CA2421949A1 - Novel nucleic acids and polypeptides - Google Patents

Novel nucleic acids and polypeptides Download PDF

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CA2421949A1
CA2421949A1 CA002421949A CA2421949A CA2421949A1 CA 2421949 A1 CA2421949 A1 CA 2421949A1 CA 002421949 A CA002421949 A CA 002421949A CA 2421949 A CA2421949 A CA 2421949A CA 2421949 A1 CA2421949 A1 CA 2421949A1
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polypeptide
polynucleotide
protein
cells
sequence
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Y. Tom Tang
Chenghua Liu
Ping Zhou
Vinod Asundi
Jie Zhang
Qing A. Zhao
Feiyan Ren
Aidong J. Xue
Yonghong Yang
Tom Wehrman
Radoje T. Drmanac
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Hyseq Inc
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    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/71Receptors; Cell surface antigens; Cell surface determinants for growth factors; for growth regulators
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00Genetically modified animals
    • A01K2217/05Animals comprising random inserted nucleic acids (transgenic)
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00Medicinal preparations containing peptides
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K2319/00Fusion polypeptide
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02ATECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

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  • Medicinal Chemistry (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Toxicology (AREA)
  • Cell Biology (AREA)
  • Immunology (AREA)
  • Peptides Or Proteins (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

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

Description

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:

NOVEL NUCLEIC ACIDS AND POLYPEPTIDES
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. 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 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 malting available large numbers of DNA/amino acid sequences for proteins that are lcnown 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 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 occurring 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: 1-444. The polypeptides sequences are designated SEQ
ID NO: 445-888. The nucleic acids and polypeptides are provided in the Sequence Listing. In the nucleic acids provided in the Sequence Listing, A is adenosine; C is cytosine;
G is guanine; T is thyrnine; and N is unknown or any of the four bases.
The nucleic acid sequences of the present invention also include, nucleic acid sequences that hybridize to the complement of SEQ ID NO: 1-444 under stringent hybridization conditions;
nucleic acid sequences which are allelic varimts 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: 1-444. A
polynucleotide comprising a nucleotide sequence having at least 90% identity to an identifying sequence.of SEQ ID NO: 1-444 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: 1-444. The sequence information can be a segment of any one of SEQ ID NO: 1-444 that uniquely identifies or represents the sequence information of SEQ ID NO: 1-444.
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: 1-444 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 ID NO: 1-444 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: 1-444; a polynucleotide comprising any of the full length protein coding sequences of SEQ ID NO: 1-444;
and a polynucleotide comprising any of the nucleotide sequences of the mature protein coding sequences of SEQ ID NO: 1-444. 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 ID NO: 1-444; (b) a nucleotide sequence encoding any one of the amiilo acid sequences set forth in the Sequence Listing; (c) a polynucleotide which is an allelic variant of any polynucleotides recited above; (d) a polynucleotide which encodes a species homolog (e.g. orthologs) of arty of the proteiils recited above; or (e) a polynucleotide that encodes a polypeptide comprising a specific domain or tr~mcation of any of the polypeptides comprising an amino acid sequence set forth in the Sequence Listing.
The isolated polypeptides of the invention include, but are not limited to, a polypeptide comprising any of the amino acid sequences set forth in SEQ ID NO: 445-888; 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 ID N0: 1-444; or (b) polynucleotides that hybridize to the complement of the polynucleotides of (a) under stringent hybridization conditions. Biologically or immunologically 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 process is a mature form of the protein.
Polynucleotides according to the invention have numerous applications in a variety of techniques lcnown to those slcilled 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 andlor 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 compotmd 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 the 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 effect 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 Table 2); fo'r 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 Table 4). 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.
Lilcewise "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 some 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 term "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 gene cells (PGCs)" refers to a small population of cells set aside from other cell lineages particularly from the yolk sac, mesenteries, or gonadal ridges dining 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 germ 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, promoter s, 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 ''oligonculeotide" 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 guanne and N
is A, C, G or T
(U). 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 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 11 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 preferably less than 30 nucleotides. Preferably the probe is from about 6 nucleotides to about 200 nucleotides, preferably from about 15 to about 50 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 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: 1-444.
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 and/or labeling are elaborated in Sambroolc, 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: 1-444. The sequence information can be a segment of any one of SEQ ID NO: 1-444 that uniquely identifies or represents the sequence information of that sequence of SEQ ID NO: 1-444. 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 fox 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 pxotein.
The terms "operably linked" or "operably associated" refer to functionally related nucleic acid sequences. For example, a promoter is operably associated or operably linlced 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 term "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 terns "polypeptide" or "peptide" or "amino acid sequence" refer to an oligopeptide, peptide, polypeptide or protein sequence or fragment thereof and to naturally OCCllrrlng 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 500 amino acids, more preferably less than 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 an 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 malting use of the "redundancy" in the genetic code. V arious 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 pxokaryotic 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 determined by systematically malting 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 degradationlW mover 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 puriFed 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 trmsported 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 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) 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}, 4$°C (for 17-base oligos}, 55°C (for 20-base oligonucleotides), and 60°C (for 23-base oligonucleotides}.
As used herein, "substantially equivalent" 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 equvalent 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 finther 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 5% (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%
identity, more preferably at least 98% identity, and most preferably at least 99% identity.
Substantially equivalent nucleotide sequences of the invention can have lower percent sequence identities, talcing into account, for example, the redundancy or degeneracy of the genetic code.
Preferably, 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 about 85% sequence identity, more preferably at least about 90% sequence identity, and most preferably at least about 95% identity, more preferably at least about 98% sequence identity, and most preferably at least about 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, tnmcation of the mature sequence (e.g., via a mutation which creates a spurious stop codon) should be disregarded. Sequence identity may be determined, e.g., using the Jotun Hein method (Hero, 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 vims 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. UMFs 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 uptalce of a linlced 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: 1-444; a polynucleotide encoding any one of the peptide sequences of SEQ ID NO: 445-888; and a polynucleotide comprising the nucleotide sequence encoding the mature protein coding sequence of the polypeptides of any one of SEQ ID NO:
445-888. 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: 1-444; (b) nucleotide sequences encoding any one of the amino acid sequences set forth in the Sequence Listing as SEQ ID NO: 445-888;
(c) a polynucleotide which is an allelic variant of any polynucleotide recited above; (d) a polynucleotide which encodes a species homolog 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: 445-888. 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-lilce proteins include the variable iinmunoglobulin-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 partially synthetic DNA, e.g., cDNA and genomic DNA, and RNA, e.g., mRNA., The polynucleotides may include all of the 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 ID NO: 1-444 can be obtained by screening appropriate cDNA or ~genomic DNA libraries under suitable hybridization conditions using any of the polynucleotides of SEQ ID NO: 1-444 or a portion thereof as a probe.
Alternatively, the polynucleotides of SEQ ID NO: 1-444 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%, 91%, 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: 1-444, 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 ID NO: 1-444, a representative fragment thereof, or a nucleotide sequence at least 90%
identical, preferably 95%
identical, to SEQ ID NO: 1-444 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 result for the nucleic acids of the present invention, including SEQ ID NO: 1-444, can be obtained by searching a database using an algoritlun or a program. Preferably, a BLAST which stands for Basic Local Alignment Search Tool 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.
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-occurring 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 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 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 insertions of single or multiple amino acid residues. Intrasequence insertions may range generally from about 1 to 10 amino residues, preferably from 1 to 5 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.
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 efFcient 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 Curl°ent 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.
Polynttcleotides encoding preferred polypeptide truncations of the invention can 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: 1-444, 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 Sambroolc 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 eulcaryotic cell and can be a unicelh~lar 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 ID NO: I-444 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: 1-444 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).
Eukaxyotic: pWLneo, pSV2cat, pOG44, PXTI, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL
(Pharmacia).
The isolated polynucleotide of the idvention 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 ifZ
Enzymology 185, 537-566 (1990). As defined herein "operably linlced" 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, lacZ, T3, T7, gpt, lambda PR, and trc. Eulcaryotic promoters include CMV immediate early, HSV
thymidine lcinase, 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 TRP 1 gene, and a promoter derived 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 3-phosphoglycerate lcinase (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 enswe maintenance of the vector and to, if desirable, provide-amplification within the host. Suitable proltaryotic hosts for transformation include E. coli, Bacillus subtilis, Salrnouella typhimurium and various species within the genera Pseudomonas, 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 stnictural 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, dismpted 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 intramuscular 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 NUCLEIC ACIDS
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: 1-4A~4, 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, 50, 100, 250 or 500 nucleotides or an entixe 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: 445-888 or antisense nucleic acids complementary to a nucleic acid sequence of SEQ ID
NO: 1-444 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 which 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: 1-444), 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 a mRNA.
For example, the antisense oligonucleotide can be complementary to the region surrounding the translatian start site of a mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 1 S, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. An 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 ofthe duplex formed 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: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 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, 5'-methoxycarboxymethyh~racil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiowacil, 4-thiouracil, 5-methyluracil, uracil-5-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-diaminopmine.
Alternatively, the antisense nucleic acid can be produced 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 ar a 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 stu-face, e.g., by lincing 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 double-stranded hybrids with complementary RNA in which, contrary to the usual (3-units, the strands run parallel to each other (Gaultier et al. (1987) Na~cleic Acids Res 15: 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) FEBS Lett 21 S: 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 a mRNA transcripts to thereby inhibit translation of a 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: 1-444). For example, a derivative of a 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 an mRNA of SEQ ID NO: 1-444 (see, e.g., Cech et al. U.S. Pat. No.
4,987,071; and Cech et al. U.S. Pat. No. 5,116,742). Alternatively, polynucleotides 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 andlor enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See generally, Helene. (1991) Afzticav~ce~~ Drwg Des. 6: 569-84; Helene. et al. (1992) Anyz. 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) Bioot~g Med Chen~ 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., S1 nucleases (Hyrup B. (1996) above); or as probes or primers for DNA sequence and hybridization (Hyrup et al. (1996), above; Peny-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 polymexases, to interact with the DNA portion while the PNA
portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linlced using linkers of appropriate lengths selected in terms of base stacking, nLUmber 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) Niacl 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., 5'-(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 5' DNA segment and a 3' PNA segment. See, Petersen et al. (1975) Bioof°g Med Chew 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, P~~oc. Natl. Acad. Sci.
U.S.A. 86:6553-6556;
Lemaitre et al., 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/I0134~. In addition, oligonucleotides can be modified with hybridization triggered cleavage agents (See, e.g., Krol et al., 1988, BioTecl2fziques 6:958-976) or intercalating agents. (See, e.g., Zon, 1988, Plzannz. Res.
5: 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. W094112650, PCT International Publication No. WO92/20808, 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 linlced 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 eulcaryotic 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 constmct into the host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, or electroporation (Davis, L. et al., Basic Metl2ads itz 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 order 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. suhtilis.
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 Sambroalc, 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 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, 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, 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 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 eularyotes such as yeast or insects or in prokaryotes such as bacteria. Potentially suitable yeast strains include Saccharomyces cerevisiae, Schizosaccharomyces pon2be, Klz~yveromyces strains, Candida, or any yeast strain capable of expressing heterologous proteins. Potentially suitable bacterial strains include Escherichia coli, Bacillus subtilis, Salmonella typhir~zzcrialyn, 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 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, 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
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 occurring 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 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.
PCTIUS92/09627 (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.
4.6 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: 445-888 or an amino acid sequence encoded by any one of the nucleotide sequences SEQ ID NO: 1-444 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: 1-444 or (b) polynucleotides encoding any one of the amino acid sequences set forth as SEQ
ID NO: 44f-888 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:
445-888 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: 445-888.
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 lcnown methods, for example, as described in H.
U. Saragovi, et al., BiolTechnology 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.
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 coding sequence is identified in the sequence listing by translation of the disclosed nucleotide sequences. The mature form of such protein may be obtained by expression of a full-length polynucleotide in a suitable mammalian cell or other host cell. 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.
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 andlor 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 prolcaryotic 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 medimn, 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 full 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 slcilled 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, immunochrornatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immuno-affinity chromatography. See, e.g., Scopes, PYOteih Purification:
Principles and Practice, Springer-Verlag (1994); Sambrook, et al., in Molecular Cloning: A
Labor-atofy Manual; Ausubel et al., Cm°f'e~t P~°otocols ih Moleculaf~
Piology. 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 Imown 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 tested for antagonist or agonist activity in in vivo tissue culture or animal models that are well known in the art. In bxief, 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 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: 445-888.
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 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 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. 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 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 baculoviruslinsect cell expression systems are commercially available in kit form from, e.g., Invitxogen, San Diego, Cali~, 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 (f. 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-toyopearlTM 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~") 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 liirther 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 othex 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 dnigs such as cyclosporin, SK506, azathioprine, CD3 antibodies and steroids. Also, polypeptides may be fused to immune modulators, and other cytolcines 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), 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. 5, 947-955), Neural Network SignalP Vl.l program (from Center for Biological Sequence Analysis, The Technical Univexsity of Denmark), and the Kyte-Doolittle hydrophobocity prediction algorithm (J. Mol Biol, 157, pp. 105-31 (1982), incorporated herein by reference). The BLAST programs are publicly available from the National Center for Biotechnology Information (NCBI) and other sources (BLAST
Manual, Altschul, S., et al. NCB NLM NIH Bethesda, MD 20894; Altschul, S., et al., J.
Mol. Biol.
215:403-410 (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.
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 fivsion 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 irz 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 linlced in-frame to the protein of the invention.
4.8 GENE THERAPY
Mutations in the polynucleotides of the invention 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 of the invention.
Delivery of a functional gene encoding polypeptides of the invention to appropriate cells is effected ex vivo, ih sitza, or iyz 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, NaW re, supplement to vol. 392, no. 6679, pp.25-20 (1998). For additional reviews of gene therapy technology see Friedmann, Science, 244: 1275-1281 (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 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 i~ 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 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 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 ih 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 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 linlced to the desired protein encoding sequences. ,See, for example, PCT International Publication No. WO 94/12650, PCT International Publication No. WO 92120808, 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 linlced 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 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 stricture 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 occurring 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 cell genome. The identification of the targeting event may also be facilitated by the use of one or more marker genes exlubiting the property of negative selection, such that the negatively selectable marker is linked to the exogenous DNA, but configlrred such that the negatively selectable marker flancs 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 pwpose 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.

(W093/09222) by Selden et al.; and International Application No.
PCTlLTS90/06436 (W091/06667) by Slcoultchi 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 viva, 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 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 ivy vivo, one or mor a 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)x. 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 tnmcations 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 marlcers 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 malting oligomers for attachment to a "gene chip" or other support, including for examination~of expression patterns; to raise anti-protein antibodies 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 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 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.
Any or all of these research utilities are capable of being developed into reagent grade or lcit format for commercialization as research products.
Methods for performing the uses listed above are well known to those skilled in the aut.
References disclosing such methods include without limitation "Molecular Cloning: A
Laboratory Manual", 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, J., E. F. Fritsch and T. Maniatis eds., 1989, and "Methods in Enzymology: Guide to Molecular Cloning Techniques", Academic Press, Berger, 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 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 soL~rce 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.
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, DA1G, T10, B9, B9ll l, BaF3, MC9/G, M+(preB M+), 2E8, RBS, DAl, 123, T1165, HT2, CTLL2, TF-l, Mole, 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. Kruisbeelc, D.
H. Margulies, E.
M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vity-o assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Talcai 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.; I. 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, Kruisbeelc, 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 Interleulcin 4, Bottomly, K., Davis, L. S. and Lipslcy, 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; Moreau et al., Nature 336:690-692, 1988;
Greenberger et al., Proc. Natl. Acad. Sci. U.S.A. 80:2931-2938, 19.83;
Measurement of mouse and human interleukin 6--Nordan, R. In Current Protocols in Immunology. J. E.
Coligan eds. Vol 1 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 of human Interleukin 11--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 1 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 vitr°o assays for Mouse Lymphocyte Function; Chapter 6, Cytolcines and their cellulax 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. 11:405-41 l, 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 ivy 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 cLU-rently 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, 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 cytolcines 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 polymerase 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 cardiornyocytes (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.
1>z 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
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, thereby indicating utility, for example, in treating vaxious 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 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 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 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, 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 forming 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 89:5907-591 l, 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 Yorlc, 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 cultL~res 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 fracW re 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, osteoartllritis, 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-lilce 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-forming 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 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 cytolcine 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.
W091107491 (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, 3.
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 autoirnmune 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 (Hoffrnann et al., Allergy 54: 446-54, 1999), guinea pig skin sensitization test (Vohr et al., Arch. Toxocol. 73: 501-9), and marine 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 invnune responses, in a number of ways. Down regulation may be in the form of inhibiting or blocking an immLme 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 suppxessive agent. Tolerance, which involves inducing non-responsiveness or anergy in T cells, is distinguishable from immunosuppression in that it is generally antigen-specific and persists after exposure to the tolexizing 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 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 as foreign by T cells, followed by an immLme 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 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 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 Turlca et al., Proc. Natl. Acad. Sci USA, 89:11102-11105 (1992). In addition, marine models of GVHD (see Paul ed., Fundamental Immunology, Raven Press, New Yorlc, 1989, pp. 846-847) can be used to determine the effect of therapeutic compositions of the invention on the development of that disease.
Bloclcing 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 cytolcines and autoantibodies involved in the pathology of the diseases. Preventing the activation of 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 blocl~ing reagents in preventing or alleviating autoimmune disorders can be determined using a number of well-characterized animal models of human autoimmune diseases. Examples include marine experimental autoimmune encephalitis, systemic lupus erythmatosis in MRLllpr/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 Yorlc, 1989, pp.
840-856).
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 (32 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 conjLmction with a peptide having the activity of a B lymphocyte antigen (e.g., B7-l, 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., 1. Immunol. 137:3494-3500, 1986;
Talcai 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 Thl/Th2 profiles) include, without limitation, those described in:
Maliszewski, J.
Immunol. 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. 3. 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; Talcai 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, 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, WlthOllt 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;
Tolci et al., Proc. Nat. Acad Sci. USA 88:7548-7551, 1991.
4.10.8 ACTIVINIINHIBIN 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 the 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., NatL~re 318:659-663,1985; Forage et al., Proc. Natl. Acad. Sci.
USA 83:3091-3095, 1986.
4.10.9 CHEMOTACTICICHEMOKINETIC ACTIVITY
A polypeptide of the present invention may be involved in chemotactic or chemolcinetic 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 chemolcinetic receptor activation can be used to mobilize or attract a desired cell population to a desired site of action. Chemotactic or chemolcinetic 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 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 fox cell chemotaxis.
Therapeutic compositions of the invention can be used in the following:
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. 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 Chemolcines 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 hemostasis 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, fox 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 cancex 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) andlor 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 advaaiced 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, slcin 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, DaLmorubicin HCl, Doxorubicin HCI, Estramustine phosphate sodium, Etoposide (V
16-213), Floxuridine, 5-Fluorouracil (5-Fu), Flutamide, Hydroxyurea (hydroxycarbamide), Ifosfamide, Interferon Alpha-2a, Interferon Alpha-2b, Leuprolide acetate (LHRH-releasing factor analog), Lomustine, Mechlorethamine HCl (nitrogen mustard), Melphalan, Mercaptopurine, Mesna, Methotrexate (MTX), Mitomycin, Mitoxantrone HCI, Octreotide, Plicamycin, Procarbazine HCI, Streptozocin, Tamoxifen citrate, Thioguanirie, 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.
In vitro models can be used to determine the effective doses of the polypeptide of the invention as a potential cancer treatment. These in vitf~o 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 tmnor cells in Boyden Chamber assays as described in Pilkington et al., Anticancer Res., 17: 4107-9 ( 1997), and angiogenesis assays such as induction of vasculaxization of the chick chorioallantoic membrane or induction of vascular endothelial cell migration as described in Ribatta et al., Intl. J. Dev. Biol., 40: 1189-97 (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, cytolcine receptors and their ligands, receptor lcinases and their ligands, receptor phosphatases and their ligands, receptors involved in cell-cell interactions and theirligands (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. 168:1145-1 l 56, 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, tritiLUn 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. Drugs 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 libraries include polyketides, non-ribosomal peptides, and (non-naturally occurring) variants thereof. For a review, see Science X82:63-68 (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 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, Cm°f~. Opin.
Biotechnol. 8:701-707 (1997). For reviews and examples of peptidomimetic libraries, see Al-Obeidi et al., Mol. Bioteclzzzol, 9(3):205-23 (1998); Hruby et al., Cuz°r Opih Chezn Biol, 1(1):114-19 (1997); Dorner et al., BioorgMed Clzezzz, 4(5):709-15 (1996) (allcylated dipeptides).
Identification of modulators through use of the various libraries described herein permits 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 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 celllanimal 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 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
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 response 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 extxacellular 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 cytolcines 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 pr omotes 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 leuemia, myeloblastic, promyelocytic, myelomonocytic, monocytic, erythroleulcemia, 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/ox 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 hmnan 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) tratunatic 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 injL~red as a result of infection, for example, by an abscess or associated with infection-by human immmodeficiency 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, Werniclce disease, tobacco-alcohol amblyopia, Marchiafava-Bignami disease (primary degeneration of the corpus callosmn), and alcoholic cerebellar degeneration;

(vi) neurological lesions associated with systemic diseases including but not limited to diabetes (diabetic neuropathy, Bell's palsy), systemic lupus erythematosus, carcinoma, or ' sarcoidosis;
(vii) lesions caused by toxic substances including alcohol, lead, or partrcu lar neLlrOtOXrnS; 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 rr~ay be useful according to the invention:
(i) increased survival time of neuxons in culture;
(ii) increased sprouting of neurons in culture or in vivo;
(iii) increased production of a neuron-associated molecule in culture or ih vivo, e.g., choline acetyltransferase or acetylcholinesterase with respect to motor neurons; or ~(iv) decreased symptoms of neuron dysfunction in viva.
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 Aralcawa et a1. (1990, J. Neurosci. 10:3507-3515); increased sprouting of neurons may be detected by methods set forth in Pestronlc et al. (1980, Exp. Neurol. 70:65-82) or Brown et al.
(1981, Arm. 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 ofmotor 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 daxriage, 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, fimgi 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); 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 the enzyme and treating deficiency-related diseases; treatment of hyperproliferative disorders (such as, for example, psoriasis);
irnmunoglobulin-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 IDENTIFICATION OF POLYMORPHISMS
The demonstration of polymorphisms 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 immtmosuppressive 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 inj ection, generally intradermally, of a suspension of lcilled 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 mglkg. The control consists of administering PBS only.
The procedure for testing the effects of the test compound would consist of intradermally inj ecting killed Mycobacterium tuberculosis in CFA followed by immediately administering the test compound and subsequent treatment every other day until day 24. At 14, 15, 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 reveah 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 ~.g/kg to 100 mg/lcg of body weight, with the preferred dose being about 0.1 ~g/lcg 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 sewm 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 lalown 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 carrier will depend on the route of administration. The pharmaceutical composition of the invention may also contain cytolcines, lympholcines, or other hematopoietic factors such as M-CSF, GM-CSF, TNF, IL-l, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IFN, TNFO, TNFl, 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-lilce growth factor (IGF), as well as cytokines described herein. , The pharmaceutical composition may fiu ther contain other agents which either enhance the activity of the protein or other active ingredient or complement its activity or 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, cytolcine, lympholcine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-inflammatory agent (such as IL-lRa, 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 ire 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 amomt 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 cytolcines, lympholcines or other hematopoietic factors. When co- administered with one or more cytolcines, lymphokines or other hematopoietic factors, protein or other active ingredient of the present invention may be administered either simultaneously with the cytolcine(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 cytolcine(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, transrnucosal, 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 pharmaceutical 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 occmTing as complication of glaucoma sL~rgery, the compounds may be administered topically, for example, as eye drops. Furthermore, one may administer the dnig in a targeted drug delivery system, for example, in a liposome coated with a specific 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 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 similax studies in appropriate animal models. Dosages can then be adjusted as necessary by the clinician to provide maximal therapeutic benefit.
4.12.2 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 carriers 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 farm, 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 administer ed 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 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 Hanlcs'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 forml~lated 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 mixtL~re 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 staxch, 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-linlced 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, 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 paxaffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration 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 compotmds 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 mufti-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 compotmds 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 1: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 vaxied 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 I 00 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, rnagnesiLUn 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 andlor 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 carriers, 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 slcill 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 natL~re 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. 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 practice the method of the present invention shoed contain about 0.01 ~,g to about 100 mg (preferably about 0.1 ~g to about 10 mg, more preferably about 0.1 p.g to about 1 mg) of protein or other active ingredient of the present invention per lcg 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 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 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 simLiltaneously 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 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 calciwn-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-cc 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 andlor repair, for example, X-rays, histomorphometric determinations and tetracycline labeling.
Polynucleotides of the present invention can also be used for gene therapy.
Such polynuoleotides 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 deternine 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 hmnans.
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 form 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 vitj~o 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 q,g/kg to 100 mgllcg of body weight daily, with the preferred dose being about 0.1 yg/lcg to 25 mg/lcg 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, tile 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, fox 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, F~b~ and F~~b~~2 fragments, and an F~,b expression library. In general, an antibody molecule obtained from humans relates to any of the classes IgG, IgM, 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 IgGI, IgG2, 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 h tunan 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 immvmogens. An antigenic peptide fragment comprises at least 6 amino acid residues of the amino acid sequence of the full length protein, such as the amino acid sequences shown in SEQ ID
NO. 445-888, and encompasses an epitope thexeof such that an antibody xaised 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. Preferred epitopes encompassed by the antigenic peptide axe 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 region of -related protein that is located on the surface of the protein, e. g., a hydrophilic region. A hydrophobicity analysis of the human related protein sequence will indicate which regions of 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 ofhydrophilicity 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 Woods, 1981, P~oc. Nat. Acad. Sci. USA 78: 3824-3828; Kyte and Doolittle 1982, J.
Mol. Biol. 157: 105-142, 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 thereof, may be utilized as an immunogen in the generation of antibodies that immunospecifzcally bind these protein components.
Various procedures known within the ant may be used for the production of polyclonal or monoclonal antibodies directed against a protein of the invention, or against derivatives, fiagments, 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 Harbox, 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 inj ections 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 imznunogenic protein, or a recombinantly expressed immunogenic protein. Furthermore, the protein may be conjugated to a second protein known to be immmzogenic 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 immwological 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 which 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 marmnal (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 cohunn to purify the immune specific antibody by immunoaffinity chromatography.
Purification of immunoglobulins is discussed, for example, by D. Willeinson (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 mique 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 I~ohler 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 (Goding, 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 (I~ozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Deldcer, Inc., 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 radioimmLmoassay (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 prefers ed 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 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;
Morrison, 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-immmoglobulin polypeptide can be substituted 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
The antibodies directed against the protein antigens of the invention can further comprise humanized antibodies or human antibodies. These antibodies are suitable fox administration to humans without engendering an immune response by the human against the administered immunoglobulin. HLUnanized forms of antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')~ 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 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 which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-~humari immunoglobulin and all or substantially all of the framework regions are those of a human immLmoglobulin 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. Stnict. 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; 5,6.61,016, and in Marks et al. (Bio/Technolo~y 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 (NatL~re Biotechnolo~y 14, 826 (1996)); and Lonberg and Huszar (Intern. Rev. Immunol. 13 65-93 (1995)).
Human antibodies may additionally be produced using transgenic nonhuman animals which 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 hmnan 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 which 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 hmnan 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 acid 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 Fab 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~a~~~2 fragment produced by pepsin digestion of an antibody molecule; (ii) an Fab fragment generated by reducing the disulfide bridges of an F~ab~>z 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 EISPECIFIC 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 malting 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 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 Enz~nologY, 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 which 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 procedL~re wherein intact antibodies are proteolytically cleaved to generate F(ab')2 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')Z 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 fox malting and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. I~ostelny et al., J. Immunol. 148(5):1547-1553 (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 hetexodimers. This method can also be utilized fox 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 malting bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) by a linlter which is too short to allow pairing between the two domains on the same chain.
Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and Vr, 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).
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 molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (FcyR), such as FcyRI (CD64), FcyRII (CD32) and FcyRIII (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 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 crosslinhing agents. For example, immunotoxins can be constructed using a disulfide exchange reaction or by forming a thioether bond.
Examples of suitable reagents for this pmpase include iminothiolate and methyl-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 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 enhmced 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, ctucin, 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~ i3~h i3lln~ 9oy~ ~d ~s6Re.
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-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 as streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal Of L111bOLlnd 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 f 1e, 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: 1-444 or a representative fragment thereof; or a nucleotide sequence at least 95% identical to any of the nucleotide sequences of SEQ ID NO: 1-444 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 ORF's 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 fox 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-ofFof 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.
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 ofthe 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.
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 tihard, 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 sputmn, 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 fox 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:
1-444, 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 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 compomds 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 fox 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.
Compounds 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 ofthe 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 pxotein. For example, one skilled in the art can readily adapt currently available procedures to generate peptides, pharmaceutical agents and the lilce, capable of binding to a specific peptide sequence, in order to generate rationally designed antipeptide peptides, for example see Hurby et al., 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 designedlselected. Targeting the ORF or EMF allows a skilled arCisan 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 - Olcano, 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 ID NO: 1-444. 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: 1-444 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, fox 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 aa-e commercially available and may be used to synthesize RNA probes in vit3~o by means of the addition of the appropriate RNA polymerase as T7 or polymerase 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 andlor 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 i~ 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 (265:1981f). 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. C11I1. Microbiol.
28(6) 1469-72);
using UV light (Nagata et al., 1985; Dahlen et al., 1987; MozTissey & Collins, (1989) Mol. Cell Probes 3(2) 189-207) or by covalent binding of base modified DNA (Keller et al., 1988; 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 Covalinlc NH. CovaLinlc NH is a polystyrene surface grafted with secondary amino groups (>NH) that serve as bridge-heads for fiu-ther 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 of DNA
(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 phosphoramidatc 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 CovaLinlc and then streptavidin used to bind the probes.
More specifically, the linkage method includes dissolving DNA in water (7.5 ng/yl) 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-MeIm~), is then added to a final concentration of 10 mM 1-MeIm~. The single-stranded DNA solution is then dispensed into CovaLinlc NH strips (75 l.~l/well) standing on ice.
Carbodiirnide 0.2 M 1-ethyl-3-(3-dimethyla~ninopropyl)-carbodiimide (EDC), dissolved in mM 1-MeIm7, is made fresh and 25 y1 added per well. The strips are incubated for 5 horns 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 further 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 carried 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., (1994) PNAS 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 aziy appropriate sotuce, 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).
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 Sambroolc et al. (1989), shearing by ultrasound and NaOH treatment.
Low pressL~re shearing is also appropriate, as described by Schriefer et cd.
(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 interniediate 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 shotgLm 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 pUC 19 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 acctunulated 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 yg instead of 2-5 p,g); 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 quicldy 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 lmow~
in the art.

