CA2460621A1 - Novel nucleic acids and polypeptides - Google Patents

Abstract

The present invention provides novel nucleic acids, novel polypeptide sequences encoded by these nucleic acids and uses thereof.

Description

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NOVEL NUCLEIC ACIDS AND POLYPEPTIDES
1. CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the priority benefit of U.S. Provisional Application Serial No.
60/323,739 filed September 19, 2001 entitled "Novel Nucleic Acids and Polypeptides", Attorney Docket No. 809, which is a continuation-in-part application of PCT
Application Serial No. PCT/LTS00/35017 filed December 22, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 784CIP3A/PCT, which in turn is a continuation-in-part application of U.S. Application Serial No. 09/552,317 filed April 25, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No.
784CIP, which in turn is a continuation-in-part application of U.S.
Application Serial No.
09/488,725 filed January 21, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 784; PCT Application Serial No.
PCT/LTSO1/02623 filed .lanuary 25, 2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 785CIP3/PCT, which in turn is a continuation-in-part application of U.S.
Application Serial No. 09/491,404 filed January 25, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 785; PCT Application Serial No.
PCT/LTSO1/03800 filed February 5, 2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 787CIP3/PCT, which in turn is a continuation-in-part application of U.S. Application Serial No. 09/560,875 filed April 27, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 787CIP, which in turn is a continuation-in-part application of U.S. Application Serial No. 09/496,914 filed February 03, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 787;
PCT Application Serial No. PCT/USO1/04927 filed February 26, 2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 788CIP3/PCT, which in turn is a continuation-in-part application of U.S. Application Serial No.
09/577,409 filed May 18, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 788CIP, which in turn is a continuation-in-part application of U.S.
Application Serial No. 09/515,126 filed February 28, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 788; PCT Application Serial No.
PCTlLJSOI/04941 filed March 5, 2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 789CIP3/PCT, which in turn is a continuation-in-part application of U.S.
Application Serial No. 09/574,454 filed May 19, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 789CIP, which in turn is a continuation-in-part application of U.S. Application Serial No. 09/519,705 filed March 07, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 789; PCT Application Serial No.
PCT/L1S01/08631 filed March 30, 2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 790CIP3/PCT, which in turn is a continuation-in-part application of U.S. Application Serial No. 09/649,167 filed August 23, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 790CIP, which in turn is a continuation-in-part application of U.S. Application Serial No. 09/540,217 filed March 31, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 790;
PCT Application Serial No. PCT/USO1/08656 filed April 18, 2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 791 CIP3/PCT, which in turn is a continuation-in-part application of U.S. Application Serial No. 09/770,160 filed January 26, 2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No.
791CIP, which is in turn a continuation-in-part application of U.S.
Application Serial No.
09/552,929 filed April 18, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 791; and PCT Application Serial No. PCT/USO1/14827 filed Mayl6, 2001 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No.
792CIP3/PCT, which in turn is a continuation-in-part application of U.S.
Application Serial No. 09/577,408 filed May 18, 2000 entitled "Novel Contigs Obtained from Various Libraries", Attorney Docket No. 792; all of which are incorporated herein by reference in their entirety.
2. BACKGROUND OF THE INVENT10N
2.1 TECHNICAL FIELD
The present invention provides novel polynucleotides and proteins encoded by such polynucleotides, along with uses for these polynucleotides and proteins, for example in therapeutic, diagnostic and research methods.
2.2 BACKGROUND
Technology aimed at the discovery of protein factors (including e.g., cytokines, such as lymphokines, interferons, circulating soluble factors, chemokines, and interleukins) has matured rapidly over the past decade. The now routine hybridization cloning and expression cloning techniques clone novel polynucleotides "directly" in the sense that they rely on information directly related to the discovered protein (i.e., partial DNA/amino acid sequence of the protein in the case of hybridization cloning; activity of the protein in the case of expression cloning). More recent "indirect" cloning techniques such as signal sequence S cloning, which isolates DNA sequences based on the presence of a now well-recognized secretory leader sequence motif, as well as various PCR-based or low stringency hybridization-based cloning techniques, have advanced the state of the art by making available large numbers of DNA/amino acid sequences for proteins that are known to have biological activity, for example, by virtue of their secreted nature in the case of leader sequence cloning, by virtue of their cell or tissue source in the case of PCR-based techniques, or by virtue of structural similarity to other genes of known biological activity.
Identified polynucleotide and polypeptide sequences have numerous applications in, for example, diagnostics, forensics, gene mapping; identification of mutations responsible for genetic disorders or other traits, to assess biodiversity, and to produce many other types 1 S of data and products dependent on DNA and amino acid sequences.

3. SUMMARY OF THE INVENTION
The compositions of the present invention include novel isolated polypeptides, novel isolated polynucleotides encoding such polypeptides, including recombinant DNA
molecules, cloned genes or degenerate variants thereof, especially naturally occurnng variants such as allelic variants, antisense polynucleotide molecules, and antibodies that specifically recognize one or more epitopes present on such polypeptides, as well as hybridomas producing such antibodies.
The compositions of the present invention additionally include vectors, including expression vectors, containing the polynucleotides of the invention, cells genetically engineered to contain such polynucleotides and cells genetically engineered to express such polynucleotides.
The present invention relates to a collection or library of at least one novel nucleic acid sequence assembled from expressed sequence tags (ESTs) isolated mainly by sequencing by hybridization (SBH), and in some cases, sequences obtained from one or more public databases. The invention relates also to the proteins encoded by such polynucleotides, along with therapeutic, diagnostic and research utilities for these polynucleotides and proteins. These nucleic acid sequences are designated as SEQ ID NO: 1-276, or 553-772 and are provided in the Sequence Listing. In the nucleic acids provided in the Sequence Listing, A
is adenine; C is cytosine; G is guanine; T is thymine; and N is any of the four bases or unknown. In the amino acids provided in the Sequence Listing, * corresponds to the stop codon.
The nucleic acid sequences of the present invention also include, nucleic acid sequences S that hybridize to the complement of SEQ >D NO: 1-276, or 553-772 under stringent hybridization conditions; nucleic acid sequences which are allelic variants or species homologues of any of the nucleic acid sequences recited above, or nucleic acid sequences that encode a peptide comprising a specific domain or truncation of the peptides encoded by SEQ
ID NO: 1-276, or 553-772. A polynucleotide comprising a nucleotide sequence having at least 90% identity to an identifying sequence of SEQ ID NO: 1-276, or 553-772 or a degenerate variant or fragment thereof. The identifying sequence can be 100 base pairs in length.
The nucleic acid sequences of the present invention also include the sequence information from the nucleic acid sequences of SEQ ID NO: 1-276, or 553-772.
The sequence information can be a segment of any one of SEQ 1D NO: 1-276, or 553-772 that uniquely identifies or represents the sequence information of SEQ >D NO: 1-276, or 553-772.
A collection as used in this application can be a collection of only one polynucleotide.
The collection of sequence information or identifying information of each sequence can be provided on a nucleic acid array. In one embodiment, segments of sequence information are provided on a nucleic acid array to detect the polynucleotide that contains the segment. The array can be designed to detect full-match or mismatch to the polynucleotide that contains the segment. The collection can also be provided in a computer-readable format.
This invention also includes the reverse or direct complement of any of the nucleic acid sequences recited above; cloning or expression vectors containing the nucleic acid sequences;
and host cells or organisms transformed with these expression vectors. Nucleic acid sequences (or their reverse or direct complements) according to the invention have numerous applications in a variety of techniques known to those skilled in the art of molecular biology, such as use as hybridization probes, use as primers for PCR, use in an array, use in computer-readable media, use in sequencing full-length genes, use for chromosome and gene mapping, use in the recombinant production of protein, and use in the generation of anti-sense DNA
or RNA, their chemical analogs and the like.
In a preferred embodiment, the nucleic acid sequences of SEQ ID NO: 1-276, or 772 or novel segments or parts of the nucleic acids of the invention are used as primers in expression assays that are well known in the art. In a particularly preferred embodiment, the nucleic acid sequences of SEQ 1D NO: 1-276, or 553-772 or novel segments or parts of the nucleic acids provided herein are used in diagnostics for identifying expressed genes or, as well known in the art and exemplified by Vollrath et al., Science 258:52-59 (1992), as expressed sequence tags for physical mapping of the human genome.
The isolated polynucleotides of the invention include, but are not limited to, a polynucleotide comprising any one of the nucleotide sequences set forth in SEQ
ID NO: 1-276, or 553-772; a polynucleotide comprising any of the full length protein coding sequences of SEQ 1D NO: 1-276, or 553-772; and a polynucleotide comprising any of the nucleotide sequences of the mature protein coding sequences of SEQ >I7 NO: 1-276, or 553-772. The polynucleotides of the present invention also include, but are not limited to, a polynucleotide that hybridizes under stringent hybridization conditions to (a) the complement of any one of the nucleotide sequences set forth in SEQ 1D NO: 1-276, or 553-772; (b) a nucleotide sequence encoding any one of the amino acid sequences set forth in SEQ ~ NO: 1-276, or 553-772; (c) a polynucleotide which is an allelic variant of any polynucleotides recited above; (d) a polynucleotide which encodes a species homologue (e.g. orthologs) of any of the proteins recited above; or (e) a polynucleotide that encodes a polypeptide comprising a specific domain or truncation of any of the polypeptides comprising an amino acid sequence set forth in SEQ >D
NO: 277-552, or 773-992, or Tables 3, 4A, 4B, 5, 6, or 8.
The isolated polypeptides of the invention include, but are not limited to, a polypeptide comprising any of the amino acid sequences set forth in the Sequence Listing;
or the corresponding full length or mature protein. Polypeptides of the invention also include polypeptides with biological activity that are encoded by (a) any of the polynucleotides having a nucleotide sequence set forth in SEQ m NO: 1-276, or 553-772; or (b) polynucleotides that hybridize to the complement of the polynucleotides of (a) under stringent hybridization conditions. Biologically active variants of any of the polypeptide sequences in the Sequence Listing, and "substantial equivalents" thereof (e.g., with at least about 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or 99% amino acid sequence identity) that preferably retain biological activity are also contemplated. The polypeptides of the invention may be wholly or partially chemically synthesized but are preferably produced by recombinant means using the genetically engineered cells (e.g. host cells) of the invention.
The invention also provides compositions comprising a polypeptide of the invention.
Polypeptide compositions of the invention may further comprise an acceptable carrier, such as a hydrophilic, e.g., pharmaceutically acceptable, carrier.

The invention also provides host cells transformed or transfected with a polynucleotide of the invention.
The invention also relates to methods for producing a polypeptide of the invention comprising growing a culture of the host cells of the invention in a suitable culture medium under conditions permitting expression of the desired polypeptide, and purifying the polypeptide from the culture or from the host cells. Preferred embodiments include those in which the protein produced by such processes is a mature form of the protein.
Polynucleotides according to the invention have numerous applications in a variety of techniques known to those skilled in the art of molecular biology. These techniques include use as hybridization probes, use as oligomers, or primers, for PCR, use for chromosome and gene mapping, use in the recombinant production of protein, and use in generation of anti-sense DNA or RNA, their chemical analogs and the like. For example, when the expression of an mRNA is largely restricted to a particular cell or tissue type, polynucleotides of the invention can be used as hybridization probes to detect the presence of the particular cell or tissue mRNA in a sample using, e.g., in situ hybridization.
In other exemplary embodiments, the polynucleotides are used in diagnostics as expressed sequence tags for identifying expressed genes or, as well known in the art and exemplified by Vollrath et al., Science 258:52-59 (1992), as expressed sequence tags for physical mapping of the human genome.
The polypeptides according to the invention can be used in a variety of conventional procedures and methods that are currently applied to other proteins. For example, a polypeptide of the invention can be used to generate an antibody that specifically binds the polypeptide. Such antibodies, particularly monoclonal antibodies, are useful for detecting or quantitating the polypeptide in tissue. The polypeptides of the invention can also be used as molecular weight markers, and as a food supplement.
Methods are also provided for preventing, treating, or ameliorating a medical condition which comprises the step of administering to a mammalian subject a therapeutically effective amount of a composition comprising a polypeptide of the present invention and a pharmaceutically acceptable carrier.
In particular, the polypeptides and polynucleotides of the invention can be utilized, for example, in methods for the prevention and/or treatment of disorders involving aberrant protein expression or biological activity.

The present invention further relates to methods for detecting the presence of the polynucleotides or polypeptides of the invention in a sample. Such methods can, for example, be utilized as part of prognostic and diagnostic evaluation of disorders as recited herein and for the identification of subjects exhibiting a predisposition to such conditions.
The invention provides a method for detecting the polynucleotides of the invention in a sample, comprising contacting the sample with a compound that binds to and forms a complex with the polynucleotide of interest for a period sufficient to form the complex and under conditions sufficient to form a complex and detecting the complex such that if a complex is detected, the polynucleotide of interest is detected. The invention also provides a method for detecting the polypeptides of the invention in a sample comprising contacting the sample with a compound that binds to and forms a complex with the polypeptide under conditions and for a period sufficient to form the complex and detecting the formation of the complex such that if a complex is formed, the polypeptide is detected.
The invention also provides kits comprising polynucleotide probes and/or monoclonal antibodies, and optionally quantitative standards, for carrying out methods of the invention. Furthermore, the invention provides methods for evaluating the efficacy of drugs, and monitoring the progress of patients, involved in clinical trials for the treatment of disorders as recited above.
The invention also provides methods for the identification of compounds that modulate (i.e., increase or decrease) the expression or activity of the polynucleotides and/or polypeptides of the invention. Such methods can be utilized, for example, for the identification of compounds that can ameliorate symptoms of disorders as recited herein.
Such methods can include, but are not limited to, assays for identifying compounds and other substances that interact with (e.g., bind to) the polypeptides of the invention. The invention provides a method for identifying a compound that binds to the polypeptides of the invention comprising contacting the compound with a polypeptide of the invention in a cell for a time sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a reporter gene sequence in the cell; and detecting the complex by detecting the reporter gene sequence expression such that if expression of the reporter gene is detected the compound that binds to a polypeptide of the invention is identified.
The methods of the invention also provide methods for treatment which involve the administration of the polynucleotides or polypeptides of the invention to individuals exhibiting symptoms or tendencies. In addition, the invention encompasses methods for treating diseases or disorders as recited herein comprising administering compounds and other substances that modulate the overall activity of the target gene products. Compounds and other substances can affect such modulation either on the level of target gene/protein expression or target protein activity.
The polypeptides of the present invention and the polynucleotides encoding them are also useful for the same functions known to one of skill in the art as the polypeptides and polynucleotides to which they have homology (set forth in Tables 2A and 2B);
for which they have a signature region (as set forth in Table 3); or for which they have homology to a gene family (as set forth in Tables 4A and 4B). If no homology is set forth for a sequence, then the polypeptides and polynucleotides of the present invention are useful for a variety of applications, as described herein, including use in arrays for detection.
4. DETAILED DESCRIPTION OF THE INVENTION
4.1 DEFINITIONS
It must be noted that as used herein and in the appended claims, the singular forms "a", "an" and "the" include plural references unless the context clearly dictates otherwise.
The term "active" refers to those forms of the polypeptide which retain the biologic and/or immunologic activities of any naturally occurring polypeptide.
According to the invention, the terms "biologically active" or "biological activity" refer to a protein or peptide having structural, regulatory or biochemical functions of a naturally occurring molecule.
Likewise "immunologically active" or "immunological activity" refers to the capability of the natural, recombinant or synthetic polypeptide to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.
The term "activated cells" as used in this application are those cells which are engaged in extracellular or intracellular membrane trafficking, including the export of secretory or enzymatic molecules as part of a normal or disease process.
The terms "complementary" or "complementarity" refer to the natural binding of polynucleotides by base pairing. For example, the sequence 5'-AGT-3' binds to the complementary sequence 3'-TCA-5'. Complementarity between two single-stranded molecules may be "partial" such that only certain portions) of the nucleic acids bind or it may be "complete" such that total complementarity exists between the single stranded molecules. The degree of complementarity between the nucleic acid strands has significant effects on the efficiency and strength of the hybridization between the nucleic acid strands.
The tem "embryonic stem cells (ES)" refers to a cell that can give rise to many differentiated cell types in an embryo or an adult, including the germ cells.
The term "germ line stem cells (GSCs)" refers to stem cells derived from primordial stem cells that provide a steady and continuous source of germ cells for the production of gametes. The term "primordial germ cells (PGCs)" refers to a small population of cells set aside from other cell lineages particularly from the yolk sac, mesenteries, or gonadal ridges during embryogenesis that have the potential to differentiate into germ cells and other cells. PGCs are the source from which GSCs and ES cells are derived. The PGCs, the GSCs and the ES cells are capable of self renewal. Thus these cells not only populate the gern~ line and give rise to a plurality of terminally differentiated cells that comprise the adult specialized organs, but are able to regenerate themselves.
The term "expression modulating fragment," EMF, means a series of nucleotides which modulates the expression of an operably linked ORF or another EMF.
As used herein, a sequence is said to "modulate the expression of an operably linked sequence" when the expression of the sequence is altered by the presence of the EMF.
EMFs include, but are not limited to, promoters, and promoter modulating sequences (inducible elements). One class of EMFs are nucleic acid fragments which induce the expression of an operably linked ORF in response to a specific regulatory factor or physiological event.
The terms "nucleotide sequence" or "nucleic acid" or "polynucleotide" or "oligonucleotide" are used interchangeably and refer to a heteropolymer of nucleotides or the sequence of these nucleotides. These phrases also refer to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA) or to any DNA-like or RNA-like material. In the sequences herein A is adenine, C is cytosine, T is thymine, G
is guanine and N is A, C, G, or T (U) or unknown. It is contemplated that where the polynucleotide is RNA, the T (thymine) in the sequences provided herein is substituted with U
(uracil).
Generally, nucleic acid segments provided by this invention may be assembled from fragments of the genome and short oligonucleotide linkers, or from a series of oligonucleotides, or from individual nucleotides, to provide a synthetic nucleic acid which is capable of being expressed in a recombinant transcriptional unit comprising regulatory elements derived from a microbial or viral operon, or a eukaryotic gene.
The terms "oligonucleotide fragment" or a "polynucleotide fragment", "portion," or "segment" or "probe" or "primer" are used interchangeably and refer to a sequence of 5 nucleotide residues which are at least about 5 nucleotides, more preferably at least about 7 nucleotides, more preferably at least about 9 nucleotides, more preferably at least about 1 1 nucleotides and most preferably at least about 17 nucleotides. The fragment is preferably less than about 500 nucleotides, preferably less than about 200 nucleotides, more preferably less than about 100 nucleotides, more preferably less than about 50 nucleotides and most 10 preferably less than 30 nucleotides. Preferably the probe is from about 6 nucleotides to about 200 nucleotides, preferably from about 15 to about SO nucleotides, more preferably from about 17 to 30 nucleotides and most preferably from about 20 to 25 nucleotides.
Preferably the fragments can be used in polymerase chain reaction (PCR), various hybridization procedures or microarray procedures to identify or amplify identical or related 1 S parts of mRNA or DNA molecules. A fragment or segment may uniquely identify each polynucleotide sequence of the present invention. Preferably the fragment comprises a sequence substantially similar to any one of SEQ ID NO: 1-276, or 553-772.
Probes may, for example, be used to determine whether specific mRNA molecules are present in a cell or tissue or to isolate similar nucleic acid sequences from chromosomal DNA as described by Walsh et al. (Walsh, P.S. et al., 1992, PCR Methods Appl 1:241-250).
They may be labeled by nick translation, Klenow fill-in reaction, PCR, or other methods well known in the art. Probes of the present invention, their preparation andlor labeling are elaborated in Sambrook, J. et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY; or Ausubel, F.M. et al., 1989, Current Protocols in Molecular Biology, John Wiley & Sons, New York NY, both of which are incorporated herein by reference in their entirety.
The nucleic acid sequences of the present invention also include the sequence information from the nucleic acid sequences of SEQ ID NO: 1-276, or 553-772.
The sequence information can be a segment of any one of SEQ ID NO: 1-276, or 553-772 that uniquely identifies or represents the sequence information of that sequence of SEQ 1D NO:
1-276, or 553-772, or those segments identified in Tables 3, 4A, 4B, 5, 6, or 8. One such segment can be a twenty-mer nucleic acid sequence because the probability that a twenty-mer is fully matched in the human genome is 1 in 300. In the human genome, there are three billion base pairs in one set of chromosomes. Because 42° possible twenty-mers exist, there are 300 times more twenty-mers than there are base pairs in a set of human chromosomes.
Using the same analysis, the probability for a seventeen-mer to be fully matched in the human genome is approximately 1 in 5. When these segments are used in arrays for expression studies, fifteen-mer segments can be used. The probability that the fifteen-mer is fully matched in the expressed sequences is also approximately one in five because expressed sequences comprise less than approximately 5% of the entire genome sequence.
Similarly, when using sequence information for detecting a single mismatch, a segment can be a twenty-five mer. The probability that the twenty-five mer would appear in a human genome with a single mismatch is calculated by multiplying the probability for a full match (1-425) times the increased probability for mismatch at each nucleotide position (3 x 25). The probability that an eighteen mer with a single mismatch can be detected in an array for expression studies is approximately one in five. The probability that a twenty-mer with a single mismatch can be detected in a human genome is approximately one in five.
The term "open reading frame," ORF, means a series of nucleotide triplets coding for amino acids without any termination codons and is a sequence translatable into protein.
The terms "operably linked" or "operably associated" refer to functionally related nucleic acid sequences. For example, a promoter is operably associated or operably linked with a coding sequence if the promoter controls the transcription of the coding sequence.
While operably linked nucleic acid sequences can be contiguous and in the same reading frame, certain genetic elements e.g. repressor genes are not contiguously linked to the coding sequence but still control transcription/translation of the coding sequence.
The teen "pluripotent" refers to the capability of a cell to differentiate into a number of differentiated cell types that are present in an adult organism. A
pluripotent cell is restricted in its differentiation capability in comparison to a totipotent cell.
The terms "polypeptide" or "peptide" or "amino acid sequence" refer to an oligopeptide, peptide, polypeptide or protein sequence or fragment thereof and to naturally occurring or synthetic molecules. A polypeptide "fragment," "portion," or "segment" is a stretch of amino acid residues of at least about 5 amino acids, preferably at least about 7 amino acids, more preferably at least about 9 amino acids and most preferably at least about 17 or more amino acids. The peptide preferably is not greater than about 200 amino acids, more preferably less than 150 amino acids and most preferably less than 100 amino acids.

Preferably the peptide is from about 5 to about 200 amino acids. To be active, any polypeptide must have sufficient length to display biological and/or immunological activity.
The term "naturally occurring polypeptide" refers to polypeptides produced by cells that have not been genetically engineered and specifically contemplates various polypeptides arising from post-translational modifications of the polypeptide including, but not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation.
The term "translated protein coding portion" means a sequence which encodes for the full-length protein which may include any leader sequence or any processing sequence.
The term "mature protein coding sequence" means a sequence which encodes a peptide or protein without a signal or leader sequence. The "mature protein portion" means that portion of the protein which does not include a signal or leader sequence. The peptide may have been produced by processing in the cell which removes any leader/signal sequence. The mature protein portion may or may not include the initial methionine residue.
The methionine residue may be removed from the protein during processing in the cell. The peptide may be produced synthetically or the protein may have been produced using a polynucleotide only encoding for the mature protein coding sequence.
The term "derivative" refers to polypeptides chemically modified by such techniques as ubiquitination, labeling (e.g., with radionuclides or various enzymes), covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of amino acids such as ornithine, which do not normally occur in human proteins.
The term "variant"(or "analog") refers to any polypeptide differing from naturally occurring polypeptides by amino acid insertions, deletions, and substitutions, created using, a g., recombinant DNA techniques. Guidance in determining which amino acid residues may be replaced, added or deleted without abolishing activities of interest, may be found by comparing the sequence of the particular polypeptide with that of homologous peptides and minimizing the number of amino acid sequence changes made in regions of high homology (conserved regions) or by replacing amino acids with consensus sequence.
Alternatively, recombinant variants encoding these same or similar polypeptides may be synthesized or selected by making use of the "redundancy" in the genetic code. Various codon substitutions, such as the silent changes which produce various restriction sites, may be introduced to optimize cloning into a plasmid or viral vector or expression in a particular prokaryotic or eukaryotic system. Mutations in the polynucleotide sequence may be reflected in the polypeptide or domains of other peptides added to the polypeptide to modify the properties of any part of the polypeptide, to change characteristics such as ligand-binding affinities, interchain affinities, or degradation/turnover rate.
Preferably, amino acid "substitutions" are the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, i.e., conservative amino acid replacements. "Conservative" amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues involved. For example, nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine; polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; positively charged (basic) amino acids include arginine, lysine, and histidine; and negatively charged (acidic) amino acids include aspartic acid and glutamic acid. "Insertions" or "deletions" are preferably in the range of about 1 to 20 amino acids, more preferably 1 to 10 amino acids. The variation allowed may be experimentally 1 S determined by systematically making insertions, deletions, or substitutions of amino acids in a polypeptide molecule using recombinant DNA techniques and assaying the resulting recombinant variants for activity.
Alternatively, where alteration of function is desired, insertions, deletions or non-conservative alterations can be engineered to produce altered polypeptides. Such alterations can, for example, alter one or more of the biological functions or biochemical characteristics of the polypeptides of the invention. For example, such alterations may change polypeptide characteristics such as ligand-binding affinities, interchain affinities, or degradation/turnover rate. Further, such alterations can be selected so as to generate polypeptides that are better suited for expression, scale up and the like in the host cells chosen for expression. For example, cysteine residues can be deleted or substituted with another amino acid residue in order to eliminate disulfide bridges.
The terms "purified" or "substantially purified" as used herein denotes that the indicated nucleic acid or polypeptide is present in the substantial absence of other biological macromolecules, e.g., polynucleotides, proteins, and the like. In one embodiment, the polynucleotide or polypeptide is purified such that it constitutes at least 95% by weight, more preferably at least 99% by weight, of the indicated biological macromolecules present (but water, buffers, and other small molecules, especially molecules having a molecular weight of less than 1000 daltons, can be present).

The term "isolated" as used herein refers to a nucleic acid or polypeptide separated from at least one other component (e.g., nucleic acid or polypeptide) present with the nucleic acid or polypeptide in its natural source. In one embodiment, the nucleic acid or polypeptide is found in the presence of (if anything) only a solvent, buffer, ion, or other component normally present in a solution of the same. The terms "isolated" and "purified" do not encompass nucleic acids or polypeptides present in their natural source.
The term "recombinant," when used herein to refer to a polypeptide or protein, means that a polypeptide or protein is derived from recombinant (e.g., microbial, insect, or mammalian) expression systems. "Microbial" refers to recombinant polypeptides or proteins made in bacterial or fungal (e.g., yeast) expression systems. As a product, "recombinant microbial" defines a polypeptide or protein essentially free of native endogenous substances and unaccompanied by associated native glycosylation. Polypeptides or proteins expressed in most bacterial cultures, e.g., E. coli, will be free of glycosylation modifications;
polypeptides or proteins expressed in yeast will have a glycosylation pattern in general different from those expressed in mammalian cells.
The term "recombinant expression vehicle or vector" refers to a plasmid or phage or virus or vector, for expressing a polypeptide from a DNA (RNA) sequence. An expression vehicle can comprise a transcriptional unit comprising an assembly of (1) a genetic element or elements having a regulatory role in gene expression, for example, promoters or enhancers, (2) a structural or coding sequence which is transcribed into mRNA
and translated into protein, and (3) appropriate transcription initiation and termination sequences.
Structural units intended for use in yeast or eukaryotic expression systems preferably include a leader sequence enabling extracellular secretion of translated protein by a host cell.
Alternatively, where recombinant protein is expressed without a leader or transport sequence, it may include an amino terminal methionine residue. This residue may or may not be subsequently cleaved from the expressed recombinant protein to provide a final product.
The term "recombinant expression system" means host cells which have stably integrated a recombinant transcriptional unit into chromosomal DNA or carry the recombinant transcriptional unit extrachromosomally. Recombinant expression systems as defined herein will express heterologous polypeptides or proteins upon induction of the regulatory elements linked to the DNA segment or synthetic gene to be expressed. This term also means host cells which have stably integrated a recombinant genetic element or elements having a regulatory role in gene expression, for example, promoters or enhancers.
Recombinant expression systems as defined herein will express polypeptides or proteins endogenous to the cell upon induction of the regulatory elements linked to the endogenous DNA segment or gene to be expressed. The cells can be prokaryotic or eukaryotic.
The term "secreted" includes a protein that is transported across or through a membrane, including transport as a result of signal sequences in its amino acid sequence when it is expressed in a suitable host cell. "Secreted" proteins include without limitation proteins secreted wholly (e.g., soluble proteins) or partially (e.g., receptors) from the cell in which they are expressed. "Secreted" proteins also include without limitation proteins that 10 are transported across the membrane of the endoplasmic reticulum.
"Secreted" proteins are also intended to include proteins containing non-typical signal sequences (e.g. Interleukin-1 Beta, see Krasney, P.A. and Young, P.R. (1992) Cytokine 4(2): 134 -143) and factors released from damaged cells (e.g. Interleukin-1 Receptor Antagonist, see Arend, W.P. et. al.
(1998) Annu. Rev. Immunol. 16:27-55) 15 Where desired, an expression vector may be designed to contain a "signal or leader sequence" which will direct the polypeptide through the membrane of a cell.
Such a sequence may be naturally present on the polypeptides of the present invention or provided from heterologous protein sources by recombinant DNA techniques.
The term "stringent" is used to refer to conditions that are commonly understood in the art as stringent. Stringent conditions can include highly stringent conditions (i.e., hybridization to filter-bound DNA in 0.5 M NaHP04, 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65°C, and washing in O.1X SSC/0.1% SDS at 68°C), and moderately stringent conditions (i.e., washing in 0.2X SSC/0.1 % SDS at 42°C). Other exemplary hybridization conditions are described herein in the examples.
In instances of hybridization of deoxyoligonucleotides, additional exemplary stringent hybridization conditions include washing in 6X SSC/0.05% sodium pyrophosphate at 37°C (for 14-base oligonucleotides), 48°C (for 17-base oligonucleotides), 55°C (for 20-base oligonucleotides), and 60°C (for 23-base oligonucleotides).
As used herein, "substantially equivalent" or "substantially similar" can refer both to nucleotide and amino acid sequences, for example a mutant sequence, that varies from a reference sequence by one or more substitutions, deletions, or additions, the net effect of which does not result in an adverse functional dissimilarity between the reference and subject sequences. Typically, such a substantially equivalent sequence varies from one of those listed herein by no more than about 35% (i.e., the number of individual residue substitutions, additions, and/or deletions in a substantially equivalent sequence, as compared to the corresponding reference sequence, divided by the total number of residues in the substantially equivalent sequence is about 0.35 or less). Such a sequence is said to have 65% sequence identity to the listed sequence. In one embodiment, a substantially equivalent, e.g., mutant, sequence of the invention varies from a listed sequence by no more than 30% (70% sequence identity); in a variation of this embodiment, by no more than 25%
(75% sequence identity); and in a further variation of this embodiment, by no more than 20% (80% sequence identity) and in a further variation of this embodiment, by no more than 10% (90% sequence identity) and in a further variation of this embodiment, by no more that S% (95% sequence identity). Substantially equivalent, e.g., mutant, amino acid sequences according to the invention preferably have at least 80% sequence identity with a listed amino acid sequence, more preferably at least 85% sequence identity, more preferably at least 90%
sequence identity, more preferably at least 95% sequence identity, more preferably at least 98% sequence identity, and most preferably at least 99% sequence identity.
Substantially equivalent nucleotide sequence of the invention can have lower percent sequence identities, taking into account, for example, the redundancy or degeneracy of the genetic code.
Preferably, the nucleotide sequence has at least about 65% identity, more preferably at least about 75% identity, more preferably at least about 80% sequence identity, more preferably at least 85% sequence identity, more preferably at least 90% sequence identity, more preferably at least about 95% sequence identity, more preferably at least 98% sequence identity, and most preferably at least 99% sequence identity. For the purposes of the present invention, sequences having substantially equivalent biological activity and substantially equivalent expression characteristics are considered substantially equivalent. For the purposes of determining equivalence, truncation of the mature sequence (e.g., via a mutation which creates a new stop codon) should be disregarded. Sequence identity may be determined, e.g., using the Jotun Hein method (Rein, J. (1990) Methods Enzymol. 183:626-645).
Identity between sequences can also be determined by other methods known in the art, e.g.
by varying hybridization conditions.
The term "totipotent" refers to the capability of a cell to differentiate into all of the cell types of an adult organism.
The term "transformation" means introducing DNA into a suitable host cell so that the DNA is replicable, either as an extrachromosomal element, or by chromosomal integration. The term "transfection" refers to the taking up of an expression vector by a suitable host cell, whether or not any coding sequences are in fact expressed.
The term "infection" refers to the introduction of nucleic acids into a suitable host cell by use of a virus or viral vector.
As used herein, an "uptake modulating fragment," UMF, means a series of nucleotides which mediate the uptake of a linked DNA fragment into a cell.
LTMFs can be readily identified using known UMFs as a target sequence or target motif with the computer-based systems described below. The presence and activity of a UMF can be confirmed by attaching the suspected UMF to a marker sequence. The resulting nucleic acid molecule is then incubated with an appropriate host under appropriate conditions and the uptake of the marker sequence is determined. As described above, a UMF will increase the frequency of uptake of a linked marker sequence.
Each of the above terms is meant to encompass all that is described for each, unless the context dictates otherwise.
4.2 NUCLEIC ACIDS OF THE INVENTION
Nucleotide sequences of the invention are set forth in the Sequence Listing.
The isolated polynucleotides of the invention include a polynucleotide comprising the nucleotide sequences of SEQ ID NO: 1-276, or 553-772; a polynucleotide encoding any one of the peptide sequences of SEQ ID NO: 1-276, or 553-772; and a polynucleotide comprising the nucleotide sequence encoding the mature protein coding sequence of the polynucleotides of any one of SEQ ID NO: 1-276, or 553-772. The polynucleotides of the present invention also include, but are not limited to, a polynucleotide that hybridizes under stringent conditions to (a) the complement of any of the nucleotides sequences of SEQ ID
NO: 1-276, or 553-772; (b) nucleotide sequences encoding any one of the amino acid sequences set forth in the Sequence Listing, or Table 8; (c) a polynucleotide which is an allelic variant of any polynucleotide recited above; (d) a polynucleotide which encodes a species homologue of any of the proteins recited above; or (e) a polynucleotide that encodes a polypeptide comprising a specific domain or truncation of the polypeptides of SEQ ID NO:
277-552, or 773-992 (for example, as set forth in Tables 3, 4A, 4B, 5, 6, or 8). Domains of interest may depend on the nature of the encoded polypeptide; e.g., domains in receptor-like polypeptides include ligand-binding, extracellular, transmembrane, or cytoplasmic domains, or combinations thereof; domains in immunoglobulin-like proteins include the variable immunoglobulin-like domains; domains in enzyme-like polypeptides include catalytic and substrate binding domains; and domains in ligand polypeptides include receptor-binding domains.
The polynucleotides of the invention include naturally occurring or wholly or S partially synthetic DNA, e.g., cDNA and genomic DNA, and RNA, e.g., mRNA.
The polynucleotides may include entire coding region of the cDNA or may represent a portion of the coding region of the cDNA.
The present invention also provides genes corresponding to the cDNA sequences disclosed herein. The corresponding genes can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include the preparation of probes or primers from the disclosed sequence information for identification and/or amplification of genes in appropriate genomic libraries or other sources of genomic materials.
Further 5' and 3' sequence can be obtained using methods known in the art. For example, full length cDNA or genomic DNA that corresponds to any of the polynucleotides of SEQ >D NO:
1-276, or 553-772 can be obtained by screening appropriate cDNA or genomic DNA
libraries under suitable hybridization conditions using any of the polynucleotides of SEQ ID NO: 1-276, or 553-772 or a portion thereof as a probe. Alternatively, the polynucleotides of SEQ >D NO:
1-276, or 553-772 may be used as the basis for suitable primers) that allow identification and/or amplification of genes in appropriate genomic DNA or cDNA libraries.
The nucleic acid sequences of the invention can be assembled from ESTs and sequences (including cDNA and genomic sequences) obtained from one or more public databases, such as dbEST, gbpri, and UniGene. The EST sequences can provide identifying sequence information, representative fragment or segment information, or novel segment information for the full-length gene.
The polynucleotides of the invention also provide polynucleotides including nucleotide sequences that are substantially equivalent to the polynucleotides recited above.
Polynucleotides according to the invention can have, e.g., at least about 65%, at least about 70%, at least about 75%, at least about 80%, 81 %, 82%, 83%, 84%, more typically at least about 85%, 86%, 87%, 88%, 89%, more typically at least about 90%, 9I%, 92%, 93%, 94%, and even more typically at least about 95%, 96%, 97%, 98%, 99% sequence identity to a polynucleotide recited above.
Included within the scope of the nucleic acid sequences of the invention are nucleic acid sequence fragments that hybridize under stringent conditions to any of the nucleotide sequences of SEQ ID NO: 1-276, or 553-772, or complements thereof, which fragment is greater than about 5 nucleotides, preferably 7 nucleotides, more preferably greater than 9 nucleotides and most preferably greater than 17 nucleotides. Fragments of, e.g. 15, 17, or 20 nucleotides or more that are selective for (i.e. specifically hybridize to) any one of the polynucleotides of the invention are contemplated. Probes capable of specifically hybridizing to a polynucleotide can differentiate polynucleotide sequences of the invention from other polynucleotide sequences in the same family of genes or can differentiate human genes from genes of other species, and are preferably based on unique nucleotide sequences.
The sequences falling within the scope of the present invention are not limited to these specific sequences, but also include allelic and species variations thereof.
Allelic and species variations can be routinely determined by comparing the sequence provided in SEQ >D NO: 1-276, or 553-772, a representative fragment thereof, or a nucleotide sequence at least 90%
identical, preferably 95% identical, to SEQ >I7 NO: 1-276, or 553-772 with a sequence from another isolate of the same species. Furthermore, to accommodate codon variability, the invention includes nucleic acid molecules coding for the same amino acid sequences as do the specific ORFs disclosed herein. In other words, in the coding region of an ORF, substitution of one codon for another codon that encodes the same amino acid is expressly contemplated.
The nearest neighbor or homology results for the nucleic acids of the present invention, including SEQ 1D NO: 1-276, or 553-772 can be obtained by searching a database using an algorithm or a program. Preferably, a BLAST (Basic Local Alignment Search Tool) program is used to search for local sequence alignments (Altshul, S.F. J Mol. Evol. 36 290-300 (1993) and Altschul S.F. et al. J. Mol. Biol. 21:403-410 (1990)). Alternatively a FASTA
version 3 search against Genpept, using FASTXY algorithm may be performed.
Species homologs (or orthologs) of the disclosed polynucleotides and proteins are also provided by the present invention. Species homologs may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source from the desired species.
The invention also encompasses allelic variants of the disclosed polynucleotides or proteins; that is, naturally-occurnng alternative forms of the isolated polynucleotide which also encode proteins which are identical, homologous or related to that encoded by the polynucleotides.
The nucleic acid sequences of the invention are further directed to sequences which encode variants of the described nucleic acids. These amino acid sequence variants may be prepared by methods known in the art by introducing appropriate nucleotide changes into a native or variant polynucleotide. There are two variables in the construction of amino acid sequence variants: the location of the mutation and the nature of the mutation. Nucleic acids encoding the amino acid sequence variants are preferably constructed by mutating the 5 polynucleotide to encode an amino acid sequence that does not occur in nature. These nucleic acid alterations can be made at sites that differ in the nucleic acids from different species (variable positions) or in highly conserved regions (constant regions). Sites at such locations will typically be modified in series, e.g., by substituting first with conservative choices (e.g., hydrophobic amino acid to a different hydrophobic amino acid) and then with 10 more distant choices (e.g., hydrophobic amino acid to a charged amino acid), and then deletions or insertions may be made at the target site. Amino acid sequence deletions generally range from about 1 to 30 residues, preferably about 1 to 10 residues, and are typically contiguous. Amino acid insertions include amino- and/or carboxyl-terminal fusions ranging in length from one to one hundred or more residues, as well as intrasequence 15 insertions of single or multiple amino acid residues. Intrasequence insertions may range generally from about 1 to 10 amino residues, preferably from 1 to S residues.
Examples of terminal insertions include the heterologous signal sequences necessary for secretion or for intracellular targeting in different host cells and sequences such as FLAG or poly-histidine sequences useful for purifying the expressed protein.
20 In a preferred method, polynucleotides encoding the novel amino acid sequences are changed via site-directed mutagenesis. This method uses oligonucleotide sequences to alter a polynucleotide to encode the desired amino acid variant, as well as sufficient adjacent nucleotides on both sides of the changed amino acid to form a stable duplex on either side of the site of being changed. In general, the techniques of site-directed mutagenesis are well known to those of skill in the art and this technique is exemplified by publications such as, Edelman et al., DNA 2:183 (1983). A versatile and efficient method for producing site-specific changes in a polynucleotide sequence was published by Zoller and Smith, Nucleic Acids Res. 10:6487-6500 (1982). PCR may also be used to create amino acid sequence variants of the novel nucleic acids. When small amounts of template DNA are used as starting material, primers) that differs slightly in sequence from the corresponding region in the template DNA can generate the desired amino acid variant. PCR
amplification results in a population of product DNA fragments that differ from the polynucleotide template encoding the polypeptide at the position specified by the primer. The product DNA

fragments replace the corresponding region in the plasmid and this gives a polynucleotide encoding the desired amino acid variant.
A further technique for generating amino acid variants is the cassette mutagenesis technique described in Wells et al., Gene 34:315 (1985); and other mutagenesis techniques well known in the art, such as, for example, the techniques in Sambrook et al., supra, and Current Protocols in Molecular Biology, Ausubel et al. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence may be used in the practice of the invention for the cloning and expression of these novel nucleic acids. Such DNA sequences include those which are capable of hybridizing to the appropriate novel nucleic acid sequence under stringent conditions.
Polynucleotides encoding preferred polypeptide truncations of the invention could be used to generate polynucleotides encoding chimeric or fusion proteins comprising one or more domains of the invention and heterologous protein sequences.
The polynucleotides of the invention additionally include the complement of any of the polynucleotides recited above. The polynucleotide can be DNA (genomic, cDNA, amplified, or synthetic) or RNA. Methods and algorithms for obtaining such polynucleotides are well known to those of skill in the art and can include, for example, methods for determining hybridization conditions that can routinely isolate polynucleotides of the desired sequence identities.
In accordance with the invention, polynucleotide sequences comprising the mature protein coding sequences corresponding to any one of SEQ ID NO: 1-276, or 553-772, or functional equivalents thereof, may be used to generate recombinant DNA
molecules that direct the expression of that nucleic acid, or a functional equivalent thereof, in appropriate host cells. Also included are the cDNA inserts of any of the clones identified herein.
A polynucleotide according to the invention can be joined to any of a variety of other nucleotide sequences by well-established recombinant DNA techniques (see Sambrook J et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY).
Useful nucleotide sequences for joining to polynucleotides include an assortment of vectors, e.g., plasmids, cosmids, lambda phage derivatives, phagemids, and the like, that are well known in the art. Accordingly, the invention also provides a vector including a polynucleotide of the invention and a host cell containing the polynucleotide.
In general, the vector contains an origin of replication functional in at least one organism, convenient restriction endonuclease sites, and a selectable marker for the host cell.
Vectors according to the invention include expression vectors, replication vectors, probe generation vectors, and sequencing vectors. A host cell according to the invention can be a prokaryotic or eukaryotic cell and can be a unicellular organism or part of a multicellular organism.
The present invention further provides recombinant constructs comprising a nucleic acid having any of the nucleotide sequences of SEQ >D NO: 1-276, or 553-772 or a fragment thereof or any other polynucleotides of the invention. In one embodiment, the recombinant constructs of the present invention comprise a vector, such as a plasmid or viral vector, into which a nucleic acid having any of the nucleotide sequences of SEQ ID NO: 1-276, or 553-772 or a fragment thereof is inserted, in a forward or reverse orientation. In the case of a vector comprising one of the ORFs of the present invention, the vector may further comprise regulatory sequences, including for example, a promoter, operably linked to the ORF. Large numbers of suitable vectors and promoters are known to those of skill in the art and are commercially available for generating the recombinant constructs of the present invention.
The following vectors are provided by way of example: Bacterial: pBs, phagescript, PsiX174, pBluescript SK, pBs KS, pNHBa, pNHl6a, pNHl8a, pNH46a (Stratagene), pTrc99A, pKK223-3, pKK233-3, pDR540, pRITS (Pharmacia); Eukaryotic: pWLneo, pSV2cat, pOG44, PXTI, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL (Pharmacia).
The isolated polynucleotide of the invention may be operably linked to an expression control sequence such as the pMT2 or pED expression vectors disclosed in Kaufman et al., Nucleic Acids Res. 19, 4485-4490 (1991), in order to produce the protein recombinantly.
Many suitable expression control sequences are known in the art. General methods of expressing recombinant proteins are also known and are exemplified in R.
Kaufman, Methods in Enzymology 185, 537-566 (1990). As defined herein "operably linked"
means that the isolated polynucleotide of the invention and an expression control sequence are situated within a vector or cell in such a way that the protein is expressed by a host cell which has been transformed (transfected) with the ligated polynucleotide/expression control sequence.
Promoter regions can be selected from any desired gene using CAT
(chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lacI, IacZ, T3, T7, gpt, lambda PR, and trc. Eukaryotic promoters include CMV
immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiae TRPI gene, and a promoter derived S from a highly expressed gene to direct transcription of a downstream structural sequence.
Such promoters can be derived from operons encoding glycolytic enzymes such as phosphoglycerate kinase (PGK), a-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein into the periplasmic space or extracellular medium.
Optionally, the heterologous sequence can encode a fusion protein including an amino terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product. Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together with suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host. Suitable prokaryotic hosts for transformation include E. coli, Bcacillus subtilis, Salmonella typhimurium and various species within the genera Pseuclomoncas, Streptomyces, and Staphylococcus, although others may also be employed as a matter of choice.
As a representative but non-limiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (Promega Biotech, Madison, WI, USA). These pBR322 "backbone" sections are combined with an appropriate promoter and the structural sequence to be expressed. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter is induced or derepressed by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period. Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification.

Polynucleotides of the invention can also be used to induce immune responses.
For example, as described in Fan et al., Nat. Biotech 17, 870-872 (1999), incorporated herein by reference, nucleic acid sequences encoding a polypeptide may be used to generate antibodies against the encoded polypeptide following topical administration of naked plasmid DNA or following injection, and preferably intra-muscular injection of the DNA. The nucleic acid sequences are preferably inserted in a recombinant expression vector and may be in the form of naked DNA.
4.3 ANTISENSE
Another aspect of the invention pertains to isolated antisense nucleic acid molecules that are hybridizable to or complementary to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1-276, or 553-772, or fragments, analogs or derivatives thereof. An "antisense" nucleic acid comprises a nucleotide sequence that is complementary to a "sense" nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. In specific aspects, antisense nucleic acid molecules are provided that comprise a sequence complementary to at least about 10, 25, S0, 100, 250 or 500 nucleotides or an entire coding strand, or to only a portion thereof. Nucleic acid molecules encoding fragments, homologs, derivatives and analogs of a protein of any of SEQ ID NO: 1-276, or 553-772 or antisense nucleic acids complementary to a nucleic acid sequence of SEQ ID NO: 1-276, or are additionally provided.
In one embodiment, an antisense nucleic acid molecule is antisense to a "coding region" of the coding strand of a nucleotide sequence of the invention. The term "coding region" refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues. In another embodiment, the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence of the invention. The term "noncoding region" refers to 5' and 3' sequences that flank the coding region that are not translated into amino acids (i.e., also referred to as 5' and 3' untranslated regions).
Given the coding strand sequences encoding a nucleic acid disclosed herein (e.g., SEQ ID NO: 1-276, or 553-772, antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick or Hoogsteen base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of an mRNA, but more preferably is an oligonucleotide that is antisense to only a portion of the coding or noncoding region of an mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of an mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. An 5 antisense nucleic acid of the invention can be constructed using chemical synthesis or enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed 10 between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used.
Examples of modified nucleotides that can be used to generate the antisense nucleic acid include: S-fluorouracil, S-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-15 carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methyl guanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 20 5'-methoxycarboxymethyluracil, S-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-S-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced 25 biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).
The antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a protein according to the invention to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II
or pol III
promoter are preferred.
In yet another embodiment, the antisense nucleic acid molecule of the invention is an a-anomeric nucleic acid molecule. An a-anomeric nucleic acid molecule forms specific 1 S double-stranded hybrids with complementary RNA in which, contrary to the usual a-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids Res 1 S:
6625-6641.). The antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide (moue et al. (1987) Nucleic Acids Res 15: 6131-6148) or a chimeric RNA -DNA analogue (moue et al. (1987) FEBSLett 215: 327-330).
4.4 RIBOZYMES AND PNA MOIETIES
In still another embodiment, an antisense nucleic acid of the invention is a ribozyme.
Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave mRNA transcripts to thereby inhibit translation of an mRNA. A ribozyme having specificity for a nucleic acid of the invention can be designed based upon the nucleotide sequence of a DNA disclosed herein (i.e., SEQ ID NO: 1-276, or 553-772). For example, a derivative of Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a mRNA. See, e.g., Cech et cal. U.5. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742.
Alternatively, mRNA of the invention can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel et al., (1993) Science 261:1411-1418.
Alternatively, gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region (e.g., promoter and/or enhancers) to form triple S helical structures that prevent transcription of the gene in target cells.
See generally, Helene.
( 1991 ) Anticancer Drug Des. 6: 569-84; Helene. et al. ( 1992) Ann. N. Y.
Acad. Sci.
660:27-36; and Maher (1992) Bioassays 14: 807-15.
In various embodiments, the nucleic acids of the invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids (see Hyrup et al. (1996) Bioorg Med Chem 4: 5-23). As used herein, the terms "peptide nucleic acids"
or "PNAs" refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for -specific hybridization to DNA and RNA under conditions of low ionic strength.
The synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup et al. (1996) above; Perry-O'Keefe et al.
(1996) PNAS 93:
14670-675.
PNAs of the invention can be used in therapeutic and diagnostic applications.
For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, e.g., inducing transcription or translation arrest or inhibiting replication. PNAs of the invention can also be used, e.g., in the analysis of single base pair mutations in a gene by, e.g., PNA directed PCR clamping; as artificial restriction enzymes when used in combination with other enzymes, e.g., S 1 nucleases (Hyrup B. ( 1996) above);
or as probes or primers for DNA sequence and hybridization (Hyrup et al.
(1996), above;
Perry-O'Keefe ( 1996), above).
In another embodiment, PNAs of the invention can be modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example, PNA-DNA chimeras can be generated that may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA
recognition enzymes, e.g., RNase H and DNA polymerases, to interact with the DNA

portion while the PNA portion would provide high binding affinity and specificity.
PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup (1996) above). The synthesis of PNA-DNA chimeras can be performed as described in Hyrup (1996) above and Finn et al. (1996) Nucl Acids Res 24: 3357-63. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry, and modified nucleoside analogs, e.g., S'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite, can be used between the PNA and the 5' end of DNA (Mag et al.
(1989) Nucl Acid Res 17: 5973-88). PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment (Finn et al.
(1996) above). Alternatively, chimeric molecules can be synthesized with a S' DNA
segment and a 3' PNA segment. See, Petersen et al. (1975) Bioorg Med Chem Lett 5:
1119-11124.
In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al., 1989, Proc. Natl. Acad.
Sci. U.S.A.
86:6553-6556; Lemaitre et u1., 1987, Proc. Natl. Acad. Sci. 84:648-652; PCT
Publication No. W088/09810) or the blood-brain barrier (see, e.g., PCT Publication No.
W089/10134).
In addition, oligonucleotides can be modified with hybridization triggered cleavage agents (See, e.g., Krol et al., 1988, BioTechnigues 6:958-976) or intercalating agents. (See, e.g., Zon, 1988, Pharm. Res. S: 539-549). To this end, the oligonucleotide may be conjugated to another molecule, e.g., a peptide, a hybridization triggered cross-linking agent, a transport agent, a hybridization-triggered cleavage agent, etc.
4.5 HOSTS
The present invention further provides host cells genetically engineered to contain the polynucleotides of the invention. For example, such host cells may contain nucleic acids of the invention introduced into the host cell using known transformation, transfection or infection methods. The present invention still further provides host cells genetically engineered to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of the polynucleotides in the cell.

Knowledge of nucleic acid sequences allows for modification of cells to permit, or increase, expression of endogenous polypeptide. Cells can be modified (e.g., by homologous recombination) to provide increased polypeptide expression by replacing, in whole or in part, the naturally occurring promoter with all or part of a heterologous promoter so that the cells express the polypeptide at higher levels. The heterologous promoter is inserted in, such a manner that it is operatively linked to the encoding sequences. See, for example, PCT International Publication No. W094/12650, PCT International Publication No. W092/20808, and PCT International Publication No. W091/09955. It is also contemplated that, in addition to heterologous promoter DNA, amplifiable marker DNA
(e.g., ada, dhfr, and the multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA
may be inserted along with the heterologous promoter DNA. If linked to the coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the desired protein coding sequences in the cells.
The host cell can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic host cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the recombinant construct into the host cell can be effected by calcium phosphate transfection, DEAE, dextran mediated transfection, or electroporation (Davis, L. et al., Basic Methods in Molecular Biology (1986)). The host cells containing one of the polynucleotides of the invention, can be used in conventional manners to produce the gene product encoded by the isolated fragment (in the case of an ORF) or can be used to produce a heterologous protein under the control of the EMF.
Any host/vector system can be used to express one or more of the ORFs of the present invention. These include, but are not limited to, eukaryotic hosts such as HeLa cells, Cv-1 cell, COS cells, 293 cells, and Sf~ cells, as well as prokaryotic host such as E. coli and B. subtilis. The most preferred cells are those which do not normally express the particular polypeptide or protein or which expresses the polypeptide or protein at low natural level.
Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al., in Molecular Cloning: A
Laboratory Manual, Second Edition, Cold Spring Harbor, New York (1989), the disclosure of which is hereby incorporated by reference.
Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines 5 of monkey kidney fibroblasts, described by Gluzman, Cell 23:175 (1981).
Other cell lines capable of expressing a compatible vector are, for example, the C127, monkey COS cells, Chinese Hamster Ovary (CHO) cells, human kidney 293 cells, human epidermal A431 cells, human Co1o205 cells, 3T3 cells, CV-1 cells, other transformed primate cell lines, normal diploid cells, cell strains derived from in vitro culture of primary tissue, primary explants, 10 HeLa cells, mouse L cells, BHK, HL-60, U937, HaK or Jurkat cells. Mammalian expression vectors will comprise an origin of replication, a suitable promoter and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5' flanking nontranscribed sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, enhancer, splice, 1 S and polyadenylation sites may be used to provide the required nontranscribed genetic elements. Recombinant polypeptides and proteins produced in bacterial culture are usually isolated by initial extraction from cell pellets, followed by one or more salting-out, aqueous ion exchange or size exclusion chromatography steps. Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. Finally, high performance 20 liquid chromatography (HPLC) can be employed for final purification steps.
Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents.
Alternatively, it may be possible to produce the protein in lower eukaryotes such as yeast or insects or in prokaryotes such as bacteria. Potentially suitable yeast strains include 25 Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces strains, Candida, or any yeast strain capable of expressing heterologous proteins. Potentially suitable bacterial strains include Escherichia coli, Bacillus subtilis, Salmonella typhimurium, or any bacterial strain capable of expressing heterologous proteins. If the protein is made in yeast or bacteria, it may be necessary to modify the protein produced therein, for example by 30 phosphorylation or glycosylation of the appropriate sites, in order to obtain the functional protein. Such covalent attachments may be accomplished using known chemical or enzymatic methods.

In another embodiment of the present invention, cells and tissues may be engineered to express an endogenous gene comprising the polynucleotides of the invention under the control of inducible regulatory elements, in which case the regulatory sequences of the endogenous gene may be replaced by homologous recombination. As described herein, gene targeting can be used to replace a gene's existing regulatory region with a regulatory sequence isolated from a different gene or a novel regulatory sequence synthesized by genetic engineering methods. Such regulatory sequences may be comprised of promoters, enhancers, scaffold-attachment regions, negative regulatory elements, transcriptional initiation sites, and regulatory protein binding sites or combinations of said sequences.
Alternatively, sequences which affect the structure or stability of the RNA or protein produced may be replaced, removed, added, or otherwise modified by targeting.
These sequence include polyadenylation signals, mRNA stability elements, splice sites, leader sequences for enhancing or modifying transport or secretion properties of the protein, or other sequences which alter or improve the function or stability of protein or RNA
1 S molecules.
The targeting event may be a simple insertion of the regulatory sequence, placing the gene under the control of the new regulatory sequence, e.g., inserting a new promoter or enhancer or both upstream of a gene. Alternatively, the targeting event may be a simple deletion of a regulatory element, such as the deletion of a tissue-specific negative regulatory element. Alternatively, the targeting event may replace an existing element;
for example, a tissue-specific enhancer can be replaced by an enhancer that has broader or different cell-type specificity than the naturally occurnng elements. Here, the naturally occurring sequences are deleted and new sequences are added. In all cases, the identification of the targeting event may be facilitated by the use of one or more selectable marker genes that are contiguous with the targeting DNA, allowing for the selection of cells in which the exogenous DNA has integrated into the host cell genome. The identification of the targeting event may also be facilitated by the use of one or more marker genes exhibiting the property of negative selection, such that the negatively selectable marker is linked to the exogenous DNA, but configured such that the negatively selectable marker flanks the targeting sequence, and such that a correct homologous recombination event with sequences in the host cell genome does not result in the stable integration of the negatively selectable marker.
Markers useful for this propose include the Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-guanine phosphoribosyl-transferase (gpt) gene.

The gene targeting or gene activation techniques which can be used in accordance with this aspect of the invention are more particularly described in U.S.
Patent No. 5,272,071 to Chappel; U.S. Patent No. 5,578,461 to Sherwin et al.; International Application No.
PCT/L1S92/09627 (W093/09222) by Selden et al.; and International Application No.
PCT/L1S90/06436 (W091/06667) by Skoultchi et al., each of which is incorporated by reference herein in its entirety.
4.6 POLYPEPTIDES OF THE INVENTION
The isolated polypeptides of the invention include, but are not limited to, a polypeptide comprising: the amino acid sequences set forth as any one of SEQ
ID NO: 277-552, or 773-992 or an amino acid sequence encoded by any one of the nucleotide sequences SEQ ID NO: 1-276, or 553-772 or the corresponding full length or mature protein.
Polypeptides of the invention also include polypeptides preferably with biological or immunological activity that are encoded by: (a) a polynucleotide having any one of the nucleotide sequences set forth in SEQ ID NO: 1-276, or 553-772 or (b) polynucleotides encoding any one of the amino acid sequences set forth as SEQ ID NO: 277-552, or 773-992 or (c) polynucleotides that hybridize to the complement of the polynucleotides of either (a) or (b) under stringent hybridization conditions. The invention also provides biologically active or immunologically active variants of any of the amino acid sequences set forth as SEQ ID NO: 277-552, or 773-992 or the corresponding full length or mature protein; and "substantial equivalents" thereof (e.g., with at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, 86%, 87%, 88%, 89%, at least about 90%, 91 %, 92%, 93%, 94%, typically at least about 95%, 96%, 97%, more typically at least about 98%, or most typically at least about 99% amino acid identity) that retain biological activity. Polypeptides encoded by allelic variants may have a similar, increased, or decreased activity compared to polypeptides comprising SEQ ID NO: 277-552, or 773-992.
Fragments of the proteins of the present invention which are capable of exhibiting biological activity are also encompassed by the present invention. Fragments of the protein may be in linear form or they may be cyclized using known methods, for example, as described in H. U. Saragovi, et al., Bio/Technology 10, 773-778 (1992) and in R. S.
McDowell, et al., J. Amer. Chem. Soc. 114, 9245-9253 (1992), both of which are incorporated herein by reference. Such fragments may be fused to carrier molecules such as immunoglobulins for many purposes, including increasing the valency of protein binding sites. Fragments are also identified in Tables 3, 4A, 4B, 5, 6, or 8.
The present invention also provides both full-length and mature forms (for example, without a signal sequence or precursor sequence) of the disclosed proteins.
The protein S coding sequence is identified in the sequence listing by translation of the disclosed nucleotide sequences. The predicted signal sequence is set forth in Table 6.
The mature form of such protein may be obtained and confirmed by expression of a full-length polynucleotide in a suitable mammalian cell or other host cell and sequencing of the cleaved product. One of skill in the art will recognize that the actual cleavage site may be different than that predicted in Table 6. The sequence of the mature form of the protein is also determinable from the amino acid sequence of the full-length form. Where proteins of the present invention are membrane bound, soluble forms of the proteins are also provided. In such forms, part or all of the regions causing the proteins to be membrane bound are deleted so that the proteins are fully secreted from the cell in which they are expressed (See, e.g., Sakal et al., Prep. Biochem. Biotechnol. (2000), 30(2), pp. 107-23, incorporated herein by reference).
Protein compositions of the present invention may further comprise an acceptable carrier, such as a hydrophilic, e.g., pharmaceutically acceptable, carrier.
The present invention further provides isolated polypeptides encoded by the nucleic acid fragments of the present invention or by degenerate variants of the nucleic acid fragments of the present invention. By "degenerate variant" is intended nucleotide fragments which differ from a nucleic acid fragment of the present invention (e.g., an ORF) by nucleotide sequence but, due to the degeneracy of the genetic code, encode an identical polypeptide sequence. Preferred nucleic acid fragments of the present invention are the ORFs that encode proteins.
A variety of methodologies known in the art can be utilized to obtain any one of the isolated polypeptides or proteins of the present invention. At the simplest level, the amino acid sequence can be synthesized using commercially available peptide synthesizers. The synthetically-constructed protein sequences, by virtue of sharing primary, secondary or tertiary structural and/or conformational characteristics with proteins may possess biological properties in common therewith, including protein activity. This technique is particularly useful in producing small peptides and fragments of larger polypeptides.
Fragments are useful, for example, in generating antibodies against the native polypeptide.
Thus, they may be employed as biologically active or immunological substitutes for natural, purified proteins in screening of therapeutic compounds and in immunological processes for the development of antibodies.
The polypeptides and proteins of the present invention can alternatively be purified from cells which have been altered to express the desired polypeptide or protein. As used herein, a cell is said to be altered to express a desired polypeptide or protein when the cell, through genetic manipulation, is made to produce a polypeptide or protein which it normally does not produce or which the cell normally produces at a lower level. One skilled in the art can readily adapt procedures for introducing and expressing either recombinant or synthetic sequences into eukaryotic or prokaryotic cells in order to generate a cell which produces one of the polypeptides or proteins of the present invention.
The invention also relates to methods for producing a polypeptide comprising growing a culture of host cells of the invention in a suitable culture medium, and purifying the protein from the cells or the culture in which the cells are grown. For example, the methods of the invention include a process for producing a polypeptide in which a host cell containing a suitable expression vector that includes a polynucleotide of the invention is cultured under conditions that allow expression of the encoded polypeptide.
The polypeptide can be recovered from the culture, conveniently from the culture medium, or from a lysate prepared from the host cells and further purified. Preferred embodiments include those in which the protein produced by such process is a fill length or mature form of the protein.
In an alternative method, the polypeptide or protein is purified from bacterial cells which naturally produce the polypeptide or protein. One skilled in the art can readily follow known methods for isolating polypeptides and proteins in order to obtain one of the isolated polypeptides or proteins of the present invention. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immuno-affinity chromatography. See, e.g., Scopes, Protein Purification: Principles and Practice, Springer-Verlag (1994); Sambrook, et al., in Molecular Cloning: A Laboratory Manual; Ausubel et al., Current Protocols in Molecular Biology. Polypeptide fragments that retain biological/immunological activity include fragments comprising greater than about 100 amino acids, or greater than about 200 amino acids, and fragments that encode specific protein domains.

