.155101 ATP synthase; H+transporting;subunit;
AA152119 mitochondrial F1 complex; alpha isoform 1; cardiac muscle 0.077 333160 CH22 FGENES.91 2 _ 0.077 337490 CH22 FGENES.799-5 _ 0.077 305403 EST singleton (not in UniGene) 0.077 AA723748 with exon hit 331747 Hs.193689 ESTs 0.077 332792 CH22-FGENES.3-2 0.078 330513 Hs.180884 carboxypeptidase B1 0.078 M81057 (tissue) 308905 Hs.8102 ribosomal protein S20 0.078 337419 CH22 FGENES.759-4 0.078 3~ 333459 CH22_FGENES.157-8 0.078 334851 CH22 FGENES.440 3 0.078 329046 CH.)~hs gi~5868569 0.078 327879 CH.06 hs gi~5868142 0.079 305830 EST singleton (not in UniGene) 0.079 AA857665 with exon hit 302928 EST duster (not in UniGene) with 0.079 AL137719 exan hit 304321 Hs.113029 ribosomal protein S25 0.079 326390 CH.19 hs gi~5867340 0.079 335230 CH22_FGENES.514-2 0.08 334622 CH22 FGENES.412 0.08 335331 _ 0.08 CH22 FGENES.535 4 304753 Hs.77961 major h!stocompaGbility 0.06 AA578840 complex; class I; B

301863 EST duster (not in UniGene) with 0.081 AI418863 axon hit 336561 CH22-FGENES.842 6 0.081 335611 CH22_FGENES.583 5 0.061 ~$ 305060 EST singleton (not in UniGene) 0.081 AA635771 with axon hit 306051 EST singleton (not in UniGene) 0.082 AA905130 with exon hit 308289 EST singleton (not in UniGene) 0.082 AI571211 with exon hit 334365 CH22_FGENES.378 13 0.082 335496 CH22 0.082 FGENES.571 4 332634 _ S38953 Human unidentified gene complementary to P450c21 gene; partial cds 0.082 337824 CH22_EM:AC005500.GENSCAN.13-18 0.082 335822 CH22-FGENES.619 7 - 0.062 334758 FGENES.428 7 0.082 55 309641 _ 0.082 AW194230 Hs.253100 EST

333064 CH22 FGENES.75 7 0.083 338695 CH22-EM:AC005500.GENSCAN.477-25 0.083 331809 Hs.97312 ESTs 0.083 326138 CH.17 hs gi~5867203 0.083 328304 CH.07-hs gi~6004478 0.083 330570 Hs.165439 arsA (bacterial) arsenite0.083 U60276 transporter; ATP-binding; homolog 334305 CH22 FGENES.373-8 0.083 335885 CH22-FGENES.632 3 0.083 325839 CH.16-hs gi~6552452 0.083 65 333531 CH22-FGENES.17518 0.084 330385 Hs.31386 ESTs; Highly similar AA449749 to secreted apoptosis related protein 1 [H.sapiens] 0.084 323305 Hs25307 Homo sapiens done 24812 0.064 AA811351 mRNA sequence 331698 Hs.65843 ESTs 0.084 335888 CH22 FGENES.633-2 0.084 306008 EST singleton 0.084 AA894390 (not in UniGene) with exon hit 334249 CH22_FGENES.365_15 0.084 318303 Hs.113418 0.084 AW451197 ESTs 330171 CH.02~2 0.084 gi~6648220 336662 CH22 FGENES.41-1 0.065 320506 Hs.157476 AI815668 suci-associated neurotrophic factor target (FGFR signalling 0.085 adaptor) 316974 Hs.128292 0.085 AI740721 ESTs 336492 CH22-FGENES.832 0.085 335750 CH22 FGENES.602 0.085 335676 CH22 FGENES.594_1 0.086 336093 CH22 FGENES.691_2 0.086 310932 Hs.222852 0.086 AI933861 ESTs IS 335160 CH22-FGENES.502 0.086 334306 CH22 FGENES.373_9 0.086 334793 CH22 FGENES.433 0.086 333936 CH22-FGENES.301 0.087 336413 CH22 FGENES.823_35 0.087 2O 333775 CH22_FGENES.272 0.087 335971 CH22 FGENES.652-4 0.087 301737 EST cluster 0.087 AI815981 (not in UniGene) with exon hit 339101 CH22-DA59H18.GENSCAN.44-6 0.067 ' 327612 CH.04_hs 6525283 0.087 gi~

25 326241 CH.17_hs 5867260 0.088 gi~

338386 CH22-EM:AC005500.GENSCAN.331-4 0.088 327762 CH.05 hs 0.088 gi~5667961 305266 EST singleton 0.088 AA679772 (not in UniGene) with exon hit 334359 CH22 FGENES.378_4 0.088 3O 335500 CH22 FGENES.571 0.088 329687 CH.14~2 0.088 gi~6117856 333654 CH22 FGENES.240 0.088 324430 EST cluster 0.088 AA464018 (not in UniGene) 325999 CH.16_hs 0.089 gi~5867073 35 334832 CH22 FGENES.439 0.089 339115 CH22_DA59H18.GENSCAN.49-3 0.089 300896 Hs.213882 0.089 AI916902 ESTs 328784 CH.07 hs 0.089 gi~5868309 335044 CH22 FGENES.480_1 0.089 329791 CH.14~2 0.089 gi~6469354 333656 CH22_FGENES.240 0.089 326180 CH.17 hs 0.089 gi~5867211 333391 CH22_FGENES.1~ 0.089 338324 EM:AC005500.GENSCAN.306-3 0.089 45 305396 _ 0.089 AA721052 EST singleton (not in UniGene) with axon hit 337483 CH22 FGENES.795-7 0.09 326424 CH.19-hs 0.09 gi~5867369 306454 EST singleton 0.09 AA977992 (not in UniGene) with axon hit 338893 CH22_DJ32110.GENSCAN.7-6 0.09 327470 CH.02_hs 0.09 gi~5867772 333165 CH22_FGENES.91 0.09 307155 Hs.182426 0.09 AI186738 ribosomal protein 330717 Hs.23635 0.09 AA233926 ESTs -335334 CH22 FGENES.535-10 0.09 55 335907 CH22 FGENES.636 0.09 333885 CH22 FGENES.292 0.09 331034 Hs.31965 N51868 ESTs; Moderately similar to 40S
RIBOSOMAL

PROTEIN 0.09 S20 ]H.sapiens]

304660 Hs.162185 0.09 AA534416 ESTs ()O328217 CH.06 hs 0.091 gi~5868096 336068 CH22-FGENES.684-13 0.091 302833 Hs.44423 0.091 AA295381 ESTs 328668 CH.07_hs 0.091 gi~5868254 335309 CH22 FGENES.532 0.091 65 338481 CH22 EM:AC005500.GENSCAN.377-5 0.091 306286 EST singleton 0.091 AA936892 (not in UniGene) with axon hit 305070 EST singleton 0.091 AA639783 (not in UniGene) with axon hit 304870 Hs.119122 0.091 AA594811 ribosomal protein Ll3a 303856 Hs.944 glucose 0.091 AA968589 phosphate isomerase 323789 Hs.170460 ESTs; Weakly similar 0.092 AI459812 to KIAA0990 protein [H.sapiens]

334910 CH22_FGENES.455 3 0.092 326382 CH.19_hs gi~5867327 0.092 332467 Hs.119004 KIAA0665 gene product 0.092 338534. CH22 EM:AC005500.GENSCAN.402-7 0.092 336449 CH22_FGENES.829 6 0.092 333709 CH22_FGENES.250 24 0.092 336559 CH22_FGENES.842 4 0.092 333230 CH22_FGENES.107-10 0.093 1~ 333133 CH22_FGENES.83-9 0.093 334885 CH22_FGENES.451 11 0.093 330605 Hs.77274 plasminogen activator; 0.093 X02419 urokinase 336392 CH22_FGENES.823 4 0.093 334083 CH22_FGENES.327_38 0.093 15 325469 CH.12_hs gi~6017034 0.093 331077 Hs.19039 ESTs 0.093 303701 EST duster (not in UniGene) with0.093 AW500732 exon hit 334218 CH22_FGENES.358-3 0.093 336542 CH22_FGENES.840-6 0.093 2~ 337151 CH22_FGENES.546-1 0.093 333642 CH22_FGENES231 2 0.093 336863 CH22_FGENES.297-4 0.093 334680 CH22_FGENES.419 2 0.093 -326365 CH.18 hs gi~5867297 0.093 2'Jr338952 CH22_DJ32110.GENSCAN.23-22 0.093 337539 CH22 FGENES.832-4 0.094 333546 CH22_FGENES.180 2 0.094 335258 CH22 FGENES.518 3 0.094 336786 CH22_FGENES.168-19 0.094 3~ 321644 Hs.237396 ESTs 0.094 335943 CH22_FGENES.646-17 0.094 327918 CH.06 hs g1(5868165 0.094 306398 EST singleton (not in UniGene) 0.094 AA970548 with exon hit 335671 CH22_FGENES.592 3 0.094 35 335033 CH22 FGENES.475_11 0.094 338277 CH22 EM:AC005500.GENSCAN.290-2 0.094 332061 Hs.192824 early B-cell factor 0.094 305153 Hs.77039 ribosomal protein S3A 0.094 333880 CH22_FGENES.292 2 0.094 4O 323940 Hs.170880 ESTs 0.094 Ai864428 313779 Hs.129771 ESTs 0.095 323109 EST duster (not in UniGene) 0.095 332930 CH22_FGENES.38 4 0.095 335368 CH22_FGENES.543 6 0.095 45 303887 Hs.193484 ESTs; Weakly simiiar 872672 to Similarity with yeast gene L3502.1 [C.elegans] 0.095 336223 CH22_FGENES.727 3 0.095 311280 Hs.197737 ESTs; Weakly similar 0.095 AI767957 to Y38A8.1 gene product [C.elegans]

337256 CH22_FGENES.648-3 0.095 5O 308814 EST singleton (not in UniGene) 0.095 AI819263 with axon hit 334659 CH22_FGENES.418 7 0.095 335895 CH22_FGENES.635 3 0.095 321697 Hs.4953 golgi autoantigen; golgin0.095 AW388061 subfamily a; 3 -336010 CH22_FGENES.668 S 0.096 55 302824 EST duster (not in UniGene) with0.096 U21260 exon hit 333612 CH22_FGENES.217 7 0.096 304823 EST singleton (not in UniGene) 0.096 AA584837 with exon hit 335665 CH22_FGENES.590_16 0.096 306518 EST singleton (not in UniGene) 0.096 AA989598 with axon hit 335243 CH22_FGENES.516 4 0.096 335436 CH22_FGENES.559 5 0.096 300243 Hs.161271 ESTs 0.096 332810 CH22_FGENES.7 12 0.097 308612 EST singleton (not in UniGene) 0.097 AI735634 with axon hit 65 335818 CH22_FGENES.618 6 0.097 325838 CH.16-hs gi~6552452 0.097 337482 CH22_FGENES.795-6 0.097 336645 CH22_FGENES.26-1 0.097 337293 CH22_FGENES.675-1 0.098 329893 CH.15~2 0.098 gi~6525313 326533 CH.19_hs 0.098 gi~5867441 334905 CH22 FGENES.452 0.098 306347 EST singleton 0.098 AA961144 (not in UniGene) with axon hit 336676 CH22_FGENES.43-4 0.098 339166 CH22 DA59H18.GENSCAN.69-7 0.098 335774 CH22 FGENES.607_10 0.098 339216 CH22 FF113D11.GENSCAN.6-11 0.098 335311 CH22 FGENES.532 0.098 l~ 329632 CH.11~2 6729060 0.098 gi~