4.22 PREPARATION 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 (subanays) 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 salve 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 I mm2 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 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. EXAMPLES
5..1. IfXAIdI:PLE I
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 hl some cases isolated from a genomic library derived from h wean 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 flauc the inserts. Clones from cDNA libraries were spotted on nylon membrane filters and screened with oligonucleotide probes (e.g., 7-mess) 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) sequences to obtain the novel nucleic acid sequences S.2 EXAMPLE 2 Assemblage of Novel Nucleic Acids The nucleic acids of the present invention, designated as SEQ ID NO: 1-444 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 was 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%.
Using PHRAP (Univ. of Washington) or CAP4 (Paracel), frill-length gene sequences and their corresponding protein sequences were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. DL~ring editing, the sequence was checked using FASTXY algorithm against Genbanlc (i.e., dbEST, gb pri, UniGene, and Genpept). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Waslungton) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.).
The full-length nucleotide sequences are shown in the Sequence Listing as SEQ ID NO: 1-444.
The corresponding polypeptide sequences are SEQ ID NO: 445-888.

Table 1 shows the various tissue soLUCes of SEQ ID NO: 1-444.
The nearest neighbor results for polypeptides encoded by SEQ ID NO: 1-444 (i.e. SEQ
ID NO: 445-888) were obtained by a BLASTP (version 2.0a1 19MP-WashU) search against Genpept release 124 using BLAST algorithm. The nearest neighbor result showed the closest homologue with functional annotation for SEQ ID NO: 1-444 from Genpept. The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologues with identifiable functions for SEQ ID NO: 1-444 are shown in Table 2 below.
Using eMatrix software package (Stanford University, Stanford, CA) (Wu et al., J.
Comp. Biol., Vol. 6 pp. 219-235 (1999) herein incorporated by reference), polypeptides encoded by SEQ ID NO: 1-444 (i.e. SEQ ID NO: 445-888) were examined to determine whether they had identifiable signature regions. Table 3 shows the signature region found in the indicated polypeptide sequences, the description of the signature, the eMatrix p-values) and the positions) of the signature within the polypeptide sequence.
Using the pFam software program (Sonnhammer et al., Nucleic Acids Res., Vol.
26(1) pp. 320-322 (1998) herein incorporated by reference) polypeptides encoded by SEQ ID NO: 1-444 (i.e. SEQ ID NO: 445-888) were examined for domains with homology to certain peptide domains. Table 4 shows the name of the domain found, the description, the p-value and the pFam score for the identified domain within the sequence.
The GeneAtlasT"~ 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: 1-444 (i.e. SEQ ID NO: 445-888). Models were generated by (1) PSI-BLAST
which is a multiple alignment sequence profile-based searching developed by Altschul et al, (NLICI. 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:l/www.msi.coml), and (3) SeqFoldTM which is a fold recognition method described by Fischer and Eisenberg (J. Mol. Biol. 209, 779-791 (1998)). Tlus 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 (PDS) 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_g/PDBn;
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 GeneAtlas~"

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. Salt, 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 follows:
Verify score (normalized) _ (raw score-1/2 high score)l(1/2 high score) The PFM score, produced by GeneAtlasT"' 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 8, 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 5 taken in totality.
The nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determined from using Neural Network SignalP V 1.1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark).
The process for identifying prolcaiyotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrilc 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, as reference, were obtained for the polypeptide sequences. Table 6 shows the position of the last amino acid of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.
Table 7 correlates each of SEQ ID NO: 1-444 to a specific chromosomal location.
Table 8 is a correlation table of the novel polynucleotide sequences SEQ ID
N0: 1-444, and their corresponding priority nucleotide sequences in the priority application USSN
09/659,671, herein incorporated by reference in its entirety.

Tissue OriginRNA Source Library SEQ 1D NO:

Name adult brain GIBCO AB3001 4 6-8 12 23 33-34 47 50 adult brain GIBCO ABD003 6 l 0 12-I 5 17-18 26 31 adult brain Clontech ABR001 5 36 43 76 108 128 182-183 adult brain Clontech ABR006 2 9 11 13 18 23 35 38 42 adult brain Clontech ABR008 1 3 7 10-14 16-17 19-23 adult brain Clontech ABRO11 174 177 360 adult brain BioChain ABR012 334 341 adult brain BioChain ABR013 41-42 60 101 163 355 adult brain Invitrogen ABR014 53 95 104-106 143 149 177 adult brain Invitrogen ABRO15 42 70-72 79 95 I 12 138-140 adult brain Invitrogen ABR016 13 31 60 79 I24 136 154 adult brain Invitrogen ABT004 1 I I-13 15 18 24-26 34 cultured Stratagene ADP001 2 11-14 24-25 40 42 47 preadipocytes 107 120 144 151 156 163 adrenal glandClontech ADR002 10-11 16 18 22-23 27-28 adult heart GIBCO AHR001 11-13 15 20-23 26-27 30 128-l 30 142 144-145 148 297 30'2 X04 adult kidneyGIBCO AICD001 4-5 8-13 15-18 20-27 33-35 adult kidneyInvitrogen AICT002 1 10-11 13 17-18 26-27 adult lung GIBCO ALG001 4 6 17-I 8 24-26 39 43-44 lymph node Clontech ALN001 17 19 26 81 85 149 166 young liver GIBCO ALV001 10 12 14 16-18 20 22 33 adult liver Invitrogen ALV002 10 15 22 24-25 33 49 66 adult liver Clontech ALV003 73 92 294 341 adult ovary Invitrogen AOV001 1 4 6-18 23 27-28 30-34 adult placentaInvitrogen APL001 17 33 157 228 232 264 placenta Invitrogen APL002 I1-12 23 31 35 51 53 88 adult spleenGIBCO ASP001 1 5 11 14 18-20 22-23 33-34 , 39-40 48-49 adult testisGIBCO ATS001 8 10-I I 13 17 28 43-44 adult bladderInvitrogen BLD001 11 24-25 44 57-58 65 141 bone marrowClontech BMD001 9 11 13-14 17 19 22-23 bone marrowClontech BMD002 1 5 7 10-11 14 16 19-20 bone marrowClontech BMD004 97 149 bone marrowClontech BMD007 53 143 149 221 colon Invitrogen CLN001 10 34 49 52-53 57-59 145 mixture various CTL016 10 56 of 16 vendors tissues/mRNAs mixture various CTL021 149 of 16 vendors tissues/mRNAs mixture various CTL028 145 358 of 16 vendors tissueslmRNAs adult cervixBioChain CVX001 1 4 6 1 I 23-25 27 30 34-35 endothelial Stratagene EDT001 1 4 6-8 10-14 16-28 31 cells 34-35 37 39 42-44 fetal brain Clontech FBR001 46 104-106 175 193 258 fetal brain Clontech FBR004 193-194 226-227 229 260 fetal brain Clontech FBR006 2-3 9-12 14 16-17 19-20 fetal brain Clontech FBRS03 199 291 402 fetal brain Invitrogen FBT002 12 15 19-20 23 30-31 47 fetal heart Invitrogen FHR001 34 43 81 87 129 134 138-139 fetal kidneyClontech FKD001 6 8 10 17 50 54 77 86 92 fetal kidneyClontech FICD002 141 264 309 341 432 fetal kidneyInvitrogen FKD007 107 123 fetal lung Clontech FLG001 16 33 92 100 149 257 337 fetal lung Invitrogen FLG003 8 13 15 32 39 48 51 56 fetal lung Clontech FLG004 122 209 fetal liver-spleenColumbia FLS001 1-13 15-46 48-51 53 55 University 121-136 138-139 141 143 fetal liver-spleenColumbia FLS002 1-3 5 11-13 15-18 20-22 University 33-34 36-40 43-44 46 49 fetal liver-spleenColumbia FLS003 I 3 19 40 49 54 57-59 68 University 106 170 176 183 256 260 fetal liver Invitrogen FLV001 2 10 14 18 20 26 35 66 fetal liver Clontech FLV002 92 126 244 fetal liver Clontech FLV004 34-35 48 51 53 92 104-106 fetal muscleInvitrogen FMS001 11-12 44 76 110-111 145 fetal muscleInvitrogen FMS002 .8 11 23 46 52 61 102 111 fetal skin Invitrogen FSIC001 5-6 8 10 12 23 26-29 32-33 288 290 ?91 294-295 298-299 fetal skin Invitrogen FSK002 9 14 22 34-35 39-40 56 fetal spleenBioChain FSP001 276 umbilical BioChain FUC001 4-6 8 11 13 16 18 21-25 cord 27 32 35 37 39-40 fetal brain GIBCO HFB001 3-4 6 11 13-14 18-20 22-23 macrophage Invitro HMP001 49 123 144 151 275 en infant brainColumbia IB2002 7-8 11-13 16 20-22 24-26 University 62-64 66 68 75 80 84 87 337-339 342=343 346-347 infant brainColumbia IB2003 4 8 I1 13-14 16 23 42 University 65-66 76 94 98 102 119-120 infant brainColumbia IBM002 33 50 54 112 131-133 163 University 331 423 infant brainColumbia IBS001 2 5 11 26 34 52 87 91 University 194 200-201 248 277 340 lung, fibroblastStratageneLFB001 13 16-17 22 26 39 46 57-58 lung tumor InvitragenLGT002 10-12 15 17-18 20 23 26-28 189 195 197-l 98 lymphocytes ATCC LPC001 7 10-11 14-15 18 20 24-25 leukocyte GIBCO LUC001 1 6-8 11 14-15 17-18 20 23-25 27 ~5 39 43 leukocyte Clontech LUC003 17 19 27 34 42-43 46 49 Melanoma Clontech MEL004 6 11 30 34 45 54-55 61-62 from 65-66 78 81 93 cell line 112 114 116 122 128 130 #CRL 1424 164 177 180 187 195 219 mamm land InvitrogenMMG001 1 5 8 10-13 IS-16 18 20 induced Stratagene NTD001 7 20 42 47 49 53 83 121 neuron 134 136 151 153 cells 195 202 218-219 223 247 retinoic Stratagene NTR001 34 70-72 104-106 110 116 acid- 197 258 392 396 induced 422 neuronal cells neuronal Stratagene NTU001 16 40 49 53-54 80 100 130 cells 136 194 2S8 pihiitary Clontech PIT004 S4 119 170 200 242 264 gland 270 319-320 333 placenta Clontech PLA003 32 304 341 421 prostate Clontech PRT001 9 13 21 23 53 59 79 83 rectum Invitrogen REC001 S 12 15 22 32 42 80 108 salivary Clontech SAL001 4 7 10 40 66 88 102 104-106 gland 126 128 151 salivary Clontech SALS03 42 gland skin fibroblastATCC SFB001 S4 skin fibroblastATCC SFB003 87 144 small intestineClontech SINO01 1 9 11 13 15 17-18 22 27 skeletal Clontech SIC.M001 13 64 76 87 92 104-106 muscle 122 176 202 302 skeletal Clontech SI~M002 246 muscle skeletal Clontech SI<MS03 49 muscle skeletal null SICMS04 88 muscle spinal cordClontech SPC001 6 12 22-23 48 60 70-72 adult spleenClontech SPLc01 2 98 120 141 164 166 244 stomach Clontech STO001 20 42 54 63 70-72 80-81 thalamus Clontech THA002 1 14 17 23 47 57-58 62 thymus Clontech TI~M001 11 33 39-40 44 49 63 73-74 ~ 90 102 108 128 thymus Clontech THMc02 9-10 I S 17 24-25 27-28 thyroid Clontech THR001 1 4-5 8-9 11-12 14-15 17 gland 19 21-25 27 34 40 trachea Clontech TRC001 17 23 34 90 93 108 142 uterus Clontech UTRDOI 18 20 30-31 50 52 I 14 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 shin 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) hLUnan thyroid mRNA (Clontech), 15) human esophagus mRNA (BioChain), 16) human conceptional umbilical cord mRNA (BioChain).

SEQ AccessionSpecies Description Score /.
ID

NO: No. Identit 445 gi4151328Homo Sapienshigh-risk human papilloma2344 48 viruses E6 oncoproteins targeted protein E6TP1 alpha mRNA, complete cds.

445 gi4151330Homo Sapienshigh-risk human papilloma1694 59 viruses E6 oncoproteins targeted protein E6TP1 beta mRNA, complete cds.

445 gi2555183Rattus SPA-I like protein p12942324 48 norveaicus 446 gi13517972Homo SapiensPR-domain containing 2496 100 protein 17 mRNA, com fete cds.

446 gi10434545Homo SapienscDNA FLJ12827 fis, clone2496 100 NT2RP2002939, weakly similar to ZINC

FINGER PROTEIN 136.

446 gi13623607Homo Sapiens, zinc finger protein 710 42 136 (clone pHZ-20), clone MGC:12711, mRNA, complete cds.

447 gi6093239Homo SapiensmRNA; cDNA DKFZp434O05151054 100 (from clone DICFZp434O0515).

447 gi3522970Homo SapiensTrio mRNA, complete cds.216 23 447 AAW27227 Homo SapiensHuman TRIO phosphoprotein.216 23 448 gi7022890Homo sapienscDNA FLJ10700 fis, clone2838 96 NT2RP3000665.

448 110438668Homo sa cDNA: FLJ22327 fis, clone1333 100 iens HRC05572.

448 a17020045Homo sa cDNA FLJ20140 fis, cloneI 074 79 iens COL07182.

449 g16102903Homo SapiensmRNA; cDNA DKFZp566D244 2601 99 (from clone DKFZp566D244);
partial cds.

449 g110434000Homo SapienscDNA FLJ12485 fis, clone1907 100 NT2RM2000420.

449 110437387Homo sapienscDNA: FLJ21308 fis, clone1519 69 COL02131.

450 g17670836Homo sapienshepatocellular carcinoma-associated3101 99 antigen 66 (HCA66) mRNA, complete cds.

450 g17959764Homo sapiensPR01289 935 100 450 g1927708 SaccharomyceYdr449cp; CAI: 0.18 288 32 s cerevisiae 451 g17020902Homo SapienscDNA FLJ20657 fis, clone3231 99 KAT01069.

451 g111037252Rattus NPL4 3156 96 norvegicus 451 g110434779Homo SapienscDNA FLJ12984 fis, clone2812 99 NT2RP3000047, weakly similar to NPL4 PROTEIN.

452 g113160469Homo SapiensWDR13 protein (WDR13) 1063 94 gene, complete cds.

452 g112044400Homo SapiensWDR13 protein (WDR13) 1063 94 mRNA, com lete cds.

452 a113751862Mus musculusWD-repeat protein 1058 93 453 g112619286Homo SapiensmRNA for spinal cord-derived1133 100 protein FI58G, complete cds.

453 g17638241Homo sapiensmesenchymal stem cell I 133 100 protein DSC92 mRNA, complete cds.

453 g1 12804543Homo Sapiens, mesenchymal stem cell 1133 100 protein DSC92, clone MGC:2824, mRNA, complete cds.

454 g113279287Homo Sapiens, clone IMAGE:3633354, 2066 100 mRNA, partial cds.

454 g15052586DrosophilaBcDNA.GH08385 334 25 melano aster -454 g110433073Homo SapienscDNA FLJI 1749 fis, clone190 26 ~

SEQ AccessionSpecies Description Score />
ID

NO: No. ldentit HEMBA1005558, weakly similar to NUCLEAR PROTEIN SNF7.

455 17019840 Homo sa cDNA FLJ20018 fis, clone1698 99 iens ADSE00909.

455 g113938166Homo Sapiens, clone MGC:12617, mRNA,1630 98 complete cds.

455 g19280376Homo Sapiensancient conserved domain1271 90 protein 3 (ACDP3) mRNA, complete cds.

456 g17020190Homo SapienscDNA FLJ20232 fis, clone1487 100 COLF5593.

456 g114249896Homo Sapiens, clone MGC:15774, rilRNA,1479 99 complete cds.

456 g19188416Homo sapiensNovel human gene mapping1479 99 to chomosome 22.

457 AAW75093 Homo sapiensHuman secreted protein 369 100 encoded by gene 37 clone HFVGS85.

457 g18895089Homo Sapiensprotein x 013 mRNA, complete145 41 ' cds.

457 g114250569Homo Sapiens, protein x 013, clone 145 41 MGC:3073, mRNA, complete cds.

458 tri7020228Homo SapienscDNA FLJ20257 fis, clone1169 100 COLF7231.

458 g17528184Drosophilabicoid-interacting protein389 4S
BINS

melano aster 459 gil 1345384Homo Sapiensvacuolar protein sorting5102 100 protein 18 (VPS18) mRNA, com Iete cds.

459 AAW48303 Homo SapiensAmino acid sequence of 2555 100 human deep oran a rotein.

459 g12832850DrosophilaEG:171 E4.1 1316 35 melanogaster 460 g16966967Homo SapiensmRNA for dipeptidyl-peptidase3814 99 III (DPP3 gene).

460 g113938201Horno , dipeptidylpeptidase 3811 99 Sapiens III, clone MGC:15061, mRNA, com lete cds.

460 AAB67571 Homo sapiensAmino acid sequence of 3807 99 a human hydrolytic enzyme HYENZ3.

461 AAY53020 Homo sapiensHuman secreted protein 657 100 clone qb56 19 protein sequence SEQ
ID NO:46.

461 AAY59788 Homo SapiensHuman normal ovarian 618 100 tissue derived protein 65.

461 AAG04028 Homo SapiensHuman secreted protein, 442 72 SEQ ID NO:

8109.

462 g113021843Homo Sapienspolyadenylate binding 679 100 protein-interacting rotein 2 mRNA, com fete cds.

462 g112052806Homo SapiensmRNA; cDNA DICFZp564F163675 99 (from clone DKFZp564F163);
com lete cds.

462 g17106826Homo SapiensHSPC218 673 99 463 g17023258Homo sapienscDNA FLJ10914 fis, clone1067 100 OVARC I 000212.

464 g17023258Homo SapienscDNA FLJ10914 fis, clone649 72 OVARC 1000212.

465 g17022147Homo sapienscDNA FLJ10233 fis, clone3464 100 HEMBB 1000266.

465 g112224837Homo SapiensmRNA; cDNA DKFZp547K202 3464 100 (from clone DI'FZ 547K202).

465 AAY99662 Homo sa Human GTPase associated 3464 100 iens protein-13.

466 g17582304Homo SapiensBM-016 584 100 466 AAW85610 Homo SapiensSecreted protein clone 330 97 eh80 1.

466 AAW78199 Homo SapiensHuman secreted protein 330 97 encoded by gene 74 clone HGBAC I 1.

467 g17018410Homo SapiensmRNA; cDNA DKFZp566K023 1010 100 (from clone DICFZp566K023).

467 a19049987Rattus X2CR1 protein 268 81 SEQ AccessionSpecies Description Score ID

NO: No. Identit norve~icus 468 gi8317213Horno histone acetyltransferase1625 100 sapiens (MOF) mRNA, artial cds.

468 gi 10433157Homo SapienscDNA FLJ11810 fis, clone1625 100 HEMBA1006347, moderately similar to MALES-ABSENT ON THE FIRST

PROTEIN (EC 2.3.1.-).

468 gi 10436400Homo SapienscDNA FLJ14040 fis, clone1613 99 HEMBA1005513, weakly similar to MALES-ABSENT ON THE FIRST

PROTEIN (EC 2.3.1.-).

469 AAY76072 Homo sapiensHuman skin cell protein,668 100 N0:327.

469 AAB56011 Homo SapiensSkin cell protein, SEQ 668 100 ID NO: 327.

470 gi29481 Homo SapiensHuman erythrocyte 2,3- 1362 100 bisphosphoglycerate mutase mRNA EC

2.7.5.4.

470 gi 179527Homo sapiensHuman 2,3-bisphosophoglycei-ate1362 100 mutase (BPGM) gene, exon 3.

470 AAB 11959Homo SapiensGlycated human erythrocyte1362 100 bisphos ho lycerate mutase (BPGM).

471 gi6841472Homo SapiensHSPC125 892 100 471 gi12001966Homo Sapiensclone O15g09 My013 protein892 100 mRNA, com fete cds.

471 gi9624483Homo SapiensHRPAP20 short form mRNA,640 72 complete cds.

472 gi9367763Homo SapiensmRNA for zinc finger 2580 100 protein Cezanne (CEZANNE gene).

472 gi6102920Homo SapiensmRNA; cDNA DKFZp434H07172197 100 (from clone DKF'Z 434H0717);
artial cds.

472 gi7332054Caenorhabditiscontains similarity to 126 25 tumor necrosis elegans factors 473 gi8489813Homo SapiensDJ963K23.2 mRNA, complete1255 100 cds.

473 AAB43861 Homo SapiensHuman cancer associated 1255 100 protein sequence SEQ ID N0:1306.

473 19858803 Mus musculusZ 228 1090 91 474 g17020223Homo sapienscDNA FLJ20254 fis, clone2278 100 COLF6926.

474 AAY25743 Homo SapiensHuman secreted protein 917 100 encoded from gene 33.

474 AAY76166 Homo sapiensHuman secreted protein 724 94 encoded by gene 43.

475 g114042066Homo SapienscDNAFLJ14503 fis, clone 159 26 NT2RM1000252, weakly similar to H.sapiens E-MAP-115 mRNA.

475 g17270600Arabidopsistrichohyalin like protein156 25 thaliana 475 g1180195 Homo SapiensHuman aorta caldesmon 145 25 mRNA, complete cds.

476 g111066250Homo Sapienspresenilins associated 2030 100 rhomboid-like rotein (PARL) mRNA, complete cds.

476 g113177766Homo Sapiens, Similar to presenilins1107 99 associated rhomboid-like protein, clone MGC:4756, mRNA, complete cds.

476 17959883 Homo sapiensPR02207 986 100 477 AAY91941 Homo SapiensHuman chaperone protein 1977 100 2 (HCHP-2).

477 g17019854Homo SapienscDNA FLJ20027 fis, clone1965 99 ADSE01901.

47? g16567172Mus musculusmDj 10 1863 93 478 g113937971Homo Sapiens; similar to RIKEN cDNA 1040 100 ene, clone MGC:14726, mRNA, SEQ AccessionSpecies Description Score ID

NO: No. ' Identit com fete cds.

478 ai13940310Homo SapiensHCC-1 ene. 1040 100 478 AAB36609 Homo SapiensHuman FLEXHT-31 protein 1040 100 sequence SEQ ID NO:31.

479 gil 1065999Homo sapiensneuronal calcium bindingI 889 99 protein NECAB3 mRNA, complete cds.

479 gi10798741Homo SapiensXB51 mRNA forXllL-binding654 99 protein 51, complete cds.

479 110798743Mus musculusX11L binding protein 1079 86 480 g16094684Homo SapiensPAC clone RP1-278D1 from3056 92 X, complete sequence.

480 g110435614Homo SapienscDNA FLJ13568 fis, clone1847 100 PLACE1008368, weakly similar to RING

CANAL PROTEIN.

480 g17023516Homo SapienscDNA FLJ11078 fis, clone1208 42 PLACE1005102, weakly similar.to RING

CANAL PROTEIN.

481 17020424 Homo sapienscDNA FLJ20369 fis, clone2727 100 HEP19364.

481 a1 1 I Mus Sp. semaphorin homolog=M-Sema2653 86 481 AAB88485 Homo SapiensHuman membrane or secretory1774 100 protein clone PSEC0078.

482 14679028 Homo SapiensHSPC021 1930 100 482 g15106781Homo SapiensHSPC025 1930 100 482 g112654535Homo sapiens, HSPC025, clone MGC:735,1930 100 mRNA, com lete cds.

483 g1 1 145789Rattus neuroligin 2 4417 98 norvegicus 483 g17960135Homo Sapiensneuroligin 3 isoform 2736 65 gene; complete cds, alternatively spliced.

483 g17960131Homo Sapiensneuroligin 3 isoform 2729 65 HNL3 mRNA, complete cds, alternatively spliced.

484 g1 14250554Homo Sapiens, hexokinase 1, clone 4725 99 MGC:1724, mRNA, com fete cds.

484 g12873349Homo Sapienshexokinase I (HK1) gene,4725 99 exon 18, complete cds, alternatively spliced.

484 g1184021 Homo sapiensHuman hexokinase 1 (HKl)4718 99 mRNA, complete cds.

485 a18453103Homo sa zinc fm er protein mRNA,3726 100 iens complete cds.

