CA2399776A1 - Novel nucleic acids and polypeptides - Google Patents

Abstract

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

Description

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

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NOVEL NUCLEIC ACIDS AND POLVPEPTIDES
1. TECHNICAL FIELD
The present invention provides novel polynucleotides and proteins encoded by such S polynucleotides, along with uses for these polynucleotides and proteins, for example in therapeutic, diagnostic and research methods.

2. BACKGROUND
Teclimology aimed at the discovery of protein factors (including e.g., cytokines, such as lymphokines, interferons, CSFs, 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 protean (i.e., partial DNAlamino 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 making available large numbers of DNA/amino acid sequences for proteins that are known to have biological activity, for example, by virtue of their secreted nature in the case of leader sequence cloning, by virtue of their cell or tissue source in the case of PCR-based techniques, or by virtue of structural similarity to other genes of known biological activity.
Identified polynucleotide and polypeptide sequences have numerous applications in, for example, diagnostics, forensics, gene mapping; identification of mutations responsible for genetic disorders or other traits, to assess biodiversity, and to produce many other types 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 engineeredto contain such 3 5 polynucleotides and cells genetically engineered to express such polynucleotides.
1.

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: 1-984,1969-2952, 3937-3942 or 3949-3954. The polypeptides sequences are designated SEQ ID NO: 985-1968, 2953-3936, 3943-3948 or 3955-3960. 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 thymine; and N
is any of the four bases. In the amino acids provided in the Sequence Listing, ~ corresponds to the stop codon.
The nucleic acid sequences of the present invention also include, nucleic acid sequences that hybridize to the complement of SEQ ID NO: 1-984,1969-2952, 3937-3942 or 3949-3954 under stringent hybridization conditions; nucleic acid sequences which are allelic variants or species homologues of any of the nucleic acid sequences recited above, or nucleic acid sequences that encode a peptide comprising a specific domain or truncation of the peptides encoded by SEQ ID
NO: 1-984,1969-2952, 3937-3942 or 3949-3954. A polynucleotide comprising a nucleotide sequence having at least 90°~° identity to an identifying sequence of SEQ ID NO: 1-984,1969-2952, 3937-3942 or 3949-3954 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:l-984,1969-2952, 3937-3942 or 3949-3954. The sequence informationcan be a segment of any one of SEQ ID N0:1-984,1969-2952, 3937-3942 or 3949-3954 that uniquely identifies or represents the sequence infomnation of SEQ ID N0:1-984, 1969-2952, 3937-3942 or 3949-3954.
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 is provided on a nucleic acid array to detect the polynucleotide that contains the segment. The array can be designed 3 0 to detect full-match or mismatch to the polynucleotide that contains the segment. The collection can also be provided in a computer-readableformat.
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 3 5 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-readablemedia, 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: l -984,1969-2952, 3937-3942 or 3949-3954 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 par ticularly preferred embodiment, the nucleic acid sequences of SEQ ID NO:l-984,1969-2952, 3937-3942 or 3949-3954 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:1-984, 1969-2952, 3937-3942 or 3949-3954 ; a polynucleotide comprising any of the full length protein coding sequences of SEQ ID NO: l -984,1969-2952, 3937-3942 or 3949-3954; and a polynucleotide comprising any of the nucleotide sequences of the mature protein coding sequences of SEQ ID
NO: l-984,1969-2952, 3937-3942 or 3949-3954. The polynueleotides 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:1-984,1969-2952, 3937-3942 or 3949-3954; (b) a nucleotide sequence encoding any one of the amino 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 any of the proteins recited above; or (e) a polynucleotide that encodes a polypeptide comprising a specific domain or truncation of any of the polypeptides comprising an amino acid sequence set forth in 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: 985-1968, 2953-3936, 3943-3948 or 3955-3960; 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 3Q polynucleotideshaving a nucleotide sequence set forth in SEQ ID NO:l-984, 1969-2952, 3937-3942 or 3949-3954; 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 known to those skilled in the art of molecular biology. These techniques include use as hybridization probes, use as oligomers, or primers, for PCR, use far chramosorne and gene mapping, use in the recombinant production of protein, and use in generation of anti-sense DNA
ox 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 axe 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 andlor 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, fax 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 fox 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 coxiprising contacting the sample with a compound that binds to and forms a complex with the polypeptide under conditions and for a period sufficient to foam the complex and detecting the formation of the complex such that if a complex is formed, the polypeptide is detected.
The invention also provides kits comprising polynucleotide probes and/or monoclonal antibodies, and optionally quantitative standards, for carrying out methods of the invention.
Furthermore, the invention provides methods for evaluating the efficacy of drugs, and monitoring the progress of patients, involved in clinical trials for the treatment of disorders as recited above.
The invention also provides methods for the identification of compounds that modulate (i.e., increase or decrease) the expression or activity of the polynucleotides andlor polypeptides of the invention. Such methods can be utilized, for example, for the identification of compounds that can ameliorate symptoms of disorders as recited herein. Such methods can include, but are not limited to, assays for identifying compounds and other substances that interact with (e.g., bind to) the polypeptides of the invention. The invention provides a method for identifying a compound that binds to the polypeptides of the invention comprising contacting the compound with a polypeptide of the invention in a cell for a time sufficient to form a polypeptide/compoun.d 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 provides 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 Tables 2 and 9); for which they have a signature region (as set forth in Tables 3 and 10); or fox which they have homology to a gene family (as set forth in Tables 4 and 11). If no homology is set forth for a sequence, then the polypeptides and polynucleotides of the present invention are useful for a variety of applications, as described herein, including use in arrays for detection.
4. DETAILED DESCRIPTION OF THE INVENTION
4.1 DEFINITIONS
It must be noted that as used herein and in the appended claims, the singular forms "a", "an" and "the" include plural references unless the context clearly dictates otherwise.
The term "active" refers to those forms of the polypeptide which retain the biologic and/or immunologic activities of any naturally occurring polypeptide.
According to the invention, the terms "biologically active" or "biological activity" refer to a protein or peptide having structural, regulatory or biochemical functions of a naturally occurring molecule.
Likewise "immunologically active" or "immunological activity" refers to the capability of the natural, recombinant or synthetic polypeptide to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.
The term "activated cells" as used in this application are those cells which are engaged in extracellular or intracellular membrane trafficking, including the export of secretory or enzymatic molecules as part of a normal or disease process.
The terms "complementary" or "complementarity" refer to the natural binding of polynucleotides by base pairing. For example, the sequence 5'-AGT-3' binds to the complementary sequence 3'-TCA-5'. Complementarity between two single-stranded molecules may be "partial" such that only 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 e~ciency 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 germ cells (PGCs)" refers to a small population of cells set aside from other cell lineages particularly from the yolk sac, mesenteries, or gonadal ridges during embryogenesis that have the potential to differentiate into germ cells and other cells. PGCs are the source from which GSCs and ES cells are derived The PGCs, the GSCs and the ES cells are capable of self renewal.
Thus these cells not only populate the germ line and give rise to a plurality ofterminallydifferentiated 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 1 S include, but are not limited to, promoters, and promoter modulating sequences (inducible elements). One class of EMFs are nucleic acid fragments which induce the expression of an operably linked ORF in response to a specific regulatory factor or physiological event.
The terms "nucleotide sequence" or "nucleic acid" or "polynucleotide" or "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 guanine 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 NOs:l-20.
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 Sambrook, J. et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY; or Ausubel, F.M. et al., 1989, Current Protocols in Molecular Biology, 3ohn 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: 1-984, 1969-2952, 3937-3942 or 3949-3954. The sequence information can be a segment of any one of SEQ ID NO:l-1-984, 1969-2952, 3937-3942 or 3949-3954 that uniquely identifies or represents the sequence information of that sequence of SEQ ID NO:1-984, 1969-2952, 3937-3942 or 3949-3954. 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 4~° possible twenty-mers exist, there are 300 times more twenty-mers than there are base pairs in a set of human chromosomes. Using the same analysis, the probability for a seventeen-mer to be fully matched in the human genome is approximately 1 in 5. When these segments are used in arrays for expression studies, fifteen-mer segments can be used. The probability that the fifteen-mer is fully matched in the expressed sequences is also approximately one in five because expressed sequences comprise less than approximately 5% of the entire genome sequence.
Similarly, when using sequence information for detecting a single mismatch, a segment can be a twenty-five mer. The probability that the twenty-five mer would appear in a human genome with a single mismatch is calculated by multiplying the probability for a full match (1425) times the s increased probability for mismatch at each nucleotide position (3 x 25). The probability that an eighteen mer with a single mismatch can be detected in an array for expression studies is approximately one in five. The probability that a twenty-mer with a single mismatch can be detected in a human genome is approximately one in five.
The term "open reading frame," ORF, means a series of nucleotide triplets coding for amino acids without any termination codons and is a sequence translatable into protein.
The terms "operably linked" or "operably associated" refer to functionally related nucleic acid sequences. For example, a promoter is operably associated or operably linked with a coding sequence if the promoter controls the transcription of the coding sequence.
While operably linked nucleic acid sequences can be contiguous and in the same reading frame, certain genetic elements e.g. repressor genes are not contiguously linked to the coding sequence but still control transcription/translation of the coding sequence.
The 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 terms "polypeptide" or "peptide" or "amino acid sequence" refer to an oligopeptide, peptide, polypeptide or protein sequence or fragment thereof and to naturally occurring or synthetic molecules. A polypeptide "fragment," "portion," or "segment" is a stretch of amino acid residues of at least about 5 amino acids, preferably at least about 7 amino acids, more preferably at least about 9 amino acids and most preferably at least about 17 or more amino acids. The peptide preferably is not greater than about 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 the initial methionine residue. The methionine residue may be removed from the protein during processing in the cell. The peptide may be produced synthetically or the pxotein 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 S ubiquitination, labeling (e.g., with radionuclides or various enzymes), covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of amino acids such as ornithine, which do not normally occur in human proteins.
The term "variant"(or "analog"} refers to any polypeptide differing from naturally occurring polypeptides by amino acid insertions, deletions, and substitutions, created using, a g., recombinant DNA techniques. Guidance in determining which amino acid residues may be replaced, added or deleted without abolishing activities of interest, may be found by comparing the sequence of the particular polypeptide with that of homologous peptides and minimizing the number of amino acid sequence changes made in regions of high homology (conserved regions) or by replacing amino acids with consensus sequence.
Alternatively, recombinant variants encoding these same or similar polypeptides may be synthesized or selected by making use of the "redundancy" in the genetic code.
Various codon substitutions, such as the silent changes which produce various restriction sites, may be introduced to optimize cloning into a plasmid or viral vector or expression in a particular prokaryotic or eukaryotic system. Mutations in the poiynueleotide 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 off nines, interchain affinities, or degradation/turnover rate.
Preferably, amino acid "substitutions" are the result of replacing one amino acid with another amino acid having similax 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 I to 20 amino acids, more preferably 1 to 10 amino acids. The variation allowed may be experimentally determined by systematically making insertions, deletions, or substitutions of amino acids in a polypeptide molecule using recombinant DNA techniques and assaying the resulting recombinant variants for activity.
Alternatively, where alteration of function is desired, insertions, deletions or non-conservative alterations can be engineered to produce altered polypeptides. Such alterations can, for example, alter one or more of the biological functions or biochemical characteristics of the polypeptides of the invention. For example, such alterations may change polypeptide characteristics such as ligand-binding affinities, interchain affinities, or degradation/turnover rate. Further, such alterations can be selected so as to generate polypeptides that are better suited for expression, scale up and the like in the host cells chosen for expression.
For example, cysteine residues can be deleted or substituted with another amino acid residue in order to eliminate disulfide bridges.
The terms "purified" or "substantially purified" as used herein denotes that the indicated nucleic acid or polypeptide is present in the substantial absence of other biological macromolecules, e.g., polynucleotides, proteins, and the like. In one embodiment, the polynucleotide or polypeptide is purified such that it constitutes at Ieast 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 eukaxyotic expression systems preferably include a leader sequence enabling extracellular secretion of translated protein by a host cell. Alternatively, where recombinant protein is expressed without a leader or transport sequence, it may include an amino terminal methionine residue. This residue may or may not be subsequently cleaved from the expressed recombinant protein to provide a final product.
The term "recombinant expression system" means host cells which\have stably integrated a recombinant transcriptional unit into chromosomal DNA or carry the recombinant transcriptional unit extrachromosomally. Recombinant expression systems as defined herein will express heterologous polypeptides or proteins upon induction of the regulatory elements linked to the DNA segment or synthetic gene to be expressed. This term also means host cells which have stably integrated a recombinant genetic element or elements having a regulatory role in gene expression, for example, promoters or enhancers. Recombinant expression systems as defined herein will express polypeptides or proteins endogenous to the cell upon induction of the regulatory elements linked to the endogenous DNA segment or gene to be expressed. The cells can be prokaryotic or eukaryotic.
The term "secreted" includes a protein that is transported across or through a membrane, including transport as a result of signal sequences in its amino acid sequence when it is expressed in a suitable host cell. "Secreted" proteins include without limitation proteins secreted wholly (e.g., soluble proteins) or partially (e.g., receptors) from the cell in which they are expressed.
"Secreted" proteins also include without limitation proteins that are transported across the membrane of the endoplasmic reticulum. "Secreted" proteins axe 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 SSC10.05% sodium pyrophosphate at 37°C (for 14-base oligonucleotides), 48°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 equivalent sequence is about 0.35 or less).
Such a sequence is said to have 65% sequence identity to the listed sequence.
In one embodiment, a substantially equivalent, e.g., mutant, sequence of the invention varies from a listed sequence by no more than 30% (70% sequence identity); in a variation of this embodiment, by no more than 25% (75% sequence identity); and in a further variation of this embodiment, by no more than 20% (80% sequence identity) and in a further variation of this embodiment, by no more than 10% (90% sequence identity) and in a further variation of this embodiment, by no more that 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% sequence identity, more preferably at least 98% sequence identity and most preferably at~ least 98% idenity. Substantially equivalent nucleotide sequences of the invention can have lower percent sequence identities, taking 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% identity, more preferably at least about 85%
identity, more preferably at least about 90% identity, and most preferably at least about 95%
identity, more preferably at least 98% and most preferably at least about 99% identity. For the purposes of the present invention, sequences having substantially equivalent biological activity and substantially equivalent expression characteristics are considered substantially equivalent.
For the purposes of determining equivalence, truncation of the mature sequence (e.g., via a mutation which creates a 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 virus or viral vector.
As used herein, an "uptake modulating fragment," UMF, means a series of nucleotides which mediate the uptake of a linked DNA fragment into a cell. 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 uptake of a linked marker sequence.
Each of the above terms is meant to encompass all that is described for each, unless the context dictates otherwise.
4.2 NUCLEIC ACIDS OF THE INVENTION
Nucleotide sequences of the invention are set forth in the Sequence Listing.
The isolated polynucleotides of the invention include a polynucleotide comprising the nucleotide sequences of SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954; a polynucleotide encoding any one of the peptide sequences of SEQ ID NO: 985-1968, 2953-3936, 3943-3948 or 3955-3960; and a polynucleotide comprising the nucleotide sequence encoding the mature protein coding sequence of the polypeptides of any one of SEQ ID NO:
985-1968, 2953-3936, 3943-3948 or 3955-3960. 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: 1-984, 1969-2952, or 3949-3954; (b) nucleotide sequences encoding any one of the amino acid sequences set forth in the Sequence Listing as SEQ ID NO: 985-1968, 2953-3936, 3943-3948 or 3955-3960; (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 N0:985-1968, 2953-3936, 3943-3948 or 3955-3960. Domains of interest may depend on the nature of the encoded polypeptide; e.g., domains in receptor-like polypeptides include ligand-binding, extracellular, transmembrane, or cytoplasmic domains, or combinations thereof; domains in immunoglobulin-like proteins include the variable immunoglobulin-like domains; domains in enzyme-like polypeptides include catalytic and substrate binding domains; and domains in ligand polypeptides include receptor-binding domains.
The polynucleotides of the invention include naturally occurring or wholly or 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 andlor 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: 1-984, 1969-2952, 3937-3942 or 3949-3954 can be obtained by screening appropriate cDNA or genomic DNA libraries under suitable hybridization conditions using any of the polynucleotides of SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954 or a portion thereof as a probe. Alternatively, the polynucleotides of SEQ ID
NO: 1-984, 1969-2952, 3937-3942 or 3949-3954 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%, and 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: 1-984, 1969-2952, 3937-3942 or 3949-3954, 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 routiilely determined by comparing the sequence provided SEQ
ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954, a representativefragmentthereof, or a nucleotide sequence at least 90% identical, preferably 95% identical, to SEQ ID NO: 1-984,1969-2952, 3937-3942 or 3949-3954 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: 1-984,1969-2952, 3937-3942 or 3949-3954, can be obtained by searching a database using an algorithm 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 efficient method for producing site-specific changes in a polynucleotide sequence was published by Zoller and Smith, Nucleic Acids Res.
10:6487-6500 (1982). PCR may also be used to create amino acid sequence variants of the novel nucleic acids.
When small amounts of template DNA are used as starting material, primers) that differs slightly in sequence from the corresponding region in the template DNA can generate the desired amino acid variant. PCR amplification results in a population of product DNA
fragments that differ from the polynucleotide template encoding the polypeptide at the position specified by the primer. The product DNA fragments replace the corresponding region in the plasmid and this gives a polynucleotide encoding the desired amino acid variant.
A further technique for generating amino acid variants is the cassette mutagenesis technique described in Wells et al., Gehe 34:315 (1985); and other mutagenesis techniques well known in the art, such as, for example, the techniques in Sambrook et al., supra, and Cu~~ent Protocols ivy Molecular Biology, Ausubel et al. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence may be used in the practice of the invention for the cloning and expression of these novel nucleic acids. Such DNA sequences include those which are capable of hybridizing to the appropriate novel nucleic acid sequence under stringent conditions.
Polynucleotides encoding preferred polypeptide truncations of the invention 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: 1-984, 1969-2952, 3937-3942 or 3949-3954, 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 axe the cDNA inserts of any of the clones identified herein.
A polynucleotide according to the invention can be joined to any of a variety of other nucleotide sequences by well-established recombinant DNA techniques (see Sambrook J et al.
(1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY). Useful nucleotide sequences for joining to polynucleotides include an assortment of vectors, e.g., plasmids, cosmids, lambda phage derivatives, phagemids, and the like, that are well known in the art. Accordingly, the invention also provides a vector including a polynucleotide of the invention and a host cell containing the polynucleotide. In general, the vector contains an origin of replication functional in at least one organism, convenient restriction endonuclease sites, and a selectable marker for the host cell. Vectors according to the invention include expression vectors, replication vectors, probe generation vectors, and sequencing vectors. A host cell according to the invention can be a prokaryotic or eukaryotic cell and can be a unicellular organism or park 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: 1-984, 1969-2952, 3937-3942 or 3949-3954or 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: 1-984, 1969-2952, 3937-3942 or 3949-3954 or a fragment thereof is inserted, in a forward or reverse orientation. In the case of a vector comprising one of the ORFs of the present invention, the vector may further comprise regulatory sequences, including for example, a promoter, operably linked to the ORF. Large numbers of suitable vectors and promoters are known to those of skill in the art and are commercially available for generating the recombinant constructs of the present invention. The following vectors are provided by way of example. Bacterial:
pBs, phagescript, PsiX174, pBluescript SK, pBs KS, pNHBa, pNHl6a, pNHl8a, pNH46a (Stratagene);
pTrc99A, pKK223-3, pKK233-3, pDR540, pRITS (Pharmacia). Eukaryotic: pWLneo, pSV2cat, pOG44, PXTI, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL (Pharmacia).
The isolated polynucleotide of the invention may be operably linked to an expression control sequence such as the pMT2 or pED expression vectors disclosed in Kaufman et al., Nucleic Acids Res. I9, 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. Kaufinan, Methods in Enzymology 185, 537-566 (1990). As defined herein "operably linked" means that the isolated polynucleotide of the invention and an expression control sequence are situated within a vector or cell in such a way that the protein is expressed by a host cell which has been transformed (transfected) with the ligated polynucleotide/expression control sequence.
Promoter regions can be selected from any desired gene using CAT
(chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, and trc. Eukaryotic promoters include CMV immediate early, HSV
thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art.
Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transfornlation of the host cell, e.g., the ampicillin resistance gene of E. coli and S. ce~evisiae TRPl 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 kinase (PGK), a-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein into the periplasmic space or extracellular medium. Optionally, the heterologous sequence can encode a fusion protein including an amino terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product.
Useful expression vectors for bacterial use are constructed by inserting a structural DNA
sequence encoding a desired protein together with suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host. Suitable prokaryotic hosts for transformation include E. coli, Bacillus subtilis, Salmonella typhimurium and various species within the genera Pseudomonas, St~eptomyces, and Staphylococcus, although others may also be employed as a matter of choice.
As a representative but non-limiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (Promega Biotech, Madison, WI, USA).
These pBR322 "backbone" sections are combined with an appropriate promoter and the structural sequence to be expressed. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter is induced or derepressed by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period. Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification.
Polynucleotides of the invention can also be used to induce immune responses.
For example, as described in Fan et al., Nat. Biotech. 17:870-872 (1999), incorporated herein by reference, nucleic acid sequences encoding a polypeptide may be used to generate antibodies against the encoded polypeptide following topical administration of naked plasmid DNA or following injection, and preferably 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
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: 1-984, 1969-2952, 3937-3942 or 3949-3954, 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 entire coding strand, or to only a portion thereof. Nucleic acid molecules encoding fragments, homologs, derivatives and analogs of a protein of any of SEQ ID NO: 985-1968, 2953-3936, 3943-3948 or 3955-3960 or antisense nucleic acids complementary to a nucleic acid sequence of SEQ ID NO:
1-984, 1969-2952, 3937-3942 or 3949-3954 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: 1-984, 1969=2952, 3937-3942 or 3949-3954), antisense nucleic acids of the invention can be designed according to the rules of Watson and Criclc or Hoogsteen base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of a 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 translation start site of a mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 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 of the 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'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-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-diaminopurine.
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 are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a protein according to the invention to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.
In yet another embodiment, the antisense nucleic acid molecule of the invention is an a-anomeric nucleic acid molecule. An a-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual [3-units, the strands run parallel to each other (Gaultier et al. (I987) Nucleic 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) FEBSLett 215: 327-330).
4.4 RIBOZYMES AND PNA MOIETIES
Tn 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 a 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: 1-984, 1969-2952, 3937-3942 or 3949-3954). 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 a SECX-encoding mRNA. See, e.g., Cech et al. U.5. Pat. No. 4,987,071; and Cech et al. U.5. Pat. No. 5,116,742.
Alternatively, SECX mRNA 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 xegion (e.g., promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in taxget cells. See generally, Helene. (1991) Anticancer Drug Des. 6: 569-84; Helene. et al. (1992) Ar~~. N. Y. Acad Sci.
660:27-36; and Maher (1992) Bioassays 14: 807-15.
In various embodiments, the nucleic acids of the invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids (see Hyrup et al.
(1996) Bioorg Med Chem 4: 5-23). As used herein, the terms "peptide nucleic acids" or "PNAs"
refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis of PhlA 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; Perry-O'Keefe (1996), above).
In another embodiment, PNAs of the invention can be modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example, PNA-DNA chimeras can be generated that may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA
recognition enzymes, e.g., RNase H and DNA polymerases, to interact with the DNA portion while the PNA
portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup (1996) above). The synthesis of PNA-DNA chimeras can be performed as described in Hyrup (1996) above and Finn et al. (1996) Nucl Acids Res 24:
3357-63. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry, and modified nucleoside analogs, e.g., 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) Bioorg Med Chern Lett 5: 1119-11124.
In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors ire vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al., 1989, Pr~oc. Natl. Acad. Sci.
U.SA. 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. W089/10134). In addition, oligonucleotides can be modified with hybridization triggered cleavage agents (See, e.g., Krol et al., 1988, BioTechniques 6:958-976) or intercalating agents. (See, e.g., Zon, 1988, Phar~r~c. 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. WO94l12650, PCT International Publication No. W092/20808, and PCT
International Publication No. W091/09955. It is also contemplated that, in addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ado, dhfr, and the multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) andlor intron DNA may be inserted along with the heterologous promoter DNA. If linked to the coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the desired protein coding sequences in the cells.
The host cell can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic host cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the recombinant construct into the host cell can be effected by calcium phosphate transfection, DEAF, dextran mediated transfection, or electroporation (Davis, L. et al., Basic Methods in Molecular Biology (1986)). The host cells containing one of the polynucleotides of the invention, can be used in conventional manners to produce the gene product encoded by the isolated fragment (in the case of an ORF) or can be used to produce a heterologous protein under the control of the EMF.
.Any hostlvector 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 Sf9 cells, as well as prokaryotic host such as E.
coli and B. subtilis.