The purified polypeptides can be used in in vitro binding assays which are well known in the art to identify molecules which bind to the polypeptides. These molecules include but are not limited to, for e.g., small molecules, molecules from combinatorial libraries, antibodies or other proteins. The molecules identified in the binding assay are then S tested for antagonist or agonist activity in in vivo tissue culture or animal models that are well known in the art. In brief, the molecules are titrated into a plurality of cell cultures or animals and then tested for either cell/animal death or prolonged survival of the animal/cells.
In addition, the peptides of the invention or molecules capable of binding to the peptides may be complexed with toxins, e.g., ricin or cholera, or with other compounds that 10 are toxic to cells. The toxin-binding molecule complex is then targeted to a tumor or other cell by the specificity of the binding molecule for SEQ ID NO: 277-552, or 773-992.
The protein of the invention may also be expressed as a product of transgenic animals, e.g., as a component of the milk of transgenic cows, goats, pigs, or sheep which are characterized by somatic or germ cells containing a nucleotide sequence encoding the 15 protein.
The proteins provided herein also include proteins characterized by amino acid sequences similar to those of purified proteins but into which modification are naturally provided or deliberately engineered. For example, modifications, in the peptide or DNA
sequence, can be made by those skilled in the art using known techniques.
Modifications of 20 interest in the protein sequences may include the alteration, substitution, replacement, insertion or deletion of a selected amino acid residue in the coding sequence.
For example, one or more of the cysteine residues may be deleted or replaced with another amino acid to alter the conformation of the molecule. Techniques for such alteration, substitution, replacement, insertion or deletion are well known to those skilled in the art (see, e.g., U.S.
25 Pat. No. 4,518,584). Preferably, such alteration, substitution, replacement, insertion or deletion retains the desired activity of the protein. Regions of the protein that are important for the protein function can be determined by various methods known in the art including the alanine-scanning method which involved systematic substitution of single or strings of amino acids with alanine, followed by testing the resulting alanine-containing variant for 30 biological activity. This type of analysis determines the importance of the substituted amino acids) in biological activity. Regions of the protein that are important for protein function may be determined by the eMATRIX program.

Other fragments and derivatives of the sequences of proteins which would be expected to retain protein activity in whole or in part and are useful for screening or other immunological methodologies may also be easily made by those skilled in the art given the disclosures herein. Such modifications are encompassed by the present invention.
The protein may also be produced by operably linking the isolated polynucleotide of the invention to suitable control sequences in one or more insect expression vectors, and employing an insect expression system. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, e.g., Invitrogen, San Diego, Calif., U.S.A. (the MaxBatTM kit), and such methods are well known in the art, as described in Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987), incorporated herein by reference. As used herein, an insect cell capable of expressing a polynucleotide of the present invention is "transformed."
The protein of the invention may be prepared by culturing transformed host cells under culture conditions suitable to express the recombinant protein. The resulting expressed protein may then be purified from such culture (i.e., from culture medium or cell extracts) using known purification processes, such as gel filtration and ion exchange chromatography. The purification of the protein may also include an affinity column containing agents which will bind to the protein; one or more column steps over such affinity resins as concanavalin A-agarose, heparin-toyopearITM or Cibacrom blue 3GA
SepharoseTM;
one or more steps involving hydrophobic interaction chromatography using such resins as phenyl ether, butyl ether, or propyl ether; or immunoaffinity chromatography.
Alternatively, the protein of the invention may also be expressed in a form which will facilitate purification. For example, it may be expressed as a fusion protein, such as those of maltose binding protein (MBP), glutathione-S-transferase (GST) or thioredoxin (TRX), or as a His tag. Kits for expression and purification of such fusion proteins are commercially available from New England BioLab (Beverly, Mass.), Pharmacia (Piscataway, N.J.) and Invitrogen, respectively. The protein can also be tagged with an epitope and subsequently purified by using a specific antibody directed to such epitope. One such epitope ("FLAG ~t ") is commercially available from Kodak (New Haven, Conn.).
Finally, one or more reverse-phase high performance liquid chromatography (RP-HPLC) steps employing hydrophobic RP-HPLC media, e.g., silica gel having pendant methyl or other aliphatic groups, can be employed to further purify the protein. Some or all of the foregoing purification steps, in various combinations, can also be employed to provide a substantially homogeneous isolated recombinant protein. The protein thus purified is substantially free of other mammalian proteins and is defined in accordance with the present invention as an "isolated protein."
The polypeptides of the invention include analogs (variants). This embraces fragments, as well as peptides in which one or more amino acids has been deleted, inserted, or substituted. Also, analogs of the polypeptides of the invention embrace fusions of the polypeptides or modifications of the polypeptides of the invention, wherein the polypeptide or analog is fused to another moiety or moieties, e.g., targeting moiety or another therapeutic agent. Such analogs may exhibit improved properties such as activity and/or stability.
Examples of moieties which may be fused to the polypeptide or an analog include, for example, targeting moieties which provide for the delivery of polypeptide to pancreatic cells, e.g., antibodies to pancreatic cells, antibodies to immune cells such as T-cells, monocytes, dendritic cells, granulocytes, etc., as well as receptor and ligands expressed on pancreatic or immune cells. Other moieties which may be fused to the polypeptide include therapeutic agents which are used for treatment, for example, immunosuppressive drugs such as cyclosporin, SK506, azathioprine, CD3 antibodies and steroids. Also, polypeptides may be fused to immune modulators, and other cytokines such as alpha or beta interferon.
4.6.1 DETERMINING POLYPEPTIDE AND POLYNUCLEOTIDE
IDENTITY AND SIMILARITY
Preferred identity and/or similarity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in computer programs including, but are not limited to, the GCG program package, including GAP
(Devereux, J., et al., Nucleic Acids Research 12(1):387 (1984); Genetics Computer Group, University of Wisconsin, Madison, WI), BLASTP, BLASTN, BLASTX, FASTA
(Altschul, S.F. et al., J. Molec. Biol. 215:403-410 (1990), PSI-BLAST (Altschul S.F. et al., Nucleic Acids Res. vol. 25, pp. 3389-3402, herein incorporated by reference), eMatrix software (Wu et al., J. Comp. Biol., Vol. 6, pp. 219-235 (1999), herein incorporated by reference), eMotif software (Nevill-Manning et al, ISMB-97, Vol. 4, pp. 202-209, herein incorporated by reference), Pfam software (Sonnhammer et al., Nucleic Acids Res., Vol. 26(1), pp. 320-322 (1998), herein incorporated by reference) and the Kyte-Doolittle hydrophobocity prediction algorithm (J. Mol Biol, 157, pp. 105-31 (1982), the GeneAtlas software (Molecular Simulations Inc. (MSI), San Diego, CA) (Sanchez and Sali (1998) Proc. Natl.
Acad. Sci., 95, 13597-13602; Kitson DH et al, (2000) "Remote homology detection using structural modeling - an evaluation" Submitted; Fischer and Eisenberg (1996) Protein Sci.
S, 947-955), Neural Network SignalP V I .1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark) incorporated herein by reference).
Polypeptide sequences were examined by a proprietary algorithm, SeqLoc that separates the proteins into three sets of locales: intracellular, membrane, or secreted.
This prediction is based upon three characteristics of each polypeptide, including percentage of cysteine residues, Kyte-Doolittle scores for the first 20 amino acids of each protein, and Kyte-Doolittle scores to calculate the longest hydrophobic stretch of the said protein. Values of predicted proteins are compared against the values from a set of 592 proteins of known cellular localization from the Swissprot database (http://www.e~asy.ch/sprot).
Predictions are based upon the maximum likelihood estimation.
Presence of transmembrane regions) was detected using the TMpred program (http://www.ch.embnet.org/software/TMPRED, for-m.ht~nl).
The BLAST programs are publicly available from the National Center for Biotechnology Information (NCBI) and other sources (BLAST Manual, Altschul, S., et al.
NCBI NLM N1H Bethesda, MD 20894; Altschul, S., et al., J. Mol. Biol. 215:403-( 1990).
4.7 CHIMERIC AND FUSION PROTEINS
The invention also provides chimeric or fusion proteins. As used herein, a "chimeric protein" or "fusion protein" comprises a polypeptide of the invention operatively linked to another polypeptide. Within a fusion protein the polypeptide according to the invention can correspond to all or a portion of a protein according to the invention. In one embodiment, a fusion protein comprises at least one biologically active portion of a protein according to the invention. . In another embodiment, a fusion protein comprises at least two biologically active portions of a protein according to the invention. Within the fusion protein, the term "operatively linked" is intended to indicate that the polypeptide according to the invention and the other polypeptide are fused in-frame to each other. The polypeptide can be fused to the N-terminus or C-terminus, or to the middle.
For example, in one embodiment a fusion protein comprises a polypeptide according to the invention operably linked to the extracellular domain of a second protein.

In another embodiment, the fusion protein is a GST-fusion protein in which the polypeptide sequences of the invention are fused to the C-terminus of the GST
(i.e., glutathione S-transferase) sequences.
In another embodiment, the fusion protein is an immunoglobulin fusion protein in which the polypeptide sequences according to the invention comprise one or more domains fused to sequences derived from a member of the immunoglobulin protein family.
The immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a ligand and a protein of the invention on the surface of a cell, to thereby suppress signal transduction in vivo. The immunoglobulin fusion proteins can be used to affect the bioavailability of a cognate ligand. Inhibition of the ligand/protein interaction may be useful therapeutically for both the treatment of proliferative and differentiative disorders, e.g., cancer as well as modulating (e.g., promoting or inhibiting) cell survival. Moreover, the immunoglobulin fusion proteins of the invention can be used as immunogens to produce antibodies in a subject, to purify ligands, and in screening assays to identify molecules that inhibit the interaction of a polypeptide of the invention with a ligand.
A chimeric or fusion protein of the invention can be produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, e.g., by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR
amplification of gene fragments can be carried out using anchor primers that give rise to complementary overhangs between two consecutive gene fragments that can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Ausubel et al. (eds.) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). A nucleic acid encoding a polypeptide of the invention can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the protein of the invention.

4.8 GENE THERAPY
Mutations in the polynucleotides of the invention gene may result in loss of normal function of the encoded protein. The invention thus provides gene therapy to restore normal activity of the polypeptides of the invention; or to treat disease states involving polypeptides 5 of the invention. Delivery of a functional gene encoding polypeptides of the invention to appropriate cells is effected ex vivo, in situ, or in vivo by use of vectors, and more particularly viral vectors (e.g., adenovirus, adeno-associated virus, or a retrovirus), or ex vivo by use of physical DNA transfer methods (e.g., liposomes or chemical treatments). See, for example, Anderson, Nature, supplement to vol. 392, no. 6679, pp.25-20 ( 1998).
For 10 additional reviews of gene therapy technology see Friedmann, Science, 244:

(1989); Verma, Scientific American: 68-84 (1990); and Miller, Nature, 357: 455-460 (1992).
Introduction of any one of the nucleotides of the present invention or a gene encoding the polypeptides of the present invention can also be accomplished with extrachromosomal substrates (transient expression) or artificial chromosomes (stable expression). Cells may 1 S also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells.
Treated cells can then be introduced in vivo for therapeutic purposes. Alternatively, it is contemplated that in other human disease states, preventing the expression of or inhibiting the activity of polypeptides of the invention will be useful in treating the disease states. It is contemplated that antisense 20 therapy or gene therapy could be applied to negatively regulate the expression of polypeptides of the invention.
Other methods inhibiting expression of a protein include the introduction of antisense molecules to the nucleic acids of the present invention, their complements, or their translated RNA sequences, by methods known in the art. Further, the polypeptides of the present 25 invention can be inhibited by using targeted deletion methods, or the insertion of a negative regulatory element such as a silencer, which is tissue specific.
The present invention still further provides cells genetically engineered in vivo to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of 30 the polynucleotides in the cell. These methods can be used to increase or decrease the expression of the polynucleotides of the present invention.
Knowledge of DNA sequences provided by the invention allows for modification of cells to permit, increase, or decrease, expression of endogenous polypeptide.
Cells can be modified (e.g., by homologous recombination) to provide increased polypeptide expression by replacing, in whole or in part, the naturally occurring promoter with all or part of a heterologous promoter so that the cells express the protein at higher levels. The heterologous promoter is inserted in such a manner that it is operatively linked to the desired protein encoding sequences.
S See, for example, PCT International Publication No. WO 94/12650, PCT
International Publication No. WO 92/20808, and PCT International Publication No. WO
91/09955. It is also contemplated that, in addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ada, dhfr, and the multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA may be inserted along with the heterologous promoter DNA. If linked to the desired protein coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the desired protein coding sequences in the cells.
In another embodiment of the present invention, cells and tissues may be engineered to express an endogenous gene comprising the polynucleotides of the invention under the control I S of inducible regulatory elements, in which case the regulatory sequences of the endogenous gene may be replaced by homologous recombination. As described herein, gene targeting can be used to replace a gene's existing regulatory region with a regulatory sequence isolated from a different gene or a novel regulatory sequence synthesized by genetic engineering methods.
Such regulatory sequences may be comprised of promoters, enhancers, scaffold-attachment regions, negative regulatory elements, transcriptional initiation sites, regulatory protein binding sites or combinations of said sequences. Alternatively, sequences which affect the structure or stability of the RNA or protein produced may be replaced, removed, added, or otherwise modified by targeting. These sequences include polyadenylation signals, mRNA
stability elements, splice sites, leader sequences for enhancing or modifying transport or secretion properties of the protein, or other sequences which alter or improve the function or stability of protein or RNA molecules.
The targeting event may be a simple insertion of the regulatory sequence, placing the gene under the control of the new regulatory sequence, e.g., inserting a new promoter or enhancer or both upstream of a gene. Alternatively, the targeting event may be a simple deletion of a regulatory element, such as the deletion of a tissue-specific negative regulatory element. Alternatively, the targeting event may replace an existing element;
for example, a tissue-specific enhancer can be replaced by an enhancer that has broader or different cell-type specificity than the naturally occurnng elements. Here, the naturally occurnng sequences are deleted and new sequences are added. In all cases, the identification of the targeting event may be facilitated by the use of one or more selectable marker genes that are contiguous with the targeting DNA, allowing for the selection of cells in which the exogenous DNA
has integrated into the cell genome. The identification of the targeting event may also be facilitated by the use of one or more marker genes exhibiting the property of negative selection, such that the negatively selectable marker is linked to the exogenous DNA, but configured such that the negatively selectable marker flanks the targeting sequence, and such that a correct homologous recombination event with sequences in the host cell genome does not result in the stable integration of the negatively selectable marker. Markers useful for this purpose include the Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-guanine phosphoribosyl-transferase (gpt) gene.
The gene targeting or gene activation techniques which can be used in accordance with this aspect of the invention are more particularly described in U.S. Patent No. 5,272,071 to Chappel; U.S. Patent No. 5,578,461 to Sherwin et al.; International Application No.
PCT/LTS92/09627 (W093/09222) by Selden et al.; and International Application No.
PCT/US90/06436 (W091/06667) by Skoultchi et al., each of which is incorporated by reference herein in its entirety.
4.9 TRANSGENIC ANIMALS
In preferred methods to determine biological functions of the polypeptides of the invention in vivo, one or more genes provided by the invention are either over expressed or inactivated in the germ line of animals using homologous recombination [Capecchi, Science 244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the regulatory control of exogenous or endogenous promoter elements, are known as transgenic animals.
Animals in which an endogenous gene has been inactivated by homologous recombination are referred to as "knockout" animals. Knockout animals, preferably non-human mammals, can be prepared as described in U.S. Patent No. 5,557,032, incorporated herein by reference.
Transgenic animals are useful to determine the roles polypeptides of the invention play in biological processes, and preferably in disease states. Transgenic animals are useful as model systems to identify compounds that modulate lipid metabolism. Transgenic animals, preferably non-human mammals, are produced using methods as described in U.S.
Patent No 5,489,743 and PCT Publication No. W094/28122, incorporated herein by reference.

Transgenic animals can be prepared wherein all or part of a promoter of the polynucleotides of the invention is either activated or inactivated to alter the level of expression of the polypeptides of the invention. Inactivation can be carried out using homologous recombination methods described above. Activation can be achieved by S supplementing or even replacing the homologous promoter to provide for increased protein expression. The homologous promoter can be supplemented by insertion of one or more heterologous enhancer elements known to confer promoter activation in a particular tissue.
The polynucleotides of the present invention also make possible the development, through, e.g., homologous recombination or knock out strategies, of animals that fail to express polypeptides of the invention or that express a variant polypeptide.
Such animals are useful as models for studying the in vivo activities of polypeptide as well as for studying modulators of the polypeptides of the invention.
In preferred methods to determine biological functions of the polypeptides of the invention in vivo, one or more genes provided by the invention are either over expressed or inactivated in the germ line of animals using homologous recombination [Capecchi, Science 244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the regulatory control of exogenous or endogenous promoter elements, are known as transgenic animals.
Animals in which an endogenous gene has been inactivated by homologous recombination are referred to as "knockout" animals. Knockout animals, preferably non-human mammals, can be prepared as described in U.S. Patent No. 5,557,032, incorporated herein by reference.
Transgenic animals are useful to determine the roles polypeptides of the invention play in biological processes, and preferably in disease states. Transgenic animals are useful as model systems to identify compounds that modulate lipid metabolism. Transgenic animals, preferably non-human mammals, are produced using methods as described in U.S.
Patent No 5,489,743 and PCT Publication No. W094/28122, incorporated herein by reference.
Transgenic animals can be prepared wherein all or part of the polynucleotides of the invention promoter is either activated or inactivated to alter the level of expression of the polypeptides of the invention. Inactivation can be carried out using homologous recombination methods described above. Activation can be achieved by supplementing or even replacing the homologous promoter to provide for increased protein expression. The homologous promoter can be supplemented by insertion of one or more heterologous enhancer elements known to confer promoter activation in a particular tissue.

4.10 USES AND BIOLOGICAL ACTIVITY
The polynucleotides and proteins of the present invention are expected to exhibit one or more of the uses or biological activities (including those associated with assays cited herein) identified herein. Uses or activities described for proteins of the present invention may be provided by administration or use of such proteins or of polynucleotides encoding such proteins (such as, for example, in gene therapies or vectors suitable for introduction of DNA). The mechanism underlying the particular condition or pathology will dictate whether the polypeptides of the invention, the polynucleotides of the invention or modulators (activators or inhibitors) thereof would be beneficial to the subject in need of treatment.
Thus, "therapeutic compositions of the invention" include compositions comprising isolated polynucleotides (including recombinant DNA molecules, cloned genes and degenerate variants thereof) or polypeptides of the invention (including full length protein, mature protein and truncations or domains thereof), or compounds and other substances that modulate the overall activity of the target gene products, either at the level of target gene/protein expression or target protein activity. Such modulators include polypeptides, analogs, (variants), including fragments and fusion proteins, antibodies and other binding proteins; chemical compounds that directly or indirectly activate or inhibit the polypeptides of the invention (identified, e.g., via drug screening assays as described herein); antisense polynucleotides and polynucleotides suitable for triple helix formation; and in particular antibodies or other binding partners that specifically recognize one or more epitopes of the polypeptides of the invention.
The polypeptides of the present invention may likewise be involved in cellular activation or in one of the other physiological pathways described herein.
4.10.1 RESEARCH USES AND UTILITIES
The polynucleotides provided by the present invention can be used by the research community for various purposes. The polynucleotides can be used to express recombinant protein for analysis, characterization or therapeutic use; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in disease states); as molecular weight markers on gels; as chromosome markers or tags (when labeled) to identify chromosomes or to map related gene positions; to compare with endogenous DNA sequences in patients to identify potential genetic disorders; as probes to hybridize and thus discover novel, related DNA

sequences; as a source of information to derive PCR primers for genetic fingerprinting; as a probe to "subtract-out" known sequences in the process of discovering other novel polynucleotides; for selecting and making oligomers for attachment to a "gene chip" or other support, including for examination of expression patterns; to raise anti-protein antibodies 5 using DNA immunization techniques; and as an antigen to raise anti-DNA
antibodies or elicit another immune response. Where the polynucleotide encodes a protein which binds or potentially binds to another protein (such as, for example, in a receptor-ligand interaction), the polynucleotide can also be used in interaction trap assays (such as, for example, that described in Gyuris et al., Cell 75:791-803 (1993)) to identify polynucleotides encoding the 10 other protein with which binding occurs or to identify inhibitors of the binding interaction.
The polypeptides provided by the present invention can similarly be used in assays to determine biological activity, including in a panel of multiple proteins for high-throughput screening; to raise antibodies or to elicit another immune response; as a reagent (including the labeled reagent) in assays designed to quantitatively determine levels of the protein (or 15 its receptor) in biological fluids; as markers for tissues in which the corresponding polypeptide is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in a disease state); and, of course, to isolate correlative receptors or ligands. Proteins involved in these binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction.
20 Any or all of these research utilities are capable of being developed into reagent grade or kit format for commercialization as research products.
Methods for performing the uses listed above are well known to those skilled in the art. References disclosing such methods include without limitation "Molecular Cloning: A
Laboratory Manual", 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, J., E. F.
25 Fritsch and T. Maniatis eds., 1989, and "Methods in Enzymology: Guide to Molecular Cloning Techniques", Academic Press, Bergen S. L. and A. R. Kimmel eds., 1987.
4.10.2 NUTRITIONAL USES
Polynucleotides and polypeptides of the present invention can also be used as 30 nutritional sources or supplements. Such uses include without limitation use as a protein or amino acid supplement, use as a carbon source, use as a nitrogen source and use as a source of carbohydrate. In such cases the polypeptide or polynucleotide of the invention can be added to the feed of a particular organism or can be administered as a separate solid or liquid preparation, such as in the form of powder, pills, solutions, suspensions or capsules. In the case of microorganisms, the polypeptide or polynucleotide of the invention can be added to the medium in or on which the microorganism is cultured.
S 4.10.3 CYTOKINE AND CELL PROLIFERATION/DIFFERENTIATION
ACTIVITY
A polypeptide of the present invention may exhibit activity relating to cytokine, cell proliferation (either inducing or inhibiting) or cell differentiation (either inducing or inhibiting) activity or may induce production of other cytokines in certain cell populations.
A polynucleotide of the invention can encode a polypeptide exhibiting such attributes.
Many protein factors discovered to date, including all known cytokines, have exhibited activity in one or more factor-dependent cell proliferation assays, and hence the assays serve as a convenient confirmation of cytokine activity. The activity of therapeutic compositions of the present invention is evidenced by any one of a number of routine factor dependent cell proliferation assays for cell lines including, without limitation, 32D, DA2, DAIG, T10, B9, B9/11, BaF3, MC9/G, M+(preB M+), 2E8, RBS, DA1, 123, T1165, HT2, CTLL2, TF-l, Mo7e, CMK, HUVEC, and Caco. Therapeutic compositions of the invention can be used in the following:
Assays for T-cell or thymocyte proliferation include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M.
Kruisbeek, D. H.
Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19;
Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986;
Bertagnolli et al., J. Immunol. 145:1706-1712, 1990; Bertagnolli et al., Cellular Immunology 133:327-341, 1991; Bertagnolli, et al., I. Immunol. 149:3778-3783, 1992;
Bowman et al., 1.
Immunol. 152:1756-1761, 1994.
Assays for cytokine production and/or proliferation of spleen cells, lymph node cells or thymocytes include, without limitation, those described in: Polyclonal T
cell stimulation, Kruisbeek, A. M. and Shevach, E. M. In Current Protocols in Immunology. J. E.
e.a. Coligan eds. Vol 1 pp. 3.12.1-3.12.14, John Wiley and Sons, Toronto. 1994; and Measurement of mouse and human interleukin-y, Schreiber, R. D. In Current Protocols in Immunology. J. E.
e.a. Coligan eds. Vol 1 pp. 6.8.1-6.8.8, John Wiley and Sons, Toronto. 1994.

Assays for proliferation and differentiation of hematopoietic and lymphopoietic cells include, without limitation, those described in: Measurement of Human and Murine Interleukin 2 and Interleukin 4, Bottomly, K., Davis, L. S. and Lipsky, P. E.
In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 6.3.1-6.3.12, John Wiley and Sons, Toronto. 1991; deVries et al., J. Exp. Med. 173:1205-1211, 1991;
lVloreau et al., Nature 336:690-692, 1988; Greenberger et al., Proc. Natl. Acad. Sci. U.S.A.
80:2931-2938, 1983; Measurement of mouse and human interleukin 6--Nordan, R. In Current Protocols in Immunology. J. E. Coligan eds. Vol I pp. 6.6.1-6.6.5, John Wiley and Sons, Toronto. 1991;
Smith et al., Proc. Natl. Aced. Sci. U.S.A. 83:1857-1861, 1986; Measurement ofhuman Interleukin I l--Bennett, F., Giannotti, J., Clark, S. C. and Turner, K. J. In Current Protocols in Immunology. J. E. Coligan eds. Vol 1 pp. 6.15.1 John Wiley and Sons, Toronto. 1991;
Measurement of mouse and human Interleukin 9--Ciarletta, A., Giannotti, J., Clark, S. C.
and Turner, K. J. In Current Protocols in Immunology. J. E. Coligan eds. Vol I
pp. 6.13.1, John Wiley and Sons, Toronto. 1991.
Assays for T-cell clone responses to antigens (which will identify, among others, proteins that affect APC-T cell interactions as well as direct T-cell effects by measuring proliferation and cytokine production) include, without limitation, those described in:
Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H.
Margulies, E. M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function; Chapter 6, Cytokines and their cellular receptors; Chapter 7, Immunologic studies in Humans); Weinberger et al., Proc.
Natl. Acad. Sci. USA 77:6091-6095, 1980; Weinberger et al., Eur. J. Immun.
11:405-411, 1981; Takai et al., J. Immunol. 137:3494-3500, 1986; Takai et al., J. Immunol.
140:508-512, 1988.
4.10.4 STEM CELL GROWTH FACTOR ACTIVITY
A polypeptide of the present invention may exhibit stem cell growth factor activity and be involved in the proliferation, differentiation and survival of pluripotent and totipotent stem cells including primordial germ cells, embryonic stem cells, hematopoietic stem cells and/or germ line stem cells. Administration of the polypeptide of the invention to stem cells in vivo or ex vivo is expected to maintain and expand cell populations in a totipotential or pluripotential state which would be useful for re-engineering damaged or diseased tissues, transplantation, manufacture of bio-pharmaceuticals and the development of bio-sensors.

The ability to produce large quantities of human cells has important working applications for the production of human proteins which currently must be obtained from non-human sources or donors, implantation of cells to treat diseases such as Parkinson's, Alzheimer's and other neurodegenerative diseases; tissues for grafting such as bone marrow, skin, cartilage, S tendons, bone, muscle (including cardiac muscle), blood vessels, cornea, neural cells, gastrointestinal cells and others; and organs for transplantation such as kidney, liver, pancreas (including islet cells), heart and lung.
It is contemplated that multiple different exogenous growth factors and/or cytokines may be administered in combination with the polypeptide of the invention to achieve the desired effect, including any of the growth factors listed herein, other stem cell maintenance factors, and specifically including stem cell factor (SCF), leukemia inhibitory factor (LIF), Flt-3 ligand (Flt-3L), any of the interleukins, recombinant soluble IL-6 receptor fused to IL-6, macrophage inflammatory protein 1-alpha (MIP-1-alpha), G-CSF, GM-CSF, thrombopoietin (TPO), platelet factor 4 (PF-4), platelet-derived growth factor (PDGF), neural growth factors and basic fibroblast growth factor (bFGF).
Since totipotent stem cells can give rise to virtually any mature cell type, expansion of these cells in culture will facilitate the production of large quantities of mature cells.
Techniques for culturing stem cells are known in the art and administration of polypeptides of the invention, optionally with other growth factors and/or cytokines, is expected to enhance the survival and proliferation of the stem cell populations. This can be accomplished by direct administration of the polypeptide of the invention to the culture medium. Alternatively, stroma cells transfected with a polynucleotide that encodes for the polypeptide of the invention can be used as a feeder layer for the stem cell populations in culture or in vivo. Stromal support cells for feeder layers may include embryonic bone marrow fibroblasts, bone marrow stromal cells, fetal liver cells, or cultured embryonic fibroblasts (see U.S. Patent No. 5,690,926).
Stem cells themselves can be transfected with a polynucleotide of the invention to induce autocrine expression of the polypeptide of the invention. This will allow for generation of undifferentiated totipotential/pluripotential stem cell lines that are useful as is or that can then be differentiated into the desired mature cell types. These stable cell lines can also serve as a source of undifferentiated totipotential/pluripotential mRNA to create cDNA libraries and templates for polymerise chain reaction experiments. These studies would allow for the isolation and identification of differentially expressed genes in stem cell populations that regulate stem cell proliferation and/or maintenance.
Expansion and maintenance of totipotent stem cell populations will be useful in the treatment of many pathological conditions. For example, polypeptides of the present invention may be used to manipulate stem cells in culture to give rise to neuroepithelial cells that can be used to augment or replace cells damaged by illness, autoimmune disease, accidental damage or genetic disorders. The polypeptide of the invention may be useful for inducing the proliferation of neural cells and for the regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders which involve degeneration, death or trauma to neural cells or nerve tissue. In addition, the expanded stem cell populations can also be genetically altered for gene therapy purposes and to decrease host rejection of replacement tissues after grafting or implantation.
Expression of the polypeptide of the invention and its effect on stem cells can also be manipulated to achieve controlled differentiation of the stem cells into more differentiated cell types. A broadly applicable method of obtaining pure populations of a specific differentiated cell type from undifferentiated stem cell populations involves the use of a cell-type specific promoter driving a selectable marker. The selectable marker allows only cells of the desired type to survive. For example, stem cells can be induced to differentiate into cardiomyocytes (Wobus et al., Differentiation, 48: 173-182, (1991); Klug et al., J. Clin.
Invest., 98(1): 216-224, (1998)) or skeletal muscle cells (Browder, L. W. In:
Principles of Tissue Engineering eds. Lanza et al., Academic Press (1997)). Alternatively, directed differentiation of stem cells can be accomplished by culturing the stem cells in the presence of a differentiation factor such as retinoic acid and an antagonist of the polypeptide of the invention which would inhibit the effects of endogenous stem cell factor activity and allow differentiation to proceed.
In vitro cultures of stem cells can be used to determine if the polypeptide of the invention exhibits stem cell growth factor activity. Stem cells are isolated from any one of various cell sources (including hematopoietic stem cells and embryonic stem cells) and cultured on a feeder layer, as described by Thompson et al. Proc. Natl. Acad.
Sci, U.S.A., 92: 7844-7848 (1995), in the presence of the polypeptide of the invention alone or in combination with other growth factors or cytokines. The ability of the polypeptide of the invention to induce stem cells proliferation is determined by colony formation on semi-solid support e.g. as described by Bernstein et al., Blood, 77: 2316-2321 (1991).
4.10.5 HEMATOPOIESIS REGULATING ACTIVITY
5 A polypeptide of the present invention may be involved in regulation of hematopoiesis and, consequently, in the treatment of myeloid or lymphoid cell disorders.
Even marginal biological activity in support of colony forming cells or of factor-dependent cell lines indicates involvement in regulating hematopoiesis, e.g. in supporting the growth and proliferation of erythroid progenitor cells alone or in combination with other cytokines, 10 thereby indicating utility, for example, in treating various anemias or for use in conjunction with irradiation/chemotherapy to stimulate the production of erythroid precursors and/or erythroid cells; in supporting the growth and proliferation of myeloid cells such as granulocytes and monocytes/macrophages (i.e., traditional CSF activity) useful, for example, in conjunction with chemotherapy to prevent or treat consequent myelo-suppression; in 15 supporting the growth and proliferation of megakaryocytes and consequently of platelets thereby allowing prevention or treatment of various platelet disorders such as thrombocytopenia, and generally for use in place of or complimentary to platelet transfusions; and/or in supporting the growth and proliferation of hematopoietic stem cells which are capable of maturing to any and all of the above-mentioned hematopoietic cells and 20 therefore find therapeutic utility in various stem cell disorders (such as those usually treated with transplantation, including, without limitation, aplastic anemia and paroxysmal nocturnal hemoglobinuria), as well as in repopulating the stem cell compartment post irradiation/chemotherapy, either in-vivo or ex-vivo (i.e., in conjunction with bone marrow transplantation or with peripheral progenitor cell transplantation (homologous or 25 heterologous)) as normal cells or genetically manipulated for gene therapy.
Therapeutic compositions of the invention can be used in the following:
Suitable assays for proliferation and differentiation of various hematopoietic lines are cited above.
Assays for embryonic stem cell differentiation (which will identify, among others, 30 proteins that influence embryonic differentiation hematopoiesis) include, without limitation, those described in: Johansson et al. Cellular Biology 15:141-151, 1995; Keller et al., Molecular and Cellular Biology 13:473-486, 1993; McClanahan et al., Blood 81:2903-2915, 1993.

Assays for stem cell survival and differentiation (which will identify, among others, proteins that regulate lympho-hematopoiesis) include, without limitation, those described in:
Methylcellulose colony fo~7~oing assays, Freshney, M. G. In Culture of Hematopoietic Cells.
R. I. Freshney, et al. eds. Vol pp. 265-268, Wiley-Liss, Inc., New York, N.Y.
1994;
Hirayama et al., Proc. Natl. Acad. Sci. USA 89:5907-5911, 1992; Primitive hematopoietic colony forming cells with high proliferative potential, McNiece, I. K. and Briddell, R. A. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 23-39, Wiley-Liss, Inc., New York, N.Y. 1994; Neben et al., Experimental Hematology 22:353-359, 1994;
Cobblestone area forming cell assay, Ploemacher, R. E. In Culture of Hematopoietic Cells.
R. I. Freshney, et al. eds. Vol pp. 1-21, Wiley-Liss, Inc., New York, N.Y.
1994; Long term bone marrow cultures in the presence of stromal cells, Spooncer, E., Dexter, M. and Allen, T. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 163-179, Wiley-Liss, Inc., New York, N.Y. 1994; Long term culture initiating cell assay, Sutherland, H. J. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 139-162, Wiley-Liss, Inc., New York, N.Y. 1994.
4.10.6 TISSUE GROWTH ACTIVITY
A polypeptide of the present invention also may be involved in bone, cartilage, tendon, ligament and/or nerve tissue growth or regeneration, as well as in wound healing and tissue repair and replacement, and in healing of burns, incisions and ulcers.
A polypeptide of the present invention which induces cartilage and/or bone growth in circumstances where bone is not normally formed, has application in the healing of bone fractures and cartilage damage or defects in humans and other animals.
Compositions of a polypeptide, antibody, binding partner, or other modulator of the invention may have prophylactic use in closed as well as open fracture reduction and also in the improved fixation of artificial joints. De novo bone formation induced by an osteogenic agent contributes to the repair of congenital, trauma induced, or oncologic resection induced craniofacial defects, and also is useful in cosmetic plastic surgery.
A polypeptide of this invention may also be involved in attracting bone-forming cells, stimulating growth of bone-forming cells, or inducing differentiation of progenitors of bone-forming cells. Treatment of osteoporosis, osteoarthritis, bone degenerative disorders, or periodontal disease, such as through stimulation of bone and/or cartilage repair or by blocking inflammation or processes of tissue destruction (collagenase activity, osteoclast activity, etc.) mediated by inflammatory processes may also be possible using the composition of the invention.
Another category of tissue regeneration activity that may involve the polypeptide of the present invention is tendon/ligament formation. Induction of tendon/ligament-like tissue or other tissue formation in circumstances where such tissue is not normally formed, has application in the healing of tendon or ligament tears, deformities and other tendon or ligament defects in humans and other animals. Such a preparation employing a tendon/ligament-like tissue inducing protein may have prophylactic use in preventing damage to tendon or ligament tissue, as well as use in the improved fixation of tendon or ligament to bone or other tissues, and in repairing defects to tendon or ligament tissue. De novo tendon/ligament-like tissue formation induced by a composition of the present invention contributes to the repair of congenital, trauma induced, or other tendon or ligament defects of other origin, and is also useful in cosmetic plastic surgery for attachment or repair of tendons or ligaments. The compositions of the present invention may provide environment to attract tendon- or ligament-forming cells, stimulate growth of tendon- or ligament-forming cells, induce differentiation of progenitors of tendon- or ligament-forniing cells, or induce growth of tendon/ligament cells or progenitors ex vivo for return in vivo to effect tissue repair. The compositions of the invention may also be useful in the treatment of tendinitis, carpal tunnel syndrome and other tendon or ligament defects. The compositions may also include an appropriate matrix and/or sequestering agent as a carrier as is well known in the art.
The compositions of the present invention may also be useful for proliferation of neural cells and for regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders, which involve degeneration, death or trauma to neural cells or nerve tissue. More specifically, a composition may be used in the treatment of diseases of the peripheral nervous system, such as peripheral nerve injuries, peripheral neuropathy and localized neuropathies, and central nervous system diseases, such as Alzheimer's, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome. Further conditions which may be treated in accordance with the present invention include mechanical and traumatic disorders, such as spinal cord disorders, head trauma and cerebrovascular diseases such as stroke. Peripheral neuropathies resulting from chemotherapy or other medical therapies may also be treatable using a composition of the invention.
Compositions of the invention may also be useful to promote better or faster closure of non-healing wounds, including without limitation pressure ulcers, ulcers associated with S vascular insufficiency, surgical and traumatic wounds, and the like.
Compositions of the present invention may also be involved in the generation or regeneration of other tissues, such as organs (including, for example, pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac) and vascular (including vascular endothelium) tissue, or for promoting the growth of cells comprising such tissues. Part of the desired effects may be by inhibition or modulation of fibrotic scarring may allow normal tissue to regenerate. A polypeptide of the present invention may also exhibit angiogenic activity.
A composition of the present invention may also be useful for gut protection or regeneration and treatment of lung or liver fibrosis, reperfusion injury in various tissues, and conditions resulting from systemic cytokine damage.
A composition of the present invention may also be useful for promoting or inhibiting differentiation of tissues described above from precursor tissues or cells; or for inhibiting the growth of tissues described above.
Therapeutic compositions of the invention can be used in the following:
Assays for tissue generation activity include, without limitation, those described in:
International Patent Publication No. W095/16035 (bone, cartilage, tendon);
International Patent Publication No. W095/05846 (nerve, neuronal); International Patent Publication No.
W091/07491 (skin, endothelium).
Assays for wound healing activity include, without limitation, those described in:
Winter, Epidermal Wound Healing, pps. 71-112 (Maibach, H. I. and Rovee, D. T., eds.), Year Book Medical Publishers, Inc., Chicago, as modified by Eaglstein and Mertz, J. Invest.
Dermatol 71:382-84 (1978).
4.10.7 IMMUNE STIMULATING OR SUPPRESSING ACTIVITY
A polypeptide of the present invention may also exhibit immune stimulating or immune suppressing activity, including without limitation the activities for which assays are described herein. A polynucleotide of the invention can encode a polypeptide exhibiting such activities. A protein may be useful in the treatment of various immune deficiencies and disorders (including severe combined immunodeficiency (SCID)), e.g., in regulating (up or down) growth and proliferation of T and/or B lymphocytes, as well as effecting the cytolytic activity of NK cells and other cell populations. These immune deficiencies may be genetic or be caused by viral (e.g., HIV) as well as bacterial or fungal infections, or may result from autoimmune disorders. More specifically, infectious diseases causes by viral, bacterial, fungal or other infection may be treatable using a protein of the present invention, including infections by HIV, hepatitis viruses, herpes viruses, mycobacteria, Leishmania spp., malaria spp. and various fungal infections such as candidiasis. Of course, in this regard, proteins of the present invention may also be useful where a boost to the immune system generally may be desirable, i.e., in the treatment of cancer.
Autoimmune disorders which may be treated using a protein of the present invention include, for example, connective tissue disease, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, autoimmune pulmonary inflammation, Guillain-Barre syndrome, autoimmune thyroiditis, insulin dependent diabetes mellitis, myasthenia gravis, graft-versus-host disease and autoimmune inflammatory eye disease. Such a protein (or antagonists thereof, including antibodies) of the present invention may also to be useful in the treatment of allergic reactions and conditions (e.g., anaphylaxis, serum sickness, drug reactions, food allergies, insect venom allergies, mastocytosis, allergic rhinitis, hypersensitivity pneumonitis, urticaria, angioedema, eczema, atopic dermatitis, allergic contact dermatitis, erythema multiforme, Stevens-Johnson syndrome, allergic conjunctivitis, atopic keratoconjunctivitis, venereal keratoconjunctivitis, giant papillary conjunctivitis and contact allergies), such as asthma (particularly allergic asthma) or other respiratory problems. Other conditions, in which immune suppression is desired (including, for example, organ transplantation), may also be treatable using a protein (or antagonists thereof) of the present invention. The therapeutic effects of the polypeptides or antagonists thereof on allergic reactions can be evaluated by in vivo animals models such as the cumulative contact enhancement test (Lastbom et al., Toxicology 125: 59-66, 1998), skin prick test (Hoffmann et al., Allergy 54: 446-54, 1999), guinea pig skin sensitization test (Vohr et al., Arch. Toxocol. 73: 501-9), and murine local lymph node assay (Kimber et al., J. Toxicol. Environ. Health 53: 563-79).
Using the proteins of the invention it may also be possible to modulate immune responses, in a number of ways. Down regulation may be in the form of inhibiting or blocking an immune response already in progress or may involve preventing the induction of an immune response. The functions of activated T cells may be inhibited by suppressing T
cell responses or by inducing specific tolerance in T cells, or both.
Immunosuppression of T
cell responses is generally an active, non-antigen-specific, process which requires continuous exposure of the T cells to the suppressive agent. Tolerance, which involves inducing 5 non-responsiveness or anergy in T cells, is distinguishable from immunosuppression in that it is generally antigen-specific and persists after exposure to the tolerizing agent has ceased.
Operationally, tolerance can be demonstrated by the lack of a T cell response upon reexposure to specific antigen in the absence of the tolerizing agent.
Down regulating or preventing one or more antigen functions (including without 10 limitation B lymphocyte antigen functions (such as, for example, B7)), e.g., preventing high level lymphokine synthesis by activated T cells, will be useful in situations of tissue, skin and organ transplantation and in graft-versus-host disease (GVHD). For example, blockage of T cell function should result in reduced tissue destruction in tissue transplantation.
Typically, in tissue transplants, rejection of the transplant is initiated through its recognition 15 as foreign by T cells, followed by an immune reaction that destroys the transplant. The administration of a therapeutic composition of the invention may prevent cytokine synthesis by immune cells, such as T cells, and thus acts as an immunosuppressant.
Moreover, a lack of costimulation may also be sufficient to anergize the T cells, thereby inducing tolerance in a subject. Induction of long-term tolerance by B lymphocyte antigen-blocking reagents may 20 avoid the necessity of repeated administration of these blocking reagents.
To achieve sufficient immunosuppression or tolerance in a subject, it may also be necessary to block the function of a combination of B lymphocyte antigens.
The efficacy of particular therapeutic compositions in preventing organ transplant rejection or GVHD can be assessed using animal models that are predictive of efficacy in 25 humans. Examples of appropriate systems which can be used include allogeneic cardiac grafts in rats and xenogeneic pancreatic islet cell grafts in mice, both of which have been used to examine the immunosuppressive effects of CTLA4Ig fusion proteins in vivo as described in Lenschow et al., Science 257:789-792 (1992) and Turka et al., Proc. Natl. Acad.
Sci USA, 89:11102-11105 (1992). In addition, murine models of GVHD (see Paul ed., 30 Fundamental Immunology, Raven Press, New York, 1989, pp. 846-847) can be used to determine the effect of therapeutic compositions of the invention on the development of that disease.

Blocking antigen function may also be therapeutically useful for treating autoimmune diseases. Many autoimmune disorders are the result of inappropriate activation of T cells that are reactive against self tissue and which promote the production of cytokines and autoantibodies involved in the pathology of the diseases. Preventing the activation of S autoreactive T cells may reduce or eliminate disease symptoms.
Administration of reagents which block stimulation of T cells can be used to inhibit T cell activation and prevent production of autoantibodies or T cell-derived cytokines which may be involved in the disease process. Additionally, blocking reagents may induce antigen-specific tolerance of autoreactive T cells which could lead to long-term relief from the disease.
The efficacy of blocking reagents in preventing or alleviating autoimmune disorders can be determined using a number of well-characterized animal models of human autoimmune diseases.
Examples include murine experimental autoimmune encephalitis, systemic lupus erythmatosis in MRL/lpr/lpr mice or NZB hybrid mice, murine autoimmune collagen arthritis, diabetes mellitus in NOD mice and BB rats, and murine experimental myasthenia gravis (see Paul ed., Fundamental Immunology, Raven Press, New York, I 989, pp.
840-85 G).
Upregulation of an antigen function (e.g., a B lymphocyte antigen function), as a means of up regulating immune responses, may also be useful in therapy.
Upregulation of immune responses may be in the form of enhancing an existing immune response or eliciting an initial immune response. For example, enhancing an immune response may be useful in cases of viral infection, including systemic viral diseases such as influenza, the common cold, and encephalitis.
Alternatively, anti-viral immune responses may be enhanced in an infected patient by removing T cells from the patient, costimulating the T cells in vitro with viral antigen-pulsed APCs either expressing a peptide of the present invention or together with a stimulatory form of a soluble peptide of the present invention and reintroducing the in vitro activated T
cells into the patient. Another method of enhancing anti-viral immune responses would be to isolate infected cells from a patient, transfect them with a nucleic acid encoding a protein of the present invention as described herein such that the cells express all or a portion of the protein on their surface, and reintroduce the transfected cells into the patient. The infected cells would now be capable of delivering a costimulatory signal to, and thereby activate, T
cells in vivo.

A polypeptide of the present invention may provide the necessary stimulation signal to T cells to induce a T cell mediated immune response against the transfected tumor cells.
In addition, tumor cells which lack MHC class I or MHC class II molecules, or which fail to reexpress sufficient mounts of MHC class I or MHC class II molecules, can be transfected with nucleic acid encoding all or a portion of (e.g., a cytoplasmic-domain truncated portion) of an MHC class I alpha chain protein and (3z microglobulin protein or an MHC
class II
alpha chain protein and an MHC class II beta chain protein to thereby express MHC class I
or MHC class II proteins on the cell surface. Expression of the appropriate class I or class II
MHC in conjunction with a peptide having the activity of a B lymphocyte antigen (e.g., B7-1, B7-2, B7-3) induces a T cell mediated immune response against the transfected tumor cell. Optionally, a gene encoding an antisense construct which blocks expression of an MHC
class II associated protein, such as the invariant chain, can also be cotransfected with a DNA
encoding a peptide having the activity of a B lymphocyte antigen to promote presentation of tumor associated antigens and induce tumor specific immunity. Thus, the induction of a T
cell mediated immune response in a human subject may be sufficient to overcome tumor-specific tolerance in the subject.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Suitable assays for thymocyte or splenocyte cytotoxicity include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.
M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19;
Chapter 7, Immunologic studies in Humans); Herrmann et al., Proc. Natl. Acad.
Sci. USA
78:2488-2492, 1981; Herrmann et al., J. Immunol. 128:1968-1974, 1982; Handa et al., J.
Immunol. 135:1564-1572, 1985; Takai et al., I. Immunol. 137:3494-3500, 1986;
Takai et al., J. Immunol. 140:508-512, 1988; Bowman et al., J. Virology 61:1992-1998;
Bertagnolli et al., Cellular Immunology 133:327-341, 1991; Brown et al., J. Immunol. 153:3079-3092, 1994.
Assays for T-cell-dependent immunoglobulin responses and isotype switching (which will identify, among others, proteins that modulate T-cell dependent antibody responses and that affect Th 1 /Th2 profiles) include, without limitation, those described in:
Maliszewski, J. lmmunol. 144:3028-3033, 1990; and Assays for B cell function:
In vitro antibody production, Mond, J. J. and Brunswick, M. In Current Protocols in Immunology. J.
E. e.a. Coligan eds. Vol 1 pp. 3.8.1-3.8.16, John Wiley and Sons, Toronto.
1994.
Mixed lymphocyte reaction (MLR) assays (which will identify, among others, proteins that generate predominantly Thl and CTL responses) include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.
M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19;
Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986;
Takai et al'., J. Immunol. 140:508-512, 1988; Bertagnolli et al., J. Immunol.
149:3778-3783, 1992.
Dendritic cell-dependent assays (which will identify, among others, proteins expressed by dendritic cells that activate naive T-cells) include, without limitation, those described in: Guery et al., J. Immunol. 134:536-544, 1995; Inaba et al., Journal of Experimental Medicine 173:549-559, 1991; Macatonia et al., Journal of Immunology 154:5071-5079, 1995; Porgador et al., Journal of Experimental Medicine 182:255-260, 1995; Nair et al., Journal of Virology 67:4062-4069, 1993; Huang et al., Science 264:961-965, 1994; Macatonia et al., Journal of Experimental Medicine 169:1255-1264, 1989; Bhardwaj et al., Journal of Clinical Investigation 94:797-807, 1994; and Inaba et al., Journal of Experimental Medicine 172:631-640, 1990.
Assays for lymphocyte survival/apoptosis (which will identify, among others, proteins that prevent apoptosis after superantigen induction and proteins that regulate lymphocyte homeostasis) include, without limitation, those described in:
Darzynkiewicz et al., Cytometry 13:795-808, 1992; Gorczyca et al., Leukemia 7:659-670, 1993;
Gorczyca et al., Cancer Research 53:1945-1951, 1993; Itoh et al., Cell 66:233-243, 1991;
Zacharchuk, 2S Journal of Immunology 145:4037-4045, 1990; Zamai et al., Cytometry 14:891-897, 1993;
Gorczyca et al., International Journal of Oncology 1:639-648, 1992.
Assays for proteins that influence early steps of T-cell commitment and development include, without limitation, those described in: Antica et al., Blood 84:111-117, 1994; Fine et al., Cellular Immunology 155:111-122, 1994; Galy et al., Blood 85:2770-2778, 1995;
'Told et al., Proc. Nat. Acad Sci. USA 88:7548-7551, 1991.
4.10.8 ACTIVIN/INHIBIN ACTIVITY

A polypeptide of the present invention may also exhibit activin- or inhibin-related activities. A polynucleotide of the invention may encode a polypeptide exhibiting such characteristics. Inhibins are characterized by their ability to inhibit the release of follicle stimulating hormone (FSH), while activins and are characterized by their ability to stimulate the release of follicle stimulating hormone (FSH). Thus, a polypeptide of the present invention, alone or in heterodimers with a member of the inhibin family, may be useful as a contraceptive based on the ability of inhibins to decrease fertility in female mammals and decrease spermatogenesis in male mammals. Administration of sufficient amounts of other inhibins can induce infertility in these mammals. Alternatively, the polypeptide of the invention, as a homodimer or as a heterodimer with other protein subunits of the inhibin group, may be useful as a fertility inducing therapeutic, based upon the ability of activin molecules in stimulating FSH release from cells of the anterior pituitary.
See, for example, U.S. Pat. No. 4,798,885. A polypeptide of the invention may also be useful for advancement of the onset of fertility in sexually immature mammals, so as to increase the lifetime reproductive performance of domestic animals such as, but not limited to, cows, sheep and pigs.
The activity of a polypeptide of the invention may, among other means, be measured by tlue following methods.
Assays for activin/inhibin activity include, without limitation, those described in:
Vale et al., Endocrinology 91:562-572, 1972; Ling et al., Nature 321:779-782, 1986; Vale et al., Nature 321:776-779, 1986; Mason et al., Nature 318:659-663, 1985; Forage et al., Proc.
Natl. Acad. Sci. USA 83:3091-3095, 1986.
4.10.9 CHEMOTACTIC/CHEMOHINETIC ACTIVITY
A polypeptide of the present invention may be involved in chemotactic or chemokinetic activity for mammalian cells, including, for example, monocytes, fibroblasts, neutrophils, T-cells, mast cells, eosinophils, epithelial and/or endothelial cells. A
polynucleotide of the invention can encode a polypeptide exhibiting such attributes.
Chemotactic and chemokinetic receptor activation can be used to mobilize or attract a desired cell population to a desired site of action. Chemotactic or chemokinetic compositions (e.g. proteins, antibodies, binding partners, or modulators of the invention) provide particular advantages in treatment of wounds and other trauma to tissues, as well as in treatment of localized infections. For example, attraction of lymphocytes, monocytes or neutrophils to tumors or sites of infection may result in improved immune responses against the tumor or infecting agent.
A protein or peptide has chemotactic activity for a particular cell population if it can stimulate, directly or indirectly, the directed orientation or movement of such cell 5 population. Preferably, the protein or peptide has the ability to directly stimulate directed movement' of cells. Whether a particular protein has chemotactic activity for a population of cells can be readily determined by employing such protein or peptide in any known assay for cell chemotaxis.
Therapeutic compositions of the invention can be used in the following:
10 Assays for chemotactic activity (which will identify proteins that induce or prevent chemotaxis) consist of assays that measure the ability of a protein to induce the migration of cells across a membrane as well as the ability of a protein to induce the adhesion of one cell population to another cell population. Suitable assays for movement and adhesion include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E.
15 Coligan, A. M. Kruisbeek, D. H. Marguiles, E. M. Shevach, W. Strober, Pub.
Greene Publishing Associates and Wiley-Interscience (Chapter 6.12, Measurement of alpha and beta Chemokines 6.12.1-6.12.28; Taub et al. J. Clin. Invest. 95:1370-1376, 1995;
Lind et al.
APMIS 103:140-146, 1995; Muller et al Eur. J. Immunol. 25:1744-1748; Gruber et al. J. of Immunol. 152:5860-5867, 1994; Johnston et al. J. of Immunol. 153:1762-1768, 1994.
4.10.10 HEMOSTATIC AND THROMBOLYTIC ACTIVITY
A polypeptide of the invention may also be involved in hemostatis or thrombolysis or thrombosis. A polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Compositions may be useful in treatment of various coagulation disorders (including hereditary disorders, such as hemophiliac) or to enhance coagulation and other hemostatic events in treating wounds resulting from trauma, surgery or other causes. A
composition of the invention may also be useful for dissolving or inhibiting formation of thromboses and for treatment and prevention of conditions resulting therefrom (such as, for example, infarction of cardiac and central nervous system vessels (e.g., stroke).
Therapeutic compositions of the invention can be used in the following:
Assay for hemostatic and thrombolytic activity include, without limitation, those described in: Linet et al., J. Clin. Pharmacol. 26:131-140, 1986; Burdick et al., Thrombosis Res. 45:413-419, 1987; Humphrey et al., Fibrinolysis 5:71-79 (1991); Schaub, Prostaglandins 35:467-474, 1988.
4.10.11 CANCER DIAGNOSIS AND THERAPY
Polypeptides of the invention may be involved in cancer cell generation, proliferation or metastasis. Detection of the presence or amount of polynucleotides or polypeptides of the invention may be useful for the diagnosis and/or prognosis of one or more types of cancer.
For example, the presence or increased expression of a polynucleotide/polypeptide of the invention may indicate a hereditary risk of cancer, a precancerous condition, or an ongoing malignancy. Conversely, a defect in the gene or absence of the polypeptide may be associated with a cancer condition. Identification of single nucleotide polymorphisms associated with cancer or a predisposition to cancer may also be useful for diagnosis or prognosis.
Cancer treatments promote tumor regression by inhibiting tumor cell proliferation, inhibiting angiogenesis (growth of new blood vessels that is necessary to support tumor growth) and/or prohibiting metastasis by reducing tumor cell motility or invasiveness.
Therapeutic compositions of the invention may be effective in adult and pediatric oncology including in solid phase tumors/malignancies, locally advanced tumors, human soft tissue sarcomas, metastatic cancer, including lymphatic metastases, blood cell malignancies including multiple myeloma, acute and chronic leukemias, and lymphomas, head and neck cancers including mouth cancer, larynx cancer and thyroid cancer, lung cancers including small cell carcinoma and non-small cell cancers, breast cancers including small cell carcinoma and ductal carcinoma, gastrointestinal cancers including esophageal cancer, stomach cancer, colon cancer, colorectal cancer and polyps associated with colorectal neoplasia, pancreatic cancers, liver cancer, urologic cancers including bladder cancer and prostate cancer, malignancies of the female genital tract including ovarian carcinoma, uterine (including endometrial) cancers, and solid tumor in the ovarian follicle, kidney cancers including renal cell carcinoma, brain cancers including intrinsic brain tumors, neuroblastoma, astrocytic brain tumors, gliomas, metastatic tumor cell invasion in the central nervous system, bone cancers including osteomas, skin cancers including malignant melanoma, tumor progression of human skin keratinocytes, squamous cell carcinoma, basal cell carcinoma, hemangiopericytoma and Karposi's sarcoma.
Polypeptides, polynucleotides, or modulators of polypeptides of the invention (including inhibitors and stimulators of the biological activity of the polypeptide of the invention) may be administered to treat cancer. Therapeutic compositions can be administered in therapeutically effective dosages alone or in combination with adjuvant cancer therapy such as surgery, chemotherapy, radiotherapy, thermotherapy, and laser therapy, and may provide a beneficial effect, e.g. reducing tumor size, slowing rate of tumor growth, inhibiting metastasis, or otherwise improving overall clinical condition, without necessarily eradicating the cancer.
The composition can also be administered in therapeutically effective amounts as a portion of an anti-cancer cocktail. An anti-cancer cocktail is a mixture of the polypeptide or modulator of the invention with one or more anti-cancer drugs in addition to a pharmaceutically acceptable carrier for delivery. The use of anti-cancer cocktails as a cancer treatment is routine. Anti-cancer drugs that are well known in the art and can be used as a treatment in combination with the polypeptide or modulator of the invention include:
Actinomycin D, Aminoglutethimide, Asparaginase, Bleomycin, Busulfan, Carboplatin, Carmustine, Chlorambucil, Cisplatin (cis-DDP), Cyclophosphamide, Cytarabine HCl (Cytosine arabinoside), Dacarbazine, Dactinomycin, Daunorubicin HC1, Doxorubicin HC1, Estramustine phosphate sodium, Etoposide (V 16-213), Floxuridine, 5-Fluorouracil (S-Fu), Flutamide, Hydroxyurea (hydroxycarbamide), Ifosfamide, Interferon Alpha-2a, Interferon Alpha-2b, Leuprolide acetate (LHRH-releasing factor analog), Lomustine, Mechlorethamine HC1 (nitrogen mustard), Melphalan, Mercaptopurine, Mesna, Methotrexate (MTX), Mitomycin, Mitoxantrone HCI, Octreotide, Plicamycin, Procarbazine HC1, Streptozocin, Tamoxifen citrate, Thioguanine, Thiotepa, Vinblastine sulfate, Vincristine sulfate, Amsacrine, Azacitidine, Hexamethylmelamine, Interleukin-2, Mitoguazone, Pentostatin, Semustine, Teniposide, and Vindesine sulfate.
In addition, therapeutic compositions of the invention may be used for prophylactic treatment of cancer. There are hereditary conditions and/or environmental situations (e.g.
exposure to carcinogens) known in the art that predispose an individual to developing cancers. Under these circumstances, it may be beneficial to treat these individuals with therapeutically effective doses of the polypeptide of the invention to reduce the risk of developing cancers.
Irr vitro models can be used to determine the effective doses of the polypeptide of the invention as a potential cancer treatment. These in vitro models include proliferation assays of cultured tumor cells, growth of cultured tumor cells in soft agar (see Freshney, (1987) Culture of Animal Cells: A Manual of Basic Technique, Wily-Liss, New York, NY
Ch 18 and Ch 21), tumor systems in nude mice as described in Giovanella et al., J.
Natl. Can. Inst., 52: 921-30 (1974), mobility and invasive potential of tumor cells in Boyden Chamber assays as described in Pilkington et al., Anticancer Res., 17: 4107-9 (1997), and angiogenesis assays such as induction of vascularization of the chick chorioallantoic membrane or induction of vascular endothelial cell migration as described in Ribatta et al., Intl. J. Dev.
Biol., 40: I 189-97 (1999) and Li et al., Clin. Exp. Metastasis, 17:423-9 (1999), respectively.
Suitable tumor cells lines are available, e.g. from American Type Tissue Culture Collection catalogs.
4.10.12 RECEPTOR/LIGAND ACTIVITY
A polypeptide of the present invention may also demonstrate activity as receptor, receptor ligand or inhibitor or agonist of receptor/ligand interactions. A
polynucleotide of the invention can encode a polypeptide exhibiting such characteristics.
Examples of such receptors and ligands include, without limitation, cytokine receptors and their ligands, receptor kinases and their ligands, receptor phosphatases and their ligands, receptors involved in cell-cell interactions and their ligands (including without limitation, cellular adhesion molecules (such as selectins, integrins and their ligands) and receptor/ligand pairs involved in antigen presentation, antigen recognition and development of cellular and humoral immune responses. Receptors and ligands are also useful for screening of potential peptide or 'small molecule inhibitors of the relevant receptor/ligand interaction. A protein of the present invention (including, without limitation, fragments of receptors and ligands) may themselves be useful as inhibitors of receptor/ligand interactions.
The activity of a polypeptide of the invention may, among other means, be measured by the following methods:
Suitable assays for receptor-ligand activity include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D.
H.
Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 7.28, Measurement of Cellular Adhesion under static conditions 7.28.1- 7.28.22), Takai et al., Proc. Natl. Acad. Sci. USA 84:6864-6868, 1987;
Bierer et al., J. Exp. Med. 168:1145-1156, 1988; Rosenstein et al., J. Exp. Med. 169:149-160 1989;
Stoltenborg et al., J. Immunol. Methods 175:59-68, 1994; Stitt et al., Cell 80:661-670, 1995.