485 ~i 13752754Homo Sapienszinc finger 1111 mRNA, 1689 56 corn fete cds.

485 g110436789Homo SapienscDNA FLJ14345 fis, clone1683 56 THYR01001189, weakly similar to ZINC FINGER PROTEIN 91.

486 AAB56937 Homo SapiensHuman prostate cancer 2341 100 antigen protein sequence SEQ ID N0:1515.

486 g112804453Homo Sapiens, Similar to Tu translation2326 100 elongation factor, mitochondrial, clone MGC:1592, mRNA, com lete cds.

486 g1899285 Homo SapiensH.sapiens mRNA for elongations2326 100 factor Tu-mitochondrial.

487 g19910111Homo Sapiensmyosin X (MYO10) mRNA, 10727 99 complete cds.

487 g16996558Mus musculusmyosin X 10089 93 487 g17108753Homo Sapiensmyosin X (MYO10) mRNA, 8029 99 partial cds.

488 g17688687Homo SapiensAD-017 protein mRNA, 1935 100 complete cds.

488 g114042251Homo SapienscDNA FLJ14611 fis, clone1935 100 NT2RP1000988.

488 AAY66671 Homo sapiensMembrane-bound protein 1935 100 PR01134.

489 g1202215 Mus musculusalpha-tubulin isotype 2387 100 M-al ha-6 489 g114328047Homo sa , tubulin alpha 4, clone2387 100 iens MGC:2379, SEQ AccessionSpecies Description Score ID

NO: No. Identit mRNA, complete cds.

489 gi1333692Macaca alpha-tubulin (ATG-initiation2382 100 codon fascicularismissin ) 490 gi5912034Homo SapiensmRNA; cDNA DKFZp434N05356810 99 (from clone DKFZp434N0535);
partial cds.

490 gi5912239Homo SapiensmRNA; cDNA DICFZp43402253442 99 (from clone DKFZp4340225);
partial cds.

490 gi3292939DrosophilaAdditional sex combs 295 39 melano aster 491 gi5912034Homo SapiensmRNA; cDNA DICFZp434N05355941 99 (from clone DKFZp434N0535);
partial cds.

491 gi5912239Homo SapiensmRNA; cDNA DKFZp434O225 2573 99 (from clone DICFZp4340225);
artial cds.

491 gi3292939DrosophilaAdditional sex combs 295 39 melanogaster 492 AAY68778 Homo SapiensAmino acid sequence of 2463 99 a human phosphorylation effector PHSP-10.

492 1479173 Homo sa H.sapiens nek3 mRNA for 2417 99 iens protein kinase.

492 g113529320Mus musculusSimilar to NIMA (never 1887 73 in mitosis gene a)-related expressed kinase 3 493 g113539686Homo Sapiensprotein kinase C and 2365 100 casein kinase substrate I (PACSIN1) mRNA, complete cds.

493 1728604 Mus musculusPACSIN 2250 95 493 g14324452Rattus syndapin 1 2250 95 norvegicus 494 g17023749Homo SapienscDNA FLJ I 1220 fis, 3994 100 clone PLACE 1008129.

494 g110433501Homo SapienscDNA FLJ12104 fis, clone2829 100 HEMBB 1002697.

494 g15788108Homo SapiensPAC clone RP5-1087M19 757 63 from 7q11.23-q21.1, complete sequence.

495 AAB54375 Homo SapiensHuman pancreatic cancer 2897 99 antigen protein sequence SEQ ID N0:827.

495 AAY57923 Homo sapiensHuman transmembrane protein2724 98 HTMPN-47.

495 AAW88628 Homo sapiensSecreted protein encoded2686 98 by gene 95 clone HPWAN23.

496 17959788 Homo SapiensPR01635 - 317 100 496 AAW74852 Homo sapiensHuman secreted protein 143 I DO
encoded by gene 124 clone HPCAD23.

497 17707424 Homo sapiensmRNA for syntaxin 18, 1705 100 com fete cds.

498 g11613858Homo SapiensHuman zinc finger protein1488 83 zfp47 (zf47) mRNA, partial eds.

498 g113938633Mus musculusRIICEN cDNA 2810435N07 1318 60 gene 498 g19837564Mus musculusSCAN-ICRAB-zinc finger 1242 58 protein 499 AAY27795 Homo SapiensHuman secreted protein 1539 99 encoded by gene No. 79.

499 g110436317Homo SapienseDNA FLJ13986 fis, clone1370 100 Y79AA1001923, weakly similar to Homo Sapiens F-box protein Fbx22 (FBX22) gene.

499 g16164747Horno F-box protein Fbx22 (FBX22)391 93 sapiens gene, artial cds.

500 g13150052Homo SapiensTGF beta receptor associated4455 100 protein-1 mRNA, complete cds.

500 g114280050Homo SapiensVps39/Vam6-like protein 382 24 gene, complete cds.

500 g112718237Neurosporarelated to TGF beta receptor174 31 associated SEQ AccessionSpecies Description Score ID

NO: No. Identit crassa rotein 1 501 gi7023051Homo SapienscDNA FLJ10796 fis, clone3360 99 NT2RP4000648, weakly similar to TRANS-ACTING TRANSCRIPTIONAL

PROTEIN ICPO.

501 gi9651170Homo Sapienscell cycle checkpoint 2491 96 protein CHFR

mRNA, complete cds.

501 AAB20219 Homo SapiensHuman Chfr (checkpoint 2491 96 with FHA and ring finger) protein.

502 gi7329074Homo Sapienscollagen type V alpha 9671 100 3 chain (COL5A3) mRNA, complete cds.

502 gi8568094Rattus alpha 4 type V collagen 8038 82 norvegicus 502 Qi7329072Mus musculuscolla en ty a V al ha 7970 82 3 chain 503 ~i12654687Homo Sapiens, clone MGC:2616, mRNA, 1161 100 complete cds.

503 gi7769617Mus musculusTCE2 1050 89 504 gi12654687Homo sa , clone MGC:2616, mRNA, 1140 96 iens complete cds.

504 ai7769617Mus musculusTCE2 1029 86 505 gi12654687Homo sapiens, clone MGC:2616, mRNA, 654 100 complete cds.

505 gi7769617Mus musculusTCE2 629 92 506 gi14249942Homo Sapiens, Similar to RIICEN cDNA1609 100 gene, clone MGC:15937, mRNA, complete cds.

506 AAB56487 Homo SapiensHuman prostate cancer 1167 98 antigen protein sequence SEQ ID NO:1065.

506 gi2828262Bos taurusaralkyl acyl-CoA:amino 597 40 acid N-acyltransferase 507 gi7688987Homo Sapiensuncharacterized bone 1295 100 marrow protein ' 507 AAB64387 Homo SapiensAmino acid sequence ofhuman1202 94 intracellular signalling molecule INTRA 19.

507 gi9437511Homo SapiensBM024 1045 98 508 AAB 18979Homo sapiensAmino acid sequence of 1203 100 a human transmembrane protein.

508 gi6808196Homo sapiensmRNA; cDNA DKFZp434P1 938 100 Ol 8 (from clone DKFZp434P1018);
partial cds.

508 gi 13960126Homo Sapiens, Similar to leucine-rich845 100 neuronal protein, clone MGC:4126, mRNA, complete cds.

509 gi13938527Homo Sapiens, Similar to RIKEN cDNA 1048 100 gene, clone MGC:2562, mRNA, complete cds.

509 AAY35994 Homo SapiensExtended human secreted 1032 98 protein sequence, SEQ ID NO.
379.

509 AAG00345 Homo SapiensHuman secreted protein, 619 98 SEQ ID NO:

4426.

510 gi773387 NeurosporaRestriction enzyme inactivation536 35 of met-10 crassa complementation in this region. Sequence similarity to S. cerevisiae chromosome VIII cosmid 9205, accession no. U10556 CDS residues 22627-24126 510 gi487945 SaccharomyceYhr070wp 528 49 s cerevisiae 510 AAG02508 Homo SapiensHuman secreted protein, 324 100 SEQ ID NO:

6589.

51 I 111493195Homo SapiensmRNA for LB1 protein. 2614 99 511 g110434688Homo SapienscDNA FLJ12920 fis, clone2604 99 NT2RP2004594.

511 g112053201Homo SapiensmRNA; cDNA DKFZp434A10312604 99 ~ (from S>GQ AccessionSpecies Description Score ID

NO: No. Identit clone DKFZ 434A1031 ;
complete cds.

512 AAW75106 Homo SapiensHuman secreted protein 47 100 encoded by gene t 50 clone HHSDZ57.

512 AAY59689 Homo SapiensSecreted protein 26-44-1-BS-CL3_l.471 100 512 AAY48331 Homo SapiensHuman prostate cancer-associated471 100 protein 28.

514 AAW67888 Homo SapiensHuman secreted protein 921 92 encoded by gene 82 clone HSKHL65.

514 gi 13436110Homo Sapiens, Similar to RIKEN cDNA 150 28 gene, clone MGC:11061, mRNA, complete cds.

514 AAY53052 Homo SapiensHuman secreted protein 132 33 clone df202 3 protein sequence SEQ
ID NO:110.

515 gi7020259Homo sa cDNA FLJ20276 fis, clone5378 100 iens HEP02437.

515 gi10432807Homo SapienscDNA FLJ11534 fis, clone3024 99 HEMBA1002679.

515 gi9916 Plasmodiumliver stage antigen 399 23 falciparum 516 AAB67448 Homo SapiensAmino acid sequence of 1190 99 a human chaperone polypeptide.

516 gi 13477189Homo Sapiens, Similar to RIKEN cDNA 1182 99 gene, clone MGC:12943, mRNA, complete cds.

516 AAG03527 Homo SapiensHuman secreted protein, 389 98 SEQ ID NO:

7608.

517 gi7023782Homo SapienscDNA FLJ11240 fis, clone2796 100 PLACE1008568.

517 AAB08869 Homo SapiensAmino acid sequence of 2792 99 a human secretory protein.

517 AAB23626 Homo SapiensHuman secreted protein 2792 99 . SEQ ID NO: 52.

518 gi6460009Deinococcuscitrate lyase, beta subunit21 30 radiodurans 518 gi 14025765Mesorhizobiucitrate lyase beta-subunit324 31 m loti 518 gi 14024477MesorhizobiuCitrate lyase beta chain316 33 (acyl lyase m loti subunit); CitE

519 gi14041831Homo SapienscDNA FLJ14357 fis, clone2873 100 HEMBA1000005, highly similar to DNAJ PROTEIN HOMOLOG
MTJ 1.

AAB67447 Homo SapiensAmino acid sequence of 2481 99 19 a human . chaperone polypeptide.

519 gi473847 Mus musculusdnaJ-lilee protein 2413 84 520 gi7669968Homo SapiensmRNA; cDNA DKFZp761G0313789 100 (from clone DICFZp761G0313).

520 gi4586315Homo sapiensORCTL3 mRNA for organic-canon348 38 trans orter like 3, complete cds.

520 gi4835384Homo SapiensDNA, DLEC1 to ORCTL4 348 38 gene region, section 1/2 (DLECI, ORCTL3, genes, complete cds).

521 gi7959805Homo SapiensPR00823 344 100 522 gi10434341Homo SapienscDNA FLJ12691 fis, clone2605 89 NT2RM4002571, weakly similar to H.sapiens mRNA for UDP-GaINAc:polypeptide N-acetyl alactosaminyltransferase (T2).

522 gi10436305Homo SapienscDNA FLJ13977 fis, clone1631 99 Y79AA1001603, weakly similar to POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANS

FERASE (EC 2.4.1.41).

SEQ AccessionSpecies Description Score />
ID

NO: No. Identit 522 gi971461 Homo SapiensH.sapiens mRNA for UDP- 1386 50 GaINAc:polypeptide N-acetyl alactosamin ltransferase (T2).

523 gi11493500Homo sa PR02979 477 100 iens 523 gi38163 Pan A-gamma-globin 477 100 tro lodytes 523 gi176779 Pan gamma-2 globin 477 100 troglodytes 524 gi5262582Homo sapiensmRNA; cDNA DKFZp434K063 3782 99 (fi~om clone DICFZ 434IC063);
artial cds.

524 Qi10438230Homo SapienscDNA: FLJ21993 fis, clone1416 100 HEP06576.

524 AAY21842 Homo SapiensHuman signal peptide-contianing1416 100 protein (SIGP) (clone ID 1273453).

525 gi1928886Rattus lin-10 protein homolog 2199 97 norvegicus 525 gi10433467Homo SapienscDNA FLJ12076 fis, clone483 98 HEMBB 1002442, weakly similar to LIN-10 PROTEIN.

525 gi5824587CaenorhabditisTOIG9.2b 668 37 ele ans 526 gi1679607Mus musculusmyosin-I 4206 84 526 gi1924940Homo SapiensH.sapiens mRNA for myosin-IE.4115 99 526 gi65324 Gallus brush border myosin IB 3812 76 gallus 527 AAB63419 Homo SapiensHuman breast cancer associated641 99 antigen protein sequence SEQ
ID N0:781.

528 gi13649967Homo Sapiensfovea-associated SH3 558 100 domain binding rotein (FASH3) mRNA, com lete cds.

528 113539561Homo sapiensmRNA for SH3BGRL2 protein.558 100 528 g15042302Mus musculussh3bar rotein 365 64 529 g110436540Homo SapienscDNA FLJ14154 fis, clone1151 99 NT2RM 1000341.

529 g113436011Mus musculusRIKEN cDNA 1200013P24 1139 97 ene 529 g11592161Methanococcuribosomal protein S18 109 36 alanine s jannaschiiacetyltransferase 530 g13135314Homo Sapienschromosome 7q22 sequence,911 100 complete sequence.

530 g16752287Homo SapiensNovel human gene mapping281 51 to chomosome X.

531 g114042818Homo SapienscDNA FLJ14937 fis, clone2548 97 PLACE 1010231, weakly similar to CELL

SURFACE GLYCOPROTEIN
EMRl PRECURSOR.

531 12117161 Homo SapiensH.sapiens mRNA for HE6 1366 52 Tm7 rece tor.

531 AAW36903 Homo SapiensHuman epididymis-specific1366 52 receptor protein.

532 g17417372Homo sapiensintracellular hyaluronan-binding2175 99 protein mRNA, complete cds.

532 g17110497Mus musculusintracellular hyaluronan-binding1862 85 protein 532 g13403154Homo SapiensHuman ICi-1/57 intracellular1591 98 antigen mRNA; partial cds.

533 g110436645Homo SapienscDNA FLJ14235 fis, clone1585 82 NT2RP4000167.

533 g17020976Homo SapienscDNA FLJ20707 fis, clone2195 84 KAIA1223.

533 g113276619Homo sapiensmRNA; cDNA DKFZp761I01121444 99 (from clone DKFZp761I0112).

534 g1438880 Rattus tropomyosin 1186 99 norvegicus 534 g12978558Xenopus Lalpha-tropomyosin 1089 89 SEQ AccessionSpecies Description Score '%
ID

NO: No. Identit laevis 534 gi438882 Rattus tropomyosin 1086 92 norveQicus 535 gi438880 Rattus tropomyosin 1120 93 norvegicus 535 gi9508585Homo Sapienstropomyosin isoform mRNA,1105 93 complete cds.

535 gi12653955Homo Sapiens, Similar to tropomyosin1094 91 4, clone MGC:3261, mRNA, complete cds.

536 gi6808111Homo sapiensmRNA; cDNA DICFZp434O1230439 100 (from clone DICFZp434O1230);
partial cds.

537 gi6807806Homo sapiensmRNA; cDNA DKFZp434K031 3007 100 (from clone DKFZp434K031);
partial cds.

537 gi13623334Homo Sapiens, Similar to DKF'ZP727C0912392 100 protein, clone MGC:10677, mRNA, complete cds.

S37 AAY25821 Homo SapiensHuman secreted protein 1967 99 fragment encoded from gene 41.

538 AAB88413 Homo sapiensHuman membrane or secretory1818 99 protein clone PSEC0170.

538 gi6457342Homo sapiensE2IG4 (E2IG4) mRNA, complete1813 99 cds.

538 AAB24026 Homo SapiensHuman PR01788 protein 1813 99 sequence SEQ

IDNO:18.

539 gi6572289Homo SapiensmRNA for mitochondrial 1820 100 tryptophanyl-tRNA synthetase (WARS2 gene).

539 gi13421159Caulobactertryptophanyl-tRNA synthetase727 46 crescentus 539 gil 1992026Zymomonastryptophanyl-tRNA synthase721 43 mobilis 540 gi7106630Homo SapiensNovel human mRNA from 6301 99 chromosome I, clone 298884, has homology to PERIOD CIRCADIAN PROTEIN
3.

540 gi13160925Homo SapiensmRNA for period (Drosophila)6274 99 homolog 3 hPER3, complete cds.

540 AAB23266 Homo SapiensHuman circadian rhythm 6274 99 protein Per3 (hPer3 ).

541 gi9621744Homo sapiensfen-itin heavy chain 968 100 subunit mRNA, complete cds.

541 gi12654093Homo Sapiens, ferritin, heavy polypeptide968 100 1, clone MGC:5580, mRNA, complete cds.

541 gi12655095Homo Sapiens, ferritin, heavy polypeptide968 I DO
1, clone MGC:1749, mRNA, complete cds.

542 gi4902699Homo sapiensNovel human gene mapping2372 57 to chomosome 13.

542 gi2341020Homo SapiensPAC clone 248015 from 1447 58 13q12-q13, complete se uence.

542 gi11907986Drosophilafry 1054 38 melano aster 543 gi7582278Homo SapiensBM-003 1386 100 S43 gi7688983Homo sapiensuncharacterized bone 1386 100 marrow protein 543 gi1752736Saccharomycegene required for phosphoylation1S0 35 of s cerevisiaeoligosaccharides/ has high homology with YJR061w 544 gi1628401Homo SapiensH.sapiens mRNA for leucine-rich3936 98 primary response protein 1.

S44 gi940821 Rattus LRPR1 2914 73 norvegicus 544 gi2196560SchizosaccharMis6 223 31 omyces pombe SEQ AccessionSpecies Description Score ID

NO: No. Identit 545 gi7022824Homo SapienscDNA FLJ10656 fis, clone1574 99 NT2 RP200603 8.

545 gi6841138Homo SapiensHSPC099 mRNA, partial 248 36 cds.

545 AAG02788 Homo SapiensHuman secreted protein, 234 85 SEQ ID NO:

6869.

546 AAB71914 Homo SapiensHuman ISOM-6. 1142 98 546 gi3876969CaenorhabditisSimilarity to Brugia 658 52 peptidylprolyl elegans isornerase (TR:G984562), contains similarity to Pfam domain:

(RNA recognition motif.
(a.k.a. RRM, RBD, or RNP domain)), Score=62.0, E-value=4.2e-15, N=1; PF00160 (Cyclophilin type peptidyl-prolyl cis-traps isomerase), Score=78.1, E-value=3.7e-22, N=1 546 AAG02246 Homo SapiensHuman secreted protein, 573 100 SEQ ID NO:

6327.

547 gi603635 SaccharomyceYe1044wp 133 25 s cerevisiae 548 gi5262665Homo SapiensmRNA; cDNA DKFZp564B07691455 99 (from clone DKF'Zp564B0769);
partial cds.

548 gi6841172Homo sapiensHSPC261 716 99 548 gi12803875Homo Sapiens, Similar to splicing 352 33 factor, arginine/serine-rich 4, clone MGC:3920, mRNA, complete cds.

549 gi7582298Homo Sa BM-013 704 100 iens 549 gi9558483Ciona PEM-3 434 55 savignyi 549 gi1644450CaenorhabditisMEX-3 362 65 elegans 550 gi4883433Homo SapiensmRNA for membrane transport2148 100 protein (XK gene).

550 16502963 Mus musculusKX antigen 1797 81 550 g12580580Homo Sapienstestis-specific XK Related157 31 Y (XICRY) mRNA, complete cds.

551 g17670746Homo SapiensUDP-glucose:glycoprotein8075 99 glucosyltransferase 1 precursor, mRNA, complete cds.

551 g113275621syntheticRat RUGT 7371 91 construct 551 g17677176Rattus UDP-glucose 7371 91 norvegicusglycoproteiii:glucosyltransferase precursor 552 g17688985Homo sapiensuncharacterized bone 390 72 marrow protein 553 g112655091Homo sapiens, AD-003 protein, clone I 177 100 MGC:783, mRNA, complete cds.

553 g16523799Homo Sapiensadrenal gland protein 1168 99 AD-003 mRNA, complete cds.

553 g17105659Caenorhabditiscontains similarity to 425 39 Streptomyces elegans peucetius carminomycin methyltransferase (GB:L13453) 554 17582282 Homo sapiensBM-005 3445 99 554 g17022933Homo sapienscDNA FLJ10725 fis, clone3312 100 NT2RP3001214.

554 g110435575Homo SapienscDNA FLJ13534 fis, clone1648 100 PLACE1006445.

555 112751374Homo Sapiensaraoxanase-3 mRNA, artial1819 99 cds.

555 g11333634Homo Sapiensparaoxonase 3 (PON3) 1741 98 mRNA, 3' end of cds.

555 g112743899Oryctolagusparaoxonase 3 1542 82~

SEQ AccessionSpecies Description Score/~
ID

NO: No. Identit cuniculus 556 g17022174Homo SapienscDNA FLJ10252 fis, clone2826 1D0 HEMBB 1000807.

556 g111596985Homo Sapienschromosome 14 clone 559 36 RP11-361H10 map 14 24.3, com lete se uence.

556 17020945Homo SapienscDNA FLJ20689 fis, clone510 39 KAIA2890.

557 g110434683Homo sapienscDNA FLJ12917 fis, clone2879 99 NT2RP2D04568, weakly similar to PUTATIVE ATP-DEPENDENT
RNA

HELICASE C30D11.03.

557 g113384106Homo SapiensRNA helicase-like protein2817 99 (RHLP) mRNA, complete cds.

557 1702081 Homo SapienscDNA FLJ20596 fiS, clone2020 99 I KAT08049.

558 g14760710Brassica SLL2-S9- rotein 284 43 ra a 558 g11669601ArabidopsisAR401 280 44 thaliana 558 g1557805Saccharomyceorf, len: 257, CAI: 327 34 0.13 s cerevisiae 559 g113548677Homo SapiensMKP-7 mRNA for MAPK 3418 100 phosphatase-7, complete cds.

559 113990989Mus musculusMAP kinase phosphatase-73093 90 559 AAB20325Homo SapiensHuman protein phosphatase3021 90 and kinase protein-4.

560 g110433965Homo SapienscDNA FLJ 12464 fis, 2196 97 clone NT2RM 1000780.

560 g110434795Homo sapienscDNA FLJ 12992 fis, 2196 97 clone NT2RP3000149.

560 g110438048Homo SapienscDNA: FLJ21857 fis, 2151 94 clone HEP02294.

561 g110438048Homo SapienscDNA: FLJ21857 fis, 2276 97 clone HEP02294.

561 g110433965Homo SapienscDNA FLJ 12464 fis, 2159 94 clone NT2RM l 000780.

561 g110434795Homo SapienscDNA FLJ12992 fis, clone2159 94 NT2RP3000149.

562 g110433965Homo SapienscDNA FLJ 12464 fis, 2443 99 clone NT2RM 1000780.

562 g110434795Homo SapienscDNA FhJ12992 fis, clone2443 99 NT2RP3000149.

562 110438048Homo sa cDNA; FLJ21857 fis, 2398 96 iens clone HEP02294.

563 g111137965Homo SapienstRNA isopentenylpyrophosphate2158 100 transferase recursor RNA, complete cds.

563 tri7019915Homo SapienscDNA FLJ20061 fis, clone1719 100 COL01383.

563 g19803035Caenorhabditiscontains similarity 407 32 to Pfam domain elegans PF00096 (zf C2H2), Score=12.0, E-value=1.1, N=1 564 g17023103Homo SapienscDNA FLJ 10826 fis, 2171 100 clone NT2RP4001100.

564 g110434339Homo SapienscDNA FLJ12690 fis, clone2171 100 NT2RM4002567.

564 g110433458Homo SapienscDNA FLJ12068 fis, clone2166 99 HEMBB 1002329.

565 g17019829Homo SapienscDNA FLJ20011 fis, clone865 100 ADKA03432.

565 110438448Homo SapienscDNA: FLJ22168 fis, 865 100 . clone HRC00618.

565 AAG02581Homo sapiensHuman secreted protein,445 98 SEQ ID N0:

6662.

566 gil 1558482Homo SapiensmRNA for B-cell lymphoma/leukaemia1543 99 11A extra long form (BCLI lA-XL ene).

566 g112150278Homo sapiensC2H2-type zinc-forger 1039 99 protein mRNA, complete cds.

566 g16652688Mus musculusC2H2-type zinc finger 1033 98 ~ protein SEQ AccessionSpecies Description Score ID

NO: No. Identit 567 gi12053249Homo sapiensmRNA; cDNA DICFZp434A155994 100 (from clone DKFZ 434A155);
complete cds_ 567 AAY73435 Homo sapiensHuman secreted protein 994 100 clone yd73'I

rotein se uence SEQ ID
N0:92.

567 AAB43698 Homo SapiensHuman cancer associated 752 95 protein sequence SEQ ID N0:1143.

568 gi12053249Homo SapiensmRNA; cDNA DICFZp434A155752 95 (from clone DICFZp434A155);
complete cds.

568 AAY73435 Homo sapiensHuman secreted protein 752 95 clone yd73_1 rotein se uence SEQ ID
NO:92.

568 AAB43698 Homo sapiensHuman cancer associated 853 100 protein se uence SEQ ID N0:1143.

569 gi8096260Homo Sapiensgene for Nopl Op, com 344 100 lete cds.

569 gi8096476Homo sapiensmRNA for Nop l Op, complete344 100 cds.

569 gi 14424489Homo sapiens, nucleolar protein family344 100 A, member 3 (HIACA small nucleolar RNPs), clone MGC:19486, mRNA, complete cds.

570 gi11595476HomosapiensmRNAforRPBllblbetaprotein633 100 (POLR2J2 gene).

570 AAB58870 Homo SapiensBreast and ovarian cancer409 100 associated antigen protein sequence SEQ ID 578.

570 gi11595474Homo SapiensmRNA for RPBllblalphaprotein247 97 (POLR2J2 gene).

571 gi7239381Homo sapiensguanine nucleotide exchange2995 99 factor smgGDS (RAP 1 GDS 1 ) mRNA, alternatively spliced, complete cds.

571 gi131 Homo Sapiens, RAP1, GTP-GDP dissociation2994 99 stimulator l, clone MGC:2897, mRNA, complete cds.

571 gi6942013Homo Sapiensexchange factor smgGDS 2991 99 mRNA, com lete cds, alternatively spliced.

572 gi12002978Homo Sapiensmitosin-associated protein1736 100 MITAPI

(MITAP1) mRNA, complete cds.

572 gi12043569Homo SapiensNudel mRNA, complete 1736 100 cds.

572 gi 13775593Homo Sapiensendooligopeptidase A 1720 99 mRNA, complete cds.

573 gi7022325Homo sapienscDNA FLJ10350 fis, clone1243 100 NT2RM2001131.

573 gi12052730Homo sapiensmRNA; cDNADKFZp761F191211243 100 (from clone DKF'Z 761F19121).

573 gi3417386Mus musculusmicrotubule-associated 428 48 protein, MAP-I 15 574 gi7022502Homo SapienscDNA FLJ10458 fis, clone2555 100 NT2RP1001457, highly similar to Homo Sapiens partial mRNA
for beta-transducin family protein.