The most preferred cells are those which do not normally express the particular polypeptide or protein or which expresses the polypeptide or protein at low natural level.
Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al., in Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, New York (1989), the disclosure of which is hereby incorporated by reference.
Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines 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, BHI~, HL-60, U937, HaI~ 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 eukaryotes such as yeast or insects or in prokaryotes such as bacteria. Potentially suitable yeast strains include Saccharomyces cey~evisiae, Schizosaccharomyces ponabe, Kluyveromyces strains, Candida, or any yeast strain capable of expressing heterologous proteins. Potentially suitable bacterial strains include Escherichia coli, Bacillus subtilis, Salmonella typhimu~ium, 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.
PCT/US92/09627 (W093/09222) by Selden et al.; and International Application No.
PCT/IJS90/06436 (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: 985-1968, 2953-3936, 3943-3948 or 3955-3960 or an amino acid sequence encoded by any one of the nucleotide sequences SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954 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: 1-984, 1969-2952, 3937-3942 or 3949-3954 or (b) polynucleotides encoding any one of the amino acid sequences set forth as SEQ ID NO: 985-1968, 2953-3936, 3943-3948 or 3955-3960 or (c) polynucleotides that hybridize to the complement of the polynucleotides of either (a) ox (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: 985-1968, 2953-3936, 3943-3948 or or the corresponding full length or mature protein; and "substantial equivalents" thereof (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%, and more typically at least about 90%, 91%, 92%, 93%, 94%, and even more typically at least about 95%, 96%, 97%, 98%, 99%, sequence 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: 98S-1968, 2953-3936, 3943-3948 or 3955-3960.
Fragments of the proteins of the present invention which are capable of exhibiting biological activity are also encompassed by the present invention. Fragments of the protein may be in linear form or they may be cyclized using known methods, for example, as described in H.
U. Saragovi, et al., Bio/Technology 10, 773-778 (1992) and in R. S. McDowell, et al., 3. 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 fiuther provides isolated polypeptides encoded by the nucleic acid fragments of the present invention or by degenerate variants of the nucleic acid fragments of the present invention. By "degenerate variant" is intended nucleotide fragments which differ from a nucleic acid fragment of the present invention (e.g., an ORF) by nucleotide sequence but, due to the degeneracy of the genetic code, encode an identical polypeptide sequence.
Preferred nucleic acid fragments of the present invention are the ORFs that encode proteins.
A variety of methodologies known in the art can be utilized to obtain any one of the isolated polypeptides or proteins of the present invention. At the simplest level, the amino acid sequence can be synthesized using commercially available peptide synthesizers.
The synthetically-constructed protein sequences, by virtue of sharing primary, secondary or tertiary structural and/or conformational characteristics with proteins may possess biological properties in common therewith, including protein activity. This technique is particularly useful in producing small peptides and fragments of larger polypeptides. Fragments are useful, for example, in generating antibodies against the native polypeptide. Thus, they may be employed as biologically active or immunological substitutes for natural, purif ed proteins in screening of therapeutic compounds and in immunological processes for the development of antibodies.
The polypeptides and proteins of the present invention can alternatively be purified from cells which have been altered to express the desired polypeptide or protein.
As used herein, a cell is said to be altered to express a desired polypeptide or protein when the cell, through genetic manipulation, is made to produce a polypeptide or protein which it normally does not produce or which the cell normally produces at a lower level. One skilled in the art can readily adapt procedures for introducing and expressing either recombinant or synthetic sequences into eukaryotic or prokaryotic cells in order to generate a cell which produces one of the polypeptides or proteins of the present invention.

The invention also relates to methods for producing a polypeptide comprising growing a culture of host cells of the invention in a suitable culture medium, and purifying the protein from the cells or the culture in which the cells are grown. For example, the methods of the invention include a process for producing a polypeptide in which a host cell containing a suitable expression vector that includes a polynucleotide of the invention is cultured under conditions that allow expression of the encoded polypeptide. The polypeptide can be recovered from the culture, conveniently from the culture medium, or from a lysate prepared from the host cells and further purified. Preferred embodiments include those in which the protein produced by such process is a 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 skilled in the art can xeadily follow known methods for isolating polypeptides and proteins in order to obtain one of the isolated polypeptides or proteins of the present invention. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immuno-affinity chromatography. See, e.g., Scopes, Protein Purification:
Principles and Practice, Springer-Verlag (1994); Sambrook, et aL, in Molecular Cloning: A Lal oratory Manual; Ausubel et al., Current Protocols in Molecular Biology. Polypeptide fragments that retain biological/immunological activity include fragments comprising greater than about 100 amino acids, or greater than about 200 amino acids, and fragments that encode specific protein domains.
The purified polypeptides can be used in in vitro binding assays which are well known in the art to identify molecules which bind to the polypeptides. These molecules include but are not limited to, for e.g., small molecules, molecules from combinatorial libraries, antibodies or other proteins. The molecules identified in the binding assay are then tested for antagonist or agonist activity in i~ vivo tissue culture or animal models that are well known in the art. In brief, the molecules are titrated into a plurality of cell cultures or animals and then tested for either cell/animal death or prolonged survival of the animal/cells.
In addition, the peptides of the invention or molecules capable of binding to the peptides may be complexed with toxins, e.g., ricin or cholera, or with other compounds that 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: 985-1968, 2953-3936, 3943-3948 or 3955-3960.
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 axe 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 1 S 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 baculovixus/insect cell expression systems are commercially available in kit form from, e.g., Invitrogen, San Diego, Calif., U.S.A.
(the MaxBatTM kit), and such methods are well known in the art, as described in Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987), incorporated herein by reference. As used herein, an insect cell capable of expressing a polynucleotide of the present invention is "transformed."
The protein of the invention may be prepared by culturing transformed host cells under culture conditions suitable to express the recombinant protein. The resulting expressed protein may then be purified from such culture (i. e., from culture medium or cell extracts) using known purification processes, such as gel filtration and ion exchange chromatography. The purification of the protein may also include an affinity column containing agents which will bind to the protein; one or more column steps over such affinity resins as concanavalin A-agarose, heparin-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 axe 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 further purify the protein. Some or all of the foregoing purification steps, in various combinations, can also be employed to provide a substantially homogeneous isolated recombinant protein. The protein thus purified is substantially free of other mammalian proteins and is defined in accordance with the present invention as an "isolated protein."
The polypeptides of the invention include analogs (variants). This embraces fragments, as well as peptides in which one or more amino acids has been deleted, inserted, or substituted.
Also, analogs of the polypeptides of the invention embrace fusions of the polypeptides or modifications of the polypeptides of the invention, wherein the polypeptide or analog is fused to another moiety or moieties, e.g., targeting moiety or another therapeutic agent. Such analogs may exhibit improved properties such as activity and/or stability. Examples of moieties which may be fused to the polypeptide or an analog include, for example, targeting moieties which provide for the delivery of polypeptide to pancreatic cells, e.g., antibodies to pancreatic cells, antibodies to immune cells such as T-cells, monocytes, dendritic cells, granulocytes, etc., as well as receptor and ligands expressed on pancreatic or immune cells. Other moieties which may be fused to the polypeptide include therapeutic agents which are used for treatment, for example, immunosuppressive drugs such as cyclosporin, SK506, azathioprine, CD3 antibodies and steroids. Also, polypeptides may be fused to immune modulators, and other cytokines such as alpha or beta interferon.
4.6.1 DETERMINING POLYPEPTIDE AND POLYNUCLEOTIDE IDENTITY
AND SIMILARITY

Preferred identity and/or similarity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in computer programs including, but are not limited to, the GCG program package, including GAP
(Devereux, J., et al., Nucleic Acids Research 12(1):387 (1984); Genetics Computer Group, University of Wisconsin, Madison, WI), BLASTP, BLASTN, BLASTX, FASTA
(Altschul, S.F.
et al., J. Molec. Biol. 215:403-410 (1990), PSI-BLAST (Altschul S.F. et al., Nucleic Acids Res.
vol. 25, pp. 3389-3402, herein incorporated by reference), eMatrix software (Wu et al., J. Comp.
Biol., Vol. 6, pp. 219-235 (1999), herein incorporated by reference), eMotif software (Nevill-Manning et al, ISMB-97, Vol. 4, pp. 202-209, herein incorporated by reference), pFam software (Sonnhammer et al., Nucleic Acids Res., Vol. 26(1), pp. 320-322 (1998), herein incorporated by reference) and the I~yte-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 axe 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 fusion protein is a GST-fusion protein in which the polypeptide sequences of the invention are fused to the C-terminus of the GST (i.e., glutathione S-transferase) sequences.
In another embodiment, the fusion protein is an immunoglobulin fusion protein in which the polypeptide sequences according to the invention comprise one or more domains fused to sequences derived from a member of the immunoglobulin protein family. The immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a ligand and a protein of the invention on the surface of a cell, to thereby suppress signal transduction in vivo. The immmoglobulin 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 reamplif ed to generate a chimeric gene sequence (see, for example, Ausubel et al. (eds.) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley ~
Sons, 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). A nucleic acid encoding a polypeptide of the invention can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the protein of the invention.
4.8 GENE THERAPY
Mutations in the polynucleotides of the invention gene may result in loss of normal function of the encoded protein. The invention thus provides gene therapy to restore normal activity of the polypeptides of the invention; or to treat disease states involving polypeptides of the invention. Delivery of a functional gene encoding polypeptides of the invention to appropriate cells is effected ex vivo, in situ, or i~c vivo by use of vectors, and more particularly viral vectors (e.g., adenovirus, adeno-associated virus, or a retrovirus), or ex vivo by use of physical DNA transfer methods (e.g., liposomes or chemical treatments). See, for example, Anderson, Nature, supplement to vol. 392, no. 6679, pp.25-20 (1998). For 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 S 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.
1 S The present invention still further provides cells genetically engineered in vivo to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of 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 2S operatively linked to the desired protein encoding sequences. See, for example, PCT International PublicationNo. WO 94/12650, PCT InternationalPublicationNo. WO 92/20808, and PCT
InternationalPublicationNo. WO 91/099SS. It is also contemplatedthat, in addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ada, dhfr, and the multifunctional GAD gene which encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA may be inserted along with the heterologous promoter DNA. If linked to the desired protein coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the desired protein coding sequences in the cells.
In another embodiment of the present invention, cells and tissues may be engineered to express an endogenous gene comprising the polynucleotides of the invention under the control of 3 S 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-attachmentregions, negative regulatory elements, transcriptional initiation sites, regulatory protein binding sites or combinations of said sequences. Alternatively, sequences which affect the structure or stability of the RNA or protein produced may be replaced, removed, added, or otherwise modified by targeting. These sequences include polyadenylation signals, mRNA stability elements, splice sites, leader sequences for enhancing or modifying transport or secretion properties of the protein, or other sequences which alter or improve the function or stability of protein or RNA molecules.
The targeting event may be a simple insertion of the regulatory sequence, placing the gene under the control of the new regulatory sequence, e.g., inserting a new promoter or enhancer or both upstream of a gene. Alternatively, the targeting event may be a simple deletion of a regulatory element, such as the deletion of a tissue-specific negative regulatory element. Alternatively, the targeting event may replace an existing element; for example, a tissue-specific enhancer can be replaced by an enhancer that has broader or different cell-type specificity than the naturally 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 exhibiting the property of negative selection, such that the negatively selectable maxker is linked to the exogenous DNA, but configured such that the negatively selectable maxker 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 Sherwinet al.; InternationalApplicationNo.

(W093/09222) by Selden et al.; and International ApplicationNo.

(W091 /06667) by Skoultchi et al., each of which is incorporated by reference herein in its entirety.
4.9 TR.ANSGENIC ANIMALS

In preferred methods to determine biological functions of the polypeptides of the invention in vivo, one or more genes provided by the invention are either over expressed or inactivated in the germ line of animals using homologous recombination [Capecchi, Science 244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the regulatory control of exogenous or endogenous promoter elements, are known as transgenic animals.
Animals in which an endogenous gene has been inactivated by homologous recombination are referred to as "knockout" animals. Knockout animals, preferably non-human mammals, can be prepared as described in U.S. Patent No. 5,557,032, incorporated herein by reference. Transgenic animals are useful to determine the roles polypeptides of the invention play in biological processes, and preferably in disease states. Transgenic animals are useful as model systems to identify compounds that modulate lipid metabolism. Transgenic animals, preferably non-human mammals, are produced using methods as described in U.S. Patent No 5,489,743 and PCT
Publication No. W094128122, 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 in vivo, one or more genes provided by the invention are either over expressed or inactivated in the germ line of animals using homologous recombination [Capecchi, Science 244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the regulatory control of exogenous or endogenous promoter elements, are known as transgenic animals.
Animals in which an endogenous gene has been inactivated by homologous recombination are referred to as "knockout" animals. Knockout animals, preferably non-human mammals, can be prepared as described in U.S. Patent No. 5,557,032, incorporated herein by .reference. Transgenic animals are useful to determine the roles polypeptides of the invention play in biological processes, and preferably in disease states. Transgenic animals are useful as model systems to identify compounds that modulate lipid metabolism. Transgenic animals, preferably non-human mammals, are produced using methods as described in U.S. Patent No 5,489,743 and PCT
Publication No. W094/28122, incorporated herein by reference.
Transgenic animals can be prepared wherein all or part of the polynucleotides of the invention promoter is either activated or inactivated to alter the level of expression of the polypeptides of the invention. Inactivation can be carried out using homologous recombination methods described above. Activation can be achieved by supplementing or even replacing the homologous promoter to provide for increased protein expression. The homologous promoter can be supplemented by insertion of one or more heterologous enhancer elements known to confer promoter activation in a particular tissue.
4.10 USES AND BIOLOGICAL ACTIVITY
The polynucleotides and proteins of the present invention are expected to exhibit one or more of the uses or biological activities (including those associated with assays cited herein) identified herein. Uses or activities described for proteins of the present invention may be provided by administration or use of such proteins or of polynucleotides encoding such proteins (such as, for example, in gene therapies or vectors suitable for introduction of DNA). The mechanism underlying the particular condition or pathology will dictate whether the polypeptides of the invention, the polynucleotides of the invention or modulators (activators or inhibitors) thereof would be beneficial to the subject in need of treatment.
Thus, "therapeutic compositions of the invention" include compositions comprising isolated polynucleotides (including recombinant DNA molecules, cloned genes and degenerate variants thereof) or polypeptides of the invention (including full length protein, mature protein and truncations or domains thereof), or compounds and other substances that modulate the overall activity of the target gene products, either at the level of target gene/protein expression or target protein activity. Such modulators include polypeptides, analogs, (variants), including fragments and fusion proteins, antibodies and other binding proteins; chemical compounds that directly or indirectly activate or inhibit the polypeptides of the invention (identified, e.g., via drug screening assays as described herein); antisense polynucleotides and polyrrucleotides suitable for triple helix formation; and in particular antibodies or other binding partners that specifically recognize one or more epitopes of the polypeptides of the invention.
The polypeptides of the present invention may likewise be involved in cellular activation or in one of the other physiological pathways described herein.
4.10.1 RESEARCH USES AND UTILITIES

The polynucleotides provided by the present invention can be used by the research community for various purposes. The polynucleotides can be used to express recombinant protein for analysis, characterization or therapeutic use; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in disease states); as molecular weight markers on gels;
as chromosome markers or tags (when labeled) to identify chromosomes or to map related gene positions; to compare with endogenous DNA sequences in patients to identify potential genetic disorders; as probes to hybridize and thus discover novel, related DNA
sequences; as a source of information to derive PCR primers for genetic fingerprinting; as a probe to "subtract-out" known sequences in the process of discovering other novel polynucleotides; for selecting and making oligomers for attachment to a "gene chip" or other support, including for examination of expression patterns; to raise anti-protein antibodies 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 irmnune 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 kit format for commercialization as research products.
Methods for performing the uses listed above are well known to those skilled in the art.
References disclosing such methods include without limitation "Molecular Cloning: A
Laboratory Manual", 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, J., E. F. 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 source of carbohydrate. In such cases the polypeptide or polynucleotide of the invention can be added to the feed of a particular organism or can be administered as a separate solid or liquid preparation, such as in the form of powder, pills, solutions, suspensions or capsules. In the case of microorganisms, the polypeptide or polynucleotide of the invention can be added to the medium in or on which the microorganism is cultured.
4.10.3 CYTOKINE AND CELL PROLIFERATIONIDIFFERENTIATION
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, DAlG, T10, B9, B9/11, BaF3, MC9/G, M+(preB M+), 2E8, RBS, DAl, 123, T1165, HT2, CTLL2, TF-1, Mo7e, CMK, HUVEC, and Caco. Therapeutic compositions of the invention can be used in the following:
Assays for T-cell or thymocyte proliferation include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D.
H. Margulies, E.
M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Yit~o assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986; Bertagnolli et al., J.
Immunol.
145:1706-1712, 1990; Bertagnolli et al., Cellular Immunology 133:327-341, 1991; Bertagnolli, et al., I. Immunol. 149:3778-3783, 1992; Bowman et al., 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, Kruisbeek, A. M. and Shevach, E. M. In Current Protocols in Immunology. J. E.
e.a. Coligan eds. Vol 1 pp. 3.12.1-3.12.14, John Wiley and Sons, Toronto. 1994; and Measurement of mouse and human interleukin-y, Schreiber, R. D. In Current Protocols in Immunology.
J. E. e.a. Coligan eds. Vol 1 pp. 6.8.1-6.8.8, John Wiley and Sons, Toronto. 1994.
Assays for proliferation and differentiation of hematopoietic and lymphopoietic cells include, without limitation, those described in: Measurement of Human and Murine Interleukin 2 and Interleukin 4, Bottomly, K., Davis, L. S. and Lipsky, P. E. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 6.3.1-6.3.12, John Wiley and Sons, Toronto. 1991;
deVries et al., J. Exp. Med. 173:1205-1211, 1991; Moreau et al., Nature 336:690-692, 1988;
Greenberger et al., Proc. Natl. Acad. Sci. U.S.A. 80:2931-2938, 1983;
Measurement of mouse and human interleukin 6--Nordan, R. In Current Protocols in Immunology. J. E.
Coligan eds. Vol 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., Claxk, 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--Ciaxletta, 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. Crreene Publishing Associates and Wiley-Interscience (Chapter 3, I~
T~'itro assays for Mouse Lymphocyte Function; Chapter 6, Cytokines and their cellular receptors;
Chapter 7, Immunologic studies in Humans); Weinberger et al.; Proc. Natl. Acad. Sci. USA
77:6091-6095, 1980; Weinberger et al., Eur. J. Immun. 11:405-411, 1981; Takai et al., J.
Immunol.
137:3494-3500, 1986; Takai et al., J. Immunol. 140:508-512, 1988.
4.10.4 STEM CELL GROWTH FACTOR ACTIVITY
A polypeptide of the present invention may exhibit stem cell growth factor activity and be involved in the proliferation, differentiation and survival of pluripotent and totipotent stem cells including primordial germ cells, embryonic stem cells, hematopoietic stem cells and/or germ line stem cells. Administration of the polypeptide of the invention to stem cells in vivo or ex vivo is expected to maintain and expand cell populations in a totipotential or pluripotential state which would be useful for re-engineering damaged or diseased tissues, transplantation, manufacture of bio-pharmaceuticals and the development of bio-sensors. The ability to produce laxge quantities of human cells has important working applications for the production of human proteins which currently must be obtained from non-human sources or donors, implantation of cells to treat diseases such as Parkinson's, Alzheimer's and other neurodegenexative 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 andlor cytokines may be administered in combination with the polypeptide of the invention to achieve the desired effect, including any of the growth factors listed herein, other stem cell maintenance factors, and specifically including stem cell factor (SCF), leukemia inhibitory factor (LIF), Flt-3 ligand (Flt-3L), any of the interieukins, recombinant soluble IL-6 xeceptor fused to IL-6, macrophage I O inflaanmatory protein I-alpha (MIP-I-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 I 5 for culturing stem cells axe 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, strama cells transfected with a polynucleotide that encodes for the polypeptide of the invention can be used as a feeder 20 layer for the stem cell populations in culture or in vivo. Stromal support cells for feeder layers rnay 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 25 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 30 proliferation andlor 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 rnay 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 35 genetic disorders. The polypeptide of the invention may be useful fox inducing the proliferation of neural cells and for-the regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders which involve degeneration, death or trauma to neural cells or nerve tissue. In addition, the expanded stem cell populations can also be genetically altered for gene therapy purposes and to decrease host rejection of replacement tissues after grafting or implantation.
Expression of the polypeptide of the invention and its effect on stem cells can also be manipulated to achieve controlled differentiation of the stem cells into more differentiated cell types. A broadly applicable method of obtaining pure populations of a specific differentiated cell type from undifferentiated stem cell populations involves the use of a cell-type specific promoter driving a selectable marker. The selectable marker allows only cells of the desired type to survive. For example, stem cells can be induced to differentiate into cardiomyocytes (Wobus et al., Differentiation, 48: 173-182, (1991); Klug et al., J. Clin. Invest., 98(1): 216-224, (1998)) or skeletal muscle cells (Browder, L. W. In: Principles of Tissue Ehgineerihg eds. Lama 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.
I~ 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 various anemias or for use in conjunction with irradiation/chemotherapy to stimulate the production of erythroid precursors and/or erythroid cells; in supporting the growth and proliferation of myeloid cells such as granulocytes and monocytes/macrophages (i.e., traditional CSF activity) useful, for example, in conjunction with chemotherapy to prevent or treat consequent myelo-suppression; in 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; andlor 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 ih-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 I5 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, Tnc., New York, N.Y. 1994;
Hirayama et al., Proc. Natl. Acad. Sci. USA 89:5907-5911, 1992; Primitive hematopoietic colony forming cells with high proliferative potential, McNiece, I. K. and Briddell, R. A. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. VoI pp. 23-39, Wiley-Liss, Inc., New York, N.Y. 1994; Neben et al., Experimental Hematology 22:353-359, 1994; Cobblestone area forming cell assay, Ploemacher, R. E. In Culture of Hematopoietic Cells. R. I. Fxeshney, et al.
eds. Vol pp. 1-21, Wiley-Liss, Tnc., New York, N.Y. 1994; Long term bone marrow cultures in the presence of stromal cells, Spooncer, E., Dexter, M, and Allen, T. In Culture of Hematopoietic Cells. R. I.
Freshney, et al. eds. Vol pp. 163-i79, Wiley-Liss, Tnc., New York, N.Y. 1994;
Long term culture initiating cell assay, Sutherland, H. J. In Culture of Hematopoietic Cells. R.
I. Freshney, et al.
eds. Vol pp. 139-162, Wiley-Liss, Inc., New York, N.Y. 1994.
4.10.6 TISSUE GROWTH ACTIVITY