By way of example, the polypeptides of the invention may be used as a receptor for a ligand(s) thereby transmitting the biological activity of that ligand(s).
Ligands may be identified through binding assays, affinity chromatography, dihybrid screening assays, BIAcore assays, gel overlay assays, or other methods known in the art.
Studies characterizing drugs or proteins as agonist or antagonist or partial agonists or a partial antagonist require the use of other proteins as competing ligands.
The polypeptides of the present invention or ligand(s) thereof may be labeled by being coupled to radioisotopes, colorimetric molecules or a toxin molecules by conventional methods.
("Guide to Protein Purification" Murray P. Deutscher (ed) Methods in Enzymology Vol. 182 (1990) Academic Press, Inc. San Diego). Examples of radioisotopes include, but are not limited to, tritium and carbon-14 . Examples of colorimetric molecules include, but are not limited to, fluorescent molecules such as fluorescamine, or rhodamine or other colorimetric molecules: Examples of toxins include, but are not limited, to ricin.
4.10.13 DRUG SCREENING
This invention is particularly useful for screening chemical compounds by using the novel polypeptides or binding fragments thereof in any of a variety of drug screening techniques. The polypeptides or fragments employed in such a test may either be free in solution, affixed to a solid support, borne on a cell surface or located intracellularly. One method of drug screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the polypeptide or a fragment thereof. Dings are screened against such transformed cells in competitive binding assays.
Such cells, either in viable or fixed form, can be used for standard binding assays. One may measure, for example, the formation of complexes between polypeptides of the invention or fragments and the agent being tested or examine the diminution in complex formation between the novel polypeptides and an appropriate cell line, which are well known in the art.
Sources for test compounds that may be screened for ability to bind to or modulate (i.e., increase or decrease) the activity of polypeptides of the invention include (1) inorganic and organic chemical libraries, (2) natural product libraries, and (3) combinatorial libraries comprised of either random or mimetic peptides, oligonucleotides or organic molecules.
Chemical libraries may be readily synthesized or purchased from a number of commercial sources, and may include structural analogs of known compounds or compounds that are identified as "hits" or "leads" via natural product screening.

The sources of natural product libraries are microorganisms (including bacteria and fungi), animals, plants or other vegetation, or marine organisms, and libraries of mixtures for screening may be created by: (1) fermentation and extraction of broths from soil, plant or marine microorganisms or (2) extraction of the organisms themselves. Natural product 5 libraries include polyketides, non-ribosomal peptides, and (non-naturally occurring) variants thereof. For a review, see Science 282:63-68 (1998).
Combinatorial libraries are composed of large numbers of peptides, oligonucleotides or organic compounds and can be readily prepared by traditional automated synthesis methods, PCR, cloning or proprietary synthetic methods. Of particular interest are peptide 10 and oligonucleotide combinatorial libraries. Still other libraries of interest include peptide, protein, peptidomimetic, multiparallel synthetic collection, recombinatorial, and polypeptide libraries. For a review of combinatorial chemistry and libraries created therefrom, see Myers, Curr. Opin. Biotechnol. 8:701-707 (1997). For reviews and examples of peptidomimetic libraries, see Al-Obeidi et al., Mol. Biotechnol, 9(3):205-23 (1998); Hruby 15 et al., Curr Opin Chem Biol, 1(1):114-19 (1997); Dorner et al., Bioorg Med Chem, 4(5):709-15 (1996) (alkylated dipeptides).
Identification of modulators through use of the various libraries described herein pern~its modification of the candidate "hit" (or "lead") to optimize the capacity of the "hit"
to bind a polypeptide of the invention. The molecules identified in the binding assay are then 20 tested for antagonist or agonist activity in in vivo tissue culture or animal models that are well known in the art. In brief, the molecules are titrated into a plurality of cell cultures or animals and then tested for either cell/animal death or prolonged survival of the animal/cells.
The binding molecules thus identified may be complexed with toxins, e.g., ricin or cholera, or with other compounds that are toxic to cells such as radioisotopes. The 25 toxin-binding molecule complex is then targeted to a tumor or other cell by the specificity of the binding molecule for a polypeptide of the invention. Alternatively, the binding molecules may be complexed with imaging agents for targeting and imaging purposes.
4.10.14 ASSAY FOR RECEPTOR ACTIVITY
30 The invention also provides methods to detect specific binding of a polypeptide e.g. a ligand or a receptor. The art provides numerous assays particularly useful for identifying previously unknown binding partners for receptor polypeptides of the invention. For example, expression cloning using mammalian or bacterial cells, or dihybrid screening assays can be used to identify polynucleotides encoding binding partners. As another example, affinity chromatography with the appropriate immobilized polypeptide of the invention can be used to isolate polypeptides that recognize and bind polypeptides of the invention. There are a number of different libraries used for the identification of compounds, and in particular small molecules, that modulate (i.e., increase or decrease) biological activity of a polypeptide of the invention. Ligands for receptor polypeptides of the invention can also be identified by adding exogenous ligands, or cocktails of ligands to two cells populations that are genetically identical except for the expression of the receptor of the invention: one cell population expresses the receptor of the invention whereas the other does not. The responses of the two cell populations to the addition of ligands(s) are then compared. Alternatively, an expression library can be co-expressed with the polypeptide of the invention in cells and assayed for an autocrine response to identify potential ligand(s). As still another example, BIAcore assays, gel overlay assays, or other methods known in the art can be used to identify binding partner polypeptides, including, (1 ) organic and inorganic chemical libraries, (2) natural product libraries, and (3) combinatorial libraries comprised of random peptides, oligonucleotides or organic molecules.
The role of downstream intracellular signaling molecules in the signaling cascade of the polypeptide of the invention can be determined. For example, a chimeric protein in which the cytoplasmic domain of the polypeptide of the invention is fused to the extracellular portion of a protein, whose ligand has been identified, is produced in a host cell. The cell is then incubated with the ligand specific for the extracellular portion of the chimeric protein, thereby activating the chimeric receptor. Known downstream proteins involved in intracellular signaling can then be assayed for expected modifications i.e.
phosphorylation. Other methods known to those in the art can also be used to identify signaling molecules involved in receptor activity.
4.10.15 ANTI-INFLAMMATORY ACTIVITY
Compositions of the present invention may also exhibit anti-inflammatory activity.
The anti-inflammatory activity may be achieved by providing a stimulus to cells involved in the inflammatory response, by inhibiting or promoting cell-cell interactions (such as, for example, cell adhesion), by inhibiting or promoting chemotaxis of cells involved in the inflammatory process, inhibiting or promoting cell extravasation, or by stimulating or suppressing production of other factors which more directly inhibit or promote an inflammatory response. Compositions with such activities can be used to treat inflammatory conditions including chronic or acute conditions), including without limitation intimation associated with infection (such as septic shock, sepsis or systemic inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement-mediated hyperacute rejection, nephritis, cytokine or chemokine-induced lung injury, inflammatory bowel disease, Crohn's disease or resulting from over production of cytokines such as TNF or IL-1. Compositions of the invention may also be useful to treat anaphylaxis and hypersensitivity to an antigenic substance or material.
Compositions of this invention may be utilized to prevent or treat conditions such as, but not limited to, sepsis, acute pancreatitis, endotoxin shock, cytokine induced shock, rheumatoid arthritis, chronic inflammatory arthritis, pancreatic cell damage from diabetes mellitus type 1, graft versus host disease, inflammatory bowel disease, inflamation associated with pulmonary disease, other autoimmune disease or inflammatory disease, an antiproliferative agent such as for acute or chronic mylegenous leukemia or in the prevention of premature labor secondary to intrauterine infections.
4.10.16 LEUKEMIAS
Leukemias and related disorders may be treated or prevented by administration of a therapeutic that promotes or inhibits function of the polynucleotides and/or polypeptides of the invention. Such leukemias and related disorders include but are not limited to acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, myeloblastic, promyelocytic, myelomonocytic, monocytic, erythroleukemia, chronic leukemia, chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia (for a review of such disorders, see Fishman et al., 1985, Medicine, 2d Ed., J.B. Lippincott Co., Philadelphia).
4.10.17 NERVOUS SYSTEM DISORDERS
Nervous system disorders, involving cell types which can be tested for efficacy of intervention with compounds that modulate the activity of the polynucleotides and/or polypeptides of the invention, and which can be treated upon thus observing an indication of therapeutic utility, include but are not limited to nervous system injuries, and diseases or disorders which result in either a disconnection of axons, a diminution or degeneration of neurons, or demyelination. Nervous system lesions which may be treated in a patient (including human and non-human mammalian patients) according to the invention include but are not limited to the following lesions of either the central (including spinal cord, brain) or peripheral nervous systems:
(i) traumatic lesions, including lesions caused by physical injury or associated with surgery, for example, lesions which sever a portion of the nervous system, or compression injuries;
(ii) ischemic lesions, in which a lack of oxygen in a portion of the nervous system results in neuronal injury or death, including cerebral infarction or ischemia, or spinal cord infarction or ischemia;
(iii) infectious lesions, in which a portion of the nervous system is destroyed or injured as a result of infection, for example, by an abscess or associated with infection by human immunodeficiency virus, herpes zoster, or herpes simplex virus or with Lyme disease, tuberculosis, syphilis;
(iv) degenerative lesions, in which a portion of the nervous system is destroyed or injured as a result of a degenerative process including but not limited to degeneration associated with Parkinson's disease, Alzheimer's disease, Huntington's chorea, or amyotrophic lateral sclerosis;
(v) lesions associated with nutritional diseases or disorders, in which a portion of the nervous system is destroyed or injured by a nutritional disorder or disorder of metabolism including but not limited to, vitamin B 12 deficiency, folic acid deficiency, Wernicke disease, tobacco-alcohol amblyopia, Marchiafava-Bignami disease (primary degeneration of the corpus callosum), and alcoholic cerebellar degeneration;
(vi) neurological lesions associated with systemic diseases including but not limited to diabetes (diabetic neuropathy, Bell's palsy), systemic lupus ervthematosus, carcinoma, or sarcoidosis;
(vii) lesions caused by toxic substances including alcohol, lead, or particular neurotoxins; and (viii) demyelinated lesions in which a portion of the nervous system is destroyed or injured by a demyelinating disease including but not limited to multiple sclerosis, human immunodeficiency virus-associated myelopathy, transverse myelopathy or various etiologies, progressive multifocal leukoencephalopathy, and central pontine myelinolysis.
Therapeutics which are useful according to the invention for treatment of a nervous system disorder may be selected by testing for biological activity in promoting the survival or differentiation of neurons. For example, and not by way of limitation, therapeutics which elicit any of the following effects may be useful according to the invention:
(i) increased survival time of neurons in culture;
(ii) increased sprouting of neurons in culture or in vivo;
(iii) increased production of a neuron-associated molecule in culture or in vivo, e.g., choline acetyltransferase or acetylcholinesterase with respect to motor neurons; or (iv) decreased symptoms of neuron dysfunction in vivo.
Such effects may be measured by any method known in the art. In preferred, non-limiting embodiments, increased survival of neurons may be measured by the method set forth in Arakawa et al. (1990, J. Neurosci. 10:3507-3515); increased sprouting of neurons may be detected by methods set forth in Pestronk et al. (1980, Exp. Neurol.
70:65-82) or Brown et al. (1981, Ann. Rev. Neurosci. 4:17-42); increased production of neuron-associated molecules may be measured by bioassay, enzymatic assay, antibody binding, Northern blot assay, etc., depending on the molecule to be measured;
and motor neuron dysfunction may be measured by assessing the physical manifestation of motor neuron disorder, e.g., weakness, motor neuron conduction velocity, or functional disability.
In specific embodiments, motor neuron disorders that may be treated according to the invention include but are not limited to disorders such as infarction, infection, exposure to toxin, trauma, surgical damage, degenerative disease or malignancy that may affect motor neurons as well as other components of the nervous system, as well as disorders that selectively affect neurons such as amyotrophic lateral sclerosis, and including but not limited to progressive spinal muscular atrophy, progressive bulbar palsy, primary lateral sclerosis, infantile and juvenile muscular atrophy, progressive bulbar paralysis of childhood (Fazio-Londe syndrome), poliomyelitis and the post polio syndrome, and Hereditary Motorsensory Neuropathy (Charcot-Marie-Tooth Disease).
4.10.18 OTHER ACTIVITIES
A polypeptide of the invention may also exhibit one or more of the following additional activities or effects: inhibiting the growth, infection or function of, or killing, infectious agents, including, without limitation, bacteria, viruses, fungi and other parasites;
effecting (suppressing or enhancing) bodily characteristics, including, without limitation, height, weight, hair color, eye color, skin, fat to lean ratio or other tissue pigmentation, or organ or body part size or shape (such as, for example, breast augmentation or diminution, change in bone form or shape); effecting biorhythms or circadian cycles or rhythms;
effecting the fertility of male or female subjects; effecting the metabolism, catabolism, anabolism, processing, utilization, storage or elimination of dietary fat, lipid, protein, carbohydrate, vitamins, minerals, co-factors or other nutritional factors or component(s);
5 effecting behavioral characteristics, including, without limitation, appetite, libido, stress, cognition (including cognitive disorders), depression (including depressive disorders) and violent behaviors; providing analgesic effects or other pain reducing effects;
promoting differentiation and growth of embryonic stem cells in lineages other than hematopoietic lineages; hormonal or endocrine activity; in the case of enzymes, correcting deficiencies of 10 the enzyme and treating deficiency-related diseases; treatment of hyperproliferative disorders (such as, for example, psoriasis); immunoglobulin-like activity (such as, for example, the ability to bind antigens or complement); and the ability to act as an antigen in a vaccine composition to raise an immune response against such protein or another material or entity which is cross-reactive with such protein.
4.10.19 IDENTIFICAT10N OF POLYMORPHISMS
The demonstration of polymotphisms makes possible the identification of such polymorphisms in human subjects and the pharmacogenetic use of this information for diagnosis and treatment. Such polymorphisms may be associated with, e.g., differential predisposition or susceptibility to various disease states (such as disorders involving inflammation or immune response) or a differential response to drug administration, and this genetic information can be used to tailor preventive or therapeutic treatment appropriately.
For example, the existence of a polymorphism associated with a predisposition to inflammation or autoimmune disease makes possible the diagnosis of this condition in humans by identifying the presence of the polymorphism.
Polymorphisms can be identified in a variety of ways known in the art which all generally involve obtaining a sample from a patient, analyzing DNA from the sample, optionally involving isolation or amplification of the DNA, and identifying the presence of the polymorphism in the DNA. For example, PCR may be used to amplify an appropriate fragment of genomic DNA which may then be sequenced. Alternatively, the DNA
may be subjected to allele-specific oligonucleotide hybridization (in which appropriate oligonucleotides are hybridized to the DNA under conditions permitting detection of a single base mismatch) or to a single nucleotide extension assay (in which an oligonucleotide that hybridizes immediately adjacent to the position of the polymorphism is extended with one or more labeled nucleotides). In addition, traditional restriction fragment length polymorphism analysis (using restriction enzymes that provide differential digestion of the genomic DNA
depending on the presence or absence of the polymorphism) may be performed.
Arrays with nucleotide sequences of the present invention can be used to detect polymorphisms. The array can comprise modified nucleotide sequences of the present invention in order to detect the nucleotide sequences of the present invention. In the alternative, any one of the nucleotide sequences of the present invention can be placed on the array to detect changes from those sequences.
Alternatively a polymorphism resulting in a change in the amino acid sequence could also be detected by detecting a corresponding change in amino acid sequence of the protein, e.g., by an antibody specific to the variant sequence.
4.10.20 ARTHRITIS AND INFLAMMATION
The immunosuppressive effects of the compositions of the invention against rheumatoid arthritis is determined in an experimental animal model system. The experimental model system is adjuvant induced arthritis in rats, and the protocol is described by J. Holoshitz, et at., 1983, Science, 219:56, or by B. Waksman et al., 1963, Int. Arch.
Allergy Appl. Immunol., 23:129. Induction of the disease can be caused by a single injection, generally intradermally, of a suspension of killed Mycobacterium tuberculosis in complete Freund's adjuvant (CFA). The route of injection can vary, but rats may be injected at the base of the tail with an adjuvant mixture. The polypeptide is administered in phosphate buffered solution (PBS) at a dose of about 1-5 mg/kg. The control consists of administering PBS only.
The procedure for testing the effects of the test compound would consist of intradermally injecting killed Mycobacterium tuberculosis in CFA followed by immediately administering the test compound and subsequent treatment every other day until day 24. At 14, I5, 18, 20, 22, and 24 days after injection of Mycobacterium CFA, an overall arthritis score may be obtained as described by J. Holoskitz above. An analysis of the data would reveal that the test compound would have a dramatic affect on the swelling of the joints as measured by a decrease of the arthritis score.
4.11 THERAPEUTIC METHODS

The compositions (including polypeptide fragments, analogs, variants and antibodies or other binding partners or modulators including antisense polynucleotides) of the invention have numerous applications in a variety of therapeutic methods. Examples of therapeutic applications include, but are not limited to, those exemplified herein.
4.11.1 EXAMPLE
One embodiment of the invention is the administration of an effective amount of the polypeptides or other composition of the invention to individuals affected by a disease or disorder that can be modulated by regulating the peptides of the invention.
While the mode of administration is not particularly important, parenteral administration is preferred. An exemplary mode of administration is to deliver an intravenous bolus. The dosage of the polypeptides or other composition of the invention will normally be determined by the prescribing physician. It is to be expected that the dosage will vary according to the age, weight, condition and response of the individual patient. Typically, the amount of polypeptide administered per dose will be in the range of about 0.01 pg/kg to 100 mg/kg of body weight, with the preferred dose being about 0.1 ~g/kg to 10 mg/kg of patient body weight. For parenteral administration, polypeptides of the invention will be formulated in an injectable form combined with a pharmaceutically acceptable parenteral vehicle. Such vehicles are well known in the art and examples include water, saline, Ringer's solution, dextrose solution, and solutions consisting of small amounts of the human serum albumin.
The vehicle may contain minor amounts of additives that maintain the isotonicity and stability of the polypeptide or other active ingredient. The preparation of such solutions is within the skill of the art.
4.12 PHARMACEUTICAL FORMULATIONS AND ROUTES OF
ADMINISTRATION
A protein or other composition of the present invention (from whatever source derived, including without limitation from recombinant and non-recombinant sources and including antibodies and other binding partners of the polypeptides of the invention) may be administered to a patient in need, by itself, or in pharmaceutical compositions where it is mixed with suitable carriers or excipient(s) at doses to treat or ameliorate a variety of disorders. Such a composition may optionally contain (in addition to protein or other active ingredient and a carrier) diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art. The term "pharmaceutically acceptable" means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The characteristics of the earner will depend on the route of administration.
The pharmaceutical composition of the invention may also contain cytokines, lymphokines, or other hematopoietic factors such as M-CSF, GM-CSF, TNF, IL-l, IL-2, IL-3, IL-4, IL-5, IL-6, 1L-7; IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IFN, TNFO, TNFI, TNF2, G-CSF, Meg-CSF, thrombopoietin, stem cell factor, and erythropoietin. In further compositions, proteins of the invention may be combined with other agents beneficial to the treatment of the disease or disorder in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet-derived growth factor (PDGF), transforming growth factors (TGF-a and TGF-(3), insulin-like growth factor (IGF), as well as cytokines described herein.
The pharmaceutical composition may further contain other agents which either enhance the activity of the protein or other active ingredient or complement its activity or 1 S use in treatment. Such additional factors and/or agents may be included in the pharmaceutical composition to produce a synergistic effect with protein or other active ingredient of the invention, or to minimize side effects. Conversely, protein or other active ingredient of the present invention may be included in formulations of the particular clotting factor, cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti- inflammatory agent to minimize side effects of the clotting factor, cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-inflammatory agent (such as IL-I Ra, IL-1 Hyl, IL-1 Hy2, anti-TNF, corticosteroids, immunosuppressive agents). A protein of the present invention may be active in multimers (e.g., heterodimers or homodimers) or complexes with itself or other proteins.
As a result, pharmaceutical compositions of the invention may comprise a protein of the invention in such multimeric or complexed form.
As an alternative to being included in a pharmaceutical composition of the invention including a first protein, a second protein or a therapeutic agent may be concurrently administered with the first protein (e.g., at the same time, or at differing times provided that therapeutic concentrations of the combination of agents is achieved at the treatment site).
Techniques for formulation and administration of the compounds of the instant application may be found in "Remington's Pharmaceutical Sciences," Mack Publishing Co., Easton, PA, latest edition. A therapeutically effective dose further refers to that amount of the compound sufficient to result in amelioration of symptoms, e.g., treatment, healing, prevention or amelioration of the relevant medical condition, or an increase in rate of treatment, healing, prevention or amelioration of such conditions. When applied to an individual active ingredient, administered alone, a therapeutically effective dose refers to that ingredient alone. When applied to a combination, a therapeutically effective dose refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
In practicing the method of treatment or use of the present invention, a therapeutically effective amount of protein or other active ingredient of the present invention is administered to a mammal having a condition to be treated. Protein or other active ingredient .of the present invention may be administered in accordance with the method of the invention either alone or in combination with other therapies such as treatments employing cytokines, lymphokines or other hematopoietic factors. When co-administered with one or more cytokines, lymphokines or other hematopoietic factors, protein or other active ingredient of the present invention may be administered either simultaneously with the cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors, or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering protein or other active ingredient of the present invention in combination with cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors.
4.12.1 ROUTES OF ADMINISTRATION
Suitable routes of administration may, for example, include oral, rectal, transmucosal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections.
Administration of protein or other active ingredient of the present invention used in the phamaceutical composition or to practice the method of the present invention can be carried out in a variety of conventional ways, such as oral ingestion, inhalation, topical application or cutaneous, subcutaneous, intraperitoneal, parenteral or intravenous injection. Intravenous administration to the patient is preferred.
Alternately, one may administer the compound in a local rather than systemic manner, for example, via injection of the compound directly into a arthritic joints or in fibrotic tissue, often in a depot or sustained release formulation. In order to prevent the scarring process frequently occurnng as complication of glaucoma surgery, the compounds may be administered topically, for example, as eye drops. Furthermore, one may administer the drug in a targeted drug delivery system, for example, in a liposome coated with a specific 5 antibody, targeting, for example, arthritic or fibrotic tissue. The liposomes will be targeted to and taken up selectively by the afflicted tissue.
The polypeptides of the invention are administered by any route that delivers an effective dosage to the desired site of action. The determination of a suitable route of administration and an effective dosage for a particular indication is within the level of skill 10 in the art. Preferably for wound treatment, one administers the therapeutic compound directly to the site. Suitable dosage ranges for the polypeptides of the invention can be extrapolated from these dosages or from similar studies in appropriate animal models.
Dosages can then be adjusted as necessary by the clinician to provide maximal therapeutic benefit.
4.1.2.2 COMPOSITIONS/FORMULATIONS
Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in a conventional manner using one or more physiologically acceptable can-iers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. These pharmaceutical compositions may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes. Proper formulation is dependent upon the route of administration chosen. When a therapeutically effective amount of protein or other active ingredient of the present invention is administered orally, protein or other active ingredient of the present invention will be in the form of a tablet, capsule, powder, solution or elixir. When administered in tablet form, the pharmaceutical composition of the invention may additionally contain a solid carrier such as a gelatin or an adjuvant. The tablet, capsule, and powder contain from about 5 to 95% protein or other active ingredient of the present invention, and preferably from about 25 to 90% protein or other active ingredient of the present invention. When administered in liquid form, a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil, mineral oil, soybean oil, or sesame oil, or synthetic oils may be added. The liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol. When administered in liquid form, the pharmaceutical composition contains from about 0.5 to 90%
by weight of protein or other active ingredient of the present invention, and preferably from S about 1 to 50% protein or other active ingredient of the present invention.
When a therapeutically effective amount of protein or other active ingredient of the present invention is administered by intravenous, cutaneous or subcutaneous injection, protein or other active ingredient of the present invention will be in the form of a pyrogen-free, parenterally acceptable aqueous solution. The preparation of such parenterally acceptable protein or other active ingredient solutions, having due regard to pH, isotonicity, stability, and the like, is within the skill in the art. A preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to protein or other active ingredient of the present invention, an isotonic vehicle such as Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection, Lactated Ringer's Injection, or other vehicle as known in the art.
The pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives known to those of skill in the art. For injection, the agents of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
For oral administration, the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the compounds of the invention to be fomulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated. Pharmaceutical preparations for oral use can be obtained from a solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, S and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration 1 S should be in dosages suitable for such administration. For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.
For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch. The compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides. In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
A pharmaceutical carrier for the hydrophobic compounds of the invention is a co-solvent system comprising benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. The co-solvent system may be the VPD co-solvent system.
VPD is a solution of 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant polysorbate 80, and 65% w/v polyethylene glycol 300, made up to volume in absolute ethanol. The VPD
co-solvent system (VPD:SW) consists of VPD diluted l :l with a 5% dextrose in water solution. This co-solvent system dissolves hydrophobic compounds well, and itself produces low toxicity upon systemic administration. Naturally, the proportions of a co-solvent system may be varied considerably without destroying its solubility and toxicity characteristics.
Furthermore, the identity of the co-solvent components may be varied: for example, other low-toxicity nonpolar surfactants may be used instead of polysorbate 80; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g. polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose. Alternatively, other delivery systems for hydrophobic pharmaceutical compounds may be employed. Liposomes and emulsions are well known examples of delivery vehicles or carriers.for hydrophobic drugs. Certain organic solvents such as dimethylsulfoxide also may be employed, although usually at the cost of greater toxicity.
Additionally, the compounds may be delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the therapeutic agent.
Various types of sustained-release materials have been established and are well known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the therapeutic reagent, additional strategies for protein or other active ingredient stabilization may be employed.
The pharmaceutical compositions also may comprise suitable solid or gel phase carriers or excipients. Examples of such carriers or excipients include but are not limited to calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin, and polymers such as polyethylene glycols. Many of the active ingredients of the invention may be provided as salts with pharmaceutically compatible counter ions. Such pharmaceutically acceptable base addition salts are those salts which retain the biological effectiveness and properties of the free acids and which are obtained by reaction with inorganic or organic bases such as sodium hydroxide, magnesium hydroxide, ammonia, trialkylamine, dialkylamine, monoalkylamine, dibasic amino acids, sodium acetate, potassium benzoate, triethanol amine and the like.
The pharmaceutical composition of the invention may be in the form of a complex of the proteins) or other active ingredients) of present invention along with protein or peptide antigens. The protein and/or peptide antigen will deliver a stimulatory signal to both B and T
lymphocytes. B lymphocytes will respond to antigen through their surface immunoglobulin receptor. T lymphocytes will respond to antigen through the T cell receptor (TCR) following presentation of the antigen by MHC proteins. MHC and structurally related proteins including those encoded by class I and class II MHC genes on host cells will serve to present the peptide antigens) to T lymphocytes. The antigen components could also be supplied as purified MHC-peptide complexes alone or with co-stimulatory molecules that can directly signal T cells. Alternatively antibodies able to bind surface immunoglobulin and other molecules on B cells as well as antibodies able to bind the TCR and other molecules on T cells can be combined with the pharmaceutical composition of the invention.
The pharmaceutical composition of the invention may be in the form of a liposome in which protein of the present invention is combined, in addition to other pharmaceutically acceptable Garners, with amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers in aqueous solution.
Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithins, phospholipids, saponin, bile acids, and the like.
Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Patent Nos. 4,235,871; 4,501,728; 4,837,028; and 4,737,323, all of which are incorporated herein by reference.
The amount of protein or other active ingredient of the present invention in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments which the patient has undergone. Ultimately, the attending physician will decide the amount of protein or other active ingredient of the present invention with which to treat each individual patient.
10 Initially, the attending physician will administer low doses of protein or other active ingredient of the present invention and observe the patient's response. Larger doses of protein or other active ingredient of the present invention may be administered until the optimal therapeutic effect is obtained for the patient, and at that point the dosage is not increased further. It is contemplated that the various pharmaceutical compositions used to 15 practice the method of the present invention should contain about 0.01 pg to about 100 mg (preferably about 0.1 pg to about 10 mg, more preferably about 0.1 pg to about 1 mg) of protein or other active ingredient of the present invention per kg body weight. For compositions of the present invention which are useful for bone, cartilage, tendon or ligament regeneration, the therapeutic method includes administering the composition 20 topically, systematically, or locally as an implant or device. When administered, the therapeutic composition for use in this invention is, of course, in a pyrogen-free, physiologically acceptable form. Further, the composition may desirably be encapsulated or injected in a viscous form for delivery to the site of bone, cartilage or tissue damage.
Topical administration may be suitable for wound healing and tissue repair.
Therapeutically 25 useful agents other than a protein or other active ingredient of the invention which may also optionally be included in the composition as described above, may alternatively or additionally, be administered simultaneously or sequentially with the composition in the methods of the invention. Preferably for bone and/or cartilage formation, the composition would include a matrix capable of delivering the protein-containing or other active 30 ingredient-containing composition to the site of bone and/or cartilage damage, providing a structure for the developing bone and cartilage and optimally capable of being resorbed into the body. Such matrices may be formed of materials presently in use for other implanted medical applications.

The choice of matrix material is based on biocompatibility, biodegradability, mechanical properties, cosmetic appearance and interface properties. The particular application of the compositions will define the appropriate formulation.
Potential matrices for the compositions may be biodegradable and chemically defined calcium sulfate, tricalcium phosphate, hydroxyapatite, polylactic acid, polyglycolic acid and polyanhydrides.
Other potential materials are biodegradable and biologically well-defined, such as bone or dermal collagen. Further matrices are comprised of pure proteins or extracellular matrix components. Other potential matrices are nonbiodegradable and chemically defined, such as sintered hydroxyapatite, bioglass, aluminates, or other ceramics. Matrices may be comprised of combinations of any of the above-mentioned types of material, such as polylactic acid and hydroxyapatite or collagen and tricalcium phosphate. The bioceramics may be altered in composition, such as in calcium-aluminate-phosphate and processing to alter pore size, particle size, particle shape, and biodegradability. Presently preferred is a 50:50 (mole weight) copolymer of lactic acid and glycolic acid in the form of porous particles having diameters ranging from 150 to 800 microns. In some applications, it will be useful to utilize a sequestering agent, such as carboxymethyl cellulose or autologous blood clot, to prevent the protein compositions from disassociating from the matrix.
A preferred family of sequestering agents is cellulosic materials such as alkylcelluloses (including hydroxyalkylcelluloses), including methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl-methylcellulose, and carboxymethylcellulose, the most preferred being cationic salts of carboxymethylcellulose (CMC). Other preferred sequestering agents include hyaluronic acid, sodium alginate, polyethylene glycol), polyoxyethylene oxide, carboxyvinyl polymer and polyvinyl alcohol). The amount of sequestering agent useful herein is 0.5-20 wt %, preferably 1-10 wt % based on total formulation weight, which represents the amount necessary to prevent desorption of the protein from the polymer matrix and to provide appropriate handling of the composition, yet not so much that the progenitor cells are prevented from infiltrating the matrix, thereby providing the protein the opportunity to assist the osteogenic activity of the progenitor cells. In further compositions, proteins or other active ingredients of the invention may be combined with other agents beneficial to the treatment of the bone and/or cartilage defect, wound, or tissue in question.
These agents include various growth factors such as epidermal growth factor (EGF), platelet derived growth factor (PDGF), transforming growth factors (TGF-a and TGF-~3), and insulin-like growth factor (IGF).
The therapeutic compositions are also presently valuable for veterinary applications.
Particularly domestic animals and thoroughbred horses, in addition to humans, are desired patients for such treatment with proteins or other active ingredients of the present invention.
The dosage regimen of a protein-containing pharmaceutical composition to be used in tissue regeneration will be determined by the attending physician considering various factors which modify the action of the proteins, e.g., amount of tissue weight desired to be formed, the site of damage, the condition of the damaged tissue, the size of a wound, type of damaged tissue (e.g., bone), the patient's age, sex, and diet, the severity of any infection, time of administration and other clinical factors. The dosage may vary with the type of matrix used in the reconstitution and with inclusion of other proteins in the pharmaceutical composition.
For example, the addition of other known growth factors, such as IGF I
(insulin like growth factor I), to the final composition, may also effect the dosage. Progress can be monitored by periodic assessment of tissue/bone growth and/or repair, for example, X-rays, histomorphometric determinations and tetracycline labeling.
Polynucleotides of the present invention can also be used for gene therapy.
Such polynucleotides can be introduced either in vivo or ex vivo into cells for expression in a mammalian subject. Polynucleotides of the invention may also be administered by other known methods for introduction of nucleic acid into a cell or organism (including, without limitation, in the form of viral vectors or naked DNA). Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells. Treated cells can then be introduced in vivo for therapeutic purposes.
4.12.3 EFFECTIVE DOSAGE
Pharmaceutical compositions suitable for use in the present invention include compositions wherein the active ingredients are contained in an effective amount to achieve its intended purpose. More specifically, a therapeutically effective amount means an amount effective to prevent development of or to alleviate the existing symptoms of the subject being treated. Determination of the effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from appropriate in vitro assays. For example, a dose can be formulated in animal models to achieve a circulating concentration range that can be used to more accurately determine useful doses in humans. For example, a dose can be formulated in animal models to achieve a circulating concentration range that includes the ICSO as determined in cell culture (i.e., the concentration of the test compound which achieves a half maximal inhibition of the protein's biological activity). Such information can be used to more accurately determine useful doses in humans.
A therapeutically effective dose refers to that amount of the compound that results in amelioration of symptoms or a prolongation of survival in a patient. Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LDSO (the dose lethal to 50%
of the population) and the EDSO (the dose therapeutically effective in 50% of the population).
The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LDso and EDSO. Compounds which exhibit high therapeutic indices are preferred. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage of such compounds lies preferably within a range of circulating concentrations that include the EDso with little or no toxicity. The dosage may vary within this range depending upon the dosage foam employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. See, e.g., Fingl et al., 1975, in "The Pharmacological Basis of Therapeutics", Ch.
1 p.1. Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the desired effects, or minimal effective concentration (MEC). The MEC will vary for each compound but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations.
Dosage intervals can also be determined using MEC value. Compounds should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%. In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.

An exemplary dosage regimen for polypeptides or other compositions of the invention will be in the range of about 0.01 ~g/kg to 100 mg/kg of body weight daily, with the preferred dose being about 0.1 ~g/kg to 25 mg/kg of patient body weight daily, varying in adults and children. Dosing may be once daily, or equivalent doses may be delivered at longer or shorter intervals.
The amount of composition administered will, of course, be dependent on the subject being treated, on the subject's age and weight, the severity of the affliction, the manner of administration and the judgment of the prescribing physician.
4.12.4 PACKAGING
The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient.
The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. Compositions comprising a compound of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.
4.13 ANTIBODIES
Also included in the invention are antibodies to proteins, or fragments of proteins of the invention. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that contain an antigen-binding site that specifically binds (immunoreacts with) an antigen. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, Fab, Fah~ and F~~b~>z fragments, and an Fab expression library. In general, an antibody molecule obtained from humans relates to any of the classes IgG, lgM, IgA, IgE and IgD, which differ from one another by the nature of the heavy chain present in the molecule.
Certain classes have subclasses as well, such as IgG~, IgGz, and others. Furthermore, in humans, the light chain may be a kappa chain or a lambda chain. Reference herein to antibodies includes a reference to all such classes, subclasses and types of human antibody species.
An isolated related protein of the invention may be intended to serve as an antigen, or a portion or fragment thereof, and additionally can be used as an immunogen to generate antibodies that immunospecifically bind the antigen, using standard techniques for polyclonal. and monoclonal antibody preparation. The full-length protein can be used or, alternatively, the invention provides antigenic peptide fragments of the antigen for use as immunogens. An antigenic peptide fragment comprises at least 6 amino acid residues of the amino acid sequence of the full length protein, such as an amino acid sequence shown in 5 SEQ >D NO: 277-552, or 773-992, or Tables 3, 4A, 4B, 5, 6, or 8, and encompasses an epitope thereof such that an antibody raised against the peptide forms a specific immune complex with the full length protein or with any fragment that contains the epitope.
Preferably, the antigenic peptide comprises at least 10 amino acid residues, or at least 15 amino acid residues, or at least 20 amino acid residues, or at least 30 amino acid residues.
10 Preferred epitopes encompassed by the antigenic peptide are regions of the protein that are located on its surface; commonly these are hydrophilic regions.
In certain embodiments of the invention, at least one epitope encompassed by the antigenic peptide is a surface region of the protein, e.g., a hydrophilic region. A
hydrophobicity analysis of the human related protein sequence will indicate which regions of 15 a related protein are particularly hydrophilic and, therefore, are likely to encode surface residues useful for targeting antibody production. As a means for targeting antibody production, hydropathy plots showing regions of hydrophilicity and hydrophobicity may be generated by any method well known in the art, including, for example, the Kyte Doolittle or the Hopp Woods methods, either with or without Fourier transformation. See, e.g., Hopp and 20 Woods, 1981, Proc. Nat. Acad. Sci. USA 78: 3824-3828; Kyte and Doolittle 1982, J. Mol.
Biol. 157: 1 OS-142, each of which is incorporated herein by reference in its entirety.
Antibodies that are specific for one or more domains within an antigenic protein, or derivatives, fragments, analogs or homologs thereof, are also provided herein.
A protein of the invention, or a derivative, fragment, analog, homolog or ortholog 25 thereof, may be utilized as an immunogen in the generation of antibodies that immunospecifically bind these protein components.
The term "specific for" indicates that the variable regions of the antibodies of the invention recognize and bind polypeptides of the invention exclusively (i.e., able to distinguish the polypeptide of the invention from other similar polypeptides despite sequence 30 identity, homology, or similarity found in the family of polypeptides), but may also interact with other proteins (for example, S. aureus protein A or other antibodies in ELISA
techniques) through interactions with sequences outside the variable region of the antibodies, and in particular, in the constant region of the molecule. Screening assays to determine binding specificity of an antibody of the invention are well known and routinely practiced in the art. For a comprehensive discussion of such assays, see Harlow et al.
(Eds), Antibodies A Laboratory Manual; Cold Spring Harbor Laboratory; Cold Spring Harbor, NY
(1988), Chapter 6. Antibodies that recognize and bind fragments of the polypeptides of the invention are also contemplated, provided that the antibodies are first and foremost specific for, as defined above, full-length polypeptides of the invention. As with antibodies that are specific for full length polypeptides of the invention, antibodies of the invention that recognize fragments are those which can distinguish polypeptides from the same family of polypeptides despite inherent sequence identity, homology, or similarity found in the family of proteins.
Antibodies of the invention are useful for, for example, therapeutic purposes (by modulating activity of a polypeptide of the invention), diagnostic purposes to detect or quantitate a polypeptide of the invention, as well as purification of a polypeptide of the invention. Kits comprising an antibody of the invention for any of the purposes described herein are also comprehended. In general, a kit of the invention also includes a control antigen for which the antibody is immunospecific. The invention further provides a hybridoma that produces an antibody according to the invention. Antibodies of the invention are useful for detection and/or purification of the polypeptides of the invention.
Monoclonal antibodies binding to the protein of the invention may be useful diagnostic agents for the immunodetection of the protein. Neutralizing monoclonal antibodies binding to the protein may also be useful therapeutics for both conditions associated with the protein and also in the treatment of some forms of cancer where abnormal expression of the protein is involved. In the case of cancerous cells or leukemic cells, neutralizing monoclonal antibodies against the protein may be useful in detecting and preventing the metastatic spread of the cancerous cells, which may be mediated by the protein.
The labeled antibodies of the present invention can be used for in vitro, in vivo, and in situ assays to identify cells or tissues in which a fragment of the polypeptide of interest is expressed. The antibodies may also be used directly in therapies or other diagnostics. The present invention further provides the above-described antibodies immobilized on a solid support. Examples of such solid supports include plastics such as polycarbonate, complex carbohydrates such as agarose and Sepharose~, acrylic resins and such as polyacrylamide and latex beads. Techniques for coupling antibodies to such solid supports are well known in the art (Weir, D.M. et al., "Handbook of Experimental Immunology" 4th Ed., Blackwell Scientific Publications, Oxford, England, Chapter 10 (1986); Jacoby, W.D. et al., Meth.
Enzym. 34 Academic Press, N.Y. (1974)). The immobilized antibodies of the present invention can be used for in vitro, in vivo, and in situ assays as well as for immuno-affinity purification of the proteins of the present invention.
Various procedures known within the art may be used for the production of polyclonal or monoclonal antibodies directed against a protein of the invention, or against derivatives, fragments, analogs homologs or orthologs thereof (see, for example, Antibodies:
A Laboratory Manual, Harlow E, and Lane D, 1988, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, incorporated herein by reference). Some of these antibodies are discussed below.
4.13.1 POLYCLONAL ANTIBODIES
For the production of polyclonal antibodies, various suitable host animals (e.g., rabbit, goat, mouse or other mammal) may be immunized by one or more injections with the native protein, a synthetic variant thereof, or a derivative of the foregoing.
An appropriate immunogenic preparation can contain, for example, the naturally occurring immunogenic protein, a chemically synthesized polypeptide representing the immunogenic protein, or a recombinantly expressed immunogenic protein. Furthermore, the protein may be conjugated to a second 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. The preparation can further include an adjuvant. Various adjuvants used to increase the immunological response include, but are not limited to, Freund's (complete and incomplete), mineral gels (e.g., aluminum hydroxide), surface-active substances (e.g., lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, etc.), adjuvants usable in humans such as Bacille Calmette-Guerin and Corynebacterium parvum, or similar immunostimulatory agents. Additional examples of adjuvants that can be employed include MPL-TDM
adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).
The polyclonal antibody molecules directed against the immunogenic protein can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as affinity chromatography using protein A or protein G, which provide primarily the IgG fraction of immune serum. Subsequently, or alternatively, the specific antigen which is the target of the immunoglobulin sought, or an epitope thereof, may be immobilized on a column to purify the immune specific antibody by immunoaffinity chromatography. Purification of immunoglobulins is discussed, for example, by D.
Wilkinson (The Scientist, published by The Scientist, Inc., Philadelphia PA, Vol. 14, No. 8 (April 17, 2000), pp. 25-28).
4.13.2 MONOCLONAL ANTIBODIES
The term "monoclonal antibody" (MAb) or "monoclonal antibody composition", as used herein, refers to a population of antibody molecules that contain only one molecular species of antibody molecule consisting of a unique light chain gene product and a unique heavy chain gene product. In particular, the complementarity determining regions (CDRs) of the monoclonal antibody are identical in all the molecules of the population. MAbs thus contain an antigen-binding site capable of immunoreacting with a particular epitope of the antigen characterized by a unique binding affinity for it.
Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and 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 can be immunized in vitro.
The immunizing agent will typically include the protein antigen, a fragment thereof or a fusion protein thereof. Generally, either peripheral blood lymphocytes are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (coding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59-103). 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 can 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.
Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, California and the American Type Culture Collection, Manassas, Virginia.
Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984);
Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, lnc., New York, (1987) pp. 51-63).
The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against the antigen.
Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem., 107, 220 (1980).
Preferably, antibodies having a high degree of specificity and a high binding affinity for the target antigen are isolated.
After the desired hybridoma cells are identified, the clones can be subcloned by limiting dilution procedures and grown by standard methods. Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown in vivo as ascites in a mammal.
The monoclonal antibodies secreted by the subclones can be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
The monoclonal antibodies can also be made by recombinant DNA methods, such as those described in U.S. Patent No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA
S also can be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences (U.S.
Patent No.
4,816,567; Mornson, Nature 368, 812-13 (1994)) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted 10 for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.
4.13.3 HUMANIZED ANTIBODIES
15 The antibodies directed against the protein antigens of the invention can further comprise humanized antibodies or human antibodies. These antibodies are suitable for administration to humans without engendering an immune response by the human against the administered immunoglobulin. Humanized forms of antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', 20 F(ab')2 or other antigen-binding subsequences of antibodies) that are principally comprised of the sequence of a human immunoglobulin, and contain minimal sequence derived from a non-human immunoglobulin. Humanization can be 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 25 rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. (See also U.S. Patent No. 5,225,539). In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies can also comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise 30 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 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., 1986; Riechmann et al., 1988; and Presta, Curr. Op. Struct.
Biol., 2, 593-596 ( 1992)).
4.13.4 HUMAN ANTIBODIES
Fully human antibodies relate to antibody molecules in which essentially the entire sequences of both the light chain and the heavy chain, including the CDRs, arise from human genes. Such antibodies are termed "human antibodies", or "fully human antibodies"
herein. Human monoclonal antibodies can be prepared by the trioma technique;
the human B-cell hybridoma technique (see Kozbor, et al., 1983 Immunol Today 4: 72) and the EBV
hybridoma technique to produce human monoclonal antibodies (see Cole, et al., 1985 In:
Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96).
Human monoclonal antibodies may be utilized in the practice of the present invention and may be produced by using human hybridomas (see Cote, et al., 1983. Proc Natl Acad Sci USA 80, 2026-2030) or by transforming human B-cells with Epstein Barr Virus in vitro (see Cole, et al., 1985 In: Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96).
In addition, human antibodies can also be produced using additional techniques, including phage display libraries (Hoogenboom and Winter, J. Mol. Biol., 227, 381 (1991 );
Marks et al., J. Mol. Biol., 222:581 (1991)). Similarly, human antibodies can be made by introducing 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, for example, 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 Marks et al.
(Bio/Technology 10, 779-783 (1992)); Lonberg et al. (Nature 368, 856-859 (1994)); Morrison (Nature 368, 812-13 (1994)); Fishwild et al, (Nature Biotechnology 14, 845-51 (1996)); Neuberger (Nature Biotechnology 14, 826 (1996)); and Lonberg and Huszar (Intern. Rev. Immunol.
13, 65-93 ( 1995)).
Human antibodies may additionally be produced using transgenic nonhuman animals that are modified so as to produce fully human antibodies rather than the animal's endogenous antibodies in response to challenge by an antigen. (See PCT
publication W094/02602). The endogenous genes encoding the heavy and light immunoglobulin chains in the nonhuman host have been incapacitated, and active loci encoding human heavy and light chain immunoglobulins are inserted into the host's genome. The human genes are incorporated, for example, using yeast artificial chromosomes containing the requisite human DNA segments. An animal which provides all the desired modifications is then obtained as progeny by crossbreeding intermediate transgenic animals containing fewer than the full complement of the modifications. The preferred embodiment of such a nonhuman animal is a mouse, and is termed the XenomouseTM as disclosed in PCT
publications WO
96/33735 and WO 96/34096. This animal produces B cells that secrete fully human immunoglobulins. The antibodies can be obtained directly from the animal after immunization with an immunogen of interest, as, for example, a preparation of a polyclonal antibody, or alternatively from immortalized B cells derived from the animal, such as hybridomas producing monoclonal antibodies. Additionally, the genes encoding the immunoglobulins with human variable regions can be recovered and expressed to obtain the antibodies directly, or can be further modified to obtain analogs of antibodies such as, for example, single chain Fv molecules.
An example of a method of producing a nonhuman host, exemplified as a mouse, lacking expression of an endogenous immunoglobulin heavy chain is disclosed in U.S.
Patent No. 5,939,598. It can be obtained by a method including deleting the J
segment genes from at least one endogenous heavy chain locus in an embryonic stem cell to prevent rearrangement of the locus and to prevent formation of a transcript of a rearranged immunoglobulin heavy chain locus, the deletion being effected by a targeting vector containing a gene encoding a selectable marker; and producing from the embryonic stem cell a transgenic mouse whose somatic and germ cells contain the gene encoding the selectable marker.
A method for producing an antibody of interest, such as a human antibody, is disclosed in U.S. Patent No. 5,916,771. It includes introducing an expression vector that contains a nucleotide sequence encoding a heavy chain into one mammalian host cell in culture, introducing an expression vector containing a nucleotide sequence encoding a light chain into another mammalian host cell, and fusing the two cells to form a hybrid cell. The hybrid cell expresses an antibody containing the heavy chain and the light chain.
In a further improvement on this procedure, a method for identifying a clinically relevant epitope on an immunogen, and a correlative method for selecting an antibody that binds immunospecifically to the relevant epitope with high affinity, are disclosed in PCT
publication WO 99/53049.
4.13.5 FAB FRAGMENTS AND SINGLE CHAIN ANTIBODIES
According to the invention, techniques can be adapted for the production of single-chain antibodies specific to an antigenic protein of the invention (see e.g., U.S. Patent No. 4,946,778). In addition, methods can be adapted for the construction of Fdb expression libraries (see e.g., Huse, et al., 1989 Science 246, 1275-1281) to allow rapid and effective identification of monoclonal Fab fragments with the desired specificity for a protein or derivatives, fragments, analogs or homologs thereof. Antibody fragments that contain the idiotypes to a protein antigen may be produced by techniques known in the art including, but not limited to: (i) an F~ab')2 fragment produced by pepsin digestion of an antibody molecule;
(ii) an Fdb fragment generated by reducing the disulfide bridges of an F~~6~~2 fragment; (iii) an Fab fragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) F,, fragments.
4.13.6 BISPECIFIC ANTIBODIES
Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for an antigenic protein of the invention. The second binding target is any other antigen, and advantageously is a cell-surface protein or receptor or receptor subunit.
Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305, 537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO
93/08829, published 13 May 1993, and in Traunecker et al., 1991 EMBO J., 10, 3655-3659.
Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the S immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al., Methods in Enzymology, 121, 210 (1986).
According to another approach described in WO 96/27011, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers that are recovered from recombinant cell culture. The preferred interface comprises at least a part of the CH3 region of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan). Compensatory "cavities" of identical or similar size to the large side chains) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g.
alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
Bispecific antibodies can be prepared as full-length antibodies or antibody fragments (e.g. F(ab')2 bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecific antibodies can be prepared using chemical linkage. Brennan et al., Science 229, 81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab')Z
fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation.
The Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives.
One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB
derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.
Additionally, Fab' fragments can be directly recovered from E. coli and chemically coupled to form bispecific antibodies. Shalaby et al., J. Exp. Med. 175, 217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab')2 molecule. Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T
cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.
Various techniques for making and isolating bispecific antibody fragments directly 5 from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al., J. Immunol. 148(5), (1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody 10 heterodimers. This method can also be utilized for the production of antibody homodimers.
The "diabody" technology described by Hollinger et al., Proc. Natl. Acad. Sci.
USA 90, 6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (V,i) connected to a light-chain variable domain (V~) by a linker which is too short to allow pairing between the 15 two domains on the same chain. Accordingly, the V,., and V~ domains of one fragment are forced to pair with the complementary V~ and V,, domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported.
See, Gruber et al., J. Immunol. 152, 5368 (1994).
20 Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al., J. Immunol. 147, 60 (1991).
Exemplary bispecific antibodies can bind to two different epitopes, at least one of which originates in the protein antigen of the invention. Alternatively, an anti-antigenic arm of an immunoglobulin molecule can be combined with an arm which binds to a triggering 25 molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (Fc~yR), such as Fc~yRI (CD64), FcyRII (CD32) and Fc~yRIII (CD16) so as to focus cellular defense mechanisms to the cell expressing the particular antigen.
Bispecific antibodies can also be used to direct cytotoxic agents to cells which express a particular antigen. These antibodies possess an antigen-binding arm and an arm which binds 30 a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA.
Another bispecific antibody of interest binds the protein antigen described herein and further binds tissue factor (TF).

4.13.7 HETEROCONJUGATE ANTIBODIES
Heteroconjugate antibodies are also within the scope of the present invention.
Heteroconjugate antibodies are composed of two covalently joined antibodies.
Such antibodies,have, for example, been proposed to target immune system cells to unwanted cells (U.S. Patent No. 4,676,980), and for treatment of HIV infection (WO 91/00360;
WO
92/200373; EP 03089). It is contemplated that the antibodies can be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins can be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S.
Patent No. 4,676,980. .
4.13.8 EFFECTOR FUNCTION ENGINEERING
It can be desirable to modify the antibody of the invention with respect to effector 1 S function, so as to enhance, e.g., the effectiveness of the antibody in treating cancer. For example, cysteine residues) can be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated can have improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp Med., 176, 1191-1195 (1992) and Shopes, J. Immunol., 148, 2918-2922 (1992).
Homodimeric antibodies with enhanced anti-tumor activity can also be prepared using heterobifunctional cross-linkers as described in Wolff et al. Cancer Research, 53, 2560-2565 (1993). Alternatively, an antibody can be engineered that has dual Fc regions and can thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design, 3, 219-230 (1989).
4.13.9 IMMUNOCONJUGATES
The invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
Chemotherapeutic agents useful in the generation of such immunoconjugates have been described above. Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A
chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A
chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, croon, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A variety of radionuclides are available for the production of radioconjugated antibodies. Examples include Z~ZBi, ~3~I, ~3'In, ~oY, and ~86Re.
Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-1 S 2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See W094/11026.
In another embodiment, the antibody can be conjugated to a "receptor" (such streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand" (e.g., avidin) that is in turn conjugated to a cytotoxic agent.
4.14 COMPUTER READABLE SEQUENCES
In one application of this embodiment, a nucleotide sequence of the present invention can be recorded on computer readable media. As used herein, "computer readable media"
refers to any medium which can be read and accessed directly by a computer.
Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM;
electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media. A skilled artisan can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising computer readable medium having recorded thereon a nucleotide sequence of the present invention. As used herein, "recorded" refers to a process for storing information on computer readable medium. A skilled artisan can readily adopt any of the presently known methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention.
A variety of data storage structures are available to a skilled artisan for creating a computer readable medium having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and Microsoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data processor structuring formats (e.g. text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information of the present invention.
By providing any of the nucleotide sequences SEQ ID NO: 1-276, or 553-772 or a representative fragment thereof; or a nucleotide sequence at least 95%
identical to any of the nucleotide sequences of SEQ ID NO: 1-276, or 553-772 in computer readable form, a skilled artisan can routinely access the sequence information for a variety of purposes. Computer software is publicly available which allows a skilled artisan to access sequence information provided in a computer readable medium. The examples which follow demonstrate how software which implements the BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993)) search algorithms on a Sybase system is used to identify open reading frames (ORFs) within a nucleic acid sequence. Such ORFs may be protein-encoding fragments and may be useful in producing commercially important proteins such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.
As used herein, "a computer-based system" refers to the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based systems are suitable for use in the present invention. As stated above, the computer-based systems of the present invention comprise a data storage means having stored therein a nucleotide sequence of the present invention and the necessary hardware means and software means for supporting and implementing a search means. As used herein, "data storage means" refers to memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.
As used herein, "search means" refers to one or more programs which are implemented on the computer-based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means.
Search means are used to identify fragments or regions of a known sequence which match a particular target sequence or target motif. A variety of known algorithms are disclosed publicly and a variety of commercially available software for conducting search means are and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, Smith-Waterman, MacPattern (EMBL), BLASTN and BLASTA
(NPOLYPEPTIDEIA). A skilled artisan can readily recognize that any one of the available algorithms or implementing software packages for conducting homology searches can be adapted for use in the present computer-based systems. As used herein, a "target sequence"
can be any nucleic acid or amino acid sequence of six or more nucleotides or two or more amino acids. A skilled artisan can readily recognize that the longer a target sequence is, the less likely a target sequence will be present as a random occurrence in the database. The most preferred sequence length of a target sequence is from about 10 to 300 amino acids, more preferably from about 30 to 100 nucleotide residues. However, it is well recognized that searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing, may be of shorter length.
As used herein, "a target structural motif," or "target motif," refers to any rationally selected sequence or combination of sequences in which the sequences) are chosen based on a three-dimensional configuration which is formed upon the folding of the target motif.
There are a variety of target'motifs known in the art. Protein target motifs include, but are not limited to, enzyme active sites and signal sequences. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences).
4.15 TRIPLE HELIX FORMATION
In addition, the fragments of the present invention, as broadly described, can be used to control gene expression through triple helix formation or antisense DNA or RNA, both of which methods are based on the binding of a polynucleotide sequence to DNA or RNA.
Polynucleotides suitable for use in these methods are preferably 20 to 40 bases in length and are designed to be complementary to a region of the gene involved in transcription (triple helix-see Lee et al., Nucl. Acids Res. 6, 3073 (1979); Cooney et al., Science 15241, 456 (1988); and Dervan et al., Science 251, 1360 (1991)) or to the mRNA itself (antisense-Olmno, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, FL (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA
hybridization 1 S blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems. Information contained in the sequences of the present invention is necessary for the design of an antisense or triple helix oligonucleotide.
4.16 DIAGNOSTIC ASSAYS AND KITS
The present invention further provides methods to identify the presence or expression of one of the ORFs of the present invention, or homolog thereof, in a test sample, using a nucleic acid probe or antibodies of the present invention, optionally conjugated or otherwise associated with a suitable label.
In general, methods for detecting a polynucleotide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polynucleotide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polynucleotide of the invention is detected in the sample.
Such methods can also comprise contacting a sample under stringent hybridization conditions with nucleic acid primers that anneal to a polynucleotide of the invention under such conditions, and amplifying annealed polynucleotides, so that if a polynucleotide is amplified, a polynucleotide of the invention is detected in the sample.

In general, methods for detecting a polypeptide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polypeptide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polypeptide of the invention is detected in the sample.
S In detail, such methods comprise incubating a test sample with one or more of the antibodies or one or more of the nucleic acid probes of the present invention and assaying for binding of the nucleic acid probes or antibodies to components within the test sample.
Conditions for incubating a nucleic acid probe or antibody with a test sample vary.
Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the nucleic acid probe or antibody used in the assay.
One skilled in the art will recognize that any one of the commonly available hybridization, amplification or immunological assay formats can readily be adapted to employ the nucleic acid probes or antibodies of the present invention. Examples of such assays can be found in Chard, T., An Introduction to Radioimmunoassay and Related Techniques, Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G.R. et al., Techniques in Immunocytochemistry, Academic Press, Orlando, FL Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, P., Practice and Theory of immunoassays: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985). The test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is compatible with the system utilized.
In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the assays of the present invention.
Specifically, the invention provides a compartment kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the probes or antibodies of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of a bound probe or antibody.