574 gi3687833Xenopus notchless 2149 82 laevis 574 gi12643028Oryza Putative Notchless protein1110 52 sativa homolog 575 AAY51115 Homo sa Human HSEC6 protein. 3767 99 iens 575 gi 1163174Rattus similar to yeast Sec6p, 3606 94 Swiss-Prot norvegicusAccession Number P32844;
similar to mammalian B94, Swiss-Prot Accession Number Q03169; Method:
conceptual franslation sup lied by author 575 AAB49655 Homo SapiensHuman SEC7 protein sequence2737 89 SEQ ID

14.

576 gi7020303Homo SapienscDNA FLJ20300 fis, clone1697 99 HEP06465.

576 AAB67575 Homo SapiensAmino acid sequence of 759 47 a human hydrolytic enzyme HYENZ7.

!, AccessionSpecies Description Score SEQ
ID

NO: No. Identit 576 gi10434892Homo SapienscDNA FLJ13055 fiS, clone755 47 NT2RP3001538, weakly similar to HYPOTHETICAL 39.0 KD
PROTEIN

T28D9.3 IN CHROMOSOME
II.

577 AAR15222 Homo SapiensChronic myelogenous leukaemia-derived513 100 myeloid-related protein.

577 gi32402 Homo SapiensHuman mRNA for HP-1, 493 100 a member of the corticostatin/defensin family.

577 gi181527 Homo SapiensHuman neutrophil peptide493 100 (defensin) 1 mRNA, complete cds.

578 AAY41716 Homo sa Human PR0860 protein 5224 100 lens sequence.

578 AAB44272 Homo SapiensHuman PR0860 (UNQ421) 5224 100 protein sequence SEQ ID N0:211.

578 gi14042832Homo sapienscDNA FLJ14946 fis, clone3746 93 PLACE2000034, weakly similar to LAR

PROTEIN PRECURSOR (EC
3.1.3.48).

579 gi7021880Homo SapienscDNA FLJ10054 fis, clone2306 100 HEMBA 1001310.

579 gi12653981Homo Sapiens, TRIAD3 protein, clone 2306 100 MGC:998, mRNA, complete cds.

579 gi7109299Homo SapiensTRIAD3 mRNA, partial 2013 100 cdS.

580 gi3288457Homo sapiensmRNA for C2 domain containing7615 99 lcinase.

580 gi3059227Rattus phosphoinositide 3-kinase3988 80 norve icus 580 gi3041786Mus musculusPhosphoinositide 3-Kinase-C2gamma3984 78 581 gi10437125Homo sa cDNA: FLJ21 103 fis, 1802 99 lens clone CAS04883.

581 17020867 Homo SapienscDNA FLJ20635 fis, clone786 52 KAT03466.

582 g113937952Homo Sapiens, Similar to upregulated297 100 during skeletal muscle growth 5, clone MGC:14697, mRNA, complete cds.

582 g16851054Rattus DAPIT protein 278 91 norvegicus 582 g19843791Mus musculusStretch regulated skeletal259 84 muscle protein 583 g17582286Homo SapiensBM-007 599 100 583 AAG02907 Homo SapiensHuman secreted protein, 477 98 SEQ ID NO:

6988.

583 g13878572CaenorhabditisMO1F1.6 161 28 elegans 584 113477103Homo Sapiens, clone MGC:1012, mRNA, 3001 99 com fete cds.

584 g112052999Homo SapiensmRNA; cDNA DICFZp434E17112619 98 (from clone DKFZp434E1711);
com lete cds.

584 g17020996Homo SapienscDNA FLJ20721 fis, clone2402 100 HEP15722.

585 AAW48892 Homo SapiensHuman guanylate binding 2645 94 protein B

(HGBPB).

585 g112803663Homo sapiens, guanylate binding protein2000 66 l, interferon-inducible, 67kD, clone MGC:3949, mRNA, complete cds.

585 g1183002 Homo sapiensHuman guanylate binding 2000 66 protein isoform I (GBP-2) mRNA, complete cds.

586 g17023366Homo SapienscDNA FLJ10983 fis, clone3218 99 PLACE1001781, weakly similar to PROBABLE

PHOSPHOMANNOMUTASE (EC

5.4.2.8).

586 g112052930Homo SapiensmRNA; cDNA DKFZp566B15243216 99 (from clone DKFZp566B 1524);
complete cds.

586 g13395586Schizosaccharsimilarity to phosphomannomutases1211 43 omyces pombe SEQ AccessionSpecies Description Score ID No. Identit NO:

587 Qi13537208Mus musculusMell 8 and Smil like 347 40 rin fin er 587 g12440074Homo SapiensmRNA for RNF3A (DONG1) 347 37 ring finger rotein.

587 g113537206Homo SapienshMBLRmRNA, complete cds.345 40 588 g114042249Homo SapienscDNA FLJ14610 fis, clone2797 99 NT2RP1000958, weakly similar to AUTOANTIGEN NGP-1.

588 g114042246Homo sapienscDNA FLJ14608 fis, clone2741 99 NT2RP1000915, weakly similar to AUTOANTIGEN NGP-1.

588 g16457340Homo SapiensE2IG3 (E2IG3) mRNA, complete2650 100 cds.

589 g17020925Homo SapienscDNA FLJ20673 fis, clone2232 100 ICAIA4464.

589 g17682684Homo Sapiensphosphoprotein associated2222 99 with GEMs (PAG) mRNA, complete cds.

589 g17707799Rattus Csk binding protein Cbp 1696 78 norve icus 590 16682873 Homo Sapiensrec mRNA, complete cds. 2002 100 590 g17230612Rattus small rec 1916 95 norvegicus 590 g13881771Caenorhabditiscontains similarity to 586 39 elegans Pfam domain:
PF01529 (DHHC zinc finger domain), Score=137.4, E-value=8.4e-38, N=1 591 g1439522 Mus musculusribosomal protein S3 678 100 591 157728 Rattus ribosomal protein S3 678 100 rattus (AA 1-243) 591 g113111933Homo Sapiens, ribosomal protein S3, 678 100 clone MGC:3657, mRNA, complete cds.

592 g16599070Homo SapiensmRNA for LIM domains 3675 99 containing rotein 1.

592 16599307 Mus musculusLIM domains containin 2728 76 rotein 1 592 g113548632Homo Sapienspartial LIMDI gene for 2690 99 LIM domains containing 1, exons 1-2, complete sequence.

593 g17020974Homo sapienscDNA FLJ20706 fis, clone2824 98 KAIA1273.

593 g112082725Mus musculusB cell phosphoinositide 411 29 3-kinase adaptor 593 AAG02945 Homo SapiensHuman secreted protein, 526 100 SEQ ID NO:
7026.

594 g111596144Homo SapiensSTE20-like kinase mRNA, 5159 99 partial cds.

594 g13452473Rattus serinelthreonine protein5117 98 norvegicuskinase TAO1 594 AAY55937 Homo sa Human SULU3 rotein. 4045 100 iens 595 g1695802 Homo sapienstranscription factor 1693 99 SL1 mRNA, partial cds.

595 g11842206Mus musculusTAFI68 1326 76 596 g17020363Homo sapienscDNA FLJ20335 fis, clone2940 99 HEP11429.

596 AAB65680 Homo SapiensNovel protein kinase, 2940 99 SEQ ID NO: 208.

596 AAB32078 Homo SapiensHuman secreted protein 826 100 BLAST search protein SEQ ID NO: 136.

597 g17020747Homo sa cDNA FL320558 fis, clone2990 100 iens KAT11870.

597 g112053175Homo SapiensmRNA; cDNA DKFZp434A172 2990 100 (from clone DKFZp434A172);
complete cds.

597 g110439123Homo SapienscDNA: FLJ22650 fis, clone2166 100 HSI07344.

598 g17023601Homo sapienscDNA FLJl 1127 fis, clone1897 100 PLACE 1006225.

598 g112224968Homo SapiensmRNA; cDNA DKFZp667E105 620 100 (from clone DKFZp667E105).

598 g114043433Homo sapiens, clone IMAGE:3952677, 549 41 mRNA, partial cds.

599 g16483296Homo SapiensCDH9 mRNA for cadherin-9,4132 100 complete cds.

SEQ AccessionSpecies Description Score ID

NO: No. Identit 599 g1867999 Gallus chicken cadherin-6B 3044 72 callus 599 1974185 Homo sa mRNA for cadherin-6, 3032 72 iens com lete cds.

600 g15734605Homo SapiensmRNA for I<ARP-1-binding750 51 protein 3, complete cds.

600 g15734601Homo SapiensmRNA for KARP-1-binding 750 51 protein 1 (KAB1), complete cds.

600 g15734603Homo SapiensmRNA for KARP-1-binding 750 51 protein 2 (KAB2), complete cds.

601 g110434848Homo sapienscDNA FLJ13028 fis, clone889 100 NT2RP3001055, weakly similar to Drosophila melanogaster separation anxiety protein (San) mRNA.

601 g110435107Homo SapienscDNA FLJ13194 fis, clone889 100 NT2RP3004378, weakly similar to Drosophila melanogaster separation anxiety rotein (san) mRNA.

601 AAB56739 Homo SapiensHuman prostate cancer 874 98 antigen protein sequence SEQ ID N0:1317.

602 g113325182Homo Sapiens, clone IMAGE:3638994, 897 100 mRNA, partial cds.

602 g1 12654203Homo Sapiens, clone IMAGE:3449323, 560 100 mRNA, partial cds.

602 g14514314Bacillus YIqF 260 39 halodurans 603 g110954046Homo Sapiensoxidation protection 1034 97 protein (OXR1) mRNA, complete cds.

603 g1 13540300Mus musculusnucleolar protein C7B 1431 94 603 g17021988Homo SapienscDNA FLJ10125 fis, clone1441 99 HEMBA1002954.

604 g1 1150495Mus musculushomology to nucleosome 211 36 assembly proteins; specifically expressed in neurons 604 g1 1 161252Glycine nucleosome assembly protein136 40 max 1 604 g15931610Homo SapiensmRNA for Nucleosome Assembly196 37 Protein 1-like 2, complete cds.

605 g17547029Homo sapiensGAP-like protein (N61) 4684 99 mRNA, complete cds.

605 g17688683Homo Sapienskinesin heavy chain-like822 100 protein (KHCHP) mRNA, complete cds.

605 AAG03378 Homo sapiensHuman secreted protein, 633 99 SEQ ID NO:

7459.

606 g17022593Homo SapienscDNA FLJ10511 fis, clone1425 100 NT2RP2000656.

606 g1 12224996Homo SapiensmRNA; cDNA DICFZp667G2481031 100 (from clone DKFZ 667G248).

606 g110436327Homo sapienscDNA FLJ13991 fis, clone803 100 Y79AA 1002115.

607 g18885998Rattus neuronal C-SRC tyrosine-specific2826 98 protein norvegicuskinase 607 g1201057 Mus musculustyrosine-s ecific protein2822 98 kinase 607 g1338460 Homo sapiensHuman c-src-1 proto-onco2815 98 ene, exon 12.

608 g17243633Homo SapiensRB-associated KRAB repressor3993 100 (RBAIC) mRNA, complete cds.

608 g17243635Mus musculusRB-associated KRAB repressor3025 78 608 g110434235Homo sapienscDNA FLJ12629 fis, clone1881 73 NT2RM4001828, moderately similar to ZINC FINGER PROTEIN 84.

609 17008402 Homo Sapienskappa B-ras 1 mRNA, complete982 100 cds.

609 g114042659Homo SapienscDNA FLJ14843 fis, clone978 99 ~

SEQ AccessionSpecies Description Score ID

NO: No. Identit PLACE 1000040, weakly similar to TRANSFORMING PROTEIN
P21/It-RAS 2B.

609 g17239257Mus musculuska aB-Rasl 952 94 610 _113625164Homo sa ankyrin mRNA, complete 426 100 iens cds.

610 g1 12698638Homo Sapiensankyrin-repeat family 426 100 A protein 2 (ANKRA2) mRNA, complete cds.

610 g110434525Homo SapienscDNA FLJ12814 fis, clone426 100 NT2RP2002520, weakly similar to Homo Sapiens transcription factor RFX-B

(RFXB) mRNA.

611 g17959841Homo sapiensPR01853 510 100 ' 611 AAGO 1282Homo SapiensHuman secreted protein, 301 100 SEQ ID NO:

53 63.

612 g15757703Mus musculussyntrophin-associated 7464 92 serine-threonine rotein kinase 612 g113537204Homo sapiensmRNA for MAST205, complete4616 68 cds.

612 g1406058 Mus musculusprotein kinase 4569 65 613 g17020724Homo sapienscDNA FLJ20545 fis, clone1780 100 I<AT11476.

613 AAB63186 Homo SapiensHuman secreted protein 1693 100 sequence encoded by gene 3 SEQ
ID N0:112.

613 g17243701DrosophilaWDS 1574 91 melanogaster 614 g113383476Homo sa NUB1 (NUB1) mRNA, com 3109 100 iens lete cds.

614 g15360093Homo SapiensNY-REN-18 antigen mRNA, 2958 95 complete cds.

614 1863014 Mus musculusBS4 peptide 2671 84 615 AAB87345 Homo sapiensHuman gene 4 encoded 4534 100 secreted protein HDPFY41, SEQ ID N0:86.

615 g14886489Homo SapiensmRNA; cDNA DKFZp564L21232892 99 (from clone DKFZp564L2123);
artial cds.

615 g112711793Homo Sapiensestrogen regulated LIV-11 171 39 protein (LIV-l ) mRNA, complete cds.

616 g17638247Homo sapiensmesenchymal stem cell 1063 100 protein DSCD75 mRNA, complete cds.

616 g112654929Homo sapiens, mesenchymal stem cell ~ 1063100 protein DSCD75, clone MGC:5515, mRNA, com lete cds.

616 AAB03956 Homo SapiensHuman mesenchymal stem 1063 100 cell polypeptide.

617 g17582304Homo SapiensBM-016 584 100 617 AAW78199 Homo SapiensHuman secreted protein 562 98 encoded by gene 74 clone HGBAC 11.

617 AAW85610 Homo sapiensSecreted protein clone 562 98 eh80_l.

618 g113603398Homo sapiensmRNA for SEZ6L, complete4199 98 cds.

618 g1 13185723Homo Sapiensn 1755 can be A, G, C, 2164 49 or T

618 AAB70537 Homo SapiensHuman PRO7 protein sequence2164 49 SEQ ID

N0:14.

619 g13880445Caenorhabditiscontains similarity to 327 40 Pfam domain:

elegans PF02214 (K+ channel teh~amerisation domain), Score=79.5, E-value=23e-20, N=1 619 AAY34129 Homo Sapiens.Human potassium channel 195 40 K+Hnov28.

619 AAZ11907~Homo SapiensHuman potassium channel 195 40 K+Hnov28 aal cDNA (5's lice variant 1).

620 110437116Homo sapienscDNA: FLJ21097 fis, clone1146 100 CAS03931.

620 g114250732Homo Sapiens, chromosome 11 open I 146 100 reading frame 14, clone MGC:12847, mRNA, complete cds.

620 113276621Homo SapiensmRNA; cDNA DKFZp761G1913378 43 (from SEQ AccessionSpecies Description Score ID

NO: No. Identit clone DKFZ 76161913 .

621 g110437078Homo sa cDNA: FLJ21069 fis, clone955 58 iens CAS01594.

621 g15911935Homo SapiensmRNA; cDNA DKFZp586N1922867 100 (from clone DICFZp586N1922);
partial cds.

621 AAB27870 Homo sa Protein fragment encoded657 l 00 iens by ene 27.

622 g113097159Homo Sapiens, tumor protein, translationally-controlled898 1, clone MGC:5308, mRNA, complete cds.

622 g114043771Homo Sapiens, clone MGC:14243, mRNA,898 100 complete cds.

622 g17573519Homo sapiensTPTI gene fortranslationally898 100 controlled tumor protein (TCTP), exons 1-6.

623 17020339 Homo~sapienscDNA FLJ20320 fis, clone1135 100 ~ HEP08923.

623 AAB18972 Homo SapiensAmino acid sequence of 1135 100 a human transmembrane protein.

623 g11314162Schizosaccharseven transmembrane protein217 29 omyces pombe 624 g16467990Mus musculusPDZ domain actin binding4816 66 protein Shroom 624 16467992 Mus musculusactin binding protein 4816 66 ShroomS

624 g113938323Homo Sapiens, Similar to shroom, 4006 99 clone IMAGE:3349317, mRNA, partial cds.

625 g112804029Homo sapiens, clone IMAGE:3940519, 1551 100 mRNA, partial cds.

625 AAY21850 Homo SapiensHuman signal peptide-contianing1109 100 protein ., (SIGP) (clone ID 1880830).

625 g18655657Homo SapiensmRNA; cDNA DKFZp762O076 593 57 (from clone DKFZp7620076).

626 g17328140Homo SapiensmRNA; cDNA DKFZp762D096 601 100 (from clone DKFZ 762D096);
artial cds.

626 g113436341Homo Sapiens, Similar to RIKEN cDNA 384 100 gene, clone MGC:10922, mRNA, complete cds.

627 11293559 Mus musculusastrotactin 4312 95 627 g16502571Mus musculusastrotactin2 2580 51 627 g16502573Homo sapiensastrotactin2 (ASTN2) 2569 51 mRNA, complete cds.

628 AAY73387 Homo SapiensHTRM clone 3340290 protein1439 95 sequence.

628 AAY48312 Homo SapiensHuman prostate cancer-associated1073 84 protein 9.

628 g112654077Homo Sapiens, clone IMAGE:3458173, 1045 86 mRNA, partial cds.

629 g111095188Homo sapiensdipeptidyl peptidase 3521 99 8 (DPPB) mRNA, complete cds.

629 g114042790Homo sapienscDNA FLJ14920 fis, clone2457 99 PLACE1007416, weakly similar to DIPEPTIDYL PEPTIDASE
IV (EC

3.4.14.5).

629 g17020273Homo SapienscDNA FLJ20283 fis, clone2483 100 HEP04088.

630 g111095188Homo Sapiensdipeptidyl peptidase 2560 99 8 (DPPB) mRNA, complete cds.

630 g114042790Homo SapienscDNA FLJ14920 fiS, clone2457 99 PLACE1007416, weakly similar to DIPEPTIDYL PEPTIDASE
IV (EC

3.4.14.5).

630 g111095192Homo sapiensdipeptidyl peptidase 2482 100 8 (DPP8) mRNA, partial cds, alternatively spliced.

631 17020611 Homo sa cDNA FLJ20481 fis, clone2211 99 iens KAT07534.

631 AAY57908 Homo sapiensHuman transmembrane protein975 44 ~ HTMPN-SEQ AccessionSpecies Description Score ID

NO: No. Identit 32.

631 AAB54284 Homo SapiensHuman pancreatic cancer 516 40 antigen protein se uence SEQ ID N0:736.

632 gi35700 Homo SapiensHuman mRNA for phosphoriobosyl1596 99 pyrophosphate synthetase subunit II (EC

2.7.6.1).

632 gi206434 Rattus phosphoribosyl pyrophosphate1585 98 synthetase norve II
icus G32 gi56979 Rattus ribose-phosphate pyrophosphokinase1585 98 norve subunit II (AA 1 ~ 18) ices 633 i 1 I Homo SapiensRag D mRNA, complete 1276 100 181620 cds.

633 gi6808148Homo SapiensmRNA; cDNA DICFZp761H1711276 100 (from clone DKFZp761H171);
partial cds.

633 AAB56443 Homo SapiensHuman prostate cancer 1276 100 antigen protein sequence SEQ ID N0:1021.

634 gi6807893Homo SapiensmRNA; cDNA DICFZp434H22261079 100 (from clone DKFZp434H2226);
partial cds.

635 gi10435042Homo SapienscDNA FLJ13152 fis, clone3495 100 NT2RP3003385, highly similar to Mus musculus SKD3 mRNA.

635 gi4958935Rattus suppressor of potassium 3085 88 transport defect 3 norvegicus 635 gi563129 Mus musculusSKD3 3066 88 636 AAB20322 Homo SapiensHuman protein phosphatase1770 100 and kinase r0tein-1.

636 gi1903458Dictyosteliummyosin heavy chain kinase236 32 B

discoideum 636 gi2104701Mus musculuselongation factor-2 kinase199 29 637 gi7670003Homo SapiensmRNA; cDNA DKFZp434P05311850 100 (from clone DKFZp434P0531).

637 gi7417474Homo Sapienschromosome 14 clone RP11-4936171251 49 and GTD-25I6D11 map 14q24.3,~
complete sequence.

637 gi7018538Homo sapiensmRNA; cDNA DKFZp434P01 330 43 l L (from clone DKFZp434P0111 );
partial cds.

638 gi7022367Homo SapienscDNA FLJ10375 fis, clone3056 100 NT2RM2001950.

638 AAY53026 Homo SapiensHuman secreted protein 1752 95 clone cn922 5 rotein sequence SEQ ID
N0:58.

638 gi4336692DrosophilaAbnormal X segregation 816 37 melanogaster 639 gi7020972Homo sapienscDNA FLJ20705 fis, clone3641 99 KAIA1571.

639 gi 12007334Homo SapiensIRS-1 PH domain binding 3632 99 protein PHIP

mRNA, complete cds.

639 gi14286226Homo Sapiens, pleckstrin homology 3632 99 domain interacting protein, clone MGC:15187, mRNA, complete cds.

640 gi7689025Homo Sapiensuncharacterized hypothalamus978 96 protein HT013 mRNA, complete cds.

641 gi9937505Homo SapiensPLIC-2 mRNA, complete 3167 100 cds.

641 gi6563288Homo Sapiensubiquitin-like product 3162 99 Chapl/Dsk2 mRNA, complete cds.

641 AAB47122 Homo SapiensHuman Chap 1. 3162 99 642 AAY53001 Homo sapienSHuman secreted protein 811 100 clone dn834~1 protein sequence SEQ
ID N0:8.

642 AAG01114 Homo SapiensHuman secreted protein, 641 99 SEQ ID NO:

5195.

642 gi12652989Homo Sapiens, clone MGC:2495, mRNA, 489 57 complete cds.

643 17021064 Homo sapienscDNA FLJ20761 fis, clone2240 100 HEP00317.

SEQ AccessionSpecies Description Score /u ID

NO: No. Identit 643 gi I 0438264Homo sa cDNA: FLJ22019 fis, clone2187 98 iens HEP07982.

643 gi577428 Rattus Ca2~--dependent activator1787 77 protein;

norvegicuscalcium-dependent actin-binding protein 644 gi702365IHomo sapienscDNA FLJ11159 fis, clone2865 99 PLACE 1006966.

644 gi7023118Homo SapienscDNA FLJ10835 fis, clone1253 100 NT2RP4001210.

644 gi600058 SaccharornyceN1342 710 39 s cerevisiae 645 gi7020012Homo SapienscDNA FLJ20121 fis, clone1334 99 COL05942.

646 gi 14336697Homo Sapiens16p13.3 sequence section609 100 2 of 8.

646 gi 13436122Homo Sapiens, non-metastatic cells 609 100 4, protein expressed in, clone MGC:11088, mRNA, complete cds.

646 gi1945762Homo sapiensH.sapiens mRNA for nucleoside-609 100 diphosphate kinase.

647 AAB24225 Homo SapiensHuman vesicle associated2946 99 protein 4 SEQ

I D N0:4.

647 gi10439139Homo SapienscDNA: FLJ22662 fis, clone2703 99 HSI08080.

647 AAB58427 Homo SapiensLung cancer associated 171 99 polypeptide I

se uence SEQ ID 765.

648 gi7020604Homo SapienscDNA FLJ20477 fis, clone2639 99 KAT07271.

648 gi6672090DrosophilaVegetable 578 32 melanogaster 649 gi 12802986Homo Sapiens, ring finger protein 81 100 24, clone MGC:I 815, I

mRNA, complete cds.

649 gi5420200Homo SapiensNovel human mRNA from 81 100 chromosome 1 20, similar to SW:GOLI_DROME

Q06003 GOLIATH PROTEIN.

649 gi5102892Homo SapiensmRNA full length insert 566 100 cDNA clone EUROIMAGE 566628.

650 gi6841346Homo sapiensHSPC054 497 98 651 gi7209305Homo SapiensmRNA for FLJ00002 protein,7637 100 partial cds.

651 gi6599226Homo SapiensmRNA; cDNA DKFZp434L08273519 100 (from clone DKFZp434L0827);
partial cds.

651 r 10440406Homo SapiensmRNA for FLJ00036 protein,3457 99 partial cds.

652 gi7018505Homo sapiensmRNA; cDNA DICFZp434E22202470 100 (from clone DKFZp434E2220).

652 gi14042579Homo SapienscDNA FLJ14796 fis, clone2466 99 NT2RP4001235.

652 gi7018507Homo SapiensmRNA; cDNA DICFZp434004202466 99 (from clone DKFZ 43400420).

653 gi552196 Plasmodiumhistidine-rich protein 192 40 lophurae 653 gi160362 Plasmodiumknob protein 178 42 falciparum 653 gi3845095Plasmodiumknob-associated His-rich172 40 protein falciparum 654 AAY70539 Homo SapiensHuman Factor 8 Homologue.1353 83 654 gi 14043498Homo Sapiens, Similar to neuropilin 189 34 1, clone MGC:12920, mRNA, complete cds.

654 gi7271465Homo Sapienssoluble neuropilin-1 189 34 mRNA, complete cds.

655 gi7019959Homo sapienscDNA FLJ20087 fis, clone3964 100 COL03793.

655 gi13569705Homo Sapienschannel kinase 2 (CHAK2)3942 99 mRNA, com fete cds.

655 AAY95433 Homo SapiensHuman calcium channel 1172 71 C-terminal polypeptide.

656 gi6094668Homo SapiensBAC clone RP11-343N14 208 100 ~ from 2, SEQ AccessionSpecies Description Score ID

NO: No. Identit com lete sequence'.

656 gi10435833Horno cDNA FLJ13729 fiS, clone208 100 Sapiens PLACE3000121, weakly similar to VESICULAR TRAFFIC CONTROL

PROTEIN SEC15.

656 gi2827162Rattus rsecl5 I60 73 norvegicus 657 gi10434153Homo SapienscDNA FLJ12580 fis, clone1806 99 NT2RM4001116, weakly similar to HYPOTHETICAL 216.3 KD
PROTEIN

R06F6.8 IN CHROMOSOME
II.

657 gi12053255Homo SapiensmRNA; cDNA DICFZp434D1051806 99 (from clone DICFZp434D105);
complete cds.

657 gi5901808DrosophilaBcDNA.GH03694 619 56 melano aster 658 gi11181618Homo SapiensRag C mRNA, complete 2072 100 cds.

658 gi 12007486Homo SapiensGTPase-interacting protein2069 99 2 mRNA, complete cds.

658 gi 13529335Mus musculusSimilar to Rag C protein2039 98 659 gi13537208Mus musculusMe118 and Bmil like ring347 40 finger 659 gi2440074Homo SapiensmRNA for RNF3A (DONG1) 347 37 ring finger rotein.

659 ai13537206Horno hMBLRmRNA, complete cds.345 40 sapiens 660 gi7023690Homo sapienscDNA FLJ11184 fis, clone1043 99 PLACE1007507.

661 gi7020878Homo SapienscDNA FLJ20641 fis, clone2552 99 I<AT02782.

661 gil 1992034Rattus antisense RNA overlapping1609 65 MCH protein norvegicus 662 AAB56646 Homo SapiensHuman prostate cancer 915 98 antigen protein sequence SEQ ID N0:1224.