328595 CH.07_hs 5868224 0.098 gi~

326928 CH.21 hs 6456782 0.098 gi~

315234 Hs.120770 0.098 A1079680 ESTs 306082 EST singleton 0.098 AA908508 (not in UniGene) with exon hit 15 305710 EST singleton 0.098 AA826544 (not in UniGene) with axon hit 318540 EST cluster 0.099 T30280 (not in UniGene) 337553 CH22-C4G1.GENSCAN.2-1 0.099 320951 Hs.202699 0.099 AA344069 neurexophilin 303845 EST cluster 0.099 T08033 (not in UniGene) with axon hit 20 338981 CH22_DA59H18.GENSCAN2-5 0.099 321313 Hs.26058 0.099 887365 ESTs; Weakly similar to p532 [H.sapiens]

328348 CH.07 hs 0.099 gi~5868383 332203 Hs.102082 0.099 301780 EST cluster 0.099 807064 (not in UniGene) with exon hit 25 332095 Hs.162681 0.099 333227 CH22_FGENES.107_5 0.099 316442 Hs.153023 0.099 AA760894 ESTs 326001 CH.i6 hs 0.099 gi~5867073 334363 CH22 FGENES.378 0.099 3~ 338895 CH22 DJ32110.GENSCAN.9-2 0.099 327460 CH.02 hs 0.099 gi~6004455 332705 Hs.76293 0.1 T59161 thymosin;
beta 10 307806 EST singleton 0.1 AI351739 (not in UniGene) with exon hit 322800 Hs.225175 0.1 F25037 ESTs 3$ 304918 EST singleton 0.1 AA602697 (not in UniGene) with exan hit 334327 CH22 FGENES.375 0.1 318359 Hs.135548 0.1 A1097439 ESTs 326644 CH20_hs 0.1 gi~5867559 334454 CH22_FGENES.388-3 0.1 327959 CH.O6_hs 0.1 gi~5868210 323783 Hs.131819 0.1 AA330586 ESTs 309198 Hs.248038 O.i AI955915 major histocompatl'bility complex;
class I;
C

339265 CH22-BA354112.GENSCAN.10-3 0.1 320576 Hs.162209 AL049977 Homo Sapiens mRNA; cDNA
DKFZp564C122 4$ (from done 0.1 DKFZp564C122) 338132 CH22 EM:AC005500.GENSCAN.200-2 0.1 333163 CH22_FGENES.91 0.101 337584 CH22_C20H12.GENSCAN.5-1 0.101 307588 EST singleton 0.101 AI285535 (not in UniGene) with exon hit 336969 CH22 FGENES.378-2 0.101 327535 CH.02_hs 0.101 gij6525279 328732 CH.07 hs 0.101 gi~5868289 336686 CH22_FGENES.46-3 0.101 -335777 CH22_FGENES.607-13 0.101 55 332944 CH22_FGENES.47 0.101 333174 CH22 FGENES.95_1 0.101 336380 CH22 FGENES.821 0.101 330571 Hs.79089 U60800 sema domain;
immunoglobulin domain (1g);

cytoplasmic 0.101 domain;
(semaphorin) 331789 Hs.186749 0.101 AA398721 ESTs 338915 CH22_DJ32110.GENSCAN.12-1 0.101 334844 CH22 FGENES.439 0.101 336642 CH22 FGENES.23-4 0.101 334906 CH22_FGENES.452 0.101 65 333188 CH22 FGENES.98_8 0.101 300088 EST cluster 0.101 AW299993 (not in UniGene) with axon hit 329373 CH.X_hs 0.102 gi~6682537 331120 Hs.23239 0.102 846576 ESTs 335856 CH22_FGENES.628_1 0.102 331888 Hs.98017 0.102 AA431337 ESTs 333154 CH22 FGENES.89 0.102 335989 CH22 FGENES.655 0.102 304385 EST singleton 0.102 AA235602 (not in UniGene) with axon hit $ 338016 CH22 EM:AC005500.GENSCAN.133-1 0.102 335190 CH22 FGENES.507 0.102 318595 Hs.6137 0.102 T39d86 ESTs 333697 CH22-FGENES.250_11 0.102 306526 EST singleton 0.103 AA989713 (not in UniGene) with axon hit 1~ 328734 CH.07-hsgi~5868289 0.103 307294 Hs.73742 0.103 AI205612 ribosomal protein;
large;
PO

327424 CH.02 hs 0.103 gi~5867751 ~

335872 CH22 FGENES.630-3 0.103 333572 CH22 FGENE5.189_1 0.103 1$ 334.774 CH22-FGENES.430 0.103 338660 CH22-EM:AC005500.GENSCAN.462-1 0.103 326713 CH.20-hs 0.103 gi~5867595 333994 CH22_FGENES.310-18 0.103 335800 CH22-FGENES.613 0.103 318113 Hs.132322 0.103 AIf87943 ESTs 337278 CH22 FGENES.665-1 0.103 336386 CH22_FGENES.822 0.103 334790 CH22-FGENES.432_15 0.103 303778 EST duster 0.104 AW505368 (not in UniGene) with axon hit 25 336524 CH22-FGENES.839 0.104 328936 CH.08-hs 0.104 gi~5868500 335102 CH22_FGENES.494 0.104 300935 Hs.222815 AA513644 ESTs; Weakly similar to Wiskott-Aldrich Syndrome protein 0.104 [H.sapiens]

3~ 307581 EST singleton 0.104 AI284415 (not in UniGene) with axon hit 317301 Hs.226056 0.104 AW291683 ESTs 335330 CH22 FGENES.535 0.104 337968 CH22 EM:AC005500.GENSCAN.103-2 0.104 335627 CH22 FGENES.584 0.104 3$ 336274 CH22_FGENES.762 0.104 334730 CH22 FGENES.424 0.105 334409 CH22 FGENES.383 0.105 327237 CH.01_hs 0.105 gi~5867544 333321 CH22_FGENES.138 0.105 4O 303181 EST duster 0.105 AA452366 (not in UniGene) with axon hit 333738 CH22_FGENES261 0.105 338255 CH22_EM:AC005500.GENSCAN.276-3 0.105 334282 CH22_FGENES.369_12 0.105 330190 CH.05,~2 0.105 gi~6165182 45 310748 Hs.158698 0.105 AW014249 ESTs 338150 CH22_EM:AC005500.GENSCAN.207-2 0.105 336719 CH22_FGENES.82-6 0.105 330228 CH.05~2 6013527 0.105 gi~

327801 CH.05_hs 5867924 0.105 gi~

$~ 330525 Hs.274 megakaryocyte-assodated 0.105 S75168 tyrosine kinase 334972 CH22_FGENES.468 0.105 335111 CH22 FGENES.494-19 0.106 334483 CH22_FGENES.395 0.106 328829 CH.07_hs 0.106 gi~5868337 $$ 302753 EST duster 0.106 M74299 (not in UniGene) with axon hit 334512 CH22 FGENES.398_10 0.106 330024 CH.16~2 0.106 gi~6671908 321030 Hs.233617 AI769930 Homo sapiens (done B3B3E13) Huntington's disease 0.107 candidate region 338410 CH22 EM:AC005500.GENSCAN.341-6 0.107 334353 CH22 FGENES.376 0.107 338276 CH22 EM:AC005500.GENSCAN.288-9 0.107 329053 CH.X-hs 0.107 gi~5868574 336560 CH22-FGENES.842 0.107 ~$ 332158 H5.112980 0.107 336447 CH22_FGENES.829 0.107 333703 CH22_FGENES250_17 O.f07 , 326207 CH.17_hs 0.107 gi~5867222 333232 CH22_FGENES.108_1 0.107 334802 CH22-FGENES.435 1 0.107 303784 EST cluster (not in UniGene) 0.107 AA704983 with axon hit 338847 CH22 DJ246D7.GENSCAN.10-2 0.107 339407 CH22-DJ579N16.GENSCAN.1-9 O.i08 337635 CH22-C20H12.GENSCAN.32-8 0.108 334650 CH22-FGENES.417_17 0.108 308511 EST singleton (not in UniGene) 0.108 AI687580 with exon hit 333392 CH22_FGENES.144_8 0.108 325840 CH.16 0.108 hs gi~6552452 1~ 315044 _ 0.108 AW205664 Hs.129568 ESTs 333298 CH22-FGENES.133 4 0.108 335157 CH22_FGENES.501 7 0.108 333305 CH22-FGENES.137_2 0.108 326379 CH.19 hs gi~5867327 0.108 15 335050 CH22-FGENES.482-1 0.108 305185 Hs.248038 major histocompatibility0.108 AA663985 complex; class I; C

335658 CH22_FGENES.590-9 0.108 323040 Hs.10862 ESTs 0.108 337326 CH22_FGENES.699-6 0.108 2O 339262 CH22 BA354112.GENSCAN.9-6 0.108 321202 Hs.i63639 ESTs; Weakly similar 854052 to INTERCELLULAR ADHESION

MOLECULE-1 PRECURSOR [H.sapiens]0.109 331792 Hs.97548 EST 0.109 333806 CH22 FGENES.278 2 0.109 25 321325 EST duster (not in UniGene) 0.109 331373 Hs.178170 ESTs; Weakly similar AA435513 to DUAL SPECIFICITY

PROTEIN PHOSPHATASE 3 0.87 328775 CH.07 hs gi~5868309 0.109 335105 CH22_FGENES.494_10 0.109 30 300975 Hs.149668 ESTs 0.109 324893 EST duster (not in UniGene) 0.109 333397 CH22-FGENES.144_15 0.109 336484 CH22 FGENES.831 3 0.109 335507 CH22-FGENES.571 22 0.109 35 336373 CH22 FGENES.820-3 0.109 336188 CH22 FGENES.717-12 0.109 313455 Hs.137329 ESTs 0.109 335185 CH22 FGENES.506 4 0.109 306814 EST singleton (not in UniGene) 0.109 A1066577 with exon hit 311130 Hs.195306 ESTs 0.109 310882 Hs.211911 ESTs 0.109 323383 Hs.135209 ESTs 0.11 300212 Hs.184552 biphenylhydrolase-like AW135925 (serine hydrolase; breast epithelial mudn-assoc. 0.11 325675 CH.14_hs gi~5867014 0.11 330095 CH.19~2 gi~6015278 0.11 331942 Hs.99309 ESTs 0.11 334723 CH22_FGENES.421 34 0.11 333614 CH22_FGENES.217_9 0.11 337316 CH22-FGENES.692-1 0.11 305057 Hs.62954 femtin; heavy polypeptide0.11 336704 CH22_EM:AC005500.GENSCAN.480-3 0.11 335385 CH22 FGENES.543 27 - 0.11 338012 CH22_EM:AC005500.GENSCAN.128-100.11 $$ 329449 CH.Y_hsgi~5868886 0.11 338980 CH22-DA59H18.GENSCAN2-4 0.11 336553 CH22 FGENES.841 10 0.111 330021 CH.16~2 gi~6671889 0.111 327579 CH.03_hs gi~5867824 0.111 60 333099 CH22_FGENES.79_4 0.111 337076 CH22_FGENES.453-4 0.111 331388 Hs.43543 suppressor of white 0.111 AA456852 apricot homolog 2 306674 Hs.180414 heat shod< 70kD protein0.111 A1005542 10 (HSC71) 305949 EST singleton (not in UniGene) O.i AA88d409 with exon hit 11 65 330748 Hs.15911 DKFZP586E1422 protein 0.111 33,9780 CH22 FGENES273 2 0.111 323676 EST duster (not in UniGene) 0.111 308952 Hs.224226 EST 0.111 309338 Hs.181165 eukaryoGc translation0.111 AW026946 elongation factor 1 alpha 1 329317 CH.X_hs gi~6381976 0.112 333518 CH22 FGENES.173 3 0.112 306982 EST singleton (not in UniGene)0.112 A1127883 with axon hit 336225 CH22 FGENES.728 2 0.112 $ 333698 CH22-FGENES250_12 0.112 302173 Hs.14068 ESTs 0.112 335510 CH22 FGENES.571 25 0.112 328042 CH.06 hs gi~5902482 0.112 336512 CH22 FGENES.834 7 0.112 1~ 328541 CH.07-hs gi~5868486 0.112 311265 Hs.199214 ESTs 0.112 323218 Hs.13396 Homo sapiens done 0.112 AF131846 25028 mRNA sequence 302002 Hs.123085 chromobox homolog 0.112 AF013956 4 (Drosophila Pc class) 315088 Hs.152448 ESTs; Moderately ADE2 AA557351 similar to MULTIFUNCTIONAL 0.112 PROTEIN