In detail, a compartment kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the antibodies used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, etc.), and containers which contain the reagents used to detect the bound antibody or probe. Types of detection reagents include labeled nucleic acid probes, labeled secondary antibodies, or in the alternative, if the primary antibody is labeled, the enzymatic, or antibody binding reagents which are capable of reacting with the labeled antibody. One skilled in the art will readily recognize that the disclosed probes and antibodies of the present invention can be readily incorporated into one of the established kit formats which are well known in the art.
4.17 MEDICAL IMAGING
The novel polypeptides and binding partners of the invention are useful in medical imaging of sites expressing the molecules of the invention (e.g., where the polypeptide of the invention is involved in the immune response, for imaging sites of inflammation or infection). See, e.g., Kunkel et al., U.S. Pat. NO. 5,413,778. Such methods involve chemical attachment of a labeling or imaging agent, administration of the labeled polypeptide to a subject in a pharmaceutically acceptable carrier, and imaging the labeled polypeptide in vivo at the target site.
4.18 SCREENING ASSAYS
Using the isolated proteins and polynucleotides of the invention, the present invention further provides methods of obtaining and identifying agents which bind to a polypeptide encoded by an ORF corresponding to any of the nucleotide sequences set forth in SEQ ID NO: 1-276, or 553-772, or bind to a specific domain of the polypeptide encoded by the nucleic acid. In detail, said method comprises the steps of:
(a) contacting an agent with an isolated protein encoded by an ORF of the present invention, or nucleic acid of the invention; and (b) determining whether the agent binds to said protein or said nucleic acid.
In general, therefore, such methods for identifying compounds that bind to a polynucleotide of the invention can comprise contacting a compound with a polynucleotide of the invention for a time sufficient to form a polynucleotide/compound complex, and S detecting the complex, so that if a polynucleotide/compound complex is detected, a compound that binds to a polynucleotide of the invention is identified.
Likewise, in general, therefore, such methods for identifying compounds that bind to a polypeptide of the invention can comprise contacting a compound with a polypeptide of the invention for a time sufficient to form a polypeptide/compound complex, and detecting the complex, so that if a polypeptide/compound complex is detected, a compound that binds to a polynucleotide of the invention is identified.
Methods for identifying compounds that bind to a polypeptide of the invention can also comprise contacting a compound with a polypeptide of the invention in a cell for a time sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a receptor gene sequence in the cell, and detecting the complex by detecting reporter gene sequence expression, so that if a polypeptide/compound complex is detected, a compound that binds a polypeptide of the invention is identified.
C'.ompounds identified via such methods can include compounds which modulate the activity of a polypeptide of the invention (that is, increase or decrease its activity, relative to activity observed in the absence of the compound). Alternatively, compounds identified via such methods can include compounds which modulate the expression of a polynucleotide of the invention (that is, increase or decrease expression relative to expression levels observed in the absence of the compound). Compounds, such as compounds identified via the methods of the invention, can be tested using standard assays well known to those of skill in the art for their ability to modulate activity/expression.
The agents screened in the above assay can be, but are not limited to, peptides, carbohydrates, vitamin derivatives, or other pharmaceutical agents. The agents can be selected and screened at random or rationally selected or designed using protein modeling techniques.
For random screening, agents such as peptides, carbohydrates, pharmaceutical agents and the like are selected at random and are assayed for their ability to bind to the protein encoded by the ORF of the present invention. Alternatively, agents may be rationally selected or designed. As used herein, an agent is said to be "rationally selected or designed"

when the agent is chosen based on the configuration of the particular protein.
For example, one skilled in the art can readily adapt currently available procedures to generate peptides, pharmaceutical agents and the like, capable of binding to a specific peptide sequence, in order to generate rationally designed antipeptide peptides, for example see Hurby et al., S Application of Synthetic Peptides: Antisense Peptides," In Synthetic Peptides, A User's Guide, W.H. Freeman, NY (1992), pp. 289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), or pharmaceutical agents, or the like.
In addition to the foregoing, one class of agents of the present invention, as broadly described, can be used to control gene expression through binding to one of the ORFs or EMFs of the present invention. As described above, such agents can be randomly screened or rationally designed/selected. Targeting the ORF or EMF allows a skilled artisan to design sequence specific or element specific agents, modulating the expression of either a single ORF or multiple ORFs which rely on the same EMF for expression control. One class of DNA binding agents are agents which contain base residues which hybridize or form a triple helix formation by binding to DNA or RNA. Such agents can be based on the classic phosphodiester, ribonucleic acid backbone, or can be a variety of sulfhydryl or polymeric derivatives which have base attachment capacity.
Agents suitable for use in these methods preferably contain 20 to 40 bases and are designed to be complementary to a region of the gene involved in transcription (triple helix -see Lee et al., Nucl. Acids Res. 6, 3073 (1979); Cooney et al., Science 241, 456 (1988); and Dervan et al., Science 251, 1360 (1991)) or to the mRNA itself (antisense-Okano, J.
Neurochem. 56, 560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, FL (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems. Information contained in the sequences of the present invention is necessary for the design of an antisense or triple helix oligonucleotide and other DNA binding agents.
Agents which bind to a protein encoded by one of the ORFs of the present invention can be used as a diagnostic agent. Agents which bind to a protein encoded by one of the ORFs of the present invention can be formulated using known techniques to generate a pharmaceutical composition.

4.19 USE OF NUCLEIC ACIDS AS PROBES
Another aspect of the subject invention is to provide for polypeptide-specific nucleic acid hybridization probes capable of hybridizing with naturally occurring nucleotide sequences. The hybridization probes of the subject invention may be derived from any of the nucleotide sequences SEQ >D NO: 1-276, or 553-772. Because the corresponding gene is only expressed in a limited number of tissues, a hybridization probe derived from any of the nucleotide sequences SEQ ID NO: 1-276, or 553-772 can be used as an indicator of the presence of RNA of cell type of such a tissue in a sample.
Any suitable hybridization technique can be employed, such as, for example, in situ hybridization. PCR as described in US Patents Nos. 4,683,195 and 4,965,188 provides additional uses for oligonucleotides based upon the nucleotide sequences. Such probes used in PCR may be of recombinant origin, may be chemically synthesized, or a mixture of both.
The probe will comprise a discrete nucleotide sequence for the detection of identical sequences or a degenerate pool of possible sequences for identification of closely related genomic sequences.
Other means for producing specific hybridization probes for nucleic acids include the cloning of nucleic acid sequences into vectors for the production of mRNA
probes. Such vectors are known in the art and are commercially available and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerise as T7 or SP6 RNA polymerise and the appropriate radioactively labeled nucleotides. The nucleotide sequences may be used to construct hybridization probes for mapping their respective genomic sequences. The nucleotide sequence provided herein may be mapped to a chromosome or specific regions of a chromosome using well-known genetic and/or chromosomal mapping techniques. These techniques include in situ hybridization, linkage analysis against known chromosomal markers, hybridization screening with libraries or flow-sorted chromosomal preparations specific to known chromosomes, and the like. The technique of fluorescent in situ hybridization of chromosome spreads has been described, among other places, in Verma et al (1988) Human Chromosomes: A Manual of Basic Techniques, Pergamon Press, New York NY.
Fluorescent in situ hybridization of chromosomal preparations and other physical chromosome mapping techniques may be correlated with additional genetic map data.
Examples of genetic map data can be found in the 1994 Genome Issue of Science (265:1981 f). Correlation between the location of a nucleic acid on a physical chromosomal map and a specific disease (or predisposition to a specific disease) may help delimit the region of DNA associated with that genetic disease. The nucleotide sequences of the subject invention may be used to detect differences in gene sequences between normal, carrier or affected individuals.
4.20 PREPARATION OF SUPPORT BOUND OLIGONUCLEOTIDES
Oligonucleotides, i.e., small nucleic acid segments, may be readily prepared by, for example, directly synthesizing the oligonucleotide by chemical means, as is commonly practiced using an automated oligonucleotide synthesizer.
Support bound oligonucleotides may be prepared by any of the methods known to those of skill in the art using any suitable support such as glass, polystyrene or Teflon. One strategy is to precisely spot oligonucleotides synthesized by standard synthesizers.
Immobilization can be achieved using passive adsorption (Inouye & Hondo, (1990) J. Clin.
Microbiol. 28(6), 1469-72); using UV light (Nagata et al., 1985; Dahlen et al., 1987; Mornssey &
Collins, (1989) Mol.
Cell Probes 3(2) 189-207) or by covalent binding of base modified DNA (Keller et al., 1988;
1 S 1989); all references being specifically incorporated herein.
Another strategy that may be employed is the use of the strong biotin-streptavidin interaction as a linker. For example, Broude et al. (1994) Proc. Natl. Acad.
Sci. USA 91 (8), 3072-6, describe the use of biotinylated probes, although these are duplex probes, that are immobilized on streptavidin-coated magnetic beads. Streptavidin-coated beads may be purchased from Dynal, Oslo. Of course, this same linking chemistry is applicable to coating any surface with streptavidin. Biotinylated probes may be purchased from various sources, such as, e.g., Operon Technologies (Alameda, CA).
Nunc Laboratories (Naperville, IL) is also selling suitable material that could be used.
Nunc Laboratories have developed a method by which DNA can be covalently bound to the microwell surface termed Covalink NH. CovaLink NH is a polystyrene surface grafted with secondary amino groups (>NH) that serve as bridgeheads for further covalent coupling.
CovaLink Modules may be purchased from Nunc Laboratories. DNA molecules may be bound to CovaLink exclusively at the 5'-end by a phosphoramidate bond, allowing immobilization of more than 1 pmol ofDNA (Rasmussen et al., (1991) Anal. Biochem. 198(1) 138-42).
The use of CovaLink NH strips for covalent binding of DNA molecules at the 5'-end has been described (Rasmussen et al., (1991). In this technology, a phosphoramidate bond is employed (Chu et al., (1983) Nucleic Acids Res. 11(8) 6513-29). This is beneficial as immobilization using only a single covalent bond is preferred. The phosphoramidate bond joins the DNA to the CovaLink NH secondary amino groups that are positioned at the end of spacer arms covalently grafted onto the polystyrene surface through a 2 nm long spacer arm. To link an oligonucleotide to CovaLink NH via an phosphoramidate bond, the oligonucleotide terminus must have a 5'-end phosphate group. It is, perhaps, even possible for biotin to be covalently bound to CovaLink and then streptavidin used to bind the probes.
More specifically, the linkage method includes dissolving DNA in water (7.5 ng/~1) and denaturing for 10 min. at 95°C and cooling on ice for 10 min. Ice-cold 0.1 M 1-methylimidazole, pH 7.0 (1-Melm~), is then added to a final concentration of 10 mM I-MeIm~.
A ss DNA solution is then dispensed into CovaLink NH strips (75 pl/well) standing on ice.
Carbodiimide 0.2 M 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC), dissolved in 10 mM 1-Melm~, is made fresh and 25 ~l added per well. The strips are incubated for 5 hours at 50°C. After incubation the strips are washed using, e.g., Nunc-Immuno Wash;
first the wells are washed 3 times, then they are soaked with washing solution for 5 min., and finally they are washed 3 times (where in the washing solution is 0.4 N NaOH, 0.25% SDS
heated to 50°C).
It is contemplated that a fizrther suitable method for use with the present invention is that described in PCT Patent Application WO 90/03382 (Southern & Maskos), incorporated herein by reference. This method of preparing an oligonucleotide bound to a support involves attaching a nucleoside 3'-reagent through the phosphate group by a covalent phosphodiester link to aliphatic hydroxyl groups carned by the support. The oligonucleotide is then synthesized on the supported nucleoside and protecting groups removed from the synthetic oligonucleotide chain under standard conditions that do not cleave the oligonucleotide from the support.
Suitable reagents include nucleoside phosphoramidite and nucleoside hydrogen phosphorate.
An on-chip strategy for the preparation of DNA probe for the preparation of DNA probe arrays may be employed. For example, addressable laser-activated photodeprotection may be employed in the chemical synthesis of oligonucleotides directly on a glass surface, as described by Fodor et al. (1991) Science 251(4995), 767-73, incorporated herein by reference. Probes may also be immobilized on nylon supports as described by Van Ness et al.
(1991 ) Nucleic Acids Res., 19(12) 3345-50; or linked to Teflon using the method of Duncan &
Cavalier (1988) Anal. Biochem. 169(1), 104-8; all references being specifically incorporated herein.
To link an oligonucleotide to a nylon support, as described by Van Ness et al.
(1991), requires activation of the nylon surface via alkylation and selective activation of the 5'-amine of oligonucleotides with cyanuric chloride.

One particular way to prepare support bound oligonucleotides is to utilize the light-generated synthesis described by Pease et al., ( I 994) Proc. Nat'1.
Acad. Sci., USA 91 ( 11 ), 5022-6, incorporated herein by reference). These authors used current photolithographic techniques to generate arrays of immobilized oligonucleotide probes (DNA
chips). These methods, in which light is used to direct the synthesis of oligonucleotide probes in high-density, miniaturized arrays, utilize photolabile 5'-protected N acyl-deoxynucleoside phosphoramidites, surface linker chemistry and versatile combinatorial synthesis strategies. A
matrix of 256 spatially defined oligonucleotide probes may be generated in this manner.
4.21 PREPARATION OF NUCLEIC ACID FRAGMENTS
The nucleic acids may be obtained from any appropriate source, such as cDNAs, genomic DNA, chromosomal DNA, microdissected chromosome bands, cosmid or YAC
inserts, and RNA, including mRNA without any amplification steps. For example, Sambrook et al. (1989) describes three protocols for the isolation of high molecular weight DNA from mammalian cells (p. 9.14-9.23).
1 S DNA fragments may be prepared as clones in M13, plasmid or lambda vectors and/or prepared directly from genomic DNA or cDNA by PCR or other amplification methods.
Samples may be prepared or dispensed in multiwell plates. About 100-1000 ng of DNA
samples may be prepared in 2-500 ml of final volume.
The nucleic acids would then be fragmented by any of the methods known to those of skill in the art including, for example, using restriction enzymes as described at 9.24-9.28 of Sambrook et al. (1989), shearing by ultrasound and NaOH treatment.
Low pressure shearing is also appropriate, as described by Schriefer et al.
(1990) Nucleic Acids Res. 18(24), 7455-6, incorporated herein by reference). In this method, DNA
samples are passed through a small French pressure cell at a variety of low to intermediate pressures. ~A lever device allows controlled application of low to intermediate pressures to the cell. The results of these studies indicate that low-pressure shearing is a useful alternative to sonic and enzymatic DNA fragmentation methods.
One particularly suitable way for fragmenting DNA is contemplated to be that using the two base recognition endonuclease, CviJI, described by Fitzgerald et al.
(1992) Nucleic Acids Res. 20(14) 3753-62. These authors described an approach for the rapid fragmentation and fractionation of DNA into particular sizes that they contemplated to be suitable for shotgun cloning and sequencing.

The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions, which alter the specificity of this enzyme (CviJI**), yield a quasi-random distribution of DNA
fragments form the small molecule pUCl9 (2688 base pairs). Fitzgerald et al. (1992) quantitatively evaluated the randomness of this fragmentation strategy, using a CviJI** digest of pUCl9 that was size fractionated by a rapid gel filtration method and directly ligated, without end repair, to a lac Z
minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI**
restricts pyGCPy and PuGCPu, in addition to PuGCPy sites, and that new sequence data is accumulated at a rate consistent with random fragmentation.
As reported in the literature, advantages of this approach compared to sonication and agarose gel fractionation include: smaller amounts of DNA are required (0.2-0.5 ~g instead of 2-S fig); and fewer steps are involved (no preligation, end repair, chemical extraction, or agarose gel electrophoresis and elution are needed).
Irrespective of the manner in which the nucleic acid fragments are obtained or prepared, it is important to denature the DNA to give single stranded pieces available for hybridization.
This is achieved by incubating the DNA solution for 2-5 minutes at 80-90°C. The solution is then cooled quickly to 2°C to prevent renaturation of the DNA fragments before they are contacted with the chip. Phosphate groups must also be removed from genomic DNA by methods known in the art.
4.22 PREPARAT10N OF DNA ARRAYS
Arrays may be prepared by spotting DNA samples on a support such as a nylon membrane. Spotting may be performed by using arrays of metal pins (the positions of which correspond to an array of wells in a microtiter plate) to repeated by transfer of about 20 n1 of a DNA solution to a nylon membrane. By offset printing, a density of dots higher than the density of the wells is achieved. One to 25 dots may be accommodated in 1 mm2, depending on the type of label used. By avoiding spotting in some preselected number of rows and columns, separate subsets (subarrays) may be formed. Samples in one subarray may be the same genomic segment of DNA (or the same gene) from different individuals, or may be different, overlapped genomic clones. Each of the subarrays may represent replica spotting of the same samples. In one example, a selected gene segment may be amplified from 64 patients. For each patient, the amplified gene segment may be in one 96-well plate (all 96 wells containing the same sample).
A plate for each of the 64 patients is prepared. By using a 96-pin device, all samples may be spotted on one 8 x 12 cm membrane. Subarrays may contain 64 samples, one from each patient.
Where the 96 subarrays are identical, the dot span may be 1 mmZ and there may be a 1 mm space between subarrays.
Another approach is to use membranes or plates (available from NUNC, Naperville, Illinois) which may be partitioned by physical spacers e.g. a plastic grid molded over the membrane, the grid being similar to the sort of membrane applied to the bottom of multiwell plates, or hydrophobic strips. A fixed physical spacer is not preferred for imaging by exposure to flat phosphor-storage screens or x-ray films.
The present invention is illustrated in the following examples. Upon consideration of the present disclosure, one of skill in the art will appreciate that many other embodiments and variations may be made in the scope of the present invention. Accordingly, it is intended that the broader aspects of the present invention not be limited to the disclosure of the following examples. The present invention is not to be limited in scope by the exemplified embodiments which are intended as illustrations of single aspects of the invention, and compositions and 1 S methods which are functionally equivalent are within the scope of the invention. Indeed, numerous modifications and variations in the practice of the invention are expected to occur to those skilled in the art upon consideration of the present preferred embodiments. Consequently, the only limitations which should be placed upon the scope of the invention are those which appear in the appended claims.
All references cited within the body of the instant specification are hereby incorporated by reference in their entirety.
5.0 EXAMPLES
5.1 EXAMPLE 1 Novel Nucleic Acid Seguences Obtained From Various Libraries A plurality of novel nucleic acids were obtained from cDNA libraries prepared from various human tissues and in some cases isolated from a genomic library derived from human chromosome using standard PCR, SBH sequence signature analysis and Sanger sequencing techniques. The inserts of the library were amplified with PCR using primers specific for the vector sequences which flank the inserts. Clones from cDNA libraries were spotted on nylon membrane filters and screened with oligonucleotide probes (e.g., 7-mers) to obtain signature sequences. The clones were clustered into groups of similar or identical sequences.
Representative clones were selected for sequencing.

In some cases, the 5' sequence of the amplified inserts was then deduced using a typical Sanger sequencing protocol. PCR products were purified and subjected to fluorescent dye terminator cycle sequencing. Single pass gel sequencing was done using a 377 Applied Biosystems (ABI) sequencer to obtain the novel nucleic acid sequences.
5.2 EXAMPLE 2 Assemblage of Novel Nucleic Acids The contigs or nucleic acids of the present invention, designated as SEQ ll~
NO: 553-772 were assembled using an EST sequence as a seed. Then a recursive algorithm was used to extend the seed EST into an extended assemblage, by pulling additional sequences from different databases (i.e., Hyseq's database containing EST sequences, dbEST, gb pri, and UniGene, and exons from public domain genomic sequences predicated by GenScan) that belong to this assemblage. The algorithm terminated when there were no additional sequences from the above databases that would extend the assemblage. Further, inclusion of component sequences into the assemblage was based on a BLASTN hit to the extending assemblage with BLAST score greater than 300 and percent identity greater than 95%.
The novel predicted polypeptides (including proteins) encoded by the novel polynucleotides (SEQ >D NO: 553-772) of the present invention, and their corresponding translation start and stop nucleotide locations to each of SEQ >D NO: 553-772 were obtained using one of two methods. Polypeptides were obtained by using a software program called FASTY (available from http://fasta.bioch.virginia,edu) which selects a polypeptide based on a comparison of the translated novel polynucleotide to known polynucleotides (W.R. Pearson, Methods in Enzymology, 183:63-98 (1990), herein incorporated by reference).
Alternatively, polypeptides were obtained by using a software program called GenScan for human/vertebrate sequences (available from Stanford University, Office of Technology Licensing) that predicts the polypeptide based on a probabilistic model of gene structure/compositional properties (C.
Burge and S. Karlin, J. Mol. Biol., 268:78-94 (1997), incorporated herein by reference).
Method C refers to a polypeptide obtained by using a Hyseq proprietary software program that translates the novel polynucleotide and its complementary strand into six possible amino acid sequences (forward and reverse frames) and chooses the polypeptide with the longest open reading frame.
5.3 EXAMPLE 3 Novel Nucleic Acids The novel nucleic acids of the present invention were assembled from sequences that were obtained from a cDNA library by methods described in Example 1 above, and in some cases sequences obtained from one or more public databases. The nucleic acids were assembled using an EST sequence as a seed. Then a recursive algorithm was used to extend the seed EST into an extended assemblage, by pulling additional sequences from different databases (Hyseq's database containing EST sequences, dbEST, gb pri, and UniGene) that belong to this assemblage. The algorithm terminated when there was no additional sequences from the above databases that would extend the assemblage. Inclusion of component sequences into the assemblage was based on a BLASTN hit to the extending assemblage with BLAST
score greater than 300 and percent identity greater than 95%.
Using PHRAP (Univ. of Washington) or CAP4 (Paracel), a full-length gene cDNA
sequence and its corresponding protein sequence were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequences were checked using FASTY and/or BLAST against Genebank (i.e., dbEST, gb pri, 1 S UniGene, and Genpept) and the Geneseq (Derwent). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and cg-zip-2 (Hyseq, Inc.). The full-length nucleotide and amino acid sequences, including splice variants resulting from these procedures are shown in the Sequence Listing as SEQ 1D NO: 1-552.
The nucleic acid sequences of the present invention were confirmed to have at least one transmembrane domain using the TMpred program (http://www.ch.embnet.orz/software/TMPRED form.html, herein incorporated by reference).
Table 1 shows the various tissue sources of SEQ >17 NO: 1-276.
The homologs for polypeptides SEQ ~ NO: 277-552, that correspond to nucleotide sequences SEQ m NO: 1-276 were obtained by a BLASTP search against Genpept release 124 and Geneseq (Derwent) release 200117 and against Genpept release 129 and Geneseq (Derwent) release (July 18, 2002). The results showing homologues for SEQ ID
NO: 277-552 from Genpept 124 are shown in Table 2A. The results showing homologues for SEQ ID
NO: 277-552 from Genpept 129 are shown in Table 2B.
Using eMatrix software package (Stanford University, Stanford, CA) (Wu et al., J.
Comp. Biol., Vol. 6, 219-235 (1999), http://motif.stanford.edu/ematrix-search/
herein incorporated by reference), all the polypeptide sequences were examined to determine whether they had identifiable signature regions. Scoring matrices of the eMatrix software package are derived from the BLOCKS, PRINTS, PFAM, PRODOM, and DOMO
databases. Table 3 shows the accession number of the homologous eMatrix signature found in the indicated polypeptide sequence, its description, and the results obtained which include accession number subtype; raw score; p-value; and the position of signature in amino acid sequence.
Using the Pfam software program (Sonnhammer et al., Nucleic Acids Res., Vol.
26(1) pp. 320-322 (1998) herein incorporated by reference) all the polypeptide sequences were examined for domains with homology to certain peptide domains. Table 4A
shows the name of the Pfam model found, the description, the e-value and the Pfam score for the identified model within the sequence as described in United States priority application serial number 60/323,739, filed September 19, 2001, herein incorporated by reference in its entirety. Table 4B shows the name of the Pfam model found, the description, the e-value and the Pfam score for the identified model within the sequence using Pfam version 7.2.
Further description of the Pfam models can be found at http://~fam.wustl.edu/.
The GeneAtlasTM software package (Molecular Simulations Inc. (MSI), San Diego, CA) was used to predict the three-dimensional structure models for the polypeptides encoded by SEQ ID NO: 1-276 (i.e. SEQ >I7 NO: 277-552). Models were generated by (1) PSI-BLAST which is a multiple alignment sequence profile-based searching developed by Altschul et al, (Nucl. Acids. Res. 25, 3389-3408 (1997)), (2) High Throughput Modeling (HTM) (Molecular Simulations Inc. (MSI) San Diego, CA,) which is an automated sequence and structure searching procedure (http://www.msi.com/), and (3) SeqFoldT~~
which is a fold recognition method described by Fischer and Eisenberg (J. Mol. Biol. 209, 779-791 (1998)).
This analysis was carried out, in part, by comparing the polypeptides of the invention with the known~NMR (nuclear magnetic resonance) and x-ray crystal three-dimensional structures as templates. Table 5 shows: "PDB ID", the Protein DataBase (PDB) identifier given to template structure; "Chain ID", identifier of the subcomponent of the PDB
template structure; "Compound Information", information of the PDB template structure and/or its subcomponents; "PDB Function Annotation" gives function of the PDB template as annotated by the PDB files (http:/www.rcsb.or~/PDB/); start and end amino acid position of the protein sequence aligned; PSI-BLAST score, the verify score, the SeqFold score, and the Potentials) of Mean Force (PMF). The verify score is produced by GeneAtlasT"~
software (MSI), is based on Dr. Eisenberg's Profile-3D threading program developed in Dr. David Eisenberg's laboratory (US patent no. 5,436,850 and Luthy, Bowie, and Eisenberg, Nature, 356:83-85 (1992)) and a publication by R. Sanchez and A. Sali, Proc. Natl.
Acad. Sci. USA, 95:13597-12502. The verify score produced by GeneAtlas normalizes the verify score for proteins with different lengths so that a unified cutoff can be used to select good models as S follows:
Verify score (normalized) _ (raw score - 1/2 high score)/(1/2 high score) The PFM score, produced by GeneAtlasTM software (MSI), is a composite scoring function that depends in part on the compactness of the model, sequence identity in the alignment used to build the model, pairwise and surface mean force potentials (MFP). As given in Table 5, a verify score between 0 to 1.0, with 1 being the best, represents a good model. Similarly, a PMF score between 0 to 1.0, with 1 being the best, represents a good model. A SeqFoldT"' score of more than 50 is considered significant. A good model may also be determined by one of skill in the art based all the information in Table S taken in totality.
Table 6 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide using Neural Network SignalP V 1.1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark). The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson, Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication " Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites" Protein Engineering, Vol.
10, no. 1, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et al reference, was obtained for the polypeptide sequences.
Table 7 correlates each of SEQ ID NO: 1-276 to a specific chromosomal location.
Table 8 shows the number of transmembrane regions, their location(s), and TMPred score obtained, for each of the SEQ ID NO: 277-552 that had a TMPred score of 500 or greater, using the TMpred program (http://www.ch.embnet.or~/software/TMPRED fonn.html).
Table 9 is a correlation table of the novel polynucleotide sequences SEQ ID
NO: 1-276, their corresponding polypeptide sequences SEQ ID NO: 277-552, their corresponding priority contig nucleotide sequences SEQ ID NO: 553-772, their corresponding priority contig polypeptide sequences SEQ ID NO: 773-992, and the US serial number of the priority application (all of which are herein incorporated in their entirety), in which the contig sequence was filed.
Table 10 is a correlation table of the novel polynucleotide sequences SEQ ID
NO: 1-276, the novel polypeptide sequences SEQ ID NO: 277-552, and the corresponding SEQ ID
NO in which the sequence was filed in priority US application bearing serial number 60/323,739, filed September 19, 2001.

Table 1 Tissue originLibrary/RNAHYSEQ LibrarySEQ ID NO:

source Name adult brainGIBCO AB3001 8 76 78 80 101-102 109-1 adult brainGIBCO ABD003 1-3 8-9 11 14 23 29 41 adult brainClontech ABR001 23 38-39 47 91 103 106 adult brainClontech ABR006 1-3 8-9 22 29-30 36 38-39 adult brainClontech ABR008 1-3 6 9-11 13 15 24 30-31 adult brainBioChain ABR012 S 28 161 211 adult brainBioChain ABR013 144 154 adult brainInvitrogen ABR014 76 115 adult brainlnvitro ABROIS 13 1S 178 211 ~en adult brainlnvitro ABR016 37 95 101-102 en adult brainInvitrogen ABT004 6 23 47 79 101-103 106 cultured Stratagene ADP001 4 26 33 81-83 86 99-102 readi ocytes 181 193 adrenal Clontech ADR002 9 13 32 40-41 57 72 76 gland 84 93 103-105 115 adult heartGIBCO AHR001 1-3 5-6 8 I 1-12 14 21 adult kidneyGIBCO AKD001 1-7 1 S-16 19-21 28 42 adult kidneyInvitrogen AKT002 1-4 6 15 20-21 41 43 45-46 adult lun GIBCO ALG001 5 24 72 78 136 158 164-166 1 m h node Clontech ALN001 64 121 154 216 235 young liverGIBCO ALV001 1-3 5 28 101-102 104 122 adult liverInvitrogen ALV002 15-16 26 42 47 51-53 58 Table 1 Tissue originLibrary/RNAHYSEQ LibrarySEQ ID NO:

source Name adult liverClontech ALV003 1-3 104 I 15 120 169 172 adult ovaryInvitrogen AOV001 1-5 21-22 26 28-29 32 adult lacentaClontech APL001 16 46 136 placenta Invitrogen APL002 4 26 47 60 101-102 109-110 adult spleenGIBCO ASP001 1-3 6 15 17 72 82-83 101-102 adult testisGIBCO ATS001 1-3 6 13 21 60 80 137 adult bladderInvitrogen BLD001 6 94 114 164-166 169 178 bone marrowClontech BMD001 1-3 11-14 29 86 99-100 bone marrowGF BMD002 6 9 13 22 32 S 1-53 55 adult colonInvitro CLN001 47 60 158 173 181 201 en 211 adult cervixBioChain CVX001 1-3 8 14 29 38-39 41-42 dia hra=m BioChain DIA002 182 endothelialStratagene EDT001 4-S 15-16 26 28-29 36 cells 47 51-53 57 60 78 fetal brainClontech FBR001 1-3 31 42 76 79 137 154 fetal brainClontech FBR004 36 79 154 fetal brainClontech FBR006 5 10-11 13 15 24-25 30-33 ' 38-39 41-42 47 fetal brainClontech FBRs03 5 28 fetal brainInvitrogen FBT002 6 15 24 35-36 41 64 101-102 fetal heartInvitrogen FHR001 6 14-15 21 30 46 51-53 Table 1 Tissue originLibrary/RNAHYSEQ LibrarySEQ ID NO:

source Name fetal kidneClontech FKD001 1-3 6 105 109-110 178 fetal kidneyClontech FKD002 10 46 S7 107 113 118 154-155 fetal lun Clontech FLG001 9 13 121 132 136 161 181 fetal lung Invitrogen FLG003 6 15 19 60 89 107 111 fetallun Clontech FLG004 99-100 fetal liver-Columbia FLS001 1-7 9 11 17 26 28-29 38-39 spleen University 57-60 72 74 76 84 90-91 fetal liverColumbia FLS002 5-6 9 11 15 18 26 28 32 spleen University 72 79-80 82-84 89-90 93 fetal liver-Columbia FLS003 5 9 21 26 28 90-91 93-94 spleen University 110113115-117121 133136143-144 fetal liverInvitrogen FLV001 32 35 101-102 106 112 fetal liverClontech FLV002 10 8S 89 107 116 120 221 fetal liverClontech FLV004 15 58 69-70 81 89-92 104-106 fetal muscleInvitrogen FMS001 6 14 32 86 107 125 132 fetal muscleInvitrogen FMS002 11 14 41 51-53 64 71 74 fetal skin Invitrogen FSK001 1-4 6 10-11 13 15 24 29 fetal skin Invitrogen FSK002 5-6 8 15 28-29 51-53 55 umbilical BioChain FUC001 4-5 28 38-39 78 80-81 cord 84 86 99-102 104-fetal brainGIBCO HFB001 1-3 8-10 14 16 22 24 26 macrophage Invitrogen HMP001 4 41 73 101-102 104 107-108 infant brainColumbia IB2002 7 10 14 16 22-23 2S 29 University 59-60 64 76 81 87 99-100 Table 1 Tissue originLibrary/RNAHYSEQ LibrarySEQ ID NO:

source Name infant brainColumbia IB2003 6 11 15-16 29 36-39 47 University 87-88 109-1 10 1 I 3 128 infant brainColumbia IBM002 139 161 242 Universit infant brainColumbia IBS001 10 37 107 109-110 112 Universit lung, fibroblastStratagene LFB001 4-5 15 28 41-42 57 72 lung tumor Invitrogen LGT002 1-3 5-6 9-10 21 27-29 lymphocytesATCC LPC001 13 41 60 78 84 91 95 99-103 leukocyte GIBCO LUC001 1-3 5-6 9 11 15 18-19 leukocyte Clontech LUC003 60 99-100 105 132 154 melanoma Clontech MEL004 99-100106120144157169191211219-from-cell-line- 220 264 ATCC-#CRL-mammary Invitrogen MMG001 4-7 11 13 15-16 25-26 gland 28 38-39 74 79 84 mixture various SUP002 15 38-39 44 85-86 112 16 vendors 117 120-121 123 tissues/mRNA 126 147 178 186 190 222 mixture various SUP008 99-100 111 114 158 246 16 vendors tissues/mRNA

mixture various SUP009 1-3 16 vendors tissues/mRNA

induced Stratagene NTD001 16 29 43 76 79 105 107 neuron- 132 162 cells retinoic Stratagene NTR001 47 109-110 1 15 118 154 acid- 157 159 178 199 induced- 230 neuronal-cells neuronal Stratagene NTU001 1-3 16 29 60 89 106 109-110 cells 118 143 200 pituitary Clontech PIT004 1-4 51-53 72 77 109-1 gland 1 1 1 13 174 240 247 placenta Clontech PLA003 1-3 30 71 89 97 104 115 Table 1 Tissue originLibrary/RNAHYSEQ LibrarySEQ ID NO:

source Name prostate Clontech PRT001 10 12 15 18 35 46 80 84 rectum Invitrogen REC001 6 32 48 67 80 90 101-102 salivary Clontech SAL001 11 15 35 49 60 84 94 104 gland 109-110 123 small intestineClontech SIN001 5-6 9 11 13 16 26 28-29 skeletal Clontech SKM001 7 9 14 24 35 42 57 107 muscle 109-110 125 150 spinal cordClontech SPC001 1-3 23-24 38-39 41 46 87 adult spleenClontech SPLc01 6 15 82-83 91 107 114 147 stomach Clontech STO001 10 15 58 91 thalamus Clontech THA002 16 76 87 90 104 132 153 thymus Clontech THM001 1-3 26 32 38-39 41 60 107 thymus Clontech THMc02 1-3 5 9 15-16 19 21 28 thyroid Clontech THR001 1-7 9 12-13 15 19 28 41 gland 43 45 47 51-52 72 trachea Clontech TRC001 18 28-29 46 101-102 113 uterus Clontech UTR001 30 38-39 86 121 132 137 bone marrowSTM001 115 199 ~

*The 16 tissue/mRNAs and their vendor sources are as follows: 1) Normal adult brain mRNA
(Invitrogen), 2) Normal adult kidney mRNA (Invitrogen), 3) Normal fetal brain mRNA (Invitrogen), 4) Normal adult liver mRNA (Invitrogen), 5) Normal fetal kidney mRNA (Invitrogen), 6) Normal fetal liver mRNA
(Invitrogen), 7) normal fetal skin mRNA (Invitrogen), 8) human adrenal gland mRNA (Clontech), 9) Human bone marrow mRNA (Clontech), 10) Human leukemia lymphoblastic mRNA (Clontech), 11) Human thymus mRNA (Clontech), 12) human lymph node mRNA (Clontech), 13) human so\spinal cord mRNA (Clontech), 14) human thyroid mRNA (Clontech), 15) human esophagus mRNA (BioChain), 16) human conceptional umbilical cord mRNA (BioChain).

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

277 11321818 Gallus RING zinc fin er rotein 1355 91 allus 277 g12746333Homo SapiensRING zinc finger protein 1455 100 (RZF) mRNA, com lete cds.

277 g13387925Homo Sapiensclone 24450 RING zinc 1455 100 finger protein RZF mRNA, com lete cds.

278 g12746333Homo SapiensRING zinc finger protein 1445 94 (RZF) mRNA, com lete cds.

278 g13387925Homo Sapiensclone 24450 RING zinc 1445 94 finger protein RZF mRNA, com lete cds.

278 g114602541Homo Sapiensring finger protein 13, 1445 94 clone MGC:13487 IMAGE:3683407, mRNA, com lete cds.

279 g12746333Homo SapiensRING zinc finger protein 1338 100 (RZF) mRNA, com lete cds.

279 g13387925Homo Sapiensclone 24450 RING zinc 1338 100 finger protein RZF mRNA, com lete cds.

279 g114602541Homo Sapiensring finger protein 13, 1338 100 clone MGC:13487 IMAGE:3683407, mRNA, com lete cds.

280 g110438603Homo sa cDNA: FLJ22282 fis, clone1341 96 iens HRC03861.

280 AAB24463 Homo SapiensHuman secreted protein 1341 96 sequence encoded by gene 27 SEQ ID N0:88.

280 AAB34813 Homo SapiensHuman secreted protein 696 93 sequence encoded b ene 41 SEQ ID NO:101.

28 16841548 Homo sa HSPC 163 423 100 I iens 281 g112653595Homo SapiensHSPC163 protein, clone 423 100 MGC:772 IMAGE:3163724, mRNA, com lete cds.

281 AAY91543 Homo SapiensHuman secreted protein 423 100 sequence encoded b gene 93 SEQ ID N0:216.

282 g12586350Homo sa tetras an NAG-2) mRNA, 842 93 iens com lete cds.

282 g12997747Homo Sapienstetraspan TM4SF (TSPAN-4)842 93 mRNA, com fete cds.

282 g112653241Homo Sapienstransmembrane 4 superfamily842 93 member 7, clone MGC:8437 IMAGE:2821236, mRNA, com lete cds.

283 g115080477Homo SapiensSimilar to RIKEN cDNA 2037 97 gene, clone MGC:9810 IMAGE:3860434, mRNA, com lete cds.

283 g19104959Xylella beta-lactamase induction 161 29 signal transducer fastidiosarotein 9a5c 283 g11778812Neisseria No definition line found 259 27 onorrhoeae 284 g1 12053215Homo sapiensmRNA; cDNA DKFZp434K2435 2762 100 (from clone DKFZ 434K2435);
com lete cds.

284 AAY87197 Homo SapiensHuman secreted protein 86 24 sequence SEQ ID

N0:236.

284 AAY27598 Homo SapiensHuman secreted protein 63 29 encoded by gene No. 32.

285 110438815Homo sa cDNA: FLJ22427 fis, clone4487 98 iens HRC09013.

285 g1 15076843Homo sapienspecanex-like protein 1 759 44 mRNA, complete cds.

285 g113171105Takifugu pecanex 685 44 rubri es 286 g12828808Bacillus glucose transporter 100 23 subtilis 286 114023148Mesorhizobiurobable fosmidom cin resistance112 25 rotein Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

m loti 286 g12650264Archaeoglobusoxalate/formate antiporter102 23 (oxlT-2) ful idus 287 g1180137Homo SapiensHuman membrane cofactor 1980 96 protein (MCP) mRNA, com lete cds.

287 AAW27484Homo sa Human MCP. 1980 96 iens 287 =1512457Homo sa membrane cofactor rotein 1976 95 iens 288 110437579Homo sa cDNA: FLJ21472 fis, clone1019 100 iens COL04936.

288 AAE01687Homo SapiensHuman gene 16 encoded 1019 100 secreted protein HDPMM88, SEQ ID N0:99.

288 g1 14043759Homo Sapiensclone IMAGE:4111596, mRNA,563 58 partial cds.

289 AAY41401Homo SapiensHuman secreted protein 392 100 encoded by gene 94 clone HLYCH68.

289 AAB08863Homo SapiensAmino acid sequence of 392 100 a human secreto rotein.

289 g1575398Saccharomyceregulator of carbon catabolite54 57 repression s cerevisiae 290 g114250010Homo sapiensclone MGC:14489 IMAGE:4244549,2035 99 mRNA, com fete cds.

290 11495419Homo sa H.sa iens ART3 gene. 1713 97 iens 290 g12677616Mus musculusNAD(P)(+)--arginine ADP- 1080 58 ribos ltransferase 291 113182757Homo sa HTPAP mRNA, com lete cds.598 100 iens 291 AAB70690Homo SapiensHuman hDPP protein sequence598 100 SEQ ID

N0:7.

291 g114020949Arabidopsisphosphatidic acid phosphatase250 38 thaliana 292 AAB88418Homo sapiensHuman membrane or secretory725 100 protein clone PSEC0181.

292 g12909844Homo Sapiensprostate stem cell antigen109 32 (PSCA) mRNA, com lete cds.

292 g19367212Homo SapiensmRNA for prostate stem 109 32 cell antigen (PSCA gene).

293 =112718841Mus musculusSkullin 283 38 293 14191356Mus musculusclaudin-6 281 38 293 g113543081Mus musculusclaudin 6 281 38 294 12618609Ca ra hircusmhc class II DRA 636 80 294 1165868 Ovis ariesMHC Ovar-DR-al ha 632 79 294 1207708 Sciurus MHC class II DR-al ha 652 82 aberti 295 g114025214Mesorhizobiuprobable amidase 348 31 m loti 295 g17226601Neisseria Glu-tRNA(Gln) amidotransferase,398 28 subunit meningitidisA

295 g17380209Neisseria Glu-tRNA(Gln) amidotransferase387 27 subunit meningitidisA

296 g1 12620132Homo Sapiensrenal sodium/sulfate cotransporter3100 100 mRNA, com lete cds.

296 g110439272Homo sa cDNA: FLJ22760 fis, clone3096 99 iens KAIA0881.

296 g1310183Rattus sodium dependent sulfate 2627 82 transporter norvegicus 297 g112653037Homo sa clone IMAGE:3355813, mRNA,1574 100 iens artial Table 2A
SEQ AccessionSpecies Description Score/~

ID No. Identity NO:

cds.

297 AAY44245 Homo sa Human cell si nallin rotein-8.1208 100 iens 297 AAW64220 Homo SapiensHuman secreted protein 1195 98 from clone CG300 3.

298 gi9588085Homo sa mRNA for TAPL, com lete 2338 99 iens cds.

298 gi9622987Homo SapiensATP-binding cassette protein2338 99 (ABCB9) mRNA, com fete cds.

298 AAE02437 Homo SapiensHuman ATP binding cassette,2338 99 trans otter rotein.

299 AAY87237 Homo SapiensHuman signal peptide containing110 30 protein HSPP-14 SEQ ID N0:14.

299 AAB87384 Homo SapiensHuman gene 43 encoded 110 30 secreted protein HSLGM81, SEQ ID N0:125.

299 AAB87410 Homo SapiensHuman gene 43 encoded 110 30 secreted protein HSYBM41, SEQ ID N0:151.

300 gi3874886CaenorhabditisC41C4.2 557 49 ele ans 300 113785612Mus musculussideroflexin 1 404 39 300 113543138Mus musculusRIKEN cDNA 2810002005 404 39 ene 301 g15114275Homo SapiensMAB21 L2 (MAB21 L2) gene,113 33 complete cds.

301 g19964007Homo SapiensMAB21L2 protein (MAB21L2)113 33 mRNA, com lete cds.

301 g114134002Homo sa MAB21L2 rotein mRNA, com 113 33 iens lete cds.

302 g17020704Homo sa cDNA FLJ20533 fis, clone 829 98 iens KAT10931.

302 g115030135Mus musculusRIKEN cDNA 1110020A09 777 60 ene 302 g15824484CaenorhabditisF32D8.Sb 111 25 ele ans 303 g110433539Homo SapienscDNA FLJ12133 fis, clone 319 30 MAMMA 1000278.

303 AAB93897 Homo SapiensHuman protein sequence 319 30 SEQ ID

N0:13 844.

303 AAW64461 Homo sa Human secreted rotein 313 30 iens from clone B 121.

304 g16841548Homo sa HSPC163 489 100 iens 304 g112653595Homo SapiensHSPC163 protein, clone 489 100 MGC:772 IMAGE:3163724, mRNA, com lete cds.

304 AAY91543 Homo SapiensHuman secreted protein 489 100 sequence encoded b ene 93 SEQ ID N0:216.

305 g14877582Homo Sapienslipoma HMGIC fusion partner222 28 (LHFP) mRNA, com lete cds.

305 AAY87336 Homo SapiensHuman signal peptide containing222 28 protein HSPP-113 SEQ ID N0:113.

305 AAW88508 Homo SapiensHuman stomach cancer clone94 26 encoded membrane rotein.

306 AAB87576 Homo sa Human PR03579. 1125 98 iens 306 g12315510Caenorhabditissimilar to 1-acyl-glycerol-3-phosphate501 4S

ele ans ac ltransferases 306 g13877657Caenorhabditiscontains similarity to 364 44 Pfam domain:

elegans PF01553 (Acyltransferase), Score=144.3, E-value=7.1e-40, N=1 307 AAY94954 Homo SapiensHuman secreted protein 596 68 clone 1w66-1 rotein se uence SEQ ID
N0:114.

307 g17259234Mus musculuscontains transmembrane _562 63 (TM region 307 AAB62810 Homo SapiensHuman nervous system associated536 60 protein ~ ~

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

NSPRT3 anuno acid se uence.

308 14580997 Mus musculusCAMP inducible 2 rotein 2377 87 308 g17543982Homo SapiensmRNA for glycerol 3-phosphate842 60 permease SLC37A1 ene).

308 g1 11095363Homo Sapiensglycerol 3-phosphate permease836 60 (SLC37A1 mRNA, com fete cds.

309 AAG71797 Homo SapiensHuman olfactory receptor 755 100 polypeptide, SEQ ID NO: 1478.

309 1 12007408Mus musculusB 1 olfacto rece for 625 79 309 112007420Mus musculusB5 olfactory rece for 609 82 310 g112803871Homo Sapiensclone MGC:4170 IMAGE:3618204,373 100 mRNA, com fete cds.

310 g13881055CaenorhabditisY48A6B.1 57 59 elegans 310 113398356Tricho ac 1-CoA delta-11 desaturase46 53 lusia pi 311 g1 1 I Homo Sapiensnicotinic acetylcholine 2370 100 128456 receptor subunit al ha 10 mRNA, com fete cds.

311 g113173184Homo Sapiensnicotinic acetylcholine 2370 100 receptor subunit al ha 10 (CHRNA I 0) gene, com fete cds.

311 g112053839Homo SapiensmRNA for neuronal nicotinic2370 100 acetylcholine alphal0 subunit (NACHRA 10 7ene).

312 g1 14328885Mus musculusspermatogenic immunoglobulin630 40 su erfamil rotein 312 g17767239Homo sapienspectin-like protein 2 628 41 (NECL2) mRNA, com fete cds.

312 114519602Homo sa IGSF4 ene, exon 10 and 625 40 iens com fete cds.

313 AAA40083 Homo SapiensHuman brain-specific transmembrane1637 54 aal 1 co rotein encodin cDNA.

313 AAB09968 Homo sapiensHuman brain-specific transmembrane1637 54 g1 co rotein.

313 AAB 12448Homo sa Human hh00149 rotein SEQ 1637 54 iens ID N0:4.

314 g114017379Homo Sapienstumor endothelial marker 2691 100 7 precursor TEM7 mRNA, com fete cds.

314 AAB31211 Homo SapiensAmino acid sequence of 1297 57 human of a tide PR06003.

314 AAW58986 Homo SapiensHomo Sapiens adult brain 560 99 clone CC194 4 encoded rotein.

315 g114017379Homo Sapienstumor endothelial marker 2592 97 7 precursor (TEM7) mRNA, com fete cds.

315 AAB31211 Homo SapiensAmino acid sequence of 1040 53 human of a tide PR06003.

315 AAW58986 Homo SapiensHomo Sapiens adult brain 461 87 clone CC194 4 encoded rotein.

316 AAG71567 Homo SapiensHuman olfactory receptor 1414 100 polypeptide, SEQ ID NO: 1248.

316 AAG71 Homo SapiensHuman olfactory receptor 726 52 S76 polypeptide, SEQ ID NO: 1257.

316 AAG72477 Homo SapiensHuman OR-like polypeptide726 52 query se uence, SEQ ID NO: 2158.

317 g114495648Homo Sapiensclone MGC:15606 IMAGE:3163718,2958 100 mRNA, com fete cds.

317 AAB74709 Homo SapiensHuman membrane associated338 31 protein MEMAP-15.

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

317 gi7020023Homo sa cDNA FLJ20127 fis, clone 149 29 iens COL06176.

318 AAB88430Homo SapiensHuman membrane or secretory2226 99 protein clone PSEC0205.

318 AAY44363Homo sa Human cell c cle regulation1827 100 iens rotein-4.

318 AAB08956Homo SapiensHuman secreted protein 1819 99 sequence encoded b ene 24 SEQ ID N0:113.

319 AAY19506Homo SapiensAmino acid sequence of 1120 100 a human secreted rotein.

319 gi 1 Homo SapiensL1M2 (LIM2) and natural 90 26 1 177546 killer group 7 (NKG7) enes, com lete cds.

319 gi13445660Homo SapiensMP19 (LIM2) mRNA, complete90 26 cds, alternativel s liced.

320 gi784990Homo sa H.sa iens DNA for 5-HTSA 1645 100 iens exonl.

320 gi6064324unidentifiedGENE DU RECEPTEUR 5HT5A 1611 98 HUMAIN

320 AAR45848Homo sa Human 5HT5a serotonin 1611 98 iens rece tor.

321 gi2695874Homo SapiensH.sapiens mRNA for P2Y-like175 28 G-protein cou led rece tor.

321 AAR53752Homo sa Seven transmembrane rece 175 28 iens for R12 .

321 AAW07617Homo sa Human G- rotein thrombin-like175 28 iens rece tor.

322 AAY25806Homo SapiensHuman secreted protein 1663 98 fragment encoded from gene 23.

322 gi5901846DrosophilaBcDNA.GH12144 627 43 melanogaster 322 AAB12140Homo SapiensHydrophobic domain protein353 36 isolated from WERI-RB cells.

323 110438949Homo sa cDNA: FLJ22529 fis, clone1290 100 iens HRC12842.

323 AAB 12119Homo SapiensHydrophobic domain protein448 100 from clone HP02869 isolated from KB cells.

323 g113384443Caenorhabditissimilar to 1-acyl-glycerol-3-phosphate294 26 ele ans acyltransferases 324 AAY25736Homo SapiensHuman secreted protein 343 100 encoded from ene 26.

324 g1 14530705CaenorhabditisSimilarity to C.elegans 75 36 UNC-7 protein elegans (SW:UNC7 CAEEL), contains similarity to Pfam domain: PF00876 (Innexin), Score=640.8, E-value=2.4e-189, N=1 324 g1142083Anabaena ribulose 1,5-bisphosphate63 41 Sp.

carbox lase/ox enase small subunit 325 AAB44336Homo SapiensHuman secreted protein 169 100 encoded by gene 2 clone HROAM11.

325 AAG03801Homo SapiensHuman secreted protein, 64 41 SEQ ID NO:

7882.

325 g16139004EchinococcusNADH dehydrogenasesubunit645 55 multilocularis 326 110566471Mus musculusGliacolin 1284 94 326 114278927Mus musculusliacolin 1284 94 326 13747097Homo sa C1 -related factor mRNA, 974 71 iens com fete cds.

327 113506225Mus musculusST7 rotein forml s lice 2996 99 variant a 327 g19230665Homo SapiensFAM4A1 splice variant 1761 96 a (FAM4A1) mRNA, com lete cds.

327 113506227Mus musculusST7 rotein forml s lice 1761 96 variant b 328 g19230665Homo SapiensFAM4A 1 splice variant 2496 97 a (FAM4A 1 ) mRNA, com lete cds.

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

328 113506227Mus musculusST7 rotein forml s lice 2489 96 variant b 328 113506225Mus musculusST7 rotein forml s lice 1366 92 variant a 329 g19230667Homo SapiensFAM4A1 splice variant 2862 97 b (FAM4A1) mRNA, com lete cds.

329 113506225Mus musculusST7 rotein forml s lice 2848 96 variant a 329 g19230665Homo sapiensFAM4A1 splice variant 1608 92 a (FAM4A1) mRNA, com lete cds.

330 g1292057Homo SapiensHuman EBV induced G-protein321 38 coupled rece for EBI2 mRNA, com lete cds.

330 AAR54080Homo SapiensEpstein Barr virus induced321 38 (EBI-2) of a tide.

330 AAW53623Homo sa E stein Ban virus induced321 38 iens ene 2 (EBI-2).

331 g110434308Homo SapienscDNA FLJ12672 fis, clone 3584 99 NT2RM4002339.

331 ~AAB94231Homo SapiensHuman protein sequence 3584 99 SEQ ID

N0:14604.

331 g110436632Homo SapienscDNA FLJ14225 fts, clone 3570 100 NT2RP3004051.

332 13462455Mus musculus'unctional adhesion molecule116 28 332 AAY23325Homo sa A33 related anti en JAM. 116 28 iens 332 g18650528Rattus functional adhesion molecule109 27 JAM

norve icus 333 g1 14250676Homo SapiensSimilar to RIKEN cDNA 1977 99 gene, clone MGC:10413 IMAGE:3954787, mRNA, com fete cds.

333 AAY27589Homo SapiensHuman secreted protein 1578 100 encoded by gene No. 23.

333 g112082328Arabidopsispara-hydroxy bezoate polyprenyl792 64 thaliana d1 hos hate transferase 334 g112655071Homo Sapienstransmembrane 4 superfamily859 98 member 4, clone MGC:1477 IMAGE:3051146, mRNA, com lete cds.

334 g1953239Homo SapiensHuman intestinal and liver859 98 tetraspan membrane protein (il-TMP) mRNA, com lete cds.

334 g1 11493837Rattus tetraspan protein LRTM4 791 85 norve icus 336 1 14336694Homo sa 16 13.3 se uence section 4100 99 iens 2 of 8.

336 g1 10716072Homo sa mRNA for M83 rotein, com 4089 99 iens fete cds.

336 110716074Mus musculusM83 rotein 3115 75 337 g1 1 Homo Sapienscorneal N-acetylglucosamine-6-O-2056 100 sulfotransferase (CHST6) mRNA, com lete cds.

337 g111023149Homo sapiensintestinal N-acetylglucosamine-6-O-2056 100 sulfotransferase (CHSTS) and corneal N-acetylglucosamine-6-O-sulfotransferase CHST6) enes, com lete cds.

337 g1 12060804Homo sapiensN-acetylglucosamine 6-O-sulfotransferase2056 100 GST-4beta mRNA, com lete cds.

338 AAG71850Homo sapiensHuman olfactory receptor 1142 71 polypeptide, SEQ ID NO: 1531.

338 AAG71809Homo SapiensHuman olfactory receptor 1049 74 polypeptide, SEQ ID NO: 1490.

~38 AAG71818Homo sapiensHuman olfactory receptor 1014 68 ~ polypeptide, Table 2A
SEQ AccessionSpecies Description Score/a ID No. Identity NO:

SEQ ID NO: 1499.

339 AAG71850Homo SapiensHuman olfactory receptor 1128 71 polypeptide, SEQ ID NO: 1531.

339 AAG71809Homo SapiensHuman olfactory receptor 1035 74 polypeptide, SEQ ID NO: 1490.

339 AAG71818Homo SapiensHuman olfactory receptor 1014 68 polypeptide, SEQ ID NO: 1499.

340 gi7960136Homo sapiensneuroligin 3 isoform gene,4557 100 complete cds, alternative) s )iced.

340 gi1145791Rattus neuroligin 3 4505 98 norvegicus 340 gi7960135Homo sapiensneuroligin 3 isoform gene,3623 96 complete cds, alternative) s )iced.

341 gi5525078Rattus seven transmembrane receptor788 31 norve icus 341 AAY57288Homo SapiensHuman GPCR protein (HGPRP)752 29 sequence clone ID 3036563 .

341 AAY40440Homo SapiensHuman brain-derived G-protein746 29 coupled rece for rotein.

342 AAG71424Homo SapiensHuman olfactory receptor 853 88 polypeptide, SEQ ID NO: 1105.

342 AAG72315Homo SapiensHuman olfactory receptor 915 96 polypeptide, SEQ ID NO: 1996.

342 AAG71431Homo SapiensHuman olfactory receptor 595 60 polypeptide, SEQ ID NO: 1112.

343 gi10434098Homo SapienscDNA FLJ12547 fis, clone 1612 84 NT2RM4000634.

343 AAB95124Homo SapiensHuman protein sequence 1612 84 SEQ ID

N0:17122.

343 gi854065Human U88 809 52 he esvirus 344 AAG71823Homo SapiensHuman olfactory receptor 1627 100 polypeptide, SEQ ID NO: 1504.

344 AAG71859Homo SapiensHuman olfactory receptor 1085 67 polypeptide, SEQ ID NO: 1540.

344 AAG72185Homo SapiensHuman olfactory receptor 980 60 polypeptide, SEQ ID NO: 1866.

345 AAY91625Homo SapiensHuman secreted protein 1968 94 sequence encoded b ene 22 SEQ ID N0:298.

345 AAU00437Homo SapiensHuman dendritic cell membrane1925 78 protein FIRE.

345 AAY59300Homo sa Human EGPCR of a tide. 1174 57 iens 346 AAY91625Homo SapiensHuman secreted protein 1968 94 sequence encoded b ene 22 SEQ ID N0:298.

346 AAU00437Homo SapiensHuman dendritic cell membrane1925 78 protein FIRE.

346 AAY59300Homo sa Human EGPCR of a tide. 1174 57 iens 347 ~i4098462Sus scrofaluteinizin hormone beta 41 53 subunit 347 gi 12232003CercopagisNADH dehydrogenase subunit81 32 en of 348 AAW74874Homo SapiensHuman secreted protein 349 100 encoded by gene 146 clone HSNAK17.

348 gi3329179Chlamydia Phosphoglycerate Mutase 68 33 trachomatis Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

348 gi9105100Xylella transport protein 68 46 fastidiosa 9a5c 349 AAY04301Homo SapiensHuman secreted protein 82 33 encoded by gene 9.

349 gi15004512Podophyllumsuccinate dehydrogenase 79 32 subunit 3 eltatum 349 gi841378SaccharomyceGpi2p 90 34 s cerevisiae 350 AAB88406Homo SapiensHuman membrane or secretory1421 99 protein clone PSEC0162.

350 AAW88579Homo SapiensSecreted protein encoded 479 9S
by gene 46 clone HCFMV39.

350 AAY4111 Homo sapiensHuman TANGO 129 (T129) 225 35 1 mature rotein.

351 gi292793Homo Sapiens(clone HBVT72) T cell 636 98 receptor beta chain (TCRB) mRNA, VDJC region, artial cds.

351 gi457274Homo SapiensHuman T-cell receptor 479 98 beta chain gene, V

region, artial cds.

351 gi495428Macaca T cell receptor beta chain477 85 mulatta 352 AAY10839Homo SapiensAmino acid sequence of 225 95 a human secreted rotein.

352 gi15163613AgrobacteriumAGR-pTi 226p 66 40 tumefaciens 352 gi903711Daucus c ochrome oxidase II 59 36 carota 353 AAY16784Homo sa Human secreted rotein 488 100 iens clone co1000 1).

353 gi1850866Macropus ATPase subunit 8 68 31 robustus 353 AAY41439Homo sapiensFragment of human secreted63 43 protein encoded b ene 24.

354 gi6573749ArabidopsisF20B24.9 58 38 thaliana 354 gi325236Influenza nb 61 34 B

virus 354 AAR1 Homo sa Human IL-4 rece tor. 60 52 1254 iens 355 gi 12652903Homo Sapiensclone MGC:3103 IMAGE:3350518,1704 100 mRNA, com lete cds.

355 AAA40083Homo SapiensHuman brain-specific transmembrane1019 43 aal g1 co rotein encodin cDNA.

355 AAB09968Homo SapiensHuman brain-specific transmembrane1019 43 1 co rotein.

356 110439087Homo sa cDNA: FLJ22625 fis, clone1792 100 iens HSI06009.

356 AAY41389Homo sapiensHuman secreted protein 1555 94 encoded by gene 82 clone HOUHHS 1.

356 AAY41747Homo sa Human PR0534 rotein se 1555 94 iens uence.

358 g113676372Homo sapiensclone MGC:4595 IMAGE:3345729,1886 98 mRNA, com fete cds.

358 AAY41690Homo sa Human PR0329 rotein se 1886 98 iens uence.

358 AAB44246Homo SapiensHuman PR0329 (UNQ291) 1886 98 protein se uence SEQ ID N0:45.

359 g113676372Homo Sapiensclone MGC:4595 IMAGE:3345729,1905 99 mRNA, com lete cds.

359 AAY41690Homo sa Human PR0329 rotein se 1905 99 iens uence.

359 AAB44246Homo sa Human PR0329 UN 291 rotein1905 99 iens Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

se uence SEQ ID N0:45.

360 AAW74807Homo SapiensHuman secreted protein 270 100 encoded by gene 79 clone HSKNE46.

360 12145070Mus musculusml7r s lice variant 49 46 360 AAB34697Homo SapiensHuman secreted protein 66 45 encoded by DNA

clone v 6 1.

361 16959684Mus musculus1 coli id transfer rotein103 26 361 g114041214Human EBNA-LP protein 76 36 he esvirus 361 g16959686Homo Sapiensglycolipid transfer protein93 24 mRNA, com fete cds.

362 g113623231Homo SapiensSimilar to RIKEN cDNA 2337 100 gene, clone MGC:3047 IMAGE:3343261, mRNA, com lete cds.

362 g114041843Homo SapienscDNA FLJ14363 fis, clone 2270 98 HEMBA 1000719.

362 AAB92464Homo SapiensHuman protein sequence 2270 98 SEQ ID

N0:10520.

363 g110438446Homo sa cDNA: FLJ22167 fis, clone1644 100 iens HRC00584.

364 g1 12053067Homo SapiensmRNA; cDNA DKFZp434I2117 1237 100 (from clone DKFZ 434I2117).

364 110438603Homo sa cDNA: FLJ22282 fis, clone649 48 iens HRC03861.

364 AAB24463Homo SapiensHuman secreted protein 649 48 sequence encoded b ene 27 SEQ ID N0:88.

365 1 12483888Homo sa solute carrier 19A3 mRNA,2549 100 iens com lete cds.

365 g114582572Homo Sapiensorphan transporter SLC19A32549 100 (SLC19A3) mRNA, com lete cds.

365 112483890Mus musculussolute carrier 19A3 1716 68 366 AAB74721Homo SapiensHuman membrane associated558 100 protein MEMAP-27.

366 AAG03412Homo SapiensHuman secreted protein, 464 100 SEQ ID NO:

7493.

366 g14929751Homo sa CGI-141 rotein mRNA, com 406 55 iens lete cds.

367 g110434145Homo sapienscDNA FLJ12576 fis, clone 2598 100 NT2RM4001032.

367 g112803561Homo Sapiensclone MGC:2991 IMAGE:3160297,2598 100 mRNA, com lete cds.

367 AAB94138Homo SapiensHuman protein sequence 2598 100 SEQ ID

N0:14406.

368 g14519535Homo sapiensCYP4F2 gene for leukotoriene1227 65 B4 omega h drox lase, exon 13.

368 g1 1857022Homo SapiensHuman mRNA for leukotriene1227 65 B4 omega-h drox lase, com lete cds.

368 110303605Homo sa CYP4F11 mRNA, com lete 1219 64 iens cds.

369 1 10438815Homo sa cDNA: FLJ22427 fis, clone4518 100 iens HRC09013.

369 g1 15076843Homo Sapienspecanex-like protein 1 762 44 mRNA, complete cds.

369 g113171105Takifugu pecanex 578 42 rubri es 370 g112656635Homo Sapienstransmembrane gamma-carboxyglutamic1201 100 acid protein 4 TMG4 mRNA, complete cds.