662 gi12053357Homo SapiensmRNA; cDNA DICFZp586G2122900 100 (from clone DICFZp586G2122);
complete cds.

662 AAB36598 Homo SapiensHuman FLEXHT-20 protein 791 59 sequence SEQ ID N0:20.

663 AAW93947 Homo SapiensHuman regulatory molecule1732 100 protein.

663 gi3288459Homo SapiensmRNA for transcription 1673 100 elongation factor TFIIS.h.

663 13288547 Mus musculustranscription elon anon 1543 90 factor TFIIS.h 664 g114042893Homo sapienscDNA FLJ14984 fis, clone3478 100 Y79AA1000349, highly similar to M.musculus Spnr mRNA
for RNA

binding rotein.

664 g113377630Homo Sapiensspermatid perinuclear 3459 99 RNA-binding protein mRNA, com lete cds.

664 g1 12053237Homo SapiensmRNA; cDNA DICFZp434N2143406 100 (from clone DICFZp434N214);
complete cds.

665 g110436573Homo SapienscDNA FLJ14183 fis, clone4423 99 NT2RP2004920, weakly similar to TRANSCRIPTIONAL REGULATOR

ATRX.

665 g110434345Homo SapienscDNA FLJ12693 fis, clone4369 99 NT2RP 1000324.

665 AAB27235 Homo sa Human EXMAD-13 SEQ ID 3346 100 iens NO: 13.

666 g19858154Homo Sapienstubby super-family protein3598 100 (TUSP) mRNA, complete cds, alternatively spliced.

666 g19502082Homo sapienstubby super-family protein3556 100 (TUSP) mRNA, complete cds.

SEQ AccessionSpecies bescription Score ID No. Identit NO:

666 819502080Mus musculustubb su er-famil rotein3505 98 667 817106796Homo so HSPC203 554 100 iens 667 19963859Homo SapiensPTD019 rnRNA, complete 554 I40 cds.

667 Homo SapiensExtended human secreted554 100 AAY35987 protein sequence, SEQ ID NQ.
236.

668 16996442Homo so CTL1 ene. 3398 99 iens 668 816996589Rattus CTL1 protein 3291 96 norvegicus 668 816996587Torpedo CTL1 protein 2454 71 marmorata 669 816808165Homo SapiensmRNA; cDNA DKFZp761 2265 100 AOS2 (from clone DKFZ 761A052).

669 Qi10439058Homo SapienscDNA: FLJ22607 fis, 1992 100 clone HSI04846.

669 176736I6Mus musculusDXImx46e rotein 1958 98 670 816808252Homo SapiensmRNA; cDNA DTCFZp434D13192336 100 (from clone DICFZ 434D1319);
partial cds.

670 81170035Glycine N-75 221 27 max 670 8318576 Glycine pre-pro pol peptide 219 27 max (AA -25 to 284) 671 AAW93947Homo SapiensHuman regulatory molecule1116 99 rotein.

6?1 813288459Homo Sapiens 105'799 mRNA
for transcription elongation factor TFIIS.h.

671 813288547Mns musculustranscri tion elongation950 86 factor TFIIS.b 672 8110434615Homo SapienscDNA FL312875 fis, clone1818 99 NT2RP2003777.

672 818778741ArabidopsisT30E16.12 254 27 thaliana 672 816520214ArabidopsisZCF61 228 29 thaliana 673 AAB88424Homo SapiensHuman membrane or secretory3032 99 protein clone PSEC0197.

673 819294464Arabidopsislong-chain-fatty-acid-CoA581 37 thaliana ligase-like protein 673 81699196Mycobacteriu4-coumarate-coA ligase 326 45 m 1e roe 674 817022969Homo SapienscDNA FLJ10747 fis, clone3378 99 NT2RP3001799.

674 AAY86211Homo sapiensNuclear transport protein1432 87 clone hfb066 protein se uenee.

674 8110439560Homo SapienseDNA: FLJ23007 6s, clone?03 1D0 LNG00451.

675 817021968Homa SapienscDNA FLJI0111 fis, clone2753 99 HEMBA1002696.

675 8114017768Mus musculusFLJ101ll 2214 92 675 110440211Homo so cDNA: FLJ23501 fis, 2160 90 iens clone LNG02837.

676 817021968Homo SapienscDNA FLJ10211 fis, clone2728 98 HEMBA 1002696.

676 8114017768Mus musculusFLJI0111 2200 90 676 a110440211Homo so cDNA: FLJ23501 fis, 2337 92 iens clone LNG02837.

677 17019869Homo SapienscDNA FLJ20036 fis, clone2834 100 COL00219.

677 8112723779LactococcusUNTCN(JWN PROTEIN 306 35 lactis subsp.
lactis 677 818885520Streptococcusstreptococcal hemagglutinin297 29 ' gordonii 678 110437508Homo SapienscDNA: FLJ21415 fis, 1129 100 clone COL04030.

679 813135314Homo sapienschromosome 7q22 sequence,1226 100 complete se uence.

679 816752287Homa SapiensNovel human gene mapping390 43 to chomosome X, SEQ AccessionSpecies Description Score ID

NO: No. Identit 679 AAB28327 Homo sapiensHuman secreted protein 265 100 BLAST search protein SEQ ID NO: 111.

680 gi3135314Homo Sapienschromosome 7q22 sequence,I 199 95 complete sequence.

680 gi6752287Homo sapiensNovel human gene mapping363 41 to chomosome X.

680 AAB28327 Homo SapiensHuman secreted protein 265 100 BLAST search rotein SEQ ID NO: 111.

681 gi10439089Homo SapienscDNA: FLJ22626 fis, clone2120 99 HSI06109.

681 gi11044557Homo SapiensHuman DNA sequence from 1185 64 clone RP11-424I5 on chromosome 6 Contains a novel gene, STSs, GSSs and a CpG island, complete sequence.

681 gi12654241Homo sapiens, Similar to splicing 949 98 factor, arginine/serine-rich 4 (SRp75), clone MGC:5283, mRNA, complete cds.

682 gi14042277Homo SapienscDNA FLJ14626 fis, clone3029 99 NT2RP2000288.

682 gi7022410Homo SapienscDNA FLJ10402 fis, clone2279 100 NT2RM4000457.

682 ~i6841196Homo SapiensHSPC273 1086 100 683 gi2815604Homo SapiensOpa-interacting protein 1364 100 OIP2 mRNA, partial cds.

683 AAB63276 Homo sapiensHuman breast cancer associated839 96 antigen protein sequence SEQ
ID N0:638.

683 AAB63406 Homo SapiensHuman breast cancer associated839 96 antigen protein sequence SEQ
ID N0:768.

684 AAB07228 Homo SapiensHuman prostate cancer 4325 100 predisposing protein HPC2.

684 AAY99850 Homo SapiensHuman sul hatase G. 4315 99 684 gi10946497Pan ELAC2 4283 98 troglodytes 685 gi7688979Homo Sapiensuncharacterized bone 895 I 00 marrow protein 685 AAB36580 Homo SapiensHuman FLEXHT-2 protein 895 100 . sequence SEQ ID N0:2.

685 AAB34771 Homo SapiensHuman secreted protein 888 99 fragment encoded by DNA clone vq23 1.

686 gi10438990Homo sa cDNA: FLJ22559 fis, clone1897 100 iens HSI01591.

686 gi8954034ArabidopsisFIOK1.17 162 31 thaliana 687 gi7020674Homo SapienscDNA FLJ20515 fis, clone2027 100 KAT09889.

687 AAB20331 Homo SapiensHuman protein phosphatase1472 92 and kinase protein-10.

687 AAB73226 Homo SapiensHuman phosphatase NP 576 83 060746 h.

688 gi6688145Homo SapiensmRNA for NICE-3 protein,1019 100 clone 1023 j 12.

688 14689120 Homo SapiensHSPC012 717 93 688 g112655055Homo Sapiens, DKF'ZP586G1722 protein,717 93 clone MGC:1147, mRNA, complete cds.

689 g17023701Homo SapienscDNA FLJ11190 fis, clone1317 100 PLACE1007583.

690 g16469703MycobacteriuDipZ 203 31 m tuberculosis 691 g113676779Mus musculusArkadia 1939 93 691 g113752369Gallus ring fin er protein 1888 91 gallus 691 g113752371Xenopus ring finger-H2 protein 1537 76 _ laevis 692 g1458255 Homo SapiensHuman X-linked PEST-containing2849 99 ~

SEQ AccessionSpecies Description Score ID

NO: No. Identit trans otter (XPCT trene, exon 6.

I 692 g1458247 Homo SapiensHuman X-linked PEST-containing2766 99 trans otter (XPCT) mRNA, partial cds.

692 g12944356Mus musculusX-linked PEST-containing2249 88 transporter 693 g114042736Homo SapienscDNA FLJ14888 ~s, clone 2034 99 PLACE 1003 762.

693 g16841178Homo SapiensHSPC264 2019 99 694 g17023413Hotno cDNA FLJ11012 fis, clone2377 99 Sapiens PLACE1003190, weakly similar to SOFI

PROTEIN.

694 g114042745Homo SapienscDNA FLJ14893 fis, clone2377 99 PLACE1004302, weakly similar to SOF1 PROTEIN.

694 g15912184Homo SapiensmRNA; cDNA DKFZp564O04631159 99 (from clone DKFZ 56400463);
partial cds.

695 g17022931Homo sapienscDNA FLJ10724 fis, clone2683 99 NT2RP3001176.

695 g1 14198202Mus musculusSimilar to melanoma antigen2126 82 recognized by T cells 2 695 g14826524Homo SapiensNovel human gene mapping982 92 to chomosome 1.

696 g17022990Homo SapienscDNA FLJ10761 fis, clone2119 99.

NT2RP3004669, weakly similar to ETHANOLAMINE KINASE (EC

2.7.1.82).

696 g19998952Homo Sapiensethanolamine kinase (EICI1)930 56 mRNA, complete cds.

696 g1532128 Drosophilaethanolamine kinase 525 45 melanoaaster 697 gil 86774Homo SapiensHuman Kruppel related 986 38 zinc finger rotein (HTF10) mRNA, complete cds.

697 g15441615Canis zinc finger protein 988 37 familiaris 697 138032 Homo sa Human ZNF43 mRNA. 947 36 iens 698 g1 13537202Homo SapiensPC-LKC mRNA for protocadherin2877 100 LKC, complete cds.

698 g17020017Homo sapienscDNA FLJ20124 f7s, clone2862 99 COL06056.

698 AAY01410 Homo sapiensSecreted protein encoded963 100 by gene 28 clone HE9ND43.

699 g17688977Homo sapiensuncharacterized bone 888 100 marrow protein 699 AAY86515 Homo SapiensHuman gene 71-encoded 888 100 protein fragment, SEQ ID N0:430.

699 g17018421Homo SapiensmRNA; cDNA DKFZp564J157 880 99 (from clone DKFZ 564J157).

700 17209307 Homo sa mRNA for FLJ00003 protein,1102 100 iens partial cds.

700 g114276857Homo SapiensPC2-glutamine-rich-associated429 93 protein (PCQAP) mRNA, complete cds.

700 g114043091Homo Sapiens, clone IMAGE:3350171, 429 93 mRNA, partial cds.

701 a17020678Homo sa cDNA FLJ20517 fis, clone2821 99 iens KAT10235.

701 g110177966Arabidopsisuridine kinase-like protein1068 44 thaliana 701 g1496728 Saccharomyceuridine kinase 775 37 s cerevisiae 702 g17022789Homo SapienscDNA FLJ10634 fis, clone1512 100 NT2RP2005654, weakly similar to CYSTEINE STRING PROTEIN.

702 AAB67446 Homo sa Amino acid sequence of 1512 100 iens a human SEQ AccessionSpecies Description Score ID

NO: No. Identit cha erone poly epode.

702 AAG01952 Homo SapiensHuman secreted protein, 422 98 SEQ ID NO:

6033.

703 gi7021321Homo sapiensGemin4 mRNA, complete 5481 99 cds.

703 gi10945430Homo Sapienschromosome 17 clone PAC 5452 100 P579 HC90, HC71 AC, HC6 and HC56 genes, complete sequence.

703 gi7018412Homo sapiensmRNA; cDNA DIGFZp434D1744359 99 (from clone DICFZp434D174).

704 gi9964287Homo sapienshypertension-related 1129 100 calcium-regulated gene mRNA, complete cds.

704 gi10434820Homo sapienscDNA FLJ13008 fis, clone1129 100 NT2RP3000456.

704 gi12803673Homo Sapiens, HT002 protein; hypertension-related1129 100 calcium-regulated gene, clone MGC:3418, mRNA, com lete cds.

705 gi10435947Homo SapienscDNA FLJ13814 fis, clone3588 99 THYR01000368.

705 gi3878402Caenorhabditissimilar to C2 domain 300 25 elegans 705 gi3002479LeishmaniaL3162.1 198 25 major 706 gi11907998Homo SapiensBCL-6 coreprescor (BOOR)2449 100 mRNA, complete cds; alternatively spliced.

706 gi7020277Homo SapienscDNA FLJ20285 fis, clone1131 99 HEP04260.

706 gi10432606Homo SapienscDNA FLJ 11362 fis, clone458 50 HEMBA 1000244.

707 gi7768662Homo sapiensC4ST mRNA for chondroitin1870 100 sulfotranseferase, complete cds.

707 gi8925966Homo Sapienschondroitin 4-O-sulfotransferase1870 100 mRNA, complete cds.

707 gi7572958Homo SapiensmRNA for chondroitin-4-SUlfotransferase1865 99 (C4ST gene).

708 gi2731561Homo SapiensATP receptor subunit 2167 96 (P2X5) mRNA, complete cds.

708 gi1552522Homo SapiensHuman ionotropic ATP 2131 96 receptor P2X5a mRNA, complete cds.

708 gi3387944Homo Sapiensclone 24793 ionotropic 1608 99 ATP receptor P2XSb mRNA, complete cds.

709 17021105 Homo SapienscDNA FLJ20793 fis, clone1587 100 COL00343.

709 g17206854Caenorhabditiscontains similarity to 435 29 Pfam family elegans PF00085 (Thioredoxins), Score 113, E=9.6e-33, N=1 709 g113775331Caenorhabditiscontains similarity to 297 28 Pfam family elegans PF00085 (Thioredoxin), score=320.7, E=1.8e-95, N=3 710 AAY04315 Homo sapiensHuman secreted protein 385 100 encoded by gene 23. ' 710 AAB12155 Homo SapiensHydrophobic domain protein385 100 isolated from HT-1080 cells.

71 g113624098Homo Sapienscervical cancer 1 protooncogene520 100 I protein 40 mRNA, complete cds.

711 g112653253Homo Sapiens, DKFZP586A011 protein, 520 100 clone MGC:8483, mRNA, complete cds.

711 g14886473Homo SapiensmRNA; cDNA DKFZp586A011 520 100 (from clone DKFZp586A011);
partial cds.

712 g1927415 Homo sapiensH.sapiens mRNA for carnitine3209 98 acet ltransferase.

712 g113879380Mus musculusSimilar to carnitine 3010 90 ~ acetyltransferase SEQ AccessionSpecies Description Score ID

NO: No. Identit 712 Qi758632 Mus musculuscarnitine acetyltransferase2967 89 ? 13 gi9437507Homo sa TERA 1198 100 iens 713 110439906Homo SapienscDNA: FLJ23279 fis, cloneI 198 100 HEP06870.

713 g112652565Homo Sapiens, TERA protein, clone 1198 100 MGC:1093, mRNA, complete cds.

714 g17023336Homo SapienscDNA FLJ10964 fis, clone1196 100 PLACE 1000748.

714 g114198104Homo sapiens, clone MGC:16981, mRNA,1196 100 complete cds.

714 g17023823Homo SapienscDNA FLJ11269 fis, clone661 100 PLACE1009190.

715 AAB67579 Homo SapiensAmino acid sequence of 2740 100 a human hydrolytic enzyme HYENZI
1.

715 g17020019Homo SapienscDNA FLJ20125 fis, clone1973 99 COL06152.

715 g113527857Drosophilapol polyprotein 298 26 melanogaster 716 g12218077Homo Sapiensaravin mRNA, complete 8920 99 cds.

716 AAW53863 Homo SapiensHuman gravin polypeptide.8868 99 716 AAB15380 Homo SapiensHuman gravin protein 8868 99 sequence.

717 g17021891Homo sapienscDNA FLJ10060 fis, clone2306 99 HEMBA1001407.

717 g110433215Homo SapienscDNA FLJI 1856 fis, clone1959 86 HEMBA 1006789.

717 g114042890Homo SapienscDNA FLJ14982 fis, clone1959 86 Y79AA1000258.

718 g16224691Homo sapiensNa+/sulfate cotransporter3271 100 SUT-I (SUT-1) mRNA, complete cds.

718 AAB36158 Homo SapiensNovel human transporter 3268 99 protein SEQ ID

NO: 2.

718 AAB23625 Homo SapiensHuman secreted protein 3268 99 SEQ ID NO: 50.

719 17020123 Homo SapienscDNA FLJ20189 fis, clone1264 99 COLF0657.

719 g114328904Homo Sapiensfetal globin-inducing 1262 99 factor (FGIF) mRNA, complete cds.

719 AAB71861 Homo SapiensHuman FGIF. 1262 99 720 g16690250Homo Sapiensclone HQ0659 PR00659 926 100 mRNA, complete cds.

720 g112654109Homo sapiens, PR00659 protein, clone926 100 MGC:4888, mRNA, complete cds.

721 g1608025 Homo SapiensHuman ankyrin G (ANI<-3)580 32 mRNA, complete cds.

721 g13885972Rattus 270 kDa ankyrin G isoform575 32 norvegicus 721 g1178646 Homo SapiensHuman erythroid ankyrin 609 35 mRNA, complete cds.

722 g17020915Homo sapienscDNA FLJ20666 fis, clone1229 96 ICAlA608.

722 g13169096Schizosaccharpossible pre-mRNA processing420 37 by omyces similarity to yeast prp39 pornbe 722 g11458279Caenorhabditiscontains similarity to 252 29 TPR domains elegans 723 17020729 Homo SapienscDNA FLJ20548 fis, clone2200 100 ICAT11542.

723 g110434720Homo SapienscDNA FLJ12942 fis, clone2200 100 NT2RP2005139, weakly similar to 2-SA-DEPENDENT RIBONUCLEASE
(EC

3.1.26.-).

723 g111967781Homo SapiensANKRD2 gene for skeletal174 30 muscle ankyrin repeat, exons 1-9.

724 g110433458Homo SapienscDNA FLJ12068 fis, clone2903 99 HEMBB 1002329.

724 110434339Homo SapienscDNA FLJ12690 fis, clone2898 99 SEQ AccessionSpecies Description Score /"
ID

NO: No. Identit NT2RM4002567.

724 gi10436665Homo sapienscDNA FLJ14252 fis, clone2167 99 OVARC 1001341.

725 gi10434638Homo sapienscDNA FLJ12889 fis, clone3026 100 NT2RP2004098, wealely similar to ADENYLATE CYCLASE (EC
4.6.1.1).

725 gi14250313Homo sapiens, clone MGC:16864, mRNA,3026 100 complete cds.

725 gi7020356Homo sapienscDNA FLJ20331 fis, clone1914 99 HEP10410.

726 AAY13947 Homo SapiensHuman transmembrane protein,655 100 HP 10495.

726 AAY07878 Homo sapienSHuman secreted protein 655 100 fragment encoded from gene 27.

726 gi6841296Homo sapiensHSPC323 449 85 727 17159733 Homo sapiensmRNA for ETAA16 roteu~. 4318 100 727 AAB 10622Homo SapiensHuman Ewing tumor associated4318 100 antigen protein.

728 17020138 Homo sa cDNA FLJ20199 fis, clone2123 99 iens COLF1162.

728 AAY91948 Homo SapiensHuman cytoskeleton associated1650 99 protein 3 (CYSICP-3).

728 g17020210Homo SapienscDNA FLJ20246 fis, clone1474 99 COLF6458.

729 g113182775Homo SapiensCDAll mRNA, com lete 1495 99 cds.

729 g113937914Homo Sapiens, clone MGC:12519, mRNA,973 97 complete cds.

729 g12257524SchizosaccharHYPOTHETICAL 47.4KD PROTEIN536 42 IN

omyces SHP1-SEC17INTERGENIC
ombe REGION

730 g17020242Homo SapienscDNA FLJ20265 fis, clone2813 99 COLF9334.

730 g114042159Homo SapienscDNA FLJ14559 fis, clone2812 99 NT2RM2001998.

730 g1499005 SaccharomyceHRC830 128 32 s cerevisiae 731 g17022375Homo SapienscDNA FLJ10379 fis, clone3182 99 NT2RM2002014.

731 g114010930Homo SapiensBAC clone RPl 1-576F1 1868 100 from 2, complete sequence.

731 g11573555HaemophiluStranscription accessory 691 42 protein (tex) influenzae Rd 732 g110434409Homo SapienscDNA FLJI2737 fis, clone1001 99 NT2RP2000337.

733 g17019597Homo sapiensclone PAC 270M7 chromosome5944 100 21 map 21 q 1 I .2, complete sequence.

733 g17407669Homo Sapienschromosome 21 PAC 30P13 5944 100 map 21 q 11.2, complete sequence, containing gene for nuclear factor RIPI40.

733 g17717256Homo sapienschromosome 21 segment 5944 100 HS21C007.

734 g17021956Homo SapienscDNA FLJ10103 fis, clone1415 100 HEMBA1002495, weakly similar to LIGHT-MEDIATED DEVELOPMENT

PROTEIN DETl.

734 AAB64828 Homo SapiensHuaan secreted protein 869 99 sequence encoded b gene 12 SE
ID NO:l 14.

734 g14038594Lycopersic0ntDETI protein 413 37 esculentum 735 g16752405StreptococcusPspA 137 24 pneumoniae 736 g15080758Homo Sapienschromosome 19, BAC 3311911486 55 (CIT-B-471f3), complete sequence.

736 g1456269 Mus musculuszinc finger protein 30 1478 54 domesticus 'I AccessionSpecies Description Score SEQ
ID

I NO: No. Identit ' gi4567179Homo sapienschromosome 19, BAC 372951281 62 736 (CIT-B-i 21A4), com lete sequence.

737 gi7023220Homo sapienscDNA FLJ10893 fis, clone4557 99 NT2RP4002791.

737 gi14042072Homo SapienscDNA FLJ14507 fis, clone4439 97 NT2RM 1000399.

737 gi7582296Homo SapiensBM-012 1807 99 738 gi11596985Homo Sapienschromosome 14 clone RP11-361H101751 100 map 14q24.3, complete sequence.

738 17020945 Homo sa cDNA FLJ2D689 fis, clone1738 99 iens KAIA2890.

738 g16067151Homo Sapienschromosome 14 BAC 98L12,1159 100 complete sequence.

739 g16941888Homo Sapiensubiquitin-specific processing5638 99 protease (USP25) mRNA, complete cds.

739 AAB31550 Homo SapiensA human ubiquitin specific5638 99 protease (USP).

739 g16693824Homo Sapiensubiquitin-specific protease4022 99 (USP21) mRNA, complete cds.

740 g16693824Homo Sapiensubiquitin-specific protease5465 99 (USP21) mRNA, complete cds.

740 AAB31546 Homo SapiensA human ubiquitin specific5465 99 protease 25 (USP25).

740 AAF24881-Homo sapiensDNA encoding a human 5465 99 ubiquitin aal specific protease 25 (USP25).

741 g17161175Homo SapiensmRNA for 19A24 protein 1726 100 ( I 9A24 gene).

741 g113021810Homo SapiensNIC cell receptor (CS1) 1349 100 mRNA, complete cds.

741 AAB32373 Homo sapiensHuman secreted protein 1349 100 sequence encoded by gene 3 SEQ
ID N0:59.

742 g17023747Homo SapienscDNA FLJ11219 fis, clone2553 100 PLACE I 008122.

742 g17022222Homo SapienscDNA FLJ10287 fis, clone880 97 HEMBB 1001387.

742 AAG01392 Homo SapiensHuman secreted protein, 569 99 SEQ ID NO:

5473.

743 g17023747Homo SapienscDNA FLJ11219 fis, clone2442 97 PLACE 1008122.

743 g17022222Homo sapienScDNA FLJ10287 fis, clone769 89 HEMBB 10013 87.

743 AAG01392 Homo SapiensHuman secreted protein, 569 99 SEQ ID NO:

5473.

744 16434857 Homo sa pallid tnRNA, complete 872 100 iens cds.

744 g113435969Homo Sapiens, pallid (mouse) homolog,872 100 pallidin, clone MGC:4983, mRNA, complete cds.

744 g16456870Mus musculussyntaxin 13-interacting 754 87 protein pallid 745 16841480 Homo sapiensHSPC129 2378 99 745 g16841354Homo SapiensHSPC058 1825 99 745 g17022613Homo SapienscDNA FLJ10523 fis, clone1489 99 NT2RP2000863.

746 g17023644Homo SapienscDNA FLJ11155 fis, clone1826 99 PLACE1006935.

746 AAB 18981Homo SapiensAmino acid sequence of 1000 99 a human transmembrane protein.

746 g113384531Caenorhabditissimilar to C. elegans 680 40 protein T16H12.10 ele ans 747 g113544089Homo Sapiens, clone IMAGE:4053618, 2749 99 mRNA, partial cds.

747 g16007859Chlamydomondynein heavy chain alpha246 30 as reinhardtii SEQ AccessionSpecies Description Score ID

NO: No. Identit 747 gi2065436Schizosacchartealp 227 28 omyces ombe 748 gi6650778Homo sapiensPR01575 297 100 749 gi8926849Homo sapiensmRNA for Pex3p, complete1892 99 cds.

749 gi4092648Homo sapiensmRNA for PEX3 rotein, 1892 99 artial.

749 gi4218426Homo Sapienspex3 gene (joined CDS, 1892 99 promoter and exon 1).
~

750 gi309209 Mus musculusearly B-cell factor 3064 99 750 gi6630994Homo Sapiensearly B-cell transcription3033 98 factor (EBF) mRNA, partial cds.

750 gi7687988Gallus early B-cell factor 3023 97 allus 751 gi10436636Homo SapienscDNA FLJ14228 fis, clone3102 99 NT2RP3004148.

751 gi14278861Homo SapiensPHD zinc finger transcription2127 100 factor mRNA, complete cds.

751 gi12804495Homo Sapiens, clone IMAGE:3356959, 1472 100 mRNA, partial cds.

752 gi6594639Homo Sapiensdynein intermediate chain1773 100 (DNAI1) mRNA, complete cds.

752 gi6635422Homo Sapiensdynein intermediate chain1768 99 (DNAI1) gene, exon 20 and complete cds.

752 gi927637 Anthocidarisdynein intermediate chain961 61 crassis ina 753 gi5924385Rattus ribosomal protein 5271 412 100 norvegicus 753 gi12803647Homo Sapiens, ribosomal protein S27 412 100 (metallopanstimulin 1), clone MGC:3659, mRNA, complete cds.

753 gi1373421Homo SapiensHuman ribosomal protein 412 100 S27 mRNA, complete cds.

754 gi1655432Mus musculusplexin 2 9646 96 754 gi6010215Homo SapiensmRNA for partial OCTlplexin-A26985 99 protein.

754 gi1665757Mus musculusplexin 1 6359 63 755 gi7770189Homo sapiensPR02325 901 100 756 gi7022885Homo SapienscDNA FLJ10697 fis, clone3318 99 NT2RP3000527, weakly similar to ZINC

FINGER PROTEIN 43.