1$ 312581 Hs.176590 ESTs 0.112 322246 Hs.125258 ESTs 0.112 333659 CH22 FGENES.241 5 0.113 327510 CH.02-hs gi~6117815 0.113 336520 CH22-FGENES.839 1 0.113 336682 CH22_EM:AC005500.GENSCAN.472-10.113 334508 CH22-FGENES.398_6 0.113 322533 EST cluster (not in UniGene) 0.113 306873 EST singleton (not in UniGene)0.113 A1086929 with axon hit 336040 CH22-FGENES.679 2 0.113 ~$ 303898 EST dusfer (not in UniGene) 0.113 T23215 with axon hit 312011 Hs.187226 ESTs 0.113 335186 CH22 FGENES.506 5 0.113 333607 CH22-FGENES.216_2 0.113 305549 EST singleton (not in UniGene)0.113 AA773530 with exon hit 3~ 333686 CH22 FGENES.249_4 0.113 334352 CH22 FGENES.376_3 0.113 338195 CH22-EM:AC005500.GENSCAN.233-180.114 , 333588 CH22-FGENES.206 2 0.114 339233 CH22 BA354112.GENSCAN2-3 0.114 35 337455 CH22 FGENES.777-1 0.114 309101 EST singleton (not in UniGene)0.114 AI925108 with exon hit 328522 CH.07 hs gi~5868477 0.114 323999 Hs.252782 ESTs 0.114 333517 CH22-FGENES.173_2 0.114 329935 CH.16,~2 gi~6165200 O.il4 326226 CH.17_hs gi~5867230 0.114 335890 CH22_FGENES.633 4 0.114 336715 CH22 FGENES.77-1 0.114 327640 CH.04_hs gi~5867890 0.114 4$ 336842 CH22_DJ246D7.GENSCAN.7-1 0.114 306534 EST singleton (not in UniGene)0.114 AA991487 with exon hit 336597 CH22_FGENES.266_1 0.114 321010 Hs.227150 Hamo sapiens LSFR2 0.114 Y17456 gene; last axon 302294 Hs.5337 isodtrate dehydrogenase0.114 AA159213 2 (NADP+); mitochondria) $~ 324895 Hs.77515 inositol 1;4;5-tdphosphate0.114 N44238 receptor; type 3 327358 CH.01 hs gi~6552411 0.114 308792 Hs.195188 glyceraldehyde-3-phosphate0.115 AI815153 dehydrogenase 325886 CH.16 hs gi~5867087 - 0.115 336850 CH22 FGENES272-11 0.115 55 305858 EST singleton (not in UniGene)0.115 AA863103 with exon hit 302569 multiple UniGene matches 0.115 336158 CH22 FGENES.707_2 0.115 327866 CH.06-hs gi~5868131 0.115 339157 CH22 DA59H18.GENSCAN.67-3 0.115 339258 CH22 BA354112.GENSCAN.8-3 0.115 336129 CH22-FGENES.701_17 0.115 333684 CH22-FGENES.249 2 0.115 309618 Hs.184776 ribosomal protein 0.115 AW190162 123a 312926 Hs.127523 ESTs 0.115 6$ 302640 EST duster (not in UniGene) 0.115 A8035698 with axon hit 328968 CH.08-hs gi~6456775 0.115 327gp2 CH.06_hs gi~5868158 0.115 321927 EST duster (not in UniGene) 0.115 335962 CH22_FGENES.651 4 0.115 334927 CH22_FGENES.460_1 0.115 330535 U11872Human interleukin-8 receptoriype B (IL8RB) mRNA, splice variant 0.856 328591 CH.07_hs 0.115 g1[5868227 334902 CH22 FGENES.452 0.115 i6 328525 CH.07 hs 0.115 gi~5868482 325870 CH.16 hs 0.116 gi~6682492 337522 CH22-FGENES.819-1 0.116 305079 AA641329EST singleton 0.116 (not in UniGene) with exon hit 1~327343 CH.Ot hsgi[6017017 0.116 333918 CH22-FGENES.296 0.116 333600 CH22 FGENES.213_2 0.116 335846 CH22 FGENES.623 0.116 333510 CH22-FGENES.171 0.116 IS327629 CH.04_hsgi~5867872 0.116 333470 CH22_FGENES.161 0.116 326855 CH.20_hs 6552460 0.116 g1[

327008 CH.2i hs 5667664 0.117 g1[

337480 CH22_FGENES.795-3 0.117 2~336425 CH22 FGENES.824_10 0.117 321964 AL079687Hs.171065 0.117 ESTs 335651 CH22 FGENES.590 0.117 308164 AI521574Hs.i81165 0.117 eukaryotic Uanslation elongation factor 1 alpha 337927 CH22-EM:AC005500.GENSCAN.80-3 0.117 2$300341 H45095Hs.153524 0.117 ESTs 300154 AI245127Hs.179331 0.117 ESTs 306295 AA937331EST singleton 0.117 (not in UniGene) with exon hit 329670 CH.14,~2 0.117 gi~6272129 335612 CH22 FGENES.583 0.117 3~307845 A1363450EST singleton 0.117 (not in UniGene) with exon hit 330401 D28383Human mRNA from for ATP the synthase B chain, 5'UTR (sequence 5'cap to 0.117 the start colon) 327127 CH.21 hs 0.117 g1[6682520 333843 CH22_FGENES.290_1 0.117 35331083 817762Hs.22292 0.117 ESTs 329140 CH.X_hs 0.117 g1[6017060 339338 CH22-BA354112.GENSCAN27-3 0.117 331974 AA464518Hs.99616 0.117 ESTs 338631 CH22_EM:AC005500.GENSCAN.454-2 0.117 330299 CH.06~2 [2905881 0.117 g1 330351 CH.09~2 [3056622 0.117 g1 305377 AA715714Hs.181357 0.117 laminin receptor 1 (67kD;
ribosomal protein SA) 333106 CH22_FGENES.79 0.117 338514 CH22 EM:AC005500.GENSCAN.392-4 0.117 45327335 CH.01 hs 0.117 g1[5902477 301970 AB028962Hs.120245 0.118 protein 326339 CH.17 hs 0.118 g1[6056311 330612 X15673Hs.93174 0.118 Human endogenous retrovirus pHE.i (ERV9) 334178 CH22_FGENES.350 0.118 328008 CH.06_hs 0.118 g1[5902482 329976 CH.16~2 0.118 g1[4878063 320952 AA897432Hs.130411 0.118 ESTs 305621 AA789095EST singleton 0.118 (not in UniGene) with exon hit -337850 CH22 EM:AC005500.GENSCAN.34-3 0.118 55333626 CH22 FGENES.224_2 0.118 337672 CH22 EM:AC000097.GENSCAN.67-1 0.118 328803 CH.07 hs 0.118 g1[6004475 325922 CH.16_hs 0.118 g1[5867122 3344gg CH22 FGENES.397-1 0.118 320638 854766Hs.101120 0.118 ESTs 321932 AA569229EST cluster 0.118 (not in UniGene) 336958 CH22 FGENES.367-1 0.118 332082 AA600176Hs.t12345 0.118 ESTs 306004 AA889992EST singleton 0.118 (not in UniGene) with axon hit 65336803 CH22 FGENES.194-1 0.118 309107 AI925823EST singleton 0.118 (not in UniGene) with axon hit 336859 CH22 FGENES.293-9 0.118 337935 CH22 EM:AC005500.GENSCAN.85-6 0.118 326492 CH.19_hs 0.118 g1[5867422 327289 CH.01 hs 5867481 0.119 gi~

325818 CH.14_hs 6682490 0.119 gi~

310787 Hs.159040 0.119 AW262580 ESTs 330028 CH.16~2 0.119 gi~6671908 $ 325317 CH.11 hs 0.119 gi~5866878 335279 CH22 FGENES.523_7 0.119 331720 Hs.221530 O.il9 AAi92i73 ESTs 329186 CH.X hs 0.119 gi~5868711 316012 Hs.119898 0.119 AA764950 ESTs 338316 CH22 EM:AC005500.GENSCAN.304-2 0.119 326033 CH.17_hs 0.119 gi~5867178 334745 CH22_FGENES.426 0.119 333051 CH22_FGENES.73_5 0.119 301763 EST cluster 0.12 801279 (not in UniGene) with exon hit 1$ 304502 Hs.172928 0.12 AA454809 collagen;
type I;
alpha 1 335680 CH22 FGENES.594 0.12 304678 EST singleton 0.12 AA548556 (not in UniGene) with exon hit 335441 CH22_FGENES.560 0.12 336187 CH22_FGENES.717-11 0.12 309422 EST singleton 0.12 AWQ87i75 (not in UniGene) with exon hit 336047 CH22_FGENES.679_9 0.12 309651 EST singleton 0.12 AW195850 (not in UniGene) with exon hit 308547 Hs.201903 0.12 304443 EST singleton 0.12 AA399444 (not in UniGene) with exon hit 336245 CH22_FGENES.746 0.12 302703 EST cluster 0.12 H72333 (not in UniGene) with exon hit 335690 CH22 FGENES.596 0.12 328941 CH.08 hs 0.12 gi~6456765 333873 CH22-FGENES.291 0.12 317246 Hs.155690 0.12 AW105092 ESTs 339288 CH22_BA354112.GENSCAN.16-6 0.12 337996 CH22_EM:AC005500.GENSCAN.116-3 0.12 333304 CH22_FGENES.137_1 0.121 308332 EST singleton 0.121 AI591235 (not in UniGene) with exon hit 3$ 329319 CH.X_hs 0.121 gi~6381976 302086 multiple 0.121 X57138 UniGene matches 333290 CH22_FGENES.i29 O.i21 323825 Hs.123525 AI793080 ESTs; Weakly similar to NEUTROPHIL
GELATINASE-ASSOCIATED

LIPOCALIN 0.121 PRECURSOR
[R.norvegicus]

330575 Hs.252280 0.121 064105 Rho guanine nucleotide exchange factor (GEF) 1 305274 Hs.181165 0.121 AA679990 eukaryoGc translation elongation factor 1 alpha 333647 CH22_FGENES.235 0.121 302251 EST cluster 0.121 AA333340 (not in UniGene) with exon hit 329777 CH.14~2 0.121 gi~6002090 333155 CH22_FGENES.89_5 0.121 326122 CH.17 hs 0.121 gi~5867194 335310 CH22_FGENES.532 0.121 335453 CH22 FGENES.562 0.122 305103 Hs.111334 0.122 AA643329 femtin;
light polypeptide $0 337284 CH22_FGENES.667-2 0.122 337418 CH22_FGENES.758-4 0.122 313073 Hs.46826 0.122 AI963740 ESTs 303759 EST cluster 0.122 AW504164 (not in UniGene) with exon hit -$$ M33197 AFFX control: 0.122 GAPDH