A polypeptide of the present invention also may be involved in bone, cartilage, tendon, ligament and/or nerve tissue growth or regeneration, as well as in wound healing and tissue repair and replacement, and in healing of burns, incisions and ulcers.
A polypeptide of the present invention which induces cartilage and/or bone growth in circumstances where bone is not normally formed, has application in the healing of bone fractures and cartilage damage or defects in humans and other animals.
Compositions of a polypeptide, antibody, binding partner, or other modulator of the invention may have prophylactic use in closed as well as open fracture reduction and also in the improved fixation of artificial joints. De novo bone formation induced by an osteogenic agent contributes to the repair of congenital, trauma induced, or oncologic resection induced craniofacial defects, and also is useful in cosmetic plastic surgery.
A polypeptide of this invention may also be involved in attracting bone-forming cells, stimulating growth of bone-forming cells, or inducing differentiation of progenitors of bone-forming cells. Treatment of osteoporosis, osteoarthritis, bone degenerative disorders, or periodontal disease, such as through stimulation of bone and/or cartilage repair or by blocking inflammation or processes of tissue destruction (collagenase activity, osteoclast activity, etc.) mediated by inflammatory processes may also be possible using the composition of the invention.
Another category of tissue regeneration activity that may involve the polypeptide of the present invention is tendon/ligament formation. Induction of tendon/ligament-like tissue or other tissue formation in circumstances where such tissue is not normally formed, has application in the healing of tendon or ligament tears, deformities and other tendon or ligament defects in humans and other animals. Such a preparation employing a tendon/ligament-like tissue inducing protein may have prophylactic use in preventing damage to tendon or ligament tissue, as well as use in the improved fixation of tendon or ligament to bone or other tissues, and in repairing defects to tendon or ligament tissue. De novo tendon/ligament-like tissue formation induced by a composition of the present invention contributes to the repair of congeutal, 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 ih 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 1 S insuff ciency, surgical and traumatic wounds, and the like.
Compositions of the present invention may also be involved in the generation or regeneration of other tissues, such as organs (including, for example, pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac) and vascular (including vascular endothelium) tissue, or for promoting the growth of cells comprising such tissues. Part of the desired effects may be by inhibition or modulation of fibrotic scarring may allow normal tissue to regenerate. A polypeptide of the present invention may also exhibit angiogenic activity.
A composition of the present invention may also be useful for gut protection or regeneration and treatment of lung or liver fibrosis, reperfusion injury in various tissues, and conditions resulting from systemic cytokine damage.
A composition of the present invention may also be useful for promoting or inhibiting differentiation of tissues described above from precursor tissues or cells; or for inhibiting the growth of tissues described above.
Therapeutic compositions of the invention can be used in the following:
Assays for tissue generation activity include, without limitation, those described in:
International Patent Publication No. W095lI6035 (bone, cartilage, tendon);
International Patent Publication No. W095/05846 (nerve, neuronal); International Patent Publication No.
W091/07491 (skin, endothelium).
Assays for wound healing activity include, without limitation, those described in: Winter, Epidermal Wound Healing, pps. 71-112 (Maibach, H. I. and Rovee, D. T., eds.), Year Book Medical Publishers, Inc., Chicago, as modified by Eaglstein and Mertz, J.
Invest. Dermatol 71:382-84 (1978).
4.10.7 IMMUNE STIMULATING OR SUPPRESSING ACTIVITY
A polypeptide of the present invention may also exhibit immune stimulating or immune suppressing activity, including without limitation the activities for which assays are described herein. A polynucleotide of the invention can encode a polypeptide exhibiting such activities. A
protein may be useful in the treatment of various immune deficiencies and disorders (including severe combined immunodeficiency (SCID)), e.g., in regulating (up or down) growth and proliferation of T and/or B lymphocytes, as well as effecting the cytolytic activity of NK cells and other cell populations. These immune deficiencies may be genetic or be caused by viral (e.g., HIV) as well as bacterial or fungal infections, or may result from autoimmune disorders. More specifically, infectious diseases causes by viral, bacterial, fungal or other infection may be treatable using a protein of the present invention, including infections by HIV, hepatitis viruses, herpes viruses, mycobacteria, Leishmania spp., malaria spp. and various fungal infections such as candidiasis. Of course, in this regard, proteins of the present invention may also be useful where a boost to the immune system generally may be desirable, i.e., in the treatment of cancer.
Autoimmune disorders which may be treated using a protein of the present invention include, for example, connective tissue disease, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, autoimmune pulmonary inflammation, Guillain-Barre syndrome, autoimmune thyroiditis, insulin dependent diabetes mellitis, myasthenia gravis, graft-versus-host disease and autoimmune inflammatory eye disease. Such a protein (or antagonists thereof, including antibodies) of the present invention may also to be useful in the treatment of allergic reactions and conditions (e.g., anaphylaxis, serum sickness, drug reactions, food allergies, insect venom allergies, mastocytosis, allergic rhinitis, hypersensitivity pneumonitis, urticaria, angioedema, eczema, atopic dermatitis, allergic contact dermatitis, erythema multiforme, Stevens-Johnson syndrome, allergic conjunctivitis, atopic keratoconjunctivitis, venereal keratoconjunctivitis, giant papillary conjunctivitis and contact allergies), such as asthma (particularly allergic asthma) or other respiratory problems. Other conditions, in which immune suppression is desired (including, for example, organ transplantation), may also be treatable using a protein (or antagonists thereof) of the present invention. The therapeutic effects of the polypeptides or antagonists thereof on allergic reactions can be evaluated by in vivo animals models such as the cumulative contact enhancement test (Lastbom et al., Toxicology 125: 59-66, 1998), skin prick test (Hoffinann et al., Allergy 54: 446-54, 1999), guinea pig skin sensitization test (Voter 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 immune responses, in a number of ways. Down regulation may be in the form of inhibiting or blocking an immune response already in progress or may involve preventing the induction of an immune response. The functions of activated T cells may be inhibited by suppressing T
cell responses or by inducing specific tolerance in T cells, or both. Immunosuppression of T
cell responses is generally an active, non-antigen-specific, process which requires continuous exposure of the T
cells to the suppressive agent. Tolerance, which involves inducing non-responsiveness or anergy in T cells, is distinguishable from immunosuppression in that it is generally antigen-specific and persists after exposure to the tolerizing agent has ceased. Operationally, tolerance can be demonstrated by the lack of a T cell response upon reexposure to specific antigen in the absence of the tolerizing agent.
Dov~m 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 immune reaction that destroys the transplant. The administration of a therapeutic composition of the invention may prevent cytokine synthesis by immune cells, such as T cells, and thus acts as an immunosuppressant. Moreover, a lack of costimulation may also be sufficient to anergize the T cells, thereby inducing tolerance in a subject. Induction of long-term tolerance by B lymphocyte antigen-blocking reagents may 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 Turka 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 York, 1989, pp. 846-847) can be used to determine the effect of therapeutic compositions of the invention on the development of that disease.

Blocking antigen function may also be therapeutically useful for treating autoimmune diseases. Many autoimmune disorders are the result of inappropriate activation of T cells that are reactive against self tissue and which promote the production of cytokines and autoantibodies involved in the pathology of the diseases. Preventing the activation of autoreactive T cells may reduce or eliminate disease symptoms. Administration of reagents which block stimulation of T
cells can be used to inhibit T cell activation and prevent production of autoantibodies or T
cell-derived cytokines which may be involved in the disease process.
Additionally, blocking reagents may induce antigen-specific tolerance of autoreactive T cells which could lead to long-term relief from the disease. The efficacy of blocking reagents in preventing or alleviating autoimmune disorders can be determined using a number of well-characterized animal models of human autoimmune diseases. Examples include marine experimental autoimmune encephalitis, systemic lupus erythmatosis in MRL/lpr/lpr mice or NZB hybrid mice, marine autoimmune collagen arthritis, diabetes mellitus in NOD mice and BB rats, and marine experimental myasthenia gravis (see Paul ed., Fundamental Immunology, Raven Press, New York, 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 pxotein and an MHC class II beta chain pxotein to thereby express MHC class I
or MHC class II
pxoteins on the cell surface. Expression of the appropriate class I or class II MHC in conjunction with a peptide having the activity of a B lymphocyte antigen (e.g., B7-1, B7-2, B7-3) induces a T
cell me'tliated 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 fox Mouse Lymphocyte Function 3.1-3.19;
Chapter 7, Immunologic studies in Humans); Herrmann et al., Proc. Natl. Acad.
Sci. USA
78:2488-2492, 1981; Herrmann et al., J. Immunol. 128:1968-1974, 1982; Handa et al., J.
Immunol. 135:1564-1572, 1985; Takai et al., I. Immunol. 137:3494-3500, 1986;
Takai et al., J.
hmnunol. 140:508-512, 1988; Bowman et al., J. Virology 61:1992-1998;
Bertagnolli et al., Cellulax 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. J. E. e.a.
Coligan eds. Vol 1 pp. 3.8.1-3.8.16, John Wiley and Sons, Toronto. 1994.
Mixed lymphocyte reaction (MLR) assays (which will identify, among others, proteins that generate predominantly Th1 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, ImmunoIogic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986; Takai et al., J.
Immunol. 140:508-512, 1988; Bertagnolli et al., J. Imrnunol. 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 so WO 01/57190 ~ PCT/USO1/04098 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 154a071-s079, 1995;
Porgador et al., Journal of Experimental Medicine 182:255-260, 199s; Nair et al., Journal of Virology 67:4062-4069, 1993; Huang et al., Science 264:961-96s, 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 53:1945-19s1, 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, without limitation, those described in: Antica et al., Blood 84:111-117, 1994; Fine et al., Cellular Immunology 155:111-122, 1994; Galy et al., Blood 85:2770-2778, 1995;
Toki et al., Proc. Nat. Acad Sci. USA 88:7548-7551, 1991.
4.10.8 ACTIVIN/INHIBIN ACTIVITY
A polypeptide of the present invention may also exhibit activin- or inhibin-related activities. A polynucleotide of the invention may encode a polypeptide exhibiting such characteristics. Inhibins are characterized by their ability to inhibit the release of follicle stimulating hormone (FSH), while activins and are characterized by their ability to stimulate the release of follicle stimulating hormone (FSH). Thus, a polypeptide of the present invention, alone or in heterodimers with a member of the inhibin family, may be useful as a contraceptive based on the ability of inhibins to decrease fertility in female mammals and decrease spermatogenesis in male mammals. Administration of sufficient amounts of other inhibins can induce infertility in these mammals. Alternatively, the polypeptide of the invention, as a homodimer or as a heterodimer with other protein subunits of the inhibin group, may be useful as a fertility inducing therapeutic, based upon the ability of activin molecules in stimulating FSH
release from cells of the anterior pituitary. See, for example, U.S. Pat. No.
4,798,885. A
polypeptide of the invention may also be useful for advancement of the onset of fertility in sexually immature mammals, so as to increase the lifetime reproductive performance of domestic animals such as, but not limited to, cows, sheep and pigs.
s1 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., Nature 318:659-663, 1985; Forage et al., Proc. Natl. Acad. Sci.
USA 83:3091-3095, 1986.
4.10.9 CHEMOTACTIC/CHEMOKINETIC ACTIVITY
A polypeptide of the present invention may be involved in chemotactic or chemokinetic activity for mammalian cells, including, for example, monocytes, fibroblasts, neutrophils, T-cells, mast cells, eosinophils, epithelial and/or endothelial cells. A
polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Chemotactic and chemokinetic receptor activation can be used to mobilize or attract a desired cell population to a desired site of action. Chemotactic or chemokinetic compositions (e.g. proteins, antibodies, binding partners, or modulators of the invention) provide particular advantages in treatment of wounds and other trauma to tissues, as well as in treatment of localized infections. For example, attraction of lymphocytes, monocytes or neutrophils to tumors or sites of infection may result in improved immune responses against the tumor or infecting agent.
A protein or peptide has chemotactic activity for a particular cell population if it can stimulate, directly or indirectly, the directed orientation or movement of such cell population.
Preferably, the protein or peptide has the ability to directly stimulate directed movement of cells.
Whether a particular protein has chemotactic activity for a population of cells can be readily determined by employing such protein or peptide in any known assay for cell chemotaxis.
Therapeutic compositions of the invention can be used in the following:
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 Chemokines 6.12.1-6.12.28; Taub et al. J. Clin. Invest. 95:1370-1376, 1995; Lind et al.
APMIS 103:140-146, 1995; Muller et al Eur. J. Immunol. 25:1744-1748; Gruber et al. J. of Immunol.
152:5860-5867, 1994; Johnston et al. J. of Immunol. 153:1762-1768, 1994.

4.10.10 HEMOSTATIC AND THROMBOLYTIC ACTIVITY
A polypeptide of the invention may also be involved in hemostatis or thrombolysis or thrombosis. A polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Compositions may be useful in treatment of various coagulation disorders (including hereditary disorders, such as hemophiliac) or to enhance coagulation and other hemostatic events in treating wounds resulting from trauma, surgery or other causes. A
composition of the invention may also be useful for dissolving or inhibiting formation of thromboses and for treatment and prevention of conditions resulting therefrom (such as, for example, infarction of cardiac and central nervous system vessels (e.g., stroke).
Therapeutic compositions of the invention can be used in the following:
Assay for hemostatic and thrombolytic activity include, without limitation, those described in: Linet et al., J. Clin. Pharmacol. 26:131-140, 1986; Burdick et al., Thrombosis Res.
45:413-419, 1987; Humphrey et al., Fibrinolysis 5:71-79 (1991); Schaub, Prostaglandins 35:467-474, 1988.
4.10.11 CANCER DIAGNOSIS AND THERAPY
Polypeptides of the invention may be involved in cancer cell generation, proliferation or metastasis. Detection of the presence or amount of polynucleotides or polypeptides of the invention may be useful for the diagnosis and/or prognosis of one or more types of cancer. For example, the presence or increased expression of a polynucleotide/polypeptide of the invention may indicate a hereditary risk of cancer, a precancerous condition, or an ongoing malignancy.
Conversely, a defect in the gene or absence of the polypeptide may be associated with a cancer condition. Identification of single nucleotide polymorphisms associated with cancer or a predisposition to cancer may also be useful for diagnosis or prognosis.
Cancer treatments promote tumor regression by inhibiting tumor cell proliferation, inhibiting angiogenesis (growth of new blood vessels that is necessary to support tumor growth) and/or prohibiting metastasis by reducing tumor cell motility or invasiveness.
Therapeutic compositions of the invention may be effective in adult and pediatric oncology including in solid phase tumors/malignancies, locally advanced tumors, human soft tissue sarcomas, metastatic cancer, including lymphatic metastases, blood cell malignancies including multiple myeloma, acute and chronic leukemias, and lymphomas, head and neck cancers including mouth cancer, larynx cancer and thyroid cancer, lung cancers including small cell carcinoma and non-small cell cancers, breast cancers including small cell carcinoma and ductal carcinoma, gastrointestinal cancers including esophageal cancer, stomach cancer, colon cancer, colorectal cancer and polyps associated with colorectal neoplasia, pancreatic cancers, liver cancer, urologic cancers including bladder cancer and prostate cancer, malignancies of the female gendtal 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, neurobiastoma, astrocytic brain tumors, gliomas, metastatic tumor cell invasion in the central nervous system, bone cancers including osteomas, skin cancers including malignant melanoma, tumor progression of human skin keratinocytes, squamous cell carcinoma, basal cell carcinoma, hemangiopericytoma and Karposi's sarcoma.
Polypeptides, polynucleotides, or modulators of polypeptides of the invention (including inhibitors and stimulators of the biological activity of the polypeptide of the invention) may be administered to treat cancer. Therapeutic compositions can be administered in therapeutically effective dosages alone or in combination with adjuvant cancer therapy such as surgery, chemotherapy, radiotherapy, thermotherapy, and laser therapy, and may provide a beneficial effect, e.g. reducing tumor size, slowing rate of tumor growth, inhibiting metastasis, or otherwise improving overall clinical condition, without necessarily eradicating the cancer.
The composition can also be administered in therapeutically effective amounts as a portion of an anti-cancer cocktail. An anti-cancer cocktail is a mixture of the polypeptide or modulator of the invention with one or more anti-cancer drugs in addition to a pharmaceutically acceptable carrier for delivery. The use of anti-cancer cocktails as a cancer treatment is routine.
Anti-cancer drugs that are well known in the art and can be used as a treatment in combination with the polypeptide or modulator of the invention include: Actinomycin D, Aminoglutethimide, Asparaginase, Bleomycin, Busulfan, Carboplatin, Carmustine, Chlorambucil, Cisplatin (cis-DDP), Cyclophosphamide, Cytarabine HCl (Cytosine arabinoside), Dacarbazine, Dactinomycin, Daunorubicin HCl, Doxorubicin HCI, Estxamustine phosphate sodium, Etoposide (V
16-213), Floxuridine, 5-Fluorouracil (5-Fu), Flutamide, Hydxoxyurea (hydroxycaxbamide), Ifosfamide, Interferon Alpha-2a, Interferon Alpha-2b, Leuprolide acetate (LHRH-releasing factor analog), Lomustine, Mechlorethamine HCl (nitrogen mustard), Melphalan, Mercaptopurine, Mesna, Methotrexate (MTX), Mitomycin, Mitoxantxone HCI, Octreotide, Plicamycin, Procarbazine HCI, Streptozocin, Tamoxifen citrate, Thioguanine, Thiotepa, Vinblastine sulfate, Vincristine sulfate, Amsacrine, Azacitidine, Hexamethylrnelamine, 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 andlor 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.

Ih vitro models can be used to determine the effective doses of the polypeptide of the invention as a potential cancer treatment. These ih viWo models include proliferation assays of cultured tumor cells, growth of cultured tumor cells in soft agar (see Fxeshney, (1987) Culture of Animal Cells: A Manual of Basic Technique, Wily-Liss, New York, NY Ch 18 and Ch 21), tumor systems in nude mice as described in Giovanella et al., J. Natl. Can.
Inst., 52: 921-30 (1974), mobility and invasive potential of tumor cells in Boyden Chamber assays as described in Pilkington et al., Anticancer Res., 17: 4107-9 (1997), and angiogenesis assays such as induction of vascularization of the chick chorioallantoic membrane or induction of vascular endothelial cell migration as described in Ribatta et al., Intl. J. Dev. BioL, 40: 1189-97 (1999) and Li et aL, Clin. Exp. Metastasis, 1.7:423-9 (1999), respectively. Suitable tumox 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 receptox/ligand interactions. A
polynucleotide of the invention can encode a polypeptide exhibiting such characteristics. Examples of such receptors and ligands include, without limitation, cytokine receptors and their ligands, receptor kinases and their ligands, receptor phosphatases and their ligands, receptors involved in cell-cell interactions and their ligands (including without limitation, cellular adhesion molecules (such as selectins, integrins and their ligands) and receptor/ligand pairs involved in antigen presentation, antigen recognition and development of cellular and humoral immune responses.
Receptors and ligands are also useful for screening of potential peptide ox 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 receptorlligand 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. I~ruisbeek, D. H.
Margulies, E. M.
Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley- Interscience (Chapter 7.28, Measurement of Cellular Adhesion under static conditions 7.28.1- 7.28.22), Takai et al., Proc.
Natl. Acad. Sci. USA 84:6864-6868, 1987; Bierer et al., J. Exp. Med. 168:1145-1156, 1988;
Rosenstein et al., J. Exp. Med. 169:149-160 1989; Stoltenborg et aL, 3.
Immunol. Methods 175:59-68, 1994; Stitt et al., Cell 80:661-670, 1995.

By way of example, the polypeptides of the invention may be used as a receptor for a ligand(s) thereby transmitting the biological activity of that ligand(s).
Ligands may be identified through binding assays; affinity chromatography, dihybrid screening assays, BIAcore assays, gel overlay assays, or other methods known in the art.
Studies characterizing drugs or proteins as agonist or antagonist or partial agonists or a partial antagonist require the use of other proteins as competing ligands. The polypeptides of the present invention or ligand(s) thereof may be labeled by being coupled to radioisotopes, colorimetric molecules or a toxin molecules by conventional methods. ("Guide to Protein Purification" Murray P. Deutscher (ed) Methods in Enzymology Vol. 182 (1990) Academic Press, Inc. San Diego). Examples of radioisotopes include, but are not limited to, tritium and carbon-14 . Examples of colorimetric molecules include, but are not limited to, fluorescent molecules such as fluorescamine, or rhodamine or other colorimetric molecules.
Examples of toxins include, but are not limited, to ricin.
4.10.13 DRUG SCREENING
This invention is particularly useful for screening chemical compounds by using the novel polypeptides or binding fragments thereof in any of a variety of drug screening techniques.
The polypeptides or fragments employed in such a test may either be free in solution, affixed to a solid support, borne on a cell surface or located intracellularly. One method of drug screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the polypeptide or a fragment thereof. 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 (l~ 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 282:63-68 (1998).
Combinatorial libraries are composed of large numbers of peptides, oligonucleotides or organic compounds and can be readily prepared by traditional automated synthesis methods, PCR, cloning or proprietary synthetic methods. Of particular interest are peptide 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, Curs. Opih.
Biotechnol. 8:701-707 (1997). For reviews and examples of peptidomimetic libraries, see Al-Obeidi et al., Mol. Biotechnol, 9(3):205-23 (1998); Hruby et al., Curr Opih Chem Biol, 1(1):114-19 (1997); Dorner et al., BioorgMed Chem, 4(5):709-15 (1996) (alkylated 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 cell/animal death or prolonged survival of the animal/cells.
The binding molecules thus identified may be complexed with toxins, e.g., ricin or cholera, or with other compounds that are toxic to cells such as radioisotopes. The 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 specif c 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 ofligands 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. Fox 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 Iigand has been identified, is produced in a host cell. The cell is then, incubated with the ligand specific for the extracellular portion of the chimeric protein, thereby activating the chimeric receptor. Known downstream proteins involved in intracellular signaling can then be assayed for expected modifications i.e. phosphorylation. Other methods known to those in the art can also be used to identify signaling molecules involved in receptor activity.
4.10.15 ANTT-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-repexfusion injury, endotoxin lethality, arthritis, complement-mediated hyperacute rejection, nephritis, cytokine or chemokine-induced lung injury, inflammatory bowel disease, Crohn's disease or resulting from over production of cytokines such as TNF or IL-1. Compositions of the invention may also be useful to treat anaphylaxis and hypersensitivity to an antigenic substance or material.
Compositions of this invention may be utilized to prevent or treat conditions such as, but not limited to, sepsis, acute pancreatitis, endotoxin shock, cytokine induced shock, rheumatoid arthritis, chronic inflammatory arthritis, pancreatic cell damage from diabetes mellitus type 1, graft versus host disease, inflammatory bowel disease, inflamation associated with pulmonary disease, other autoimmune disease or inflammatory disease, an antiproliferative agent such as for acute or chronic mylegenous leukemia or in the prevention of premature labor secondary to intrauterine infections.
4.10.16 LEUKEMIAS
Leukemias and related disorders may be treated or prevented by administration of a therapeutic that promotes or inhibits function of the polynucleotides and/or polypeptides of the invention. Such leukemias and related disorders include but are not limited to acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, myeloblastic, promyelocytic, myelomonocytic, monocytic, erythroleukemia, chronic leukemia, chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia (for a review of such disorders, see Fishman et al., 1985, Medicine, 2d Ed., J.B. Lippincott Co., Philadelphia).
4.10.17 NERVOUS SYSTEM DISORDERS
Nervous system disorders, involving cell types which can be tested for efficacy of intervention with compounds that modulate the activity of the polynucleotides and/or polypeptides of the invention, and which can be treated upon thus observing an indication of therapeutic utility, include but are not limited to nervous system injuries, and diseases or disorders which result in either a disconnection of axons, a diminution or degeneration of neurons, or demyelination. Nervous system lesions which may be treated in a patient (including human and non-human mammalian patients) according to the invention include but are not limited to the following lesions of either the central (including spinal cord, brain) or peripheral nervous systems:
(i) traumatic lesions, including lesions caused by physical injury or associated with surgery, for example, lesions which sever a portion of the nervous system, or compression injuries;
(ii) ischemic lesions, in which a lack of oxygen in a portion of the nervous system results in neuronal injury or death, including cerebral infarction or ischemia, or spinal cord infarction or ischemia;
(iii) infectious lesions, in which a portion of the nervous system is destroyed or injured as a result of infection, for example, by an abscess or associated with infection by human immunodeficiency virus, herpes zoster, or herpes simplex virus or with Lyme disease, tuberculosis, syphilis;