756 gi10434872Homo SapienscDNA FLJ13043 fis, clone957 43 NT2RP3001338, weakly similar to ZINC

FINGER PROTEIN 81.

756 gi38032 Homo SapiensHuman ZNF43 mRNA. 346 25 757 gi14042238Homo SapienscDNA FLJ14604 fis, cloneI 107 93 NT2RP1000363, moderately similar to R.norve icus LL5 mRNA.

757 AAB43723 Homo SapiensHuman cancer associated 647 86 protein se uence SEQ ID NO:1168.

757 gi14044043Homo Sapiens, clone IMAGE:4299555, 467 66 mRNA, partial cds.

758 17106766 Homo sa HSPC188 532 100 iens 758 g112804349Homo Sapiens, clone MGC:4355, mRNA, 529 99 complete cds.

758 g11002516SaccharomyceHghlp 115 27 s cerevisiae 759 g16175593Homo Sapienstranscription factor 4326 99 IIIC90 mRNA, complete cds.

760 g17023345Homo SapienscDNA FLJ10970 fis, clone647 99 PLACE1000948.

760 AAG03409 Homo sapiensHuman secreted protein, 239 100 SEQ ID NO:

SEQ AccessionSpecies Description Score ID

NO: No. Identit 7490.

761 gi5441541Canis Ribosomal protein 447 94 familiaris 761 gi304526 Cricetulusribosomal protein S17 447 94 riseus 761 gi10439453Homo SapienscDNA: FLJ22917 fis, clone447 94 KAT06430.

762 16635353 Homo SapiensRU1 (RU1) mRNA, complete4638 99 cds.

762 18100079 Mus musculuspolycomb-group roteins 4176 88 762 g18100077Rattus polycomb-group protein 4152 88 norvegicus 763 g112804681Homo sapiens, S100 calcium-binding 479 100 protein, beta (neural), clone MGC:1323, mRNA, complete cds.

763 g1337730 Homo sapiensHuman 5100 protein beta-subunit479 100 gene, exon 3.

763 g1404769 MuS musculuSS100 beta protein 473 98 764 17106782 Homo SapiensHSPC196 617 98 764 17106786 Homo SapiensHSPC 198 617 98 764. AAW74871 Homo SapiensHuman secreted protein 617 98 encoded by gene 143 clone HBMDM46.

765 g13851206Homo Sapienschromosome 19, costnid 1282 100 F19847, complete sequence.

765 g113276629Homo SapiensmRNA; cDNA DICFZp761D221815 35 (from clone DKFZp761D221);
complete cds.

765 g15701573Caenorhabditissimilar to S. pombe phosphoprotein430 33 elegans (GB:X86179) 766 17020238 Homo SapienscDNA FLJ20262 fis, clone1393 100 COLF7748.

766 g112653607Homo Sapiens, clone IMAGE:3162218, 1019 98 mRNA, partial cds.

766 AAY86358 Homo sapiensHuman gene I I-encoded 996 95 protein fra ment, SEQ ID N0:273.

767 g12588619Homo SapiensBAC clone CTB-104F4 from2037 100 7q21-q22, complete sequence.

767 g11707507Homo SapiensH.sapiens mRNA for mitochondrial2037 100 transcription termination factor.

767 g112654289Homo Sapiens, transcription termination2033 99 factor, mitochondrial, clone MGC:5000, mRNA, com lete cds.

768 g11314373Homo sapiensHuman aquaporin-5 (AQPS)1336 100 gene, exon 4 and complete cds.

768 g1664760 Rattus aquaporin-5 1245 91 norvegicus 768 g14894460Mus musculusaquaporin 5 1235 91 769 g113097624Homo Sapiens, clone IMAGE:3608084, 1093 100 mRNA, partial cds.

769 g110438279Homo sapienscDNA: FLJ22029 fis, clone615 60 HEP08661.

769 g113325154Homo Sapiens, clone IMAGE:3635709, 609 45 mRNA, partial cds.

770 AAB48789 Homo sapiensHuman prostate cancer-predisposing2878 100 protein, CA7 CG04.

770 g111321424Mus musculusRal-A exchange factor 2073 96 RaIGPS2 770 g17637906Homo SapiensRal guanine nucleotide 1224 70 exchange factor RaIGPS 1A mRNA, com fete cds.

771 g113623239Homo Sapiens, Similar to SGC32445 1080 99 protein, clone MGC:10610, mRNA, complete cds.

771 g17547035Homo SapiensSGC32445 protein (SGC32445)687 100 mRNA, com lete cds.

771 g110434977Homo SapienscDNA FLJ13110 fis, clone519 64 ~ ~ ~
NT2RP3002549, moderately similar to SEQ AccessionSpecies Description Score '%
ID

NO: No. Identit HYPOTHETICAL 26.6 KD
PROTEIN

T19C3.4 IN CHROMOSOME
III.

772 gi13939858Homo sa RITA 2614 100 iens 772 gi 10048470Homo SapiensC2H2-like zinc finger 2614 100 protein (ZNF463) mRNA, com lete cds.

772 gi8575775Homo SapiensKR.AB zinc finger protein2614 100 (RITA) mRNA, complete cds.

773 gi12654989Homo sapiens, clone MGC:5623, mRNA, 2300 100 complete cds.

773 gi3329425Homo sapienshuntingtin interacting 963 100 protein HYPE

mRNA, partial cds.

773 gi429189 Haemophilussurface protein 152 41 somnus 774 gi14028017Mesorhizobiuargininosuccinate lyase 199 26 m loti 774 gi2182606RhizobiumY4rH 179 29 Sp.

775 gi3098311Oryctolaguselongation factor 1 A2 2410 100 cuniculus 775 gi8886507Homo Sapienselongation factor 1 A-2 2410 100 (EF1A-2) gene, complete cds.

775 gi 12653327Homo Sapiens, eukaryotic translation2410 100 elongation factor 1 alpha 2, clone MGC:8362, mRNA, complete eds.

776 gi6624095Homo SapiensBAC clone RP11-294L11 2515 97 from 2, com fete se uence.

776 AAY66674 Homo SapiensMembrane-bound protein 2515 97 PR01277.

776 AAB87542 Homo sa Human PR01277. 2515 97 iens 777 gi6049162Homo Sapiensrhabdoid tumor deletion 1732 100 region protein 1 (RTDRI) mRNA, complete cds.

777 gi14290442Homo Sapiens, rhabdoid tumor deletion1732 100 region protein 1, clone MGC:16968, mRNA, complete cds.

778 AAB66071 Homo SapiensHuman INTERCEPT 296. 1787 99 778 AAB 18992Homo SapiensAmino acid sequence of 880 58 a human transmembrane protein.

778 AAB26325 Homo sa Human CASB618 rotein. 880 58 iens 779 gi643656 Rattus synaptotagmin VII 1851 95 norvegicus 779 gi12667446Rattus synaptotagmin VIIs 1851 95 norvegicus 779 ~i6136786Mus musculussynaptota min VII 1842 95 780 gi7020988Homo sapienscDNA FLJ20716 fis, clone1048 100 HEP19742.

780 gi4033606Adiantum Extensin 131 38 capillus-veneris 780 gi169347 Phaseolushydroxyproline-rich glycoprotein130 38 vulgaris 781 gi7020477Homo SapienscDNA FLJ20401 fis, clone1644 96 ICAT00901.

781 gi7022002Homo SapienscDNA FLJ10135 fis, clone590 40 .

HEMBA1003117.

781 gi7022284Horno cDNA FLJ10324 fis, clone590 40 Sapiens NT2RM2000567.

782 gi6808186Homo SapiensmRNA; cDNA DKFZp434D02181322 99 (from clone DKFZp434D0218);
partial cds.

783 gi505544 Homo SapiensH.sapiens mRNA for Zinc-finger1211 99 protein (ZNF TI).

783 AAY58627 Homo SapiensProtein regulating gene 688 50 expression PRGE-20.

783 gi9187356Homo SapiensmRNA full length insert 687 50 cDNA clone SEQ AccessionSpecies Description Score ID

NO: No. Identit EUROIMAGE 2107395.

784 gi8896094Homo SapiensSH3-containing protein 1975 97 mRNA, complete cds.

784 14929591 Homo SapiensCGI-61 protein mRNA, 706 69 complete cds.

784 g18896092Homo SapiensSH3-containing protein 706 69 mRNA, complete cds.

785 a17770175Homo SapiensPR02249 1827 99 785 gil 1527602Homo sapiensmRNA for MCM10 homolog, 1827 99 complete cds.

785 g112053187Homo SapiensmRNA; cDNA DI<FZp434H1521682 99 (from clone DKFZp434H152);
complete cds.

786 g17023364Homo SapienscDNA FLJ10982 fis, clone1413 99 PLACE1001692, moderately similar to S-ACYL FATTY ACID SYNTHASE

THIOESTERASE, MEDIUM
CHAIN

(EC 3.1.2.14 .

786 g17023563Homo sapienscDNA FLJ11106 fis, clone1099 98 PLACE1005763, moderately similar to S-ACYL FATTY ACID SYNTHASE

THIOESTERASE, MEDIUM
CHAIN

(EC 3.1.2.14).

786 g1205326 Rattus S-acyl fatty acid sunthetase807 55 thio ester norve hydrolase, medium chain icus 787 g12599502Homo Sapiensprotocadherin 68 (PCH68)327 43 mRNA, complete eds.

787 AAY24913 Homo SapiensHuman ontherin. 327 43 787 AAY94991 Homo sapiensHuman secreted protein 296 28 vc35_l, SEQ ID

N0:22.

788 g17023688Homo SapienscDNA FLJ11183 fis, clone2260 I00 PLACE1007488, weakly similar to PUTATIVE RHOIRAC GUANINE

NUCLEOTIDE EXCHANGE FACTOR.

788 g13342246Rattus actin-filament binding 725 32 protein Frabin norve icus 788 g1595425 Homo SapiensHuman faciogenital dysplasia759 32 (FGD1) mRNA, complete cds.

789 g16554165Homo Sapiensreceptor protein tyrosine7734 99 phosphatase (RPTP-rho) mRNA, alternatively spliced, complete cds.

789 g113378306Mus musculusbrain RPTPmam4 isoform 7499 97 I

789 g132456 Homo sapiensH.sapiens hR-PTPu gene 4995 64 for protein tyrosine phosphatase.

790 g17020479Homo SapienscDNA FLJ20402 fis, clone2024 99 KAT00919.

790 17770205 Homo SapiensPR02521 1957 97 790 g110241843Mus musculusasdermin 282 29 791 g15262472Homo SapiensmRNA; cDNA DKFZp564J102 1602 100 (from clone DKFZp564J102);
partial cds:

792 g110436457Homo SapienscDNA FLJ14084 fis, clone830 100 HEMBB 1002383.

792 AAY94940 Homo SapiensHuman secreted protein 830 100 clone y162 1 protein sequence SEQ
ID N0:86.

792 AAY57922 Homo SapiensHuman transmembrane protein830 100 HTMPN-46.

793 g17328061Homo SapiensmRNA; cDNA DICFZp761I23122723 100 (from clone DKFZp761I2312);
partial cds.

793 114039825Mus musculusaroma-1 syntrophin 2579 93 793 g18247279Homo SapiensmRNA for synti~ophin 2271 97 4.

794 g16164674Homo sapiensheterogeneous nuclear 730 66 ribonucleoprotein, alternate transcript (RALY) mRNA, SEQ AccessionSpecies Description Score '%
ID

SEQ AccessionSpecies Description Score ID No. Identit NO:

complete cds.

794 gi14250048Homo Sapiens, heterogeneous nuclear 705 53 ribonucleoprotein C (CllC2), clone MGC:14574, mRNA, complete cds.

794 gi13937888Homo sapiens, Similar to heterogeneous704 53 nuclear ribonucleoprotein C, clone MGC:12469, mRNA, complete cds.

795 gi12653905Homo sapiens, Similar to Max dimerization1045 100 protein 3, clone MGC:2383, mRNA, complete cds.

795 AAY93137 Homo sa Human M rotein. 1023 98 iens 795 AAB35713 Homo sapiensHuman Mad3 rotein sequence.1010 97 796 17020704 Homo sa cDNA FLJ20533 fis, clone585 98 iens KAT10931.

797 g17106878Homo SapiensHSPC244 398 98 797 AAY07855 Homo SapiensHuman secreted protein 398 98 fran"~. vent encoded fi-om gene 4.

797 g113274582Mus musculusth mus atro hy-related 383 95 rotein 798 g18886483Gallus FURL 1178 74 gallus 798 g110435877Homo SapienscDNA FLJ13763 fis, clone873 98 PLACE4000089.

798 AAGOl Homo SapiensHuman secreted protein, 561 100 108 SEQ ID NO:
5189.

799 AAY33297 Homo SapiensHurnan membrane spanning,781 100 protein MSP-4.

799 AAB61149 Homo SapiensHuman NOV I 8 protein. 781 100 799 AAB61150 Homo SapiensHuman NOV 19 protein. 781 100 800 g18099348Homo sapienszinc finger protein (ZFP)4066 99 mRNA, complete cds.

800 g12293535Homo Sapienszinc finger protein (ZnF20)1863 49 mRNA, complete cds.

800 1l 1527849Mus musculuszinc finger protein SKAT21323 58 801 g17023523Homo SapienscDNA FLJI 1082 fis, clone2693 99 PLACE1005206.

801 g19558010Leishmaniapossible cDNA flj 11082 134 26 major fis, clone place1005206 802 g16841558Homo sa HSPC168 1502 100 iens 802 g16453346Homo SapiensNovel human gene on chromosome1502 100 . 20.

802 g113542748Mus musculusRIKEN cDNA 3230401D17 1314 86 gene 803 g17020468Homo sa cDNA FLJ20396 fis, clone931 100 iens KAT00561.

803 AAB 18980Homo SapiensAmino acid sequence of 931 100 a human transmembrane protein.

803 AAY91632 Homo SapiensHuman secreted protein 914 98 sequence encoded by gene 25 SEQ
ID N0:305.

804 g16650345Homo Sapiensalpha-catenin-like protein4478 99 VR22 mRNA, complete cds.

804 g1222788 Gallus alpha N-catenin 2765 60 gallus 804 AAR58778 Homo sa Neural al ha-catenin 2765 60 iens rotein.

805 g110434911Homo SapienscDNA FLJ13068 fis, clone587 38 NT2RP3001739, weakly similar to HYPOTHETICAL 72.5 KD
PROTEIN
C2F7.10 IN CHROMOSOME
I.

805 g15912258Homo SapiensmRNA; cDNA DKFZp586K0524190 41 (from clone DICFZp586K0524);
artial cds.

805 g17022673Homo SapienscDNA FLJ10562 fis, clone154 44 NT2RP2002701.

806 g110435877Homo sapienscDNA FLJ13763 fis, clone876 99 PLACE4000089.

806 g18886483Gallus FURL 868 72 gallus 806 AAG01108 Homo SapiensHuman secreted protein, 561 100 SEQ ID NO:
5189.

SEQ AccessionSpecies Description Score ID No. Identit NO:

807 Qi4521254Mus musculuscornichon-like rotein 867 100 807 AAB60464 Homo SapiensHuman cell cycle and 729 81 proliferation rotein CCYPR-12, SEQ
ID N0:12.

807 AAY76218 Homo SapiensHuman secreted protein 716 81 encoded by gene 95.

808 gi7407144Homo Sapiensprotocadherin Fat 2 (FAT2)22667 99 mRNA, complete cds.

808 gi3449286Rattus MEGF1 18806 81 norve icus 808 gi6688786Mus musculusmouse fat 1 cadherin 8928 47 809 gi7407144Homo sapiensprotocadherin Fat 2 (FAT2)19770 99 mRNA, com lete cds.

809 gi3449286Rattus MEGF1 16567 82 norvegicus 809 gi6688786Mus musculusmouse fat 1 cadherin 8928 47 810 gi7020201Homo SapienscDNA FLJ20241 fis, clone2420 100 COLF6335.

810 gi10435321Homo SapienscDNA FLJ13337 fis, clone1279 99 OVARC1001880.

810 gi7020600Homo sapienscDNA FLJ20475 fis, clone634 60 ICAT07206.

811 gi6483290Homo sapiensCDH7 mRNA for cadherin-7,4032 100 complete cds.

811 gi10803408Homo SapiensmRNA for cadherin-7 (CDH73965 98 gene).

811 gi868001 Gallus chicken cadherin-7 3830 93 gallus 812 gi 13276621Homo SapiensmRNA; cDNA DKFZp761 G 1204 97 1913 (from clone DKFZp761G1913).

812 18977983 Musmusculusneuronal interactin factorX699 78 I (NIXI) 812 g110437116Homo SapienscDNA: FLJ21097 fis, clone297 42 CAS03931.

814 g113279269Homo Sapiens, clone IMAGE:3631943, 1480 100 mRNA, partial cds.

814 g16808028Homo SapiensmRNA; cDNA DKFZp76l C029857 100 (from clone DICFZ 761C029);
artial cds.

814 AAW88657 Homo SapiensSecreted protein encoded436 94 by gene 124 clone HPMCJ92.

815 g17959853Homo SapiensPR01966 281 100 816 g17259234Mus musculuscontains transmembrane 718 65 (TM) region 816 AAY94954 Homo SapiensHuman secreted protein 679 58 clone 1w66-1 protein sequence SEQ
ID N0:114.

816 AAB62810 Homo SapiensHuman nervous system 678 61 associated protein NSPRT3 amino acid sequence.

817 g15921144Schizosaccharmipl 1489 48 omyces pombe 817 g1458938 SaccharomyceYhr186cp ~ 469 30 s cerevisiae 817 g19366720Trypanosomapossible t16o11.22 protein.277 45 brucei 819 17020799 Homo sa cDNA FLJ20590 fis, clone727 100 iens KAT09052.

820 17020555 Homo SapienscDNA FLJ20449 fis, clone1857 99 ICAT05575.

820 AAY79269 Homo SapiensHuman testis-specific 1696 99 transcription factor PHELIX.

821 g16482350Homo SapiensCAC-1 mRNA, partial cds.1136 100 821 g113937595Homo Sapiens, Similar to RIKEN cDNA 560 94 gene, clone MGC:2583, mRNA, complete cds.

821 AAY25770 Homo SapiensHuman secreted protein 560 94 encoded from gene 60.

822 g110434608Homo SapienscDNA FLJ12871 fis, clone2023 100 NT2RP2003751.

822 g16093227Homo SapiensmRNA; cDNA DKFZp434I08501607 100 (from clone DKFZ 434I0850);
artial cds.

SEQ AccessionSpecies Description Score /"
ID

NO: No. Identit 822 gi6453452Homo SapiensmRNA; cDNA DI<FZp434L08501607 100 (from clone DKFZp434L0850).

823 AAY13402 Homo SapiensAmino acid sequence of 1079 63 rotein PR0310.

823 AAB I Homo SapiensAmino acid sequence of 1079 63 8988 a human transmembrane protein.

823 AAB80270 Homo sapiensHuman PR0310 protein. 1079 63 824 gi13938181Homo sapiens, clone IMAGE:2905978, 2722 99 mRNA, partial cds.

824 gi6453540Homo SapiensmRNA; cDNA DICFZp434D04282455 99 (from clone DKFZp434D0428);
partial cds.

824 gi10440436Homo SapiensmRNA for FLJ00053 protein,807 100 partial cds.

825 gi7022318Homo SapienscDNA FLJ10346 fis, clone1475 100 NT2RM2001004.

826 gi7110152Mus musculusselenocysteine lyase 1219 80 SCLY

826 gi7022600Homo sapienscDNA FLJ10515 fis, clone592 98 NT2RP2000764, weakly similar to NIFS

PROTEIN.

826 gi9887215Methanosarcincysteine desulfurase 315 43 NifS

a thermophila 827 gi7022560Homo SapienscDNA FLJ10491 fis, clone1266 100 NT2RP2000239.

827 gi7022033Homo SapienscDNA FLJ10156 fis, clone1161 97 HEMBA 1003447.

828 gi8247250Homo SapiensmRNA for neutral sphingomyelinase3489 100 II

(nSMase2 ene).

828 AAB70772 Homo SapiensHuman neutral cerebral 3489 100 sphingomyelinase protein.

828 gi8247281Mus musculusneutral sphingomyelinase3187 91 II

829 17020945 Homo sa cDNA FLJ20689 fis, clone2459 100 iens KAIA2890.

829 g111596985Homo sapienschromosome 14 clone RPl 1819 97 l-361H10 map 14q24.3, complete sequence.

829 g16067151Homo Sapienschromosome 14 BAC 98L12,1153 99 complete sequence.

830 g110039443Homo SapiensNEDLI mRNA forNEDD4-like4335 56 ubiquitin ligase 1, complete cds.

830 AAW93167 Homo SapiensHuman ZGGBP1 protein. 992 47 830 g1 1374782Mus musculuspossible ubiquitin protein1062 50 ligase 831 g17021974Homo sapienscDNA FLJ10115 fis, clone1882 99 HEMBA 1002777.

831 g17021027Homo SapienscDNA FLJ20739 fis, clone1252 98 HEP07341.

831 g15002381Takifugu BAW 776 72 rubri es 832 g17022523Homo SapienscDNA FLJ10469 fis, clone3772 99 NT2RP2000008, weakly similar to ZINC

FINGER PROTEIN 84.

832 g11020145Homo SapiensHuman DNA binding protein1714 48 (HPF2) mRNA, complete cds.

832 g17243633Homo SapiensRB-associated KRAB repressor1653 46 (RBAK) mRNA, complete cds.

833 g16433864Homo sa CLDN12 ene for claudin-12.1295 100 iens 833 g112053057Homo SapiensmRNA; cDNA DICFZp434I18161295 100 (from clone DICFZp434I1816);
complete cds.

833 g19799020Mus musculusclaudin-12 1125 91 834 g1 12053151Homo SapiensmRNA; cDNA DKF'Zp434G03265605 99 (from clone DKFZp434G0326 ;
complete cds.

834 17020102 Homo SapienscDNA FLJ20176 fis, clone1268 88 COL09928.

834 g17023725Homo SapienscDNA FLJl 1205 fis, clone719 100 PLACE 1007843.

835 g17020789Homo SapienscDNA FLJ20583 fis, clone2153 99 KAT09685.

SEQ AccessionSpecies Description Score ID

NO: No. Identit 835 AAG02503 Homo sapiensHuman secreted protein, 423 98 SEQ ID NO:

6584.

835 g114289183Homo sa chac mRNA for chorein, 193 24 iens complete cds.

836 g17022600Homo sapienscDNA FLJ10515 fis, clone1301 100 NT2RP2000764, weakly similar to NIFS

PROTEIN.

836 17110152 Mus musculusselenocysteine lyase 1107 83 . SCLY

836 g113592392CaenorhabditisContains similarity to 468 44 Pfam domain:

elegans PF00266 (aminotran 5), Score=51.6, E-value=5.7e-12, N=1 837 g17274380Homo Sapiensgroup III secreted phospholipase2813 99 mRNA, com lete cds.

837 g14314431Homo SapiensPAC clone RP3-412A9 from596 99 22, com Iete se uence.

837 15627 Apis melliferaphosphalipase A-2 243 41 838 g18331760Homo SapiensX28 region near ALD locus3242 100 containing dual specificity phosphatase 9 (DUSP9), ribosomal protein LlBa (RPLl8a), Ca2+/Calmodulin-dependent protein kinase I (CAMICI), creative transporter (CRTR), CDM protein (CDM), adrenoleukodystrophy protein (ALD), plexin-related protein (PLXB3), muscle-specific serine kinase (MSSK), NAD-isocitrate dehydrogenase (IDH), translocon-associated protein delta (TRAP), and LU1 protein (LU1) genes, complete cds; and CCp pseudogene, complete sequence.

838 g16651019Mus musculussemaphorin cytoplasmic 1583 50 domain-associated protein 3A

838 g16651021Mus musculussemaphorin cytoplasmic 1583 50 domain-associated protein 3B

839 g17023290Homo SapienscDNA FLJ10932 fis, clone718 100 OVARCI 000588.

840 g16094681Homo SapiensPAC clone RP5-1049N15 4804 100 from 7q31.2-7q32, complete sequence.

840 g17264724Homo Sapiensalpha-aminoadipate semialdehyde4804 100 synthase mRNA, complete cds.

840 g14938304Homo SapiensmRNA for lysine-ketoglutarate4799 99 reductaselsaccharopine dehydrogenase, partial CDS.

841 AAY66700 Homo SapiensMembrane-bound protein 1164 95 PR01137.

841 AAB65223 Homo SapiensHuman PR01137 (UNQ575) 1164 95 protein sequence SEQ ID N0:250.

84I AAY50917 Homo SapiensHuman fetal brain cDNA 1023 100 clone vc4_1 derived protein.

842 AAW56477 Homo SapiensAmino acid sequence ofhuman1183 I00 bone morphogenetic rotein-16 (BMP-16).

842 AAY03849 Homo sapiensHuman nodal protein. 1183 100 842 g1296605 Mus musculusnodal 986 84 843 17020399 Homo SapienscDNA FLJ20356 fis, clone5470 100 HEP15821.

843 g110435659Homo SapienscDNA FLJ13605 fis, clone224 44 'PLACE 1 O 10562.

844 g14886471Homo SapiensmRNA; cDNA DKFZp586N0819531 100 (from clone DICFZp586N0819). ' 845 13288470 Homo sa surf5c mRNA, clone 10.9.728 100 iens 845 g13288452Homo SapiensSurf 5 and Surf 6 genes.334 94 845 Qi3288468Homo sa surf5b mRNA, clone L5. 334 94 iens 846 g114149050Drosophilaturtle protein, isoform 1037 32 ~ 4 SEQ AccessionSpecies Description Score ID

NO: No. Tdentit melanoaaster 846 gi14149048Drosophilaturtle protein, isoform 1037 32 melanoaaster 846 gi 14149046Drosophilaturtle protein, isoform 939 34 melano aster 847 gi7021049Homo SapienscDNA FLT20753 fis, clone2930 99 ~ HEP02714.

847 gi9886896Human Orf73 175 20 herpesvirus 847 gi 11037008Human latent nuclear antigen 172 20 herpesvirus 848 gi 12597293Homo sapiensacidic mammalian chitinase2018 100 precursor, mRNA, complete cds.

848 gi6467177Homo sapiensTSA1902-L mRNA for novel2010 99 member of chitinase family, complete cds.

848 gi6467179Homo SapiensTSA1902-S mRNA for novel1725 99 member of chitinase family, complete cds.

849 gi32391 Homo SapiensHuman HOX4C mRNA for 1802 98 a homeobox protein.

849 gi51416 Mus musculusHox-4.4 1591 88 849 Qi4322104Danio homeobox rotein 425 82 rerio 850 gi 1359443Homo SapiensHuman gene for hepatitis2299 99 C-associated microtubular aggregate protein p44, exon 9 and complete cds.

850 AAY05371 Homo SapiensHuman HCMV inducible 2299 99 gene protein, SEQ ID NO 10.

850 gi218576 Pan p44 2242 97 troglodytes 851 gi575494 Homo sapiensMHC class II lymphocyte 437 72 antigen beta-chain (HLA-DPBla) mRNA, complete cds.

851 gi 188479Homo sapiensHuman MHC class II lymphocyte437 72 antigen (HLA-DP) beta chain mRNA, complete cds.

851 gi 14044082Homo Sapiens, Similar to major histocompatibility429 70 complex, class II, DP
beta 1, clone MGC:14112, mRNA, complete cds.

852 gi 181547Homo Sapiensdefensin 6 mRNA, complete318 90 cds.