316725 Hs.127264 0.122 AW135084 ESTs 330738 Hs.120980 0.122 AA293153 nuclear receptor co-repressor 336466 CH22 FGENES.829 0.122 335956 CH22-FGENES.647-3 0.122 60 315308 Hs.189053 0.122 AA780564 ESTs 338925 CH22 DJ32110.GENSCAN.14-3 0.122 334969 CH22 FGENES.466 0.122 322050 EST duster 0.122 AL137589 (not in UniGene) 339084 CH22 DA59H18.GENSCAN.38-2 0.122 6$ 338323 CH22_EM:AC005500.GENSCAN.306-2 0.122 337003 CH22 FGENES.419-7 0.122 325470 CH.12 hs 0.123 gi~6017034 336503 CH22_FGENES.833_10 0.123 330786 Hs258712 0.123 329446 CH.Y_hs 0.123 gi~5868886 303326 AA229433Hs.222634 ESTs; Moderately similar to ubiquitin-like protein ribosomal 0.123 protein 309067 AI916313Hs.212788 0.123 EST

317464 AA968472Hs.130463 0.123 ESTs 328755 CH.07 hs ~5868301 0.123 g1 326036 CH.17 hs ~5867178 0.123 g1 327208 CH.01 hs 5867447 0.123 gi~

326124 CH.17_hs 5916395 0.123 gi~

1 327509 CH.02 hs 6117815 0.123 O gi~

338398 CH22-EM:AC005500.GENSCAN.336-5 0.123 304652 AA527782Hs.84298 CD74 antigen (invariant polypeptide of major histocompatibility 0.123 complex;
class II
antigen-associated) 335797 CH22 FGENES.612 0.124 B .

15 336714 CH22 FGENES.76-29 0.124 327204 CH.01 h5 0.124 gi~5867447 331881 AA430672Hs.123778 0.124 ESTs 306971 A1126509EST singleton 0.124 (not in UniGene) with exon hit 336174 CH22_FGENES.710_1 0.124 2O 336126 CH22_FGENES.70113 0.124 329129 CH.)Lhs 0.124 gi~6588026 303049 AW407562EST duster 0.124 (not in UniGene) with exon hit 335778 CH22 FGENES.607_14 0.124 336601 CH22_FGENES.369-2 0.124 25 334340 CH22_FGENES.37517 0.124 337436 CH22_FGENES.767-1 0.124 306013 AA896990EST singleton 0.124 (not in UniGene) with exon hit 339213 CH22 FF113D11.GENSCAN.6-8 0.124 335355 CH22 FGENES.541 0.124 336552 CH22 FGENES.841 0.124 336384 CH22 FGENES.822 0.124 310485 AI286202Hs.149800 0.125 ESTs 335840 CH22 FGENES.622 0.125 336444 CH22 FGENES.827_10 0.125 35 315703 N36070EST duster 0.125 (not in UniGene) 327763 CH.05_hs 0.125 gi~5867961 336383 CH22_FGENES.822 0.125 333496 CH22_FGENES.168_6 0.125 328662 CH.07_hs 0.125 gi~6004473 4O 338986 CH22_DA59H18.GENSCAN.S-1 0.125 328311 CH.07 hs 0.125 gij586837i 337241 CH22_FGENES.644-2 0.125 336933 CH22_FGENES.350-7 0.125 313483 AW294432Hs.144252 0.125 ESTs 45 326116 CH.17 hs 0.125 gi~5867193 330450 HG363-HT363Epidermal 0.125 Growth Factor Receptor-Related Protein 307491 AI268539EST singleton 0.125 (not in UniGene) with axon hit 331852 AA418988Hs.98314 Homo sapiens mRNA; d)NA
DKFZp586L0120 (from done 0.125 OKFZp586L0120) 5O 330462 HG944-HT944Dopamine 0.125 Receptor 304410 AA284508EST singleton 0.125 (not in UniGene) with exon hit 336365 CH22 FGENES.822 0.125 336793 CH22 FGENES.176-3 0.125 -326243 CH.17 5867261 0.125 hs gi~

55 327266 _ 5867462 0.125 CH.01 hs gi~

320753 AF070579Hs.lBi 544 0.125 Homo Sapiens clone 24487 mRNA sequence 336960 CH22 FGENES.369-5 0.125 329667 CH.14~2 0.125 gi~6272129 328168 CH.06 hs 0.125 gi~5868071 336534 CH22 FGENES.839 0.125 i6 339289 CH22 BA354112.GENSCAN.16-9 0.126 309230 AI970747EST singleton 0.126 (not in UniGene) with axon hit 339190 CH22 FF113D11.GENSCAN.1-2 0.126 337086 CH22 FGENES.458-14 0.126 6$ 319233 821054Hs.211522 0.126 ESTs 339396 CH22_BA232E17.GENSCAN.6-8 0.126 331930 AA449077Hs.179765 Homo sapiens mRNA; d)NA
DKFZp586H1921 (from done 0.126 DKFZp586H192 308099 AI475914EST singleton 0.126 (not in UniGene) with axon hit 338477 CH22 EM:AC005500.GENSCAN.373-5 0.126 334286 CH22 FGENES.369_16 0.126 317245 A1025039Hs.131732 0.126 ESTs 335249 CH22 FGENES.516 0.126 333327 CH22 FGENES.138 0.126 304240 AA009802EST singleton 0.126 (not in UniGene) with axon hit 335464 CH22 FGENES.562 0.126 335236 CH22 FGENES.515_8 0.126 334154 CH22 FGENES.340 0.126 1 309257 AI984183EST singleton 0.126 O (not in UniGene) with axon hit 310015 AI220122Hs.201981 ESTs; Weakly similar to breast carcinoma-associated antigen [H.sapiens] 0.126 328280 CH.07_hs 0.126 gi~5868352 305744 AA831819EST singleton 0.126 (not in UniGene) with exan hit I 327430 CH.02_hs 0.126 S gi~5867754 328323 CH.07_hs 0.126 gi~5868373 333274 CH22-FGENES.123 0.126 337193 CH22 FGENES.575-3 0.127 334820 CH22_FGENES.437 0.127 2~ 328706 CH.07_hs 0.127 gi~5868270 331228 W67267Hs.174911 0.127 ESTs 307205 A1192479EST singleton 0.127 (not in UniGene) with axon hit 337123 CH22 FGENES.519-3 0.127 ' 326201 CH.17_hs 0.127 gi~5867216 25 335276 CH22 FGENES.523-2 0.127 331202 T81115Hs.191136 0.127 ESTs 330532 003187Hs.121544 0.127 interleukin 12 receptor, beta 1 321235 N49521EST cluster 0.127 (not in UniGene) 301743 F12605Hs.204529 0.127 ESTs; Weakly similar to reverse transcriptase [H.sapiens]

328175 CH.06 hs 0.127 gi~5868073 306407 AA971985EST singleton 0.127 (not in UniGene) with axon hit 327145 CH.01 hs 5867548 0.127 gi~

327649 CH.04-hs 5867899 0.127 gi~

335142 CH22_FGENES.498 0.127 35 333909 CH22-FGENES.295 0.127 330608 X04325Hs.2679 gap junction protein;
beta 1;
32kD (connexin 32;

Charcot-Marie-Tooth 0.127 neuropathy;
X-linked) 330158 CH.21~2 0.127 gi[6580367 320153 AF064594Hs.120360 0.127 phospholipase A2; group VI

4~ 314407 AA098835Hs.224432 0.127 ESTs 333383 CH22_FGENES.143_22 0.127 320663 AI734242Hs244473 0.128 ESTs 326233 CH.17_hs 0.128 gi~5867232 326598 CH.20_hs 0.128 gi~5867634 45 335174 CH22 FGENES.504 0.128 319843 H29920Hs.99486 0.128 ESTs; Weakly similar to aralari [H.sapiens]

335458 CH22_FGENES.562 0.128 332997 CH22_FGENES.58 0.128 334188 CH22_FGENES.352 0.128 329759 CH.14~2 0.128 gi~6048280 330348 CH.09~2 0.128 gi~4544475 326958 CH.21 hs 0.128 gi[6469836 305263 AA679467EST singleton 0.128 (not in UniGene) with axon hit -337693 CH22_EM:AC000097.GENSCAN.78-14 0.128 326812 CH.20_hs 0.128 gi~6682504 333237 CH22_FGENES.108 0.128 333699 CH22_FGENES250_13 0.128 311496 AI768677Hs.209888 ESTs; Weakly similar to phosphatidylserine synthase-2 0.128 [M.musculus]

6O 336499 CH22-FGENES.833 0.128 320087 AF032387Hs.113265 0.128 small nuclear RNA activating complex;
polypeptide 4;190kD

309989 AI184186Hs.197813 0.128 ESTs 301490 AW298468Hs.250461 0.128 ESTs 337011 CH22_FGENES.427-6 0.128 65 315052 AA876910Hs.134427 0.128 ESTs 301611 W22172Hs.59038 0.128 ESTs 336497 CH22_FGENES.833 0.129 302068 Y16280Hs.132049 0.129 endothelin type b receptor-like protein 334502 CH22_FGENES.397_18 0.129 304332 EST singleton (not in UniGene) 0.129 AA158884 with axon hit 304522 EST singleton (not in UniGene) 0.129 AA465405 with axon hit 312407 Hs.153485 ESTs 0.129 310098 Hs.161354 ESTs 0.129 S 301119 EST cluster (not in UniGene) 0.129 AF142579 with axon hit 309268 Hs.62954 ferritin; heavy polypeptide0.129 330989 Hs.226396 DEADM (Asp-Glu-Ala-AspMis) H42142 box polypeptide 19 (DbpS; yeast; homology 0.129 336949 CH22 FGENES.361-4 0.129 IO 330115 CH.19~2 gi~6015202 0.129 339212 CH22_FF113D11.GENSCAN.6-7 0.129 326951 CH.21 hs gi~6004446 0.129 305165 EST singleton (not in UniGene) 0.129 AA662939 with axon hit 308238 EST singleton (not in UniGene) 0.129 AI559492 with axon hit IS 337140 CH22-FGENES.537-5 0.13 321758 EST cluster (not in UniGene) 0.13 304619 Hs.119598 ribosomal protein 0.13 312469 Hs.173088 ESTs 0.13 339017 CH22-DA59H18.GENSCAN20-6 0.13 2O 330116 CH.19~2 gi~6015202 0.13 333312 CH22 FGENES.138 4 0.13 338004 CH22 EM:AC005500.GENSCAN.121-1 O.i3 _ 314141 Hs.190028 ESTs 0.13 300509 Hs.128494 ESTs; Weakly similar 0.13 AI239845 to EG:95B72 [D.melanogaster]