(iv) degenerative lesions, in which a portion of the nervous system is destroyed or injured as a result of a degenerative process including but not limited to degeneration associated with Parkinson's disease, Alzheimer's disease, Huntington's chorea, or amyotrophic lateral sclerosis;
S (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 def ciency, folic acid deficiency, Wernicke disease, tobacco-alcohol amblyopia, Marchiafava-Bignami disease (primary degeneration of the corpus callosum), and alcoholic cerebellar degeneration;
(vi) neurological lesions associated with systemic diseases including but not limited to diabetes (diabetic neuropathy, Bell's palsy), systemic lupus erythematosus, carcinoma, or sarcoidosis;
(vii) lesions caused by toxic substances including alcohol, lead, or particular neurotoxins; and (viii) demyelinated lesions in which a portion of the nervous system is destroyed or injured by a demyelinating disease including but not limited to multiple sclerosis, human immunodeficiency virus-associated myelopathy, transverse myelopathy or various etiologies, progressive multifocal leukoencephalopathy, and central pontine myelinolysis.
Therapeutics which are useful according to the invention for treatment of a nervous system disorder may be selected by testing for biological activity in promoting the survival or differentiation of neurons. For example, and not by way of limitation, therapeutics which elicit any of the following effects may be useful according to the invention:
(i) increased survival time of neurons in culture;
(ii} increased sprouting of neurons in culture or in vivo;
(iii) increased production of a neuron-associated molecule in culture or in vivo, e.g., choline acetyltransferase or acetylcholinesterase with respect to motor neurons; or (iv) decreased symptoms of neuron dysfunction in vivo.
Such effects may be measured by any method known in the art. In preferred, non-limiting embodiments, increased survival of neurons may be measured by the method set forth in Arakawa et al. (1990, 3. Neurosci. 10:3507-3515); increased sprouting of neurons may be detected by methods set forth in Pestronk et al. (1980, Exp. Neurol. 70:65-82) or Brown et al.
(1981, Ann. Rev. Neurosci. 4:17-42); increased production of neuron-associated molecules may be measured by bioassay, enzymatic assay, antibody binding, Northern blot assay, etc., depending on the molecule to be measured; and motor neuron dysfunction may be measured by assessing the physical manifestation of motor neuron disorder, e.g., weakness, motor neuron conduction velocity, or functional disability.
In specific embodiments, motor neuron disorders that may be treated according to the invention include but are not Iimified to disorders such as infarction, infection, exposure to toxin, trauma, surgical damage, degenerative disease or malignancy that may affect motor neurons as well as other components of the nervous system, as well as disorders that selectively affect neurons such as amyotrophic lateral sclerosis, and including but not limited to progressive spinal muscular atrophy, progressive bulbar palsy, primary lateral sclerosis, infantile and juvenile muscular atrophy, progressive bulbar paralysis of childhood (Fazio-Londe syndrome), poliomyelitis and the post polio syndrome, and Hereditary Motorsensory Neuropathy (Charcot-Marie-Tooth Disease).
4.10.18 OTHER ACTIVITIES
A polypeptide of the invention may also exhibit one or more of the following additional activities or effects: inhibiting the growth, infection or function of, or killing, infectious agents, including, without limitation, bacteria, viruses, fungi and other parasites;
effecting (suppressing or enhancing) bodily characteristics, including, without limitation, height, weight, hair color, eye color, skin, fat to lean ratio or other tissue pigmentation, or organ or body part size or shape (such as, far 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 Iineages; 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); immunoglobulin-like activity (such as, for example, the ability to bind antigens or complement); and the ability to act as an antigen in a vaccine composition to raise an immune response against such protein or another material or entity which is cross-reactive with such protein.
4.10.19 IDENTIFICATION OF POLYMORPHISMS
m 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 immunosuppressive effects of the compositions of the invention against rheumatoid arthritis is determined in an experimental animal model system. The experimental model system is adjuvant induced arthritis in rats, and the protocol is described by J.
Holoshitz, et at., 1983, Science, 219:56, or by B. Waksman et al., 1963, Int. Arch. Allergy Appl.
Immunol., 23:129.
Induction of the disease can be caused by a single injection, generally intradermally, of a suspension of killed Mycobacterium tuberculosis in complete Freund's adjuvant (CFA). The route of injection can vary, but rats may be injected at the base ofthe tail with an adjuvant mixture. The polypeptide is administered in phosphate buffered solution (PBS) at a dose of about 1-5 mg/kg. The control consists of administering PBS only. .
The procedure for testing the effects of the test compound would consist of intradermally injecting killed Mycobacterium tuberculosis in CFA followed by immediately administering the test compound and subsequent treatment every other day until day 24. At 14, 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 reveal that the test compound would have a dramatic affect on the swelling of the joints as measured by a decrease of the arthritis score. .
4.11 THERAPEUTIC METHODS
The compositions (including polypeptide fragments, analogs, variants and antibodies or other binding partners or modulators including antisense polynucleotides) of the invention have numerous applications in a variety of therapeutic methods. Examples of therapeutic applications include, but are not limited to, those exemplified herein.
4.11.1 EXAMPLE
One embodiment of the invention is the administration of an effective amount of the polypeptides or other composition of the invention to individuals affected by a disease or disorder that can be modulated by regulating the peptides of the invention.
While the mode of administration is not particularly important, parenteral administration is preferred. An exemplary mode of administration is to deliver an intravenous bolus. The dosage of the polypeptides or other composition of the invention will normally be determined by the prescribing physician. It is to be expected that the dosage will vary according to the age, weight, condition and response of the individual patient. Typically, the amount of polypeptide administered per dose will be in the range of about 0.01 ~,g/kg to 100 mg/kg of Body weight, with the preferred dose being about 0.1 ~g/kg to 10 mg/kg of patient body weight.
For parenteral administration, polypeptides of the invention will be formulated in an injectable form combined with a pharmaceutically acceptable parenteral vehicle. Such vehicles are well known in the art and examples include water, saline, Ringer's solution, dextrose solution, and solutions consisting of small amounts of the human serum albumin. The vehicle may contain minor amounts of additives that maintain the isotonicity and stability of the polypeptide or other active ingredient.
The preparation of such solutions is within the skill of the art.

4.12 PHARMACEUTICAL FORMULATIONS AND ROUTES OF
ADMINISTRATION
A protein or other composition of the present invention (from whatever source derived, including without limitation from recombinant and non-recombinant sources and including antibodies and other binding partners of the polypeptides of the invention) may be administered to a patient in need, by itself, or in pharmaceutical compositions where it is mixed with suitable carriers or excipient(s) at doses to treat or ameliorate a variety of disorders. Such a composition may optionally contain (in addition to protein or other active ingredient and a carrier) diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art. The term "pharmaceutically acceptable" means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The characteristics of the carrier will depend on the route of administration. The pharmaceutical composition of the invention may also contain cytokines, lymphokines, or other hematopoietic factors such as M-CSF, GM-CSF, TNF, IL-1, 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, TNF1, TNF2, G-CSF, Meg-CSF, thrombopoietin, stem cell factor, and erythropoietin. In further compositions, proteins of the invention may be combined with other agents beneficial to the treatment of the disease or disorder in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet-derived growth factor (PDGF), transforming growth factors (TGF-a and TGF-(3), insulin-like growth factor (IGF), as well as cytokines described herein.
The pharmaceutical composition may further contain other agents which either enhance the activity of the protein or other active ingredient or complement its activity or 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, lymphokine, 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 in such multimeric or complexed form.

As an alternative to being included in a pharmaceutical composition of the invention including a first protein, a second protein or a therapeutic agent may be concurrently administered with the first protein (e.g., at the same time, or at differing times provided that therapeutic concentrations of the combination of agents is achieved at the treatment site).
Techniques for formulation and administration of the compounds of the instant application may be found in "Remington's Pharmaceutical Sciences," Mack Publishing Co., Easton, PA, latest edition. A therapeutically effective dose further refers to that amount of the compound sufficient to result in amelioration of symptoms, e.g., treatment, healing, prevention or amelioration of the relevant medical condition, or an increase in rate of treatment, healing, prevention or amelioration of such conditions. When applied to an individual active ingredient, administered alone, a therapeutically effective dose refers to that ingredient alone. When applied to a combination, a therapeutically effective dose refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
In practicing the method of treatment or use of the present invention, a therapeutically effective amount of protein or other active ingredient of the present invention is administered to a mammal having a condition to be treated. Protein or other active ingredient of the present invention may be administered in accordance with the method of the invention either alone or in combination with other therapies such as treatments employing cytokines, lymphokines or other hematopoietic factors. When co- administered with one or more cytokines, lymphokines or other herilatopoietic factors, protein or other active ingredient of the present invention may be administered either simultaneously with the cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors, or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering protein or other active ingredient of the present invention in combination with cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors.
4.12.1 ROUTES OF ADMINISTRATION
Suitable routes of administration may, for example, include oral, rectal, transmucosal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections. Administration of protein or other active ingredient of the present invention used in the 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 occurring as complication of glaucoma surgery, the compounds may be administered topically, for example, as eye drops. Furthermore, one may administer the drug in a targeted drug delivery system, for example, in a liposome coated with a specific 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 similar studies in appropriate animal models. Dosages can then be adjusted as necessary by the clinician to provide maximal therapeutic benefit.
4.12.2 COMPOSITIONS/FORMiTLATIONS
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 form, the pharmaceutical composition of the invention may additionally contain a solid carrier such as a gelatin or an adjuvant. The tablet, capsule, and powder contain from about 5 to 95% protein or other active ingredient of the present invention, and preferably from about 25 to 90% protein or other active ingredient of the present invention. When administered in liquid form, a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil, mineral oil, soybean oil, or sesame oil, or synthetic oils may be added. The liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol.
When administered in liquid form, the pharmaceutical composition contains from about 0.5 to 90% by weight of protein or other active ingredient of the present invention, and preferably from 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, paxenterally 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 I S 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 inj ection, the agents of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
For oral administration, the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated. Pharmaceutical preparations for oral use can be obtained from a solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, 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 plasticizes, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for such administration. For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.
For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch. The compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion.
Formulations for injection may be presented in unit dosage form, e.g., in ampules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated WO 01/57190 . PCT/USO1/04098 solutions. Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use..
The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides. In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection.
Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
A pharmaceutical carrier for the hydrophobic compounds of the invention is a co-solvent system comprising benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. The co-solvent system may be the VPD co-solvent system. VPD
is a solution of 3% w/v benzyl alcohol, 8% w/v of the nonpolax surfactant polysorbate 80, and 65% w/v polyethylene glycol 300, made up to volume in absolute ethanol. The VPD co-solvent system (VPD:SV~ consists of VPD diluted 1:1 with a 5% dextrose in water solution.
This co-solvent system dissolves hydrophobic compounds well, and itself produces low toxicity upon systemic administration. Naturally, the proportions of a co-solvent system may be varied considerably without destroying its solubility and toxicity characteristics. Furthermore, the identity of the co-solvent components may be varied: for example, other low-toxicity nonpolar surfactants may be used instead of polysorbate 80; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g. polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose. Alternatively, other delivery systems for hydrophobic pharmaceutical compounds may be employed. Liposomes and emulsions are well known examples of delivery vehicles or carriers for hydrophobic drugs. Certain organic solvents such as dimethylsulfbxide also may be employed, although usually at the cost of greater toxicity.
Additionally, the compounds may be delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the therapeutic agent.
Various types of sustained-release materials have been established and are well known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the therapeutic reagent, additional strategies for protein or other active ingredient stabilization may be employed.
The pharmaceutical compositions also may comprise suitable solid or gel phase carriers or excipients. Examples of such carriers or excipients include but axe 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 axe those salts which retain the biological effectiveness and properties of the free acids and which are obtained by reaction with inorganic or organic bases such as sodium hydroxide, magnesium hydroxide, ammonia, trialkylamine, dialkylarnine, 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 ingxedient(s) of present invention along with protein or peptide antigens. The protein and/or peptide antigen will deliver a stimulatory signal to both B and T
lymphocytes. B lymphocytes will respond to antigen through their surface immunoglobulin receptor. T lymphocytes will respond to antigen through the T cell receptor (TCR) following presentation of the antigen by MHC proteins. MHC and structurally related proteins including those encoded by class I and class II MHC genes on host cells will serve to present the peptide antigens) to T lymphocytes. The antigen components could also be supplied as purified MHC-peptide complexes alone or with co-stimulatory molecules that can directly signal T cells.
Alternatively antibodies able to bind surface immunoglobulin and other molecules on B cells as well as antibodies able to bind the TCR and other molecules on T cells can be combined with the pharmaceutical composition of the invention.
The pharmaceutical composition of the invention may be in the form of a liposome in which protein of the present invention is combined, in addition to other pharmaceutically acceptable 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 skill in the art, as disclosed, fox example, in U.S.
Patent Nos. 4,235,871; 4,501,728; 4,837,028; and 4,737,323, all of which are incorporated herein by reference.
The amount of protein or other active ingredient of the present invention in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments which the patient has undergone. Ultimately, the attending physician will decide the amount of protein or other active ingredient of the present invention with which to treat each individual patient. Initially, the attending physician will administer low doses of pxotein 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 should contain about 0.01 ~,g to about 100 mg (preferably about 0.1 ~g to about 10 mg, more preferably about 0.1 ~g to about 1 mg) of protein or other active ingredient of the present invention per kg body weight. For compositions of the present invention which are useful for bone, cartilage, tendon or ligament regeneration, the therapeutic method includes administering the composition 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 simultaneously or sequentially with the composition in the methods of the invention. Preferably for bone and/or cartilage formation, the composition would include a matrix capable of delivering the protein-containing or other active 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 axe comprised of pure proteins or extracellular matrix components.
Other potential matrices are nonbiodegradable and chemically defined, such as sintered hydroxyapatite, bioglass, aluminates, or other ceramics. Matrices may be comprised of combinations of any of the above mentioned types of material, such as polylactic acid and hydroxyapatite or collagen and tricalcium phosphate. The bioceramics may be altered in composition, such as in calcium-aluminate-phosphate and processing to alter pore size, particle size, particle shape, and biodegradability. Presently preferred is a 50:50 (mole weight) copolymer of lactic acid and glycolic acid in the form of porous particles having diameters ranging from 150 to 800 microns.

In some applications, it will be useful to utilize a sequestering agent, such as carboxymethyl cellulose or autologous blood clot, to prevent the protein compositions from disassociating from the matrix.
A preferred family of sequestering agents is cellulosic materials such as alkylcelluloses (including hydroxyalkylcelluloses), including methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl-methylcellulose, and carboxymethylcellulose, the most preferred being cationic salts of carboxymethylcellulose (CMC). Other preferred sequestering agents include hyaluronic acid, sodium alginate, polyethylene glycol), polyoxyethylene oxide, carboxyvinyl polymer and polyvinyl alcohol).
The amount of sequestering agent useful herein is 0.5-20 wt %, preferably 1-10 wt % based on total formulation weight, which represents the amount necessary to prevent desorption of the protein from the polymer matrix and to provide appropriate handling of the composition, yet not so much that the progenitor cells are prevented from infiltrating the matrix, thereby providing the protein the opportunity to assist the osteogenic activity of the progenitor cells. In further compositions, proteins or other active ingredients of the invention may be combined with other agents beneficial to the treatment of the bone and/or cartilage defect, wound, or tissue in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet derived growth factor (PDGF), transforming growth factors (TGF-a, and TGF-(3), and insulin-like growth factor (IGF).
The therapeutic compositions are also presently valuable for veterinary applications.
Particularly domestic animals and thoroughbred horses, in addition to humans, are desired patients for such treatment with proteins or other active ingredients of the present invention. The dosage regimen of a protein-containing pharmaceutical composition to be used in tissue regeneration will be determined by the attending physician considering various factors which modify the action of the proteins, e.g., amount of tissue weight desired to be formed, the site of damage, the condition of the damaged tissue, the size of a wound, type of damaged tissue (e.g., bone), the patient's age, sex, and diet, the severity of any infection, time of administration and other clinical factors. The dosage may vary with the type of matrix used in the reconstitution and with inclusion of other proteins in the pharmaceutical composition. For example, the addition of other known growth factors, such as IGF I (insulin like growth factor I), to the final composition, may also effect the dosage. Progress can be monitored by periodic assessment of tissue/bone growth and/or repair, for example, X-rays, histomorphometric determinations and tetracycline labeling.
Polynucleotides of the present invention can also be used for gene therapy.
Such polynucleotides can be introduced either in vivo or ex vivo into cells for expression in a mammalian subject. Polynucleotides of the invention may also be administered by other known methods for introduction of nucleic acid into a cell or organism (including, without limitation, in the form of viral vectors or naked DNA). Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells. Treated cells can then be introduced in viva fox therapeutic purposes.
4.12.3 EFFECTIVE DOSAGE
Pharmaceutical compositions suitable for use in the present invention include compositions wherein the active ingredients are contained in an effective amount to achieve its intended purpose. More specifically, a therapeutically effective amount means an amount effective. to prevent development of or to alleviate the existing symptoms of the subject being treated. Determination of the effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from appropriate in vitro assays. For example, a dose can be formulated in animal models to achieve a circulating concentration range that can be used to more accurately determine useful doses in humans. For example, a dose can be formulated in animal models to achieve a circulating concentration range that includes the ICso as determined in cell culture (i.e., the concentration of the test compound which achieves a half maximal inhibition of the protein's biological activity).
Such information can be used to more accurately determine useful doses in humans.
A therapeutically effective dose refers to that amount of the compound that results in amelioration of symptoms ox 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 SO% 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 ih vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations.
Dosage intervals can also be determined using MEC value. Compounds should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%. In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.
An exemplary dosage regimen for polypeptides or other compositions of the invention will be in the range of about 0.01 ~,g/kg to 100 mg/kg of body weight daily, with the preferred dose being about 0.1 ~,g/kg to 25 mg/kg of patient body weight daily, varying in adults and children. Dosing may be once daily, or equivalent doses may be delivered at longer or shorter intervals.
The amount of composition administered will, of course, be dependent on the subject being treated, on the subject's age and weight, the severity of the affliction, the manner of administration and the judgment of the prescribing physician.
4.12.4 PACKAGING
The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. Compositions comprising a compound of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.
4.13 ANTIBODIES
Also included in the invention are antibodies to proteins, or fragments of proteins of the invention. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, Fab, Fab' and F(ab~)2 fragments, and an Fab 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 human antibody species.
An isolated related protein of the invention may be intended to serve as an antigen, or a portion or fragment thereof, and additionally can be used as an immunogen to generate antibodies that immunospecifically bind the antigen, using standard techniques for polyclonal and monoclonal antibody preparation. The full-length protein can be used or, alternatively, the invention provides antigenic peptide fragments of the antigen fox use as immunogens. An antigenic peptide fragment comprises at least 6 amino acid residues of the amino acid sequence of the full length protein, such as an amino acid sequence shown in SEQ ID
N0:985, and encompasses an epitope thereof such that an antibody raised against the peptide forms a specific immune complex with the full length protein or with any fragment that contains the epitope.
Preferably, the antigenic peptide comprises at least I O 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 are regions of the protein that are located on its surface; commonly these are hydrophilic regions.
In certain embodiments of the invention, at least one epitope encompassed by the antigenic peptide is a 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 shoving regions of hydrophilicity and hydrophobicity may be generated by any method well known in the art, including, for example, the Kyte Doolittle or the Hopp Woods methods, either with or without Fourier transformation. See, e.g., Hopp and 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 immunospecifically bind these protein components.
Various procedures known within the art may be used for the production of polyclonal or monoclonal antibodies directed against a protein of the invention, or against derivatives, fragments, analogs homologs or orthologs thereof (see, for example, Antibodies: A Laboratory Manual, Harlow E, and Lane D, 1988, Cold Spring Harbor Laboratory Press, Cold Spring Haxbor, NY, incorporated herein by reference). Some of these antibodies are discussed below.
5.13.1 Polyclonal Antibodies For the production of polyclonal antibodies, various suitable host animals (e.g., rabbit, goat, mouse or other mammal) may be immunized by one or more injections with the native protein, a synthetic variant thereof, or a derivative of the foregoing. An appropriate immunogenic preparation can contain, for example, the naturally occurring immunogenic protein, a chemically synthesized polypeptide representing the immunogenic protein, or a recombinanlly expressed immunogenic protein. Furthermore, the protein may be conjugated to a second protein known to be immunogenic in the mammal being immunized.
Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The preparation can further include an adjuvant. Various adjuvants used to increase the immunological response include, but axe not limited to, Freund's (complete and incomplete), mineral gels (e.g., aluminum hydroxide), surface active substances (e.g., lysolecithin, platonic 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 mammal (e.g., from the blood) and further purified by well known techniques, such as affinity chromatography using protein A or protein G, which provide primarily the IgG
fraction of immune serum. Subsequently, or alternatively, the specific antigen which is the target of the immunoglobulin sought, or an epitope thereof, may be immobilized on a column to purify the immune specific antibody by inununoaffinity chromatography.
Purification of immunoglobulins is discussed, for example, by D. Wilkinson (The Scientist, published by The Scientist, Inc., Philadelphia PA, Vol. 14, No. 8 (April 17, 2000), pp. 25-28).
5.13.2 Monoclonal Antibodies The term "monoclonal antibody" (MAb) or "monoclonal antibody composition", as used herein, refers to a population of antibody molecules that contain only one molecular species of antibody molecule consisting of a unique light chain gene product and a unique heavy chain gene product. In particular, the complementarily determining regions (CDRs) of the monoclonal antibody are identical in alI the molecules of the population. MAbs thus contain an antigen binding site capable of immunoreacting with a particular epitope of the antigen characterized by a unique binding affinity for it.
Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes can be immunized in vitro.
The immunizing agent will typically include the protein antigen, a fragment thereof or a fusion protein thereof. Generally, either peripheral blood lymphocytes are used if cells of human origin are desired, or spleen cells or lymph node cells 'are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (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 irmnortalized cell lines axe 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 marine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, California and the American Type Culture Collection, Manassas, Virginia. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Maxcel Dekker, Inc., New York, (1987) pp.
51-63).
The culture medium in which the hybridoma cells axe cultured can then be assayed for the presence of monoclonal antibodies directed against the antigen.
Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the axt. 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-Sephaxose, 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 marine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also can be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous marine 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-immunoglobulin 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.
5.13.2 Humanized Antibodies The antibodies directed against the protein antigens of the invention can further comprise humanized antibodies or human antibodies. These antibodies are suitable for administration to humans without engendering an immune response by the human against the administered immunoglobulin. Humanized forms of antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or other antigen-binding subsequences of antibodies) that are principally comprised of the sequence of a human immunoglobulin, and contain minimal sequence derived from a non-human immunoglobulin.
Humanization can be performed following the method of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988);
Verhoeyen et al., Science, 239:1534-1536 (1988)), by substituting 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-human immunoglobulin and all or substantially all of the framework regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., 1986; Riechmann et al., 1988; and Presta, Curr.
On. Struct. Biol., 2:593-596 (1992)).
5.13.3 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 I~ozbor, et al., 1983 Immunol Today 4: 72) and the EBV hybridoma technique to produce human monoclonal antibodies (see Cole, et al., 1985 In:
MONOCLONAL
ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96). Human monoclonal antibodies may be utilized in the practice of the present invention and may be produced by using human hybridomas (see Cote, et al., 1983. Proc Natl Acad Sci USA 80: 2026-2030) or by transforming human B-cells with Epstein Barr Virus in vitro (see Cole, et al., 1985 In:
MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96).
In addition, human antibodies can also be produced using additional techniques, including phage display libraries (Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991);
Marks et al., J. Mol. Biol., 222:581 (1991)). Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated.
Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Patent Nos. 5,545,807; 5,545,806;
5,569,825; 5,625,126;
5,633,425; 5,661,016, and in Marks et al. (Bio/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 (Nature Biotechnolo~y 14, 826 (1996)); and Lonberg and Huszar (Intern. Rev. Irnmunol. 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 W094102602). The endogenous genes encoding the heavy and light immunoglobulin chains in the nonhuman host have been incapacitated, and active loci encoding hmnan heavy and light chain immunoglobulins are inserted into the host's genome. The human genes are incorporated, for example, using yeast artificial chromosomes containing the requisite human DNA segments. An animal which provides all the desired modifications is then obtained as progeny by crossbreeding intermediate transgenic animals containing fewer than the full complement of the modifications. The preferred embodiment of such a nonhuman animal is a mouse, and is termed the XenomouseTM
as disclosed in PCT publications WO 96/33735 and WO 96/34096. This animal produces B cells 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 human variable regions can be recovered and expressed to obtain the antibodies directly, or can be further modified to obtain analogs of antibodies such as, for example, single chain Fv molecules.
An example of a method of producing a nonhuman host, exemplified as a mouse, lacking expression of an endogenous immunoglobulin heavy chain is disclosed in U.S.
Patent No.
5,939,598. It can be obtained by a method including deleting the J segment genes from at least one endogenous heavy chain locus in an embryonic stem cell to prevent rearrangement of the locus and to prevent formation of a transcript of a rearranged immunoglobulin heavy chain locus, the deletion being effected by a targeting vector containing a gene encoding a selectable marker;
and producing from the embryonic stem cell a transgenic mouse whose somatic and germ cells contain the gene encoding the selectable marker.
A method for producing an antibody of interest, such as a human antibody, is disclosed in U.S. Patent No. 5,916,771. It includes introducing an expression vector that contains a nucleotide sequence encoding a heavy chain into one mammalian host cell in culture, introducing an expression vector containing a nucleotide sequence encoding a light chain into another so 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.
5.13.4 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~ab~~2 fragment produced by pepsin digestion of an antibody molecule; (ii) an Fab fragment generated by reducing the disulfide bridges of an F(ab')2 fragment; (iii) an Fab fragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) F~ fragments.
5.13.5 Bispecific Antibodies Bispecific antibodies.are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for an antigenic protein of the invention. The second binding target is any other antigen, and advantageously is a cell-surface protein or receptor or receptor subunit.
Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published 13 May 1993, and in Traunecker et al., 1991 EMBO J., 10:3655-3659.
Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CHl) 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 Enzymolo~y, 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 procedure wherein intact antibodies axe 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')2 molecule. Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.

Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al., J. Immunol. 148(5):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 heterodimers. This method can also be utilized for the production of antibody homodimers. The "diabody"
technology described by Hollinger et al., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) by a linker which is too short to allow pairing between the two domains on the same chain.
Accordingly, the VH arid VL domains of one fragment are forced to pair with the complementary VL and VH
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 (CD 16) 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).
5.13.6 Heteroconjugate Antibodies Heteroconjugate antibodies are also within the scope of the present invention.
Heteroconjugate antibodies are composed of two covalently joined antibodies.
Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Patent No. 4,676,980), and for treatment of HIV infection (WO 91/00360; WO 92/200373;
EP 03089).
It is contemplated that the antibodies can be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins can be constructed using a disulfide exchange reaction or by forming a thioether bond.
Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Patent No.
4,676,980.
5.13.7 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 cellulax cytotoxicity (ADCC). See Caron et al., J. Exp Med., 176:
1191-1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumor activity can also be prepared using heterobifunctional cross-linkers as described in Wolff et al. Cancer Research, 53: 2560-2565 (1993). Alternatively, an antibody can be engineered that has dual Fc regions and can thereby have enhanced complement lysis and ADCC
capabilities.
See Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989).
5.13.8 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 radioconj ugate).
Chemotherapeutic agents useful in the generation of such immunoconjugates have been described above. Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, croon, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A
variety of radionuclides are available for the production of radioconjugated antibodies.
Examples include aiaBi~ i3ih isiln~ 9oY~ ~d is6Re.
Conjugates of the antibody and cytotoxic agent axe 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 streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand" (e.g., avidin) that is in turn conjugated to a cytotoxic agent.
4.14 COMPUTER READABLE SEQUENCES
In one application of this embodiment, a nucleotide sequence of the present invention can be recorded on computer readable media. As used herein, "computer readable media" refers to any medium which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM
and ROM; and hybrids of these categories such as magnetic/optical storage media. A slcilled artisan can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising computer readable medium having recorded thereon a nucleotide sequence of the present invention. As used herein, "recorded"
refers to a process for storing information on computer readable medium. A skilled artisan can readily adopt any of the presently known methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention.
A variety of data storage structures are available to a skilled artisan for creating a computer readable medium having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and Microsoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data processor structuring formats (e.g. text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information, of the present invention.
By providing any of the nucleotide sequences SEQ ID NO: 1-984, 1969-2952, 3937-or 3949-3954 or a representative fragment thereof; or a nucleotide sequence at least 95%
identical to any of the nucleotide sequences of SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954 in computer readable form, a skilled artisan can routinely access the sequence information for a variety of purposes. Computer software is publicly available which allows a skilled artisan to access sequence information provided in a computer readable medium. The examples which follow demonstrate how software which implements the BLAST
(Altschul et al., J. Mol. Biol. 215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem.
17:203-207 (1993)) search algorithms on a Sybase system is used to identify open reading frames (ORFs) within a nucleic acid sequence. Such ORFs may be protein encoding fragments and may be useful in producing commercially important proteins such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.
As used herein, "a computer-based system" refers to the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based systems are suitable for use in the present invention. As stated above, the computer-based systems of the present invention comprise a data storage means having stored therein a nucleotide sequence of the present invention and the necessary hardware means and software means for supporting and implementing a search means. As used herein, "data storage means" refers to memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.
As used herein, "search means" refers to one or more programs which are implemented on the computer-based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Seaxch 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), BLAST'N and BLASTA (NPOLYPEPTIDEIA). A
skilled artisan can readily recognize that any one of the available algorithms or implementing software packages for conducting homology searches can be adapted for use in the present computer-based systems. As used herein, a "target sequence" can be any nucleic acid or amino acid sequence of six or more nucleotides or two or more amino acids. A skilled artisan can readily recognize that the longer a target sequence is, the less likely a target sequence will be present as a random occurrence in the database. The most preferred sequence length of a target sequence is from about 10 to 300 amino acids, more preferably from about 30 to 100 nucleotide residues. However, it is well recognized that searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing, may be of shorter length.
As used herein, "a target structural motif," or "target motif," refers to any rationally selected sequence or combination of sequences in which the sequences) are chosen based on a three-dimensional configuration which is formed upon the folding of the target motif. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzyme active sites and signal sequences. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences).
4.15 TRIPLE HELIX FORMATION
In addition, the fragments of the present invention, as broadly described, can be used to control gene expression through triple helix formation or antisense DNA or RNA, both of which methods are based on the binding of a polynucleotide sequence to DNA or RNA.
Polynucleotides suitable for use in these methods are preferably 20 to 40 bases in length and are designed to be complementary to a region of the gene involved in transcription (triple helix - see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 15241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense - Olmno, J.
Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC
Press, Boca Raton, FL (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA
molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems.
Information contained in the sequences of the present invention is necessary for the design of an antisense or triple helix oligonucleotide.
4.16 DIAGNOSTIC ASSAYS AND KITS
The present invention further provides methods to identify the presence or expression of one of the ORFs of the present invention, or homolog thereof, in a test sample, using a nucleic acid probe or antibodies of the present invention, optionally conjugated or otherwise associated with a suitable label.
In general, methods for detecting a polynucleotide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polynucleotide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polynucleotide of the invention is detected in the sample. Such methods can also comprise contacting a sample under stringent hybridization conditions with nucleic acid primers that anneal to a polynucleotide of the invention under such conditions, and amplifying annealed polynucleotides, so that if a polynucleotide is amplified, a polynucleotide of the invention is detected in the sample.
In general, methods for detecting a polypeptide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polypeptide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polypeptide of the invention is detected in the sample.
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 Chaxd, T., An Introduction to Radioimmunoassay and Related Techniques, Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G.R. et al., Techniques in Immunocytochemistry, Academic Press, Orlando, FL Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985);
Tijssen, P., Practice and Theory of immunoassays: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985). The test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is compatible with the system utilized.
8s 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 axe 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., I~unkel 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 ih 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:

1-9~4, 1969-2952, 3937-3942 or 3949-3954, 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 fox a time sufficient to form a polynucleotidelcompound 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 compounds that bind to a polypeptide of the invention can comprise contacting a compound with a polypeptide of the invention for a time sufficient to form a polypeptide/compound complex, and detecting the complex, so that if a polypeptide/compound complex is detected, a compound that binds to a polynucleotide of the invention is identified.
Methods for identifying compounds that bind to a polypeptide of the invention can also comprise contacting a compound with a polypeptide of the invention in a cell for a time sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a receptor gene sequence in the cell, and detecting the complex by detecting reporter gene sequence expression, so that if a polypeptide/compound complex is detected, a compound that binds a polypeptide of the invention is identified.
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 of the present invention. Alternatively, agents may be rationally selected or designed.

As used herein, an agent is said to be "rationally selected ox designed" when the agent is chosen based on the configuration of the particular protein. For example, one skilled in the art can readily adapt currently available procedures to generate peptides, pharmaceutical agents and the Like, capable of binding to a specific peptide sequence, in order to generate rationally designed antipeptide peptides, for example see Hurby et al., Application of Synthetic Peptides: Antisense Peptides," Tn Synthetic Peptides, A User's Guide, VJ.H. Freeman, NY (1992), pp. 289-307, and Kaspczak et al., Biochemistry 28:9230-8 (I989), or pharmaceutical agents, or the like.
Tn 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 ox rationally designed/selected. Targeting the ORF or EMF allows a skilled artisan to design sequence specific or element specific agents, modulating the expression of either a single ORF or multiple ORFs which rely on the same EMF for expression control. One class of DNA binding agents are agents which contain base residues which hybridize or form a triple helix formation by binding to DNA or RNA. Such agents can be based on the classic phosphodiester, ribonucleic acid backbone, or can be a variety of sullhydryl ox 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); Coaney et al., Science 241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense - Okano, J.
Neurochem. 56:560 {1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC
Press, Boca Baton, 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.
Tnformation 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.
x.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: 1-984, 1969-2952, 3937-3942 or 3949-3954. Because the corresponding gene is only expressed in a limited number of tissues, a hybridization probe derived from of any of the nucleotide sequences SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954 can be used as an indicator of the presence of RNA of cell type of such a tissue in a sample.
Any suitable hybridization technique can be employed, such as, for example, in situ hybridization. PCR as described in US Patents Nos. 4,683,195 and 4,965,188 provides additional uses for oligonucleotides based upon the nucleotide sequences. Such probes used in PCR may be of recombinant origin, may be chemically synthesized, or a mixture of both. The probe will comprise a discrete nucleotide sequence for the detection of identical sequences or a degenerate pool of possible sequences for identification of closely related genomic sequences.
Other means for producing specific hybridization probes for nucleic acids include the cloning of nucleic acid sequences into vectors for the production of mRNA
probes. Such vectors are known in the art and are commercially available and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA 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 and/or chromosomal mapping techniques.
These techniques include in situ hybridization, linkage analysis against known chromosomal markers, hybridization screening with libraries or flow-sorted chromosomal preparations specific to known chromosomes, and the like. The technique of fluorescent in situ hybridization of chromosome spreads has been described, among other places, in Verma et al (1988) Human Chromosomes: A Manual of Basic Techniques, Pergamon Press, New York NY.
Fluorescent 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 (265:1981 f). Correlation between the location of a nucleic acid on a physical chromosomal map and a specific disease (or predisposition to a specific disease) may help delimit the region of DNA
associated with that genetic disease. The nucleotide sequences of the subj ect invention may be used to detect differences in gene sequences between normal, carrier or affected individuals.

4.20 PREPARATION OF SUPPORT BOUND OLIGONUCLEOTIDES
Oligonucleotides, i.e., small nucleic acid segments, may be readily prepared by, for example, directly synthesizing the oligonucleotide by chemical means, as is commonly practiced using an automated oligonucleotide synthesizer.
Support bound oligonucleotides may be prepared by any of the methods known to those of skill in the art using any suitable support such as glass, polystyrene or Teflon. One strategy is to precisely spot oligonucleotides synthesized by standard synthesizers.
Immobilization can be achieved using passive adsorption (Inouye & Hondo, (1990) J. Clin. Microbiol.
28(6) 1469-72);
using UV light (Nagata et al., 1985; Dahlen et al., 1987; Morrissey & Collins, (1989) Mol. Cell Probes 3 (2) 189-207) or by covalent binding of base modified DNA (I~eller 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 Covalink NH. CovaLink NH is a polystyrene surface grafted with secondary amino groups (>NH) that serve as bridge-heads for further covalent coupling.
CovaLink Modules may be purchased from Nunc Laboratories. DNA molecules may be bound to CovaLink exclusively at the 5'-end by a phosphoramidate bond, allowing immobilization of more than 1 pmol 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 phosphoramidatebond is employed (Chu et al., (1983) Nucleic Acids Res. 11(8) 6513-29). This is beneficial as immobilizationusing only a single covalent bond is preferred. The phosphoramidatebond joins the DNA to the CovaLink NH secondary amino groups that are positioned at the end of spacer arms covalently grafted onto the polystyrene surface through a 2 nm long spacer arm. To link an oligonucleotide to CovaLink NH via an phosphoramidate bond, the oligonucleotide terminus must have a 5'-end phosphate group. It is, perhaps, even possible for biotin to be covalently bound to CovaLink and then streptavidin used to bind the probes.

More specifically, the linkage method includes dissolving DNA in water (7.5 ng/ul) 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-MeIm7), is then added to a final concentration of 10 mM 1-MeIm7. A
ss DNA solution is then dispensed into CovaLink NH strips (75 ul/well) standing on ice.
Carbodiimide 0.2 M 1-ethyl-3-(3-dimethylaminopropyl)-caxbodiimide (EDC), dissolved in mM 1-MeIm7, is made fresh and 25 u1 added per well. The strips are incubated for 5 hours at 50°C. After incubation the strips are washed using, e.g., Nunc-Immuno Wash; first the wells are washed 3 times, then they are soaked with washing solution for 5 min., and finally they are washed 3 times (where in the washing solution is 0.4 N NaOH, 0.25% SDS heated to 50°C).
10 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), incorporatedherein 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-activatedphotodeprotectionmay 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 specificallyincorporatedherein.
To link an oligonucleotideto 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 describedby Pease et al., (1994) PNAS USA 91(11) 5022-6, incorporated herein by reference). These authors used current photolithographictechniques 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'-protectedN acyl-deoxynucleosidephosphoramidites, surface linker chemistry and versatile combinatorial synthesis strategies. A matrix of 256 spatially defined oligonucleotideprobes may be 3 5 generated in this manner.

4.21 PREPARATION OF NUCLEIC ACID FRAGMENTS
The nucleic acids may be obtained from any appropriate source, such as cDNAs, genomic DNA, chromosomal DNA, microdissected chromosome bands, cosmid or YAC inserts, and RNA, including mRNA without any amplification steps. For example, Sambrook et al.
(1989) describes three protocols for the isolation of high molecular weight DNA from mammalian cells (p.
9.14-9.23).
DNA fragments may be prepared as clones in M 13, plasmid or lambda vectors and/or prepared directly from genomic DNA or cDNA by PCR or other amplificationmethods. Samples rnay be prepared or dispensed in multiwell plates. About 100-1000 ng of DNA
samples may be prepared in 2-500 ml of final volume.
The nucleic acids would then be fragmented by any of the methods known to those of skill in the art including, for example, using restriction enzymes as described at 9.24-9.28 of Sambrook et al. (1989), shearing by ultrasound and NaOH treatment.
Low pressure shearing is also appropriate, as described by Schriefer et al.
(1990) Nucleic Acids Res. 18(24) 7455-6, incorporated herein by reference). In this method, DNA samples are passed through a small French pressure cell at a variety of low to intermediatepressures. A lever device allows controlled application of low to intermediate pressures to the cell. The results of these studies indicate that low-pressure shearing is a useful alternative to sonic and enzymatic DNA
fragmentation methods.
One particularly suitable way for fragmenting DNA is contemplated to be that using the two base recognition endonuclease, CviJI, described by Fitzgerald et al. (1992) Nucleic Acids Res.
20(14) 3753-62. These authors described an approach for the rapid fragmentation and fractionation of DNA into particular sizes that they contemplated to be suitable for shotgun cloning and sequencing.
The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions, which alter the specificity of this enzyme (CviJI* *), yield a quasi-random distribution of DNA fragments form the small molecule pUC 19 (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 fractionatedby a rapid gel filtrationmethod and directly ligated, without end repair, to a lac Z minus M 13 cloning vector. Sequence analysis of 76 clones showed that CviJI* *
restricts pyGCPy and PuGCPu, in addition to PuGCPy sites, and that new sequence data is accumulated at a rate consistent with random fragmentation.
As reported in the literature, advantages of this approach compared to sonication and agarose gel fractionation include: smaller amounts of DNA are required (0.2-0.5 ug instead of 2-5 ug); and fewer steps are involved (no preligation, end repair, chemical extraction, or agarose gel electrophoresis and elution are needed Irrespective of the manner in which the nucleic acid fragments are obtained or prepared, it is important to denature the DNA to give single stranded pieces available for hybridization. This is achieved by incubating the DNA solution for 2-5 minutes at 80-90°C. The solution is then cooled quickly to 2°C to prevent renaturation of the DNA fragments before they are contacted with the chip. Phosphate groups must also be removed from genomic DNA by methods known in the art.
4.22 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 preselectednumber of rows and columns, separate subsets (subarrays) may be formed. Samples in one subarray may be the same genomic segment of DNA
(or the same gene) from different individuals, or may be different, overlapped genomic clones. Each of the subarrays may represent replica spotting of the same samples. In one example, a selected gene segment may be amplified from 64 patients. For each patient, the amplified gene segment may be in one 96-well plate (all 96 wells containing the same sample). A plate for each of the 64 patients is prepared. By using a 96-pin device, all samples may be spotted on one 8 x 12 cm membrane.
Subarrays may contain 64 samples, one from each patient. Where the 96 subarrays are identical, the dot span may be 1 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.
5.0 EXAMPLES
5.1 EXAMPLE 1 Novel Nucleic Acid Seduences Obtained From Various Libraries A plurality of novel nucleic acids were obtained from cDNA libraries prepared from various human tissues and in some cases isolated from a genomic library derived from human chromosome using standard PCR, SBH sequence signature analysis and Sanger sequencing techniques. The inserts of the library were amplified with PCR using primers specific for the vector sequences which flank the inserts. Clones from cDNA libraries were spotted on nylon membrane filters and screened with oligonucleotide probes (e.g., 7-mers) to obtain signature sequences. The clones were clustered into groups of similar or identical sequences. Representative clones were selected for sequencing.
In some cases, the 5' sequence of the amplified inserts was then deduced using a typical Sanger sequencing protocol. PCR products were purified and subj ected to fluorescent dye terminator cycle sequencing. Single pass gel sequencing was done using a 377 Applied Biosystems (ABI) sequencerto obtain the novel nucleic acid sequences. In some cases RACE
(Random Amplification of cDNA Ends) was performed to further extend the sequence in the 5' direction.
5,2 EXAMPLE 2 Assemblage of Novel Nucleic Acids The contigs or nucleic acids of the present invention, designated as SEQ ID
NO: 1969-2951, and 3949-3954 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
version 114, gb pri 114, and UniGene version 1 O 1 ) that belong to this assemblage. The algorithm terminated when there was no additional sequences from the above databases that would extend the assemblage.
Inclusion of component sequences into the assemblage was based on a BLASTN hit to the extending assemblage with BLAST score greater than 300 and percent identity greater than 95%.
Tables 6 and 8 sets forth the novel predicted polypeptides (including proteins) encoded by the novel polynucleotides (SEQ ID N0:2953-3936, and 3949-3954) of the present invention, and their corresponding nucleotide locations to each of SEQ ID NO: 2953-3936 and 3955-3960. Tables 6 and 8 also indicates the method by which the polypeptide was predicted.
Method A refers to a polypeptide obtained by using a software program called FASTY (available from http://fasta.bioch.virginia,edu) which selects a polypeptide based on a comparison of the translated novel polynucleotide to known polynucleotides (W.R. Pearson, Methods in Enzymology,183:63-98 ( 1990), herein incorporated by reference). Method B refers to a polypeptide obtained by using a software program called GenScan for human/vertebrate sequences (available from Stanford University, Office of Technology Licensing) that predicts the polypeptide based on a probabilistic model of gene structure/compositionalproperties (C SBurge and S. Karlin, J.
Mol. Biol., 268:78-94 ( I 997), incorporated herein by reference). Method C refers to a polypeptide obtained by using a Hyseq proprietary software program that translates the novel polynucleotide and its complementary strand into six possible amino acid sequences (forward and reverse frames) and chooses the polypeptide with the longest open reading frame.
5.3 EXAMI':L.:~~ 3 Novel Nucleic Acids Using PHRAP (Univ. of Washington) or CAP4 (Paracel), full length gene cDNA
sequences and their corresponding protein sequences were generated from the assemblage.
A,ny frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTY and/or BLAST against Genebank. Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). The full-length nucleotide sequences are shown in the Sequence Listing as SEQ ID NO:l-351. The amino acids are SEQ ID N0:985-1335.
Table 1 shows the various tissue sources of SEQ ID NO: 1-351.
The nearest neighbor results for SEQ ID NO: 1-351 were obtained by a BLASTP
version 2.0a1 19MP-WashU search against Genpept release 120 and Geneseq October 12, 2000 release 21 (Derwent), using BLAST algorithm. The nearest neighbor result showed the closest homologue for SEQ ID NO: 1-351 from Genpept . The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologs with identifiable functions for SEQ ID NO: 1-351 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), all the sequences 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) all the polypeptide sequences 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 nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determine from using Neural Network SignalP V 1.1 program (from Center for Biological Sequence Analysis, The Technical Uuversity of Denmark).
The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson, Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication "
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites"
Protein Engineering, Vol. 10, no. 1, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et as reference, was obtained for the polypeptide sequences. Table 7 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.
5.4 EXAMPLE 4 Novel Nucleic Acids Using PHRAP (Univ. of Washington) or CAP4 (Paracel), a full length gene cDNA
sequence and its corresponding protein sequence were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTY and/or BLAST against Genbank (i.e. dbEST version 117, gb pri 117, UniGene version 117, Genpept release 117). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). The full-length nucleotide, including splice variants resulting from these procedures are shown in the Sequence Listing as SEQ ID NOS: 352-766. The corresponding amino acids are SEQ ID NO: 1336-1750.
Table 1 shows the various tissue sources of SEQ ID NO: 352-766.
The nearest neighbor results for SEQ ID NO: 352-766 were obtained by a BLASTP
version 2.0a1 19MP-WashU search against Genpept release 120 and Geneseq October 12, 2000 release 21 (Derwent), using BLAST algoritlun. The nearest neighbor result showed the closest homologue for SEQ ID NO: 352-766 from Genpept . The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologs with identifiable functions for SEQ ID NO: 352-766 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), all the sequences 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) all the polypeptide sequences 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 nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determine from using Neural Network SignalP V 1.1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark).
The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson, Jacob Engelbrecht, Soren Brunak, and Gunnax von Heijne in the publication " Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites" Protein Engineering, Vol. 10, no. l, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et as reference, was obtained for the polypeptide sequences. Table 7 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.
5.5 ~XAMPL:C 5 Novel Nucleic Acids Using PHRAP (Univ. of Washington) or CAP4 (Paracel), a full length gene cDNA
sequence and its corresponding protein sequence were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTY and/or BLAST against Genbank (i.e., dbEST version 118, gb pri 118, UniGene version 118, Genpept release 118). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). The full-length nucleotide, including splice variants resulting from these procedures are shown in the Sequence Listing as SEQ ID NOS: 767-930. The corresponding amino acid sequences axe SEQ ID N0:1751-1914.
Table 1 shows the various tissue sources of SEQ ID NO: 767-930.
loo The homology results for SEQ ID NO: 767-930 were obtained by a BLASTP version 2.0a1 19MP-WashU search against Genpept release 120 and Geneseq October 12, 2000 release 21 (Derwent), using BLAST algorithm. The nearest neighbor result showed the homologs for SEQ.ID NO: 767-930 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: 767-930 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), all the sequences 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) all the polypeptide sequences 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 nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determine from using Neural Network SignalP V 1.1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark).
The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson, Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication " Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites" Protein Engineering, Vol. 10, no. 1, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et as reference, was obtained for the polypeptide sequences. Table 7 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.
5.6 EXAMPLE 6 Novel Nucleic Acids Using PHR.AP (Univ. of Washington) or CAP4 (Paracel), a full length gene cDNA
sequence and its corresponding protein sequence were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTY and/or BLAST against Genbank (i.e. dbEST version 118, gb pri 118, UniGene version 118, Genpept release 118). Other computer programs which may have been used 10i WO 01/57190 . PCT/USO1/04098 in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). The full-length nucleotide, including splice variants resulting from these procedures are shown in the Sequence Listing as SEQ ID NOS: 931-965. The corresponding amino acid sequences are shown in SEQ ID N0:1915-1949.
Table 1 shows the various tissue sources of SEQ ID NO: 931-965.
The nearest neighbor results for SEQ ID NO: 931-965 were obtained by a BLASTP
version 2.0a1 19MP-WashU search against Genpept release 120 and Geneseq October 12, 2000 release (Derwent), using BLAST algorithm. The nearest neighbor result showed the closest homologue for SEQ ID NO: 931-965 from Genpept . The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologs with identifiable functions for SEQ ID NO: 931-965 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), all the sequences 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) all the polypeptide sequences 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 nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determine from using Neural Network SignalP V 1.1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark).
The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson, Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication " Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites" Protein Engineering, Vol. 10, no. 1, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et as reference, was obtained for the polypeptide sequences. Table 7 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.
5.7 EXAMPLE 7 Novel Nucleic Acids Using PHRAP (Univ. of Washington) or CAP4 (Paracel), a full length~gene cDNA
sequence and its corresponding protein sequence were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTY and/or BLAST against Genbank (i.e. dbEST version 119, gb pri 119, UniGene version 119, Genpept release 119). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). The full-length nucleotide, including splice variants resulting from these procedures axe shown in the Sequence Listing as SEQ ID NOS:966-974. The corresponding amino acid sequences are SEQ ID N0:1950-1958.
Table 1 shows the various tissue sources of SEQ ID NO: 966-974.
The nearest neighbor results for SEQ ID NO: 966-974 were obtained by a BLASTP
version 2.0a1 19MP-WashU search against Genpept release 120 and Geneseq October 12, 2000 release (Derwent), using BLAST algorithm. The nearest neighbor result showed the closest homologue for SEQ ID NO: 966-974 from Genpept . The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologs with identifiable functions for SEQ ID NO: 966-974 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), all the sequences 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) all the polypeptide sequences 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 nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determine from using Neural Network SignalP V 1.1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark).
The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson, Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication " Identification of pro~Caryotic 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 as reference, was obtained for the polypeptide sequences. Table 7 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.
5,8 EXAMPLE 8 Novel Nucleic Acids Using PHR.AP (Univ. of Washington) or CAP4 (Paracel), a full length gene cDNA
sequence and its corresponding protein sequence were generated from the assemblage, Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTY and/ox BLAST against Genbank (i.e. dbEST version 120, gb pri 120, UniGene version 120, Genpept release 120). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). The full-length nucleotide, including splice variants resulting from these procedures are shown in the Sequence Listing as SEQ ID NOS:975-984. The corresponding amino acid sequences are SEQ ID N0:1959-1968.
Table 1 shows the various tissue sources of SEQ ID NO: 975-984.
The nearest neighbor results for SEQ ID NO: 975-984 were obtained by a BLASTP
version 2.0a1 19MP-WashU search against Genpept release 120 and Geneseq October 21, 2000 release (Derwent), using BLAST algorithm. The nearest neighbor result showed the closest homologue for SEQ ID NO: 975-984 from Genpept . The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologs with identifiable functions for SEQ ID NO: 975-984 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 (I999) herein incorporated by reference), all the sequences 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) all the polypeptide sequences 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 nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determine from using Neural Network SignaIP V 1.1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark).
The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson, Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication " Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites" Protein Engineering, Vol. 10, no. l, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et as reference, was obtained for the poiypeptide sequences. Table 7 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.
5.9 EXAMPLE 9 Novel Nucleic Acids Using PHRAP (Univ. of Washington) or CAP4 (Paracel), a full length gene cDNA
sequence and its corresponding protein sequence were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTY and/or BLAST against Genbank (i.e. dbEST version 120, gb pri I20, UniGene version I20, Genpept release 120). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). The full-length nucleotide, including splice variants resulting from these procedures are shown in the Sequence Listing as SEQ ID NOS:3937-3942.
The correspondingpeptide sequence is SEQ ID NO: 3943-3948.
Table 1 shows the various tissue sources of SEQ ID NO: 3937-3942.
The nearest neighbor results for SEQ ID NO: 3937-3942 were obtained by a BLASTP
version 2.OaI 19MP-WashU search against Genpept release 120 and Geneseq October 12, 2000 release 21 (Derwent), using BLAST algorithm. The nearest neighbor result showed the closest homologue for SEQ ID NO: 3937-3942 from Genpept . The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologs with identifiable functions for SEQ ID NO: 3937-3942 are shown in Table 9 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}, all the sequences were examined to determine whether they had identifiable signature regions. Table 10 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., Val.
26(1) pp. 320-322 (1998} herein incorporated by reference) all the polypeptide sequences were examined for domains with homology to certain peptide domains. Table 11 shows the name of 1os the domain found, the description, the p-value and the pFam score for the identified domain within the sequence.
The nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determine from using Neural Network SignalP V 1.1 program (from Center for Biological Sequence Analysis, The Technical University of Denmark).
The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson, Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication " Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites" Protein Engineering, Vol. 10, no. l, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et as reference, was obtained for the polypeptide sequences. Table 12 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.
Tables 5 and 13 are correlation tables of all of the sequences and the SEQ ID
NOS.