370 g114603178Homo sapienstransmembrane gamma-carboxyglutamic1201 100 acid rotein 4, clone MGC:19793 Table 2A
SEQ AccessionSpecies Description Score/a ID No. Identity NO:

IMAGE:3841745, mRNA, com fete cds.

370 AAB61219Homo sa Human TANGO 292 rotein. 1201 100 iens 371 gi7689031Homo Sapiensuncharacterized hypothalamus1847 100 protein HARP11 mRNA, com lete cds.

371 gi15080516Homo SapiensSimilar to uncharacterized1847 100 hypothalamus protein HARP11, clone MGC:9273 IMAGE:3862712, mRNA, com fete cds.

371 AAY53029Homo SapiensHuman secreted protein 1847 100 clone cw1640-1 rotein se uence SEQ ID
N0:64.

372 gi 10440079Homo sa cDNA: FLJ23403 fis, clone2817 100 iens HEP 18857.

372 AAY53635Homo sapiensA bone marrow secreted 758 50 protein desi nated BMS53.

372 gi10439735Homo sa cDNA: FLJ23144 fis, clone771 100 iens LNG09262.

373 gi7023450Homo sapienscDNA FLJ11036 fis, clone 980 87 PLACE 1004289.

373 AAB93444Homo SapiensHuman protein sequence 980 87 SEQ ID

N0:12686.

373 gi1199697Athalia vitello enin 107 42 rosae 374 gi13447851Macaca killer immunoglobulin-like77 31 receptor mulatta KIR3DL7 374 gi190203Homo SapiensHuman cardiac potassium 83 33 channel (KCNAS) mRNA, com fete cds.

374 gi308765Homo SapiensHuman voltage-gated potassium82 35 channel (HK2 mRNA, com lete cds.

375 gi5542014Homo sa DKC1 ene, exons 1 to 11. 1574 99 iens 375 13873221Homo sa d skerin (DKC1) mRNA, 1574 99 iens com lete cds.

375 g114603090Homo Sapiensdyskeratosis congenita 1574 99 1, dyskerin, clone MGC:15313 IMAGE:4303933, mRNA, com lete cds.

376 15542014Homo sa DKC1 gene, exons 1 to 2399 95 iens 11.

376 13873221Homo sa d skerin (DKCI) mRNA, 2326 94 iens com lete cds.

376 g114603090Homo Sapiensdyskeratosis congenita 2326 94 l, dyskerin, clone MGC:15313 IMAGE:4303933, mRNA, com lete cds.

377 g1 12653555Homo Sapienslysophospholipase-like, 907 100 clone MGC:1216 IMAGE:3163689, mRNA, com lete cds.

377 g1 13623261Homo Sapienslysophospholipase-like, 907 100 clone MGC:10338 IMAGE:3945191, mRNA, com lete cds.

377 g11763011Homo sapiensHuman lysophospholipase 907 100 homolog (HU-K5 mRNA, com lete cds.

378 g112653555Homo Sapienslysophospholipase-like, 903 100 clone MGC:1216 IMAGE:3163689, mRNA, com lete cds.

378 g113623261Homo Sapienslysophospholipase-like, 903 100 clone MGC:10338 IMAGE:3945191, mRNA, com lete cds.

378 g11763011Homo SapiensHuman lysophospholipase 903 100 homolog (HU-K5) mRNA, com fete cds.

379 AAY94946Homo SapiensHuman secreted protein 571 93 clone cd205 2 rotein se uence SEQ ID
N0:98.

379 AAY53051Homo SapiensHuman secreted protein 324 63 clone dd119_4 rotein se uence SEQ ID
N0:108.

379 g14097381Heteractispotassium channel toxin 61 41 HmK

ma nifica Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

380 gi6523817Homo sa S1R rotein S1R mRNA, com 928 93 iens lete cds.

380 gi4929707Homo sa CGI-119 rotein mRNA, com 928 93 iens lete cds.

380 AAY77122 Homo SapiensHuman neurotransmission-associated928 93 rotein NTAP) 414692.

381 16739575 Mus musculusTBX2 rotein 696 80 381 16980032 Mus musculusARL-6 interactin rotein-1696 80 381 AAB54057 Homo SapiensHuman pancreatic cancer 70 28 antigen protein se uence SEQ ID N0:509.

382 g113432057Homo sa NYD-TSPG mRNA, com lete 206 25 iens cds.

382 AAB95759 Homo SapiensHuman protein sequence 142 29 SEQ ID

N0:18680.

382 g114550463Homo SapiensDKFZP434B103 protein, 106 32 clone MGC:15207 IMAGE:3841498, mRNA, com lete cds.

383 AAY48312 Homo SapiensHuman prostate cancer-associated1509 100 protein 9.

383 g1 12654077Homo Sapiensclone IMAGE:3458173, mRNA,1191 100 partial cds.

383 AAY73387 Homo sa HTRM clone 3340290 rotein763 82 iens se uence.

384 g114042559Homo SapienscDNA FLJ14784 fis, clone 2492 100 NT2RP4000713.

384 AAB93185 Homo SapiensHuman protein sequence 2492 100 SEQ ID

N0:12134.

384 AAB56514 Homo SapiensHuman prostate cancer 765 98 antigen protein se uence SEQ ID N0:1092.

385 g112044473Homo SapiensmRNA; cDNA DKFZp761D0211 2875 100 (from clone DKFZ 761 D0211 ).

385 g114336686Homo sa 16 13.3 se uence section 2786 98 iens 1 of 8.

385 AAB58984 Homo SapiensBreast and ovarian cancer759 94 associated anti en rotein se uence SEQ ID 692.

386 g114336686Homo sa 16 13.3 se uence section 2811 100 iens 1 of 8.

386 g112044473Homo sapiensmRNA; cDNA DKFZp761D0211 2799 98 (from clone DKFZ 761D0211).

386 AAB58984 Homo SapiensBreast and ovarian cancer683 89 associated anti en rotein se uence SEQ ID 692.

387 g13879783CaenorhabditisSimilarity to Salmonella 281 53 regulatory protein ele ans UHPC SW:UHPC SALTY) 387 g17268507Arabidopsisglycerol-3-phosphate permease207 44 like thaliana rotein 387 AAB39202 Homo SapiensHuman secreted protein 194 38 sequence encoded b ene 24 SEQ ID N0:82.

388 g114860862Homo Sapienspolyamine oxidase isoform-1638 52 mRNA, com lete cds.

388 17021037 Homo sa cDNA FLJ20746 fis, clone 637 52 iens HEP06040.

388 AAB 12164Homo SapiensHydrophobic domain protein637 52 from clone HP10673 isolated from Th us cells.

389 g15911897Homo sapiensmRNA; cDNA DKFZpS86B 14176467 96 (from clone DKFZ 586B1417 ;
artial cds.

389 g114424668Homo Sapiensclone MGC:14927 IMAGE:4298580,4267 94 mRNA, com lete cds.

389 110438036Homo sa cDNA: FLJ21846 fis, clone4259 94 iens HEP01887.

390 g113529623Mus musculusSimilar to RIKEN cDNA 1408 81 ene 390 g15656743Homo sa BAC clone CTB-122E10 from105 25 iens 7 11.23-Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

21.1, com lete se uence.

390 AAB58323Homo sapiensLung cancer associated 105 25 polypeptide se uence SEQ ID 661.

391 gi14603247Homo SapiensSimilar to RIKEN cDNA 754 96 gene, clone MGC:19636 IMAGE:2822323, mRNA, com lete cds.

391 AAB36613Homo SapiensHuman FLEXHT-35 protein 754 96 sequence SEQ ID N0:35.

391 gi7022832Homo SapienscDNA FLJ10661 fis, clone 240 90 NT2RP2006106.

392 110439204Homo sa cDNA: FLJ22709 fis, clone304 39 iens HSI13338.

392 AAB56085Homo SapiensHuman secreted protein 304 39 sequence encoded b gene 9 SEQ ID N0:179.

392 g17407643Canis occludin 1B 177 32 familiaris 393 AAB 18993Homo SapiensAmino acid sequence of 1212 70 a human transmembrane rotein.

393 g115079979Homo SapiensSimilar to RIKEN cDNA 1211 70 gene, clone MGC:19609 IMAGE:3640970, mRNA, com lete cds.

393 g113111831Homo Sapiensclone IMAGE:3451448, mRNA,980 68 partial cds.

394 AAY59713Homo sa Secreted rotein 76-20-3-H1-FL1.865 92 iens 394 g14220892Homo Sapienstranscriptional co-activator920 95 (CRSP34) mRNA, com lete cds.

394 g17141322Homo Sapiensp37 TRAP/SMCC/PC2 subunit919 95 mRNA, com lete cds.

395 g13880799CaenorhabditisY39A 1 B.2 837 33 elegans 395 g1 1707052Caenorhabditissimilar to drosophilia 616 35 and mouse patched ele ans roteins 395 g1861251Caenorhabditisweakly similar to C. elegans475 31 protein elegans F54G8.5 and to C. elegans protein F44F4.4 396 g1765240human, hPPAR alpha ~eroxisome 2011 99 liver, proliferator mRNA, 1731activated receptor alpha nt]. [Homo sa iens 396 AAR74053Homo SapiensHuman peroxisome proliferator2011 99 activated rece tor.

396 AAB20342Homo SapiensPeroxisome proliferator-activated2011 99 receptor al ha.

397 AAB43983Homo SapiensHuman cancer associated 1692 100 protein sequence SEQ ID N0:1428.

397 AAA88691Homo SapiensHuman transmembrane protein1410 100 aal NPCAHHO1 cDNA.

397 g15565977Homo Sapienstransmembrane protein 1409 100 BRI (BRI) mRNA, com lete cds.

398 g14894991Drosophilasodium-hydrogen exchangerNHEI1362 61 melano aster 398 g13979941Caenorhabditiscontains similarity to 1059 46 Pfam domain:

elegans PF00999 (Sodium/hydrogen exchanger family), Score=354.0, E-value=5.3e-103, N=1 Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

398 gi14150471Homo sapiensnonselective sodium potassium/proton679 40 exchan er (NHE7 mRNA, com lete cds.

399 gi7023154Homo SapienscDNA FLJ10856 fis, clone 1617 99 NT2RP4001547.

399 AAY28810Homo sa nn296 2 secreted rotein. 1617 99 iens 399 AAB93258Homo SapiensHuman protein sequence 1617 99 SEQ ID

N0:12282.

400 AAG00388Homo SapiensHuman secreted protein, 316 100 SEQ ID NO:

4469.

400 gi 11967794Echinops NADH dehydrogenase subunit61 29 telfairi 400 gi321 Homo Sapienssarco-/endoplasmic reticulum54 39 1979 Ca-ATPase 3 (ATP2A3) mRNA, alternatively spliced, artial cds.

401 gi14043649Homo Sapiensclone MGC:14161 IMAGE:4111078,253 33 mRNA, com lete cds.

401 gi2623016Methanothermheterodisulfide reductase,88 30 subunit C

obacter thermautotrop hicus 401 gi4262178Arabidopsis25726 87 28 thaliana 402 gi6164616Homo SapiensF-box protein Fbl3b (FBL3B)128 26 mRNA, artial cds.

402 AAY83075Homo sa F-box rotein FBP-3b. 128 26 iens 402 AAY83043Homo sa F-box rotein FBP-3. 109 23 iens 403 AAB98207Homo sa Human P24 rotein-22 SEQ 1009 99 iens ID N0:2.

403 gi1890141Mus musculusP24 rotein 940 91 403 110439977Homo sa cDNA: FLJ23329 fis, clone274 38 iens HEP12646.

404 g113276693Homo SapiensmRNA; cDNA DKFZp761F069 807 70 (from clone DKFZ 761F069); com lete cds.

404 g17020303Homo sa cDNA FLJ20300 fis, clone 539 39 iens HEP06465.

404 AAB67575Homo SapiensAmino acid sequence of 435 33 a human h drol tic enz me HYENZ7.

405 g13878748CaenorhabditisM 176.4 98 24 ele ans 405 g17542459TaeniopygiaSWS1 opsin 92 29 =uttata 405 AAB76874Homo SapiensHuman lung tumour protein65 51 related rotein se uence SEQ ID
N0:799.

406 g13880799CaenorhabditisY39A1B.2 634 25 ele ans 406 g1861251Caenorhabditisweakly similar to C. elegans261 24 protein elegans F54G8.5 and to C. elegans protein F44F4.4 406 g11255388Caenorhabditissimilar to drosophila 255 26 membrane protein ele ans PATCHED SP: P 18502) 407 g114603058Homo Sapiensclone IMAGE:4134852, mRNA,1067 100 partial cds.

407 g11016178CyanophoraPsaE 53 32 aradoxa 407 g112724543LactococcusUNKNOWN PROTEIN 78 43 lactis Subsp.

lactis Table 2A
SEQ AccessionSpecies Description Score/.

ID No. Identity NO:

408 AAB 12150Homo SapiensHydrophobic domain protein952 100 isolated from HT-1080 cells.

408 gi13096862Mus musculusRIKEN cDNA 9430096L06 845 88 ene 408 AAB29651Homo SapiensHuman membrane-associated502 100 protein HUMAP-8.

409 gi15074997SinorhizobiumCONSERVED HYPOTHETICAL 98 32 meliloti PROTEIN

409 AAG73357Homo SapiensHuman gene 12-encoded 57 35 secreted protein HBXAM53, SEQ ID N0:128.

409 AAG73405Homo SapiensHuman gene 12-encoded 57 35 secreted protein HBXAM53, SEQ ID N0:176.

410 gi1669689Homo sa H.sa iens TAFII105 mRNA, 3902 98 iens artial.

410 AAW31494Homo sa Human hTAFII105 rotein. 3902 98 iens 410 AAY57279Homo SapiensTranscription factor subunit3902 98 of a tide.

411 AAG71672Homo SapiensHuman olfactory receptor 1202 94 polypeptide, SEQ ID NO: 1353.

411 AAG72062Homo SapiensHuman olfactory receptor 1068 66 polypeptide, SEQ ID NO: 1743.

411 AAG71847Homo SapiensHuman olfactory receptor 1051 67 polypeptide, SEQ ID NO: 1528.

412 AAY 16630Homo SapiensHuman Putative Adrenomedullin1592 99 Receptor (PAR .

412 gi292419Homo SapiensHuman homologue of the 1580 98 canine orphan rece for (RDC 1 ) mRNA, 5' end.

412 gi899 Canis RDC1 receptor (AA 1-362) 1503 92 familiaris 413 AAY95002Homo SapiensHuman secreted protein 98S 71 vc34-1, SEQ ID

N0:44.

413 gi14550480Homo sapiensclone MGC:16377 IMAGE:3936171,917 97 mRNA, com fete cds.

413 gi7020918Homo sa cDNA FLJ20668 fis, clone 179 37 iens KAIA585.

414 AAB56877Homo SapiensHuman prostate cancer 1004 98 antigen protein se uence SEQ ID N0:1455.

414 gi13991373HymenolepisNADH dehydrogenase subunit4L62 38 diminuta 414 gi 14487711Hepatitis polyprotein 62 50 C

virus 415 gi179165Homo SapiensHuman Na,K-ATPase subunit5238 99 alpha 2 (ATP1A2) ene, com lete cds.

415 gi203029Rattus (Na+ and K+) ATPase, alpha+5205 98 catalytic norve icussubunit recursor 415 1212406 Gallus Na,K-ATPase al ha-2-subunit4977 93 anus 416 AAB90649Homo sa Human secreted rotein, 563 92 iens SEQ ID NO: 192.

416 AAB90565Homo sa Human secreted rotein, 472 100 iens SEQ ID NO: 103.

416 AAB90651Homo sa Human secreted rotein, 203 97 iens SEQ ID NO: 194.

417 g16599290Homo SapiensmRNA; cDNA DKFZp586C1021 81 25 (from clone DKFZ 586C1021 ;
artial cds.

417 g17190652Chlamydia phosphoenolpyruvate-protein89 21 muridarum hos hotransferase 417 g1 14700035Aspergillusnuclear transport factor 76 37 nidulans 418 g113249295Homo Sapiensanion exchanger AE4 mRNA,4951 100 complete cds.

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

418 gi 13517508Homo Sapienssodium bicarbonate cotransporter4493 95 (SLC4A9) mRNA, artial cds.

418 gi 11611537Oryctolagusanion exchanger 4a 4231 85 cuniculus 419 gi2564913Homo Sapiensclk2 kinase (CLK2), propinl,1109 82 cotel, glucocerebrosidase (GBA), and metaxin genes, complete cds; metaxin pseudogene and glucocerebrosidase pseudogene;and thrombospondin3 (THBS3) gene, partial cds.

419 gi1326108Homo SapiensHuman metaxin (MTX) gene,1109 82 complete cds.

419 gi12804907Homo SapiensSimilar to metaxin 1, 1100 99 clone MGC:2518 IMAGE:3546178, mRNA, com lete cds.

420 gi2564913Homo Sapiensclk2 kinase (CLK2), propinl,1665 100 cotel, glucocerebrosidase (GBA), and metaxin genes, complete cds; metaxin pseudogene and glucocerebrosidase pseudogene;and thrombospondin3 (THBS3) gene, partial cds.

420 gi1326108Homo SapiensHuman metaxin (MTX) gene,1665 100 complete cds.

420' gi807670 Mus musculusmetaxin 1519 91 421 gi6094684Homo SapiensPAC clone RP1-278D'1 from580 30 X, complete se uence.

421 gi7023516Homo SapienscDNA FLJ11078 fis, clone 547 30 PLACE1005102, weakly similar to RING

CANAL PROTEIN.

421 AAB93480 Homo SapiensHuman protein sequence 547 30 SEQ ID

N0:12768.

422 gi14715068Homo SapiensSimilar to RIKEN cDNA 2062 100 gene, clone MGC:9907 IMAGE:3870073, mRNA, com lete cds.

422 gi3342906Homo Sapiens2-amino-3-ketobutyrate-CoA853 89 ligase mRNA, nuclear gene encoding mitochondria) rotein, com lete cds.

422 gi4093159Mus musculus2-amino-3-ketobutyrate-coenzyme834 87 A

1i ase 423 AAB24058 Homo SapiensHuman PR0290 protein sequence1972 100 SEQ ID

N0:7.

423 AAY66639 Homo sa Membrane-bound rotein 1972 100 iens PR0290.

423 AAB65162 Homo sapiensHuman PR0290 (UNQ253) 1972 100 protein se uence SEQ ID N0:33.

424 gi167835 Dictyosteliummyosin heavy chain 152 24 discoideum 424 gi14042847Homo SapienscDNA FLJ14957 fis, clone 135 26 PLACE4000009, weakly similar to MYOSIN HEAVY CHAIN, NONMUSCLE TYPE B.

424 AAB95546 Homo SapiensHuman protein sequence 135 26 SEQ ID

N0:18167.

425 AAB43587 Homo SapiensHuman cancer associated 427 100 protein sequence SEQ ID N0:1032.

425 AAG00658 Homo sapiensHuman secreted protein, 360 97 I SEQ ID NO: ~ ~

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

4739.

425 AAG00657Homo SapiensHuman secreted protein, 243 72 SEQ ID NO:

4738.

426 gi13325388Homo SapiensSimilar to RIKEN cDNA 535 99 gene, clone MGC:11115 IMAGE:3833318, mRNA, com lete cds.

426 AAB93133Homo SapiensHuman protein sequence 77 30 SEQ ID

N0:12027.

427 gi7023138Homo SapienscDNA FLJ10847 fis, clone 731 49 NT2RP4001379.

427 AAB93249Homo SapiensHuman protein sequence 731 49 N0:12263.

427 AAB 18977Homo SapiensAmino acid sequence of 616 89 a human transmembrane rotein.

428 AAB 18977Homo SapiensAmino acid sequence of 1008 100 a human transmembrane rotein.

428 gi7023138Homo sapienscDNA FLJ10847 fis, clone 765 43 NT2RP4001379.

428 AAB93249Homo SapiensHuman protein sequence 765 43 SEQ ID

N0:12263.

429 AAG03349Homo SapiensHuman secreted protein, 59 28 SEQ ID NO:

7430.

429 gi12620543BradyrhizobiuID263 63 30 m 'a onicum 429 AAY20368Homo SapiensHuman microtubule associated53 40 protein 2 mutant fra ment 64.

430 gi7209839Homo SapiensmRNA for casein kinase 1564 99 I epsilon, com lete cds.

430 gi13676318Homo Sapienscasein kinase 1, epsilon,1564 99 clone MGC:10398 IMAGE:3937782, mRNA, com lete cds.

430 gi852057Homo sapienscasein kinase I epsilon 1564 99 mRNA, complete cds.

431 gi2642187Rattus endo-alpha-D-mannosidase 1973 87 norvegicus 431 gi10434559Homo SapienscDNA FLJ12838 fis, clone 1559 99 NT2RP2003230, moderately similar to Rattus norvegicus endo-alpha-D-mannosidase Enman mRNA.

431 AAB95204Homo SapiensHuman protein sequence 1559 99 SEQ ID

N0:17303.

432 gi12044469Homo sapiensmRNA; cDNA DKFZp761H1710 141 37 (from clone DKFZ 761H1710 ;
com lete cds.

432 115079305Mus musculusRIKEN cDNA 9130020610 126 37 ene 432 g16599277Homo SapiensmRNA; cDNA DKFZp434E1818 114 41 (from clone DKFZ 434E1818);
artial cds.

433 g112803977Homo Sapiensclone MGC:4175 IMAGE:3634983,611 100 mRNA, com lete cds.

433 AAB34781Homo SapiensHuman secreted protein 58 39 sequence encoded b gene 9 SEQ ID N0:69.

433 AAW39938Homo SapiensPeptide effecting G-protein-coupled57 37 rece for activit .

434 g12150013Homo Sapienstransmembrane protein 1159 100 mRNA, complete cds.

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

434 gi12803197Homo Sapiensclaudin 5 (transmembrane 1159 100 protein deleted in velocardiofacial syndrome), clone MGC:8543 IMAGE:2822745, mRNA, com fete cds.

434 AAY91533Homo SapiensHuman secreted protein 1159 100 sequence encoded b ene 83 SEQ ID N0:206.

435 gi15082442Homo Sapiensclone MGC:20235 IMAGE:4562851,1368 100 mRNA, com lete cds.

435 gi7023829Homo SapienscDNA FLJ11273 fis, clone 503 42 PLACE 1009338.

435 AAB93645Homo SapiensHuman protein sequence 503 42 SEQ ID

N0:13146.

436 gi11640570Homo sa MSTP031 mRNA, com lete 777 100 iens cds.

436 AAY91516Homo SapiensHuman secreted protein 70 44 sequence encoded b ene 66 SEQ ID N0:189.

436 AAY91657Homo SapiensHuman secreted protein 70 44 sequence encoded b ene 66 SEQ ID N0:330.

437 AAG73464Homo SapiensHuman gene 7-encoded secreted2267 98 protein fra ment, SEQ ID N0:239.

437 AAG73462Homo SapiensHuman gene 7-encoded secreted1898 99 protein fragment, SEQ ID N0:237.

437 AAG73463Homo SapiensHuman gene 7-encoded secreted1881 98 protein fra ment, SEQ ID N0:238.

438 gi9886738Homo SapiensJP3 mRNA for junctophilin3916 99 type3, com lete cds.

438 gi9927307Mus musculus'uncto hilin t a 3 3549 90 438 gi9886757Homo SapiensJP3 gene for junctophilin3172 100 type3, exon 5 and artial cds.

439 AAB08894Homo SapiensHuman secreted protein 240 64 sequence encoded b ene 4 SEQ ID N0:51.

439 gi7414441porcine envelope protein 147 28 endogenous retrovirus 439 gi348952Rat leukemiaenvelope protein 145 26 virus 440 gi13623369Homo Sapiensclone IMAGE:3957135, mRNA,2617 100 partial cds.

440 AAB43484Homo SapiensHuman cancer associated 761 100 protein sequence SEQ ID N0:929.

440 gi14247685Staphylococcunicotinate phosphoribosyltransferase370 40 s aureus homolog subsp.

aureus Mu50 441 gi13623369Homo Sapiensclone IMAGE:3957135, mRNA,2077 94 partial cds.

441 AAB43484Homo SapiensHuman cancer associated 761 100 protein sequence SEQ ID N0:929.

441 gi14247685Staphylococcunicotinate phosphoribosyltransferase370 40 s aureus homolog subsp.

aureus Mu50 442 gi13623369Homo Sapiensclone IMAGE:3957135, mRNA,2517 97 partial cds.

442 AAB43484Homo SapiensHuman cancer associated 761 100 protein sequence SE ID N0:929.

442 gi14247685Sta h lococcunicotinate hos horibos 370 40 ltransferase Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

s aureus homolog subsp.

aureus Mu50 443 gi 13182757Homo sa HTPAP mRNA, com lete cds.639 65 iens 443 AAB70690Homo SapiensHuman hDPP protein sequence639 65 SEQ ID

N0:7.

443 gi14020949Arabidopsisphosphatidic acid phosphatase460 39 thaliana 444 gi 10436254Homo SapienscDNA FLJ 13948 fis, clone529 41 Y79AA 1001023.

444 AAB94837Homo SapiensHuman protein sequence 529 41 SEQ ID

N0:16006.

444 gi7022187Homo SapienscDNA FLJ 10261 fis, clone521 42 HEMBB 1000975.

445 gi1403547SaccharomyceP2558 protein 162 26 s cerevisiae 445 gi2621070Methanothermribosomal protein S18 79 33 (E.coli S13) obacter thermautotrop hicus 445 gi4097361Human nucleocapsid protein 59 30 parainfluenza virus 1 446 gi15157363AgrobacteriumAGR C 4025p 259 32 tumefaciens 446 gi15075368SinorhizobiumCONSERVED HYPOTHETICAL 251 31 meliloti PROTEIN

446 gi15024663ClostridiumUncharacterized protein, 198 28 YfiH family acetobutylicu m 447 gi12584947Homo Sapiensovary-specific acidic 1195 100 protein mRNA, com lete cds.

447 gi632549PetromyzonNF-180 152 30 marinus 447 gi4678807Homo SapiensHuman gene from PAC 179D3,140 32 chromosome X, isoform of mitochondrial apoptosis inducing factor, AIF, AF 100928.

448 AAX23994Homo SapiensHuman CAR receptor DNA. 1495 99 aal 448 gi458542Homo SapiensH.sapiens mRNA for orphan1494 99 nuclear hormone rece tor.

448 AAR41346Homo sa Human CAR rece for of 1494 99 iens a tide.

449 gi14625447Rattus MT-protocadherin 2566 83 norve icus 449 AAB 12154Homo SapiensHydrophobic domain protein895 100 isolated from WERI-RB cells.

449 gi 13537202Homo SapiensPC-LKC mRNA for protocadherin445 31 LKC, com lete cds.

450 110880797Mus musculusS ne-lA 124 27 450 g15262574Homo SapiensmRNA; cDNA DKFZp434G 173 108 26 (from clone DKFZ 4346173); com lete cds.

450 1 10880799Mus musculusS ne-1 B 124 27 451 g1 11967375Rattus Dvl-binding protein Idax 1062 100 norve icus Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

451 gi11967377Homo SapiensDvl-binding protein IDAX 1062 100 mRNA, com fete cds.

451 gi7023269Homo SapienscDNA FLJ 10920 fis, clone348 48 OVARC 1000384.

452 gi4929538Rarius Olg-1 bHLH protein 1088 87 norvegicus 452 111602814Mus musculusOligl bHLH rotein 1070 86 452 g17385152Mus musculusoligodendrocyte-specific 1070 86 bHLH

transcri tion factor Oligl 453 g13851514Phytophthoracyst germination specific874 31 acidic repeat infestans rotein recursor 453 g1454154 Homo Sapiensintestinal mucin (MUC2) 746 26 mRNA, com lete cds.

453 g1296881 ClostridiumS-layer protein 678 34 thermocellum 454 g14929577Homo sa CGI-54 rotein mRNA, com 1552 100 iens lete cds.

454 AAY13942 Homo sa Human transmembrane rotein,1552 100 iens HP01737.

454 AAB36611 Homo SapiensHuman FLEXHT-33 protein 1546 99 sequence SEQ ID N0:33.

455 g1295671 Saccharomyceselected as a weak suppressor108 21 of a mutant s cerevisiaeof the subunit AC40 of DNA dependant RNA of merase I and III

455 g12425111DictyosteliumZipA 107 20 discoideum 455 g11279563Medicago nuMl 104 21 sativa 456 AAB58236 Homo SapiensLung cancer associated 286 88 polypeptide se uence SEQ ID 574.

456 g12065288Doryctobraconcytochrome b 61 30 crawfordi 456 g11653554SynechocystisCDP-diacylglycerol--glycerol-3-phosphate48 45 s . PCC 3- hos hand ltransferase 457 13273731 Homo sa MHC class 1 re ion. 603 95 iens 457 g1312407 Homo SapiensHuman HLA-F gene for human603 95 leukocyte anti en F.

457 g114349362Homo SapiensSinular to major histocompatibility599 95 complex, class I, F, clone MGC:15399 IMAGE:4039990, mRNA, com lete cds.

458 AAG71945 Homo sapiensHuman olfactory receptor 1 96 polypeptide, 106 SEQ ID NO: 1626.

458 AAG71532 Homo SapiensHuman olfactory receptor 1104 96 polypeptide, SEQ ID NO: 1213.

458 AAG71525 Homo SapiensHuman olfactory receptor 641 53 polypeptide, SEQ ID NO: 1206.

459 g111612079Homo SapiensDC-specific transmembrane2448 100 protein mRNA, com lete cds.

459 AAE02638 Homo SapiensHuman dendritic cell specific2448 100 transmembrane rotein (DC-STAMP
.

459 AAB87357 Homo SapiensHuman gene 16 encoded 1798 99 secreted protein HMADJ14, SEQ ID N0:98.

460 g13006230Homo SapiensPAC clone RP4-60465 from 85 35 7q22-q31.1, com lete se uence.

460 g147373 Streptococcus7 kDa protein 59 42 neumoniae Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

46U gi5880698Nephroselmistranslational initiation 57 30 factor 1 olivacea 461 AAG73470 Homo SapiensHuman gene 14-encoded 699 100 secreted protein fragment, SEQ ID N0:245.

461 gi10436625Homo sapienscDNA FLJ14220 fis, clone 489 53 NT2RP3003828.

461 AAB95779 Homo SapiensHuman protein sequence 489 53 SEQ ID

N0:18726.

462 gi7021367Drosophilacll.l 522 27 melano aster 462 gi12724134LactococcusHYPOTHETICAL PROTEIN 84 33 lactis subsp.

lactis 463 17322066 Droso hilaHls 367 28 s .

463 g13309579Rattus A-kinase anchor protein121;155 27 norvegicus 463 g12072307Mus musculusAKAP121 154 27 464 .AAB47106Homo sa Second s lice variant 4193 99 iens of MAPP.

464 AAB47105 Homo sa First s lice variant of 3311 100 iens MAPP.

464 g1 14550175Mus musculusADAM33 2684 72 465 g114091952Rattus KIDINS220 324 27 norvegicus 465 g111321435Rattus ankyrin repeat-rich membrane-spanning320 27 norve icusrotein 465 g16599237Homo SapiensmRNA; cDNA DKFZp434F0621 220 27 (from clone DKFZ 434F0621).

466 g19864747LeishmaniaL165.9 225 35 ma' or 466 g13021392Homo SapiensH.sapiens mRNA for nuclear118 34 protein SDK3, artial.

466 15734402 Homo sa mRNA for GANP rotein. 96 27 iens 467 g112002028Homo Sapiensbrain my040 protein mRNA,482 100 complete cds.

467 AAB56147 Homo SapiensHuman secreted protein 74 36 sequence encoded b gene 71 SEQ ID N0:241.

467 AAB56272 Homo SapiensHuman secreted protein 74 36 sequence encoded b gene 71 SEQ ID N0:366.

468 AAY94938 Homo SapiensHuman secreted protein 2290 97 clone ye78_1 rotein se uence SEQ ID
N0:82.

468 113603412Homo sa B29 mRNA, com lete cds. 187 30 iens 468 ~AAY17227Homo sa Human secreted rotein 203 26 iens clone al-1 .

469 AAY27721 Homo SapiensHuman secreted protein I 88 encoded by gene 118 No. 29.

469 AAB87068 Homo sapiensHuman secreted protein 621 99 TANGO 365, SEQ ID N0:46.

469 AAB87146 Homo SapiensHuman secreted protein 617 98 A5V variant, SEQ ID N0:161.

470 110438739Homo sa cDNA: FLJ22376 fis, clone1931 99 iens HRC07327.

470 AAE03639 Homo SapiensHuman extracellular matrix1934 99 and cell adhesion molecule-3 (XMAD-3).

470 g14033606Adiantum Extensin 200 33 capillus-veneris 471 g11769467Homo SapiensHuman p126 (ST5) mRNA, 1504 70 complete cds. ~ ~

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

471 gi1769472Homo SapiensHuman p82 (STS) mRNA, 1504 70 alternatively s liced, com fete cds.

471 gi257387human, HTS1=HeLa tumor suppressor1504 70 gene revertant clone F2, mRNA

Partial, nt]. [Homo sa iens 472 gi9944535Amsacta AMV012 69 29 moorei entomopoxviru s 472 giS59500CaenorhabditisND2 protein (AA 1 - 282) 81 35 ele ans 472 gi15042251Chilo 1508 62 36 iridescent virus 473 gi559500CaenorhabditisND2 protein (AA 1 - 282) 91 26 ele ans 473 gi9944535Amsacta AMV012 69 29 moorei entomopoxviru s 473 gi9944642Amsacta AMV 119 73 29 moorei entomopoxviru s 474 gi5739566Homo SapiensBAC clone CTA-332P12 from907 100 7q22-31.1, com lete se uence.

474 132474 Homo sa H.sa iens h-S 1 mRNA. 907 100 iens 474 g1632790human, pantophysin 907 100 keratinocyte line HaCaT, mRNA, 2106 nt]. [Homo sa iens 475 g114603247Homo SapiensSimilar to RIKEN cDNA 937 100 gene, clone MGC:19636 IMAGE:2822323, mRNA, com lete cds.

475 AAB36613Homo SapiensHuman FLEXHT-35 protein 937 100 sequence SEQ ID N0:3S.

475 g17022832Homo SapienscDNA FLJ10661 fis, clone 240 90 NT2RP2006106.

476 g15052674DrosophilaBcDNA.LD29892 162 38 melano aster 476 AAB21007Homo SapiensHuman nucleic acid-binding167 39 protein, NuABP-11.

476 g19295345Homo SapiensHSKM-B (HSKM-B) mRNA, 173 31 complete cds.

477 .AAG71509Homo SapiensHuman olfactory receptor 1510 96 polypeptide, SEQ ID NO: 1190.

477 AAG71669Homo SapiensHuman olfactory receptor 1198 77 polypeptide, SEQ ID NO: 1350.

477 AAG71820Homo SapiensHuman olfactor rece for 1181 75 pol eptide, Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

SEQ ID NO: 1501.

478 AAY73483Homo SapiensHuman secreted protein 582 47 clone y118 1 rotein se uence SEQ ID
N0:188.

478 AAW85723Homo sa Novel rotein (Clone AX56 246 34 iens 28).

478 AAG03191Homo SapiensHuman secreted protein, 112 30 SEQ ID NO:

7272.

479 gi15079907Homo SapiensSimilar to secretory carrier1182 94 membrane protein 4, clone MGC:19661 IMAGE:3161979, mRNA, com lete cds.

479 gi9837305Rattus secretory carrier membrane1012 79 protein 4 norve icus 479 17021484Mus musculussecreto carrier membrane 1006 77 rotein 4 480 g11345560Oryza sativanitrate reductase apoenzyme72 44 (AA 394-471 ) ( 130 is 2nd base in codon) 481 g1 13517508Homo sapienssodium bicarbonate cotransporter5138 100 (SLC4A9) mRNA, artial cds.

481 g114582760Homo Sapiensanion exchanger AE4 mRNA,4603 96 complete cds.

481 gil 1611537Oryctolagusanion exchanger 4a 4080 86 cuniculus 482 g12570933Rattus vanilloid receptor subtype986 44 norve icus 482 g17544146Rattus vanilloid receptor type 979 45 1 like protein 1 norve icus 482 gil 1055318Rattus vanilloid receptor-related951 43 osmotically norvegicusactivated channel 483 g114669436Homo Sapiensalkaline phytoceramidase 110 54 (APHC) mRNA, com lete cds.

483 AAB 18986Homo SapiensAmino acid sequence of 110 54 a human transmembrane rotein.

483 g114488266ArabidopsisAcyl-CoA independent ceramide91 33 synthase thaliana 484 g112053091Homo SapiensmRNA; cDNA DKFZp434F1719 615 97 (from clone DKFZ 434F1719);
com lete cds.

484 AAE01546Homo SapiensHuman gene 1 encoded secreted76 39 protein HMVCQ82, SEQ ID N0:96.

484 g1 1574439Haemophilusleucine responsive regulatory77 36 protein (lrp) influenzae Rd 485 AAY99347Homo SapiensHuman PRO11 13 (LJNQ556) 2250 99 amino aacid se uence SEQ ID N0:24.

485 AAB71863Homo sa Human h15571 GPCR. 1834 48 iens 485 g17407148Homo Sapiensprotocadherin Flamingo 306 27 2 (FMI2) mRNA, com lete cds.

486 AAW94654Homo SapiensG-protein coupled receptor887 52 rotein.

486 1219867 Homo sa Human mRNA for HM74. 882 52 iens 486 AAY90637Homo sa Human G rotein-cou led 882 52 iens rece for HM74.

487 g13337385Homo SapiensChromosome 16 BAC clone 1158 83 A-761H5, com lete se uence.

487 g12342743Homo SapiensHuman Chromosome 16 BAC 709 59 clone CIT987SK-A-589H1, com lete se uence.

487 g14959568Homo Sapiensnuclear pore complex interacting705 58 protein NPIP NPIP mRNA, com fete cds.

488 g17021167Homo sa cDNA FLJ20839 fis, clone 551 98 iens ADKA02346.

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

488 g19309293Homo Sapienshasc-1 mRNA for asc-type 551 98 amino acid trans orter 1, com lete cds.

488 g17415938Mus musculusasc 1 460 83 489 g1 14248997Homo Sapienslung seven transmembrane 2239 97 receptor 1 (LUSTR1) mRNA, com lete cds.

489 g110439034Homo sa cDNA: FLJ22591 fis, clone1515 98 iens HSI03124.

489 g1 14248999Mus musculuslun seven transmembrane 813 49 rece for 2 490 AAY87079Homo SapiensHuman secreted protein 927 82 sequence SEQ ID

N0:118.

490 g13851540Homo Sapiensbrain mitochondria) carrier927 82 protein-1 (BMCP1) mRNA, nuclear gene encoding mitochondria) rotein, com fete cds.

490 g111094335Homo Sapiensmitochondria) uncoupling 927 82 protein 5 long form mRNA, complete cds;
nuclear gene for mitochondria) roduct.

491 AAG71803Homo SapiensHuman olfactory receptor 1616 100 polypeptide, SEQ ID NO: 1484.

491 AAG71807Homo SapiensHuman olfactory receptor 1165 69 polypeptide, SEQ ID NO: 1488.

491 AAG71805Homo SapiensHuman olfactory receptor 1099 83 polypeptide, SEQ ID NO: 1486.

492 ~gi10440458Homo sa mRNA for FLJ00065 rotein,992 100 iens artial cds.

492 g1938175Gallus al ha) (XIV) collagen 102 32 gallus 492 1211358 Gallus al ha-1 collagen t a 1X 63 45 gallus 493 19963845Homo sa HT017 mRNA, com lete cds.558 38 iens 493 AAW09405Homo sa Pineal land s ecific ene-1558 38 iens rotein.

493 AAB69185Homo sa Human hISLR-iso rotein 558 38 iens SEQ ID N0:7.

494 g16179740Homo Sapiensparaneoplastic neuronal 421 51 antigen MA3 MA3) mRNA, com lete cds.

494 g112053257Homo SapiensmRNA; cDNA DKFZp434K225 421 51 (from clone DKFZ 434K225); com lete cds.

494 AAB 12529Homo sa Human Ma5 rotein SEQ ID 421 51 iens N0:13.

495 g113384467Caenorhabditiscontains similarity to 391 35 CDP-alcohol ele ans hos hotransferases 495 g13661595Arabidopsisaminoalcoholphosphotransferase411 32 thaliana 495 1530088 Gl cine aminoalcohol hos hotransferase410 31 max 496 19963853Homo sa HT018 mRNA, com lete cds.1368 100 iens 496 AAG71359Homo SapiensHuman gene 10-encoded 50 50 secreted protein fra ment, SEQ ID N0:210.

496 AAY20863Homo SapiensHuman presenilin I mutant61 36 protein fra ment 9.

497 g113241761Homo Sapienstransmembrane protein 1286 70 induced by tumor necrosis factor alpha (TMPIT) mRNA, com lete cds.

497 AAB 12123Homo SapiensHydrophobic domain protein1286 70 from clone HP 10608 isolated from Saos-2 cells.

497 AAB38371Homo SapiensHuman secreted protein 331 67 encoded by gene 51 clone HLDQC46.

498 AAY86234Homo SapiensHuman secreted protein 126 32 HNTNC20, SEQ

ID N0:149.

498 AAB24074Homo SapiensHuman PR01153 protein 113 54 sequence SEQ

ID N0:49.

498 AAY66735Homo SapiensMembrane-bound protein 113 54 ~ ~ ~ PR01153. I ~

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

499 AAB93704 Homo SapiensHuman protein sequence 3677 99 SEQ ID

N0:13287.

499 g12792496Rattus tulip 2 1339 70 norvegicus 499 g12792494Rattus tulip 1 1159 48 norvegicus 500 g110438718Homo sa cDNA: FLJ22362 fis, clone1224 100 iens HRC06544.

500 g1310897 Thermobifidabeta-1,4-endoglucanase 138 36 precursor fusca 500 AAY59066 Homo SapiensHuman tie receptor FNIII 99 26 repeat fragment 2.

501 g14519607Homo sa Nurrl gene, com lete cds.1342 100 iens 501 g14760535Homo Sapiensgene for T-cell nuclear 1342 100 receptor NOT

(Nurrl , com lete cds.

501 g114424530Homo Sapiensnuclear receptor subfamily1342 100 4, group A, member 2, clone MGC:14354 IMAGE:4298967, mRNA, com lete cds.

502 g17288872Ratios taste receptor rT2R6 398 32 norvegicus 502 g17262617Homo Sapienscandidate taste receptor 397 33 T2R9 gene, com lete cds.

502 AAB87739 Homo SapiensHuman T2R09 amino acid 397 33 sequence SEQ

ID N0:17.

503 g17022610Homo SapienscDNA FLJ10521 fis, clone 3005 98 NT2RP2000841.

503 AAB92909 Homo SapiensHuman protein sequence 3005 98 SEQ ID

N0:11539.

503 g113111772Homo Sapiensclone MGC:2899 IMAGE:3010245,649 99 mRNA, com lete cds.

504 AAB51244 Homo sapiensHuman haemopoietin receptor3066 99 protein NR10.3 SEQ ID N0:17.

504 AAB51242 Homo SapiensHuman haemopoietin receptor3018 100 protein NR10.1 SEQ ID N0:2.

504 AAB51243 Homo SapiensHuman haemopoietin receptor885 100 protein NR10.2 SEQ ID N0:4.

505 AAG71668 Homo SapiensHuman olfactory receptor 1547 97 polypeptide, SEQ ID NO: 1349.

505 AAG71507 Homo SapiensHuman olfactory receptor 1399 90 polypeptide, SEQ ID NO: 1188.

505 AAG71676 Homo SapiensHuman olfactory receptor 1126 70 polypeptide, SEQ ID NO: 1357.

506 110438252Homo sa cDNA: FLJ22009 fis, clone2022 99 iens HEP07114.

506 g112654279Homo Sapiensclone IMAGE:3451160, mRNA,1975 100 partial cds.

506 14102877 Mus musculusShc bindin rotein 1915 70 507 g1 12248917Homo sa mRNA for s inesin, com 1404 100 iens lete cds.

507 AAB 11699Homo SapiensHuman serine protease 1404 100 BSSP2 (hBSSP2), SEQ ID NO:10.

507 AAB08950 Homo SapiensHuman secreted protein 1207 100 sequence encoded b gene 22 SEQ ID N0:107.

508 g17715916Mus musculusSorCSb splice variant 4966 96 of the VPS 10 domain rece for SorCS

508 166_92583Mus musculusVPS10 domain rece for 4_96_196 rotein SORCS

508 g112007720Mus musculusVPS10 domain receptor 2613 49 ~ ~ protein SorCS2 ~ ~

Table 2A
SEQ AccessionSpecies Description Score'%

ID No. Identity NO:

509 110566471Mus musculusGliacolin 1284 94 509 114278927Mus musculusliacolin 1284 94 509 13747097 Homo sa C1 -related factor mRNA, 974 71 iens com fete cds.

510 g17332063Caenorhabditiscontains similarity to 147 41 Strongylocentrotus elegans uratus S ec3 rotein SP:P
16537) 510 g112247892SterkiellaSPEC3-like protein 85 36 histriomuscoru m 510 g1483822 Gallus vitellogenin gene-binding73 47 gallus protein, al halal ha isoform 511 AAB25755 Homo SapiensHuman secreted protein 648 100 sequence encoded b ene 33 SEQ ID N0:144.

511 AAB25754 Homo SapiensHuman secreted protein 301 100 sequence encoded by ene 33 SEQ ID N0:143.

511 AAB25697 Homo SapiensHuman secreted protein 278 100 sequence encoded b ene 33 SEQ ID N0:86.

512 g113810306Homo SapiensmRNA for transmembrane 1271 100 protein 7 (TMEM7 ene).

512 g111065721Homo SapiensmRNA for 28kD interferon 420 45 responsive rotein (IFRG28 gene).

512 AAB84453 Homo SapiensAmino acid sequence of 420 45 a human interferon-al ha induced rotein.

513 AAG72504 Homo SapiensHuman OR-like polypeptide1615 99 query se uence, SEQ ID NO: 2185.

513 AAG71709 Homo SapiensHuman olfactory receptor 1611 99 polypeptide, SEQ ID NO: 1390.

513 AAG72127 Homo SapiensHuman olfactory receptor 829 99 polypeptide, SEQ ID NO: 1808.

514 AAB83079 Homo sa Human CASB6411 rotein. 1806 100 iens 514 AAB08764 Homo SapiensA human leukocyte and 1424 100 blood related rotein (LBAP).

514 g110435645Homo SapienscDNA FLJ13593 fis, clone 1124 100 PLACE 1009493.

515 AAB74716 Homo SapiensHuman membrane associated1094 99 protein MEMAP-22.

515 g16093235Homo SapiensmRNA; cDNA DKFZp566N034 424 94 (from clone DKFZ 566N034); artial cds.

515 g115157430AgrobacteriumAGR C 4131p 131 25 tumefaciens 516 g113447610Homo SapiensVTS20631 mRNA, g-protein 3804 99 coupled rece for famil , artial cds.

516 g110441732Homo Sapiensleucine-rich repeat-containing3782 100 G protein-coupled receptor 6 (LGR6) mRNA, partial cds.

516 g13366802Homo Sapiensorphan G protein-coupled 1805 52 receptor HG38 mRNA, com lete cds.

517 AAB24465 Homo SapiensHuman secreted protein 447 98 sequence encoded b ene 29 SEQ ID N0:90.

517 g11749851Human tat protein 60 36 immunodeficie ncy virus type 517 g12245481Human Tat protein 59 33 immunodeficie Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

ncy virus type 518 15802879 Homo sa AIM-1 rotein mRNA, com 458 44 iens lete cds.

518 g115028433Mus musculusB/AIM-1-like rotein 453 45 518 g14680229Homo sa DNb-5 mRNA, artial cds. 498 41 iens 519 g15525078Rattus seven transmembrane receptor788 31 norvegicus 519 AAY57288 Homo sapiensHuman GPCR protein (HGPRP)752 29 sequence clone ID 3036563 .

519 AAY40440 Homo SapiensHuman brain-derived G-protein746 29 coupled rece for rotein.

520 AAY27577 Homo SapiensHuman secreted protein 598 100 encoded by gene No. 11.

520 g11617316Homo sa H.sa iens mRNA for tenascin-R.97 26 iens 520 g14379056Homo SapiensH.sapiens mRNA for tenascin-R97 26 restrictin).

521 g110434488Homo SapienscDNA FLJ12791 fis, clone 1523 100 NT2RP2001991, highly similar to SODIUM- AND CHLORIDE-DEPENDENT TRANSPORTER
NTT73.

521 ~AAB94304Homo SapiensHuman protein sequence 1523 100 SEQ ID

N0:14767.

521 g1 11907841Homo Sapiensorphan neurotransmitter 1353 92 transporter v7-3 mRNA, com lete cds.

522 g1 10437307Homo sa cDNA: FLJ21240 fis, clone677 38 iens COL01132.

522 AAY94906 Homo SapiensHuman secreted protein 644 37 clone rb649 3 rotein se uence SEQ ID
N0:18.

522 AAB74730 Homo SapiensHuman membrane associated644 37 protein MEMAP-36.

523 AAB43665 Homo SapiensHuman cancer associated 1254 100 protein sequence SEQ ID NO:1110.

523 AAY19759 Homo sa SEQ ID NO 477 from W09922243.966 100 iens 523 g112804249Homo SapiensSimilar to gene rich cluster,411 46 C9 gene, clone MGC:2519 IMAGE:3546861, mRNA, com lete cds.

524 AAB03625 Homo sa Human G- rotein cou led 1925 94 iens rece for fb4la.

524 AAB70143 Homo SapiensHuman G protein-coupled 1925 94 receptor rotein.

524 AAW79258 Homo sa Human G rotein cou led 1877 93 iens rece for ISE.

525 g17023154Homo SapienscDNA FLJ10856 fis, clone 943 53 NT2RP4001547.

525 AAY28810 Homo sa nn296 2 secreted rotein. 943 53 iens 525 AAB93258 Homo SapiensHuman protein sequence 943 53 SEQ ID

N0:12282.

526 1l 1878036Sus scrofasomatostatin rece for 198 25 526 g112056166Yaba-like 7L protein 196 26 disease virus 526 g1 13876663lumpy skinG-protein-coupled chemokine197 25 receptor-disease like rotein virus 527 g13880799CaenorhabditisY39A1B.2 441 24 ele ans 527 g11707052Caenorhabditissimilar to drosophilia 368 23 and mouse patched ele ans roteins ~27 g11255388Caenorhabditissimilar to drosophila 191 23 ~ ~ ~ membrane protein Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

elegans PATCHED SP: P18502) 528 AAB34321 Homo SapiensHuman secreted protein 74 38 sequence encoded b ene 23 SEQ ID N0:82.

528 AAB51693 Homo sapiensHuman secreted protein 51 55 related amino acid se uence SEQ ID N0:133.

528 AAB87388 Homo SapiensHuman gene 47 encoded 68 44 secreted protein HFXDK20, SEQ ID N0:129.

529 AAY94297 Homo SapiensHuman coenzyme A-utilising1581 69 enzyme CoAEN-5.

529 AAY66699 Homo sa Membrane-bound rotein 1581 69 iens PRO1 108.

529 AAB65222 Homo SapiensHuman PRO1 108 (UNQ551) 1581 69 protein se uence SEQ ID N0:248.

530 AAY29332 Homo SapiensHuman secreted protein 1282 99 clone pe584_2 rotein se uence.

530 AAB58289 Homo SapiensLung cancer associated 1282 99 polypeptide se uence SE ID 627.

530 AAB75246 Homo SapiensHuman secreted protein 1282 99 sequence encoded b ene 7 SEQ ID N0:65.

531 AAB08538 Homo SapiensA human G-protein coupled787 100 receptor desi nated 14273.

531 AAY44662 Homo SapiensHuman 14273 G-protein 765 98 coupled receptor (GPCR).

531 AAY44815 Homo SapiensHuman 14273 G-protein 761 97 coupled receptor (GPCR) version 2.

532 AAG71706 Homo SapiensHuman olfactory receptor 1579 99 polypeptide, SEQ ID NO: 1387.

532 AAG71705 Homo SapiensHuman olfactory receptor 1180 74 polypeptide, SEQ ID NO: 1386.

532 ~AAG71679Homo SapiensHuman olfactory receptor 1089 68 polypeptide, SEQ ID NO: 1360.

533 g1557822 Saccharomycemal5, stal, len: 1367, 362 27 CAI: 0.3, s cerevisiaeAMYH_YEAST P08640 GLUCOAMYLASE S1 (EC 3.2.1.3) 533 g11304387Saccharomyceglucoamylase 362 27 s cerevisiae var. diastaticus 533 g17332056Caenorhabditiscontains similarity to 345 27 Pfam family elegans PF00078 (Reverse transcriptase (RNA-de endent , score=79.6, E=6.3e-20, E=1 534 AAU00437 Homo SapiensHuman dendritic cell membrane1841 91 protein FIRE.

534 AAY91625 Homo sapiensHuman secreted protein 1840 90 sequence encoded b ene 22 SE ID N0:298.

534 AAY59300 Homo sa Human EGPCR of a tide. 1121 58 iens 535 g110438710Homo sa cDNA: FLJ22357 fis, clone4572 100 iens HRC06404.

535 114336678Homo sa 16 13.3 se uence section 4547 99 iens I of 8.

535 AAB61148 Homo sa Human NOV 17 rotein. 1955 67 iens 536 110438710Homo sa cDNA: FLJ22357 fis, clone4379 100 iens HRC06404.

536 114336678Homo sa 16 13.3 se uence section 4354 99 iens 1 of 8.

536 AAB61148 Homo sa Human NOV 17 rotein. 1955 67 iens 537 1 10439790Homo sa cDNA: FLJ23186 fis, clone753 99 iens LNG 11945.

537 g1310100 Rattus developmentally regulated86 30 protein norve icus 537 15824457 Caenorhabditiscontains similarit to 78 30 Pfam domain:

Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

elegans PF00615 (Regulator of G protein signaling domain), Score=200.4, E-value=9.1e-57, N=1 538 AAG71899 Homo SapiensHuman olfactory receptor 1603 100 polypeptide, SEQ ID NO: 1580.

538 15869925 Mus musculusolfactor rece for 1322 82 538 AAG71954 Homo SapiensHuman olfactory receptor 883 54 polypeptide, SEQ ID NO: 1635.

539 g1466604 EscherichiaNo definition line found 90 25 coli 539 g152952 Mus musculusdelta-aminolevulinate 82 35 dehydratase (AA 1 -539 g14262032Bos taurusD5 do amine rece for 59 64 540 g112803977Homo Sapiensclone MGC:4175 IMAGE:3634983,611 100 mRNA, com fete cds.

540 AAB34781 Homo sapiensHuman secreted protein 58 39 sequence encoded by gene 9 SEQ ID N0:69.

540 AAW39938 Homo SapiensPeptide effecting G-protein-coupled57 37 rece for activit .

541 AAY73442 Homo SapiensHuman secreted protein 596 95 clone ya66-1 rotein se uence SEQ ID
N0:106.

541 AAB63255 Homo sapiensHuman breast cancer associated95 40 antigen rotein se uence SEQ ID
N0:617.

541 g113182890Macaca collagen type III alpha 79 46 mulatta 542 g19929914Homo sapiensMUC3B gene for intestinal4024 99 mucin, partial cds.

542 g19929918Homo SapiensMUC3B mRNA for intestinal4024 99 mucin, artial cds.

542 g111990203Homo Sapienspartial MUC3B gene for 3985 98 MUC3B mucin, exons 1-11.

543 g114043332Homo SapiensSimilar to ring finger 925 40 protein 23, clone MGC:2475 IMAGE:3051389, mRNA, com fete cds.

543 g110716078Mus musculustestis-abundant fin er 919 40 rotein 543 112407417Mus musculustri artite motif rotein 671 35 544 g157131 Rattus ribosomal protein S26 260 68 norve icus 544 g112803549Homo Sapiensribosomal protein S26, 260 68 clone MGC:1963 IMAGE:3143099, mRNA, com fete cds.

544 1456351 Homo sa H.sa fens RPS26 mRNA. 260 68 iens 545 g110438861Homo sa cDNA: FLJ22461 fis, clone1258 42 iens HRC10107.

545 g115079400Homo Sapiensclone MGC:16796 IMAGE:3855477,1258 42 mRNA, com fete cds.

545 g16683905DrosophilaDispatched 412 37 melano aster 546 AAY72910 Homo SapiensHuman IGS3 G-protein coupled589 58 receptor GPCR rotein.

546 AAB67654 Homo sapiensAmino acid sequence of 589 58 a human G-rotein cou led rece for (Ant).

546 AAF55661 Homo SapiensNucleotide sequence of 589 58 a human G-protein aal cou led rece for (Ant).

547 g16740013Homo Sapiensclone cDSCI Down syndrome6373 60 cell adhesion molecule (DSCAM
mRNA, Table 2A
SEQ AccessionSpecies Description Score ID No. Identity NO:

com fete cds.

547 AAW42086Homo SapiensHuman Down syndrome-cell 6347 62 adhesion molecule DS-CAM 1.

547 111066998Mus musculusDown s ndrome cell adhesion6344 60 molecule 548 g112656633Homo Sapienstransmembrane gamma-carboxyglutamic1192 100 acid protein 3 TMG3 mRNA, complete cds.

548 g12338290Homo Sapiensproline-rich Gla protein 283 49 1 (PRGP 1 ) mRNA, com fete cds.

548 g1506601Rattus factor X 206 49 norve icus 549 g112698682Homo Sapienstestis-expressed transmembrane-4588 95 protein (TETM4 mRNA, com fete cds.

549 111559214Homo sa mRNA for MS4A5, com fete 588 95 iens cds.

549 g113649401Homo sa MS4A5 rotein mRNA, com 588 95 iens fete cds.

550 g112054393Homo Sapiens6M1-10*O1 gene for olfactory1853 100 receptor, cell line BM28.7.

550 g112054395Homo Sapiens6M1-10*O1 gene for olfactory1853 100 receptor, cell line BM19.7.

550 g112054397Homo Sapiens6M1-10*O1 gene for olfactory1853 100 receptor, cell line LG2.

551 g1 11275360Homo SapiensSLC4A 10 mRNA for NCBE, 5677 99 complete cds.

551 111182364Mus musculusNCBE 5542 96 551 g17385123Mus musculussodium bicarbonate cotransporter4364 76 isoform 3 kNBC-3 552 AAE04178Homo SapiensHuman gene 3 encoded secreted1111 98 protein fra ment, SEQ ID N0:169.

552 AAE04127Homo SapiensHuman gene 3 encoded secreted1078 98 protein HSDJL42, SEQ ID N0:114.

552 AAE04102Homo SapiensHuman gene 3 encoded secreted1068 98 protein HSDJL42, SEQ ID N0:88.

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 277 AAY55787 Homo 1NCY- Human zinc RING (ZIRI)1859 95 protein.

sa iens 277 AAW81821 Homo INCY- Human ZIRI protein. 1859 95 sa iens 277 gi3387925Homo RING zinc finger protein 1859 95 RZF

sa iens 278 AAY55787 Homo 1NCY- Human zinc RING (ZIRI)1703 88 protein.

sa iens 278 AAW81821 Homo INCY- Human ZIRI protein. 1703 88 sa iens 278 gi3387925Homo RING zinc finger protein 1703 88 RZF

sa iens 279 AAY55787 Homo 1NCY- Human zinc RING (ZIRI)1769 92 protein.

sa iens 279 AAW81821 Homo INCY- Human ZIRI protein. 1769 92 sa iens 279 gi3387925Homo RING zinc finger protein 1769 92 RZF

sa iens 280 AAB24463 Homo HUMA- Human secreted protein1346 96 sequence sa iens encoded b gene 27 SEQ ID
N0:88.

280 AAU27674 Homo ZYMO Human protein AFP669232.1334 95 sa iens 280 AAB34813 Homo HUMA- Human secreted protein701 93 sequence sa iens encoded b gene 41 SEQ ID
NO:101.

281 ABB89737 Homo HUMA- Human polypeptide 614 87 SEQ ID NO

sa iens 2113.

281 AAG89173 Homo GEST Human secreted protein,614 87 SEQ ID NO:

sa iens 293.

281 AAM25811 Homo HYSE- Human protein sequence614 87 SEQ ID

sa iens N0:1326.

282 AAW61622 Homo HUMA- Clone HTPBA27 of TM4SF841 93 sa iens su erfamil .

282 gi2997747Homo tetraspan TM4SF; Tspan-4 841 93 sa iens 282 gi2586350Homo tetraspan 841 93 sa iens 283 gi 15080477Homo Similar to RIKEN cDNA 23100106132034 97 gene sa iens 283 gi17512422Mus Similar to RIKEN cDNA 23100106131577 76 gene musculus 283 gi17427162RalstoniaTRANSPORT TRANSMEMBRANE 315 28 solanacearuPROTEIN

m 284 ABB05645 Homo BODE- Human thyroglobulin 1858 100 38 protein sa iens SEQ ID N0:2.

284 ABB05646 Homo BODE- Human thyroglobulin 88 100 38 protein N-sa iens terminal a tide SEQ ID N0:7.

284 gi21322795CorynebacteABC-type transporter, permease78 22 rium components glutamicum ATCC

285 gi18157547Mus pecanex-like 3 1791 93 musculus 285 gi15076843Homo ecanex-like rotein 1 871 34 Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa iens 285 AAM42412Homo HUMA- Human polypeptide 743 100 SEQ ID NO

sa iens 145.

286 gi17390957Mus Similar to RIKEN cDNA 2010001E11184 26 gene musculus 286 gi2650264Archaeogloboxalate/formate antiporter 95 22 (oxlT-2) us ful idus 286 gi 19712705FusobacteriuMultidrug resistance protein94 18 m nucleatum subsp.

nucleatum ATCC

287 AAW27484Homo IMUT- Human MCP. 1991 96 sa iens 287 gi180137Homo membrane cofactor protein 1991 96 sa iens 287 AAR93939Homo AUST- CD46 wild-type. 1986 96 sa iens 288 AAE01687Homo HUMA- Human gene 16 encoded1019 100 secreted sa iens rotein HDPMM88, SEQ ID N0:99.