2S 338530 CH22 EM:AC005500.GENSCAN.398-110.13 335968 CH22 FGENES.652_1 0.13 314121 Hs.187619 ESTs 0.13 337593 CH22_C20H12.GENSCAN.6-8 0.13 332881 CH22 FGENES.33-1 0.13 3O 305836 EST singleton (not in UniGene) 0.13 AA858043 with axon hit , 339059 CH22 DA59H18.GENSCAN.30-5 0.13 305610 EST singleton (not in UniGene) 0.13 AA782319 wish axon hit 305852 EST singleton (not in UniGene) 0.13 AA862455 with axon hit 327409 CH.02_hs gi~5867750 0.13 3S 312751 Hs.i64178 ESTs 0.13 308726 Hs.209929 EST 0.13 325961 CH.16-hs gi~5867147 0.13 311159 Hs.197636 ESTs 0.13 322715 Hs.182135 ESTs 0.13 4O 336441 CH22 FGENES.827 7 0.13 336339 CH22_FGENES.814_12 0.13 306911 EST singleton (not in UniGene) 0.13 A1095365 with axon hit 333613 CH22_FGENES.217 8 0.13 338489 CH22_EM:AC005500.GENSCAN.384-170.131 4S 326904 CH.21 hs gi~5867684 0.131 337337 CH22-FGENES.717-1 0.131 326752 CH.20_hs gi~5867615 0.131 303977 EST singleton (not in UniGene) 0.131 AW512978 with axon hit 301373 EST cluster (not in UniGene) 0.131 AA595235 with axon hit SO 338448 CH22 EM:AC005500.GENSCAN.359-220.131 333774 CH22-FGENES.272 5 0.131 332986 CH22 FGENES.54-8 0.131 335362 CH22 FGENES.541 12 - 0.131 335896 CH22 FGENES.635 4 0.131 SS 337825 CH22-EM:AC005500.GENSCAN.13-19 0.131 325257 CH.11 hs gi~5866895 0.131 331188 Hs.i67837 ESTs 0.131 330645 Hs.144879 dual specificity phosphatase0.131 331760 Hs.154434 ESTs; Weakly similar 0.131 AA292721 to unknown [H.sapiens]

6O 322995 Hs.29797 ribosomal protein L10 0.131 335497 CH22 FGENES.571 5 0.131 334824 CH22 FGENES.437_6 0.131 319480 Hs.184221 ESTs 0.131 334842 CH22 FGENES.439 21 0.131 6S 333335 CH22 FGENES.139 4 0.131 317252 Hs.130124 ESTs 0.131 329034 CH.X_hs gi~5868561 0.131 305186 EST singleton (not in UniGene) 0.131 AA664230 with axon hft 335755 CH22_FGENES.604 4 0.131 302143 Hs.189847 0.131 H15270 putative neuronal cell adhesion molecule 334939 CH22 FGENES.465 0.131 318994 Hs.17802 0.131 C15110 ESTs 334498 CH22 FGENES.397 0.131 333413 CH22 FGENES.146 0.132 329676 CH.14~2 0.132 gi~6272128 327277 CH.01 hs 0.132 gi~5867473 305022 EST singleton 0.132 AA627416 (not in UniGene) with axon hit 336805 CH22 FGENES.196-3 0.132 IO 320121 EST duster 0.132 T93657 (not in UniGene) 334761 CH22_FGENES.428_10 0.132 339400 CH22 BA232E17.GENSCAN.7-6 0.132 330301 CH.06~2 0.132 gi~2905862 316822 Hs.129967 AA827691 ESTs; Weakly similar to neuronal thread protein 1$ AD7o-NTP 0.132 [H.sapiens) 328020 CH.O6_hs 5902482 0.132 gi~

325327 CH.11 hs 5866875 0.132 gi~

321163 EST duster not in UniGene) 0.132 AA209530 ( 336393 CH22 FGENES.823 0.132 325905 CH.16_hs 0.132 gi~5867104 305237 Hs2186 eukaryotic 0.132 AA676286 translation elongation factor 1 gamma 339046 CH22-DA59H18.GENSCAN.28-6 0.132 325375 CH.12 hs 0.132 gi~5866920 -333961 CH22-FGENES.304-7 0.132 25 335450 CH22_FGENES.562 0.133 302286 EST duster 0.133 858438 (not in UniGene) with axon hit 335116 CH22 FGENES.496 0.133 327333 CH.01_hs 0.133 gi~5902477 308070 EST singleton 0.133 AI470948 (not in Un!Gene) with axon hit 30 308311 EST singleton 0.133 AI581855 (not in UniGene) with axon hit 320813 Hs.208839 0.133 AW360847 ESTs 323665 EST duster 0.133 AW248307 (not in UniGene) 328318 CH.07 hs 5868373 0.133 gi~

320603 EST duster not in Un!Gene) 0.133 851419 ( 3$ 332791 CH22_FGENES.3_1 0.133 314976 Hs.162108 0.133 AA524725 ESTs 303309 Hs224868 0.133 AL134164 ESTs 320581 Hs.170187 0.133 839753 ESTs 333944 CH22_FGENES.302 0.133 317992 Hs.130901 0.133 AI733512 ESTs 330935 Hs.26492 0.133 F02383 beta-1;3-glucuronyltransferase 3 (glucuronosyltransferase 1) 336659 CH22_FGENES.36-5 0.133 338887 CH22_DJ32110.GENSCAN.6-10 0.133 305273 Hs.181165 0.133 AA679979 eukaryotic translation elongation factor 1 alpha 45 333566 CH22_FGENES.183 0.134 316952 Hs.163312 0.134 AW450033 ESTs 333818 CH22_FGENES283 0.134 328687 CH.07_hs 5868262 0.134 gi~

302879 EST duster not in UniGene) with 0.134 H11802 ( axon hit SO 336557 CH22_FGENES.842-2 0.134 335222 CH22-FGENES.513 0.134 338094 CH22_EM:AC005500.GENSCAN.179-3 0.134 337384 CH22-FGENES.745-1 0.134 -327360 CH.01 hs 6552411 0.134 gi~

55 328132 CH.O6 hs 5868038 0.134 gi~

323604 Hs.182827 ly similar to !1!!
AI751438 ESTs; Weak ALU SUBFAMILY SQ

WARNING 0.134 ENTRY !!!!

337591 CH22_C20H12.GENSCAN.6-6 0.134 307018 EST singleton 0.134 A1140639 (not in UniGene) with axon hit 326896 CH.21 hs 0.134 gi~5867680 333479 CH22 FGENES.163 0.134 337915 CH22 EM:AC005500.GENSCAN.61-3 0.134 335110 CH22_FGENES.494-18 0.134 333481 CH22 FGENES.163 O.i34 327512 CH.02 hs 0.134 gi~6117815 300096 Hs.83575 0.134 AW328639 ESTs; Weakly similar to ZC328.3 (C.elegans) 330163 CH.02~2 0.135 gi~6042042 335752 CH22_FGENES.604-1 0.135 334857 CH22_FGENES.443_1 0.135 244.

301872 EST duster (not in UniGene) with 0.135 H84730 axon hit 337529 CH22 FGENES.823-29 0.135 335734 CH22_FGENES.601 4 0.135 337551 CH22-FGENES.847-8 0.135 $ 309078 Hs.77961 ma]or histocompaUbility 0.135 AI920965 complex; class I; 8 335513 CH22 FGENES.571 28 0.135 339078 CH22 DA59Hi8.GENSCAN.37-6 0.135 321907 Hs.148722 ESTs; Weakly similar 0.135 N56660 to large tumor suppressor 1 [H.sapiens]

337189 CH22 FGENES.571-32 0.135 1~ 329635 CH.12~2 gi~5302817 0.135 308601 EST singleton (not in UniGene) 0.135 AI719930 with axon hit 305020 Hs.2064 vimentin 0.135 333894 CH22 FGENES.293-1 0.135 322465 Hs.3784 ESTs; Highly similar to AA137152 phosphoserine aminotransferase 15 [H.sapiensJ 0.135 305601 EST singleton (not in UniGene) 0.135 AA780975 with axon hit 332186 Hs.141051 ESTs; Moderately similar H10781 to !!!! ALU SUBFAMILY SB

WARNING ENTRY 0.135 327822 CH.05-hs gi]5867968 0.135 2~ 310087 Hs.160624 ESTs; Weakly similar AI393914 to similar to CR16; SH3 domain binding protein 0.135 328752 CH.07 hs gi~5868298 0.135 337611 CH22 C20H12.GENSCAN.19-4 0.135 334470 CH22 FGENES.394-1 0.136 25 335115 CH22 FGENES.496-2 0.136 328730 CH.07 hs gi~5868289 0.136 330350 CH.09~2 gi~3056622 0.136 336971 CH22 FGENES.378-6 0.136 308258 EST singleton (not in UniGene) 0.136 AI565612 with axon hit 326745 CH.20_hs gi~5867611 0.136 335440 CH22 FGENES.560 3 0.136 320257 EST duster (not in UniGene) 0.136 328677 CH.07_hs gi~5868256 0.136 329731 CH.14~2 gi~6065783 0.136 35 315950 Hs.206974 ESTs 0.136 330049 CH.17,~2 gi~4567182 0.136 337070 CH22_FGENES.448-3 0.136 304095 Hs.31059 EST 0.136 309304 Hs.232820 EST 0.136 4~ 333458 CH22_FGENES.157 7 0.136 329899 CH.15~2 gi]6563505 0.136 322202 Hs.200133 ESTs 0.136 333991 CH22_FGENES.310_15 0.136 318617 Hs.75514 nudeoside phosphorylase 0.136 45 310623 Hs.195588 ESTs 0.136 330489 Hs.3003 CD3E antigen; epsilon 0.136 M23323 polypeptide (TT3 complex) 309646 EST singleton (not in UniGene) 0.136 AW194694 with axon hit 331068 Hs.191199 ESTs 0.136 334285 CH22_FGENES.369_15 0.136 332178 Hs.100725 EST 0.136 305724 EST singleton (not in UniGene) 0.136 AA827608 with axon hit 303158 Hs.8594 Homo sapiens mRNA containing0.136 AL138110 (CAG)4 repeat; clone CZ-CAG-7 334543 CH22 FGENES.403 8 - 0.136 335384 CH22 FGENES.543 26 0.136 55 336527 CH22 FGENES.839-8 0.136 334951 CH22_FGENES.465-20 0.136 325882 CH.16 hs gi~5867087 0.137 305134 EST singleton (not in UniGene) 0.137 AA653159 with axon hit 307058 EST singleton (not in UniGene) 0.137 A1148709 with axon hit 6O 331943 Hs.178272 ESTs 0.137 331116 Hs.22634 ESTs 0.137 306094 EST singleton (not in UniGene) 0.137 AA908877 with axon hit 333561 CH22-FGENES.180_18 0.137 321439 EST duster (not in UniGene) 0.137 324594 EST duster (not in UniGene) 0.137 337926 CH22_EM:AC005500.GENSCAN.77-4 0.137 337353 CH22_FGENES.726-1 0.137 331836 Hs.104774 EST 0.137 308981 EST singleton (not in UniGene) 0.137 AI873242 with axon hit 329424 CH.Y_hs 0.137 gi~5868879 325829 CH.15_hs 0.137 gi~5867052 331845 Hs.98183 0.137 AA416863 ESTs 333854 CH22_FGENES.290_13 0.137 $ 306591 EST singleton 0.137 AI000248 (not in UniGene) with axon hit 328948 CH.OB hs 0.137 gi~6456765 338935 CH22_DJ32110.GENSCAN.18-12 0.137 325960 CH.16 hs ~5867147 0.137 g1 328377 CH.07 hs ~5868390 0.138 g1 1~ 308851 EST singleton 0.138 AI829820 (not in UniGene) with axon hit 314620 Hs.210586 0.138 AA424352 ESTs 337592 CH22-C20H12.GENSCAN.6-7 0.138 338684 CH22 EM:AC005500.GENSCAN.472-3 0.138 331800 Hs.97543 0.138 AA400498 ESTs 1$ 304587 EST singleton 0.138 AA505535 (not in UniGene) with axon hit 333981 CH22-FGENES.310-4 0.138 332452 Hs.1 1 170 0.138 AA040369 SYT interacting protein 305752 EST singleton 0.138 AA835278 (not in UniGene) with axon hit .