852 AAR44819 Homo sapiensSequence ofthe gastrointestinal318 90 defensin (GID) peptide calledhuman defensin 6.

852 gi1200182Homo SapiensHuman defensin 6 (HD-G) 314 89 gene, complete cds.

853 gi 13396914Homo SapiensThe gene of C2GnT3 2389 100 853 gi7527464Homo Sapienscore 2 beta-1,6-N- 2389 100 acetylglucosaminyltransferase (C2GnT3) mRNA, complete cds.

853 AAU00037 Homo SapiensHuman C2GnT3. 2389 100 855 tri7959772Homo sapiensPR01483 252 100 856 gi5911169Homo Sapienstransmembrane mucin 12 2914 99 (MUC12) mRNA, artial cds.

856 AAY59290 Homo SapiensHuman MUC12 polypeptide.2914 99 856 gi2589172Rattus mucin Muc3 595 36 norvegicus 857 AAE00508 Homo sa Human 1i ase protein, 1456 100 iens MLip-1.

857 gi56600 Rattus triacylglycerollipase 776 58 norvegicus 857 13108175 Mus musculusancreatic lipase related772 57 protein 1 858 AAY94954 Homo sapiensHuman secreted protein 1112 100 clone 1w66-1 protein sequence SEQ
ID NO:I 14.

~58 g1 10434269Homo sapienscDNA FL.T12650 fis, clone872 100 ~

SEQ AccessionSpecies Description Score ID

NO: No. Identit NT2RM4002054.

858 17259234 Mus musculuscontains transmembrane 660 60 (TM) region 859 g17021851Homo SapienscDNA FLJ10035 fis, clone1589 100 HEMBA 1000919.

859 110440420Homo sa mRNA for FLJ00045 protein,654 89 iens partial cds.

859 AAY99671 Homo sa Human GTPase associated 654 89 iens rotein-22.

860 g17022523Homo sapienscDNA FLJ10469 fis, clone3573 99 NT2RP2000008, weakly similar to ZINC

FINGER PROTEIN 84.

860 g11020145Homo SapiensHuman DNA binding protein1604 48 (HPF2) mRNA, complete cds.

860 g1 12584159Homo Sapienszinc finger protein 268 1542 48 (ZNF268) mRNA, complete cds.

861 16539434 Homo SapiensSPRl mRNA, complete cds.808 100 861 g16523547Volvox hydroxyproline-rich glycoprotein185 39 carteri DZ-f. nagariensisHRGP

861 g1904359 Beta vulgarischitinase 1 185 41 862 g17021924Horno cDNA FLJ10081 fis, clone2742 100 Sapiens HEMBA 1002018.

862 g110435862Homo SapienscDNA FLJ13751 fis, clone2687 99 PLACE3000339, weakly similar to PRECURSOR (EC 3.2.1.3).

862 g111275988Homo Sapienstestis development protein2454 99 PRTD mRNA, com lete cds.

863 g17019913Homo sapienscDNA FLJ20060 fis, clone1830 100 COL01358.

863 g110434817Homo SapienscDNA FLJ13006 fis, clone1823 .99 NT2RP3000449.

863 g110434659Homo SapienscDNA FLJ12902 fis, clone1724 99 NT2RP2004347.

864 g17329718Homo SapiensNovel human gene mapping11682 99 to chomosome 1.

864 g17022765Homo sapienscDNA FLJ10619 fis, clone3153 99 NT2RP2005472.

864 g114388939Homo Sapienschorea-acanthocytosis 462 30 (CHAC) mRNA, complete cds.

865 g128971 Homo sapiensH.sapiens mRNA for autoantigen3813 100 NOR-90.

865 g1509241 Homo SapiensHuman mRNA for upstream 2661 78 binding factor (hUBF).

865 AAB44430 Homo sapiensHuman lung tumour-specific2649 78 antigen encoded by cDNA

866 113445482Homo SapiensHP43.8KD mRNA, complete 282 47 cds.

866 g110434108Homo SapienscDNA FLJ12552 fis, clone219 36 NT2RM4000712, moderately similar to Homo Sapiens ubiquitin hydrolyzing enzyme I (UBHl) mRNA.

866 g110436670Homo SapienscDNA FLJ14256 fis, clone219 36 PLACE1000007, weakly similar to PROBABLE UBIQUITIN CARBOXYL-TERMINAL HYDROLASE R10E11.3 (EC 3.1.2.15).

867 AAB73229 Homo SapiensHuman phos hatase MTMR7 743 57 h.

867 g15901814DrosophilaBcDNA.GH04637 503 48 melanogaster 867 g17020021Homo sa cDNA FLJ20126 fis, clone697 73 iens COL06160.

868 g17959801Homo SapiensPRO0800 392 100 869 g112654971Homo Sapiens, calcium-regulated heat-stable417 97 protein ' (24kD), clone MGC:5586, mRNA, SEQ AccessionSpecies Description Score ID

NO: No. Identit com lete cds.

869 gi13097198Homo sapiens, calcium-regulated heat-stable417 97 protein (24kD), clone MGC:5235, mRNA, com lete cds.

869 AAW61023 Homo SapiensHuman RNA binding protein.417 97 870 Qi6650832Homo SapiensPR02086 243 100 871 gi2217942Rattus glycoprotein specific 1802 97 UDP-norvegicusglucuronyltransferase 871 gi8051678Homo Sapienshu-GIcAT-P mRNA for 1757 99 glucuronyltransferase, complete cds.

871 gi4519214Rattus UDP-glucuronyltransferase-S760 50 norveaicus 872 gi14286288Homo Sapiens, Similar to RIKEN cDNA 715 100 gene, clone MGC:2734, mRNA, complete cds.

872 113529665Mus musculusRIKEN cDNA 2010004P11 706 98 gene 872 g12565364Musca Sex-lethal protein 134 33 domestica 873 g1190406 Homo SapiensHuman profilaggrin gene 6301 99 exons 1-3, 5' end.

873 g1190396 Homo SapiensHuman profda grin gene, 5133 99 3' end.

873 g1190404 Homo sapiensHuman profdaggrin mRNA, 3696 89 3' end.

874 g1791002 Homo SapiensARSD ene, complete CDS. 1761 99 874 g16651286Homo Sapiensarylsulfatase D beta l 756 99 (ARSD) mRNA, complete cds.

874 g1791004 Homo sapiensARSE ene, complete CDS. 947 58 875 g113097675Homo sapiens, Similar to uncharacterized612 96 hypothalamus protein HCDASE, clone MGC:1171, mRNA, complete cds.

875 AAY87599 Homo SapiensHuman fatty acid beta-oxidation612 96 enzyme HUFA-2.

875 AAG03352 Homo SapiensHuman secreted protein, 591 100 SEQ ID NO:

7433.

876 g16180180Homo Sapienstranscription factor 908 I 00 IGHM enhancer 3, JM11 protein, JM4 protein, JM5 protein, T54 protein, JM10 protein, differentiation-dependent protein, triple LIM domain protein 6, and synaptophysin genes, complete cds;
and L-type calcium channel alpha-1 subunit gene, partial cds, complete sequence.

876 g13114826Homo sapiensmRNA for JM4 protein, 908 100 complete CDS

(clone IMAGE 546750 and LLNLc110F1857Q7 (RZPD
Berlin)).

876 g17673612Mus musculusDXImx39e protein 831 91 877 g113543663Homo Sapiens, ubiquitin-conjugating 805 100 enzyme E2D 1 (homologous to yeast UBC4/5), clone MGC:14673, mRNA, complete cds.

877 g1460810 Homo SapiensH.sapiens UBCHS mRNA 805 100 for ubiquitin con'u ating enzyme.

877 g14868140Homo sapiensubiquitin-conjugating 747 91 enzyme HBUCE1 mRNA, com fete cds.

878 17020915 Homo sapienscDNA FLJ20666 fis, clone1288 100 KAIA608.

878 g13169096Schizosaccharpossible pre-mRNA processing279 33 by omyces similarity to yeast prp39 pombe 878 g110177721Arabidopsisgene id:MPL12.20-- 146 22 thaliana 879 17020681 Homo sapienscDNA FLJ20519 fis, clone891 100 KAT10365.

879 AAY87267 Homo SapiensHuman signal peptide 824 95 ~ containing protein SEQ AccessionSpecies Description Score ID

NO: No. Identit HSPP-44 SEQ ID N0:44.

879 AAB65245 Homo SapiensHuman PR01104 (LJNQ547) 824 95 protein sequence SEQ ID NO:297.

880 16560622 Homo SapiensPR00611 501 100 881 AAB57079 Homo SapiensHuman prostate cancer 668 100 antigen protein sequence SEQ ID N0:1657.

881 AAY99372 Homo sapiensHuman PR01430 (L1NQ736) 668 100 amino acid sequence SEQ ID NO:I
16.

881 AAB88356 Homo sapiensHuman membrane or secretory661 99 protein clone PSEC0082.

882 g11381181Oryctolagusubiquitin-conjugating 663 100 enzyme E2-32k cuniculus 882 g113436071Homo Sapiens, clone MGC:10481, mRNA,663 100 complete cds.

882 g17020506Homo SapienscDNA FLJ20419 fis, clone658 99 ICAT02435.

883 g11381181Oryctolagusubiquitin-conjugating 1265 99 enzyme E2-32k cuniculus 883 g113436071Homo sapiens, clone MGC:10481, mRNA,1265 99 complete cds.

883 a17020506Homo SapienscDNA FLJ20419 fis, clone1256 98 KAT02435.

884 g11381181Oryctolagusubiquitin-conjugating 383 97 enzyme E2-32k cuniculus 884 g113436071Homo Sapiens, clone MGC:10481, mRNA,383 97 complete cds.

884 17020506 Homo SapienscDNA FLJ20419 fis, clone383 97 KAT02435.

885 g114424536Homo Sapiens, Similar to septin 6, 2183 99 clone MGC:16619, mRNA, complete cds.

885 g15689158Mus musculusSeptin6 2114 95 885 g17023141Homo SapienscDNA FLJ I 0849 fis, 1840 82 clone NT2RP4001414, highly similar to SEPTIN 2 FIOMOLOG.

886 g114424536Homo Sapiens, Similar to septin 6, 1213 63 clone MGC:16619, mRNA, complete cds.

886 g15689158Mus musculusSeptin6 1162 62 886 g17023141Homo sapienscDNA FLJ10849 fis, clone995 51 NT2RP4001414, highly similar to SEPTIN 2 HOMOLOG.

887 g14309951Homo SapiensBAC clone RP11-121A8 684 100 from 7p14-p13, complete sequence.

887 AAG00417 Homo sapierisHurnan secreted protein,684 100 SEQ ID NO:

4498.

887 g1339159 Homo SapiensHuman T-cell receptor 392 73 germline gamma-chain gene V-region (V3;
subgroup I).

888 g12570015Homo SapiensH.sapiens PAX7 gene, 2756 100 exon 1 (and joined CDS).

888 g12570021Homo SapiensH.sapiens mRNA for paired2756 100 box containing transcription factor, PAX7.

888 g12570014Homo SapiensH.sapiens PAX7 gene, 2735 99 exon 1 (and joined CDS).

SEQ AccessionDescription Results*
ID

NO: No.

445 BL00434 HSF-type DNA-bindingBL00434C 23.85 7.l l 1e-09 domain proteins.

446 PD00066 PROTEIN ZINC-FINGERPD00066 13.92 1.000e-13 METAL-BINDI. PD00066 13.92 2.286e-12 PD00066 13.92 4.522e-11 PD00066 13.92 6.538e-10 PD00066 13.92 7.923e-10 453 PR00037 LACR BACTERIAL PR00037A 12.66 6.786e-09 REGULATORY PROTEIN

HTH SIGNATURE

465 PR00320 G-PROTEIN BETA PR00320C 13.01 6.100e-09 REPEAT SIGNATURE PR00320C 13.01 6.400e-09 PR00320A 16.74 8.683e-09 PR00320B 12.19 9.775e-09 466 DM00215 PROLINE-RICH PROTEINDM00215 19.43 5.881 e-09 470 BL00175 Phosphoglycerate BL00175D 27.67 8.500e-40 mutase 175-227 family phosphohistidineBL00175C 23.75 S.OOOe-25 proteins. BL00175A 15.42 8.333e-20 BL00175B 12.60 I.OOOe-12 472 BL00315 Dehydrins proteins.BL00315A 9.35 8.119e-09 473 BL00518 Zinc finger, C3HC4BL00518 12.23 4.000e-1 type I 44-53 (RING finger), roteins.

475 PD02448 TRANSCRIPTION PD02448A 9.37 4.293e-09 PROTEIN DNA-BINDIN.

477 PR00625 DNAJ PROTEIN FAMILYPR00625A 12.84 8.500e-19 SIGNATURE PR00625B 13.48 3.204e-15 478 PD02102 SUBUNIT E V-ATPASEPD02102A 16.74 5.853e-10 VACUOLAR ATP

SYNTHASE HYDROL.

479 BL00018 EF-hand calcium-bindingBL00018 7.41 4.706e-11 domain roteins.

480 PR00501 ICELCH REPEAT PR00501A 8.25 9.182e-09 SIGNATURE

483 PR00878 CHOLINESTERASE PR00878F 5.37 5.179e-12 SIGNATURE

484 BL00378 Hexokinases proteins.BL00378C 16.14 1.000e-40 BL00378E 22.92 1.000e-40 BL00378C 16.14 3.520e-40 BL00378E 22.92 3.382e-36 BL00378B 14.23 5.333e-35 BL00378B 14.23 8.953e-28 BL00378A 19.01 1.346e-22 BL00378F 8 ~7 2.688e-17 BL00378D 10.94 6.294e-17 BL00378D 10.94 S.SOOe-16 BL00378F 8:Z7 9.609e-13 BL00378A 19.01 3.017e-12 485 BL00028 Zinc forger, C2H2BL00028 16.07 2.688e-15 type, 352-369 domain proteins. BL00028 16.07 4.375e-15 BL00028 16.07 4.176e-14 BL00028 16.07 8.412e-14 BL00028 16.07 9.471e-14 BL00028 16.07 1.450e-13 BL00028 16.07 2.350e-13 BL00028 16.07 4.150e-13 BL00028 16.07 5.050e-13 BL00028 16.07 1.783e-12 SEQ AccessionDescription Results' ID

NO: No.

BL00028 16.07 3.348e-12 BL00028 16.07 5.304e-12 BL00028 16.07 5.304e-12 BL00028 16.07 4.808e-11 BL00028 16.07 7.000e-10 .486 BL00301 GTP-binding elongationBL00301B 20.09 1.429e-26 factors proteins.BL00301A 12.41 6.400e-15 487 PD00301 PROTEIN REPEAT PD00301B 5.49 7.600e-12 MUSCLE CALCIUM-BI.

489 BL00227 Tubulin subunits BL00227B 19.29 1.000e-40 alpha, beta, 52-107 and gamma proteins.BL00227C 25.48 l .000e-40 BL00227D 18.46 1.000e-40 BL00227F 21.16 1.000e-40 BL00227E 24.15 6.727e-36 BL00227A 24.55 2.125e-33 490 BL00479 Phorbol esters BL00479B 12.57 6.625e-09 diacylglycerol binding domain roteins.

491 BL00479 Phorbol esters BL00479B 12.57 6.625e-09 diacylglycerol binding domain proteins.

492 BL00107 Protein kinases BL00107A 18.39 5.500e-19 ATP-binding 138-169 region proteins. BL00107B 13.31 1.000e-16 493 BL50002 Src homology 3 BL50002A 14.19 S.OOOe-15 (SH3) 392-411 domain proteins BL50002B 15.18 2.500e-09 profile. 430-444 494 PR00049 WILM'S TUMOUR PR00049D 0.00 6.949e-09 PROTEIN SIGNATURE

497 BL00914 Syntaxin / epimorphinBL00914 24.91 6.172e-09 family proteins.

498 PD00066 PROTEIN ZINC-FINGERPD00066 I3.92 8.200e-16 METAL-BINDI. PD00066 13.92 4.462e-15 PD00066 13.92 8.615e-15 PD00066 13.92 5?OOe-14 PD00066 13.92 3.000e-13 500 PF00780 Domain found in PF00780I 14.69 7.863e-09 NIKI-like 293 X23 kinases, mouse citron and yeast ROM.

501 BL00518 Zinc finger, C3HC4BL00518 12.23 7.333e-09 type 279-288 (RING fin er), proteins:

502 DM01418 352 FIBRILLAR DM01418A 20.83 2.050e-23 COLLAGEN CARBOXYL-DM01418B 22.51 5.895e-21 TERMINAL. DM01418C 20.48 8.571e-18 508 BL01052 Calponin family BL01052B 15.31 1.000e-09 repeat 131-157 proteins.

512 BL01310 ATP1G1 / PLM / BL01310 14.74 7.107e-36 family proteins.

515 DM00475 w LOW TRANSPOSASEDM00475B 12.12 6.019e-09 SAPA 12K.

516 BL00636 Nt-dnaJ domain BL00636A 8.07 5.865e-11 proteins. 64-81 519 PR00625 DNAJ PROTEIN FAMILYPR00625A 12.84 2.019e-14 SIGNATURE PR00625B 13.48 5.714e-11 520 BL00216 Su ar traps ort BL00216B 27.64 6.400e-10 roteins. 92-142 523 BL01033 Globins rofile. BL01033B 13.81 1.000e-15 526 BL50002 Src homology 3 BL50002B 15.18 4.750e-12 (SH3) 1075-1089 domain roteins rofile.

531 PR00249 SECRETIN-LIKE PR00249G 15.72 8.892e-10 SUPERFAMILY PR00249C 17.08 6.609e-09 SIGNATURE

532 BL00528 Ribosomal proteinBL00528D 27.17 8.012e-09 S4e 341-395 proteins.

SEQ AccessionDescription Results ID

NO: No.

534 PR00194 TROPOMYOSIN PR00194C 6.38 1.900e-35 SIGNATURE PR00194E 8.74 1.000e-30 PR00194D 9.57 8.714e-27 PR00194B 10.24 2.800e-25 PR00194A 7.86 5.500e-22 535 PR00194 TROPOMYOSIN PR00194C 6.38 1.900e-35 SIGNATURE PR00194E 8.74 1.000e-30 PR00194B 10.24 2.800e-25 PR00194D 9.57 1.900e-23 PR00194A 7.86 5.500e-22 538 PR00019 LEUCINE-RICH REPEATPR00019A 1 l .19 5.050e-11 SIGNATURE

541 BL00540 Ferritin iron-bindingBL00540A 15.06 1.000e-40 regions 32-73 proteins. BL00540B 18.82 1.000e-40 BL00540C 13.00 7.750e-14 546 PR00153 CYCLOPHILIN PR00153E 9.10 2.385e-15 PEPTIDYL-PROLYL
CIS-TRANS ISOMERASE

SIGNATURE

548 BL00115 Eulcaryotic RNA BL00115Z 3.12 8.213e-09 polymerase 63-112 II heptapeptide repeat roteins.

549 BL01282 BIR repeat proteins.BL01282B 30.49 2.373e-12 551 BL00570 Bacterial ring BL00570B 19.03 9.357e-09 hydroxylating 277-309 dioxygenases alpha-subunit signa.

553 PD01427 TRANSFERASE PD01427B 22.45 7.000e-1 METHYLTRANSFERASE

BI.

554 PR00048 C2H2-TYPE ZINC PR00048A 10.52 7.632e-1 SIGNATURE

555 PD02637 SERUM PD02637A 14.26 1.000e-40 PARAOXONASE/ARYLESPD02637G 13.82 1.000e-40 TERASE P. PD02637D 13.69 6.053e-36 PD02637B 10.33 8.875e-34 PD02637E 1 I .92 8.200e-28 PD02637C 7.53 3.520e-27 PD02637F 15.62 9.438e-26 556 DM00892 3 RETROVIRAL DM00892C 23.55 2.768e-16 PROTEINASE.

557 BL00039 DEAD-box subfamilyBL00039D 21.67 5.179e-36 dependent helicasesBL00039A 18.44 7.955e-29 proteins. 15-54 BL00039C 15.63 1.300e-16 BL00039B 19.19 2.465e-12 558 PR00507 N12 CLASS N6 ADENINE-PR00507B 14.16 8.932e-09 SPECIFIC DNA

METHYLTRANSFERASE

SIGNATURE

559 BL00383 Tyrosine specificBL00383E 10.35 8.683e-12 protein 242-253 hos hatases roteins.

566 PD00066 PROTEIN ZINC-FINGERPD00066 13.92 5.500e-13 METAL-BINDI.

572 BL01160 Kinesin light BL01160B 19.54 4.432e-09 chain repeat 76-130 roteins.

573 BL00422 Granins proteins.BL00422C 16.18 4.638e-10 574 PR00319 BETA G-PROTEIN PR00319A 15.27 7.911 e-10 (TRANSDUCIN) PR00319A 15.27 2.180e-09 SIGNATURE

577 BL00269 Mammalian defensinsBL00269C 16.52 6.786e-26 proteins. BL00269A 8.53 2.607e-20 SEQ AccessionDescription Results' ID

NO: No.

19.17 5.500e-17 35-64 578' PD02327 GLYCOPROTEIN PD02327B 19.84 2.241e-1 ANTIGEN PRECURSOR

IMMUNOGLO.

579 BL00596 High potential BL00596B 13.07 9.743e-09 iron-sulfur 273-285 proteins.

580 BL00915 PhosphatidylinositolBL00915C 22.43 8.147e-32 3- and 1015-1054 4-kinases proteins.BL00915D 27.02 9 ? 17e-27 BL00915B 22.78 3.382e-25 BL00915A 10.09 5.500e-10 584 BL00038 Myc-type, 'helix-loop-helix'BL00038B 16.97 7.488e-09 dimerization domain proteins.

585 BL00795 Involucrin roteins.BL00795C 17.06 9.200e-09 586 BL00710 PhosphoglucomutaseBL00710 12.98 9.100e-17 and 159-174 phosphomannomutase phosphoserine si na.

587 BL00518 Zinc finger, C3HC4BL00518 12.23 5.714e-10 type 34-43 (RING finger), roteins.

588 PR00326 GTP1/OBG GTP-BINDINGPR00326A 8.75 5.979e-14 PROTEIN FAMILY

S IGNATURE

591 BL00548 Ribosomal proteinBL00548 20.58 7.000e-19 proteins.

592 BL00478 LIM domain proteins.BL00478B 14.79 1.250e-12 BL00478B 14.79 6.000e-12 BL00478B 14.79 2.400e-1 l 624-639 594 PR00109 TYROSINE KINASE PR00109B 12.27 3.681e-13 CATALYTIC DOMAIN

SIGNATURE

596 PR00049 WILM'S TUMOUR PR00049D 0.00 9.063e-12 PROTEIN SIGNATUREPR00049D 0.00 8.286e-10 PR00049D 0.00 9.000e-10 PR00049D 0.00 9.429e-10 599 BL00232 Cadherins extracellularBL00232B 32.79 4.750e-40 repeat proteins BL00232A 27.72 3.793e-22 domain 48-81 proteins. BL00232B 32.79 1.257e-16 BL00232C 10.65 5.935e-14 BL00232D 16.25 3.368e-13 BL00232B 32.79 3.512e-11 600 DM00215 PROLINE-RICH PROTEINDM00215 19_43 9.695e-09 601 PF00583 AcetyltransferasePF00583B 10.18 9.100e-10 (GNAT) 120-130 family.

602 PR00326 GTP1/OBG GTP-BINDINGPR00326A 8.75 5.950e-11 PROTEIN FAMILY

SIGNATURE

604 BL00319 Amyloidogenic BL00319C 17.12 6.000e-10 glycoprotein 136-170 extracellular domain proteins.

607 BL00239 Receptor tyrosineBL00239F 28.15 4.717e-25 kinase 477-522 class II proteins.BL00239E 17.14 5.897e-23 BL00239C 18.75 7.600e-17 608 PD01066 PROTEIN ZINC FINGERPD01066 19.43 3.357e-32 ZINC-FINGER METAL-BINDING NU.

609 PR00449 TRANSFORMING PR00449A 13.20 4.808e-10 PROTEIN P21 RAS PR00449D 10.79 5.636e-09 SIGNATURE

610 PF00791 Domain present PF00791 C 20.98 2.412e-09 ~ in ZO-1 and 1-40 SEQ ID AccessionDescription Results''=

NO: No.

UncS-like netrin rece tors.

612 PR00109 TYROSINE KINASE PR00109B 12.27 9.234e-13 CATALYTIC DOMAIN

SIGNATURE

613 BL00678 Trp-Asp (WD) repeatBL00678 9.67 1.600e-10 proteins proteins.BL00678 9.67 5.737e-09 9.67 8.105e-09 146-157 BL00678 9.67 8.105e-09 276-287 G 15 PR00334 HMW KININOGEN PR00334B 8.69 5.230e-10 SIGNATURE PR00334B 8.69 1.771 e-09 PR00334B 8.69 2.886e-09 PR00334B 8.69 8.200e-09 617 DM00215 PROLINE-RICH PROTEINDM00215 19.43 5.881e-09 3.

618 PF00084 Sushi domain proteinsPF00084B 9.45 7.188e-10 (SCR 539-551 repeat proteins. PF00084B 9.45 7.300e-09 619 PR00169 POTASSIUM CHANNELPR00169A 16.77 4.316e-09 SIGNATURE

621 BL00845 CAP-Gly domain BL00845 16.43 1.900e-25 proteins. 321-346 BL00845 16.43 9.325e-22 622 BL01002 Translationally BLO l 002D 18.24 4.706e-26 controlled 143-171 tumor protein. BLO 1002C 21.97 6.143e-26 BL01002A 1;.19 1.360e-24 BL01002B 7.39 3.118e-14 624 PR00049 WILM'S TUMOUR PR00049D 0.00 8.857e-10 PROTEIN SIGNATURE

627 PR00011 TYPE TII EGF-LACEPR0001 1A 14.06 4.822e-09 SIGNATURE

629 PF00930 Dipeptidyl peptidasePF00930I I 5.96 S.OOOe-15 (DPP IV) N-terminalPF00930J 8.78 6.045e-12 re ion. 708-729 630 PF00930 Dipeptidyl peptidasePF009301 15.96 S.OOOe-15 (DPP IV) N-terminalPF00930J 8.78 6.045e-12 region. 650-671 631 BL00303 S-100lICaBP type BL00303B 26.15 1.844e-10 calcium 365-402 bindin protein.

632 BL00114 Phosphoribosyl BL00114A 17.22 1.000e-40 pyrophosphate BL00114B 15.90 I.OOOe-40 synthetase 107-153 proteins. BL001 I 4D 21.45 1.000e-40 BL00114C 18.22 2.895e-34 BL00114E 14.48 3.647e-25 635 BL00870 Chaperonins clpABBL00870F 8.73 4.833e-36 proteins. BL00870G 8.07 6.553e-27 BL00870E 17.62 3.333e-16 639 BL00633 Bromodomain proteins.BL00633B 13.82 9.775e-13 BL00633B 13.82 4.75.0e-11 641 BL00299 Ubi uitin domain BL00299 28.84 7.962e-17 proteins. 47-99 642 PD02102 SUBUNIT E V-ATPASEPD02102A 16.74 4.176e-10 VACUOLAR ATP

SYNTHASE HYDROL.

643 PD02080 T-CELL GLYCOPROTEINPD02080D 15.22 6.557e-09 ALPHA PRE.

644 BL01245 RIO1/ZK632.3/MJ0444BL01245F 18.75 7.805e-14 family proteins.

646 BL00469 Nucleoside diphosphateBL00469 22.22 1.000e-40 kinases roteins.

649 PR00217 43 KD POSTSYNAPTICPR00217C 10.91 5.945e-09 PROTEIN SIGNATURE

651 PR00326 GTPIIOBG GTP-BINDINGPR00326A 8.75 7.600e-11 PROTEIN FAMILY

SIGNATURE

SEQ ID AccessionDescription Results''' NO: No.