288 AA014187Homo INCY- Human transporter 560 58 and ion channel sa iens TRICH-4.

288 gi20988041Homo Similar to ATPase, Class 560 58 I, type 8B, sa iens member 2 289 AAG81436Homo ZYMO Human AFP protein sequence392 100 SEQ

sa fens ID N0:390.

289 AAG74872Homo HUMA- Human colon cancer 392 100 antigen sa iens rotein SEQ ID N0:5636.

289 AAB08863Homo INCY- Amino acid sequence 392 100 of a human sa iens secretor rotein.

290 gi1226246Homo mono-ADP-ribosyltransferase1880 94 sa iens 290 gi2677616Mus NAD(P)(+)--arginine ADP- 1142 60 musculus ribos ltransferase 290 gi20067374Mus ART3 mono(ADP-ribosyl)transferase1071 58 musculus 291 AAB70690Homo SREN- Human hDPP protein 598 100 sequence SEQ

sa iens ID N0:7.

291 AAG89279Homo GEST Human secreted protein,598 100 SEQ ID NO:

sa iens 399.

291 gi 13182757Homo HTPAP 598 100 sa iens 292 AAU83599Homo GETH Human PRO protein, 760 100 Seq ID No 16.

sa iens 292 AAB88418Homo HELI- Human membrane or 725 100 secretory sa iens rotein clone PSEC0181.

292 ABK09980_Homo JAKO/ Human prostate stem 101 32 cell antigen as 1 sa iens (PSCA) cDNA se uence.

293 gi12718841Mus Skullin 279 38 musculus 293 gi4191356Mus claudin-6 277 38 musculus 293 gi 13543081Mus claudin 6 277 38 musculus Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 294 ABB50276Homo USSH HLA-DR alpha chain 1214 92 ovarian tumour sa iens marker rotein, SE ID N0:41.

294 AAB58160Homo ROSE/ Lung cancer associated1214 92 polypeptide sa iens se uence SEQ ID 498.

294 gi15929084Homo major histocompatibility 1214 92 complex, class II, sa iens DR al ha 295 AAE15283Homo INCY- Human RNA metabolism 2777 99 protein-46 sa iens (RMEP-46).

295 gi16768810DrosophilaLD05247p 1133 46 melanogaste r 295 gi16185327DrosophilaLD38433p 906 40 melanogaste r 296 gi12620132Homo renal sodium/sulfate cotransporter3100 100 sa iens 296 gi469555Rattus Na/Sulfate cotransporter 2627 82 norve icus 296 gi310183Rattus sodium dependent sulfate 2627 82 transporter norve icus 297 AAY44245Homo 1NCY- Human cell signalling1522 89 protein-8.

sa iens 297 AAE06590Homo SAGA Human protein having 1327 80 hydrophobic sa iens domain, HP 10785.

297 AAM93721Homo HELI- Human polypeptide, 1205 99 SEQ ID NO:

sa iens 3671.

298 AAE 13277Homo INCY- Human transporters 3306 92 and ion channels sa iens (TRICH)-4.

298 AAD06381_Homo ACTI- Human ATP binding 2338 99 cassette, aal sa iens ABCB9 trans otter cDNA.

298 AAE02437Homo ACTI- Human ATP binding 2338 99 cassette, sa iens ABCB9 trans orter rotein.

299 gi20072551Mus RIKEN cDNA 4930511J11 gene 342 40 musculus 299 gi17974542Homo voltage-dependent calcium 118 25 channel gamma-sa iens 8 subunit 299 gi13357180Homo calcium channel gamma subunit117 25 sa iens 300 gi20258606Homo siderollexin 5 1178 100 sa iens 300 gi3874886CaenorhabdiC41C4.2 592 46 tis ele ans 300 gi13543138Mus RIKEN cDNA 2810002005 gene 401 38 musculus 301 AAE07054Homo HUMA- Human gene 4 encoded 612 29 secreted sa iens rotein HSYAB05, SEQ ID N0:71.

301 AAE07077Homo HUMA- Human gene 4 encoded 143 23 secreted sa iens rotein HSYAB05, SEQ ID N0:94.

301 gi9964007Homo MAB21 L2 protein 105 33 sa iens 302 ABB89405Homo HUMA- Human polypeptide 1337 98 SEQ ID NO

sa iens 1781.

302 gi15030135Mus RIKEN cDNA 1110020A09 gene 769 60 musculus 302 gi16767870DrosophilaGH02466p 284 36 ~

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit melanogaste r 303 AAE13349Homo SENO- Human TSTP protein, 1652 100 165-015D.

sa iens 303 AAE13348Homo SENO- Human TSTP protein, 589 40 165-015C.

sa iens 303 AAE13350Homo SENO- Human TSTP protein, 314 31 165-015E.

sa iens 304 ABB89737Homo HUMA- Human polypeptide 489 100 SEQ ID NO

sa iens 2113.

304 AAG89173Homo GEST Human secreted protein,489 100 SEQ ID NO:

sa iens 293.

304 AAM25811Homo HYSE- Human protein sequence489 100 SEQ ID

sa iens N0:1326.

305 gi16648454DrosophilaSD01285p 290 30 melanogaste r 305 AAY87336Homo INCY- Human signal peptide 222 28 containing sa iens rotein HSPP-113 SEQ ID N0:113.

305 gi4877582Homo lipoma HMGIC fusion partner222 28 sa iens 306 AAE14439Homo INCY- Human drug metabolising1123 98 enzyme sa iens (DME)-2.

306 ABB84932Homo GETH Human PR03579 protein 1123 98 sequence sa iens SEQ ID N0:232.

306 AAB87576Homo GETH Human PR03579. 1123 98 sa iens 307 gi18857903Homo TCBA1 867 100 sa iens 307 AAG78000Homo BIOW- Human actin 14. 663 100 sa iens 307 ABB89045Homo HUMA- Human polypeptide 644 98 SEQ ID NO

sa iens 1421.

308 gi4580997Mus CAMP inducible 2 protein 2377 87 musculus 308 gi 18676548Homo FLJ00171 protein 1877 100 sa iens 308 gi20073163Mus Similar to solute carrier 1572 60 family 37 (glycerol-musculus 3- hos hate trans orter , member 1 309 AAG71797Homo YEDA Human olfactory receptor755 100 sa iens of a tide, SEQ ID NO: 1478.

309 AAG66336Homo CURA- Human NOV 16 protein 755 100 sequence.

sa iens 309 AAU24615Homo SENO- Human olfactory receptor755 100 sa iens AOLFR108.

31 AAS01280-Homo JANC Human alpha nicotinic 2370 100 1 acetylcholine aal sa iens rece for cDNA se uence.

311 AAD27812-Homo GLAX Human nicotinic acetylcholine2370 100 aal sa iens rece for ene, sb 471005nAChR.

311 AAE17317Homo GLAX Human nicotinic acetylcholine2370 100 sa iens rece for rotein, sb 471005nAChR.

312 gi21518639Homo TSLC1-like 2 1991 97 sa iens 312 gi19068139Mus membrane glycoprotein 1970 96 musculus Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 312 AAM78418 Homo HYSE- Human protein SEQ 1905 97 ID NO 1080.

sa iens 313 AAG67512 Homo SMIK Amino acid sequence 3994 100 of a human sa iens secreted of a tide.

313 AAH78215-Homo SMIK Nucleotide sequence 1659 57 of a human aal sa iens secreted of a tide.

313 AAG67523 Homo SMIK Amino acid sequence 1659 57 of a human sa iens secreted of a tide.

314 ABB90749 Homo UYJO Human Tumour Endothelial2691 100 Marker sa iens of a tide SEQ ID NO 230.

314 ABB90723 Homo UYJO Human Tumour Endothelial2691 100 Marker sa iens of a tide SEQ ID NO 179.

314 gi15987487Homo tumor endothelial marker 2691 100 3 precursor sa iens 315 ABB90749 Homo UYJO Human Tumour Endothelial2600 97 Marker sa iens of a tide SEQ ID NO 230.

315 ABB90723 Homo UYJO Human Tumour Endothelial2600 97 Marker sa iens of a tide SEQ ID NO 179.

315 gi15987487Homo tumor endothelial marker 2600 97 3 precursor sa iens 316 AAG66705 Homo CURA- Human GPCR3 polypeptide.1494 100 sa iens 316 AAG71567 Homo YEDA Human olfactory receptor1414 100 sa iens of a tide, SEQ ID NO: 1248.

316 gi18480740Mus olfactory receptor MOR267-141017 67 musculus 317 AAU83597 Homo GETH Human PRO protein, 690 31 Seq ID No 12.

sa fens 317 ABB 10293Homo HUMA- Human cDNA SEQ ID 651 100 NO: 601.

sa iens 317 ABB10483 Homo HUMA- Human cDNA SEQ ID 642 99 NO: 791.

sa iens 318 gi 10944274Homo bA346K 17.2 (A novel protein2235 100 similar to the Sapiens cell division control protein 91 (CDC91, YLR459W or L9122.2 from Yeast) 318 gi20988986Homo CDC91 cell division cycle 2235 100 91-like 1 (S.

sa iens cerevisiae 318 AAB88430 Homo HELI- Human membrane or 2226 99 secretory sa iens rotein clone PSEC0205.

319 AAY19506 Homo HUMA- Amino acid sequence 1120 100 of a human sa iens secreted rotein.

319 gi~17540010~CaenorhabdiF26D10.11.p 83 28 ref~NP tis elegans 66.1 319 gi~14149748~Mus claudin 15 72 20 ref~NP musculus 65.1 320 gi784990 Homo 5-HTSA serotonin receptor 1645 100 sa iens 320 gi20379144Homo 5-hydroxytryptamine receptor1645 100 sa fens 320 AAR45848 Homo INRM Human 5HT5a serotonin 1611 98 receptor.

sa iens 321 AAS07947-Homo AREN- Human cDNA encoding 1734 100 G-protein as 1 Sapiens coupled rece tor, hRUP20.

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 321 AAD13260_Homo MILL- Human 39406 cDNA. 1734 100 aal sa iens 321 AAM50774 Homo INGE- Human G protein coupled1734 100 receptor sa iens IGPcR20.

322 AAY25806 Homo HUMA- Human secreted protein1663 98 fragment sa iens encoded from gene 23.

322 gi19528215DrosophilaAT30101p 1012 38 melanogaste r 322 AAM93717 Homo HELI- Human polypeptide, 1011 100 SEQ ID NO:

sa iens 3663.

323 AAB 12119Homo PROT- Hydrophobic domain 448 100 protein from sa fens clone HP02869 isolated from KB cells.

323 gi4827164Gluconacetosimilar to melibiose carrier89 26 protein of E.coli bacter x linus 323 gi595475 Homo hFcRn 84 31 sa iens 324 AAY25736 Homo HUMA- Human secreted protein343 100 encoded sa iens from ene 26.

325 AAB44336 Homo HUMA- Human secreted protein169 100 encoded sa iens b ene 2 clone HROAM11.

325 gi~12045265~MycoplasmaATP synthase F0, subunit 65 44 B (atpF) ref)NP genitalium 76.1 325 gig 18447301DrosophilaLD26265p 65 31 ~

gb~AAL682melanogaste 25.1 r 326 gi 14278927Mus gliacolin 1291 94 musculus 326 gi10566471Mus Gliacolin 1291 94 musculus 326 gi3747097Homo Clq-related factor 976 70 sa iens 327 gi13506225Mus ST7 protein forml splice 2996 99 variant a musculus 327 gi 19353275Mus Similar to suppression of 2940 98 tumorigenicity 7 musculus 327 gi9230665Homo FAM4A1 splice variant a 2857 95 sa iens 328 gi9230665Homo FAM4A1 splice variant a 2709 94 sa iens 328 gi13506227Mus ST7 protein forml splice 2702 94 variant 6 musculus 328 gi 13506225Mus ST7 protein forml splice 2668 90 variant a musculus 329 gi9230667Homo FAM4A1 splice variant b 2859 99 sa iens 329 gi13506225Mus ST7 protein forml splice 2848 96 variant a musculus 329 gi19353275Mus Similar to suppression of 2792 95 tumorigenicity 7 musculus 330 AAU19222 Homo PHAA Human G protein-coupled467 100 receptor sa iens nGPCR-2343.

330 AAV25491 Homo BGHM cDNA for E stein Barr 317 38 virus Table 2B
SEQ Hit ID Species Description S Percent ID score identit aal sa iens induced ene 2 (EBI-2).

330 AAY90630Homo AREN- Human G protein-coupled317 38 receptor sa iens EBI2.

331 AAB94231Homo HELI- Human protein sequence3584 99 SEQ ID

sa iens N0:14604.

331 AAB95784Homo HELI- Human protein sequence3570 100 SEQ ID

sa iens N0:18737.

331 gi10880791Homo PP791 protein 3329 99 sa iens 332 AAY23325Homo GETH A33 related antigen 105 27 JAM.

sa iens 332 gi3462455Mus functional adhesion molecule105 27 musculus 332 gi8650528Rattus functional adhesion molecule98 26 JAM

norvegicus 333 AAG93279Homo NISC- Human protein HP03145.1977 99 sa iens 333 gi14250676Homo Similar to RIKEN cDNA 2310002F181977 99 gene sa iens 333 AAY27589Homo HUMA- Human secreted protein1578 100 encoded sa iens b ene No. 23.

334 gi953239Homo tetraspan membrane protein996 91 sa iens 334 gi 12655071Homo transmembrane 4 superfamily996 91 member 4 sa iens 334 gi11493837Rattus tetraspan protein LRTM4 91 81 norve icus 335 AAB94238Homo HELI- Human protein sequence3039 99 SEQ ID

sa iens N0:14621.

335 AAB87342Homo HUMA- Human gene 1 encoded3033 99 secreted sa iens rotein HETHR73, SEQ ID
N0:83.

335 AAU23815Homo UROG- Human prostate-related3016 99 gene sa iens 103P2D6 encoded rotein.

336 gi14336694Homo M83 4100 99 sa iens 336 gi18204292Homo transmembrane protein 8 4096 99 (five membrane-sa iens s arming domains) 336 gi10716072Homo M83 protein 4089 99 sa iens 337 AAD02700_Homo REGC Human glycosyl sulfotransferase-2056 100 aal sa iens 4beta (GST-4beta cDNA.

337 AAE 15438Homo 1NCY- Human drug metabolising2056 100 enzyme sa iens DME -5.

337 AAY72640Homo REGC Human glycosyl sulfotransferase-2056 100 sa iens 4beta (GST-4beta).

338 AAB82971Homo MILL- G protein coupled 1631 99 receptor 43238.

sa iens 338 gi18480770Mus olfactory receptor MOR271-11373 83 musculus 338 gi18479336Mus olfactory receptor MOR270-11367 83 musculus 339 AAB82971Homo MILL- G protein coupled 1562 99 receptor 43238.

sa iens 339 gi18479336Mus olfactory receptor MOR270-11338 85 musculus Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 339 gi18480770Mus olfactory receptor MOR271-11336 84 musculus 340 gi7960136Homo neuroligin 3 isoform 4557 100 sa iens 340 gi1145791Rattus neuroligin 3 4505 98 norve icus 340 gi7960135Homo neuroligin 3 isoform 4419 97 sa iens 341 ABB07253Homo LEXI- Human novel GPCR (NGPCR)3943 99 sa iens rotein.

341 AAM69607Homo MOLE- Human bone marrow 1770 82 expressed sa iens robe encoded rotein SEQ
ID NO: 29913.

341 AAM57201Homo MOLE- Human brain expressed1770 82 single exon sa iens robe encoded rotein SEQ
ID NO: 29306.

342 AAG72315Homo YEDA Human olfactory receptor1140 76 sa iens of a tide, SEQ ID NO: 1996.

342 AAE18020Homo CURA- Human G-protein coupled915 96 receptor-sa iens 7 GPCR-7 rotein.

342 AAU24629Homo SEND- Human olfactory receptor859 89 sa iens AOLFR123.

343 AAB95124Homo HELI- Human protein sequence1552 81 SEQ ID

sa iens N0:17122.

343 gi854065Human U88 802 46 herpesvirus 343 AAM40934Homo HYSE- Human polypeptide 435 36 SEQ ID NO

sa iens 5865.

344 AAG71823Homo VEDA Human olfactory receptor1627 100 sa iens of a tide, SEQ ID NO: 1504.

344 AAU24669Homo SENO- Human olfactory receptor1627 100 sa iens AOLFR 167.

344 AAE11910Homo CURA- Human G-protein coupled1627 100 receptor sa iens 15a GPCRISa) rotein.

345 AAU00437Homo COUN- Human dendritic cell 2867 88 membrane sa iens rotein FIRE.

345 AAY91625Homo HUMA- Human secreted protein1966 97 sequence sa iens encoded b ene 22 SEQ ID
N0:298.

345 gi16930385Mus seven-span membrane protein1838 55 FIRE

musculus 346 AAU00437Homo COUN- Human dendritic cell 2341 87 membrane sa iens rotein FIRE.

346 AAY91625Homo HUMA- Human secreted protein1966 97 sequence sa iens encoded b ene 22 SEQ ID
N0:298.

346 gi16930385Mus seven-span membrane protein1535 59 FIRE

musculus 347 ABB94047Homo HUMA- Human secreted protein84 31 SEQ ID

sa iens NO: 90.

347 ABB94023Homo HUMA- Human secreted protein84 31 SEQ ID

sa iens NO: 66.

347 gi~21288752~AnophelesebiP7790 537 34 gb~EAA010gambiae str.

45.1 PEST

348 AAW75000Homo HUMA- Human secreted protein349 100 encoded sa iens b ene 146 clone HSNAK17.

348 ABB03792Homo ~ HUMA- Human musculoskeletal70 28 system Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa iens related of a tide SEQ ID
NO 1739.

348 gi~17542842~CaenorhabdiW08E12.8.p 69 39 reflNP tis elegans 10.1 349 gi19684136Homo Similar to RIKEN cDNA 4933413N12178 26 gene sa iens 349 gi841378SaccharomyGpi2p 90 30 ces cerevisiae 349 gi295139StaphylococORFB 79 31 cus 1u dunensis 350 AAB88406Homo HELI- Human membrane or 1421 99 secretory sa iens rotein clone PSEC0162.

350 ABB50346Homo HUMA- Human secreted protein476 95 encoded sa iens b ene 46 SEQ ID N0:294.

350 AAW88579Homo HUMA- Secreted protein encoded476 95 by gene sa iens 46 clone HCFMV39.

351 gi292793Homo T-cell receptor beta 636 98 sa iens 351 AAM76093Homo MOLE- Human bone marrow 594 93 expressed sa iens robe encoded rotein SEQ
ID NO: 36399.

351 AAM63281Homo MOLE- Human brain expressed594 93 single exon sa iens robe encoded rotein SEQ
ID NO: 35386.

352 AAY10839Homo HUMA- Amino acid sequence 225 95 of a human sa iens secreted rotein.

353 AAY16784Homo GEMY Human secreted protein488 100 (clone sa iens co 1000 1 .

353 gi1850866Macropus ATPase subunit 8 69 31 robustus 353 gi2935032RhodococcuCIcR 68 42 s o acus 354 gi~21293186~AnophelesagCP9246 71 26 gb~EAA053gambiae str.

31.1 PEST

355 AAA40083-Homo ICAZU- Human brain-specific1553 51 aal Sapiens transmembrane glycoprotein encoding cDNA.

355 AAB 12448Homo CHUG- Human hh00149 protein1553 51 SEQ ID

sa iens N0:4.

355 AAB09968Homo ICAZU- Human brain-specific1553 51 sa iens transmembrane 1 co rotein.

356 AAB50953Homo GETH Human PR0534 protein. 1760 95 sa iens 356 AAB73689Homo INCY- Human oxidoreductase 1760 95 protein ORP-sa iens 22.

356 AAB44303Homo GETH Human PR0534 (UNQ335) 1760 95 protein sa iens se uence SEQ ID N0:410.

357 gi12276180Homo metalloprotease-disintegrin5255 99 meltrin beta sa iens 357 AAE19181Homo 1NCY- Human protease, PRTS-184967 99 protein.

sa iens 357 gi12802370Homo disintegrin and metalloproteinase4967 99 sa iens 358 gi18056675Homo FREB 1969 98 Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa fens 358 gi21245136Homo FCRLaI 1940 99 sa iens 358 AAE03451Homo HUMA- Human gene 25 encoded1888 98 secreted sa iens rotein HRGBL78, SEQ ID NO:
134.

359 gi18056675Homo FREB 1986 99 sa iens 359 AAE03451Homo HUMA- Human gene 25 encoded1905 99 secreted sa iens rotein HRGBL78, SEQ ID NO:
134.

359 AAB34744Homo ALPH- Human secreted protein1905 99 encoded by sa iens DNA clone v 24 1.

360 AAW74807Homo HUMA- Human secreted protein270 100 encoded sa iens b gene 79 clone HSKNE46.

360 AA002082Homo HYSE- Human polypeptide 69 41 SEQ ID NO

sa iens 15974.

360 AAB34697Homo ALPH- Human secreted protein66 45 encoded by sa iens DNA clone v 6 1.

361 gi17861418DrosophilaGH03649p 226 35 melanogaste r 361 gi6959684Mus glycolipid transfer protein95 24 musculus 361 gi16741551Mus Similar to glycolipid transfer95 24 protein musculus 362 AAE06578Homo SAGA Human protein having 2337 100 hydrophobic sa iens domain, HP 10769.

362 gi13623231Homo Similar to RIKEN cDNA 1200013A082337 100 gene sa iens 362 AAB92464Homo HELI- Human protein sequence2272 98 SEQ ID

sa iens N0:10520.

363 AAU12211Homo GETH Human PR01886 polypeptide1639 99 sa iens se uence.

363 gi~17542564~CaenorhabdiT26A8.2.p 189 21 ref~NP tis elegans 34.1 363 gi~21298000~AnophelesagCP15426 127 18 gb~EAA101gambiae str.

45.1 PEST

364 ABB05715Homo GEHU- Human transmembrane 1237 100 protein sa iens clone tes3 17121.

364 AAU27674Homo ZYMO Human protein AFP669232.649 48 sa iens 364 AAB24463Homo HUMA- Human secreted protein648 48 sequence sa iens encoded b ene 27 SEQ ID
N0:88.

365 g114582572Homo orphan transporter SLC19A3 2549 100 sa iens 365 gi1~2483888Homo solute carrier 19A3 2549 100 sa iens 365 g1 12483890Mus solute carrier 19A3 1713 68 musculus 366 AAM41254Homo HYSE- Human polypeptide 632 90 SEQ ID NO

sa iens 6185.

366 ABB11854Homo HYSE- Human secreted protein632 90 homologue, sa iens SEQ ID N0:2224.

366 ABB89257Homo HUMA- Human of a tide SEQ 631 99 ID NO

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa iens 1633.

367 AAB94138Homo HELI- Human protein sequence2598 100 SEQ ID

sa iens N0:14406.

367 gi15866720Homo fukutin-related protein 2598 100 sa iens 367 gi17945162DrosophilaRE09574p 354 23 melanogaste r 368 AAE 14448Homo INCY- Human drug metabolising2002 99 enzyme sa iens (DME -11.

368 AAB85780Homo INCY- Human drug metabolizing1797 98 enzyme sa iens (ID No. 7256116CD 1 .

368 gi4519535Homo Leukotriene B4 omega-hydroxylase1222 64 sa iens 369 gi18157547Mus pecanex-like 3 1809 95 musculus 369 gi15076843Homo pecanex-like protein 1 872 34 sa iens 369 AAM42412Homo HUMA- Human polypeptide 743 100 SEQ ID NO

sa iens 145.

370 AAB61219Homo MILL- Human TANGO 292 protein.1201 100 sa iens 370 gi14603178Homo transmembrane gamma-carboxyglutamic1201 100 sa iens acid rotein 4 370 gi12656635Homo transmembrane gamma-carboxyglutamic1201 100 sa iens acid rotein 4 TMG4 371 AAM40584Homo HYSE- Human polypeptide 2045 95 SEQ ID NO

sa iens 5515.

371 ABB 10286Homo HUMA- Human cDNA SEQ ID 2045 95 NO: 594.

sa iens 371 ABB 10269Homo HUMA- Human cDNA SEQ ID 2045 95 NO: 577.

sa iens 372 gi1510143Homo similar to C.elegans protein1624 55 encoded in sa iens cosmid T20D3 (Z68220 .

372 ABB89128Homo HUMA- Human polypeptide 1359 98 SEQ ID NO

sa iens 1504.

372 AAY53635Homo CHIR A bone marrow secreted1148 51 protein sa iens designated BMS53.

373 AAB93444Homo HELI- Human protein sequence1006 87 SEQ ID

sa iens N0:12686.

373 ABB89562Homo HUMA- Human polypeptide 998 86 SEQ ID NO

sa iens 1938.

373 gi15209353CaenorhabdiY39B6A.1 138 45 tis ele ans 374 AAM06271Homo HYSE- Human foetal protein,426 98 SEQ ID NO:

sa iens 2.

374 gi190203Homo potassium channel 76 32 sa iens 374 gi10176968Arabidopsisreceptor-like protein kinase76 31 thaliana 375 gi5542014Homo dyskerin 2616 91 sa iens 375 AAY33675Homo DEKR- Human DKC1 protein. 2549 90 sa iens 375 gi3.135028Homo dyskerin 2549 90 Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa iens 376 gi5542014Homo dyskerin 2492 94 sa iens 376 AAY33675 Homo DEKR- Human DKC1 protein. 2425 92 sa iens 376 gi3135028Homo dyskerin 2425 92 sa iens 377 gi1763011Homo lysophospholipase homolog 1444 90 sa iens 377 gi13623261Homo lysophospholipase-like 1444 90 sa iens 377 gi14594904Homo monoglyceride lipase 1390 90 sa iens 378 gi1763011Homo lysophospholipase homolog 1589 92 sa iens 378 gi13623261Homo lysophospholipase-like 1589 92 sa iens 378 gi14594904Homo monoglyceride lipase 1535 92 sa iens 379 ABB90165 Homo HUMA- Human polypeptide 571 93 SEQ ID NO

sa iens 2541.

379 AAY94946 Homo GEMY Human secreted protein571 93 clone sa iens cd205 2 rotein se uence SEQ ID N0:98.

379 AAY53051 Homo GEMY Human secreted protein318 59 clone sa iens dd119 4 rotein se uence SEQ ID N0:108.

380 AAM93503 Homo HELI- Human polypeptide, 1082 92 SEQ ID NO:

sa iens 3213.

380 AAY77122 Homo INCY- Human neurotransmission-associated1082 92 sa iens rotein NTAP) 414692.

380 gi6523817Homo SlRprotein 1082 92 sa iens 381 AAE07124 Homo HUMA- Human gene 16 encoded931 91 secreted sa iens rotein fra ment, SEQ ID
N0:141.

381 AAE07099 Homo HUMA- Human secreted protein,931 91 SEQ ID

sa iens N0:116.

381 gi6980032Mus ARL-6 interacting protein-1907 88 musculus 382 gi21430284DrosophilaLD38689p 1292 40 melanogaste r 382 AAM80289 Homo HYSE- Human protein SEQ 191 30 ID NO 3935.

sa iens 382 AAM79305 Homo HYSE- Human protein SEQ 191 30 ID NO 1967.

sa iens 383 AAG73684 Homo HUMA- Human colon cancer 1863 98 antigen sa iens rotein SEQ ID N0:4448.

383 AAY48312 Homo META- Human prostate cancer-associated1509 100 sa iens rotein 9.

383 gi17389322Homo Similar to NICE-5 protein 1419 74 sa iens 384 AAB93185 Homo HELI- Human protein sequence2492 100 SEQ ID

sa iens N0:12134.

384 AAM93581 Homo HELI- Human polypeptide, 1971 96 SEQ ID NO:

sa iens 3373.

384 AAE10328 Homo INCY-Human transporter and 1873 100 ~ ~ ion channel-5 ~

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa iens (TRICH-5 rotein.

385 ABB89951Homo HUMA- Human polypeptide 2862 99 SEQ ID NO

sa iens 2327.

385 AAB58984Homo HUMA- Breast and ovarian 759 94 cancer Sapiens associated antigen protein sequence SEQ ID

692.

385 ABB04610Homo BODA- Human quinoprotein 244 27 dehydrogenase sa iens 33 rotein SEQ ID N0:2.

386 ABB89951Homo HUMA- Human polypeptide 2791 98 SEQ ID NO

sa iens 2327.

386 AAB58984Homo HUMA- Breast and ovarian 688 89 cancer Sapiens associated antigen protein sequence SEQ ID

692.

386 ABB04610Homo BODA- Human quinoprotein 251 28 dehydrogenase sa iens 33 rotein SEQ ID N0:2.

387 AAM93354Homo HELI- Human polypeptide, 531 100 SEQ ID NO:

sa iens 2907.

387 AAM00917Homo HYSE- Human bone marrow 495 99 protein, SEQ

sa iens ID NO: 393.

387 gi18308220Xenopus transmembrane protein quicken333 77 laevis 388 AAU12232Homo GETH Human PR04398 polypeptide2696 100 sa iens se uence.

388 ABB90111Homo HUMA- Human polypeptide 1784 99 SEQ ID NO

sa iens 2487.

388 gi14860862Homo polyamine oxidase isoform-1932 39 sa iens 389 AAM00947Homo HYSE- Human bone marrow 6659 98 protein, SEQ

sa iens ID NO: 423.

389 AAM00834Homo HYSE- Human bone marrow 4723 100 protein, SEQ

sa iens ID NO: 197.

389 AAY99666Homo 1NCY- Human GTPase associated3647 97 protein-sa iens 17.

390 AAE17492Homo INCY- Human secretion and 1705 100 trafficking sa iens rotein-1 SAT-1).

390 gi13529623Mus Similar to RIKEN cDNA 4930418P061408 81 gene musculus 390 gi~21313292~Mus RIKEN cDNA 4930418P06 1401 80 ref)NP musculus 53.1 391 AAB36613Homo INCY- Human FLEXHT-35 protein1121 85 sa iens se uence SEQ ID N0:35.

391 gi14603247Homo Similar to RIKEN cDNA 57304096151121 85 gene sa iens 391 AAB93042Homo HELI- Human protein sequence240 90 SEQ ID

sa iens N0:11827.

392 AAB82940Homo UYNY Human androgen receptor299 39 trapped sa iens rotein 5 ARTS).

392 AAB56085Homo HUMA- Human secreted protein299 39 sequence sa iens encoded b ene 9 SE ID N0:179.

392 gi18043859Mus Similar to RIKEN cDNA 9430098E02251 42 gene musculus 393 AAM39990Homo HYSE- Human polypeptide 1209 70 SEQ ID NO

sa iens 3135.

393 AAM38999Homo NYSE- Human of a tide SEQ 1209 70 ID NO

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa iens 2144.

393 AAB 18993Homo INCY- Amino acid sequence 1209 70 of a human sa iens transmembrane rotein.

394 gi4220892Homo transcriptional co-activator919 97 sa iens 394 gi7141322Homo p37 TRAP/SMCC/PC2 subunit 918 97 sa iens 394 gi16741439Mus RIKEN cDNA 1500015J03 gene 918 97 musculus 395 gi1.825729CaenorhabdiC. elegans PTR-2 protein 1024 30 (corresponding tis elegansse uence C32E8.8) 395 gi3880799CaenorhabdiY39A1B.2 940 29 tis ele ans 395 gi15718594CaenorhabdiC. elegans PTR-10 protein 818 28 (corresponding tis elegansse uence F55F8.1) 396 AAB20342Homo UYMC- Peroxisome proliferator-activated2265 94 sa iens rece toral ha.

396 AAR74053Homo LIGA- Human peroxisome proliferator2265 94 sa iens activated rece tor.

396 gi765240Homo peroxisome proliferator 2265 94 activated receptor sa iens al ha; PPAR al ha 397 ABB 11934Homo HYSE- Human transmembrane 1692 100 protein sa iens homologue, SEQ ID N0:2304.

397 AAB43983Homo HUMA- Human cancer associated1692 100 protein sa iens se uence SEQ ID N0:1428.

397 AAH47123-Homo NIGE- Human B 1466 protein 1409 100 encoding aal sa iens cDNA.

398 gi19526687Mus Na-H exchanger isoform NHE82829 96 musculus 398 gi5304871Homo dJ963K23.4 (continues in 2236 100 dJ1041C10 sa iens (AL162615 398 gi17862784DrosophilaLP02993p 1535 55 melanogaste r 399 AAB93258Homo HELI- Human protein sequence1617 99 SEQ ID

sa iens N0:12282.

399 AAY28810Homo GEMY nn296 2 secreted protein.1617 99 sa iens 399 ABB89196Homo HUMA- Human polypeptide 1319 99 SEQ ID NO

sa iens 1572.

400 AAG00388Homo GEST Human secreted protein,316 100 SEQ ID NO:

sa iens 4469.

401 AAU21958Homo HUMA- Human cardiovascular 97 26 system sa iens anti en of a tide SEQ ID
No 732.

401 gi 1814196CaenorhabdiA013 ankyrin 87 31 tis ele ans 401 gi19110782Homo DNA helicase HEL308 81 25 sa iens 402 gi21438549Homo humane cDNA 2566 99 sa iens 402 gi21438547Rattus Ratten cDNA 2444 93 norve icus 402 gi21438551Mus genomische DNA Exon I der 691 91 Maus musculus 403 AAE04759Homo INCY- Human vesicle trafficking1013 100 protein-2 ~

Table 2B
SEQ Hit ID Species Description S Percent ID score identit sa iens (VETRP-2) rotein.

403 AAB98207Homo SHAN- Human P24 protein-221009 99 SEQ ID

sa iens N0:2.

403 gi16118876Homo vesicular membrane protein1009 99 sa iens 404 ABB 14761Homo HUMA- Human nervous system873 95 related sa iens of a tide SEQ ID NO 3418.

404 AAU25439Homo INCY- Human mddt protein 524 38 from clone sa iens LG:403872.1:2000MAY19.

404 AAU75787Homo INCY- Human protein phosphatase444 36 5 (PP5) sa iens rotein se uence.

405 AAM93259Homo HELI- Human polypeptide, 1257 100 SEQ ID NO:

sa iens 2709.

405 gi16877659Homo Similar to RIKEN cDNA 18100540131157 98 gene sa iens 405 AAG81420Homo ZYMO Human AFP protein 137 40 sequence SEQ

sa iens ID N0:358.

406 gi12214288Homo dJ402H5.2 (novel protein 1397 50 similar to worm sa iens and fl roteins) 406 gi3880799CaenorhabdiY39A 1 B.2 707 25 tis ele ans 406 gi 1825729CaenorhabdiC. elegans PTR-2 protein 602 24 (corresponding tis ele se uence C32E8.8) ans 407 gi19338984Homo fat cell-specific low molecular135 44 weight sa iens rotein beta 407 gi19071802Homo fat cell-specific low molecular135 44 weight sa iens rotein al ha 407 gi20380358Mus RIKEN cDNA 1110025612 gene121 31 musculus 408 ABB90225Homo HUMA- Human polypeptide 952 100 SEQ ID NO

sa iens 2601.

408 AAB 12150Homo PROT- Hydrophobic domain 952 100 protein sa iens isolated from HT-1080 cells.

408 ABB06157Homo COMP- Human NS protein 944 98 sequence SEQ

sa iens ID N0:249.

409 gi15074997SinorhizobiuCONSERVED HYPOTHETICAL 96 32 m melilotiPROTEIN

409 gi~20868002~Mus similar to expressed sequence75 28 rellXP-1373musculus 98.1 410 AAY57279Homo YEDA Transcription factor 3902 98 subunit sa iens TAFII105 0l a tide.

410 AAW31494Homo REGC Human hTAFII105 protein.3902 98 sa iens 410 gi1669689Homo TBP associated factor 3902 98 sa iens 411 AAE04639Homo MILL- Human novel transmembrane1588 98 sa iens rotein, 32164 rotein.

411 AAE18658Homo INCY- Human G-protein coupled1548 98 receptor sa iens (GCREC-19).

411 AAG71672Homo YEDA Human olfactory receptor1202 94 sa iens of a tide, SEQ ID NO: 1353.

412 ABB 11920Homo HYSE- Human adrenomedullin1795 95 receptor sa iens homolo ue, SEQ ID N0:2290.

412 AAY16630Homo SMIK Human Putative Adrenomedullin1789 94 ~ ~

Table 2B
SEQ Hit ID Species Description S Percent ID score identit sa iens Rece for (PAR).

412 gi292419Homo orphan receptor 1774 93 sa iens 413 AAY95002Homo ALPH- Human secreted protein1027 56 vc34-1, sa iens SEQ ID N0:44.

413 ABB 12222Homo HYSE- Human secreted protein697 76 homologue, sa iens SEQ ID N0:2592.

413 AAM95374Homo HUMA- Human reproductive 477 65 system related sa iens anti en SEQ ID NO: 4032.

414 ABB89474Homo HUMA- Human polypeptide 1004 98 SEQ ID NO

sa iens 1850.

414 AAB56877Homo ROSE/ Human prostate cancer1004 98 antigen sa iens rotein se uence SEQ ID
N0:1455.

414 gi18044902Mus Similar to RIKEN cDNA 3110005623851 65 gene musculus 415 gi179165Homo Na,K-ATPase subunit alpha 5238 99 sa iens 415 gi203029Rattus (Na+ and K+) ATPase, alpha+5205 98 catalytic norve subunit recursor icus 415 gi212406Gallus Na,K-ATPase alpha-2-subunit4977 93 anus 416 gi18606367Mus RIKEN cDNA 4930570003 gene715 92 musculus 416 AAB90649Homo HUMA- Human secreted protein,562 97 SEQ ID

sa iens NO: 192.

416 AAB90565Homo HUMA- Human secreted protein,472 100 SEQ ID

sa iens NO: 103.

417 gi18512192Homo polycystic kidney and hepatic1871 100 disease 1 sa iens 417 gi178273Homo alanine:glyoxylate aminotransferase77 26 sa iens 417 gi28S61 Homo L- alanine:glyoxylate aminotransferase77 26 sa iens 418 gi13249295Homo anion exchanger AE4 4951 100 sa iens 418 gi7363254Homo sodium bicarbonate cotransporter4898 98 S

sa iens 418 gi13517508Homo sodium bicarbonate cotransporter4873 95 sa iens 419 gi2564913Homo metaxin 1108 82 sa iens 419 gi12804907Homo Similar to metaxin 1 1100 99 sa iens 419 gi807670Mus metaxin 995 89 musculus 420 gi2564913Homo metaxin 1665 100 sa iens 420 gi18606009Mus metaxin 1528 91 musculus 420 gi12804907Homo Similar to metaxin 1 1470 90 sa iens 421 gi6094684Homo similar to Kelch proteins;694 31 similar to sa iens BAA77027 PID: 4650844 421 AAB93480Homo HELI- Human protein sequence630 29 SEQ ID

sa iens N0:12768.

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 421 AAU28187Homo HYSE- Novel human secretory628 29 protein, Seq sa iens ID No 356.

422 gi14715068Homo Similar to RIKEN cDNA 2600001A112062 100 gene sa iens 422 gi4808241Homo dJ466N1.2 (glycine C-acetyltransferase853 89 (2-sa iens amino-3-ketobut ate coenz me A 1i ase) 422 gi3342906Homo 2-amino-3-ketobutyrate-CoA 853 89 ligase sa iens 423 AAB65162Homo GETH Human PR0290 (UNQ253) 1972 100 protein sa iens se uence SE ID N0:33.

423 AAY66639Homo GETH Membrane-bound protein1972 100 PR0290.

sa iens 423 AAB24058Homo GETH Human PR0290 protein 1972 100 sequence sa iens SEQ ID N0:7.

424 gi167835Dictyosteliumyosin heavy chain 142 24 m discoideum 424 gi2983243Aquifex chromosome assembly protein140 20 homolog aeolicus 424 AAB95546Homo HELI- Human protein sequence132 25 SEQ ID

sa iens N0:18167.

425 AAB43587Homo HUMA- Human cancer associated427 100 protein sa iens se uence SEQ ID N0:1032.

425 AAM52659Homo BIOW- Human phosphatase 423 98 9.

sa iens 425 AAG00658Homo GEST Human secreted protein,360 97 SEQ ID NO:

sa iens 4739.

426 gi13325388Homo Similar to RIKEN cDNA 1110007009821 88 gene sa iens 426 ABB89804Homo HUMA- Human polypeptide 814 87 SEQ ID NO

sa iens 2180.

426 AAG73935Homo HUMA- Human colon cancer 299 95 antigen sa iens rotein SEQ ID N0:4699.

427 AAB93249Homo HELI- Human protein sequence731 49 SEQ ID

sa iens N0:12263.

427 AAB 18977Homo INCY- Amino acid sequence 615 89 of a human sa iens transmembrane rotein.

427 AAE01518Homo HUMA- Human gene 2 encoded 495 98 secreted sa iens rotein fra ment, SEQ ID
N0:175.

428 AAB 18977Homo INCY- Amino acid sequence 1008 100 of a human sa iens transmembrane rotein.

428 AAB93249Homo HELI- Human protein sequence756 43 SEQ ID

sa iens N0:12263.

428 AAY00276Homo HUMA- Human secreted protein603 100 encoded sa iens b gene 19.

430 gi7644318Mesocricetucasein kinase I epsilon; 1564 99 CKI epsilon s auratus 430 gi13122442Rattus casein kinasel epsilon-2 1564 99 norve icus 430 gi9650968Rattus casein kinase 1 epsilon-3 1564 99 norve icus 431 gi2642187Rattus endo-alpha-D-mannosidase 1973 87 norve icus 431 AAB95204Homo HELI- Human protein sequence1559 99 SEQ ID

sa iens N0:17303.

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 431 AAE04255Homo HUMA- Human gene 4 encoded 1408 98 secreted sa iens rotein fra ment, SEQ ID
N0:116.

432 ABB05662Homo GEHU- Human signal transduction139 36 protein sa iens clone am 2 10h17.

432 AAU16313Homo HUMA- Human novel secreted 139 36 protein, Seq sa iens ID 1266.

432 gi21040537Homo Similar to RIKEN cDNA 9130020610132 35 gene sa iens 433 AAG89209Homo GEST Human secreted protein,460 97 SEQ ID NO:

sa iens 329.

433 gi1890812Flexamia NADH dehydrogenase 1 71 24 raminea 433 gi~21295981AnophelesagCP 1281 73 28 ~

gb~EAA081gambiae str.

26.1 PEST

434 AAY91533Homo HUMA- Human secreted protein1159 100 sequence sa iens encoded b gene 83 SEQ ID
N0:206.

434 gi2150013Homo transmembrane protein 1159 100 sa iens 434 gi12803197Homo claudin 5 (transmembrane 1159 100 protein deleted in sa iens velocardiofacial s ndrome) 435 AAE06609Homo SAGA Human protein having 498 42 hydrophobic sa iens domain, HP 10800.

435 ABB89766Homo HUMA- Human polypeptide 497 42 SEQ ID NO

sa iens 2142.

435 AAB93645Homo HELL- Human protein sequence497 42 SEQ ID

sa iens N0:13146.

436 gi 11640570Homo MSTP031 777 100 sa iens 436 ABB50826Homo HUMA- Human secreted protein75 40 encoded sa iens b ene 77 SEQ ID N0:779.

436 gi15291231DrosophilaGH13214p 72 25 melanogaste r 437 AAG73464Homo HUMA- Human gene 7-encoded 2264 98 secreted sa iens rotein fra ment, SEQ ID
N0:239.

437 AAG73462Homo HUMA- Human gene 7-encoded 1897 100 secreted sa iens rotein fra ment, SEQ ID
N0:237.

437 AAG73463Homo HUMA- Human gene 7-encoded 1878 98 secreted sa iens rotein fra ment, SEQ ID
N0:238.

438 gi9886738Homo junctophilin type3 3916 99 sa iens 438 gi9927307Mus junctophilin type 3 3551 90 musculus 438 gi9886757Homo junctophilin type3 3172 100 sa iens 439 ABB89241Homo HUMA- Human polypeptide 739 96 SEQ ID NO

sa iens 1617.

439 i 18762530Danio envelo a rotein 380 47 rerio 439 AAB08894Homo HUMA- Human secreted protein240 64 sequence sa iens encoded b ene 4 SEQ ID N0:51.

440 AAB43484Homo HUMA- Human cancer associated761 100 protein sa iens se uence SEQ ID N0:929.

440 gi10834676Homo PP3856 673 99 sa iens Table 2B
SEQ Hit ID Species Description S Percent ID score identit 440 gi21428806DrosophilaGH04243p 636 49 melanogaste r 441 AAB43484Homo HUMA- Human cancer associated761 100 protein sa iens se uence SEQ ID N0:929.

441 gi21428806DrosophilaGH04243p 636 49 melanogaste r 441 gi14247685Staphylococnicotinate phosphoribosyltransferase544 34 cus aureushomolog subsp.

aureus Mu50 442 AAB43484Homo HUMA- Human cancer associated761 100 protein sa iens se uence SEQ ID N0:929.

442 gi21428806DrosophilaGH04243p 636 49 melanogaste r 442 gi10834676Homo PP3856 582 89 sa iens 443 ABB 11177Homo HYSE- Human phosphatidate 952 98 Sapiens phosphohydrolase homologue, SEQ ID

N0:1547.

443 AAG89279Homo GEST Human secreted protein,641 66 SEQ ID NO:

sa iens 399.

443 AAB70690Homo SREN- Human hDPP protein 639 65 sequence SEQ

sa iens ID N0:7.

444 AAM40391Homo HYSE- Human polypeptide 672 48 SEQ ID NO

sa iens 3536.

444 AAM42177Homo HYSE- Human polypeptide 567 49 SEQ ID NO

sa iens 7108.

444 ABB90382Homo HUMA- Human polypeptide 559 42 SEQ ID NO

sa iens 2758.

445 gi19354040Mus Similar to RIKEN cDNA 1810038N08853 95 gene musculus 445 gi 1403547SaccharomyP2558 protein 175 26 ces cerevisiae 445 AAE15269Homo INCY- Human RNA metabolism78 28 protein-32 sa iens (RMEP-32 .

446 gi15157363AgrobacteriAGR C 4025p 256 31 um tumefaciens str. C58 (Cereon 446 gi15075368SinorhizobiuCONSERVED HYPOTHETICAL 243 3l m melilotiPROTEIN

446 gi21324924CorynebacteUncharacterized ACR 192 28 rium glutamicum ATCC

447 gi20069113Homo corneal endothelium specific1201 100 protein 1 sa iens 447 112584947Homo ovar -s ecific acidic rotein1195 100 Table 2B
SEQ Hit ID Species Description S Percent ID score identit sa iens 447 gi15214757Mus Similar to RIKEN cDNA 4930583H14558 50 gene musculus 448 AAT92305-Homo SALK Constitutively active1686 94 receptor-alpha as 1 sa iens encoding cDNA.

448 AAG63170Homo TULA- Amino acid sequence 1686 94 of human sa iens CAR-a of a tide.

448 AAW93902Homo GEHO Human CAR receptor 1686 94 protein.

sa iens 449 118182375Bos taurushotorece for cadherin 2693 86 449 g114625447Rattus MT-protocadherin 2563 83 norve icus 449 g118182377Mus photoreceptorcadherin 2561 83 musculus 450 AAM39421Homo HYSE- Human polypeptide 126 27 SEQ ID NO

sa iens 2566.

450 g1 18676458Homo FLJ00126 protein 126 27 sa iens 450 g117861384Homo nesprin-2 gamma 126 27 sa iens 451 gil 1967375Rattus Dvl-binding protein Idax 1062 100 norve icus 451 g111967377Homo Dvl-binding protein IDAX 1062 100 sa iens 451 ABB 16307Homo HUMA- Human nervous system1006 100 related sa iens of a tide SEQ ID NO 4964.

452 g120073201Homo Similar to Olg-I bHLH protein1301 100 sa iens 452 g14929538Rattus Olg-1 bHLH protein 1086 87 norve icus 452 g17385152Mus oligodendrocyte-specific 1069 86 bHLH

musculus transcri tion factor Oligl 453 AAM68085Homo MOLE- Human bone marrow 6900 99 expressed sa iens robe encoded rotein SEQ
ID NO: 28391.

453 AAM55707Homo MOLE- Human brain expressed6900 99 single exon sa iens robe encoded rotein SEQ
ID NO: 27812.

453 g118146660Homo DPCR1 1206 100 sa iens 454 AAG75611Homo HUMA- Human colon cancer 1759 89 antigen sa iens rotein SEQ ID N0:6375.

454 AAY13942Homo SAGA Human transmembrane 1759 89 protein, sa iens HP01737.

454 g115559308Homo Similar to serologically 1759 89 defined breast sa iens cancer antigen 84 455 g1 I Mus heart alpha-kinase 100 24 musculus 455 g1602255Rattus protein tyrosine phosphatase99 22 norve icus 455 g12425111DictyosteliuZipA 94 20 m discoideum 456 AAB58236Homo ROSE/ Lung cancer associated283 88 polypeptide sa iens se uence SEQ ID 574.

457 g15420183Homo dJ377H14.9 (major histocompatibility611 96 sa iens com lex, class I, F CDA12 Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 457 AAG64617Homo KIMU/ Human cancer cell 603 95 specific HLA-F

sa iens anti en SEQ ID 4.

457 ABB50296Homo USSH HLA-Cw ovarian tumour 603 95 marker sa iens rotein, SEQ ID N0:82.

458 AAE 18015Homo CURA- Human G-protein coupled1116 97 receptor-sa iens 3 GPCR-3 rotein.

458 AAU24535Homo SEND- Human olfactory receptor1 97 sa iens AOLFR20.

458 AAG71945Homo YEDA Human olfactory receptor1106 96 sa iens of a tide, SEQ ID NO: 1626.

459 AAE02638Homo SCHE Human dendritic cell 2448 100 specific sa iens transmembrane rotein DC-STAMP
.

459 gi11612079Homo DC-specific transmembrane 2448 100 protein sa iens 459 AAB87357Homo HUMA- Human gene 16 encoded1798 99 secreted sa iens rotein HMADJ14, SEQ ID N0:98.

460 ABB89120Homo HUMA- Human polypeptide 403 87 SEQ ID NO

sa iens 1496.

460 gi17742567dipeptideABC transporter, membrane 71 29 spanning protein [Agrobacterium tumefaciens str.

C58 (U.

460 gi 15159154AgrobacteriAGR L-1477p 71 29 um tumefaciens str. C58 (Cereon) 461 AAG73470Homo HUMA- Human gene 14-encoded699 100 secreted sa iens rotein fra ment, SEQ ID
N0:245.

461 ABB90038Homo HUMA- Human polypeptide 486 53 SEQ ID NO

sa iens 2414.

461 AAB95779Homo HELI- Human protein sequence486 53 SEQ ID

sa iens N0:18726.

462 gi7021367Drosophilac 11.1 511 25 melanogaste r 462 gi 17862452DrosophilaLD28902p 511 25 melanogaste r 462 gi12724134LactococcusHYPOTHETICAL PROTEIN 81 33 lactis subsp.

lactis 463 AAM42407Homo HUMA- Human polypeptide 606 100 SEQ ID NO

sa iens 140.

463 AAM95921Homo HUMA- Human reproductive 606 100 system related sa iens anti en SE ID NO: 4579.

463 gi7322066DrosophilaHls 335 27 s.

464 gi 18147612Homo metalloprotease disintegrin4206 100 sa iens 464 AAB47106Homo ZYMO Second splice variant 4190 99 of MAPP.

sa iens 464 gi13157560Homo dJ964F7.1 (novel disintegrin4104 100 and reprolysin sa iens metallo roteinase famil rotein 465 gi 14091952Rattus KIDINS220 294 26 norve icus Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 465 gil 1321435Rattus ankyrin repeat-rich membrane-spanning292 26 norve rotein icus 465 AAM39025Homo HYSE- Human polypeptide 288 27 SEQ ID NO

sa iens 2170.

466 gi16648368DrosophilaLD35341p 177 49 melanogaste r 466 gi 19744967Dictyosteliu80 kda MCM3-associated protein153 22 m discoideum 466 gi4995703Mus GANP protein 141 25 musculus 467 gi12002028Homo brain my040 protein 482 100 sa iens 467 gi~20453865~Utriculariacytochrome C oxidase subunit67 48 I

gb~AAM221geminiscapa 67.1 ~AF482 467 gi~20453861Utriculariacytochrome C oxidase subunit67 48 ~ I

gb~AAM221adpressa 65.1 ~AF482 468 AAY94938Homo GEMY Human secreted protein2288 97 clone sa iens e78 1 rotein se uence SEQ
ID N0:82.

468 AAG81379Homo ZYMO Human AFP protein sequence1701 99 SEQ

sa iens ID N0:276.

468 AAG81387Homo ZYMO Human AFP protein sequence1570 99 SEQ

sa iens ID N0:292.

469 AAY27721Homo HUMA- Human secreted protein1114 98 encoded sa iens b ene No. 29.

469 AAB87068Homo MILL- Human secreted protein621 99 TANGO

sa iens 365, SEQ ID N0:46.

469 AAB87148Homo MILL- Human secreted protein617 98 TANGO

sa iens 365 T20S variant, SEQ ID
N0:165.

470 gi 12140288Homo bA 12M 19.1.3 (novel protein)2537 100 I

sa iens 470 gi 12140289Homo bA 12M 19.1.1 (novel protein)2203 88 sa iens 470 AAE03639Homo INCY- Human extracellular 2114 88 matrix and cell sa iens adhesion molecule-3 (XMAD-3 .

471 AAR90766Homo USSH Tumour suppressor protein1502 70 HTS-1.

sa iens 471 gi257387Homo HTS1 1502 70 sa iens 471 gi 1769472Homo p82 1502 70 sa iens 472 gi19684136Homo Similar to RIKEN cDNA 4933413N12645 100 gene sa iens 472 gi559500CaenorhabdiND2 protein (AA 1 - 282) 75 35 tis ele ans 472 gi6687124ConvolvulusNADH dehydrogenase subunit 72 30 F

arvensis 473 gi19684136Homo Similar to RIKEN cDNA 4933413N12972 100 gene sa iens 473 gi2258350ReclinomonSect-t a trans orter rotein78 24 Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit as americana 473 gi559500CaenorhabdiND2 protein (AA 1 - 282) 76 29 tis ele ans 474 gi32474 Homo h-Sp 1 1250 93 sa iens 474 gi632790Homo pantophysin 1250 93 sa iens 474 gi16877127Homo Similar to synaptophysin-like1161 92 protein sa iens 475 AAB36613Homo 1NCY- Human FLEXHT-35 protein1304 88 sa iens se uence SEQ ID N0:35.

475 gi14603247Homo Similar to RIKEN cDNA 57304096151304 88 gene sa iens 475 AAB93042Homo HELI- Human protein sequence240 90 SEQ ID

sa iens N0:11827.

476 gi5052674DrosophilaBcDNA.LD29892 349 24 melanogaste r 476 gi 16768704DrosophilaHL04910p 329 24 melanogaste r 476 gi17945748DrosophilaRE32936p 277 22 melanogaste r 477 AAG71509Homo YEDA Human olfactory receptor1510 96 sa iens of a tide, SEQ ID NO: 1190.

477 gi2792016Homo olfactory receptor 1388 99 sa iens 477 gi4092819Homo BC319430-5 1381 99 sa iens 478 AAY73483Homo GEMY Human secreted protein579 47 clone sa iens 118 1 rotein se uence SEQ
ID N0:188.

478 AAM92890Homo HUMA- Human digestive system384 52 antigen sa iens SEQ ID NO: 2239.

478 AAU83621Homo GETH Human PRO protein, 333 28 Seq ID No 60.

sa iens 479 AAM93439Homo HELI- Human polypeptide, 1182 94 SEQ ID NO:

sa iens 3078.

479 gi15079907Homo Similar to secretory carrier1182 94 membrane sa iens rotein 4 479 ABB06156Homo COMP- Human NS protein sequence1020 83 SEQ

sa iens ID N0:248.

480 gi 1497861fowl fiber 81 24 adenovirus 8J [Fowl adenovirus 480 gi6572647fowl short fiber homolog [Fowl 81 24 adenovirus 480 gi3808227Sphaeropsiscoat protein 79 32 sapinea RNA virus 481 gi13517508Homo sodium bicarbonatecotransporter5138 100 sa iens 481 gi14582760Homo anion exchanger AE4 4979 97 sa iens Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 481 gi7363254Homo sodium bicarbonate cotransporter4973 97 sa iens 482 AAM50714 Homo MILL- Human TRP-like calcium2810 99 channel-4 sa iens (TLCC-4 .

482 gi21435923Homo cation channel TRPV3 2810 99 sa iens 482 gi20908451Mus TRP ion channel TRPV3 2665 94 musculus 483 AAB86365 Homo MEMO- Human ceramidase K3 1069 76 protein.

sa iens 483 gi17529684Mus cancer related gene-liver 1020 70 musculus 483 gi18028135Drosophilabrain washing 442 36 melanogaste r 484 ABB89360 Homo HUMA- Human polypeptide 251 78 SEQ ID NO

sa iens 1736.

484 gi1574439Haemophiluleucine responsive regulatory73 38 protein (lrp) s influenzae Rd 484 gi12720483PasteurellaLrp 73 38 multocida 485 AAY99347 Homo GETH Human PR01113 (UNQS56)2250 99 amino sa iens aacid se uence SEQ ID N0:24.

485 gi 15987499Mus tumor endothelial marker 1863 48 5 precursor musculus 485 AAU74824 Homo INCY- Human REPTR 7 protein.1812 47 sa iens 486 AAS12581-Homo PEKE cDNA encoding novel 1853 100 human G

aal sa iens rotein-cou led rece for (GPCR).

486 AAS07946-Homo AREN- Human cDNA encoding 1853 100 G-protein as 1 sa iens cou led rece tor, hRUP 19.

486 AAD27497_Homo EURO- Human G-protein coupled1853 100 receptor as 1 sa iens GPCRx 14) DNA.

487 gi4959568Homo nuclear pore complex interacting1087 67 protein sa iens NPIP

487 ABB90262 Homo HUMA- Human polypeptide 852 71 SEQ ID NO

sa iens 2638.

487 gi 14603481Homo Similar to nuclear pore 644 82 complex interacting sa iens rotein 488 AAM25630 Homo HYSE- Human protein sequence554 90 SEQ ID

sa iens N0:1145.

488 AAG63804 Homo NISC- Amino acid sequence 551 98 of a human sa iens amino acid trans orter.

488 gi9309293Homo asc-type amino acid transporter551 98 sa iens 489 AAM39751 Homo HYSE- Human polypeptide 2304 99 SEQ ID NO

sa iens 2896.

489 AAM41538 Homo HYSE- Human polypeptide 2294 99 SEQ ID NO

sa iens 6469.

489 AAM41537 Homo HYSE- Human polypeptide 2294 99 SEQ ID NO

sa iens 6468.

490 AAE06056 Homo HUMA- Human gene 16 encoded1006 75 secreted sa iens rotein HMIAP86, SEQ ID N0:118.

490 AAY87079 Homo HUMA- Human secreted rotein1006 75 se uence Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa iens SEQ ID N0:118.

490 AAY78511Homo AMYL- Human uncoupling protein1006 75 4 (UCP-sa iens 4 amino acid se uence.

491 AAG71803Homo YEDA Human olfactory receptor1616 100 sa iens of a tide, SEQ ID NO: 1484.

491 ABB06625Homo CURA- G protein-coupled 1608 99 receptor sa iens GPCR13 rotein SEQ ID N0:60.

491 ABB06626Homo CUBA- G protein-coupled 1605 99 receptor sa iens GPCRI3b rotein SEQ ID N0:62.

492 gi10440458Homo FLJ00065 protein 992 100 sa iens 492 gi15545993Homo Bcl-2 modifying factor 992 100 sa iens 492 gi 15545991Mus Bcl-2 modifying factor 864 87 musculus 493 AAG67525Homo SMIK Amino acid sequence 1841 99 of a human sa iens secreted of a tide.

493 ABB90207Homo HUMA- Human polypeptide 557 38 SEQ ID NO

sa iens 2583.

493 AAB69185Homo SREN- Human hISLR-iso protein557 38 SEQ ID

sa iens N0:7.

494 ABB05727Homo GEHU- Human signal transduction777 46 protein sa iens clone tes3 5k22.

494 AAB 12529Homo SLOK Human Ma5 protein SEQ 777 46 ID N0:13.

sa iens 494 gi6179740Homo paraneoplastic neuronal 777 46 antigen MA3 sa iens 495 gi17862902DrosophilaSD02518p 845 43 melanogaste r 495 gi17861532DrosophilaGH11618p 833 42 melanogaste r 495 gi530088Gl cine aminoalcohol hos hotransferase398 28 max 496 gi9963853Homo HT018 1368 100 sa iens 497 ABB90073Homo HUMA- Human polypeptide 1286 70 SEQ ID NO

sa iens 2449.

497 AAB 12123Homo PROT- Hydrophobic domain 1286 70 protein from sa iens clone HP10608 isolated from Saos-2 cells.

497 gi13241761Homo transmembrane protein induced1286 70 by tumor sa iens necrosis factor al ha 498 ABB85001Homo GETH Human PR028631 protein131 27 sequence sa iens SEQ ID N0:370.

498 AAY86234Homo HUMA- Human secreted protein123 38 sa iens HNTNC20, SEQ ID N0:149.

498 AAB65258Homo GETH Human PR01153 (UNQ583)111 54 protein sa iens se uence SEQ ID N0:351.

499 AAB93704Homo HELI- Human protein sequence3677 99 SEQ ID

sa iens N0:13287.

499 ABB07504Homo INCY- Human GTP-binding 2960 57 protein sa iens GTPB ID:4028409CD1 .

499 ABB07686Homo MERE Human GTPase-like protein,2456 56 MFQ-sa iens _111.

500 gi21212948Mus ~ peroxisomal protein (PeP) 462 5~
l ~ ~

Table 2B
SEQ Hit ID Species Description S Percent ID score identit musculus 500 gi310897Thermobifidbeta-1,4-endoglucanase 124 35 precursor a fusca 500 gi485747Gallus protein-tyrosine phosphatase115 32 allus 501 AAB35156Homo SMIK Human nuclear receptor2750 88 NOTIa sa iens s lice variant related rotein.