311947 Hs.251591 0.138 333783 CH22_FGENES.273-5 0.138 337406 CH22-FGENES.754-14 0.138 327976 CH.06_hs 5868212 0.138 gi~

325593 CH.13_hs 5866992 0.138 gi~ ' 339425 CH22_DJ579N16.GENSCAN.14-4 0.138 2$ 304475 EST singleton 0.138 AA428879 (not in UniGene) with axon hit 309488 EST singleton 0.138 AW131104 (not in UniGene) with axon hit 337532 CH22-FGENES.827-6 0.138 317234 Hs.126368 0.138 AA904448 ESTs 312261 Hs.144455 0.138 AA854425 ESTs 328927 CH.08 hs 0.138 gi~5868500 336424 CH22 FGENES.824-9 0.138 326667 CH.20_hs 6552455 0.138 gi~

325988 CH.16-hs 5867064 0.138 gi~

318446 EST clusternot in UniGene) 0.139 AW300287 ( 35 336511 CH22_FGENES.834_6 0.139 335204 CH22 FGENES.50B 0.139 303244 EST cluster 0.139 AA147472 (not in UniGene) with axon hit 330870 Hs.187593 0.139 AA115804 ESTs 329376 CH.X-hs 0.139 gi~5868859 4~ 304703 EST singleton 0.139 AA563898 (not in UniGene) with axon hit 333653 CH22_FGENES.239 0.139 306799 EST singleton 0.139 A1051696 (not in UniGene) with axon hit 304872 EST singleton 0.139 AA595289 (not in UniGene) with axon hit 330812 Hs.60563 0.139 AA013001 ESTs 45 329568 CH.10~2 0.139 gi~3962490 319210 Hs.146261 0.139 AA253074 ESTs 334320 CH22 FGENES.374 0.139 300860 Hs.149748 0.139 AI916949 ESTs; Weakly similar to weak similarity to collagens [C.elegans]

305866 EST singleton 0.139 AA864533 (not in UniGene) with axon hit $~ 312943 Hs.119064 0.139 AA984364 ESTs 330523 Hs.83958 0.139 M99439 transducin-like enhancerof split4;
homolog of Drosophila E(spi) 312708 Hs.135440 0.139 A1076204 ESTs 309366 EST singleton 0.139 AW072970 (not in UniGene) with axon hit -303273 EST cluster 0.139 AA316069 (not in UniGene) with axon hit $$ 317484 Hs.143921 0.139 AW274696 ESTs 333239 CH22 FGENES.111 0.139 307126 EST singleton 0.139 A1184951 (not in UniGene) with axon hit 316813 Hs.124517 0.139 AA826505 ESTs 331746 Hs.121640 0.139 AA281365 ESTs; Weakly similar to KIAA0386 [H.sapiens]

308558 Hs.172182 0.139 AI700145 poly(A)-binding protein;
cytoplasmic 310784 Hs.159017 0.139 AW086142 ESTs 323831 Hs.200299 0.139 AA335715 ESTs 307692 EST singleton 0.139 AI318342 (not in UniGene) with axon hit 310570 EST cluster 0.139 AI318327 (not in UniGene) 65 327934 CH.06 hs 0.139 gi~5868184 305232 Hs.195188 0.139 AA670052 glyceraldehyde-3-phosphate dehydrogenase 334756 CH22 FGENES.428 0.139 331938 Hs.99255 0.139 AA451867 ESTs 301393 Hs.150898 0.139 AI474722 ESTs; Weakly similar to KIAA0644 protein [H.sapiens]

312005 T78450Hs.13941 0.139 ESTs 338431 CH22_EM:AC005500.GENSCAN.351-4 0.14 331214 T90496Hs.16757 0.14 ESTs 333601 CH22 FGENES.213_4 0.14 323481 AA278449Hs.137429 0.14 ESTs 336911 CH22 FGENES.344-4 0.14 338157 CH22_EM:AC005500.GENSCAN.209-5 0.14 327845 CH.05-hs 0.14 gi~6531962 319109 245662Hs.90797 0.14 Homo sapiens done 23620 mRNA sequence l0 334763 CH22 FGENES.428_12 0.14 329384 CH.X_hs 0.14 gi~5868869 302996 AF054663EST cluster 0.14 (not in Un!Gene) with axon h!t 323751 AW452656Hs.209824 0.14 ESTs 329916 CH.16~2 0.14 gi~6223624 15 301993 N49826Hs.18602 0.14 ESTs 338129 CH22-EM:AC005500.GENSCAN.197-2 0.14 325704 CH.14-hs 0.14 gi~5867028 335656 CH22 FGENES.590 0.14 331673 W72366Hs.40033 0.14 ESTs 2~ 316807 A1018331Hs.172444 0.14 ESTs; Highly similar to transcription regulator [M.musculus]

310743 AW449754Hs.158665 0.14 ESTs 326941 CH.21 hs 6004446 0.14 gi~

328809 CH.07_hs 5868327 0.14 gi~

323855 AI653164Hs.128665 0.14 ESTs 25 304705 AA564064EST singleton 0.14 (not in UniGene) with axon hit 325666 CH.14-hs 0.14 gi~6469822 333747 CH22 FGENES.265 0.14 318287 AW015616Hs.143321 0.141 ESTs 332972 CH22 FGENES.51 0.141 3O 305704 AA825266EST singleton 0.141 (not in UniGene) with exon hit 315699 AW182805Hs.189183 0.141 ESTs; Weakly similar to Nod1 [H.sapiens]

327296 CH.01 hs 0.141 gi~5867492 336400 CH22 FGENES.823-15 0.141 321033 H26214Hs.20733 ESTs; Weakly similar to !!!!
ALU SUBFAMILY
SX

WARNING 0.141 ENTRY

316522 AI475995Hs.122910 0.141 ESTs 335715 CH22 FGENES.599 0.141 335959 CH22_FGENES.650-2 0.141 333259 CH22_FGENES.118 0.141 4~ 337382 CH22_FGENES.744-8 0.141 322346 AA227618Hs.10882 0.141 HMG-box containing protein 325378 CH.12_hs 0.141 gi~5866920 338500 CH22 EM:AC005500.GENSCAN.390-1 0.141 338460 CH22_EM:AC005500.GENSCAN.362-5 0.141 45 315279 AW511138Hs.256581 0.141 ESTs 314439 AI539443Hs.137447 0.141 ESTs 333624 CH22 FGENES.222 0.141 329237 CH.X_hs 0.141 gi~5868729 330117 CH.19~2 0.141 gi~6015201 SO 338017 CH22_EM:AC005500.GENSCAN.134-1 0.141 337854 CH22 EM:AC005500.GENSCAN.38-12 0.142 329984 CH.16~2 0.142 gi~4646193 305004 AA622328Hs.162762 0.142 EST -302815 N40373EST cluster 0.142 (not in UniGene) with exon hit 327823 CH.05_hs 5867968 0.142 gi~

326753 CH.20_hs 5867616 0.142 gi~

301201 AA904482Hs.197775 0.142 ESTs 334303 CH22 FGENES.373_6 0.142 326453 CH.19_hs 0.142 gi~5867399 6O 311050 AI864581Hs.215477 0.142 ESTs 308740 AI802711Hs.210337 0.142 EST; Weakly similar to aldolase A [H.sapiens]

331003 H63959Hs.142722 0.142 ESTs 338010 CH22 EM:AC005500.GENSCAN.128-8 0.142 336326 CH22_FGENES.812 0.142 d f)5318100 844308Hs.242302 0.142 ESTs 320641 855421EST cluster(not in UniGene) 0.142 325855 CH.16_hs ~5867067 0.142 gi 330425 HG1728-HT1734 Non-Specific Cross Reacting Antigen (Gb:D90277), Alt. Splice 0.142 Form 2 324583 Hs.22581 0.142 AA425411 ESTs 326268 CH.17 hs 0.142 gij5867267 331390 Hs.45008 0.142 AA460341 ESTs 338904 CH22-DJ32110.GENSCAN.10-16 0.143 333096 CH22_FGENES.79_1 0.143 331919 Hs.119316 0.143 AA446869 ESTs 312214 Hs.125187 0.143 AI248004 ESTs 323198 Hs.7984 ESTs 0.143 316107 Hs.184014 0.143 AI204001 ribosomal protein 301335 Hs.190511 0.143 AA885317 ESTs 337392 CH22 FGENES.747-3 0.143 325543 CH.12 hs 0.143 gij6682452 305903 EST singleton 0.143 AA873085 (not in UniGene) with axon hit 332707 Hs.174185 0.143 L35594 phosphodiesterase I/nudeotide pyrophosphatase 2 (autotaxin) IS 337913 CH22-EM:AC005500.GENSCAN.59-10 0.143 301436 Hs.131696 0.143 AA961061 ESTs 335078 CH22 FGENES.486 0.143 338451 CH22_EM:AC005500.GENSCAN.359-39 0.143 302777 EST cluster 0.143 AJ230640 (not in UniGene) with axon hit 330464 Hs.78223 0.143 J03068 N-acylaminoacyl-peptide hydrolase 330988 Hs.33855 0.143 H414i1 ESTs 328939 CH.08_hs 0.143 gij6004481 308015 Hs.228907 AI440174 EST; Weakly similar to GUANINE
NUCLEOTIDE-BINDING

PROTEIN BETA
SUBUNIT-LIKE
PROTEIN

12.3 [H.sapiens] 0.143 328504 CH.07 hs 0.143 gij5868471 332599 Hs.32951 0.143 AA402891 solute carrier family 29 {nucleoside transporters);
member 2 335744 CH22 FGENES.601 O.i43 322394 EST duster 0.143 AF077208 {not in UniGene) 30 323892 EST cluster 0.143 AL042661 (not in UniGene) 318443 Hs.157714 AI939323 ESTs; Weakly similar to NEURONAL
ACETYLCHOLINE

RECEPTOR
PROTEIN;

CHAIN PRECURSOR

[H.sapiens]
0.143 336568 CH22_FGENES.843-7 0.143 35 330958 Hs.159824 0.143 327672 CH.04-hs 0.143 gij5867843 335900 CH22_FGENES.635 0.144 336044 CH22_FGENES.679 O.i44 318845 Hs.33183 AI815951 ESTs; Weakly similar to estrogen-responsive finger protein;

40 efp [H.sapiens] 0.144 333483 CH22-FGENES.165 0.144 333337 CH22_FGENES.139_6 0.144 305993 EST singleton 0.144 AA889197 {not in UniGene) with axon hit 335719 CH22-FGENES.599 0.144 45 325682 CH.14_hs 6138923 0.144 gij 327350 CH.01 hs 6249563 0.144 gij 339291 CH22-BA354112.GENSCAN.18-1 0.144 326358 CH.18_hs 0.144 gij5867293 330316 CH.08~2 gij6007576 0.144 50 308150 Hs.174131 0.144 AI499346 ribosomal protein 338065 CH22_EM:AC005500.GENSCAN.164-1 0.144 339009 CH22_DA59H18.GENSCAN.18-7 0.144 327776 CH.05 hs 0.145 gij5867964 -336664 CH22-FGENES.41-8 0.145 55 321921 EST duster O.i45 AF070619 (not in UniGene) 319346 Hs.12024 0.145 T70147 ESTs 304265 EST singleton 0.145 AA062892 (not in UniGene) with axon hit 303818 Hs.250178 0.145 245986 coping II