Tissue OriginRNA Library SE(~ ID NOS:

Source Name lung 3 11 25 49 65 75 114 141 156 adult brain GIBCO AB3001 1 3 12-13 16 22-24 28-29 41 adult brain GIBCO ABD003 3 19 21-25 28-29 31 33-34 37 adult brain Clontech ABR001 3 53 66 113 115 126 135 160 adult brain Clontech ABR006 19 32 49 53 60 72 91 103 118 adult brain Clontech ABR008 2-3 9-11 14 17 21 23-25 28-29 adult brain Clontech ABRO11 57 196 270 304 344 436 834 adult brain BioChain ABR012 14 82 121-122 168 691 adult brain InvitrogenABR013 72 108 263 270 336 425 492-494 adult brain InvitrogenABR014 293 394 399 764 768-769 928 adult brain InvitrogenABRO15 738-739 764 adult brain InvitrogenABR016 320 374 396 399 405 684 742-743 adult brain InvitrogenABT004 21 33-34 37-38 47 52 57-58 69 cultured StrategeneADP001 4 28-29 69 93 114 121 132-133 preadipocytes 152159167172178181 184190194-~

1os adrenal glandClontech ADR002 1 3 12-13 21 23-24 27-29 67 adult heart 41 48 54-57 65 69-72 75 78 80 adult kidney GIBCO AKD001 1.3 8 12-14 17 19-25 28-29 33-34 adult kidneyInvitrogenAI~T002 1 3 1621 30 32 35 38-41 46-47 adult lung GIBCO ALG001 1 3 14 18 28-29 38 54-56 59 mo lymph node Clontech ALN001 3 10 110 146 160 168 196 209 young liver GIBCO ALV001 3 14 16 37-38 41 51 56 60 97 adult liver InvitrogenALV002 3 37 42 56 60 71 82 104-105 adult liver Clontech ALV003 60 134 169-171 275 adult ovary InvitrogenAOV001 1 3 9-10 12-14 16 18 20 22-25 m adult placentaInvitrogenAPL001 41 56 67 253 301 304 334 380 placenta InvitrogenAPL002 3 21 31 38 63-64 78 135 143 adult spleenGIBCO ASP001 1 3 21-22 46 52 54-55 57-58 testis GIBCO ATS001 6 22 28-29 33-34 41 48 52 62 Genomic DNA Research BAC001 515 from BAC Genetics 63I18 (CITB BAC

Library) Genomic DNA Research BAC002 640 from BAC Genetics 393I6 (CITB BAC

Library) Genomic DNA Research BAC003 ~ 640 from BAC Genetics 393I6 (CITB BAC

Library) adult bladderInvitrogenBLD001 50 55 66 71 111 143-144 148 bone marrow Clontech BMD001 3 10-13 16 18 20-21 25 28-29 .

bone marrow Clontech BMD002 3 9-10 15-19 30 33-34 39 45 bone marrow Clontech BMD004 54 bone marrow Clontech BMD007 766 887 928 adult colon InvitrogenCLN001 22 37 67 97 117 121 148-149 Mixture of Various CTL016 358 740 760 tissues - Vendors*

mRNAs*

Mixture of Various CTL021 468 527 928 tissues - Vendors*

mRNAs*

adult cervixBioChain CVX001 1 3 10 14 22 28-30 37 41 47-48 * The 16 tissue-mRNAs and their vendor source, are as follows: 1) Normal adult brain mRNA (Invitrogen), 2) normal adult kidney mRNA (Invitrogen), 3) normal adult liver mRNA
(Invitrogen), 4) normal fetal brain mRNA
(Invitrogen), 5) normal fetal kidney mRNA (Invitrogen), 6) normal fetal liver mRNA (Invitrogen), 7) normal fetal skin mRNA (Invitrogen), 8) human adrenal gland mRNA (Clontech), 9) human bone marrow mRNA (Clontech), 10) human leukemia lymphablastic mRNA (Clontech), 11) human thymus mRNA
(Clontech), 12) human lymph node mRNA (Clontech), 13) human spinal cord mRNA (Clontech), 14) human thyroid mRNA (Clontech), 15) human esophagus mRNA (BioChain), 16) human conceptional umbilical cord mRNA
(BioChain).

diaphragm BioChain DIA002 3 39 184 203 431 563 ~54~5 yd ~
endothelial Stxategene EDT001 3 6 8-10 1419-24 28-29 33-34 37 39 41 cells 46 48 52 55-58 62-65 67 69 71-72 75 78 Genomic Genomic EPM001 324 515 640 clones fromDNA from the short arm Genetic of chromosome Research esophagus BioChain ES0002 97 103 128 371 474 fetal brainClontech FBR001 67 129 156 159 232 267 433 446 fetal brainClontech FBR004 28-29 185 213 277 350 384 432 fetal brain Clontech FBR006 10-11 14 21 30 32 47 49 56 65 69 72 77-WO

.

fetal FBRs03 130-131 312 517 637 691 738-739 brain Clontech fetal FBT002 3 22 28-31 47 57 63-64 72 75 brain 77-78 86 Invitrogen fetal FHR001 19 57 130-131 394 431 6_42 769 heart 844 Invitrogen fetal FKD001 3 31 33-34 38 48 54 72160 208-209 kidney 211 Clontech fetal kidneyClontech FKD002 19 474 726 903 fetal kidneyInvitrogenFKD007 3 118 186-187 230 244 271 432 fetal lung Clontech FLG001 69 132-133 156 168 208-209 217 fetal lung InvitrogenFLG003 3 8 28-29 32 39 50 66 82 88 fetal lung Clontech FLG004 130-I31 394 664 769 942 fetal liver-Columbia FLS001 3 8-10 12-13 16-17 19-25 27-29 spleen University 38 41 45-46 48 52 55-58 60-67 374 376-380 382-383 388-389'394-396 fetal liver-Columbia FLS002 3 8-13 15-17 19-20 22 25 28-29 spleen University 41 45-46 52 54-56 60-61 63-64 fetal liver-Columbia FLS003 19 60 78 224 273 275 370 373-374 spleen University 602-603 639 643 730 732 738-739 fetal liver InvitrogenFLV001 37 55 60 69 72-73 97 104-105 fetal liver Clontech FLV002 72 418-419 632 fetal liver Clontech FLV004 3 160 169-171 355 367 374 376 fetal muscleInvitrogenFMS001 15 27 32 37 67 72 83 99 112 fetal muscleInvitrogenFMS002 15 99 130-131 223 361-362 431 fetal skin InvitrogenFSI~001 3 6 20-22 32-34 41-45 47 49-52 fetal skin InvitrogenFSK002 3 130-131 146 194 306 354 367 fetal spleenBioChain FSP001 276 563 842 umbilical BioChain FUC001 3 20 33-34 39 48 50 52 55-57 cord 65 67 69 72 fetal brain GIBCO HFB001 3 9-10 12-14 16 21 25 28-30 32-34 macrophage InvitrogenHMP001 86 168 186-187 297 537 608 681 infant brain Columbia IB2002 2-3 9-10 12-14 16 21 25 27-30 University 46-47 49 55-56 58 65 69 71-72 84-86 91-92 98-99 106 109-l 2?7-279 284-285 287 293-294 613 616-618 620 622 624 bzy-b;~z t~j~-635 637 641 643-644 650-b51 653 661 711 720-722 724 730 732 735 740 74S-.

brain Columbia 1B2003 3 12-13 21 27-29 32 39 49 69 72 82 91 University 113 116 126 128 132-133 I42 144 1 S6 nt brain Columbia IBM002 16 47 82 84 201263 302 376 394 4~,1 44C
University 488 537 592 606-607 635 740 769 887 nt brain Columbia IBS001 84 86 i 80 185 198 201 203 230 279 312 University 326 346 354 366 388 488 542 S81 588 g, fibroblast Strategene LFB001 3 11 25 49 65 7S 114 141 156 160 172 688 691 745 752 761 768 ?94 822 837 ~g tumor Invitrogen LGT002 1 3 9-10 12-13 20 31 38 41 46 48 51-52 209 212 2i6-217 226 228-229 232 234-lymphocytes ATCC LPC001 3 9-11 32 47 50 56 71 75 88 leukocyte GIBCO LUC001 1 3 9 11 18-19 21 23-25 27 31-34 leukocyte Clontech LUC003 1 41 82 106 119 123-124 160 627 642 655 697 761 767 769.

melanoma Clontech MEL004 3 25 55-56 67 71 78 109 121 from cell 172-173 176 200 209 212 258-259 line 263 ATCC #CRL 278 297 301 306 312 335 338 mammary InvitrogenMMG001 1 14 19 21 28-29 31-37 47 49-51 gland 63-67 69 71-72 75-78 92 108-109 637 639 642-644 646-647 650'657 d neuron StrategeneNTD001 9 65 82 92 106 113 142 146 156 d 172 176 i uce 191 208 221 258 277 328 333 346 n 361-cells 362 371-372 375 388 410 414 418-419 retinaid acidStrategeneNTR001 19 87 184 305 385 440 474 626-627 induced neuron 748 799 834 977 cells neuronal cellsStrategeneNTU001 19 33-34 42 70 82 87 109 115 pituitary Clontech PIT004 3 19 123-124 194 255 354 358 gland 373-374 placenta Clontech PLA003 138 176 574 896 972 Clontech PRT001 3 9 16 57 65 75 83 108 130-134 prostate 146 149-150 159 182 186-187 190 505-506 523 53.7 543 564 583 t InvitrogenREC001 19 30 33-34 66 108-109 123-124 e 126 129-c 131 143 149 151 156 164 190 201 um 240 r salivary glandClontech SAL001 16 68 74 84 121 123-124 156172 salivary Clontech SALs03 217 254 270 388 610 gland skin fibroblastATCC SFB001 517 949 skin fibroblastATCC SFB002 269 688 skin fibroblastATCC SFB003 3 203 897 907 small intestineClontech SIN001 3-4 47 57 68-69 92 99 125-126 skeletal Clontech SI~MM001 15 75 135 146 172 190 218 267 muscle 282 308 skeletal Clontech SI~Ms04 215 muscle spinal cord Clontech SPC001 14 20-21 25 28-29 31 39 46 524 537 539.558 581 586 604-605 adult spleenClontech SPLc01 3 6 12-13 66 130-131 178 365 stomach Clontech STO001 35 114 130-131 144 155 176 thalamus Clontech THA002 30-32 48 66 109 127 130-131 thymus Clonetech THM001 10 16 20 28-29 32 37 41 52 569 577-5'78 582 586 598 608 thymus Clontech THMc02 1 3 9-11 16 21 27 32-34 38-39 ' 297 313-314 322 334 343 354-355 thyroid glandClontech THR001 3 8-9 14-15 19-22 28-29 39 trachea Clontech TRC001 33-34 55-56 69 74 163 172 190 WO 01/57190 PCTlUSOI/04098 uterus Clontech UTR001 4 9 18 37 63-64 74 108 114-11S

400 403 406 411' 42S 431 434 SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY

NO: SCORE

1 L06175 Homo Sapiensoccurs in MHC class 308 98 I region; ORF

2 Y70775 Homo sapiensFollistatin-related 3094 98 protein zfsta.

3 X15187 Homo Sapiensprecursor polypeptide 4112 100 (AA -21 to 782) 4 AF110640Homo Sapiensorphan seven-transmembrane344 100 receptor 603798 Homo sapiensHuman secreted protein,158 72 SEQ ID

NO: 7879.

6 W85607 Homo sapiensSecreted protein clone 1477 100 da228_6.

7 Y30162 Homo SapiensHuman dorsal root receptor884 88 hDRR4.

8 Y15227 Homo SapiensLeul 391 100 9 Y28817 Homo Sapienspt326 4 secreted protein.3338 100 X92I06 Homo sapiensbleomycin hydrolase 2445 100 I1 Y15228 Homo sapiensLeu2 445 100 12 TJ27838 Mus musculusglycosyl-phosphatidyl-inositol-432 34 anchored protein homolog 13 U27838 Mus musculusglycosyl-phosphatidyl-inositol-320 27 anchored protein homolog 14 'Y71062 Homo SapiensHuman membrane transport2323 99 protein, MTRP-7.

U96781 Homo SapiensCa2+ ATPase of fast-twitch5145 100 skeletal muscle sacroplasmic reticulum, adult isoform 16 M16653 Homo sapienspancreatic elastase 1435 99 IIB zymogen 17 Y13398 Homo SapiensAmino acid sequence 1749 99 ofprotein PR0346.

18 Y02283 Homo SapiensSecreted protein clone 1399 99 br342 11 polypeptide sequence.

19 Y53030 Homo sapiensHuman secreted protein 1371 100 clone d24 1 protein sequence SEQ
ID N0:66.

AL031320Homo SapiensdJ20N2.S (novel protein2597 99 similar to fucosidase, alpha-L-1, tissue (EC

3.2.1.51, alpha-1-fucosidase fucohydrolase)) 21 BOI384 Homo SapiensNeuron-associated protein.1876 100 22 Y68778 Homo SapiensAmino acid sequence 2470 100 of a human phosphorylation effector PHSP-10.

SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

23 Y55935 Homo SapiensHuman KHS2 protein. 4781 99 24 Y55935 Homo SapiensHuman KHS2 protein. 2807 100 25 AC024792Caenorhabditiscontains similarity 463 31 elegans to TR:095029 26 Y07972 787 Human secreted protein1540 100 fragment 27 X97630 Homo Sapiensserine/threonine protein3781 98 kinase 28 AF150755Mus musculusmicrotubule-actin crosslinking3514 68 factor 29 AF150755Mus musculusmicrotubule-actin crosslinking3725 70 factor 30 238011 Mus musculusDMR-N9 2988 86 31 AJ000522Homo Sapiensaxonemal dynein heavy 6058 99 chain 32 AF037256Mus musculusES2 protein 2260 91 33 562140 Homo SapiensTLS=nuclear RNA-binding2917 100 protein 34 S62140 Homo SapiensTLS=nuclear RNA-binding2890 98 protein 36 AB038237Homo SapiensG protein-coupled receptor1767 100 37 D79994 Homo Sapienssimilar to ankyrin 6089 99 of Chromatium vinosum.

38 X63380 Homo Sapiensserum response factor-related1966 99 protein 39 AL022072Schizosaccharlipoic acid synthetase1067 61 omyces pombe 40 J03930 Homo Sapiensalkaline phosphatase 2751 100 41 AF132968Homo SapiensCGI-34 protein 1088 98 42 AL117637Homo Sapienshypothetical protein 2208 100 43 AL021393Homo SapiensbK747E2.1 (novel protein)1526 100 44 X68011 Homo SapiensZNF81 1886 100 45 AC002464Homo Sapiensorganic cation transporter;2423 100 SO%
similarity to JC4884 (PID:g2143892) 46 W78245 Homo SapiensFragment of human secreted1949 100 protein encoded by gene 19.

47 Y41765 Homo SapiensHuman PR01083 protein 3604 100 sequence.

48 AF097330Homo SapiensH1 chloride channel; 1305 99 p64H1; CLIC4 50 U09413 Homo Sapienszinc finger protein 1361 57 51 AF061812Homo Sapienskeratin 16 2374 100 52 W63681 Homo SapiensHuman secreted protein1326 99 1.

53 AB035303Homo Sapienscadherin-10 4094 100 54 A12022 synthetic MRP-8 485 100 construct 55 AL121897Homo SapiensbA392M18.3 (KIAA0180) 1867 100 56 Y73330 Homo SapiensHTRM clone 397663 protein818 96 sequence.

57 AF151018Homo SapiensHSPC184 955 100 58 AF125042Homo Sapiensbisphosphate 3'-nucleotidase' 1586 100 59 AF118670Homo Sapiensorphan G protein-coupled1971 100 receptor 60 X04494 Homo sapiensprecursor polypeptide 1903 100 61 AF208865Homo SapiensEDRF 528 100 62 D15057 Homo sapiensDAD-1 567 100 63 AF260665Homo sapienshistone acetyltransferase1510 100 64 AF260665Homo Sapienshistone acetyltransferase1429 96 65 AJ277145Homo Sapiensras-related small GTPase1073 100 66 Y94950 Homo SapiensHuman secreted protein348 100 clone dh1073_12 protein sequence SEQ ID
N0:106.

67 Y82744 Homo SapiensDNA replication and 1028 100 repair associated protein (DRASP).

68 Y44486 Homo SapiensHuman GPRW receptor 1721 100 polypeptide.

69 AL031228Homo SapiensdJ1033B10.2 (WD40 protein3196 100 BING4 _ (similar to S. cerevisiae YER082C, M. sexta MNG 10 and C. elegans F28D1.1) SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

70 AJ276316Homo Sapienszinc finger protein 1751 52 71 Y 18314 Homo Sapiensparaplegin-like protein4146 99 72 AF157028Homo Sapiensprotein phosphatase 2017 100 methylesterase-1 74 Y71082 Homo SapiensHuman B-aggressive lymphoma1765 99 (BAL) protein.

75 AF225420Homo SapiensAD025 734 100 76 X95235 Homo Sapienstranscription factor 217 100 77 AF108420Takifugu 1-aminocyclopropane-carboxilate733 56 rubripes synthase 78 601349 Homo SapiensHuman secreted protein,650 99 SEQ ID
NO: 5430.

79 AL117635Homo Sapienshypothetical protein 922 99 81 285986 Homo SapiensdJ108K11.3 (similar 865 77 to yeast suppressor protein SRP40) 82 AF183414Homo Sapienshemin-sensitive initiation3231 99 factor 2a kinase 83 GO 1143 Homo SapiensHuman secreted protein,495 98 SEQ ID
NO: 5224.

84 U03985 Homo SapiensN-ethylinaleimide-sensitive3744 99 factor 85 Y17791 Homo SapiensVAX2 protein 1496 100 87 AF263538Homo Sapiensgrowth differentiation 1944 99 factor 3 88 Y19757 Homo SapiensSEQ ID NO 475 from W09922243.1361 100 89 AF161493Homo SapiensHSPC144 1185 100 90 AF161493Homo SapiensHSPC144 856 100 91 B25780 787 Human secreted protein 647 41 SEQ ID

92 U57344 Mus musculusMeis3 1007 89 93 AF172854Homo Sapienscardiotrophin-like cytokine1197 98 CLC

94 AL390114Leishmaniaextremely cysteine/valine223 29 major rich protein 95 AB016886Arabidopsiscontains similarity 287 38 thaliana to adenylate kinase~gene id:MCA23.18 96 AC005525Homo SapiensF22162_1 1855 96 97 B20997 Homo SapiensHuman nucleic acid-binding3836 99 protein, NuABP-1.

98 AJ006692Homo Sapiensultra high sulfer keratin507 70 99 AF172264Homo SapiensTraf2 and NCK interacting6942 99 kinase, splice variant 1 100 L11239 Homo Sapienshomeoboxprotein 717 100 101 AC004890Homo Sapienssimilar to zinc forger 2154 98 proteins;
similar to AAC01956 (PID:g2843171) 102 AC003682Homo SapiensR28830_2 1287 48 103 AF201839Rattus dynamin IIIbb isoform 4270 95 norvegicus 104 Y79510 Homo SapiensHuman carbohydrate-associated1394 100 protein CRBAP-6.