501 AAU09156Homo SMIK Human NOT1 orphan 2750 88 nuclear sa iens rece tor.

501 AAR48631Homo MAGE/ Sequence of nuclear 2750 88 receptor of T-sa iens cells NPT steroidrece for rotein.

502 AAU11383Homo SENO- Human T2R55 (hT2R55)1632 98 sa iens of a tide.

502 gi20336515Homo candidate taste receptor 1632 98 sa iens 502 AAU11382Homo SENO- Human T2R54 (hT2R54)894 57 sa iens of a tide.

503 AAB92909Homo HELI- Human protein sequence3006 98 SEQ ID

sa iens N0:11539.

503 gi17862912DrosophilaSD02996p 1037 31 melanogaste r 503 ABB90736Homo UYJO Human Tumour Endothelial410 24 Marker sa iens of a tide SEQ ID NO 204.

504 ABB05730Homo ZYMO Human zcytorl7 protein3070 99 sequence sa iens SEQ ID N0:2.

504 gi20563277Homo gp130-like monocyte receptor3070 99 sa iens 504 ABB05741Homo ZYMO Human zcytorl7 protein3066 99 sequence sa iens SEQ ID N0:54.

505 AAU80509Homo INCY- Human G-coupled receptor1781 100 sa iens GCREC rotein, Se ID No 17.

505 AAU11885Homo CURA- Human novel G protein-coupled1595 100 sa iens rece tor, GPCRIa.

505 AAU11886Homo CURA- Human novel G protein-coupled1589 99 sa iens rece tor, GPCRlb.

506 gi4102877Mus Shc binding protein 2283 69 musculus 506 gi12017952Homo GE36 464 30 sa iens 506 gi20906085Methanosarcsurface layer protein B 128 23 ina mazei Goe 1 507 AAB11699Homo FUSO Human serine protease1404 100 sa fens (hBSSP2 , SEQ ID NO:10.

507 gi12248917Homo spinesin 1404 100 sa iens 507 AAE14342Homo INCY- Human protease PRTS-71236 99 protein.

sa iens 508 gi 18032273Mus VPS 10 domain receptor 5 I 96 SorCS 1 c splice 98 musculus variant 508 gi 18032275Homo VPS 10 domain receptor 5121 99 SorCS

sa iens 508 gi7715916Mus SorCSb splice variant of 4963 96 the VPS10 domain musculus rece for SorCS

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 509 gi14278927Mus gliacolin 1291 94 musculus 509 gi10566471Mus Gliacolin 1291 94 musculus 509 gi3747097Homo Clq-related factor 976 70 sa iens 510 gi12247892SterkiellaSPEC3-like protein 90 31 histriomusco rum 510 AAA99908_Homo GETH cDNA encoding human 71 30 protein as 1 sa iens PR0321.

510 ABB84833Homo GETH Human PR0321 protein 71 30 sequence sa iens SE ID N0:34.

511 ABB90246Homo HUMA- Human polypeptide 648 100 SEQ ID NO

sa iens 2622.

511 AAB25755Homo HUMA- Human secreted protein648 100 sequence sa iens encoded b ene 33 SEQ ID
N0:144.

511 AAB25754Homo HUMA- Human secreted protein301 100 sequence sa iens encoded b gene 33 SEQ ID
N0:143.

512 gi13810306Homo transmembrane protein 7 1271 100 sa iens 512 gi18250724Mus transmembrane protein 7 639 64 musculus 512 gi15341942Homo 28kD interferon responsive 428 38 protein sa iens 513 AAG72504Homo YEDA Human OR-like polypeptide1615 99 query sa iens se uence, SEQ ID NO: 2185.

513 AAU24651Homo SENO- Human olfactory receptor1615 99 sa iens AOLFR147.

513 AAG71709Homo YEDA Human olfactory receptor1611 99 sa iens of a tide, SEQ ID NO: 1390.

514 gi20381191Homo Similar to RIKEN cDNA 4932443L082831 99 gene sa iens 514 AAB83079Homo SMIK Human CASB6411 protein.1806 100 sa iens 514 AAB08764Homo INCY- A human leukocyte 1424 100 and blood sa iens related rotein (LBAP).

515 gi20072886Homo Similar to RIKEN cDNA 2610024A011456 100 gene sa iens 515 AAB74716Homo INCY- Human membrane associated1094 99 protein sa iens MEMAP-22.

515 ABB89524Homo HUMA- Human polypeptide 513 98 SEQ ID NO

sa iens 1900.

516 AAG66141Homo MILL- Human LGR6 polypeptide3804 99 (clone sa iens Fbh150881 .

516 AAG66140Homo MILL- Human LGR6 polypeptide3804 99 (clone sa iens fahr).

516 gi10441732Homo leucine-rich repeat-containing3782 100 G protein-sa iens cou led rece for 6 517 AAB24465Homo HUMA- Human secreted protein447 98 sequence sa iens encoded b ene 29 SEQ ID
N0:90.

518 AAM40227Homo HYSE- Human polypeptide 909 34 SEQ ID NO

sa iens 3372.

518 gi21321124Rattus proton-associated sugar 898 34 transporter A

norve icus Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 518 gi4680229Homo DNb-5 537 29 sa iens 519 ABB07253Homo LEXI- Human novel GPCR (NGPCR)3943 99 sa iens rotein.

519 AAM69607Homo MOLE- Human bone marrow 1770 82 expressed sa iens robe encoded rotein SEQ
ID NO: 29913.

519 AAM57201Homo MOLE- Human brain expressed1770 82 single exon sa iens robe encoded rotein SEQ
ID NO: 29306.

520 AAM43601Homo HUMA- Human polypeptide 1229 99 SEQ ID NO

sa iens 279.

520 AAU18290Homo HUMA- Human endocrine polypeptide1228 99 SEQ

sa iens ID No 245.

520 AAY27577Homo HUMA- Human secreted protein598 100 encoded sa iens b ene No. 11.

521 AAB94304Homo HELI- Human protein sequence1523 100 SEQ ID

sa iens N0:14767.

521 AAD23974_Homo INCY- Human neurotransmitter1350 92 transporter, aal sa iens NTT-2 cDNA.

521 AAE 14404Homo 1NCY- Human neurotransmitterI 92 transporter, 350 sa iens NTT-2.

522 AAB74730Homo INCY- Human membrane associated637 37 protein sa iens MEMAP-36.

522 AAY94906Homo GEMY Human secreted protein637 37 clone sa iens rb649 3 rotein se uence SEQ ID N0:18.

522 AAM40237Homo HYSE- Human polypeptide 523 37 SEQ ID NO

sa iens 3382.

523 AAB43665Homo HUMA- Human cancer associated1254 100 protein sa iens se uence SEQ ID NO: I 110.

523 AAY19759Homo HUMA- SEQ ID NO 477 from 966 100 sa iens W09922243.

523 gi21428606DrosophilaLD47425p 939 70 melanogaste r 524 AAH42183_Homo PHAA Nucleotide sequence 1925 94 of a G-protein aa2 sa iens cou led rece tor.

524 ABB06303Homo TAKE Human ZAQ protein sequence1925 94 SEQ

sa iens ID NO:1.

524 AAB70143Homo TAKE Human G protein-coupled1925 94 receptor sa iens rotein.

525 AAB93258Homo HELI- Human protein sequence930 53 SEQ ID

sa iens N0:12282.

525 AAY28810Homo GEMY nn296_2 secreted protein.930 53 sa iens 525 gi 17944467DrosophilaRH03777p 749 48 melanogaste r 526 AAM48989Homo TAKE Human testis originated1061 97 G-protein sa iens cou led rece for TGR10.

526 gi13876663lumpy G-protein-coupled chemokine191 25 skin receptor-like disease rotein virus 526 gi7108517Oryctolaguschemokine receptor 190 29 cuniculus 527 gi12214288Homo dJ402H5.2 (novel protein 2655 100 similar to worm sa iens and fl roteins 527 13880799CaenorhabdiY39A1B.2 431 23 Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit tis ele ans 527 gi15718594CaenorhabdiC. elegans PTR-10 protein 430 23 (corresponding tis ele se uence F55F8.1) ans 528 ABB89636Homo HUMA- Human polypeptide 817 100 SEQ ID NO

sa iens 2012.

528 gi21483396DrosophilaLD22376p 813 40 melanogaste r 528 gi18480372Mus olfactory receptor MOR145-382 25 musculus 529 AAM50125Homo MILL- Human acyltransferase1874 100 46743.

sa iens 529 AAB65222Homo GETH Human PR01108 (UNQ551)1583 69 protein sa iens se uence SEQ ID N0:248.

529 AAM00959Homo HYSE- Human bone marrow 1583 69 protein, SEQ

sa iens ID NO: 435.

530 ABB 11531Homo HYSE- Human secreted protein1290 99 homologue, sa iens SEQ ID N0:1901.

530 AAM25596Homo HYSE- Human protein sequence1289 99 SEQ ID

sa iens NO:1111.

530 ABB55767Homo FECH/ Human polypeptide 1282 99 SEQ ID NO

sa iens 140.

531 AAI66039-Homo KYOW Human G protein-coupled787 100 receptor aal sa iens encodin cDNA SEQ ID NO 2.

531 AAA64346-Homo MILL- DNA encoding a human 787 100 G-protein as 1 sa iens cou led rece for desi nated 14273.

531 AAE04564Homo INCY- Human G-protein coupled787 100 receptor-sa iens 20 (GCREC-20 rotein.

532 AAU11888Homo CURA- Human novel G protein-coupled1747 99 sa iens rece tor, GPCR3a.

532 AAU24662Homo SENO- Human olfactory receptor1747 99 sa iens AOLFR160.

532 AAU11889Homo CURA- Human novel G protein-coupled1632 98 sa iens rece tor, GPCR3b.

533 gi557822Saccharomymal5, stal, len: 1367, CAI:314 25 0.3, ces AMYH_YEAST P08640 cerevisiaeGLUCOAMYLASE S1 EC 3.2.1.3) 533 gi1304387Saccharomyglucoamylase 314 25 ces cerevisiae var.

diastaticus 533 1915208 Sus scrofaastric mucin 307 25 534 AAU00437Homo COUN- Human dendritic cell 1997 88 membrane sa iens rotein FIRE.

534 AAY91625Homo HUMA- Human secreted protein1836 96 sequence sa iens encoded b ene 22 SEQ ID
N0:298.

534 g116930385Mus seven-span membrane protein1445 62 FIRE

musculus 535 AAB61148Homo CURA- Human NOV 17 protein.2306 59 sa iens 535 g118676416Homo FLJ00080 protein 1900 57 sa iens 535 AAB61147Homo CURA- Human NOV 16 protein.1378 53 sa iens Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit 536 AAB61148Homo CURA- Human NOV 17 protein.2306 59 sa iens 536 gi18676416Homo FLJ00080 protein 1900 57 sa iens 536 AAB61147Homo CURA- Human NOV 16 protein.1378 53 sa iens 537 gi14325132Thetmoplastricorn protease 75 29 ma volcanium 537 gi21064441DrosophilaRE29777p 74 30 melanogaste r 537 gi~13541726~ThermoplasTricorn protease 75 29 ref~NP-1114ma 14.1 volcanium 538 AAG71899Homo VEDA Human olfactory receptor1603 100 sa iens of a tide, SEQ ID NO: 1580.

538 AAU24548Homo SENO- Human olfactory receptor1603 100 sa iens AOLFR35.

538 AAE06770Homo INCY- Human G-protein coupled1598 100 receptor-sa iens 20 GCREC-20) rotein.

539 AAG81420Homo ZYMO Human AFP protein sequence403 98 SEQ

sa iens ID N0:358.

539 AAM93259Homo HELI- Human polypeptide, 327 38 SEQ ID NO:

sa iens 2709.

539 gi16877659Homo Similar to RIKEN cDNA 1810054013314 38 gene sa iens 540 AAG89209Homo GEST Human secreted protein,460 97 SEQ ID NO:

sa iens 329.

540 gi 1890812Flexamia NADH dehydrogenase 1 71 24 raminea 540 gi~~1295981~AnophelesagCP1281 73 28 gb~EAA081gambiae str.

26.1 PEST

541 ABB89210Homo HUMA- Human polypeptide 851 99 SEQ ID NO

sa iens 1586.

541 AAY73442Homo GEMY Human secreted protein596 95 clone sa iens a66 1 rotein se uence SEQ
ID N0:106.

541 AAB63255Homo LUDW- Human breast cancer 88 40 associated sa iens anti en rotein se uence SEQ ID N0:617.

542 gi9929918Homo intestinal mucin 4024 99 sa iens 542 gi11990203Homo MUC3B mucin 3985 98 sa iens 542 gi9929920Homo intestinal mucin 3908 96 sa iens 543 gi17483744Mus RING finger protein 33 1115 47 musculus 543 gi14043332Homo Similar to ring finger protein913 40 sa iens 543 gi 10716078Mus testis-abundant finger protein907 40 musculus 544 AAG76127Homo HUMA- Human colon cancer 260 68 antigen sa iens rotein SEQ ID N0:6891.

544 AAG03891Homo GEST Human secreted protein,260 68 SEQ ID NO:

Table 2B
SEQ Hit ID Species Description S Percent ID scoreidentit sa iens 7972.

544 gi57131 Rattus ribosomal protein S26 260 68 norve icus 545 AAU74820Homo 1NCY- Human REPTR 3 protein.1737 42 sa iens 545 gi6683905DrosophilaDispatched 1073 31 melanogaste r 545 AAU03497Homo UYZU- Human sterol sensing 885 43 domain sa iens rotein.

546 AAM78329Homo HYSE- Human protein SEQ 933 70 ID NO 991.

sa iens 546 ABL41227-Homo SWIT- Human G-protein coupled585 58 receptor aal sa iens encoding cDNA SEQ ID NO
8.

546 AAS16914-Homo PEKE Human G-protein coupled585 58 receptor aal sa iens (GPCR) cDNA.

547 gi20067221Homo Down syndrome cell adhesion11077100 molecule 2 sa fens 547 gi18033452Homo Down syndrome cell adhesion1074599 molecule sa iens DSCAML1 547 AAM39040Homo HYSE- Human polypeptide 9116 100 SEQ ID NO

sa iens 2185.

548 gi 12656633Homo transmembrane gamma-carboxyglutamic1192 100 sa iens acid rotein 3 TMG3 548 AAM93243Homo HELL- Human polypeptide, 1186 99 SEQ ID NO:

sa iens 2675.

548 gi20977032Xenopus mitotic phosphoprotein 77 359 38 laevis 549 AAG89138Homo GEST Human secreted protein,709 74 SEQ ID NO:

sa iens 258.

549 AAE13062Homo AMGE- Human CD20/IgE-receptor709 74 like sa iens rotein, a -96614-al.

549 gi11559214Homo MS4A5 709 74 sa iens 550 AAG72074Homo YEDA Human olfactory receptor1853 100 sa iens of a tide, SEQ ID NO: 1755.

550 AAG71493Homo VEDA Human olfactory receptor1853 100 sa iens of a tide, SEQ ID NO: 1174.

550 gi12054409Homo olfactory receptor 1853 100 sa iens 551 AAB47932Homo SE1N/ Human Na+-driven CI-/HC03-5677 99 sa iens exchanger.

551 gi11275360Homo NCBE 5677 99 sa iens 551 gi 1 Mus NCBE 5542 96 musculus 552 AAE04178Homo HUMA- Human gene 3 encoded 1111 98 secreted sa iens rotein fra ment, SEQ ID
N0:169.

552 AAE04127Homo HUMA- Human gene 3 encoded 1078 98 secreted sa iens rotein HSDJL42, SEQ ID N0:114.

552 AAE04102Homo HUMA- Human gene 3 encoded 1068 98 secreted sa iens rotein HSDJL42, SEQ ID N0:88.

Table 3 SEQ Database Description Results*
ID

NO: entr ID

277 PR00217 43 KD POSTSYNAPTIC PROTEINPR00217C 10.91 3.753e-10 SIGNATURE

278 PR00217 43 KD POSTSYNAPTIC PROTEINPR00217C 10.91 3.753e-10 SIGNATURE

281 PD01572 PHOTOSYSTEM II REACTIONPD01572 8.77 4.083e-09 CENTRE T PROTEIN PHOTOS.

282 BL00421 Transmembrane 4 family BL00421 E 20.97 4.000e-20 proteins. 137-166 BL00421 C 12.89 6.571 e-12 77-88 BL00421A 11.79 1.563e-11 282 PR00259 TRANSMEMBRANE FOUR FAMILYPR00259D 13.50 8.200e-12 SIGNATURE PR00259C 16.40 1.684e-09 PR00259A 9.27 4.405e-09 282 PR00218 PERIPHER1N (RDS)/ROM-1 PR00218D 6.22 4.894e-09 SIGNATURE

286 PR00237 RHODOPS1N-LIKE GPCR PR00237A 11.48 5.355e-09 SUPERFAMILY SIGNATURE

290 PR00970 ARGININE ADP- PR00970A 17.73 6.906e-21 RIBOSYLTRANSFERASE PR00970D 9.96 8.920e-20 SIGNATURE PR00970F 12.30 9.250e-15 PR00970E 11.23 1.265e-14 PR00970G 9.97 3.700e-14 PR00970C 11.05 7.000e-14 PR00970B 16.37 7.387e-13 290 BL01291 NAD:arginine ADP-ribosyltransferasesBL01291F 23.30 5.974e-40 proteins. BL01291D 19.99 9.471e-31 BL01291A 22.07 4.892e-26 BL01291C 14.06 7.387e-17 BL01291 G 15.18 4.176e-16 BL01291 B 9.15 2.800e-11 BL01291 E 7.03 1.000e-09 292 BL00983 L -6 / u-PAR domain BL00983C 12.69 4.326e-10 roteins. 92-107 292 BL00272 Snake toxins roteins. BL00272C 8.27 9.372e-09 294 BL00290 Immunoglobulins and BL00290B 13.17 9.308e-15 major 168-185 histocom atibilit com BL00290A 20.89 1.450e-12 lex roteins. 129-151 295 BL00571 Amidases roteins. BL00571 25.69 4.188e-31 296 BL01271 Sodiumaulfate symporterBL01271D 25.26 1.000e-40 family 505-559 proteins. BL01271 C 13.62 6.824e-21 BL01271B 12.02 9.206e-21 BL01271A 8.06 8.800e-20 298 PD00131 ATP-BINDING TRANSPORT PD00131B 34.97 9.308e-32 TRANSMEMBR. PD00131C 19.59 1.000e-29 298 BL0021 ABC transporters familyBL00211B 13.37 7.750e-29 I proteins. 580-611 BL00211A 12.23 2.588e-10 298 PR00988 URIDINE KINASE SIGNATUREPR00988A 6.39 6.838e-09 304 PD01572 PHOTOSYSTEM II REACTIONPD01572 8.77 4.083e-09 CENTRE T PROTEIN PHOTOS.

308 BL00942 glpT family of transportersBL00942B 20.36 1.750e-10 proteins. 82-124 BL00942F 15.07 1.771e-10 BL00942C 14.04 6.610e-09 308 PD02963 COMPONENT PD02963B 5.41 6.776e-09 PHOSPHOTRANSFERASE SYST.

309 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 5.909e-21 SIGNATURE

309 BL00237 G- rotein cou led rece BL00237A 27.68 9.743e-13 tors roteins. 90-129 309 PR00237 ~RHODOPSIN-LIKE GPCR PR00237B 13.50 9.280e-12 ~ 59-80 Table 3 SEQ Database Description Results*
ID

NO: entr ID

SUPERFAMILY SIGNATURE PR00237C 15.69 6.914e-10 PR00237A 11.48 4.774e-09 311 PR00254 NICOTINIC ACETYLCHOLINEPR00254A 11.23 5.765e-14 RECEPTOR SIGNATURE PR00254D 15.50 2.023e-12 PR00254B 12.97 1.973e-11 311 BL00236 Neurotransmitter-gated BL00236A 21.96 5.050e-25 ion-channels 57-94 proteins. BL00236C 25.16 7.097e-25 BL00236D 25.66 8.105e-21 BL00236B 14.67 3.813e-11 311 PR00252 NEUROTRANSMITTER-GATED PR00252A 14.28 5.696e-14 ION CHANNEL FAMILY PR00252C 17.49 9.77Se-12 SIGNATURE PR00252B 15.17 2.406e-10 312 PD02327 GLYCOPROTEIN ANTIGEN PD02327B 19.84 2.091e-09 PRECURSOR IMMUNOGLO.

312 DM00179 w KINASE ALPHA ADHESIONDM00179 13.97 7.652e-09 CELL.

313 PR00019 LEUCINE-RICH REPEAT PR00019A 1 1.19 8.043e-10 SIGNATURE PR00019B 1 1.36 7.120e-09 313 BL00240 Receptor tyrosine kinaseBL00240B 24.70 7.319e-09 class III 319-342 roteins.

316 BL00237 G- rotein cou led rece BL00237A 27.68 2.600e-10 tors roteins. 45-84 316 PR00534 MELANOCORTIN RECEPTOR PR00534A 11.49 9.446e-10 FAMILY SIGNATURE

316 PR00245 OLFACTORY RECEPTOR PR00245C 7.84 4.750e-18 SIGNATURE PR00245A 18.03 4.808e-15 PR00245E 12.40 9.043e-11 PR00245B 10.38 2.102e-09 316 PR00237 RHODOPS1N-LIKE GPCR PR00237C 15.69 8.875e-09 SUPERFAMILY SIGNATURE

320 PR00518 S-HYDROXYTRYPTAMINE PR00518D 8.59 9.471e-21 RECEPTOR SIGNATURE PR00518E 11.20 8.898e-12 PR00518C 5.94 1.000e-11 320 PR00237 RHODOPS1N-LIKE GPCR PR00237C 15.69 4.462e-19 SUPERFAMILY SIGNATURE PR00237G 19.63 7.261e-16 PR00237F 13.57 1.857e-15 PR00237E 13.03 4.600e-14 PR00237D 8.94 1.900e-11 PR00237B 13.50 7.517e-11 320 BL00237 G-protein coupled receptorsBL00237A 27.68 4.938e-27 proteins. 104-143 BL00237C 13.19 2.500e-17 BL00237D 11.23 5.846e-11 BL00237B 5.28 6.727e-09 321 PR00237 RHODOPSIN-LIKE GPCR PR00237A 11.48 8.714e-12 SUPERFAMILY SIGNATURE PR00237G 19.63 4.600e-11 PR00237B 13.50 3.531e-10 326 PR00007 COMPLEMENT C1Q DOMAIN PR00007B 14.16 6.657e-15 SIGNATURE PR00007C 15.60 2.047e-14 PR00007A 19.33 8.412e-12 326 BL00415 S a sins roteins. BL0041SN 4.29 7.307e-09 326 BLO1 I Clq domain proteins. BL01113B 18.26 3.647e-27 BL01113A 17.99 1.000e-13 BL01113C 13.18 2.532e-13 BL01113A 17.99 7.081e-13 BL01113A 17.99 8.297e-13 BL01113A 17.99 3.538e-12 Table 3 SEQ Database Description Results*
ID

NO: entr ID

BL01113A 17.99 5.385e-12 BL01113A 17.99 5.909e-11 BLOI 113A 17.99 8.773e-11 BLO11 13A 17.99 9.135e-09 326 BL00420 Speract receptor repeatBL00420A 20.42 4.808e-12 proteins domain 56-84 proteins. BL00420A 20.42 8.967e-10 BL00420A 20.42 7.231e-09 BL00420A 20.42 9.169e-09 330 PR00237 RHODOPSIN-LIKE GPCR PR00237E 13.03 6.400e-12 SUPERFAMILY SIGNATURE PR00237D 8.94 1.450e-11 330 BL00237 G-protein coupled receptorsBL00237C 13.19 7.000e-09 proteins. 114-140 BL00237B 5.28 9.182e-09 333 BL00943 Cytochrome c oxidase BL00943A 22.06 6.087e-17 assembly factor 117-155 COX10/ctaB/c of si natur.

334 PD00866 GLYCOPROTE1N PROTEIN PD00866L 3.73 6.902e-09 E2 PRECURSOR PEPLOMER.

338 PR00237 RHODOPSIN-LIKE GPCR PR00237C 15.69 5.371e-10 SUPERFAMILY SIGNATURE

338 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 2.473e-14 SIGNATURE PR00245B 10.38 5.500e-13 PR00245E 12.40 2.149e-11 PR00245D 10.47 5.814e-10 338 BL00237 G-protein coupled receptorsBL00237A 27.68 4.818e-14 proteins. 89-128 BL00237D 11.23 5.364e-09 339 PR00237 RHODOPSIN-LIKE GPCR PR00237C 15.69 5.371e-10 SUPERFAMILY SIGNATURE

339 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 2.473e-14 SIGNATURE PR00245B 10.38 5.500e-13 PR00245D 10.47 5.814e-10 339 BL00237 G-protein coupled receptorsBL00237A 27.68 4.818e-14 proteins. 89-128 BL00237D 11.23 5.364e-09 340 PR00878 CHOLINESTERASE SIGNATUREPR00878F 5.37 4.780e-13 340 BL00122 Carboxylesterases type-BBL00122E 22.02 1.563e-25 serine 254-294 proteins. BL00122A 12.04 5.929e-16 BL00122D 12.53 4.484e-14 BL00122B 16.84 5.800e-14 BL00122G 11.67 8.615e-13 BL00122C 7.91 3.118e-11 BL00122F 11.10 3.000e-10 340 BL01173 Lipolytic enzymes G-D-X-GBL01173A 9.41 5.245e-10 family, 203-215 histidine.

341 BL00649 G-protein coupled receptorsBL00649C 17.82 6.564e-13 family 2 711-736 roteins.

341 PR00249 SECRET1N-LIKE GPCR PR00249C 17.08 4.323e-10 SUPERFAMILY SIGNATURE

341 BL01187 Calcium-binding EGF-likeBL01187B 12.04 9.775e-09 domain 122-137 roteins attern roteins.

342 BL00237 G- rotein cou led rece BL00237A 27.68 5.629e-13 tors roteins. 90-129 342 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 2.565e-17 SIGNATURE PR00245E 12.40 9.735e-13 PR00245C 7.84 3.591e-09 343 PF00954 S-locus 1 co rotein PF00954E 23.75 6.798e-09 famil . 152-202 343 BL00246 Wnt-1 famil roteins. BL00246E 20.32 8.306e-09 344 BL00237 G- rotein cou led rece BL00237A 27.68 9.455e-14 tors roteins. 93-132 344 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 1.000e-18 Table 3 SEQ DatabaseDescription Results*
ID

NO: entr ID

SIGNATURE PR00245B 10.38 9.143e-16 PR00245C 7.84 1.360e-13 PR00245E 12.40 7.882e-13 PR00245D 10.47 1.000e-10 344 ' PR00237RHODOPS1N-LIKE GPCR PR00237C 15.69 4.600e-10 SUPERFAMILY SIGNATURE PR00237G 19.63 1.209e-09 345 PR00249 SECRETIN-LIKE GPCR PR00249C 17.08 9.129e-1 SUPERFAMILY SIGNATURE PR00249E 14.90 4.493e-10 345 BL00649 G-protein coupled receptorsBL00649C 17.82 6.073e-13 family 2 462-487 proteins. BL00649E 15.34 2.857e-12 BL00649G 13.52 8.826e-11 BL00649B 20.68 8.548e-09 345 BL01187 Calcium-binding EGF-likeBLO1 1878 12.04 7.600e-11 domain 87-102 roteins attern roteins. BL01187A 9.98 1.000e-08 346 PR00249 SECRETIN-LIKE GPCR PR00249C 17.08 9.129e-11 SUPERFAMILY SIGNATURE PR00249E 14.90 4.493e-10 346 BL00649 G-protein coupled receptorsBL00649C 17.82 6.073e-13 family 2 366-391 proteins. BL00649E 15.34 2.857e-12 BL00649G 13.52 8.826e-11 BL00649B 20.68 8.548e-09 355 PR00019 LEUCINE-RICH REPEAT PR00019B 11.36 9.500e-11 SIGNATURE PR00019A 11.19 5.696e-10 PR00019B 11.36 6.400e-10 PR00019B 11.36 5.320e-09 355 PR00014 FIBRONECTIN TYPE III PR00014C 15.44 8.043e-09 SIGNATURE

357 BL00427 Disinte rins roteins. 8L00427 13.93 9.384e-24 357 PR00289 DISINTEGRIN SIGNATURE PR00289A 13.62 4.000e-14 PR00289B 11.79 6.745e-1 357 BL00142 Neutral zinc metallopeptidases,BL00142 8.38 2.125e-10 zinc- 343-353 bindin re ion roteins.

358 PD01270 RECEPTOR FC PD01270C 19.54 4.919e-14 IMMUNOGLOBULIN AFFIN. PD01270B 22.18 4.462e-10 359 PD01270 RECEPTOR FC PD01270C 19.54 4.919e-14 IMMUNOGLOBULIN AFFIN. PD01270B 22.18 4.462e-10 368 PR00463 E-CLASS P450 GROUP I PR00463E 17.37 4.667e-12 SIGNATURE

368 PR00385 P450 SUPERFAMILY SIGNATUREPR00385A 14.97 1.783e-13 PR00385B 10.22 5.950e-12 368 PR00464 E-CLASS P450 GROUP II PR00464C 18.84 7.750e-22 SIGNATURE PR00464A 20.47 7.300e-17 PR00464D 17.40 6.538e-14 PR00464B 20.41 1.000e-11 368 PR00408 MITOCHONDRIAL P450 PR00408D 15.44 8.099e-09 SIGNATURE

370 PR00001 COAGULATION FACTOR GLA PROOOO1B 10.75 9.000e-15 DOMAIN SIGNATURE PROOOOlA 12.78 5.800e-10 371 BL00406 Actins proteins. BL00406D 12.58 3.143e-19 BL00406A 9.95 5.729e-13 BL00406B 5.47 7.429e-12 BL00406C 6.75 9.682e-12 371 PR00735 GLYCOSYL HYDROLASE FAMILYPR00735D 12.75 1.000e-08 377 BL00120 Li ases, serine roteins.8L001208 11.37 1.383e-10 377 PR00793 PROLYL AMINOPEPTIDASE PR00793C 12.24 9.500e-09 Table 3 SEQ DatabaseDescription Results*
ID

NO: entr ID

FAMILY SIGNATURE

378 BL00120 Li ases, serine roteins.BL00120B 11.37 1.383e-10 378 PR00793 PROLYL AMINOPEPTIDASE PR00793C 12.24 9.500e-09 (533) 128-142 FAMILY SIGNATURE

382 PR00761 B1NDIN PRECURSOR SIGNATUREPR00761E 14.32 1.663e-09 388 PR00420 AROMATIC-RING HYDROXYLASEPR00420A 14.78 4.638e-13 (FLAVOPROTE1N

MONOOXYGENASE SIGNATURE

388 PR00757 FLAVIN-CONTAINING AMINE PR00757A 6.64 1.414e-10 OXIDASE SIGNATURE

388 PR00419 ADRENODOX1N REDUCTASE PR00419A 14.89 4.094e-10 FAMILY SIGNATURE

388 PR00072 MALIC ENZYME SIGNATURE PR00072F 8.87 5.922e-09 388 BL00623 GMC oxidoreductases roteins.BL00623A 12.60 8.200e-09 388 PR00368 FAD-DEPENDENT PYRIDINE PR00368A 17.76 9.839e-09 NUCLEOTIDE REDUCTASE

SIGNATURE

396 BL00031 Nuclear hormones receptorsBL00031A 19.55 9.471e-34 bindin re ion roteins. BL00031B 22.25 2.216e-22 396 PR00398 STEROID HORMONE RECEPTORPR00398A 14.44 3.328e-16 SIGNATURE PR00398C 13.47 1.450e-10 396 PR00350 VITAMIN D RECEPTOR PR00350B 9.35 2.125e-12 SIGNATURE PR00350F 8.61 4.385e-10 PR00350A 10.48 7.871e-09 396 PR00047 C4-TYPE STEROID RECEPTORPR00047A 15.70 5.500e-19 ZINC FINGER SIGNATURE PR00047B 7.63 4.522e-17 PR00047D 13.53 9.550e-10 PR00047C 5.40 8.788e-09 398 PD01672 + TRANSPORT EXCHANGER PD01672B 15.16 1.115e-24 TRANS. PD01672D 10.50 5.275e-18 PD01672I 17.98 5.939e-16 PD01672G 15.27 1.600e-12 PD01672C 16.18 3.933e-12 PD01672H 22.99 4.949e-10 403 PD02797 HYDROLASE CELL WALL N- PD02797D 19.90 9.032e-09 ACETYLMURAMOYL-L-AL.

405 PR00456 RIBOSOMAL PROTEIN P2 PR00456E 3.06 8.861e-09 SIGNATURE

411 PR00237 RHODOPS1N-LIKE GPCR PR00237C 15.69 2.575e-09 SUPERFAMILY SIGNATURE

411 BL00237 G-protein coupled receptorsBL00237A 27.68 9.419e-15 proteins. 90-129 BL00237D 11.23 5.636e-09 411 PR00896 VASOPRESSIN RECEPTOR PR00896B 9.01 7.577e-09 SIGNATURE

411 PR00245 OLFACTORY RECEPTOR PR00245C 7.84 9.053e-19 SIGNATURE PR00245A 18.03 7.907e-18 PR00245E 12.40 2.731e-14 PR00245D 10.47 8.531e-09 412 PR00646 RDCI ORPHAN RECEPTOR PR00646I 10.54 1.110e-26 SIGNATURE PR00646D 15.99 1.540e-26 PR00646G 14.95 1.281e-25 PR00646B 6.02 1.978e-25 PR00646A 16.77 9.438e-24 PR00646F 10.13 1.150e-23 PR00646C 18.45 1.170e-23 Table 3 SEQ Database Description Results*
ID

NO: entr ID

PR00646E 9.52 5.500e-23 PR00646H 6.32 I.lOle-20 412 BL00237 G-protein coupled receptorsBL00237A 27.68 4.789e-24 proteins. 92-131 BL00237C 13.19 9.280e-14 BL00237D 11.23 7.857e-13 412 PR00237 RHODOPSIN-LIKE GPCR PR00237C 15.69 8.800e-18 SUPERFAMILY SIGNATURE PR00237B 13.50 2.000e-15 PR00237G 19.63 2.800e-15 PR00237F 13.57 I.OOOe-14 PR00237E 13.03 4.333e-11 PR00237D 8.94 4.375e-10 412 PR00425 BRADYKININ RECEPTOR PR00425C 13.23 8.286e-10 SIGNATURE

412 PR00526 FORMYL-METHIONYL PEPTIDEPR00526C 13.54 9.550e-10 RECEPTOR SIGNATURE

412 PR00241 ANGIOTENSIN II RECEPTORPR00241C 8.90 4.536e-09 SIGNATURE

413 PR00049 WILM'S TUMOUR PROTEIN PR00049D 0.00 3.438e-12 SIGNATURE

415 PR00120 H+-TRANSPORTING ATPASE PR00120C 9.90 5.800e-19 (PROTON PUMP) SIGNATURE

415 PR00121 SODIUM/POTASSIUM- PR00121D 16.72 1.209e-28 TRANSPORTING ATPASE PR00121I 15.47 2.500e-26 SIGNATURE 1061 PR00121B 7.83 6.786e-26 218-238 PR00121G 6.89 8.875e-26 941-961 PR00121 H 12.14 9.1 OOe-6.70 4.214e-25 874-895 PR00121C
9.40 7.652e-23 382-404 PR00121E
13.97 1.563e-22 592-610 PR00121A
6.71 7.429e-19 191-205 415 BL00154 E1-E2 ATPases phosphorylationBL00154E 20.37 8.615e-38 site 680-720 proteins. BL00154B 15.44 2.800e-31 BL00154G 21.18 9.526e-30 BL00154F 8.23 6.400e-28 BL00154C 12.38 6.000e-23 BL00154A 11.86 9.500e-16 BL00154D 12.57 3.769e-13 415 PR00119 P-TYPE CATION-TRANSPORTINGPR00119E 8.48 6.250e-25 ATPASE SUPERFAMILY PR00119B 13.94 2.800e-20 SIGNATURE PR00119A 17.34 3.000e-15 PR00119D 9.56 3.571e-13 PR00119C 11.01 6.143e-13 PR00119F 11.81 7.750e-13 415 BL01228 H othetical cof famil BL01228D 17.44 6.250e-11 roteins. 800-824 415 BL01047 Heavy-metal-associated BL01047B 19.73 6.063e-10 domain 808-828 roteins.

418 BL00219 Anion exchangers familyBL00219K 12.73 9.883e-24 proteins. 677-718 BL00219M 9.98 5.208e-23 BL00219H 10.06 5.034e-22 BL00219N 10.66 7.545e-22 BL00219B 14.47 6.104e-20 BL00219I 6.16 9.818e-17 BL00219G 12.86 9.697e-16 BL00219A 17.13 I.OOOe-15 Table 3 SEQ Database Description Results*
ID

NO: entr ID

BL00219F 10.52 8.024e-15 BL00219C 17.29 4.470e-14 BL002190 14.02 1.000e-13 BL00219E 11.63 2.019e-10 BL00219L 18.71 3.560e-10 418 PR00165 ANION EXCHANGER SIGNATUREPR00165B 15.26 1.549e-13 PR00165I 10.02 2.521e-13 PR00165E 8.63 8.859e-11 PR00165F 10.39 7.674e-10 PR00165G 11.41 8.180e-09 421 DM00099 4 kw A55R REDUCTASE DM00099B 14.73 2.125e-09 TERMINAL DIHYDROPTERIDINE.464 421 PR00501 KELCH REPEAT SIGNATURE PR00501 B 18.88 8.342e-09 421 BL00292 C clins roteins. BL00292B 20.31 1.000e-08 422 BL00599 Aminotransferases class-IIBL00599B 18.93 7.894e-12 pyridoxal- 394-422 hos hate attachment sit.

422 PR00320 G-PROTEIN BETA WD-40 PR00320B 12.19 5.500e-09 SIGNATURE PR00320C 13.01 6.400e-09 PR00320A 16.74 6.927e-09 PR00320A 16.74 8.024e-09 423 DM00215 PROLINE-RICH PROTEIN DM00215 19.43 8.780e-09 3. 862-894 423 PF00761 Pol omavirus coat rotein.PF00761A 12.61 8.925e-09 427 PR00902 VP6 BLUE-TONGUE VIRUS PR00902J 18.54 6.400e-09 CAPSID PROTEIN SIGNATURE

428 PR00902 VP6 BLUE-TONGUE VIRUS PR00902J 18.54 6.400e-09 CAPSID PROTEIN SIGNATURE

430 BL00107 Protein kinases ATP-bindingBL00107A 18.39 4.273e-15 region 118-148 roteins.

430 ' PR00109TYROSINE KINASE CATALYTICPR00109B 12.27 9.426e-13 DOMAIN SIGNATURE

430 BL00240 Receptor tyrosine kinaseBL00240E 11.56 6.743e-09 class III 104-141 roteins.

432 BL00518 Zinc finger, C3HC4 typeBL00518 12.23 6.333e-09 (RING 32-40 fin er), roteins.

435 PR00625 DNAJ PROTEIN FAMILY PR00625D 11.93 9.077e-09 SIGNATURE

438 DM00215 PROLINE-RICH PROTEIN DM00215 19.43 6.186e-09 3. 460-492 448 BL00031 Nuclear hormones receptorsBL00031A 19.55 5.320e-30 bindin re ion roteins. BL00031B 22.25 6.604e-16 448 PR00350 VITAMIN D RECEPTOR PR00350A 10.48 1.692e-16 SIGNATURE PR00350F 8.61 6.400e-11 PR00350B 9.35 7.581e-11 PR00350E 11.55 9.693e-11 448 PR00047 C4-TYPE STEROID RECEPTORPR00047A 15.70 2.200e-16 ZINC FINGER SIGNATURE PR00047B 7.63 3.813e-16 PR00047C 5.40 S.OOOe-10 PR00047D 13.53 6.850e-10 448 PR00546 THYROID HORMONE RECEPTORPR00546H 16.85 6.523e-09 SIGNATURE

448 PR00398 STEROID HORMONE RECEPTORPR00398A 14.44 7.750e-14 SIGNATURE PR00398C 13.47 4.857e-09 PR00398F 13.87 7.943e-09 449 PR00205 CADHERIN SIGNATURE PR00205B 11.39 2.473e-10 PR00205B 11.39 8.691e-10 449 BL00232 Cadherins extracellularBL00232B 32.79 5.279e-20 re eat roteins 219-266 Table 3 SEQ DatabaseDescription Results*
ID

NO: entr ID

domain proteins. BL00232C 10.65 6.268e-12 BL00232C 10.65 9.308e-10 449 PR00291 SOYBEAN TRYPSIN INHIBITORPR00291A 19.85 9.366e-09 KUNITZ-TYPE SIGNATURE

449 PR00649 GPR6 ORPHAN RECEPTOR PR00649B 8.21 1.000e-08 SIGNATURE

452 PD00306 PROTEIN GLYCOPROTEIN PD00306B 5.57 9.000e-09 PRECURSOR RE.

457 BL00290 Immunoglobulins and majorBL00290B 13.17 7.750e-19 histocom atibilit com lex roteins.

458 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 4.966e-13 SIGNATURE PR00245B 10.38 8.875e-13 458 BL00237 G- rotein cou led rece BL00237A 27.68 5.500e-12 tors roteins. 90-129 458 PR00237 RHODOPSIN-LIKE GPCR PR00237B 13.50 2.688e-10 SUPERFAMILY SIGNATURE PR00237C 15.69 7.171e-10 PR00237A 11.48 2.161e-09 464 BL00427 Disinte rins roteins. BL00427 13.93 7.592e-26 464 PR00138 MATRIXIN SIGNATURE PR00138D 16.56 S.lOle-11 464 BL00142 Neutral zinc metallopeptidases,BL00142 8.38 7.545e-11 zinc- 278-288 bindin re ion roteins.

464 PR00289 DISINTEGRIN SIGNATURE PR00289A 13.62 2.500e-14 PR00289B 11.79 4.226e-10 464 PR00480 ASTACIN FAMILY SIGNATUREPR00480B 15.41 8.909e-10 464 PR00907 THROMBOMODULIN SIGNATUREPR00907E 11.70 3.647e-09 464 BL00546 Matrixins c steine switch.BL00546C 16.41 4.255e-09 464 BL00024 Hemo exin domain roteins.BL00024D 17.28 5.596e-09 466 DM01206 CORONAVIRUS NUCLEOCAPSIDDM01206B 10.69 1.000e-08 PROTEIN.

470 PR00211 GLUTELIN SIGNATURE PR00211B 0.86 5.673e-10 470 PR00910 LUTEOVIRUS ORF6 PROTEIN PR00910A 2.51 8.607e-09 SIGNATURE

470 DM00215 PROLINE-RICH PROTEIN DM00215 19.43 4.051e-09 3. 522-554 DM00215 19.43 6.644e-09 DM00215 19.43 9.085e-09 474 PR00220 SYNAPTOPHYSIN/SYNAPTOPORINPR00220D 8.32 7.585e-26 FAMILY SIGNATURE PR00220C 11.05 4.477e-25 PR00220A 10.93 8.244e-24 PR00220E 3.46 6.932e-23 474 BL00604 Synaptophysin / synaptoporinBL00604E 8.32 1.444e-23 proteins. 182-223 BL00604B 9.95 1.329e-19 BL00604C 14.66 5.639e-12 BL00604D 12.28 5.410e-11 476 PR00785 NUCLEAR TRANSLOCATOR PR00785H 15.80 7.692e-09 SIGNATURE

477 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 7.300e-19 SIGNATURE PR00245C 7.84 8.579e-19 PR00245D 10.47 4.000e-15 PR00245B 10.38 4.405e-12 PR00245E 12.40 1.509e-10 477 BL00237 G-protein coupled receptorsBL00237A 27.68 6.143e-13 proteins. 93-132 BL00237D 11.23 5.091 e-09 285-301 478 BL00297 Heat shock hsp70 proteinsBL00297D 11.95 8.835e-09 family 86-125 roteins.

481 BL00219 Anion exchangers family BL00219E 11.63 4.838e-24 proteins. 376-415 BL00219K 12.73 9.883e-24 Table 3 SEQ Database Description Results*
ID

NO: entr ID

BL00219M 9.98 5.208e-23 BL00219H 10.06 5.034e-22 BL00219N 10.66 7.545e-22 BL00219B 14.47 6.104e-20 BL00219I 6.16 9.818e-17 BL00219G 12.86 9.697e-16 BL00219F 10.52 8.024e-15 BL00219C 17.29 4.470e-14 BL002190 14.02 1.000e-13 BL00219L 18.71 9.422e-10 481 PR00165 ANION EXCHANGER SIGNATUREPR00165A 9.84 8.000e-18 PR00165B 15.26 1.549e-13 PR00165I 10.02 2.521e-13 PR00165E 8.63 8.859e-11 PR00165F 10.39 7.674e-10 PR00165G 11.41 8.180e-09 486 PR00237 RHODOPSIN-LIKE GPCR PR00237G 19.63 2.552e-13 SUPERFAMILY SIGNATURE PR00237B 13.50 3.045e-13 PR00237F 13.57 1.000e-10 PR00237A 11.48 9.333e-10 PR00237C 15.69 2.800e-09 486 BL00237 G-protein coupled receptorsBL00237A 27.68 3.032e-15 proteins. 81-120 BL00237C 13.19 2.324e-10 BL00237D 11.23 2.607e-10 BL00237B 5.28 7.136e-09 490 BL00215 Mitochondrial ener transferBL00215A 15.82 7.618e-14 roteins. 67-91 491 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 8.364e-14 SIGNATURE PR00245C 7.84 5.500e-12 PR00245B 10.38 4.600e-11 PR00245E 12.40 9.830e-10 491 PR00237 RHODOPSIN-LIKE GPCR PR00237G 19.63 3.605e-10 SUPERFAMILY SIGNATURE PR00237C 15.69 6.175e-09 491 BL00237 G-protein coupled receptorsBL00237A 27.68 5.371e-13 proteins. 90-129 BL00237D 11.23 9.455e-09 493 PR00019 LEUCINE-RICH REPEAT PR00019B 11.36 4.150e-10 SIGNATURE PR00019B 11.36 9.100e-10 PR00019A 11.19 8.000e-09 493 PR00500 POLYCYSTIC KIDNEY DISEASEPR00500B 7.74 9.337e-09 PROTEIN SIGNATURE

495 BL00379 CDP-alcohol phosphatidyltransferasesBL00379 24.64 8.855e-16 roteins.

500 BL00790 Receptor tyrosine kinaseBL00790I 20.01 9.550e-10 class V 107-137 roteins.

501 BL00031 Nuclear hormones receptorsBL00031B 22.25 6.538e-34 bindin re ion roteins.

501 PR00047 C4-TYPE STEROID RECEPTORPR00047C 5.40 3.250e-14 ZINC FINGER SIGNATURE PR00047D 13.53 3.250e-12 501 PR00398 STEROID HORMONE RECEPTORPR00398C 13.47 5.299e-14 SIGNATURE PR00398G 15.17 7.081e-09 504 PR00500 POLYCYSTIC KIDNEY DISEASEPR00500A 5.70 8.768e-10 PROTEIN SIGNATURE

504 PD02382 RECEPTOR CHAIN PRECURSORPD02382B 4.60 3.100e-09 TRANSME.

504 BL00790 Receptor tyrosine kinaseBL00790I 20.01 7.643e-09 class V 535-565 roteins.

Table 3 SEQ Database Description Results*
ID

NO: entr ID

505 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 6.870e-24 SIGNATURE PR00245C 7.84 2.421e-19 PR00245E 12.40 8.714e-16 PR00245D 10.47 6.786e-13 PR00245B 10.38 6.906e-13 505 BL00237 G-protein coupled receptorsBL00237A 27.68 8.839e-15 proteins. 132-171 BL00237D 11.23 2.364e-09 505 PR00237 RHODOPSIN-LIKE GPCR PR00237B 13.50 1.750e-09 SUPERFAMILY SIGNATURE PR00237C 15.69 4.600e-09 PR00237A 11.48 5.065e-09 PR00237G 19.63 5.605e-09 505 PR00023 ZONA PELLUCIDA SPERM- PR00023E 22.27 9.813e-09 BINDING PROTEIN SIGNATURE

507 PR00722 CHYMOTRYPS1N SERINE PR00722A 12.27 4.960e-15 PROTEASE FAMILY (S1) PR00722C 10.87 2.929e-14 SIGNATURE

507 BL00134 Serine proteases, trypsinBL00134B 15.99 3.571e-19 family, 510-533 histidine proteins. BL00134A 11.96 3.160e-17 BL00134C 13.45 3.250e-13 507 BL00495 Apple domain proteins. BL00495N 11.04 4.729e-24 BL004950 13.75 6.127e-15 BL00495M 8.50 6.400e-12 507 BL01253 Type I fibronectin domainBL01253H 13.15 8.364e-19 proteins. 528-562 BL01253G 11.34 1.574e-17 BL01253F 14.35 6.850e-14 BL01253E 16.01 8.861e-14 BL01253D 4.84 6.400e-10 507 BL00021 Kringle domain proteins.BL00021D 24.56 8.500e-28 BL00021B 13.33 5.154e-15 BL00021C 22.21 6.943e-09 509 PR00007 COMPLEMENT C1Q DOMAIN PR00007B 14.16 6.657e-15 SIGNATURE PR00007C 15.60 2.047e-14 PR00007A 19.33 8.412e-12 509 BL0041 S na sins roteins. BL00415N 4.29 7.307e-09 509 BL01113 Clq domain proteins. BL01113B 18.26 3.647e-27 BL01113A 17.99 1.000e-13 BL01113C 13.18 2.532e-13 BL01113A 17.99 7.081e-13 BL01113A 17.99 8.297e-13 BL01113A 17.99 3.538e-12 BL01113A 17.99 5.385e-12 BL01113A 17.99 5.909e-11 BL01113A 17.99 8.773e-11 BL01113A 17.99 9.135e-09 509 BL00420 Speract receptor repeatBL00420A 20.42 4.808e-12 proteins domain 150-178 proteins. BL00420A 20.42 8.967e-10 BL00420A 20.42 7.231e-09 BL00420A 20.42 9.169e-09 513 BL00237 G- rotein cou led rece BL00237A 27.68 9.486e-13 tors roteins. 92-131 513 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 6.714e-12 SIGNATURE PR00245C 7.84 8.000e-10 513 PR00237 RHODOPSIN-LIKE GPCR PR00237A 11.48 5.355e-09 SUPERFAMILY SIGNATURE PR00237C 15.69 9.550e-09 516 PR00237 RHODOPS1N-LIKE GPCR PR00237G 19.63 2.543e-11 SUPERFAMILY SIGNATURE PR00237A 11.48 3.000e-10 Table 3 SEQ DatabaseDescription Results*
ID

NO: entr ID

516 PR00373 GLYCOPROTEIN HORMONE PR00373D 11.16 2.403e-09 RECEPTOR SIGNATURE

516 BL00237 G-protein coupled receptorsBL00237A 27.68 6.600e-10 proteins. 491-530 BL00237D 11.23 4.545e-09 516 PR00019 LEUCINE-RICH REPEAT PR00019A 11.19 7.300e-11 SIGNATURE PR00019A 11.19 8.043e-10 PR00019B 11.36 5.320e-09 516 PR00910 LUTEOVIRUS ORF6 PROTEIN PR00910A 2.51 7.429e-09 SIGNATURE

519 BL00649 G-protein coupled receptorsBL00649C 17.82 6.564e-13 family 2 578-603 roteins.

519 PR00249 SECRETIN-LIKE GPCR PR00249C 17.08 4.323e-10 SUPERFAMILY SIGNATURE

521 PR00176 SODIUM/NEUROTRANSMITTER PR00176C 10.84 2.667e-24 SYMPORTER SIGNATURE PR00176A 16.82 5.500e-23 PR00176B 7.31 9.308e-17 521 BL00610 Sodium:neurotransmitter BL00610A 17.73 1.000e-40 symporter 69-118 family proteins. BL00610B 23.65 1.000e-40 BL00610C 12.94 6.157e-14 524 PR00237 RHODOPSIN-LIKE GPCR PR00237B 13.50 7.750e-14 SUPERFAMILY SIGNATURE PR00237C 15.69 1.667e-12 PR00237F 13.57 8.333e-12 PR00237E 13.03 6.667e-11 PR00237D 8.94 7.750e-10 524 BL00419 Photos stem I saA and BL00419L 20.03 7.850e-09 saB roteins. 11-59 524 BL00237 G-protein coupled receptorsBL00237A 27.68 3.739e-20 proteins. 126-165 BL00237C 13.19 4.808e-13 BL00237B 5.28 8.773e-09 526 PR00237 RHODOPSIN-LIKE GPCR PR00237D 8.94 2.000e-09 SUPERFAMILY SIGNATURE

526 BL00237 G- rotein cou led rece BL00237A 27.68 3.020e-09 tors roteins. 121-160 526 PR00641 EBI1 ORPHAN RECEPTOR PR00641E 10.22 8.975e-09 SIGNATURE

527 BL00519 Bacterial regulatory BL00519C 29.50 6.595e-09 proteins, asnC 110-154 famil roteins.

531 BL00237 G- rotein cou led rece BL00237A 27.68 8.258e-15 tors roteins. 143-182 531 PR00237 RHODOPSIN-LIKE GPCR PR00237A 11.48 7.375e-11 SUPERFAMILY SIGNATURE PR00237B 13.50 4.094e-10 PR00237C 15.69 2.575e-09 532 BL00237 G- rotein cou led rece BL00237A 27.68 2.029e-13 tors roteins. 111-150 532 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 9.000e-23 SIGNATURE PR00245C 7.84 3.543e-14 PR00245B 10.38 9.357e-14 PR00245E 12.40 8.286e-12 532 PR00237 RHODOPSIN-LIKE GPCR PR00237A 11.48 2.161 e-09 47-71 SUPERFAMILY SIGNATURE PR00237C 15.69 4.150e-09 533 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 I.OOOe-17 SIGNATURE

534 PR00249 SECRETIN-LIKE GPCR PR00249C 17.08 9.129e-11 SUPERFAMILY SIGNATURE PR00249E 14.90 4.493e-10 534 BL00649 G-protein coupled receptorsBL00649C 17.82 6.073e-13 family 2 245-270 proteins. BL00649E 15.34 2.857e-12 BL00649G 13.52 8.826e-11 BL00649B 20.68 8.548e-09 538 PR00245 OLFACTORY RECEPTOR PR00245C 7.84 6.049e-15 Table 3 SEQ Database Description Results*
ID

NO: entr ID

SIGNATURE PR00245A 18.03 6.192e-15 PR00245E 12.40 4.643e-12 PR00245B 10.38 4.886e-10 538 BL00237 G-protein coupled receptorsBL00237A 27.68 S.SOOe-12 proteins. 90-129 BL00237D 11.23 7.545e-09 538 PR00237 RHODOPSIN-LIKE GPCR PR00237G 19.63 2.674e-09 SUPERFAMILY SIGNATURE PR00237E 13.03 7.088e-09 PR00237C 15.69 8.875e-09 542 BL00243 Integrins beta chain BL00243H 17.53 4.375e-10 cysteine-rich 411-436 domain roteins.

542 PR00011 TYPE III EGF-LIKE SIGNATUREPROOO11D 14.03 3.508e-11 PROOO11B 13.08 4.522e-10 PROOO11A 14.06 2.479e-09 542 PR00962 LETHAL(2) GIANT LARVAE PR00962F 12.39 6.855e-09 PROTEIN SIGNATURE

543 BL00518 Zinc finger, C3HC4 typeBL00518 12.23 4.857e-10 (RING 31-39 finger , roteins.

544 BL00733 Ribosomal protein S26e BL00733A 11.62 8.784e-25 proteins. 1-43 BL00733B 12.04 6.870e-20 544 BL00127 Pancreatic ribonucleaseBL00127B 26.57 3.455e-09 famil roteins. 134-178 546 PR00237 RHODOPSIN-LIKE GPCR PR00237B 13.50 8.313e-10 SUPERFAMILY SIGNATURE PR00237D 8.94 7.000e-09 547 BL00790 Receptor tyrosine kinaseBL00790I 20.01 7.480e-11 class V 1216-proteins. 1246 BL00790I20.01 6.963e-10 1115-1145 BL00790I20.01 8.988e-13.42 9.514e-10 1266-1291 547 DM00215 PROLINE-RICH PROTEIN DM00215 19.43 1.305e-09 3. 2034-547 PD02870 RECEPTOR 1NTERLEUKIN-1 PD02870B 18.83 8.024e-12 PRECURSOR. 1440 PD02870D 15.74 9.900e-10 1408-1442 PD02870B 18.83 7.415e-09 339-371 547 PR00014 FIBRONECTIN TYPE III PR00014A 8.22 3.864e-09 SIGNATURE 1274 PR00014D 12.04 7.750e-09 547 DM00179 w KINASE ALPHA ADHESIONDM00179 13.97 8.043e-09 CELL.

547 PD02327 GLYCOPROTEIN ANTIGEN PD02327B 19.84 9.591e-09 PRECURSOR IMMUNOGLO. PD02327B 19.84 9.591 e-09 676-697 547 BL00240 Receptor tyrosine kinaseBL00240B 24.70 7.907e-10 class III 487-510 roteins. BL00240B 24.70 1.000e-08 548 PR00001 COAGULATION FACTOR GLA PROOOOIA 12.78 2.174e-13 DOMAIN SIGNATURE PR00001B 10.75 8.364e-13 PROOOO1 C 16.60 6.327e-09 550 PR00245 OLFACTORY RECEPTOR PR0024SA 18.03 2.500e-22 SIGNATURE PR00245C 7.84 7.000e-18 PR00245B 10.38 7.480e-15 PR0024SE 12.40 6.029e-13 550 BL00237 G-protein coupled receptorsBL00237A 27.68 6.182e-14 proteins. 90-129 BL00237D 11.23 7.750e-10 550 PR00237 RHODOPSIN-LIKE GPCR PR00237G 19.63 5.219e-12 SUPERFAMILY SIGNATURE PR00237E 13.03 1.000e-10 PR00237C 15.69 3.925e-09 551 PR00165 ANION EXCHANGER SIGNATUREPR00165A 9.84 1.652e-16 ~ 453-475 Table 3 SEQ DatabaseDescription Results*
ID entr NO: ID

PR00165B 15.26 7.835e-14 PR00165I 10.02 5.378e-12 PR00165D 7.84 8.159e-11 PR00165F 10.39 8.729e-11 PR00165H 8.01 1.321e-10 551 BL00219 Anion exchangers family BL00219C 17.29 7.474e-25 proteins. 338-376 BL00219N 10.66 4.575e-24 BL00219E 11.63 9.471e-24 BL00219K 12.73 2.098e-22 BL00219B 14.47 8.571e-22 BL00219M 9.98 7.222e-21 BL00219H 10.06 9.693e-21 BL00219A 17.13 4.176e-20 BL00219I 6.16 3.106e-19 BL00219L 18.71 3.889e-19 BL00219G 12.86 3.198e-17 BL00219F 10.52 7.152e-16 BL002190 14.02 I .83 5e-11 959-998 BL00219D 15.15 3.148e-10 *Results include in order: accession number subtype; raw score; p-value;
position of signature in amino acid sequence.

Table 4A
SEQ Pfam Model Description E-value Score ID
NO:

277 zf C3HC4 Zinc fin er, C3HC4 t a (RING5.2e-10 36.7 fin er 278 zf C3HC4 Zinc fin er, C3HC4 t a RING 5.2e-10 36.7 finger 279 PA PA domain 1.3e-18 75.3 282 transmembrane4Tetras anin famil 1.7e-48 161.4 287 sushi Sushi domain SCR re eat 1.8e-56 201.1 290 ART NAD:ar mine ADP-ribos ltransferase6.5e-207700.8 292 UPAR LY6 u-PAR/L -6 domain 0.01 14.2 293 PMP22 ClaudinPMP-22/EMP/MP20/Claudin famil9.4e-06 32.5 294 MHC_II alpha Class II histocompatibility 4.1 e-44160.0 d antigen, alpha omain 295 Amidase Amidase 4.6e-71 249.5 296 Na sul h s Sodiumaulfate s m orter transmembrane1.3e-73 258.0 m re ion 298 ABC membrane ABC traps orter transmembrane1.6e-56 201.2 re ion.