327498 CH.02 hs 0.145 gij6017023 60 335227 CH22_FGENES.513_13 0.145 339022 CH22-DA59H1 0.145 S.GENSCAN22-1 302597 Hs.33026 H55661 ESTs; Weakly similar to similar to Enterococcus faecalis TRAB [C.elegans] 0.145 308550 Hs.201811 0.145 65 302175 Hs.156015 0.145 AA262760 Homo sapiens chromosome 19; cosmid 303252 EST duster 0.145 AA156760 {not in UniGene) with axon hit 337414 CH22-FGENES.757-2 0.145 310382 EST duster 0.145 AI734009 (not in UniGene) 329333 CH.X_hs gij5868806 0.145 336857 CH22 FGENES.291-7 0.145 332565 Hs.25272 0.145 AA234896 E1A binding protein p300 318634 Hs.156832 0.145 AI928098 ESTs 336318 CH22 FGENES.801 0.145 310960 Hs.170843 0.145 AI923551 ESTs 335346 CH22 FGENES.537_2 0.145 331196 Hs.12826 0.145 T65416 ESTs 337607 CH22_C20H12.GENSCAN.17-3 0.146 331206 Hs.15284 0.146 T84096 ESTs 1 301793 EST cluster 0.146 ~ T80698 (not in UniGene) with axon hit 319590 ' EST cluster 0.146 AA210878 (not in UniGene) 311394 Hs.256231 0.146 A1695374 ESTs 324773 Hs.163401 0.146 AA632554 ESTs 324841 Hs.155316 0.146 A1142359 ESTs IS 332260 Hs.138467 0.146 N70088 ESTs 329276 CH.X_hs 0.146 gi~5868762 335887 CH22_FGENES.633-1 0.146 338294 CH22 EM:AC005500.GENSCAN.297-1 O.i46 336993 CH22 FGENES.409-4 0.146 2~ 334135 CH22 FGENES.336 0.146 326251 CH.17-hs 0.146 gi~5867263 337396 CH22 FGENES.749-1 0.146 339167 CH22 DA59H18.GENSCAN.69-8 0.146 316838 Hs.161210 0.146 AW135418 ESTs 25 325313 CH.11 hs 0.146 gi~5866865 331047 Hs.32205 0.146 N66918 ESTs 323915 EST duster 0.146 AL043362 (not in UniGene) 302747 EST cluster 0.146 AF062275 (not in UniGene) with axon hit 306317 EST singleton 0.146 AA947909 (not in UniGene) with axon hit 334399 CH22 FGENES.382 0.146 326472 CH.19 hs 0.146 gij5867404 333061 CH22-FGENES.75 0.146 337072 CH22_FGENES.448-5 0.146 334328 CH22 FGENES.375_5 0.146 35 327039 CH.21 hs 6531965 0.146 gi~

325576 CH.12-hs 6552443 0.147 gi~

315935 Hs.132660 0.147 A1075804 ESTs 319638 EST duster 0.147 AA323758 (not in UniGene) 334501 CH22-FGENES.397_17 0.147 4~ 338238 CH22_EM:AC005500.GENSCAN264-4 0.147 308636 EST singleton 0.147 AI744063 (not in UniGene) with axon hit 336567 CH22_FGENES.843 0.147 335819 CH22_FGENES.619-2 0.147 336950 CH22_FGENES.361-8 0.147 45 307055 EST singleton 0.147 AI148477 (not in UniGene) with axon hit 315134 Hs.126714 0.147 AW504854 ESTs 335834 CH22-FGENES.621 0.147 327870 CH.06_hs 0.147 gi~5868131 323802 Hs.250138 0.147 AA332011 protein phosphatase 2C; magnesium-dependent;
catalytic subunit 329412 CH.~hs gi~6682553 0.147 323791 EST duster 0.147 AA333068 (not in UniGene) 324126 EST duster 0.147 AA385315 (not in UniGene) 327865 CH.O6 hs 0.147 gi~5868130 ' 333445 CH22_FGENES.154 0.147 55 321302 Hs.158497 0.147 gene product 336744 CH22-FGENES.118-9 0.147 323731 EST cluster 0.148 AA323414 (not in UniGene) 320289 EST duster 0.148 H07989 (not in UniGene) 305488 EST singleton 0.148 AA749000 (not in UniGene) with axon hit 305592 Hs.62954 0.148 AA780594 ferritin;
heavy polypeptide 304094 EST singleton 0.148 H11295 (not in UniGene) with axon hit 325040 EST duster 0.148 AW296368 (not in UniGene) 339034 CH22_DA59Hi8.GENSCAN26-2 0.148 334504 CH22-FGENES.398-2 0.148 65 334778 CH22_FGENES.4312 0.148 320148 Hs.119687 0.148 077494 RAN binding protein 303584 Hs.203401 0.148 AW173759 ESTs 325826 CH.15 hs 0.148 gi~5867048 331192 Hs.152571 0.148 T55182 ESTs; Highly similar to IGF-II
mRNA-binding protein 2 [H.sapiens]

325785 CH.14_hs 0.148 gi~6381957 333166 CH22 FGENES.91 0.148 336548 CH22 FGENES.841 0.148 337552 CH22-C4G1.GENSCAN.1-4 0.148 331775 Hs.97151 0.148 338936 CH22 DJ32110.GENSCAN.19-6 0.148 331869 Hs.104894 0.148 AA428554 ESTs; Weakly similar to fibronedin precursor [H.sapiens]

332865 CH22_FGENES.28-5 0.148 328663 CH.07-hs 6004473 0.148 gi~

IO 328436 CH.07-hs 5868417 0.148 gi~

311158 Hs.250789 0.148 AI634864 ESTs; Highly similar to similar to NEDD-4 [H.sapiensJ

336942 CH22 FGENES.354-2 0.148 302262 Hs.246091 0.149 853169 ESTs 333296 CH22 FGENES.132_3 0.149 1$ 333365 CH22 FGENES.142 0.149 311706 Hs.252854 0.149 AW452392 ESTs 337109 CH22 FGENES.489-2 0.149 .

315062 Hs.190201 0.149 AW173300 ESTs 333454 CH22 FGENES.157 0.149 334784 CH22 FGENE5.432 0.149 333255 CH22 FGENES.118_3 0.149 337518 CH22 FGENES.814-7 0.149 320651 EST cluster 0.149 AA489268 (not in ' UniGene) 323437 EST duster 0.149 AA287567 (not in UniGene) 328761 CH.07 hs 0.149 gi~5868302 328787 CH.07-hs 0.149 gi~5868309 335261 CH22 FGENES.520 0.149 300827 Hs.106004 0.149 816689 ESTs 339263 CH22 BA354112.GENSCAN.10-1 0.149 3O 337412 CH22 FGENES.756-6 0.149 334414 CH22 FGENES.384_1 0.149 332931 CH22 FGENES.38 0.149 310801 Hs.106346 0.149 AW270980 novel centrosomal protein RanBPM

305216 EST singleton 0.149 AA669056 (not in UniGene) with axon h8 35 314779 Hs.190261 0.149 AA470122 ESTs 338414 ~ CH22 EM:AC005500.GENSCAN.341-27 0.149 303342 EST duster 0.149 AW247361 (not in UniGene) with axon hit 337509 CH22_FGENES.80fi-4 0.149 306631 EST singleton 0.149 A1001149 (not in UniGene) with axon hit 302533 Hs248116 0.149 L36149 chemokine (C motif) XC receptor 336536 CH22_FGENES.839_18 0.149 324666 Hs.14285 0.149 T32458 ESTs 310173 Hs.170013 0.149 AI767433 ESTs 333595 CH22_FGENES.211 0.149 45 335975 CH22-FGENES.652 0.15 306654 EST singleton 0.15 A1003654 (not in UniGene) with axon hit 335025 CH22_FGENES.475 0.15 328711 CH.07_hs ~5868271 0.15 gi 328274 CH.07 hs ~5868219 0.15 gi 325505 CH.12-hs ~6682451 0.15 gi 329641 CH.14~2 ~6468233 0.15 gi 304955 EST singleton 0.15 AA613504 (not in UniGene) with axon hit 339103 CH22 DA59H18.GENSCAN.44-10 0.15 -329636 CH.12,~2 0.15 gi~5302817 55 310118 Hs.157489 0.15 AI203293 ESTs 326056 CH.17-hs ~5867184 0.15 gi 303773 EST cluster(not in UniGene) 0.15 AA769074 with axon hit 303153 Hs.8325 0.15 009759 mitogen-activated protein kinase TABLE 13A shows the accession numbers for those primekeys lacking unigene)D's for Table 13. 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 321666 13653_22BE259906 AA232518 AA013359 AL035788 AW160822 BE387134 300088 622937_1AW576245 BE207878 AW299993 AI199558 AI285442 AW299994 322303 704603_1AI357412 AI870708 AI590539 W07459 AW401920 AA321636 AA354474 C17297 Ci 6938 AA311774 AA214723 A1014482 AW949347 T27749 AW804226 AW79696d AW404581 AF077208 NM_014029 W68830 W79652 321758 44275_1029112 AI656540 AI364875 AI656246 AI990940 323109 155498_1AA169345 AI762857 AI949997 AI809601 AI681948 AI221079 321921 34680_1AF070619 820302 T80358 321927 21620_1AJ223366 BE305086 AW820106 AA621983 BE305208 A1738475 AA621975 AI587036 AA665743 AW204003 AI692234 A1002242_AI692219 Aw732ns 321932 265316 N72324 N52825 Wi9526 BE143464 AA376060 306971 14694_7M83667 NM_005195 S63168 M83667 AW068039 AW630649 AI338577 AI9i46i9 AI380585 AI767501 AI823759 A1564i16 AI190991 AI377369 A1814122 AI221623 AI354793 Ai081988 AI391740 AI337435 8E467366 AI824347 AI565325 AI280038 AI640d55 AI702936 BE221985 AId98727 AI918196 AI279735 AW771497 (75 AI360180 AW611715 AI871777 BE045447 BE326444 AI266547 AI800237 AI8233i5 AI478368 AI264281 AI675841 A1690041 AI498018 AI554124 AI239893 AI864054 AI280099 A1i92815 $ AI796752 AI765290 AI301155 AW470358 BE222764 AI823569 AI799810 AA931170 BE048559 AI809606 AI13861d AI220732 AI681633 AI768783 AI684d63 AI307339 AI263203 2O AI458934 AI3428d8 AI693227 AI912642 AI689993 AA932572 AI765579 AI338263 AI431721 AI3942d9 A1186462 AI823571 AI953665 Ai497954 AI761057 AI678228 AI640302 AI948742 AA126417 AA971455 AA557319 Aid99738 AA911438 AI913637 25 AA046840 AI262557 AAi 31729 AA594926 T59467 AA436907 AA04d630 AI589177 Af279237 AI880d98 A1431822 AA708934 AA501478 Af621069 AA468534 AA503715 AA658457 323437 189513_1AA287567 AA252404 AW967735 AA287568 AA761222 AA865644 AW770140 AW379805 A1581609 AW36414d AA078921 45 315703 119175_1AA402307 D60405 061237 D59891 AW964877 AA325215 Ai459739 AI472001 AI648568 817676 841625 Al 1 23237 817677 AW514577 D80420 AW149850 240953 AI867861 AA9275d7 AA974344 AI825793 AI635565 AI652i57 BE504748 AW295759 302086 23306-1X57138 NM-003514 298744 BE253911 BE256314 A10950i3 Af138475 325040 23854_1AW296368 AA247632 AK002030 815304 T08775 AW975664 d 324594 330528_1AA497090 AI351879 AI350914 65 301737 65_1AI815981 AF287269 BE260960 BE263991 AA311733 F12145 AA505716 A1049661 Ai499239 854072 A1023394 1~ 303049 102592AW408042 AW407562 BE172835 BE396893 BE269184 AA045741 301863 19477-1BE263301 AI418863 NM_005194 X52560 AW328663 BE298869 AI281358 AW591213 A1017724 AI262859 Hi6997 838991 303181 74060_2AA452366 AA351338 BE262590 BE262591 AA074050 AA389667 302569 17513_2AC004472 BE312721 BE273942 F11928 T65358 BE612432 2~ 324893 4670_1AA324119 AW246199 BE395368 BE261676 BE382334 BE3947018E304548 AW956831 AW06291~ AL040397 BE305160 AA315419 3~ AA490611 AA715039 AW590666 AW590447 AI864512 AA204731 244257 Ri 2986 AA448446 AI734041 AA422167 BE220551 AA687257 AI261661 AA747442 AA48i351 AA206339 AA903407 AW473306 A1688930 AA262281 AA4483i0 AA748820 302640 21194_1AW973784 AW843642 AA557573 AA578088 A1125161 AA349349 AA366908 A~085652 843207 877954 A1672848 T28547 AA427734 BE541378 AA358274 AA213391 T88771 NM_015493 5~ AA056181 Ai753611 AA046428 AA488007 AA300764 N44732 AA864950 T94173 AId75634 AI701411 AI287696 T94091 318446 604736_1AW779971 AW300287 AW152002 AW069505 AI866447 AI298231 304332 28696_41AA158883 AA171835 AA187049 AA143546 BE299538 BE614280 BE614483 BE293447 BE270710 BE28107i BE267458 BE542095 BE512885 BE616638 BE266i73 BE258933 BE2597i0 BE268569 BE386i10 BE260368 BE250186 BE265875 BE537229 25 AW859229 8E170489 BE620i49 8E548218 AA316696 AA484426 AAi58269 AI282220 W25297 AI580710 BE262453 AI185868 AId32725 AW732011 AA872254 BE205807 T59435 AI282712 8E299000 AA196413 BE613327 BE26i523 AA866599 AW844713 4$ 303773 356632AA769074 AA570769 AA808585 AA808682 303778 174437_1AW505368 AA218610 F11852 T65345 AA397806 305186 17456_1M13560 AA336951 AA161015 872814 T69687 875705 T61319 T&3894 AA013050 AA079133 W96364 AA487926 AI762796 320257 163534_1817531 AW960899 AA338366 AW673294 BE047729 BE047722 320289 115941_1H07989 AJ239462 H24544 AA078369 874153 (S W56857 A1028525 BE617241 BE531271 AW856227 T56489 AW371449 AW945864 AW948447 AW9d5910 AA643002 AA522680 AA522715 AA578840 AA523279 AA826i50 AW945809 DEMANDE OU BREVET VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVET COMPREND
PLUS D'UN TOME.