105 Y79510 Homo SapiensHuman carbohydrate-associated1209 90 protein CRBAP-6.

106 AL096748Homo Sapienshypothetical protein 1216 100 108 X97260 Homo SapiensMetallothionein 2 381 100 109 AL034422Homo SapiensdJ1141E15.2 (novel protein)433 100 110 AF191338Homo sapiensanaphase-promoting complex683 100 subunit 111 AL021712Arabidopsisputative protein 185 26 thaliana 112 AF250138Homo Sapienssmall stress protein-like1063 100 protein 113 AL109976Homo sapiensdJ794I6.1.1 (novel protein)4176 99 114 Y36151 787 Human secreted protein 668 100 SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

115 AF110399 Homo Sapienselongation factor Ts 1666 100 116 AF210317 Homo Sapiensfacilitative glucose 2052 99 transporter family member GLUTS

117 Y73328 Homo sapiensHTRM clone 082843 protein931 100 sequence.

118 X0408S Homo Sapienscatalase 2846 100 119 AF147717 Homo Sapiensubiquitin C-terminal 1695 100 hydrolase 120 X73882 Homo sapiensmicrotubule associated3801 99 protein 121 AC004882 Homo Sapienssimilar to CAA16821 3223 100 (PID:g32SS9S2) 122 M93311 Homo Sapiensmetallothionein-III 421 100 123 603827 Homo SapiensHuman secreted protein,SS7 94 SEQ ID
NO: 7908.

124 603827 Homo SapiensHuman secreted protein,222 S3 SEQ ID
NO: 7908.

12S AF232009 Homo Sapiensperoxisomal trans 2-enoyl1565 99 CoA
reductase 126 AB004906 Ipomoea transposase 146 20 purpurea 127 M6016S Homo Sapiensguanine nucleotide-binding1832 ~ 99 regulatory protein 128 Y10319 Homo Sapienscarnitine carrier 1592 100 129 U7S467 DrosophilaAtu 937 36 .
melanogaster 130 Z21S07 Homo Sapienshuman elongation factor-1-delta494 87 131 Z21S07 Homo sapienshuman elongation factor-1-delta938 100 132 YS8633 Homo SapiensProtein regulating 6745 100 gene expression PRGE-26.

133 YS8633 Homo sapiensProtein regulating 4818 9S
gene expression PRGE-26.

134 M13692 Homo Sapiensalpha-1 acid glycoprotein1064 99 precursor 13S U72970 Sus scrofacalcium/calinodulin-dependent2723 99 protein kinase II isoform gamma-B

136 G032I3 Homo SapiensHuman secreted protein,4S0 100 SEQ ID
NO: 7294.

137 ACOOS Homo Sapienssmall inducible cytokine627 99 102 subfamily A
member 24 138 AF1SS648 Homo Sapiensputative zinc fmgerproteinS8SS 92 139 AF144638 Homo Sapienssphingosine-1-phosphate2977 100 lyase 140 AFIS2318 HomosapiensprotocadheringammaAl 4778 100 141 B08S 17 Homo SapiensAmino acid sequence 5841 100 of a beta-tubulin antigen.

142 XS6667 Homo Sapienscalretinin 1410 99 143 X92763 Homo Sapienstafazzins 1605 100 x44 Y9S293 Homo SapiensHuman GEF containing 4092 99 NEK-like kinase substrate sGNK.

14S AF226046 Homo SapiensGK003 1198 100 146 M22877 Homo Sapienscytochrome c SS4 98 147 AJ272212 Homo Sapiensprotein serine kinase 2196 100 148 AB026491 Homo sapiensPICKl 2114 98 149 AB018S80 Homo SapienshIuPGFS 1699 100 1S0 X91868 Homo sapienssixl 1509 100 151 AF266S05 Mus musculuspseudouridine synthase2135 84 1S2 U29170 DrosophilaANON-23D 883 43 melanogaster 1S3 G0407S Homo SapiensHuman secreted protein,S67 99 SEQ ID
NO: 8156.

1S4 AY009128 Homo SapiensISCU2 138 100 wo ons7igo rcTmsonoa.o9s SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NiJMBER WATERMAN IDENTITY
NO: SCORE

155 AF141315 Homo Sapiensalpha-I,4-N- 1842 100 acetylglucasaminyltransferase 156 AF110645 Homo sapienscandidate tumor suppressor1294 g9 p33 INGl homolog 15'7 AF159297 Zea ways extensin-like protein 238 25 158 ALI33325 _ dJ984P4.3 (Homeobox 1437 100 Homo Sapiensprotein NI~.X2B) 159 AF073298 Homo Sapienssmall EDRK-rich factor294 100 160 AC004858 Homo SapiensUI small ribonucleoprotein4032 100 ISNRP
homolog; match to PID:g4050087 161 AB012109 Homa SapiensAPC10 990 I00 162 AL162751 Arabidopsisputative protein 194 32 thaliana I63 AJ005698 Homo Sapienspoly(A)-specific ribonuclease3351 100 I64 AF117646 Homo Sapienslong CBL-3 protein 2547 99 165 AC004002 Homo Sapienssimilar to ciliary 5065 100 dynein beta heavy chain; 78% Similarity to P23098 (PID:g118965) 166 M10942 Homo sapienshuman metallothionein-Ie381 100 167 AF126484 Homo sapiensCARD4 4961 100 168 AF161518 Homo SapiensHSPC169 1604 I00 169 M64983 Homo Sapiensfibrinogen beta chain 2482 100 170 M64983 Homo Sapiensfibrinogen beta chain 2679 I00 I7I M58514 Galius fibrinogen beta chain 1059 78 gallus 172 AF078845 Homo Sapiens16.7Kd protein 786 100 173 AC004774 Homo SapiensDlx-6 923 I00 174 298974 Schizosaccharputative vacuolar protein185 31 omyces sorting-pombe associated protein 175 X56203 PlasmodiumLiver stage antigen 283 23 falciparum I76 W74726 Homo SapiensHuman secreted protein1879 z 00 fg949 3.

177 AJ222967 Homo Sapienscystinosin 1920 100 178 AC024796 Caenorhabditiscontains similarity 221 27 elegans to TR:076167 179 Y66632 Homo sapiensMembrane-bound protein1370 100 PRO276.

180 AF15I803 Homo SapiensCGI-45 protein 215 28 181 602694 Homo SapiensHuman secreted protein,283 i00 SEQ ID
NO: 6775.

182 Y17292 Homo SapiensHuman cell death preventing2676 100 kinase {DPK-1) protein sequence.

183 AF234765 ____ serine-arginine-rich 148 27 Rattus splicing norvegicusregulatory protein 184 AF151855 Homo SapiensCGI-97 protein 1214 96 185 AF289664 Mus musculusCYLN2 4673 g0 I86 AL022238 Homo SapiensdJI042K10.2 (supported4059 I00 by GENSCAN, FGENES and GENEbVISE) 187 AL022238 Homo SapiensdJ1042K10.2 (supported2332 x00 by GENSCAN, FGENES and GENE WISE) 188 X83543 Homo SapiensAPXL 8513 99 189 AF059569 Homo sapiensactin binding protein 3106 99 MAYVEN

190 M18135 Rattus smooth-muscle alphatropomyosin1306 95 norvegicus 191 _ Drosophilabrakeless-B I47 S2 AF242194 melanogaster I92 D30689 Bacillus subunit of nitrite 113 29 subtilis reductase ' Y44984 Homo SapiensHuman epidermal protein-1.538 97 393 ~
~

i31 , SEQ ACCESSIONSPECIES DESCRIPTION SMITH- %
ID NUMBER WATERMAN IDENTITY
NO: SCORE

194 B25679 Homo sapiensHuman secreted protein760 100 sequence encoded by gene 15 SEQ ID N0:68.

195 AB020315787 homologue of mouse 1466 100 dkk-1 gene:Acc 196 U35730 Mus musculusjerky 2021 75 197 AL136450Homo SapiensdJ510O21.1 (novel protein)632 - 100 198 X56203 Plasmodium liver stage antigen 512 24 falciparum 199 Y70775 Homo SapiensFollistatin-related 2027 63 protein zfsta.

200 X87237 Homo Sapiensa-glucosidase I 4447 99 201 AF101078CaenorhabditisCLU-1 1393 46 elegans 202 X04571 Homo Sapiensprecursor polypeptide 6611 100 (AA -22 to 1185) 203 X00474 Homo SapienspS2 precursor 466 100 204 AB029333HalocynthiaHrPET-1 974 54 roretzi 205 AF146019Homo Sapienshepatocellular carcinoma998 100 antigen gene 520 206 AF071002Homo Sapiensminx-related peptide 632 100 1; MiRPl 207 AB038162Homo Sapienstrefoil factor 2 744 100 208 U30521 Homo SapiensP311 HUM 363 100 209 AB000911Sus scrofa ribosomal protein 782 100 210 AB021227Homo sapiensmembrane-type-5 matrix3545 100 metalloproteinase 211 AF180920Homo Sapienscycliri L ania-6a 2722 100 212 AF105365Homo SapiensK-Cl cotransporter 5624 100 213 U29244 Caenorhabditissimilar to human (TRE)602 32 elegans transforming protein (PIR:S22157) 214 AL033538Homo SapiensdJ477H23.1 (novel protein)3195 100 215 X52011 Homo Sapiensmuscle determination 1262 100 factor 216 AF083248Homo Sapiensribosomal protein L26 739 100 homolog 217 AF006751Homo SapiensES/130 4793 99 218 AB007859Homo SapiensKIAA0399 protein 3559 99 219 AK026291Homo Sapiensunnamed protein product826 100 221 Y84045 Homo SapiensSplice variant of cancer5851 97 associated polypeptide CH1-9a11-2.

222 267996 Homo Sapienstenascin-R (restrictin)7186 100 223 AF134802Homo Sapienscofilin isoform 1 846 100 224 Y17711 Homo sapiensatopy related autoantigen1611 99 CALC

225 AF190051Gallus gallushepatocyte nuclear 443 81 factor la dimerization cofactor isoform 226 AK026256Homo sapiensunnamed protein product866 98 227 269368 Schizosaccharnuf2-like coiled-coil 230 25 omyces pombeprotein 228 AF275948Homo SapiensABCA1 11763 99 229 AF161384Homo SapiensHSPC266 2006 98 230 Y16270 Homo Sapiensparalemin 1951 100 231 AJ245599Homo Sapiensputative secreted ligand2379 99 232 W88499 Homo SapiensHuman stomach carcinoma1545 99 clone HP10412-encoded protein.

233 AF096286Mus musculuspecanex 1 3623 93 234 V64619_cdHomo Sapiens30-NOV-1990 Human HE1 796 100 1 cDNA.

235 V64619_cdHomo Sapiens30-NOV-1990 Human HE1 470 98 1 cDNA.

236 AF227258Bos taurus RPGR-interacting protein-11262 38 237 AJ132445Homo Sapiensclaudin-14 1181 100 238 AL034562Homo SapiensdJ684024.2 (prodynorphin1330 100 (Beta-SEQ ACCESSIONSPECIES DESCRIPTION SMTTH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

Neoendorphin-Dynorphin precursor, Proenkephalin B precursor)) 239 AF262027Homo SapienseIF-5A2 808 100 240 AL079344Arabidopsisputative protein 194 33 thaliana 241 AC002394Homo SapiensGene product with similarity1 S42 51 to dynein beta subunit 242 AJ271361Takifugu FRANK2 protein 303 30 rubripes 243 AL02I9I8Homo Sapiensb34I8.I (Kruppel related1476 48 Zinc Finger protein 184) 244 AF190167Homo Sapiensmembrane associated 1736 99 protein SLP-2 245 Y10601 Homo Sapiensankyrin-like protein 5877 100 246 AL121771Homo SapiensdJ548G19.1.1 (novel 3628 100 protein (ortholog of mouse zinc finger protein ZFP64) (translation of cDNA
NTZRP3001398 (Em:AK001596)) (isoform 1)) 247 L25314 Drosophila~actin-related protein 984 47 melanogaster 248 X63745 Homo SapiensKDEL receptor 1095 100 249 AF112208Homo Sapiensl3kDa differentiation-associated816 100 protein 250 AP001707Homo Sapienshuman gene for claudin-8,1172 100 Accession No. AJ2507I 1 251 AL136125Homo SapiensdJ304B14.1 (novel protein)778 100 252 AL031186Homo SapiensbK984G1.1 (supported 532 100 by FGENES) 253 Y17531 Homo SapiensHuman secreted protein639 100 clone BL205 14 protein.

254 AL049843Homo SapiensdJ392M17.3 (KIAA0349 6741 99 protein) 25S AJ242972Homo SapiensTOLLIP protein 1424 99 256 Y94873 Homo SapiensHuman protein clone 1876 100 HP02632.

257 AF279865Homo Sapienskinesin-like protein 2903 100 GAKIN

258 AL024498Homo SapiensdJ417M14.1 (novel protein)589 100 259 866278 Homo SapiensTherapeutic polypeptide830 100 from glioblastoma cell line.

260 AF101784Homo Sapiensb-TRCP variant E3RS-IkappaB3226 99 261 AF101784Homo Sapiensb-TRCP variant E3RS-IkappaB2821 100 262 AF101784Homo sapiensb-TRCP variant E3RS-IkappaB3149 99 263 AF197060Homo sapienssrc homology 3 domain-containing2257 100 protein HIP-55 264 Y86262 Homo SapiensHuman secreted protein766 100 HAQAR23, SEQ ID N0:177.

265 Y56966. Homo SapiensHuman SBPSAPL polypeptide.2779 100 266 Y56966 Homo sapiensHuman SBPSAPL polypeptide.1018 99 267 AJ300465Homo Sapiensputative white family 1557 95 ATP-binding cassette transporter 268 AC004030Homo SapiensF21856_2 3579 99 269 X55954 Homo sapiensHL23 ribosomal protein714 100 270 AB033921Mus musculusNdrl related protein 1855 94 Ndr2 271 AF081886Homo sapiensERO1-like protein 1905 99 272 AF166492Homo sapienssmall GTPase RAB6B 1060 100 273 AL022238Homo SapiensdJ1042K10.4 (novel 2201 100 protein) 274 W88667 Homo SapiensSecreted protein encoded1530 99 by gene 134 clone HAIBP89.

275 X00129 Homo sapiensprecursor RBP 1044 97 276 247500 Homo sapiens11-MAY-1998 Human RHOH1161 100 cdl gene sequence.

277 AB049188Equus caballusubiquitin C-terminal 1118 ~ 96 ~ ~ f hydrolase ~

SEQ ACCESSIONSPECIES DESCRH'TION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

278 AF270647 Homo sapiensGTTl 1564 100 279 AF143956 Mus musculuscoronin-2 2414 94 280 885151 Homo SapiensEndothelial cell polypeptide.911 92 281 885151 Homo SapiensEndothelial cell polypeptide.1031 100 282 D83948 Rattus S1-1 protein 3975 90 norvegicus 283 Y14768 Homo SapiensI Kappa B-like protein2037 100 286 AL031316 Homo sapiensdJ28O10.3(HSD11B1 294 100 (hydroxysteroid (11-beta) dehydrogenase 1) . D64109 Homo sapienstob family 1773 99 288 AB026043 Homo SapiensMS4A7 1230 100 289 M61866 Homo SapiensKrueppel-related DNA-binding209 90 protein 290 AJ001810 Homo SapiensmRNA cleavage factor 1217 100 I 25 kDa subunit 291 Y99454 Homo SapiensHuman PR01605 (UNQ786)694 100 amino acid sequence SEQ ID
N0:395.

292 Y44824 Homo SapiensHuman molecule associated2370 100 with cell proliferation, MACP-4.

293 AJ276101 Homo sapiensGPRCSB protein 2099 100 294 AF161406 Homo sapiensHSPC288 719 100 295 Y58628 Homo SapiensProtein regulating 1276 100 gene expression PRGE-21.

296 U91561 Rattus pyridoxine 5'-phosphate1239 87 norvegicusoxidase 297 L02956 Xenopus ribonucleoprotein 1624 83 laevis 298 AF226730 Homo SapiensCytl9 1729 99 299 AF226730 Homo SapiensCytl9 906 98 300 Y54324 Homo SapiensAmino acid sequence 718 89 of a human gastric cancer antigen protein.

301 AF125533 Homo SapiensNADH-cytochrome b5 1606 100 reductase isoform 302 Y32206 Homo SapiensHuman receptor molecule1676 98 (REC) encoded by Incyte clone 2825826.

303 AF247565 Homo Sapienshepatocellular carcinoma525 100 associated ring forger protein 304 AF208844 Homo SapiensBM-002 428 100 305 AC004983 Homo sapienssimilar to PID:g38779441988 100 306 AL132978 Arabidopsisputative protein 210 25 thaliana 307 Y10530 Homo Sapiensolfactory receptor 1645 100 308 AF180681 Homo Sapiensguanine nucleotide 3597 100 exchange factor 309 AF111856 Homo Sapienssodium dependent phosphate3591 99 transporter isoform NaPi-3b 310 Y13583 Homo SapiensG-protein coupled receptor2171 100 311 273420 Homo SapienscE146D10.2 (mercaptopyruvate1598 100 .
sulfurtransferase (EC
2.8.1.2)) 312 X79535 Homo Sapiensbeta tubulin 2348 100 313 AF070658 Homo SapiensHSPC002 861 100 314 AF078866 Homo SapiensSURF-4 1395 100 317 237986 Homo Sapiensphenylalkylamine binding1258 100 protein 320 AB047892 Macaca hypothetical protein 258 82 fascicularis 321 Y25755 Homo sapiensHuman secreted protein1440 100 encoded from gene 45.

322 AB016531 Homo sapiensPEX16 1741 100 323 AL391141 Arabidopsisputative protein 274 49 SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

thaliana 325 AF140501 Homo SapiensDNA polymerise iota 3691 99 326 X96698 Homo sapiensD1075-like 1450 96 327 AF152325 Homo Sapiensprotocadherin gamma 4769 100 AS

328 AF151803 Homo SapiensCGI-45 protein 1970 100 329 X74070 Homo Sapienstranscription factor 639 81 330 AF171102 Homo Sapiensretinal degeneration 1302 95 B beta 331 W54040 Homo SapiensHuman interferon-inducible484 98 protein, HIFI.

332 AF024617 Homo Sapienstranscription-associated691 100 zinc ribbon protein 333 U19181 Rattus Rabin3 2129 90 norvegicus 334 603877 Homo sapiensHuman secreted protein,621 100 SEQ ID
NO: 7958.

335 AL008582 Homo SapiensbK223H9.2 (ortholog 626 100 of A. thaliana F23F 1.8) 336 AF110774 Homo Sapiensadrenal gland protein 647 100 337 AB011414 Homo SapiensKruppel-type zinc finger1674 58 protein 338 AF207600 Homo Sapiensethanolamine kinase 129 100 340 AC020579 Arabidopsisputative 3283 50 thaliana phosphoribosylformylglycinamidine synthase; 25509-29950 341 Y28576 Homo sapiensSecreted peptide clone944 100 pe503 1.

342 U32274 SaccharomyceYdr386wp; CAI: 0.12 191 37 s cerevisiae 343 A01771 synthetic vascular anticoagulating1661 - 99 construct protein 344 AF220052 Homo sapiensuncharacterized hematopoietic1285 100 stem/progenitor cells protein 345 Y70400 Homo sapiensHuman cell-signalling 754 100 protein-2.

346 Y50926 Homo SapiensHuman fetal brain cDNA962 100 clone vcl6_1 derived protein.

347 AF183428 Homo Sapiens28.4 kDa protein 1329 100 348 AC006069 Arabidopsisputative cleavage and 1383 55 thaliana polyadenylation specifity factor 349 AL032631 CaenorhabditisY106G6H.8 194 39 elegans 350 U70669 Homo SapiensFas-ligand associated 167 23 factor 3 351 Y93468 Homo sapiensAmino acid sequence 1182 92 of a potassium channel interactor protein.

352 AF005856 Drosophilaanon2A5 111 45 yakuba 353 AJ271684 Homo Sapiensmyeloid DAP12-associating1013 100 lectin 354 AF099100 Homo SapiensWD-repeat protein 6 2882 99 355 U51730 Murine reverse transcriptase 316 42 leukemia virus 356 D50617 SaccharomyceYFL042C 279 27 s cerevisiae 357 D50617 SaccharomyceYFL042C 279 27 s cerevisiae 358 AF161432 Homo SapiensHSPC314 1059 93 359 AB029488 Homo SapiensCl lorf2l 758 99 360 AJ251024 Homo Sapiensputative odorant binding1239 100 protein ag 361 U43281 SaccharomyceLpg22p 2074 74 s cerevisiae 362 U43281 SaccharomyceLpg22p 2153 74 s cerevisiae SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

363 AC007153 Arabidopsis100632 156 24 thaliana 364 AF197927 Homo SapiensAF.5q31 protein 3992 99 365 D28500 Homo Sapiensmitochondria) isoleucine4286 98 tRNA
synthetase 366 X97868 Homo Sapiensarylsulphatase 3141 98 367 AL162048 Homo Sapienshypothetical protein 1532 100 368 L36062 Mus musculussteroidogenic acute 189 25 regulatory protein 369 AF113249 Homo Sapiensmultiple domain putative1022 59 nuclear protein 370 M15888 Bos taurusendozepine-related 2425 84 protein precursor 371 X66363 Homo Sapiensserine/threonine protein2562 100 kinase 372 W74802 Homo SapiensHuman secreted protein1532 89 encoded by gene 73 clone HSQEL25.

373 AF100772 Homo Sapienstenascin-M1 11535 99 374 . AF090934Homo SapiensPR00518 382 100 375 AB021643 Homo Sapiensgonadotropin inducible2761 99 transcription repressor-3 376 AB049758 Homo SapiensMAWD binding protein 1331 100 377 AF070666 Homo SapiensKruppel-associated 466 97 box protein 378 559342 Mus Sp. nuclear pore complex 464 60 glycoprotein p62 379 AF149205 Mus musculusSu(var)3-9 homolog 1690 88 Suv39h2 380 AF227906 Homo SapiensUDP-glucose:glycoprotein7851 99 glucosyltransferase 2 precursor 381 AF118566 Mus musculushematopoietic zinc 1769 92 finger protein 382 AK000619 Homo sapiensunnamed protein product810 100 383 AF227906 Homo SapiensUDP-glucose:glycoprotein7851 99 glucosyltransferase 2 precursor 384 AF117946 Homo SapiensLink guanine nucleotide2363 100 exchange factor II

385 AF125390 DrosophilaL82G 139 41 melanogaster 386 Y94907 Homo SapiensHuman secreted protein1092 50 clone ca106_19x protein sequence SEQ ID
N0:20.

387 U18795 SaccharomyceYe1064cp 206 28 s cerevisiae 388 AF177388 Homo Sapienscancer-amplified transcriptional10748 99 coactivator ASC-2 389 AJ002744 Homo SapiensUDP-GaINAc:polypeptide3469 96 N-acetylgalactosaminyltransferase 390 AF097366 Homo sapienscone sodium-calcium 3166 100 potassium exchanger 391 AF217525 Homo SapiensDown syndrome cell 5337 60 adhesion molecule 392 U81035 Rattus ankyrin binding cell 3967 91 norvegicusadhesion molecule neurofascin 393 X65224 Gallus neurofascin 4097 78 gallus 394 X13916 Homo sapiensLDL-receptor related 4292 99 precursor (AA
-19 to 4525) 395 AF151083 Homo SapiensHSPC249 444 98 396 AB017026 Mus musculusoxysterol-binding protein2173 98 397 AL035587 Homo SapiensdJ475N16.4 (KIAA0240) 2393 100 398 W74813 Homo sapiensHuman secreted protein722 92 encoded by gene 85 clone HSDFV29.

399 Y71110 Homo SapiensHuman Hydrolase protein-81637 99 (HYDRL-8).

SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

400 AF0397I8Caenorhabditiscontains similarity 325 43 elegans to lupus LA
protein homologs 401 AE000877Methanothermconserved protein 231 36 obacter thermoautotro phicus 402 Y27795 Homo SapiensHuman secreted protein 1539 99 encoded by gene No. 79.

403 250853 Homo SapiensCLPP 615 100 405 X03475 Rattus ribosomal protein L35a _ 99 norvegicus(aa 1-110) 576 406 AF144237Homo SapiensLOMP protein 252 44 407 U20239 Mus musculusfibrosin 288 76 409 AL033378Homo SapiensdJ323M4.1 (I~IAA0790 6026 99 protein) 4I0 X54326 Homo Sapiensglutaminyl-tRNA synthetase7577 99 411 X61585 Bos tauruspolynucleotide adenylyltransferase3715 97 412 AF217190Homo SapiensMLEL1 protein 5271 99 414 602815 Homo SapiensHuman secreted protein,_ 95 NO: 6896.