299 PMP22 ClaudinPMP-22/EMP/MP20/Claudin famil0.048 -29.1 306 Ac ItransferaseAc ltransferase 9.6e-06 30.8 309 7tm 1 7 transmembrane rece for 4.1 e-3097.8 (rhodo sin family) 311 Neur chap Neurotransmitter-gated ion-channel2.2e-83 290.4 LBD ligand bindin domain 312 i Immuno lobulin domain 4.7e-20 69.7 313 LRR Leucine Rich Re eat 1.9e-23 91.3 314 Plexin re Plexin re eat 0.02 20.2 eat 315 Plexin re Plexin re eat 0.02 20.2 eat 316 7tm 1 7 transmembrane rece for 1.2e-25 83.6 (rhodo sin famil 320 7tm 1 7 transmembrane rece for 1.9e-95 305.4 rhodo sin famil ) 321 7tm 1 7 transmembrane rece for 3.3e-19 63.2 (rhodo sin famil 322 TPR TPR Domain 4.8e-16 66.7 326 C1 C1 domain 2.7e-31 117.4 330 7tm 1 7 transmembrane rece for 4.3e-15 50.1 rhodo sin famil ) 333 UbiA UbiA rep ltransferase famil 1.5e-62 221.3 338 7tm 1 7 transmembrane rece for 5.6e-38 122.8 (rhodo sin famil 339 7tm 1 7 transmembrane rece for 5.6e-38 122.8 rhodo sin famil ) 340 COesterase Carbox lesterase 3.9e-134459.0 341 7tm 2 7 transmembrane rece for 2.3e-21 84.4 (Secretin famil 342 7tm 1 7 transmembrane rece for 3.8e-25 82.1 (rhodo sin famil ) 344 7tm 1 7 transmembrane rece for 1.3e-31 102.6 (rhodo sin famil 345 7tm 2 7 transmembrane rece for 3.3e-73 256.6 (Secretin famil ) 346 7tm 2 7 transmembrane rece for 3.3e-73 256.6 (Secretin family) 351 i lmmuno lobulin domain 6.6e-07 27.3 355 LRR Leucine Rich Re eat 6.1e-29 109.6 357 Re rol sin Re rol sin M12B famil zinc 3.7e-93 322.9 metallo rotease 358 i Immuno lobulin domain 2.7e-08 31.8 359 i Immuno lobulin domain 2.7e-08 31.8 362 i= Immuno lobulindomain 4.1e-08 31.2 365 Folate carrierReduced folate carrier 3.5e-145495.7 368 450 C ochrome P450 4.4e-57 203.1 370 gla Vitamin K-dependent carboxylation/gamma-6.1e-15 63.1 carboxy lutamic GLA domain 371 actin Actin 5.7e-27 89.8 375 TruB N TruB family pseudouridylate 6.6e-69 242.3 synthase (N
terminal domain 376 TruB N TruB family pseudouridylate 6.6e-69 242.3 synthase (N
terminal domain) 377 abh drolase al ha/beta h drolase fold 0.015_ 15.7 378 abhydrolase alpha/beta hydrolase fold 1.1e-10 49.0 ~

Table 4A
SEQ Pfam Model Description E-value Score ID
NO:

382 TTL Tubulin-t osine 1i ase famil4.1e-122419.1 383 UQ con Ubi uitin-con'u atin enz 0.0067 -45.5 me 388 Amino oxidaseFlavin containin amine oxidase1.3e-17 71.9 389 RUN RUN domain 8e-51 182.3 390 Rhomboid Rhomboid famil 4.7e-05 30.2 392 Occludin Occludin/ELL famil 1.2e-11 46.2 393 DUF6 Inte ral membrane rotein 0.037 14.8 395 Patched Patched famil 5.2e-105362.3 396 zf C4 Zinc finger, C4 t a two domains1.4e-44 152.5 398 Na H ExchangerSodium/h dro en exchan er 9.9e-103354.7 famil 402 F-box F-box domain 0.022 21.4 404 PAP2 PAP2 su erfamil 1.4e-30 115.0 406 Patched Patched famil 5.8e-17 -4.9 411 7tm 1 7 transmembrane rece for 5.4e-43 138.7 (rhodo sin famil 412 7tm 1 7 transmembrane rece for 2.8e-91 292.1 (rhodo sin famil ) 415 E1-E2 ATPase E1-E2 ATPase 1.1e-116387.9 418 HC03 cotrans HC03- trans orter famil 1.2e-3021018.9 421 Kelch Kelch motif 6.5e-40 146.0 422 WD40 WD domain, G-beta re eat 7.5e-16 66.1 423 Beach Bei eBEACH domain 7.3e-23 86.9 424 bZIP bZIP transcri lion factor 0.0074 15.5 430 kinase Protein kinase domain 1.8e-36 134.6 432 zf C3HC4 Zinc fin er, C3HC4 t a (RING9.4e-06 22.9 fin er) 434 PMP22 ClaudinPMP-22/EMP/MP20/Claudin famil1.7e-39 144.7 438 MORN MORN re eat 1.4e-34 128.3 443 PAP2 PAP2 su erfamil 2.9e-29 110.7 448 hormone rec Ligand-binding domain of 1e-41 139.0 nuclear hormone rece for 449 cadherin Cadherin domain 1.6e-37 138.1 451 zf CXXC CXXC zinc fin er 2.1 e-0634.7 452 HLH Helix-loo -helix DNA-bindin 2.6e-09 44.4 domain 457 ig Immuno lobulin domain 0.0098 13.9 458 7tm 1 7 transmembrane rece for 1.2e-25 83.6 rhodo sin famil 463 TUDOR Tudor domain 6.6e-13 56.3 464 Re rol sin Re rol sin M 12B famil zinc 3.1 e-88306.6 metallo rotease 468 HEAT HEAT re eat 0.0013 25.4 469 DUF6 Inte ral membrane rotein 1.4e-05 32.0 471 DENN DENN (AEX-3 domain 7.1e-59 209.0 474 S a to h sin S na to h sin / s na to orin4.2e-38 140.0 476 zf MYND MYND finger 4.4e-05 29.5 477 7tm 1 7 transmembrane rece for 2.4e-33 108.1 (rhodo sin famil ) 481 HC03 cotrans HC03- trans orter family 0 1065.8 482 ank Ank re eat 1e-19 79.0 485 LRRCT Leucine rich re eat C-terminal1.1e-08 42.3 domain 486 7tm 1 7 transmembrane rece for 5.3e-42 135.6 (rhodo sin famil 490 mito carr Mitochondria) carrier rotein5.6e-24 93.1 491 7tm 1 7 transmembrane rece for 3.8e-28 91.6 (rhodo sin famil ) 493 LRR Leucine Rich Re eat 1.7e-15 64.9 499 Ra GAP Ra /ran-GAP 2e-20 81.3 500 fn3 Fibronectin t a III domain 1.1e-12 55.6 501 hormone rec Ligand-binding domain of 2e-46 154.4 nuclear hormone rece for 503 RhoGEF RhoGEF domain 2.8e-33 124.0 504 fn3 Fibronectin t a III domain 1.5e-09 45.1 Table 4A
SEQ Pfam Model Description E-value Score ID
NO:

505 7tm 1 7 transmembrane rece for 3.1e-45 145.8 rhodo sin famil 507 tr sin T sin 7e-87 276.1 508 PKD PKD domain 1.2e-09 45.5 509 Cl C1 domain 2.7e-31 117.4 513 7tm 1 7 transmembrane rece for 3.3e-12 40.9 (rhodo sin famil ) 516 LRR Leucine Rich Re eat 7.3e-31 116.0 519 7tm 2 7 transmembrane rece for 2.3e-21 84.4 Secretin famil ) 521 SNF Sodium:neurotransmitter s 1.7e-124427.0 m orter famil 523 SPRY SPRY domain 9.8e-20 79.0 524 7tm 1 7 transmembrane rece for 5.3e-59 189.6 rhodo sin famil 527 Patched Patched famil 0.00021 -419.9 531 7tm 1 7 transmembrane rece for 3.1e-18 60.1 (rhodo sin famil ) 532 7tm 1 7 transmembrane rece for 1.7e-37 121.3 rhodo sin famil 533 7tm 1 7 transmembrane rece for 6.7e-10 33.6 (rhodo sin famil 534 7tm 2 7 transmembrane rece for 3.3e-73 256.6 Secretin famil ) 535 Rhomboid Rhomboid famil 8.5e-18 72.6 536 Rhomboid Rhomboid famil 8.5e-18 72.6 538 7tm 1 7 transmembrane rece for 4.6e-38 123.1 rhodo sin famil 542 SEA SEA domain 5.1e-10 46.7 543 SPRY SPRY domain 2.6e-17 70.9 544 Ribosomal Ribosomal rotein S26e 2.1e-20 81.2 S26e 547 fn3 Fibronectin t a III domain 4.1e-102352.6 548 gla Vitamin K-dependent carboxylation/gamma-3e-15 64.1 carbox lutamic (GLA) domain 550 7tm 1 7 transmembrane rece for 4e-43 139.1 (rhodo sin famil ) 551 HC03 cotrans HC03- trans orter famil 0 1704.8 552 DUF6 Integral membrane rotein 0.069 10.4 Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

277 zf C3HC4 Zinc finger, C3HC4 1.6e-0738.5 1 222-263 type (RING
fin er 277 PA PA domain 1.4e-0635.3 1 58-144 277 PHD PHD-fin er 0.019 5.9 1 221-266 278 zf C3HC4 Zinc finger, C3HC4 1.6e-0738.5 1 198-239 type (RING
finger 278 PA PA domain 0.004 21.3 1 28-120 278 PHD PHD-fin er 0.019 5.9 1 197-242 279 PA PA domain 1.4e-1875.2 1 58-162 281 Cornichon Cornichon rotein 4.4e-37136.6 1 2-113 281 PsbT Photosystem II reaction3.8 6.4 1 1-24 centre T
rotein 282 transmembraneTetraspanin family 1.6e-2494.9 1 10-166 286 su ar tr Su ar (and other) 3.9 -186.51 19-494 trans orter 286 Na sulph-symSodium: sulfate 9 -362.51 78-453 symporter transmembrane 287 sushi Sushi domain (SCR 1.8e-56201.1 4 35-94:99-repeat) 157:162-223:228-290 ART NAD:arginine ADP- 1.8e-207702.6 1 1-326 ribos ltransferase 291 PAP2 PAP2 su erfamil 1.3 -21.2 1 88-175 292 UPAR LY6 u-PAR/L -6 domain 0.0034 12.8 1 23-108 292 Keratin Keratin, high sulfur0.48 -63.3 1 7-124 B2 B2 rotein 293 PMP22_ClaudiPMP-22/EMP/MP20/Claudin9.4e-0632.5 1 7-169 n famil 294 MHC II alphaClass II histocompatibility4.1e-44160.0 1 29-109 antigen, al 294 i Immuno lobulin domain0.016 21.8 1 125-172 295 Amidase Amidase 2.1e-65230.7 1 69-513 296 Na sulph Sodiumaulfate symporter4.1e-71249.7 1 3-579 sym transmembran 296 Na H antiporteNa+/H+ antiporter 3.3 -108.51 241-572 family 296 Pe tidase T a IV leader a 6.8 -187.41 1-307 C20 tidase famil 296 PH04 Phos hate trans 9 -206.11 129-510 orter famil 298 ABC membranABC transporter 1.7e-56201.1 1 188-459 a transmembrane re ion 298 ABC tran ABC trans orter 1.2e-53191.7 1 469-653 298 APS kinase Aden l lsulfate 2.6 -117.01 468-587 kinase 298 DUF258 Protein of unknown 3.6 -79.4 1 446-596 function, 299 PMP22_ClaudiPMP-22/EMP/MP20/Claudin0.048 -29.1 1 4-168 n famil 300 Mtc Tricarbox late carrier1.2e-67238.1 1 1-236 301 Mab-21 Mab-21 rotein 2.3 -192.11 189-524 304 Cornichon Cornichon rotein 3.4e-1977.2 1 2-98 304 PsbT Photosystem II reaction3.8 6.4 1 1-24 centre T
rotein 305 PMP22_ClaudiPMP-22/EMP/MP20/Claudin1.6 -55.5 1 1-192 n famil 306 Ac ItransferaseAc ltransferase 4.9e-0530.2 1 70-229 Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

308 su ar tr Su ar (and other) 0.33 -155.61 9-490 trans orter 308 PUCC PUCC rotein 0.6 -253.11 93-486 308 Nucleoside Nucleoside transporter2.1 -151.41 143-456 tra n 308 oxidored-qlNADH- 7 -168.71 151-478 Ubi uinone/ lasto uinone 309 7tm 1 7 transmembrane 7.1e-05-4.8 1 41-235 receptor rhodo sin famil ) 311 Neur_chan_LBNeurotransmitter-gated1.4e-85297.7 1 30-236 ion-D channel lig 311 Neur_chan_meNeurotransmitter-gated6.5e-38139.4 1 243-446 ion-mb channel tra 312 ig Immunoglobulin domain2.1e-1771.3 3 37-106:138-208:245-313 LRR Leucine Rich Repeat1.3e-2391.9 7 66-89:90-113:114-137:138-161:163-186:

210:211-313 i Immuno lobulin domain2.7e-0737.7 1 314-372 313 fn3 Fibronectin t a 2.4e-0634.5 1 422-502 III domain 313 LRRCT Leucine rich repeat5.6e-0530.0 1 252-297 C-terminal domain 313 LRRNT Leucine rich repeat3.7 8.7 1 33-64 N-terminal domain 313 APS kinase Aden 1 lsulfate 5.6 -120.41 541-646 kinase 314 PSI Plexin re eat 0.02 20.2 1 303-348 315 PSI Plexin re eat 0.02 20.2 1 303-348 316 7tm 1 7 transmembrane 4.7e-1976.7 1 3-245 receptor rhodo sin famil 316 DUF40 Domain of unknown 3.1 -127.11 2-206 function 317 Filamin Filamin/ABP280 re 5.5 -34.0 1 100-192 eat 318 Polysacc Polysaccharide biosynthesis7 -87.4 1 107-368 synt rotein 320 7tm 1 7 transmembrane 1.2e-90314.5 1 54-335 receptor rhodo sin famil ) 321 7tm 1 7 transmembrane 2.6e-0841.0 1 32-309 receptor rhodo sin famil ) 321 7tm 5 7TM chemorece for 8.3 -169.81 14-317 322 TPR TPR Domain 4.3e-1666.9 3 493-526:527-560:561-322 PMT Dolichyl-phosphate-mamose-3.2 -54.0 I 6-245 rotein mannos It 326 C1 C1 domain 7.3e-32119.3 1 117-241 326 Collagen Collagen triple 3.8e-0633.8 1 50-109 helix repeat (20 co ies 326 L sis col L sis rotein 9.3 -10.9 1 1-36 330 7tm 1 7 transmembrane 0.027 -64.6 1 1-183 rece for Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

rhodo sin famil 331 PICD PICD domain 1.7e-0841.7 4 407-495:502-591:596-685:690-331 REJ REJ domain 0.99 -314.61 327-806 331 fn3 Fibronectin t a III 3.7 -2.3 1 408-486 domain 331 Arthro defensiArthropod defensin 4.6 4.0 1 879-907 n 333 UbiA UbiA ren Itransferase3.2e-56200.2 1 86-351 famil 338 7tm_1 7 transmembrane receptor1.1e-34128.7 1 40-289 (rhodo sin famil ) 338 EII-Sor PTS system sorbose-specific9.1 -143.41 20-226 iic com onent 339 7tm 1 7 transmembrane receptor1.1e-34128.7 1 40-289 (rhodo sin famil 339 EII-Sor PTS system sorbose-specific9.1 -143.41 20-226 iic com onent 340 COesterase Carbox lesterase 2.3e-133456.4 1 19-624 341 7tm 2 7 transmembrane rece2.3e-2184.4 1 637-897 for 341 GPS Latrophilin/CL-1-like2.7e-1357.6 1 581-634 GPS

domain 341 HRM Hormone rece for 0.008515.8 1 298-351 domain 341 Me-amine- Methylamine dehydrogenase,4 -30.1 1 190-321 L

deh L chain 342 7tm 1 7 transmembrane receptor3.4e-0625.9 1 41-225 (rhodo sin famil 342 DUF32 Domain of unknown 1.9 -145.91 37-242 function 342 DUF40 Domain of unknown 9.1 -135.51 26-240 function 344 7tm_1 7 transmembrane receptor2.2e-28107.8 1 44-293 (rhodo sin famil ) 344 Abi CAAX amino terminal 5.4 -25.4 1 101-190 protease farm I

345 7tm 2 7 transmembrane rece3.3e-73256.6 1 396-739 for 345 GPS Latrophilin/CL-1-like3.1e-1564.0 1 345-394 GPS

domain 345 metalthio Metallothionein 1.7 -4.1 1 33-100 345 7tm 5 7TM chemorece for 1.7 -157.41 392-650 345 CbiM CbiM 2.1 -83.3 1 497-654 345 DUF26 Domain of unknown 2.9 -12.6 1 64-109 function 345 cytochrome Cytochrome b(C- 4 -28.5 1 369-471 b_ -C terminal /66/ etD

345 TIL Trypsin Inhibitor 9.7 -15.4 1 23-74 like cysteine rich d 346 7tm 2 7 transmembrane rece3.3e-73256.6 1 300-643 for 346 GPS Latrophilin/CL-1-like3.1e-1564.0 1 249-298 GPS

domain 346 7tm 5 7TM chemorece for 1.7 -157.41 296-554 346 CbiM CbiM 2.1 -83.3 1 401-558 346 cytochrome Cytochrome b(C- 4 -28.5 I 273-375 b--C terminal /b6/ etD

Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

351 i Immuno lobulin domain0.0003327.4 1 72-150 355 LRR Leucine Rich Repeat 4.6e-29110.0 7 49-72:73-96:97-120:121-144:146-169:170-193:194-355 fn3 Fibronectin t a III 2.7e-0841.0 1 387-470 domain 355 i Immunoglobulin domain2.4e-0737.9 1 278-336 355 LRRCT Leucine rich repeat 0.054 17.5 1 218-262 C-terminal domain 355 LRRNT Leucine rich repeat 1 12.9 1 16-47 N-terminal domain 356 thiored Thioredoxin 0.0088-10.1 1 172-279 357 Reprolysin Reprolysin (M128) 3.6e-93322.9 1 21 1-409 family zinc metallo 357 Pep M12B-proReprolysin family 7.7e-43155.7 1 80-196 propeptide a 357 disintegrinDisinte rin 2.2e-2597.8 1 426-501 357 Adeno E3 Adenovirus E3 region5.1 -2.5 1 698-738 CR protein 357 EB EB module 9.3 -12.3 1 633-682 358 ig Immunoglobulin domain6.7e-0736.4 2 115-168:208-359 ig Immunoglobulin domain6.7e-0736.4 2 109-162:202-362 ig Immunoglobulin domain6.9e-0736.3 2 47-139:179-365 Folate carrierReduced folate carrier3.8e-145495.6 1 10-441 365 ion trans Ion trans ort rotein8.3 -13.4 1 85-337 365 Nucleoside Nucleoside transporter8.7 -163.11 113-367 tra n 365 FecCD FecCD trans ort famil9.4 -220.81 274-457 365 su ar tr Sugar (and other) 9.7 -198.01 11-459 trans orter 368 450 C ochrome P450 4.6e-1976.8 1 60-379 370 gla Vitamin K-dependent 3.5e-1563.9 1 57-98 carbox lation/ anima-carb 371 actin Actin 1.6e-1255.0 1 8-371 372 DUF140 Domain of unknown 5.9 -162.81 1-204 function 375 TruB N TruB family pseudouridylate6.6e-69242.3 1 107-247 s nthase 375 PUA PUA domain 5e-18 73.3 1 339-414 376 TruB N TruB family pseudouridylate6.6e-69242.3 1 78-218 s nthase 376 PUA PUA domain 1.8e-2598.0 1 266-341 377 abh drolaseal ha/beta h drolase0.015 15.7 1 80-270 fold 377 Li ase 3 Li ase class 3 0.6 -26.8 1 68-184 377 ThioesteraseThioesterase domain 1.9 -44.1 1 53-270 378 abh drolaseal ha/beta h drolase1.1e-1049.0 1 80-326 fold 378 Lipase 3 Lipase (class 3) 0.98 -29.1 1 68-198 ~

Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

378 ThioesteraseThioesterase domain 1.6 -43.0 1 53-297 382 TTL Tubulin-t osine 1i 1.5e-120413.9 1 468-764 ase famil 383 UQ con Ubi uitin-con'u atin4.2e-1047.0 1 249-412 enz me 384 sugar tr Su ar (and other 1.2 -171.71 54-471 traps orter 384 voltage Volta a ated chloride9.2 -243.01 92-393 CLC channel 388 Amino oxidaseFlavin containing 1.9e-69244.2 1 23-497 amine oxidoreductase 389 DENN DENN AEX-3 domain 2.1e-87303.8 1 202-390 389 RUN RUN domain 8e-51 182.3 1 801-946 389 uDENN uDENN domain 1.2e-32121.9 1 4-138 389 dDENN dDENN domain 3.2e-31117.1 1 512-588 389 PLAT PLAT/LH2 domain 7.4e-1769.4 1 957-1059 390 Rhomboid Rhomboid famil 4.7e-0530.2 1 . 59-214 390 UIM Ubi uitin interaction2.1 14.6 1 268-285 motif 392 Occludin Occludin/ELL famil 1.1e-05-92.9 1 183-550 392 7tm 5 7TM chemorece for 4 -164.01 184-451 393 DUF6 Integral membrane 0.042 15.4 1 80-186 protein 393 Nramp Natural resistance-associated5.3 -290.41 123-381 macro hage ro 393 EII-GUT PTS system enzyme 5.8 -135.71 192-300 II sorbitol-s ecific facto 395 Patched Patched famil 3.2e-105363.0 1 166-965 395 Srg C.elegans Srg family2.7 -213.31 214-464 integral membrane rote 395 UPF0132 Uncharacterised protein4.8 -39.8 1 402-494 family UPF0132) 395 Sec62 Translocation rotein5.6 -132.61 311-502 Sec62 396 zf C4 Zinc finger, C4 type1.8e-42154.5 1 100-174 (two domains) 396 hormone Ligand-binding domain7e-17 69.5 1 281-441 rec of nuclear hormone 398 Na H ExchangSodium/hydrogen exchanger9.9e-103354.7 1 62-478 er famil 398 ABC2 membraABC-2 type transporter0.92 -112.61 254-479 ne 398 GntP ermeaseGntP famil ermease 4.9 -374.71 64-366 398 Transp cyt-purPermease for cytosine/purines,5 -194.91 50-427 uracil 398 ABC-3 ABC 3 traps ort famil7.8 -194.61 260-469 398 TrkH Sodium traps ort 7.9 -214.71 12-411 rotein 398 DUF6 Integral membrane 8 -23.3 1 338-462 protein 398 ER lumen ER lumen protein 8.7 -158.21 274-435 rece retaining t rece for 399 DUF284 Eukaryotic protein 1.5e-114394.0 1 68-309 of unknown function, DUF2 402 F-box F-box domain 0.009122.6 1 8-55 404 PAP2 PAP2 su erfamil 1.4e-30115.0 1 129-283 406 Patched Patched famil 5.8e-17-4.9 1 I-756 406 oxidored-qlNADH- 0.55 -146.01 77-319 Ubiquinone/plastoquinone (com lex I) 406 UPF0118 Domain of unknown 9.3 -133.51 377-719 ~ ~ function ( Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

411 7tm 1 7 transmembrane 7.1e-38139.3 1 41-290 receptor rhodo sin famil 411 7tm 5 7TM chemorece for 6.7 -168.11 16-258 412 7tm 1 7 transmembrane 1.3e-85297.9 1 43-297 receptor rhodo sin famil 412 7tm 5 7TM chemorece for 1.8 -157.81 51-305 413 PHD PHD-fin er 0.21 -3.5 1 150-199 413 zf MIZ MIZ zinc fin er 3.9 -18.2 1 150-200 415 E1-E2 ATPaseE1-E2 ATPase 1.7e-113390.5 1 223-454 415 Cation ATPaseCation transporting1.7e-69244.3 1 921-1099 ATPase, C-C terminu 415 Cation-ATPaseCation transporter/ATPase,4.2e-42153.3 1 121-204 N-N terminus 415 Hydrolase haloacid dehalogenase-like3.7e-1563.8 1 458-825 h drolase 415 7tm 5 7TM chemorece for 9.4 -170.71 170-438 416 MAPEG MAPEG famil 2.1 -21.7 1 98-183 416 Cation ATPaseCation transporting5.6 -47.5 1 81-221 ATPase, C-C terminu 418 HC03 cotransHC03- transporter 0 1024.41 84-853 family 418 xan ur~ermeaPermease family 0.9 -176.01 375-836 se 421 Kelch Kelch motif 3.9e-49176.7 5 258-308:310-355:357-417:419-471:473-421 BTB BTB/POZ domain 0.88 -10.1 1 2-70 422 WD40 WD domain, G-beta 1.6e-2081.6 4 16-56:62-repeat 98:162-199:313-422 aminotran Aminotransferase 0.0091 -46.1 1 391-597 1 2 class I and II

422 Cys Met Cys/Met metabolism 9.6 -318.81 371-600 Meta PLP-PP de endentenz 423 ribonuc_red_sRibonucleotide reductase,5.6 -142.11 989-1265 small m chain 424 DUF87 Domain of unknown 3.9 -134.31 48-354 function 427 DUF6 Integral membrane 3.8 -17.8 1 143-271 protein 427 Frizzled Frizzled/Smoothened7.2 -246.31 79-280 family membrane re io 427 oxidored_qlNADH- 9 -170.91 70-270 Ubiquinone/plastoquinone com lex I) 428 DUF6 Integral membrane 3.8 -17.8 1 143-271 protein 428 Frizzled Frizzled/Smoothened7.2 -246.31 79-280 family membrane re io 428 oxidored-qlNADH- 9 -170.91 70-270 Ubi uinone/ lasto uinone Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

(com lex I) 430 kinase Protein kinase domain5.6e-33123.0 1 9-273 432 zf C3HC4 Zinc finger, C3HC4 0.0015 24.7 1 13-59 type (RING

fin er 432 FYVE FYVE zinc fin er 9.5 -26.0 I 10-65 434 PMP22_ClaudiPMP-22/EMP/MP20/Claudin1.7e-39144.7 1 89-266 n famil 434 Grpl Fun34 GPR1/FUN34/yaaH 5.9 -120.31 71-240 Y family aaH

435 DnaJ_CXXCX DnaJ central domain3.5 -46.2 1 37-92 (4 repeats) GXG

437 AT hook AT hook motif 3.1 10.6 1 713-725 438 MORN MORN repeat 1.4e-34128.3 7 15-37:39-60:61-81:107-129:130-152:288-310:311-443 PAP2 PAP2 su erfamil 2.9e-29110.7 1 82-230 448 hormone Ligand-binding domain3.6e-39143.6 1 148-329 rec of nuclear hormone 448 zf C4 Zinc finger, C4 3.3e-2597.2 1 9-66 type (two domains 449 cadherin Cadherin domain 3.2e-37137.1 4 15-108:127-227:241-331:342-449 SMP-30 Senescence marker 9 -180.91 223-467 protein-30 (SMP-30) 450 s ectrin S ectrin re eat 0.86 -8.7 1 97-203 451 zf CXXC CXXC zinc fin er 2.1e-0634.7 1 131-172 452 HLH Helix-loop-helix 4.4e-0943.6 1 106-165 DNA-binding domain 453 TP2 Nuclear transition 8.8 -60.2 1 200-335 rotein 2 458 7tm 1 7 transmembrane 2.1e-057.3 1 41-233 receptor rhodo sin famil 463 TUDOR Tudor domain 6.6e-1356.3 1 13-134 464 Reprolysin Reprolysin (M12B) 3e-88 306.6 1 146-345 family zinc metallo 464 Pep M12B-proReprolysin family 1.3e-31118.4 1 16-134 propeptide a 464 disinte Disinte rin 2.5e-2390.9 1 362-437 rin 464 EGF EGF-like domain 0.65 16.5 1 589-616 464 metalthio Metallothionein 8.7 -12.3 1 362-428 466 SAC3 GANP SAC3/GANP famil 8.8e-77268.5 1 159-358 468 HEAT HEAT re eat 0.0012 25.5 1 546-584 469 DUF6 Integral membrane 0.0002827.7 2 50-protein DL1F6 179:197-469 PhaG_MnhG_ Na+/H+ antiporter 2 -50.3 1 66-168 subunit YufB

469 DUF7 Integral membrane 3.9 -34.6 1 227-318 protein Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

469 Com etence Com etence rotein 7.5 -104.91 93-330 471 DENN DENN (AEX-3 domain 4.9e-87302.6 1 57-241 471 dDENN dDENN domain 1.4e-2598.4 1 286-353 471 uDENN uDENN domain 0.0068-0.5 I I-50 474 S na to S na to h sin / s 4.2e-38140.0 1 25-241 h sin a to orin 476 zf MYND MYND fin er 3e-05 30.9 1 296-335 476 SET SET domain 2.3 -50.9 1 450-577 476 Antifreeze Antifreeze-like domain8.4 -10.3 1 246-295 477 7tm 1 7 transmembrane receptor2.4e-30114.2 1 44-293 (rhodo sin famil ) 481 HC03 cotransHC03- transporter 0 1072.81 108-891 family 481 xan ur_permeaPermease family 0.64 -172.11 410-874 se 482 ank Ankyrin repeat 9.3e-2079.1 4 172-207:219-251:266-299:345-485 LRRCT Leucine rich repeat 9.7e-0942.5 1 9-58 C-terminal domain 485 GPS Latrophilin/CL-1-like0.001225.4 1 519-571 GPS

domain 485 7tm 2 7 transmembrane receptor0.0055-90.7 1 578-784 (Secretin family) 485 i Immuno lobulin domain0.007822.8 1 79-148 485 HRM Hormone rece for 0.069 6.8 1 168-241 domain 486 7tm 1 7 transmembrane rece2.9e-38140.6 1 32-278 for 486 7tm 5 7TM chemorece for 0.23 -141.71 55-268 486 V1R Vomeronasal organ 0.4 -145.61 42-291 pheromone rece for farm 486 oxidored-qlNADH- 4.1 -164.01 20-268 Ubiquinone/plastoquinone (com lex I) 486 UPF0032 MttB famil UPF0032 7.3 -94.8 1 54-248 490 mito carr Mitochondrial carrier6e-24 93.0 2 61-protein 1 52:155-491 7tm 1 7 transmembrane receptor5.3e-2699.8 1 41-289 rhodo sin famil 493 LRR Leucine Rich Repeat 1.2e-1565.5 5 95-118:119-142:143-166:167-190:191-493 LRRNT Leucine rich repeat 3e-08 40.9 1 64-93 N-terminal domain 493 LRRCT Leucine rich repeat 7.8e-0736.1 1 224-277 C-terminal domain 494 Retrotrans Retrotrans oson a 2 -5.1 1 180-273 a rotein 495 CDP- CDP-alcohol 5.8e-0839.9 1 94-242 OH P transfhos hand Itransferase 495 Cons_hypoth69Conserved hypothetical3 -173.71 136-379 protein Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

497 oxidored_qlNADH-Ubiquinone 7.2 -66.0 1 27-276 C

oxidoreductase 499 Rap GAP Rap/ran-GAP 1.7e-2184.9 1 1335-500 fn3 Fibronectin t a 1.1e-1255.6 1 47-130 III domain 501 hormone Ligand-binding domain2e-45 164.4 1 364-545 rec of nuclear hormone 501 zf C4 Zinc finger, C4 1.4e-1668.5 1 269-316 type (two domains) 502 7tm 5 7TM chemorece for 4.3 -164.61 9-304 503 RhoGEF RhoGEF domain 2.7e-33124.0 1 320-502 504 fn3 Fibronectin type 1.5e-0945.1 2 174-III domain 267:473-505 7tm 1 7 transmembrane 1.7e-41151.3 1 83-332 receptor (rhodo sin famil ) 505 7tm 5 7TM chemorece for 4.5 -165.11 89-327 505 DUF40 Domain of unknown 4.8 -130.61 79-274 function 506 PFEMP Plasmodium falciparum0.16 -65.7 1 919-1028 a hrocyte membrane 507 tr sin T sin 2.6e-79276.9 1 218-559 507 SRCR Scavenger receptor 6.2 -22.5 1 120-207 cysteine-rich domain 508 PKD PICD domain 2.6e-0944.4 1 641-732 508 BNR BNR/Asp-box repeat 1e-06 35.7 5 54-65:102-113:338-349:415-426:457-509 C1 C1 domain 7.3e-32119.3 1 211-335 509 Collagen Collagen triple 3.8e-0633.8 1 144-203 helix repeat (20 co ies) 509 L sis col L sis rotein 9.3 -10.9 1 95-130 513 7tm 1 7 transmembrane 1.7e-1048.3 1 43-294 rece for 513 Com etence Com etence rotein 6.8 -104.01 197-459 513 Na H antiporteNa+/H+ antiporter 8.9 -119.11 126-404 family r 514 7tm 5 7TM chemorece for 1 -153.51 164-454 514 su ar tr Su ar (and other 2.8 -182.41 50-547 trans orter 515 Pe tidase T a IV leader a 3.3 -182.31 99-278 C20 tidase famil 515 MadM Malonate/sodium 4.7 -20.6 1 209-271 symporter MadM subunit 516 LRR Leucine Rich Repeat4.8e-31116.6 8 114-137:138-161:162-184:185-208:209-230:231-254:255-278:279-516 LRRNT Leucine rich repeat0.0003827.2 1 24-55 N-terminal domain Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

516 7tm 1 7 transmembrane 0.0032 -43.2 1 434-683 rece for 516 EII-Sor PTS system sorbose-specific5.8 -140.2I 427-629 iic com on 516 CytidylyltransPhosphatidate 7.1 -89.9 1 515-612 c id 1 ltransferase 516 oxidored_qlNADH- 9.7 -171.51 470-680 Ubi uinone/ lasto uinone 516 MerC MerC mercury resistance9.8 -87.5 1 529-627 rotein 519 7tm 2 7 transmembrane 2.3e-2184.4 1 504-764 rece for 519 GPS Latrophilin/CL-1-like2.7e-1357.6 1 448-501 GPS
domain 519 HRM Hormone rece for 0.0085 15.8 1 165-218 domain 519 Me-amine- Methylamine dehydrogenase,4 -30.1 1 57-188 deh L L
chain 521 SNF Sodium:neurotransmitter4.3e-207.1 1 61-289 s orter famil 523 SPRY SPRY domain 6.1e-2079.7 1 153-284 524 7tm 1 7 transmembrane 1.6e-52187.9 1 75-338 receptor (rhodo sin famil ) 524 V 1 R Vomeronasal organ 7.7 -169.01 82-351 pheromone rece for famil 525 DUF284 Eukaryotic protein 2.1e-113390.1 1 53-350 of unknown function, DUF2 526 7tm 1 7 transmembrane 0.037 -67.9 1 71-379 receptor rhodo sin famil ) 527 Patched Patched famil 0.00021-419.91 1-484 528 PSS Phos hand 1 serine 7.3 -242.71 115-277 s thase 529 Ac ltransferaseAc ltransferase 0.27 -15.8 1 352-517 531 7tm 1 7 transmembrane 0.0063 -49.9 1 96-253 receptor (rhodo sin famil ) 532 7tm 1 7 transmembrane 8.6e-35129.0 1 62-311 receptor rhodo sin famil 534 7tm 2 7 transmembrane 3.3e-73256.6 1 179-522 rece for 534 GPS Latrophilin/CL-1-like2.8e-1564.2 1 128-177 GPS
domain 534 7tm 5 7TM chemorece for 1.7 -157.41 175-433 534 CbiM CbiM 2.1 -83.3 1 280-437 534 cytochrome Cytochrome b(C- 4 -28.5 1 152-254 b- terminal)/b6/ etD
C

535 Rhomboid Rhomboid famil 8.5e-1872.6 1 647-789 535 Com etence Com etence rotein 4.4 -100.31 640-849 536 Rhomboid Rhomboid famil 8.5e-1872.6 I 670-812 536 Com etence Com etence rotein 4.4 -100.31 663-872 538 7tm-1 7 transmembrane 6.5e-34126.1 1 41-290 receptor rhodo sin famil ) 542 SEA SEA domain S.le-1046.7 1 472-S91 542 EGF EGF-like domain 0.57 16.7 2 425-462:633-542 EB EB module 4.8 -9.1 1 412-462 542 Bowman- Bowman-Birk serine 7.2 -18.4 1 628-672 Birk 1e protease inhibitor 542 Keratin Keratin, hi hsulfurB28.8 -83.0 1 254-385 B2 rotein 543 SPRY SPRY domain 7.8e-1769.4 1 ~ 347-468 ~

Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

543 zf C3HC4 Zinc finger, C3HC4 3.1e-1150.7 1 16-56 type (RING

fin er 543 zf B box B-box zinc fin er 5.7e-0529.9 1 92-133 544 Ribosomal Ribosomal protein 2.1e-2081.2 1 1-110 526 S26e a 544 rnaseA Pancreatic ribonuclease1.3e-0732.0 1 106-232 545 Patched Patched famil 0.33 -525.21 37-846 545 oxidored-q3NADH- 4.3 -79.9 1 201-368 ubiquinone/plastoquinone oxidoreduct 545 oxidored_qlNADH- 9.7 -171.51 663-851 Ubiquinone/plastoquinone (com lex I) 545 Keratin Keratin, hi h sulfur10 -83.9 1 1 I-141 B2 B2 rotein 546 7tm 1 7 transmembrane receptor0.028 -65.2 1 47-249 rhodo sin famil 547 fn3 Fibronectin type 4.1e-102352.6 6 947-III domain 1034:104 1138:115 1239:125 1337:144 1527:154 547 ig Immunoglobulin domain1.8e-87304.0 9 199-260:300-356:389-448:482-547:579-637:670-731:764-829:863-929:1364-548 gla Vitamin K-dependent 3.7e-1563.8 1 24-65 carbox lation/ anima-Garb 550 7tm 1 7 transmembrane receptor1.1e-39145.3 1 41-290 rhodo sin famil 550 DUF40 Domain of unknown 2 -123.71 39-229 function 551 HC03 cotransHC03- transporter 0 1723.01 146-959 family 551 xan ur-permeaPermease family 3.3 -190.71 477-941 se 551 Plant vir Plant virus coat 9.3 -51.7 1 772-865 rot rotein 551 DENN DENN (AEX-3) domain 9.5 -71.3 1 593-719 552 DUF6 Integral membrane 0.092 9.6 1 68-174 protein 552 DUF250 Domain of unknown 2.8 -98.0 1 180-351 function, 552 oxidored-q3NADH- 5.9 -82.1 1 81-236 ubi uinonel lasto uinone Table 4B
SEQ Model Description E-valueScore RepeatsPosition ID

oxidoreduct 552 7tm 5 7TM chemoreceptor 9.2 -170.61 ~ 54-338 ~

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(~ 'i ~ ~ ~ ~ ..r ~ In b ~ ,.~ ~'~ 'b v' t.~- O ~ ~ ~o Wd~'~~Wd°'~~ ~ x O~~°~~ x O~r~ ~~ o ~~r ~~~~ ~~r ~~~~ a d d dzd ~d ~zv ~Z°
~x o '~
~d r~ ~
~o o.

"' 0 0 0 o Z ~ ~
~o ~o ~ J J J p d ~
l/ V~ Cn N
W '~ 'b 'C3 'a 'a ~ ~ v d r n ~x d z W W N W
J O~ O~o Oo ado N N cn In W c.n 0 oN, ~ °c,~ p ~ ~ z v O~ W W W W
v °° o ~ c~ ~ ~ ro J J W 1 ~
tn O~ 01 N 01 O O O O O
N D W N W
00 Cn Ov 00 . ~7 O
A ~G
O
n Np O ~ 00 !D
A ~ V7 a' CD
O fD
~~a z~v ~v ~v~~~~x ra ra ra~xW°d r x~a ~~ ~ ~. ~ ~. ~~~N~o fro ~ b ~~N~~~ o y ~,~~, Z Z ~~~o~~ a Cxn O ~ x ~ W ~ 'b ro c m On r t" ~ C7 "'7 C7 CJ ~ G7 C7 t~ ~ C7 C7 b~ ''d x a n n 'v r~ v~ ~o v~ r~ ~wn v~
~~~z~~aaY~do~~°~ zr~r~zm~z~rn r~~~r~rr~
o~r~~x ~~o~x ~oo~oo~oo ~~ag ro~~°~v~x~~ N~~NHHN~~~ v ~~~~'~r~zor ~~'°zo NtrltiiNh7CrJNti'ltrl dnr~~~d ~~,~,~ n n~~n °rx°rx°dx b~W~ro ~ ~ °a v~ ~c~~~c~d~'c~d o o~~~H ~ ~ ~~ a~ ~~o~~o~~o r.~ ~ ~~ ~ ~'oa~'oa~'oa Z~m~ ~ rz~rz~rz~

Table 6 SEQ ID NO: Position of SignalmaxS (Maximum means (Mean score) in score) Amino Acid Se uence 277 34 0.972 0.868 278 34 0.972 0.868 279 34 0.972 0.868 280 17 0.994 0.966 281 28 0.983 0.868 282 37 0.997 0.957 283 16 0.917 0.844 284 31 0.931 0.621 285 22 0.972 0.883 286 40 0.972 0.632 287 34 0.964 0.760 288 49 0.936 0.594 289 19 0.952 0.897 290 26 0.914 0.727 291 27 0.911 0.682 292 22 0.996 0.941 293 24 0.986 0.955 294 25 0.938 0.818 295 32 0.969 0.872 296 32 0.986 0.926 297 16 0.971 0.564 298 23 0.982 0.801 299 28 0.995 0.945 300 27 0.908 0.613 301 22 0.981 0.771 302 19 0.958 0.722 304 32 0.983 0.825 305 21 0.991 0.897 306 20 0.990 0.957 307 24 0.948 0.690 308 36 0.959 0.788 309 41 0.979 0.594 310 34 0.943 0.677 311 24 0.974 0.934 312 24 0.974 0.882 313 31 0.952 0.767 314 18 0.956 0.868 315 18 0.956 0.868 316 24 0.910 0.559 317 30 0.992 0.941 318 25 0.989 0.809 319 40 0.971 0.570 321 32 0.967 0.612 322 21 0.913 0.732 323 40 0.945 0.778 324 28 0.949 0.828 325 49 0.987 0.628 326 19 0.990 0.910 327 39 0.996 0.766 328 39 0.996 0.766 329 39 0.996 0.766 330 42 0.988 0.594 33_1 49 0.976 0.581 332 28 0.959 0.747 Table 6 SEQ ID NO: Position of SignalmaxS (Maximum means (Mean score) in score) Amino Acid Se uence 333 26 0.934 0.688 334 36 0.959 0.880 335 24 0.961 0.843 336 34 0.929 0.666 337 32 0.984 0.903 338 42 0.970 0.642 339 42 0.970 0.642 340 37 0.969 0.747 341 2S 0.983 0.861 342 43 0.979 0.635 343 20 0.990 0.944 344 49 0.981 0.658 345 24 0.984 0.91 S

346 24 0.984 0.878 347 26 0.982 0.899 348 41 0.959 0.578 349 21 0.947 0.760 350 23 0.908 0.781 351 39 0.997 0.792 352 32 0.971 0.794 353 36 0.978 0.716 354 16 0.992 0.973 355 16 0.990 0.967 356 3S 0.988 0.849 357 25 0.936 0.710 358 49 0.993 0.675 359 44 0.993 0.648 360 44 0.994 0.700 361 36 0.966 0.818 362 19 0.981 0.958 363 42 0.991 0.608 364 25 0.958 0.613 365 30 0.883 0.630 366 49 0.971 0.749 367 29 0.977 0.879 368 48 0.995 0.760 369 22 0.972 0.883 370 17 0.983 0.915 443 21 0.899 0.686 489 39 0.925 0.610 Table 7 SEQ ID Chromsomal location 14 4 15.1- 14 26 8 22- 21.13 27 6 22.1-22.33 00001456Fb082 31 6 22.2-22.33 35 11 15.5 60 16 13.3 61 16 23.1 64 X 13.1 Table 7 SEQ ID Chromsomal location 96 18 11.2 97 3 ter-3 25.1 103 17 21.2 106 22.

120 22 13.1-13.33 122 20 13.11-13.2 123 6 13-14.3 124 3 21.2- 14.3 125 9 22.2-31.1 _1_48 2 149 3q Table 7 SEQ ID Chromsomal location 156 9 32-33.2 178 20 ter- 12 181 6 21.32-22.1 190 19 13.4 195 1 12-13.2 196 6 ter- 24.1 197 6 ter- 24.1 Table 7 SEQ ID Chromsomal location 236 3 21.3 245 12 21.3- 21.4 251 6 12.3-21.1 259 16 ter- 13 260 16 ter- 13 262 9 13.1-13.3 Table 8 SEQ Number of For Each Transmembrane Domain, its Transmembrane ID Transmembrane Domain NO: Domains Position in SEQ ID NO: and its TM Pred Score 277 2 15-34;1045 171-185;1944 278 2 15-34;1045 147-161;1944 279 2 15-34; 1045 189-203; 1944 280 6 42-58; 666 76-94; 864 119-136; 871 145-162;

188-210;1170 223-247;1433 281 2 43-65;1330 104-119;1947 282 2 18-42; 2872 143-158; 1292 283 8 21-48;787 73-92;1024 95-114;1804 167-182;1499 210-225;997 256-275;1133 314-345;939 389-405; 1337 284 9 16-32;1965 40-59;506 66-86;2091 111-126;1647 155-172;669 199-217;1521 240-255;1130 314;951 399-414;2605 285 5 576-592;578 754-769;2335 771-793;1265 811-832;1715 863-878;1373 286 11 24-40; 2230 53-70; 1120 84-99; 2458 107-122;

144-160;1641 221-237;961 305-320;1305 362; 1022 380-398; 2785 400-415; 1417 466-487; 2904 287 2 16-31; 1313 314-336; 3340 288 2 26-42; 1404 71-88; 2248 289 1 36-54; 2289 290 I 371-390; 2292 291 4 14-33; 887 59-75; 2149 89-104; 1046 152-170;

292 2 70-87;742 123-139;630 293 2 82-97;1433 120-141;1650 294 1 200-221; 2645 295 4 9-31;1859 208-227;607 394-414;1433 469-491;775 296 11 55-72;1655 85-99;938 123-138;1548 242-254;897 284-303; 2550 347-363; 1621 381-401; 1905 445; 902470-484; 1799 514-540; 888 559-574;

297 5 29-45;1401 82-100;1251 143-163;2820 201-216;1686 228-251; 831 298 8 40-62;634 84-99;2577 114-133;1654 185-201;2433 228-245;1509 328-346;2079 414-432;1097 451; 1182 299 4 68-84;2529 77-112;1338 98-120;2138 147-182;1036 300 5 7-31; 1206 62-77; 1120 98-115; 1219 155-170;

182-206; 1989 301 1 100-119; 1816 302 2 109-128;932 143-162;2178 303 4 17-33; 540 54-71; 2700 99-122; 1064 183-203;

304 1 60-72; 1513 305 3 89-107;3007 125-143;1461 174-193;2228 306 3 6-34; 1804 48-64; 980 117-132; 599 307 3 37-52;1351 67-80;2411 151-166;523 308 11 20-36; 1794 93-108; 1358 118-138; 2196 146-159; 779 209-223;2351 294-316;850 309-325;967 362-379; 1578 386-402; 1996 428-454; 1188 462-477; 1965 309 4 25-41; 1707 36-59; 852 61-83; 773 101-120;

310 1 18-35; 2169 311 4 236-258;1342 270-285;1522 304-322;1138 429-447;2437 312 1 332-356; 3221 Table 8 SEQ Number of For Each Transmembrane Domain, its Transmembrane Domain ID Transmembrane Position in SEQ ID NO: and its TM Pred Score NO: Domains 313 2 17-52; 564 536-556; 3165 314 2 151-165;836 427-443;3134 315 2 151-165; 836 415-431; 3134 316 5 56-72;1759 104-118;1739 152-181;3025 199-215;987 230-247;1737 317 1 438-453; 762 318 10 44-77; 590 82-97; 1267 160-194; 1095 174-208;

230-251;1703 253-278;1268 287-302;1352 326; 1252 355-373; 2066 386-403; 1499 319 4 16-38; 2449 77-94; 1750 109-131; 2443 153-171; 1698 320 7 42-59; 1401 75-99; 1751 I 10-134; 1209 160-179; 2116 200-216; 1212 283-296; 2687 319-335; 790 321 6 16-35;2306 60-76;1207 101-115;1890 155-172;1646 201-225; 2512 250-268; 1697 322 11 89-105;1259 108-124;1058 139-157;1802 168-185;1278 189-205;915 224-240;1616 311-328;1587 408; 1074 423-444; 1905 450-468; 1163 552-572; 540 323 10 1 I-38; 1993 50-65; 859 106-128; 1632 117-140; 870 164-184; 1886 194-209; 1335 299-324; 1463 352; 930413-431; 835 466-481; 1566 324 1 35-55;694 325 1 22-43; 2636 326 1 152-168; 610 327 4 22-38; 3134 65-80; 1300 512-531; 2076 542-555; 746 328 3 22-38; 3134 65-80; 1300 493-507; 936 329 3 22-38; 3134 65-80; 1313 512-531; 2076 330 4 27-48;1144 69-92;2697 119-134;1835 160-182;552 331 3 31-47;1577 652-667;592 930-952;3003 332 1 148-169; 2982 333 7 83-99; 1049 110-125; 1190 182-198; 1150 206-222; 1406 232-246;953 278-295;1834 338-353;1407 334 5 9-35; 1516 26-49; 2339 69-87; 1588 141-155;

154-180;579 335 3 58-73; 589 285-300; 1231 493-509; 2248 336 8 285-303;1598 417-430;866 549-566;1758 569-583;995 634-650;1821 659-674;1429 691-709;2005 737; 825 337 1 66-92; 508 338 7 24-39; 2590 60-73; 600 91-119; 1337 148-163;

196-214;2187 236-259;878 272-291;1508 339 7 24-39; 2590 60-73; 600 91-119; 1337 148-163;

196-214; 2187 236-259; 878 272-291; 1508 340 5 18-33; 955 222-237; 670 282-299; 1484 310-325; 786 710-731; 2486 341 9 447-464; 826 548-563; 848 646-666; 2709 680-702; 1087 712-727;1843 752-770;1193 799-818;2230 860; 1402 877-893; 1767 342 5 25-51;2632 61-75;1133 92-120;1945 141-158;1186 177-196;1468 343 5 41-59;1627 54-85;2078 141-162;1510 178-199;2300 241-266; 1378 344 7 28-52; 2109 64-85; 1007 95-123; 1859 147-161;

200-219; 1807 247-263; 1555 276-295; 1639 345 11 91-109;760 245-262;900 405-424;2528 436-454;1166 ~

Table 8 SEQ Number of For Each Transmembrane Domain, its Transmembrane ID Transmembrane Domain NO: Domains Position in SEQ ID NO: and its TM Pred Score 460-478;1710 514-530;1043 551-573;2733 615;1300 625-644;1509 688-707;1446 773-790;617 346 10 149-166; 900 309-328; 2528 340-358; 1166 364-382; 1710 418-434; 1043 455-477; 2733 501-519; 1300 548; 1509 592-611; 1446 677-694; 617 347 7 38-54; 1710 64-80; 1230 150-169; 1096 177-189; 660 205-220;1089 247-259;583 294-311;1199 348 1 25-44;1754 349 4 61-78;1267 92-107;1758 96-132;910 125-145;1211 350 1 63-81; 2993 351 1 21-37; 3067 352 1 33-49; 829 353 1 14-32; 1792 354 1 53-72; 1987 355 1 501-522; 2686 356 2 235-254; 582 307-322; 1905 357 3 _ 305-324;989 359-385;512 704-723;3256 358 1 20-39; 1897 359 1 20-39; 1897 360 1 21-36; 3076 361 2 13-32; 2338 110-126; 621 362 1 342-363; 3126 363 4 25-43;2055 148-164;770 232-258;718 270-283;1272 364 6 43-59; 1008 80-95; 798 130-149; 886 157-175;

191-212; 1337 226-250; 1425 365 10 58-74;1806 81-103;1546 115-127;710 174-189;1420 278-299;1477 321-337;1182 347-363;1923 398; 1258 403-426; 1703 439-454; 1202 366 3 22-52; 1371 65-89; 1862 100-121; 994 367 1 217-236; 652 368 2 21-36; 2696 95-110; 1111 369 5 576-592;578 747-762;2335 764-786;1265 804-825;1715 856-871; 1373 370 1 120-140; 3089 371 3 100- 115;939 284-302;707 332-347;933 372 7 47-64;1640 87-101;700 119-134;1949 143-159;507 184-199; 593 208-223; 744 456-477; 2177 373 2 163-175;1638 182-207;1865 374 1 32-51; 3413 375 3 225-243; 1004 324-339; 1291 386-402; 1266 376 2 196-214;1004 313-329;1173 377 2 126-143;1381 149-161;668 378 3 126-143;1381 149-161;668 195-220;807 379 1 80-103; 3414 380 7 20-41; 602 52-71; 1552 83-98; 1700 103-120;

136-151;2709 162-178;1788 193-211;1280 381 3 44-62;2777 65-80;1045 141-156;1507 382 1 92-112; 1518 383 2 73-88; 605 334-356; 1208 384 12 54-69;1830 90-109;2293 118-133;1498 156-176;884 184-200;1166 232-251;1806 282-297;1680 335; 2405 349-364; 1374 377-401; 1798 423-437; 1391 444-463; 2164 Table 8 SEQ Number of For Each Transmembrane Domain, its Transmembrane ID Transmembrane Domain NO: Domains Position in SEQ ID NO: and its TM Pred Score 385 5 49-66; 2934 135-149; 610 177-197; 653 275-289; 698 397-417; 1229 386 5 49-66; 2934 166-188; 504 190-208; 500 266-280; 698 388-408; 1229 387 2 35-61;782 69-85;2708 388 2 13-32;1026 364-383;1294 389 5 297-315; 565 321-336; 515 340-363; 626 934-954; 875 1131-1147; 556 390 4 27-43; 1142 103-122; 1568 138-154; 868 174-204; 1058 391 3 90-112;638 127-145;669 209-229;733 392 5 195-216;2012 224-246;640 258-279;2594 294-313;1189 342-362; 2675 393 9 68-88;2263 115-130;1131 142-162;2103 172-187;986 212-229; 2963 236-251; 1166 274-291; 2044 326; 1229 337-357; 2709 394 1 126-141; 896 395 14 134-159;1969 296-312;1030 394-418;2134 427-440;1532 432-458; 2248 452-469; 1111 500-518; 1407 549;1051 616-633;2001 817-832;1658 841-858;2487 866-889; 943 912-934; 1900 940-957; 1433 396 2 311-344;667 373-390;788 397 1 204-228; 2681 398 11 61-80;3083 91-107;866 120-142;886 154-169;1501 196-208; 865 267-286; 1159 315-331; 2009 375; 1205 377-404; 2067 416-433; 913 447-463;

399 2 53-72; 2827 291-307; 809 400 2 28-59; 982 54-69; 843 401 1 188-207; 2756 402 2 120-138; 631 196-211; 534 403 2 64-86; 2717 120-136; 1251 404 6 21-42; 555 76-100; 1949 130-150; 1051 204-219; 943 232-248; 1740 260-278; 1996 405 8 84-101;750 135-154;1635 162-178;1545 187-204;1038 211-227;2064 232-245;1277 265-286;1440 313; 1011 406 10 167-182; 1236 192-213; 2175 202-237; 869 270-284; 1296 296-316; 1177 309-327; 1613 400-412; 1434 614;1965 624-660;681 722-744;2309 407 1 45-67;3251 408 3 53-83;1832 107-121;1361 128-151;1826 409 1 165-186;1496 410 2 328-350; 819 433-448; 634 411 7 26-48;2329 61-83;815 95-120;2154 143-159;947 205-222;1700 237-260;1060 270-292;1172 412 6 73-87;1184 104-122;2026 145-160;2008 196-215;2624 235-256; 1873 281-300; 1350 413 ' 2 226-245; 2251 263-287; 800 414 4 48-64;1636 92-110;1288 139-157;930 171-192;2385 415 10 64-84; 854 188-201; 2590 218-237; 1364 386-401; 2666 405-425;1179 874-895;1854 944-961;1011 1022;1158 1040-1065;894 1072-1088;1850 416 4 105-120;2238 127-148;1679 167-183;2605 202-217;1098 417 2 49-64;631 159-173;822 418 13 241-255; 643 382-400; 1292 413-428; 1275 ~ 433-448; 852 Table 8 SEQ Number of For Each ID Transmembrane Transmembrane NO: Domains Domain, its Transmembrane Domain Position in SEQ
ID NO:
and its TM Pred Score 463-485;

491-509;
732 589-605;

645;1543 679-691;1481 720-735;2038 775-794;1386 801-817;1752 849-864;1553 419 3 154-172;1020185-200;629231-251;1947 420 5 34-50; 264-282; 295-310;
668 70-85; 1020 629 341-361;

421 2 18-34;53052-73;703 422 3 208-226; 542-558; 570-599;

423 8 56-71;
578 211-228;

328-346;
644 454-473;

587-601;
587 699-714;
553 1039-1055;

1518;

424 1 411-432;

425 1 51-68;

426 1 106-120;

427 9 42-57;

81-93;

95-111;

103-139;

131-148;

160-178;

199-220;

276; 1647 311-326;

428 10 42-57;1250 81-93;1131 95-111;1306 103-139;901 131-148;1307 160-178;1366 199-220;1093 276; 1647 314-332;
902 368-384;

429 1 85-101;

430 3 198-216; 389-404; 429-445;

431 1 42-60;

432 1 215-230;2143 433 3 29-52;226362-82;155794-113;2561 434 4 96-112;1641167-187;2265202-224;1612257-272;2465 435 1 94-114;2794 436 2 73-92;2179123-137;779 437 1 271-292;

438 1 727-744;2924 439 1 78-102;

440 4 90-110; 114-131; 183-195; 268-291;

441 4 90-110; 114-131; 183-195; 268-291;

442 4 90-110;536114-131;907183-195;654268-291;977 443 5 53-69;2297 145-163;1504179-194;1353 83-98;1058 206-222;2021 444 3 78-98; 134-150; 224-243;

445 4 17-42;70653-70;159297-112;1041142-160;2123 446 4 198-214; 274-289; 306-321; 330-345;

447 1 46-64;

448 1 129-154;569 449 1 468-489;

450 1 354-373;

451 2 64-79; 73-97;

452 3 151-166; 186-208; 255-270;

453 3 82-95; 112-129; 1470-1491;

454 2 30-43; 302-320;

455 2 84-96; 892-911;

456 1 28-48;

457 1 77-103;

458 5 25-50; 92-120; 140-155;

61-82;

199-214;

459 7 33-50;247958-73;139394-115;882 144-162;671 ~

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

NOTE : Pour les tomes additionels, veuillez contacter 1e Bureau canadien des brevets JUMBO APPLICATIONS/PATENTS
THIS SECTION OF THE APPLICATION/PATENT CONTAINS MORE THAN ONE
VOLUME

NOTE: For additional volumes, please contact the Canadian Patent Office NOM DU FICHIER / FILE NAME
NOTE POUR LE TOME / VOLUME NOTE:

Claims (26)

WHAT IS CLAIMED IS:

1. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-276.

2. An isolated polynucleotide encoding a polypeptide with biological activity, wherein said polynucleotide hybridizes to the polynucleotide of claim 1 under stringent hybridization conditions.

3. An isolated polynucleotide encoding a polypeptide with biological activity, wherein said polynucleotide has greater than about 99% sequence identity with the polynucleotide of claim 1.

4. The polynucleotide of claim 1 wherein said polynucleotide is DNA.

5. An isolated polynucleotide of claim 1 wherein said polynucleotide comprises the complementary sequences.

6. A vector comprising the polynucleotide of claim 1.

7. An expression vector comprising the polynucleotide of claim 1.

8. A host cell genetically engineered to comprise the polynucleotide of claim 1.

9. A host cell genetically engineered to comprise the polynucleotide of claim operatively associated with a regulatory sequence that modulates expression of the polynucleotide in the host cell.

10. An isolated polypeptide, wherein the polypeptide is selected from the group consisting of:
(a) a polypeptide encoded by any one of the polynucleotides of claim 1;
and (b) a polypeptide encoded by a polynucleotide hybridizing under stringent conditions with any one of SEQ ID NO: 1-276.

11. A composition comprising the polypeptide of claim 10 and a carrier.

12. An antibody directed against the polypeptide of claim 10.

13. A method for detecting the polynucleotide of claim 1 in a sample, comprising:
a) contacting the sample with a compound that binds to and forms a complex with the polynucleotide of claim 1 for a period sufficient to form the complex; and b) detecting the complex, so that if a complex is detected, the polynucleotide of claim 1 is detected.

14. A method for detecting the polynucleotide of claim 1 in a sample, comprising:
a) contacting the sample under stringent hybridization conditions with nucleic acid primers that anneal to the polynucleotide of claim 1 under such conditions;
b) amplifying a product comprising at least a portion of the polynucleotide of claim 1; and c) detecting said product and thereby the polynucleotide of claim 1 in the sample.

15. The method of claim 14, wherein the polynucleotide is an RNA molecule and the method further comprises reverse transcribing an annealed RNA molecule into a cDNA
polynucleotide.

16. A method for detecting the polypeptide of claim 10 in a sample, comprising:
a) contacting the sample with a compound that binds to and forms a complex with the polypeptide under conditions and for a period sufficient to form the complex; and b) detecting formation of the complex, so that if a complex formation is detected, the polypeptide of claim 10 is detected.

17. A method for identifying a compound that binds to the polypeptide of claim 10, comprising:
a) contacting the compound with the polypeptide of claim 10 under conditions sufficient to form a polypeptide/compound complex; and b) detecting the complex, so that if the polypeptide/compound complex is detected, a compound that binds to the polypeptide of claim 10 is identified.

18. A method for identifying a compound that binds to the polypeptide of claim 10, comprising:
a) contacting the compound with the polypeptide of claim 10, in a cell, under conditions sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a reporter gene sequence in the cell; and b) detecting the complex by detecting reporter gene sequence expression, so that if the polypeptide/compound complex is detected, a compound that binds to the polypeptide of claim 10 is identified.

19. A method of producing the polypeptide of claim 10, comprising, a) culturing a host cell comprising a polynucleotide sequence selected from the group consisting of any of the polynucleotides from SEQ ID NO: 1-276, under conditions sufficient to express the polypeptide in said cell; and b) isolating the polypeptide from the cell culture or cells of step (a).

20. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of any one of the polypeptides SEQ ID NO: 277-552.

21. The polypeptide of claim 20 wherein the polypeptide is provided on a polypeptide array.

22. A collection of polynucleotides, wherein the collection comprising of at least one of SEQ ID NO: 1-276.

23. The collection of claim 22, wherein the collection is provided on a nucleic acid array.

24. The collection of claim 23, wherein the array detects full-matches to any one of the polynucleotides in the collection.

25. The collection of claim 23, wherein the array detects mismatches to any one of the polynucleotides in the collection.

26. The collection of claim 22, wherein the collection is provided in a computer-readable format.