652 DM00215 PROLINE-RICH PROTEINDM002I5 19.43 8.322e-09 3.

653 PF01298 Transferrin bindingPF01298C 15.13 1.000e-08 protein. 413-440 658 PR00443 G-PROTEIN ALPHA PR00443A 15.16 9.451e-09 SUBUNIT GROUP

SIGNATURE

659 BL00518 Zinc finger, C3HC4BL00518 12.23 5.714e-10 type 34-43 (RING finger), proteins.

663 BL00466 TFIIS zinc ribbonBL00466 25.88 I .000e-32 domain 294-331 roteins.

664 PD00567 PROTEIN RNA-BINDINGPD00567B 18.23 3.172e-10 RNA REPEAT HYD.

665 BL00030 Eukaryotic RNA-bindingBL00030A 14.39 7.882e-11 region RNP-1 proteins.

669 PR00124 ATP SYNTHASE C PR00124A 8.81 8.347e-11 SUBUNIT SIGNATURE

670 PD01234 PROTEIN NUCLEAR PD01234B 15.53 2.500e-10 BROMODOMAIN TRAMS.

671 BL00466 TFI1S zinc ribbonBL00466 25.88 1.000e-32 domain 219-256 proteins.

672 BL01282 BIR repeat proteins.BL01282B 30.49 2.068e-12 673 BL00455 Putative AMP-bindingBL00455 13.31 4.176e-14 domain proteins.

674 BL01160 Kinesin light BL01160B 19.54 8_703e-10 chain repeat 407-461 proteins. BL01160B 19.54 2.373e-09 675 BL00518 Zinc finger, C3HC4BL00518 12.23 5.286e-1 type 0 326-335 (RING finger), proteins.

676 BL00518 Zinc finger, C3HC4BL00518 12.23 5.286e-10 type 335-344 (RING finger), proteins.

682 PR00761 BINDIN PRECURSOR PR00761E 14.32 4.789e-09 SIGNATURE

691 BL00415 S na sins roteins.BL00415Q 2.23 2.885e-09 692 PR00211 GLUTELIN SIGNATUREPR00211B 0.86 6.167e-09 694 PR00320 G-PROTEIN BETA PR00320C 13.01 7.300e-09 REPEAT SIGNATURE

696 PD02952 ICINASE TRANSFERASEPD02952C 15.76 5.701 e-16 CHOLINE PROTEIN PD02952B 15.57 7.242e-11 MULTIGENE FAMI. PD02952A 11.84 9.625e-09 697 PD00066 PROTEIN ZINC-FINGERPD00066 13.92 7.231e-15 METAL-BINDI. PD00066 13.92 5.800e-14 PD0D066 13.92 1.000e-11 PDOD066 13.92 5.696e-11 PD00066 13.92 2.500e-09 698 PR00205 CADHERIN SIGNATUREPR00205B 11.39 6.571 e-13 699 PR00049 WILM'S TUMOUR PR00049D 0.00 4.966e-09 PROTEIN SIGNATUREPR00049D 0.00 9.237e-09 701 PR00988 URIDINE ICINASE PR00988A 6.39 6.600e-15 SIGNATURE PR00988C I3.64 5.605e-13 PR00988E 8.27 8.393e-13 PR00988D 5.95 8.250e-11 PR00988F 12.23 9.820e-11 PR00988B 11.60 2.317e-10 702 PR00625 DNAJ PROTEIN FAMILYPR00625A 12.84 1.804e-13 SIGNATURE PR00625B 13.48 5.821e-13 706 PF00023 Ank repeat proteins.PF00023A 16.03 2.286e-09 708 BL01212 ATP P2X receptorsBL01212A 34.89 1.000e-40 proteins. 43-96 BL01212E 24.87 1.000e-40 BL01212D 11.42 6.700e-25 BL01212G 11.86 2.800e-24 BL01212B 19.25 3.571e-21 SEQ AccessionDescription Resultsx ID

NO: No.

BL01212C 8.4D 1.214e-14 BL01212F 10.12 4.774e-14 709 BL00194 Thioredoxin familyBL00194 12.16 3.455e-17 proteins. 45-58 712 BL00439 Acyltransferases BL00439F 26.22 1.000e-40 ChoActase 418-471 / COT / CPT familyBL00439E 19.05 2.440e-24 proteins. BL00439B 16.82 I.OOOe-20 BL00439H 18.24 4.600e-20 BL00439A 9.40 1.237e-15 BL00439D 13.11 4.545e-15 BL00439C 13.53 1.730e-11 BL00439G 13.40 9.719e-11 716 BL00412 Neuromodulin (GAP-43)BL00412D 16.54 8.990e-09 proteins.

718 BL01271 Sodiumaulfate BL01271D 25.26 5.979e-32 symporter 537-592 family proteins. BL01271A 8.06 6.250e-18 BL01271C 13.62 7.750e-17 BL01271B 12.D2 1.563e-16 719 PF00023 Ank repeat proteins.PF00023B 14.20 2.500e-10 PF00023A 16.03 4.000e-10 721 PF00023 Ank repeat proteins.PF00023A 16.03 1.750e-10 PF00023B 14.20 5.500e-09 PF00023A 16.03 8.714e-09 725 PR00019 LEUCINE-RICH REPEATPR00019B 11.36 1.500e-11 SIGNATURE PR00019A 11.19 2.800e=11 PR00019A 1 I .19 5.050e-11 PR00019B 11.36 3.520e-09 PR00019B I 136 4.6DOe-09 PR00019B 11.36 5.320e-09 PR00019A I 1.19 6.000e-09 PR00019B 11.36 8.200e-09 PR00019B 11.36 9.640e-09 731 PR00681 RIBOSOMAL PROTEINPRD0681I 8.81 9.897e-09 SIGNATURE

736 PD01066 PROTEIN ZINC FINGERPD01066 19.43 9.581e-31 ZINC-FLNGER METAL-BINDING NU.

739 BL00972 Ubiquitin carboxyl-terminalBLD0972A 11.93 1.587e-13 hydrolases familyBL00972D 22.55 8.826e-11 2 proteins. 590-615 740 BL00972 Ubiquitin carboxyl-terminalBL00972A 11.93 1.587e-13 hydrolases familyBLOD972D 22.55 8.826e-11 2 roteins. 590-615 741 DM01688 2 POLY-IG RECEPTOR.DM01688G 16.45 6.936e-10 747 PF00646 F-box domain roteins.PF00646A 14.37 6.625e-09 753 BL01168 Ribosomal proteinBLOI 168 15.74 1.000e-40 S27e 20-75 proteins.

756 PD00066 PROTEIN ZINC-FINGERPD00066 13.92 6.885e-10 METAL-BINDI.

757 PD00301 PROTEIN REPEAT PDOD301B 5.49 7.231e-09 MUSCLE CALCIUM-BI.

761 BL00712 Ribosomal proteinBL00712B 12.56 1.000e-40 Sl7e 28-66 proteins. BL00712A 6.23 8.855e-19 762 PF00878 Cation-independentPF00878T 17.51 3.818e-09 mannose-6-phosphate rece torre eat roteins.

763 BL00303 S-100/ICaBP type BL00303A 21.77 9.526e-31 calcium 3-40 bindin protein. BL00303B 26.15 5.737e-30 766 BL00018 EF-hand calcium-bindingBL00018 7.41 6.087e-09 domain proteins.

768 BL00221 MIP family proteins.BL00221D 12.33 6.143e-19 BL00221C 13.36 1.000e-14 BL00221E 8.47 3.739e-13 SEQ AccessionDescription Resultsr ID

NO: No.

BL00221B 10.22 1.750e-12 BL00221A 6.39 5.200e-12 769 PF00992 Troponin. PF00992A 16.67 8.859e-10 770 BL00720 Guanine-nucleotideBL00720B 16.57 8.297e-15 dissociation stimulators CDC25 family sign.

77I PR00883 HIGH MOBILITY PR00883A 6.49 8.920e-09 LIKE NUCLEAR

PROTEIN SIGNATURE

772 PD01066 PROTEIN ZINC FINGERPD01066 19.43 6.786e-32 ZINC-FINGER METAL-BINDING NU.

775 BL00301 GTP-binding elongationBL00301B 20.09 5.500e-31 factors proteins.BL00301C 11.73 8.200e-15 BL00301A 12.41 3.842e-13 ?76 PR00453 VON WILLEBRAND PR00453A 12.79 4.892e-12 FACTOR TYPE A PR00453B 14.65 1.614e-10 DOMAIN SIGNATURE PR00453A 12.79 3.152e-10 779 PR00399 SYNAPTOTAGMIN PR00399A 9.52 1.730e-13 SIGNATURE PR00399B 14.27 2.059e-13 PR00399C 12.82 7.324e-12 PR00399D 14.48 3.930e-l PR00399B 14.27 1.915e-09 780 BL00115 Eukaryotic RNA BL00115Z 3.12 8.395e-10 polymerase 123-172 II heptapeptide BL001 I5Z 3.12 4.375e-09 repeat 137-186 proteins.

783 PD00066 PROTEIN ZINC-FINGERPD00066 13.92 8.800e-14 METAL-BINDI. PD00066 13.92 8.800e-14 PD00066 13.92 5.286e-12 PD00066 13.92 8.269e-10 786 PF00975 Thioesterase domainPF00975B 10.82 2.688e-12 proteins.

788 DM01970 0 kw ZK632.12 DM01970B 8.60 9.833e-16 ENDOSOMAL III.

789 BL00740 MAM domain proteins.BL00740B 19.76 5.378e-12 BL00740C 15.93 4.000e-11 793 PD00289 PROTEIN SH3 DOMAINPD00289 9.97 9.500e-12 REPEAT PRESYNA.

795 BL00038 Myc-type, 'helix-loop-helix'BL00038A 13.61 3.400e-09 dimerization domain_ proteins.

800 PD01066 PROTEIN ZINC FINGERPD01066 19.43 5.050e-15 ZINC-FINGER METAL-BINDING NU.

804 BL00663 Vinculin family BL00663G 24.17 1.000e-40 talin- 364-414 binding region BL00663K 21.52 9.816e-40 proteins. 735-790 BL00663I 27.27 4.447e-35 BL00663J 18.16 3.000e-33 BL00663L 20.67 9.118e-27 BL00663F 20.78 2.000e-25 BL00663H 27.09 1.703e-24 BL00663C 22.59 2.853e-23 BL00663B 27.86 4.629e-23 BL00663D 24.77 3.789e-18 BL00663A 11.51 2.350e-15 BL00663E 21.19 9.566e-10 808 PR00010 TYPE II EGF-LIKE PROOOlOC 11.16 7.545e-10 SIGNATURE

809 PR00010 TYPE II EGF-LIKE PROOOIOC 11.16 7.545e-10 SIGNATURE

SEQ AccessionDescription Results ID

NO: No.

810 DM00215 PROLINE-RICH PROTEINDM00215 19.43 2.929e-10 3.

811 PR00205 CADHERIN SIGNATUREPR00205B 11.39 9.182e-15 ~ 243-261 PR00205A 14.73 1.000e-12 PR00205C 13.65 1.783e-12 PR00205B I 1.39 9.294e-1 813 PR00456 RIBOSOMAL PROTEINPR00456E 3.06 5.146e-11 SIGNATURE PR00456E 3.06 5.146e-11 PR00456E 3.06 5.146e-11 PR00456E 3.06 7.938e-10 PR00456E 3.06 7.938e-10 818 BL01071 grpE protein. BL01071A 24.88 8.277e-21 BL01071B 18.21 5.286e-15 826 DM00813 AMINOTRANSFERASESDM00813A 20.30 8.898e-17 CLASS-V PYRIDOXAL-PHOSPHATE

ATTACHMENT SI.

828 BL00415 Synapsins proteins.BL00415P 2.37 9.814e-09 830 PF00632 HECT-domain (ubiquitin-PF00632C 20.66 5.186e-23 transferase). PF00632B 18.45 8.393e-22 831 DM00215 PROLINE-RICH PROTEINDM00215 19.43 9.695e-09 3.

832 PDO1066 PROTEIN ZINC FINGERPD01066 19.43 4.231 e-33 ZINC-FINGER METAL-BINDING NU.

834 BL00120 Lipases, serine BL00120B 11.37 5.846e-09 proteins. 1319-1334 836 DM00813 AMINOTRANSFERASESDM00813A 20.30 8.898e-17 CLASS-V PYRIDOXAL-PHOSPHATE

ATTACHMENT SI.

838 PD00289 PROTEIN SH3 DOMAINPD00289 9.97 8.000e-12 REPEAT PRESYNA.

840 BL00053 Ribosomal proteinBL00053B 14.56 1.000e-08 proteins.

841 PR00970 ARGININE ADP- PR00970D 9.96 3.357e-17 . 129-146 RIBOSYLTRANSFERASEPR00970A 17.73 8.600e-17 SIGNATURE PR00970E 11.23 6.464e-15 PR00970B 16.37 2.756e-1 PR00970C 11.05 9.357e-11 842 BL00250 TGF-beta family BL00250A 21.24 7.120e-25 proteins. 114-150 - BL00250B 27.37 4.774e-18 846 BL00240 Receptor tyrosineBL00240B 24.70 7.488e-10 kinase 156-180 class III proteins.

848 BL01095 Chitinases familyBL01095B 10.82 5.500e-14 proteins. BL01095C 10.76 7.207e-10 849 BL00027 'Homeobox' domainBL00027 26.43 2.500e-34 proteins.

850 PR00318 ALPHA G-PROTEIN PR00318A 7.84 7.088e-09 (TRANSDUCIN) SIGNATURE

851 PF00969 Class II histocompatibilityPF00969A 22.07 5.846e-29 antigen, beta PF00969B 9.97 6.211 e-25 domain 56-92 proteins. PF00969C 27.72 7.324e-16 852 BL00269 Mammalian defensinsBL00269B 19.17 6.824e-21 proteins. BL00269A 8.53 6.108e-18 853 PF00777 SialyltransferasePF00777B 29.69 8.767e-10 family. 407-450 856 DM00191 w SPAC8A4.04C DM00191D 13.94 9.083e-10 RESISTANCE

SPAC8A4.05C

DAUNORUBICIN.

SEQ AccessionDescription Results*
ID

NO: No.

857 PR00823 PANCREATIC LIPASEPR00823A 18.01 3.143e-14 SIGNATURE PR00823C 6.88 6_ 164e-12 859 BL00678 Trp-Asp (WD) repeatBL00678 9.67 6.684e-09 roteins roteins.

860 BL00028 Zinc forger, C2H2BL00028 16.07 8.650e-13 type, 425-442 domain proteins. BL00028 16.07 5.696e-12 BL00028 16.07 8.826e-12 BL00028 16.07 7.577e-1 BL00028 16.07 7.577e-1 BL00028 16.07 7.923e-11 BL00028 16.07 8.615e-11 BL00028 16.07 l .G00e-10 BL00028 16.07 2.200e-10 BL00028 16.07 3.400e-10 BL00028 16.07 6.100e-10 BL00028 16.07 7.OOOe-I

BL00028 16.07 8.200e-10 BL00028 16.07 5.114e-09 864 BL01126 Elongation factorBL01126A 18.48 5.01 1e-10 Ts 2637-2680 roteins.

865 BL00353 HMG1/2 proteins. BL00353B I 1.47 1.330e-13 BL00353B 11.47 5.692e-11 866 BL00972 Ubiquitin carboxyl-terminalBL00972A I 1.93 4.600e-18 hydrolases familyBL00972D 22.55 1.947e-13 2 proteins. 576-601 ' BL00972E 20.72 2.038e-1 867 BL00383 Tyrosine specificBL00383E 10.35 2.756e-12 protein 255-266 phosphatases proteins.

872 BL00030 Eukaryotic RNA-bindingBL00030B 7.03 5.737e-09 re ion RNP-1 roteins.

873 BL00303 S-100/ICaBP type BL00303B 26.15 4.405e-19 calcium 50-87 bindin rotein. BL00303A 21.77 8.765e-15 874 BL00523 Sulfatases proteins.BL00523A 13.36 6.500e-I7 BL00523B 8.64 5.909e-15 _ BL00523C 12.64 5.500e-13 BL00523D 9.89 9.438e-11 877 BLOOI83 Ubiquitin-conjugatingBL00183 28.97 1.000e-40 enzymes proteins.

881 PR00081 GLUCOSE/RIBITOL PR00081B 10.38 6.727e-11 DEHYDROGENASE PR00081A 10.53 3.106e-10 FAMILY SIGNATURE

882 BL00183 Ubiquitin-conjugatingBL00183 28.97 1.391e-39 enzymes proteins.

883 BL00183 Ubiquitin-conjugatingBL00183 28.97 1.391e-39 enzymes proteins.

888 BL00027 'Homeobox' domainBL00027 26.43 2.929e-30 proteins.

Results include Accession number, sub type, eMatrix p-value and the position of the signature.

SEQ ID Pfam Model Description E-value Pfam NO: Score 445 Rap GAP Rap/ran-GAP 6.2e-121 415.2 446 zf C2H2 Zinc finger, C2H2 ty 7.4e-65 228.9 a 452 WD40 WD domain, G-beta repeat0.00017 28.4 465 WD40 WD domain, G-beta repeat1.3e-19 78.6 483 COesterase Carboxylesterases 2.1e-128 440.0 484 hexokinase Hexokinase 0 2009.4 485 zf G2H2 Zinc finger, C2H2 type1e-135 464.2 486 GTP EFTU Elongation factor Tu 3.2e-125 424.7 family 487 myosin head Myosin head (motor 1.5e-283 955.3 domain) 488 Glyco transfGlycosyl transferase 4e-12 53.7 8 family 8 489 tubulin Tubulin/FtsZ family 3.2e-293 987.5 492 kinase Eukaryotic rotein kinase7.9e-85 295.2 domain 493 SH3 SH3 domain 1 ~e-18 75.4 497 S ntaxin S ntaxin 0.074 -75.1 498 SCAN SCAN domain 5.4e-67 236.0 499 F-box F-box domain 0.0002 28.
I

501 FHA FHA domain 1.7e-13 58.3 502 Colla en Collagen tri 1e helix 6.5e-197 667.6 re eat (20 co ies) 507 PH PH domain 3e-15 59.5 508 CH Calponin homology (CH)0.0069 16.3 domain 512 ATP I G 1 ATP I G 1 /PLM/MAT8 5.7e-3 1 I
PLM M family I 6.3 516 DnaJ DnaJ domain 1.4e-24 95.1 519 DnaJ DnaJ domain 6.8e-26 99.5 522 Glycos transfGlycosyl transferases 1.2e-13 58.8 523 lobin Globin 4.1 e-38 137.3 526 myosin head Myosin head (motor 0 1057.8 domain) 529 AcetyltransfAcetyltransferase (GNAT)5e-I 1 50.1 family 530 MSP domain MSP (Major sperm protein)1.7e-16 68.2 domain 531 7tm 2 7 transmembrane receptor1.3e-59 211.5 (Secretin family) 534 Tro omyosin Tropomyosin 7e-177 553.3 535 Tro omyosin Tropomyosin 3.1e-173 541.9 538 LRR LeucineRichRe eat 2.9e-23 90.7 539 tRNA-synt tRNA synthetases class7.9e-79 275.3 1b I (W and Y) 540 PAS PAS domain 2.8e-05 24.9 541 ferritin Ferritin 9.9e-116 391.6 546 pro isomeraseCyclophilin type peptidyl-prolyl3.5e-33 117.6 cis-tr 549 KII-domain ICH domain 0.0004 27.1 551 Glyco transfGlycosyl transferase 0.01 -47.7 8 family 8 554 zf C2H2 Zinc fin er, C2H2 type2.6e-22 87.5 555 ArylesteraseArylesterase 2.3e-211 715.6 556 G-patch G-patch domain 2.4e-17 71.1 557 DEAD DEAD/DEAH box helicase8.7e-67 214.2 558 MethyltransfPutative methyltransferase0.0095 -48.4 559 DSPc Dual specificity phosphatase,4.8e-70 246.1 catalytic dom 563 IPPT IPP transferase 6.7e-66 232.4 566 zf C2H2 Zinc fin er, C2H2 ty 2.6e-19 77.6 a 570 RNA_pol_L RNA polymerises L / 0.043 -12.1 13 to 16 kDa subunit 571 Armadillo Armadillo/beta-catenin-like8.6e-33 122.4 se repeat 574 WD40 WD domain, G-beta repeat1.1e-65 231.6 576 PAP2 PAP2 su erfamily 1.2e-19 78.7 577 Defensin Defensin propeptide 3e-25 97.3 propep 578_ i Immunoglobulin domain 3.5e-16 57.2 580 ~ PI3 PI4 kinasePhosphatidylinositol 6.5e-93 322.1 3- and 4-kinase SEQ ID NO: Pfam Model Description E-value Pfam Score 585 GBP Guanylate-binding protein,43e-16S 548.2 N-terminal domain 586 PGM PMM_I Phosphoglucomutase/phosphomannom7.6e-06 4.4 utase, alp 587 zf C3HC4 Zinc finger, C3HC4 type1.3e-1 41.9 (RING fin er) I

588 MMR HSRl GTPase of unknown function5.9e-48 172.7 590 zf DHHC DHHC zinc finger domain1.8e-36 134.6 591 Ribosomal Ribosomal protein S3, 1.3e-07 28.0 S3 C C-terminal domai _592 LIM LIM domain 4.4e-27 103.4 594 pkinase Protein kinase domain 3.7e-77 269.7 596 PX PX domain 2.2e-17 71.2 599 Cadherin Cadherin cytoplasrnic 3.3e-88 306.5 C teen re ion 600 FHA FHA domain 3.4e-20 80.5 601 AcetyltransfAcetyltransferase (GNAT)3.2e-17 70.6 family 604 NAP family Nucleosome assembly S.Se-12 46.4 protein (NAP) 605 RhoGAP RhoGAP domain 1e-28 108.9 606 Armadillo Armadillo/beta-catenin-like0.00022 28.0 se repeat 607 pkinase Protein kinase domain 5.9e-77 269.1 608 zf C2H2 Zinc finger, C2H2 type 5.4e-110378.8 609 ras Ras family 1.2e-16 52.8 610 ank Ank repeat 1.6e-08 41.8 612 pkinase Protein kinase domain 1.6e-69 244.3 613 WD40 WD domain, G-beta repeat4.7e-55 196.3 614 UBA UBA/TS-N domain 3.6e-12 53.9 615 Zi ZIP Zinctrans orter 8.1e-59 208.8 618 sushi Sushi domain (SCR repeat)1.3e-58 208.2 619 K_tetra K+ channel tetramerisation1.3e-19 78.6 domain 621 CAP GLY CAP-Gly domain 1.9e-48 174.3 622 TCTP Translationally controlled5.2e-109375.5 tumor protein 628 UQ con Ubiquitin-conjugating 0.0046 -43.3 enzyme 629 DPPIV_N_tennDipeptidyl peptidase 5.1e-07 -82.1 IV (DPP IV) N-termi 630 DPPIV_N_termDipeptidyl peptidase 5.5e-07 -83.2 IV (DPP IV) N-termi 631 efhand EF hand 2.3e-14 61.1 632 PribosyltranPhosphoribosyl transferase4_3e-37 136.7 domain 635 ank Ank re eat 1.8e-25 98.0 636 MHCK EF2 MHCK/EF2 kinase domain 1.2e-12 5.6 kinas family a 637 DUF221 Domain of unknown function1.2e-89 311.2 639 bromodomain Bromodomain 2.2e-29 106.0 641 ubiquitin Ubi uitin family 2.2e-21 81.9 644 RIO1 RTO1/ZK632.31MJ0444 1.1e-07 -14.9 famil 646 NDK Nucleoside diphos hate 1.1e-52 188.4 kinase 649 zf C3HC4 Zinc fin er, C3HC4 t 9.4e-12 42.4 a (RING finger) 651 ABC tran ABC transporter 7.9e-84 291.9 654 CUB CUB domain 3e-30 113.9 655 MHCK_EF2_lcinasMHCIC/EF2 kinase domain2.6e-09 -353 a family 659 zf C3HC4 Zinc finger, C3HC4 type1.3e-11 41.9 (RING finger) 661 UvrD-helicaseUvrD/REP helicase 0.078 9.7 663 TFIIS Transcription factor 2e-22 87.9 S-II (TFIIS) 664 dsrm Double-stranded RNA 4.3e-42 153.3 binding motif 66S rrm RNA recognition motif. 0.002 24.8 669 OTU OTU-like c steine rotease1e-19 78.9 671 TFIIS Transcription factor 2e-22 87.9 S-II (TFIIS) 672 zf C3HC4 Zinc finger, C3HC4 type1.5e-05 22.3 (RING finger) 673 ~ AMP-binding AMP-binding enzyme ~ 1.6e-86 300.9 ~

SEQ ID Pfam Model Description E-value Pfam NO: Score 679 MSP domain MSP (Ma'or sperm rotein)5.4e-18 73.2 domain 680 MSP domain MSP (Major sperm rotein)S.Se-11 49.9 domain 683 RNase PH 3' exoribonuclease family3e-42 153.8 684 lactamase Metallo-beta-lactamase 0.088 -15.6 B superfamily 686 tRNA anti OB-fold nucleic acid 0.031 20.9 bindin domain 690 NHL NHL repeat 8.2e-18 72.6 691 zf C3HC4 Zinc finer, C3HC4 type 6.Ie-09 33.2 (RING fin er) 693 WD40 WD domain, G-beta re 0.025 21.2 eat 694 WD40 WD domain, G-beta re I.le-23 92.1 eat 696 Choline_kinaseCholine/ethanolamine 1.6e-51 184.6 kinase 697 zf C2H2 Zinc fin er, C2H2 t 3.4e-74 259.9 a 698 cadherin Cadherin domain 2.2e-05 3I.3 701 PRK Phosphoribulokinase 1.1e-79 278.1 / Uridine kinase family 702 DnaJ DnaJ domain Se-26 99.9 888 ~ PAX 'Paired box' domain 1.1e-87 304.7 Q ~ ~ ~ H ~ ~ z z z w W w ~~ ~'?~ Nz ~?~
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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

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Claims (28)

WHAT IS CLAIMED IS:
1. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-444, a mature protein coding portion of SEQ ID NO:
1-444, an active domain coding portion of SEQ ID NO: 1-444, and complementary sequences thereof.
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 90% 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 1 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: 1-444
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 SEQ ID NO: 1-444, a mature protein coding portion of SEQ ID NO: 1-444, an active domain coding portion of SEQ ID NO: 1-444, complementary sequences thereof and a polynucleotide sequence hybridizing under stringent conditions to SEQ ID NO: 1-444, 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: 217-432, or 649-864, the mature protein portion thereof, or the active domain thereof.
21. The polypeptide of claim 20 wherein the polypeptide is provided on a polypeptide array.
22. A collection of polynucleotides, wherein the collection comprising the sequence information of at least one of SEQ ID NO: 1-444.
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.
27. A method of treatment comprising administering to a mammalian subject in need thereof a therapeutic amount of a composition comprising a polypeptide of claim 10 or 20 and a pharmaceutically acceptable carrier.
28. A method of treatment comprising administering to a mammalian subject in need thereof a therapeutic amount of a composition comprising an antibody that specifically binds to a polypeptide of claim 10 or 20 and a pharmaceutically acceptable carrier.
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