~~ TTENANT LES PAGES 1 A 254 NOTE : Pour les tomes additionels, veuillez contacter 1e Bureau canadien des brevets JUMBO APPLICATIONS/PATENTS
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Claims (70)

WHAT IS CLAIMED IS:

1. A method of detecting a prostate 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 1-16.

2. The method of claim 1, wherein the polynucleotide selectively hybridizes to a sequence at least 95% identical to a sequence as shown in Tables 1-16.

3. The method of claim 1, wherein the biological sample is a tissue sample.

4. The method of claim 1, wherein the biological sample comprises isolated nucleic acids.

5. The method of claim 4, wherein the nucleic acids are mRNA.

6. The method of claim 4, further comprising the step of amplifying nucleic acids before the step of contacting the biological sample with the polynucleotide.

7. The method of claim 1, wherein the polynucleotide comprises a sequence as shown in Tables 1-16.

8. The method of claim 1, wherein the polynucleotide is labeled.

9. The method of claim 8, wherein the label is a fluorescent label.

10. The method of claim 1, wherein the polynucleotide is immobilized on a solid surface.

11. The method of claim 1, wherein the patient is undergoing a therapeutic regimen to treat prostate cancer.

12. The method of claim 1, wherein the patient is suspected of having prostate cancer.

13. A method of monitoring the efficacy of a therapeutic treatment of prostate 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 prostate 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 1-16, thereby monitoring the efficacy of the therapy.

14. The method of claim 13, further comprising the step of: (iii) comparing the level of the prostate cancer-associated transcript to a level of the prostate cancer-associated transcript in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.

15. The method of claim 13, wherein the patient is a human.

16. A method of monitoring the efficacy of a therapeutic treatment of prostate 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 prostate cancer-associated antibody in the biological sample by contacting the biological sample with a polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80%
identical to a sequence as shown in Tables 1-16, wherein the polypeptide specifically binds to the prostate cancer-associated antibody, thereby monitoring the efficacy of the therapy.

17. The method of claim 16, further comprising the step of: (iii) comparing the level of the prostate cancer-associated antibody to a level of the prostate cancer-associated antibody in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.

18. The method of claim 16, wherein the patient is a human.

19. A method of monitoring the efficacy of a therapeutic treatment of prostate 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 prostate cancer-associated polypeptide in the biological sample by contacting the biological sample with an antibody, wherein the antibody specifically binds to a polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1-16, thereby monitoring the efficacy of the therapy.

20. The method of claim 19, further comprising the step of: (iii) comparing the level of the prostate cancer-associated polypeptide to a level of the prostate cancer-associated polypeptide in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.

21. The method of claim 19, wherein the patient is a human.

22. An isolated nucleic acid molecule consisting of a polynucleotide sequence as shown in Tables 1-16.

23. The nucleic acid molecule of claim 22, which is labeled.

24. The nucleic acid of claim 23, wherein the label is a fluorescent label

25. An expression vector comprising the nucleic acid of claim 22.

26. A host cell comprising the expression vector of claim 25.

27. An isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1-16.

28. An antibody that specifically binds a polypeptide of claim 27.

29. The antibody of claim 28, further conjugated to an effector component.

30. The antibody of claim 29, wherein the effector component is a fluorescent label.

31. The antibody of claim 29, wherein the effector component is a radioisotope or a cytotoxic chemical.

32. The antibody of claim 29, which is an antibody fragment.

33. The antibody of claim 29, which is a humanized antibody

34. A method of detecting a prostate cancer cell in a biological sample from a patient, the method comprising contacting the biological sample with an antibody of claim 28.

35. The method of claim 34, wherein the antibody is further conjugated to an effector component.

36. The method of claim 35, wherein the effector component is a fluorescent label.

37. A method of detecting antibodies specific to prostate cancer in a patient, the method comprising contacting a biological sample from the patient with a polypeptide encoded by a nucleic acid comprises a sequence from Tables 1-16.

38. A method for identifying a compound that modulates a prostate cancer-associated polypeptide, the method comprising the steps of:
(i) contacting the compound with a prostate 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 1-16; and (ii) determining the functional effect of the compound upon the polypeptide.

39. The method of claim 38, wherein the functional effect is a physical effect.

40. The method of claim 38, wherein the functional effect is a chemical effect.

41. The method of claim 38, wherein the polypeptide is expressed in a eukaryotic host cell or cell membrane.

42. The method of claim 38, wherein the functional effect is determined by measuring ligand binding to the polypeptide.

43. The method of claim 38, wherein the polypeptide is recombinant.

44. A method of inhibiting proliferation of a prostate cancer-associated cell to treat prostate cancer in a patient, the method comprising the step of administering to the subject a therapeutically effective amount of a compound identified using the method of claim 38.

45. The method of claim 44, wherein the compound is an antibody.

46. The method of claim 45, wherein the patient is a human.

47. A drug screening assay comprising the steps of (i) administering a test compound to a mammal having prostate 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 1-16 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 prostate cancer.

48. The assay of claim 47, wherein the control is a mammal with prostate cancer or a cell therefrom that has not been treated with the test compound.

49. The assay of claim 47, wherein the control is a normal cell or mammal.

50. A method for treating a mammal having prostate cancer comprising administering a compound identified by the assay of claim 47.

51. A pharmaceutical composition for treating a mammal having prostate cancer, the composition comprising a compound identified by the assay of claim 47 and a physiologically acceptable excipient.

52. The method according to claim 1,wherein said biological sample is contacted with a plurality of polynucleotides comprising a first polynucleotide that selectively hybridizes to a sequence at least 80% identical to a first sequence as shown in Tables 1-16; and a second polynucleotide that selectively hybridizes to a second sequence at least 80% identical to a second sequence as shown in Tables 1-16.

53. A method according to claim 52, wherein the plurality of polynucleotides comprises a third polynucleotide that selectively hybridizes to a sequence at least 80% identical to a third sequence as shown in Tables 1-16..

54. A method of detecting a prostate cancer associated transcript, the method comprising contacting a biological sample from the patient with a plurality of polynucleotides wherein at least two of said polynucleotides selectively hybridize to a difference sequence at least 80% identical to a sequence as shown in Tables 1-16.

55. A method of detecting a prostate cancer, the method comprising the steps of:
(i) providing a biological sample from a patient;
(ii) contacting the biological sample with a first polynucleotide that selectively hybridizes to a sequence at least 80% identical to a first sequence as shown in Tables 1-16 to determine the level of a prostate cancer-associated transcript in the biological sample; and with a second polynucleotide that selectively hybridizes to a second sequence at least 80%
identical to a sequence not shown in Tables 1-16; wherein the expression of said second sequence is not substantially changed in prostate cancer, to detemine the level of expression of a control transcript in the biological sample;

(iii) comparing the level of the prostate cancer-associated transcript to a level of the normal tissue associated transcript in the biological sample.

56. A method of quantitating a prostate 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 1-16.

57. The method of claim 56, wherein the polynucleotide selectively hybridizes to a sequence at least 95% identical to a sequence as shown in Tables 1-16.

58. The method of claim 56, wherein the biological sample is a tissue sample.

59. The method of claim 56, wherein the biological sample comprises isolated nucleic acids.

60. The method of claim 56, wherein the nucleic acids are mRNA.

61. The method of claim 59, further comprising the step of amplifying nucleic acids before the step of contacting the biological sample with the polynucleotide.

62. The method of claim 56, wherein the polynucleotide comprises a sequence as shown in Tables 1-16.

63. The method of claim 56, wherein the polynucleotide is labeled.

64. The method of claim 63, wherein the label is a fluorescent label.

65. The method of claim 56, wherein the polynucleotide is immobilized on a solid surface.

66. The method of claim 56, wherein the patient is undergoing a therapeutic regimen to treat metastatic prostate cancer.

67. The method of claim 56, wherein the patient is suspected of having metastatic prostate cancer.

68. A biochip comprising a plurality of polynucleotides that selectively hybridize to a sequence at least 80% identical to a sequence as shown in Tables 1-16.

69. A method of screening drug candidates comprising:
i) providing a cell that expresses an expression profile gene selected from the group consisting of an expression profile gene set forth in Tables 1-16 or fragment thereof;
ii) adding a drug candidate to said cell; and iii) determining the effect of said drug candidate on the expression of said expression profile gene.

70. A method according to claim 59 wherein said determining comprises comparing the level of expression in the absence of said drug candidate to the level of expression in the presence of said drug candidate.