41 AJ245922Homo Sapiensalpha-tubulin 8 2370 100 S

416 AF203032Homo Sapiensneurofilament protein 220 21 417 297653 Homo Sapiensc380A1.2.1 (novel protein1567 100 (isoform 1)) 418 AJ404326Homo sapiensSR+89 1871 99 419 AJ404326Homo SapiensSR+89 ~ 902 64 420 AF134726Homo SapiensG9A ' 5334 99 421 L2812S Podospora beta transducin-like _ 39 anserina protein 288 422 W21733 Homo SapiensNIP-1 encoded by clone 110 72 59.

423 567970 Homo SapiensZNF75=KRAB zinc forger 951 76 424 L28035 Mus musculusprotein kinase C gamma 3768 98 426 Y73373 Homo SapiensHTRM clone 921803 protein555 56 sequence.

427 Y73373 Homo SapiensHTRM clone 921803 protein266 49 sequence.

428 X61118 Homo SapiensTTG-2a/RBTN-2a 876 100 429 296932 Homo sapiensnuclear autoantigen 496 83 fo 14 kDa 430 AJ277291Homo SapiensHELG protein 678 72 431 X82157 Homo Sapienshevin 3525 99 432 AC007192Homo SapiensP85B HUMAN; PTDINS-3- _ 99 433 AL021918Homo Sapiensb34I8.1 (Kruppel related1713 50 Zinc Finger protein 184) 434 AF084464Rattus GTP-binding protein 141 29 norvegicusREM2 435 AL049795Homo SapiensdJ622L5.2 (novel protein)1756 98 436 M14513 Rattus (Na+ and K+) ATPase, 4269 99 norvegicusalpha(III) catalytic subunit 437 U33460 Homo SapiensDNA-directed RNA polymerase8777 98 I, largest subunit 438 D87076 Homo Sapienssimilar to human bromodomain3067 100 protein BR140(JC2069) 439 L43912 Macaca mannose-binding protein589 93 mulatta A

440 D31763 Homo Sapiensha0946 protein is Kruppel-related.927 49 441 U70976 Homo Sapiensarrestin 2068 99 442 B08069 Homo SapiensA human beta-alanine-pyruvate2343 99 aminotransferase (NAPA).

443 AF10066,2Caenorhabditiscontains similarity 166 24 to ubiquitin SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY

NO: SCORE

elegans carboxyl-terminal hydrolase (Pfam:

UCH-l.hmm, score: 28.46) (Pfam:

UCH-2.hmm, score: 47.53) 444 D78017 Rattus NFI-A1 2667 98 norvegicus 445 AL049569Homo sapiensdJ37C10.3 (novel ATPase)2418 100 448 AJ242540Volvox hydroxyproline-rich 165 34 carteri glycoprotein f. nagariensisDZ-HRGP

449 AJ133352Homo SapiensZNF237 protein 2006 100 450 AJ133352Homo SapiensZNF237 protein 1025 96 451 AF170708Homo SapiensT-box protein TBX3 3700 99 452 AK002080Homo Sapiensunnamed protein product1546 99 453 L32977 Homo sapiensRieske Fe-S protein 1239 93 454 X51760 Homo sapienszinc forger protein 1533 57 (583 AA) 455 Y01141 Homo SapiensSecreted protein encoded1453 99 by gene 7 clone HTLFA90.

456 AB006631Homo SapiensThe human homolog of 6559 100 mouse Cux-2 457 AF067165Homo Sapienszinc forger protein 977 64 458 AF038169Homo Sapiensunknown 154 38 459 W75214 Homo SapiensHuman secreted protein 1180 95 encoded by gene 19 clone HRSMC69.

460 U97002 Caenorhabditissimilar to acyl-CoA 583 37 dehydrogenases elegans and epoxide hydrolases;~Pfam domain PF00441 (Acyl-CoA_dh), Score=57.4, E-value=1.7e-16, N=2;

contains similarity to Pfam domain PF00702 (Hydrolase), Score=57.4, E-value=le-13, N=1 461 AK023 Homo Sapiensunnamed protein productI 041 99 462 M93134 Friend pol protein 289 44 murine leukemia virus 463 AF055473Homo SapiensGAGE-8 232 47 466 Y51415 Homo sapiensHuman wild type pKe83 2625 100 protein.

467 Y51417 787 Human pKe83 splice variant2433 100 protein 468 Y57936 Homo sapiensHuman transmembrane 1629 96 protein HTMPN-60.

469 D38552 Homo SapiensThe ha1539 protein is 2995 100 related to cyclophilin.

470 Y70013 Homo sapiensHuman Protease and associated3530 100 protein-7 (PPRG-7).

471 AJ224747Homo SapiensC-terminal variant of 7969 100 hINADL

including 2 amino acid exchanges and an insertion of 28 amino acids in frame.

472 W99665 Homo SapiensHuman secreted protein 1546 100 clone du157_12 protein.

473 W99665 Homo SapiensHuman secreted protein 998 98 clone du157_12 protein.

474 X63526 Homo Sapienshomologue to elongation2273 99 factor 1-gamma from A.salina 475 X15940 Homo Sapiensribosomal protein L31 644 100 (AA 1-125) 476 M60832 Homo Sapiensalpha-2 type VIII collagen3581 99 477 AF039697Homo Sapiensantigen NY-CO-31 1213 97 478 AF156929Sus scrofainflammatory response 1588 83 protein 6 479 AF264717Homo SapiensFYVE domain-containing 5610 99 dual specificity protein phosphatase 480 AF044578Homo sapiensputative DNA polymerase;2478 94 481 X89750 Homo sapiensTGIF protein 1413 100 SEQ ACCESSIONSPECIES DESCRIPTION SMITFI- % y ID NUMBER . WATERMAN IDENTITY

NO: SCORE

482 M93107 Homo Sapiens(R)-3-hydroxybutyrate 1663 96 dehydrogenase 483 U58334 Homo SapiensBbp/53BP2 1556 41 484 AF1S1538Homosapiensdeoxycytidyltransferase;Revlp4281 99 485 298884 Homo SapiensdJ467L1.1 (KIAA0833) 699 73 486 AJ243874Homo sapiensoligophrenin-4 3682 100 48? 211737 Homo sapiensflavin-containing monooxygenase2969 100 488 X56123 Mus musculustalin 4353 77 489 AJ278112Homo sapiensputative cell cycle 335 23 control protein 490 W74843 Homo SapiensHuman secreted protein 1013 98 encoded by gene 115 clone HOVBA03.

491 Y41337 Homo SapiensHuman secreted protein 509 36 encoded by gene 30 clone HRDDV47.

492 X90530 Homo Sapiensraga 1926 99 493 X90530 Homo Sapiensraga 1405 99 494 X90530 Horno Sapiensraga 1893 96 495 AL022394Homo sapiensdJ511B24.3 (KIAA0395 4990 99 (probable homeobox protein)) 496 Y11395 Homo Sapienslanthionine synthetase 2168 100 C-like protein 497 AJ010119Homo SapiensRibosomal protein kinase4001 100 B (RSK-B) 498 601563 Homo SapiensHuman secreted protein,330 100 SEQ ID

NO: 5644.

499 X54131 Homo sapiensprotein-tyrosine phasphatase10465 99 500 601082 Homo SapiensHuman secreted protein,549 100 SEQ ID

NO: 5163.

501 AC004142Homo sapienssimilar to murine leucine-rich3676 100 repeat protein; possible role in neural development by protein-protein interactions; 93% similarity to D49802 (PID:g1369906) 502 AL117544Homo Sapienshypothetical protein 1226 100 503 AF203032Homo Sapiensneurofilament protein 5115 99 504 AL034417Homo SapiensbK21SD11.2 (similar 2476 100 to rat gene 33) 505 X69090 Homo sapiens190kD protein 7546 99 506 U58755 Caenorhabditiscoded for by C. elegans782 55 cDNA

elegans yk34b1.5; coded for by C. elegans cDNA yk13h10.5; coded for by C.

elegans cDNA yk46e8.5;
coded for by C. elegans cDNA yk46d5.5;

coded for by C. elegans cDNA

yk43c2.5; coded for by C. elegans cDNA yk46e8.3; coded for by C.

elegans cDNA yk43c2.3;
coded fox by C. elegans cDNA yk46d5.3;

coded for by C. elegans cDNA

yk13f10,3; coded for by C. elegans cDNA yk34b1.3 507 AJ293309Homo SapiensNHP2 protein 801 100 508 U3904S Rattus cytoplasmic dynein intermediate3241 97 norvegicuschain 2B

509 AF063231Mus musculuscytoplasmic dynein intermediate3159 97 chain 2 510 AF202893Mus musculusKitZlb 4336 95 511 Y13115 Homo Sapiensserine/threonine protein5071 99 kinase 512 AB030207Homo SapiensG gamma subunit 364 100 513 AF039571Homo Sapiensperipheral benzodiazepine495 33 receptor interacting protein;
PBR-IP/PRAXl 514 AB037883Homo SapiensGb3/CD77 synthase 1916 99 SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

515 D90868 Escherichiasimilar to 1489 100 coli 516 X98834 Homo Sapienszinc forger protein 5290 100 Hsal2 517 AF055668Mus musculusapoptosis-linked gene 2904 78 4, deltaC form 518 AF019926Mus musculusprotein kinase 1694 90 519 M34513 Homo Sapiensomega protein 317 91 520 Y08612 Homo Sapiens88kDa nuclear pore 2313 99 complex protein 521 Y08612 Homo Sapiens88kDa nuclear pore 1561 99 complex protein 522 AL096766Homo SapiensdA59H18.1 (KIAA0767 2497 100 protein) 523 AF186249Homo sapienssix transmembrane epithelial1790 100 antigen of prostate 524 AB029012Homo SapiensKIAA1089 protein 4933 100 525 AB026893Homo Sapiensvascular cadherin-2 5962 100 526 X74331 Homo SapiensDNA primase (p58 subunit)1720 100 528 AC007228Homo SapiensR31665_2 1488 47 529 X14830 Homo Sapiensacetylcholine receptor2639 100 beta-subunit preprotein 530 U80446 Caenorhabditiscoded for by C. elegans420 39 elegans cDNA
yk172e6.3; coded for by C. elegans cDNA yk158f7.3; coded for by C.
elegans cDNA yk158f7.5;
coded for by C. elegans cDNA
yk172e6.5 531 576838 Mus Sp. Dbs 4821 88 532 282215 Homo SapiensdJ68O2.2 (myosin, heavy9828 100 polypeptide 9, non-muscle) 533 AF245505Homo Sapiensadlican 277 31 534 AF300612Homo SapiensN-acetylgalactosamine-4-O-993 59 sulfotransferase 535 AL121928Homo SapiensbA18I14.3 (pleckstrin 3333 99 and Sec7 domain protein) 536 AJ27I055Mus musculusIroquois homeobox protein1724 76 537 AF180473Homo SapiensNot2p 2267 100 538 AF071059Mus musculuszinc forger RNA binding1089 . 51 protein 539 AF023453Homo Sapiensactin-related protein 2219 100 3-beta 540 AC003030Homo SapiensR29828_1 1401 70 541 AC003030Homo SapiensR29828_1 2294 100 542 AL121889Homo SapiensdJ1076E17.1 (KIAA0823 2152 100 protein (continues in AL023803)) 543 AB006135Rattus db83 1238 98 norvegicus 544 602650 Homo SapiensHuman secreted protein,644 97 SEQ ID
NO: 6731.

545 Y07595 Homo Sapienstranscription factor 2373 - 100 TFIIH

546 AL133545Homo SapiensbA386N14.1 (novel protein964 99 similar to a dual specificity phosphatase) 547 X83618 Homo Sapienshydroxymethylglutaryl-CoA2647 100 synthase 548 AF134726Homo SapiensNG37 4359 99 549 AB035356Homo Sapiensneurexin I-alpha protein6948 99 551 AB037901Homo sapiensgene amplified in squamous5215 99 cell carcinoma-1 552 AB043634Homo sapiensPAR-6A 885 100 553 AP000693Homo Sapienspartial CDS 4875 99 554 AF002223Homo Sapiensmyotubularin related 3490 100 555 AC004893Homo Sapienssimilar to NEDD-4 (KIA0093);1611 100 similar to P46934 (PID:g1171682) 556 AJ404468Homo Sapiensaxonemal dynein heavy 8328 100 chain 557 AJ404468Homo Sapiensaxonemal dynein heavy 11137 100 chain WO 01!57190 PCT/US01/04098 SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

558 X65873 Homo Sapienskinesin heavy chain 4860 100 559 AJ277365Homo sapienspolyglutamine-containing592 36 protein 560 AF205600Homo sapienstransposase-like protein407 27 561 X71125 Homo Sapiensglutaminyl-peptide cyclotransferase1914 100 562 X71125 Homo Sapiensglutaminyl-peptide cyclotransferase1456 97 563 X54304 Homo sapiensmyosin regulatory light897 100 chain 564 AF250842Drosophilamultiple asters 130 23 melanogaster 565 Y58608 Homo SapiensProtein regulating gene1619 99 expression PRGE-1.

566 AL121893Homo sapiensbA189K.21.5 (novel protein1012 100 similar to retinoblastoma binding protein (RBBP9)) 567 AL117352Homo sapiensdJ876B10.2 (novel protein3713 99 (ortholog of xat EX084)) 568 AF228603Homo Sapienspleckstrin 2 1841 100 569 AF239243Homo Sapienshistone deacetylase 3244 86 570 AF087695Mus musculusveii 3 989 100 571 AB046381Homo sapienstestis-abundant forger 1346 99 protein 572 AC005551Homo SapiensR26529_2, partial CDS 1020 100 573 Y90290 Homo sapiensHuman peptidase, HPEP-7274 52 protein sequence.

574 W76734 Homo SapiensHuman mDia Rho targeting712 32 protein.

575 AL121935Homo SapiensbA5-17H2.3 (t-complex 853 78 10 (a marine tcp.homolog)) 576 Y86217 Homo SapiensHuman secreted protein 2123 99 HWHGU54, SEQ ID N0:132.

577 AL121716Homo SapiensdJ202D23.2 (novel protein)6329 99 578 AL121716Homo SapiensdJ202D23.2 (novel protein)6329 99 579 X92715 Homo SapiensKRAB 1C2H2 zinc finger 3102 97 protein 580 X54637 Homo Sapiensprotein tyrosine kinase5564 98 581 X78817 Homo Sapiensp115 1148 44 582 AJ251245Rattus SECIS binding protein 3086 71 norvegicus2 583 AF113125Homo SapiensE-1 enzyme 581 100 584 M19529 Sus scrofafollistatin A 1906 98 585 AF169677Homo Sapiensleucine-rich repeat 3403 100 transmembrane protein FLRT3 586 D87685 Homo Sapienssimilar to human transcription8083 99 factor TFIIS (534159).

587 Y00876 Homo SapiensHuman LAPH-1 protein 2110 100 sequence.

588 Y99674 Homo sapiensHuman GTPase associated2111 99 protein-25.

589 D86973 Homo sapienssimilar to Yeast translation12033 99 activator GCN1 (P1:A48126) 590 AL034452Homo SapiensdJ682J1S.1 (novel Collagen1979 100 triple helix repeat containing protein) 591 YS7396 Horno SapiensHuman lysoenzyme LYC4 814 100 polypeptide.

592 AJ297743Mus musculustorsinB protein 1448 85 593 AF164796Homo SapiensNADH:ubiquinone oxidoreductase469 100 Q subunit homolog MLR

594 Y41312 Homo sapiens_ 749 94 Human secreted protein encoded by gene 5 clone HLDRM43.

595 Y41312 Homo SapiensHuman secreted protein 824 100 encoded by gene 5 clone HLDRM43.

596 Y77123 Homo SapiensHuman neurotransmission-associated2102 98 protein (NTAP) 998868.

597 AF215703DrosophilaKISMET-L long isoform 1880 65 SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

melanogaster 598 AF070447Homo Sapiensbarrier-to-autointegration290 90 factor 599 X56203 Plasmodiumliver stage antigen 372 22 falciparum 600 X79828 Mus musculusNK10 202 53 601 AB004109Cricetulusphosphatidylserine synthase2262 92 griseus II

602 U94988 Mus musculusNulpl 2912 89 603 U94988 Mus musculusNulp 1 2800 86 604 AF006264Homo Sapiensrecombination and sister2850 100 chromatid cohesion protein homolog 605 AF006264Homo Sapiensrecombination and sister2530 100 chromatid cohesion protein homolog 606 X82260 Homo SapiensRanGAPl 2929 100 607 X82260 Homo sapiensRanGAPl 1843 97 608 AF160909DrosophilaBcDNA.LD03471 943 58 melanogaster 610 X74801 Homo sapiensgamma subunit of CCT 2745 99 chaperonin 6I1 AL03I427Homo SapiensdJ167A19.1 (novel protein)1608 100 612 Y71072 Homo SapiensHuman membrane transport445 100 protein, MTRP-17.

613 X16396 Homo Sapiensprecursor polypeptide 1749 100 (AA -29 to 315) 614 AK000281Homo Sapiensunnamed protein product1814 99 615 AB011128Homo SapiensKIAA0556 protein 5761 99 616 U19361 PetromyzonNF-180 205 21 marinus 617 AF045555Homo Sapienswbscrl 1208 100 618 AF045555Homo Sapienswbscrl alternative spliced1318 100 product 619 U22229 Felis catusribosomal protein L41 I28 100 620 Y 17169 Homo SapiensA6 related protein 1819 100 621 Y12065 Homo SapienshNop56 2956 99 622 AF177758Homo Sapiensubiquitin specific protease2998 100 623 AF317425Homo SapiensGAC-1 3866 100 624 AL050297Homo Sapienshypothetical protein 1227 99 625 AC007204Homo SapiensBC273239_1 3398 99 626 268747 Homo Sapiensimogen 38 2024 99 627 268747 Homo Sapiensimogen 38 1958 97 628 Y70229 Homo SapiensHuman RNA-associated 3424 99 protein-10 (RNAAP-10).

629 AF191492Homo Sapiensnasopharyngeal carcinoma613 100 associated gene protein-8 630 AF119664Homo Sapienstranscriptional regulator1574 100 protein HCNGP

631 AF119664Homo Sapienstranscriptional regulator1150 89 protein HCNGP

632 Y17849 Homo sapiensganglioside-induced 1839 98 differentiation associated protein 1 633 X55740 Homo Sapiens5'-nucleotidase 3012 100 634 AF039688Homo Sapiensantigen NY-CO-3 931 100 635 AF119662Homo SapiensE46 protein 2424 100 636 AB007836Homo SapiensHic-5 2544 100 637 AF077818Mus musculussyntrophin-associated 2027 44 serine-threonine protein kinase 638 AL035455Homo SapiensdJ1018E9.1 (VAMP (vesicle-150 26 associated membrane protein)-associated protein B
and C) 639 AF078844Homo sapienshqp0376 protein 416 81 ~ ~

SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

640 U28377 EscherichiaORF f239; was ORF f191I 198 100 coli and ORF'_f194 before splice 641 AK024442Homo SapiensFLJ00032 protein 1677 56 642 U58682 Homo sapienSribosomal protein S28 340 100 643 X57432 Rattus rattusribosomal protein S2 1520 98 644 AB002348Homo SapiensI~IAA0350 protein 5186 ~ 99 646 Y96202 Homo sapiensIkappaB kinase (IKK) I 178 98 binding protein, Y2H56.

647 AB029482Mus musculusJNK-binding protein 4609 81 648 AB009053Arabidopsiscontains similarity 407 44 thaliana to isoamyl acetate-hydrolyzing esterase~gene_id:MQB2.25 650 AC002550Homo SapiensUnknown gene product 858 99 651 U26592 Homo Sapiensdiabetes mellitus type253 66 I autoantigen 6S2 X60155 Homo Sapienszinc finger 41 4349 100 653 XS3330 PlatynereisH4 protein (AA 1 - 523 100 dumerilii 103) 654 AC003682Homo Sapiens827945 2 2558 100 ~

655 X80473 Mus musculusrabl9 596 56 656 J02649 Rarius unknown protein 201 95 norvegicus 657 AC006014Homo Sapienssimilar to RFP transforming1331 99 protein;
similar to P14373 (PID:g132517) 658 X92972 Homo Sapiensprotein phosphatase 1666 100 659 L35269 Homo Sapienszinc finger protein 2803 99 660 AC003682Homo SapiensF18547_1 3184 96 661 X79204 Homo Sapiensataxin-1 4195 99 662 X17620 Homo SapiensNm23 protein 965 99 663 AB015617Homo SapiensELKS _ 80 664 256281 Homo Sapiensinterferon regulatory 2331 100 factor 3 665 AJ248283Pyrococcus LACTOYLGLUTATHIONE 254 40 abyssi LYASE (EC 4.4.1.5) METHYLGLYOXALASE) (ALDOKETOMUTASE) (GLYOXALASE I).

666 270200 Homo SapiensU5 snRNP-specific 200kD8819 99 protein 667 270200 Homo SapiensU5 snRNP-specific 200kD_ 97 protein 8589 668 AF153450Manduca juvenile hormone esterase_ 32 sexta binding 225 protein 669 AF227198Homo sapiensCrkRS 7231 99 670 X99586 Homo sapiensSMT3C protein 441 87 671 261589 Homo Sapiens17-AUG-1998 DNA encoding2593 100 cdI a human OC-2 protein.

672 AJ132702Mus musculusATFa-associated factor3240 88 673 AF204159Homo Sapienspotassium large conductance_ 100 calcium-activated channel1486 beta 3a subunit 674 602061 Homo SapiensHuman secreted protein,558 99 SEQ ID
NO: 6142.

675 601246 Homo sapiensHuman secreted protein,141 77 SEQ ID
NO: 5327.

676 AB016839Homo Sapiensmobl 419 42 677 D86970 Homo sapienssimilar to myosin heavy__ 28 chain: 161 Containing ATP/GTP-binding site motif A(P-loop) 678 U83115 Homo Sapiensnon-lens beta gamma-crystallin. 8569 99 like protein 679 AF203687Homo Sapiensprolactin regulatory 2181 100 element-binding protein SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

680 M27685 Mus musculusulna-high sulphur keratin650 58 681 U04968 Cricetulus nucleotide excision 3712 97 griseus repair protein 682 AF119663Homo SapiensG-protein gamma-12 356 100 subunit 683 603733 Homo sapiensHuman secreted protein,342 100 SEQ ID
NO: 7814.

684 X67699 Homo SapiensCDw52 antigen 297 100 685 AF022789Homo Sapiensubiquitin hydrolyzing 1892 100 enzyme I

686 AJ001006Mus musculusEMeg32 protein 938 96 687 W03S16 Homo SapiensProstaglandin DP receptor.1864 100 688 AF019661Mus musculuszeta proteasome chain;1214 100 PSMAS

689 AF156557Homo Sapiensstomatin related protein2036 100 690 603960 Homo SapiensHuman secreted protein,593 100 SEQ ID
NO: 8041.

691 AFI61512Homo SapiensHSPC163 738 100 692 AL031115Homo SapiensZXDA, ZXDB (zinc finger4298 100 X-linked protein) 693 L40410 Homo sapiensthyroid receptor interactor806 100 694 AC004542Homo SapiensOXYSTEROL-BINDING 2533 99 PROTEIN-like; similar to P22059 (PID:g129308) 695 AFI69411Rattus PAPIN 4144 S2 norvegicus 696 YS8168 Homo SapiensHuman hydrolase homologue2144 100 HHH-4.

697 AF271994Homo Sapiensdopamine responsive 1613 I00 protein DRG-1 698 Y41741 Homo SapiensHuman PRO704 protein 1323 100 sequence.

699 AL133S06Unknown /prediction=(method:"""genscan"",825 48 version:""1.0"", score:""109.13"");
/prediction=(method:

700 Y96870 Homo SapiensHuman goose-type lysozyme1032 100 (GOLY).

701 AC003034Homo sapiensGene with similarity 1190 100 to rat kidney-specific (KS) gene 702 AC003034Homo SapiensGene with similarity 937 95 to rat kidney-specific (KS) gene 703 AJ242832Homo sapienscalpain 3756 100 704 SS2624 Homo Sapiensunknown 18S 100 705. AFOOS081Homo Sapiensskin-specific protein 652 100 706 Y16793 Homo Sapienskeratin, type I 2232 100 707 Y44985 Homo SapiensHuman epidermal protein-2.455 69 708 AF113220Homo SapiensMSTP040 686 100 709 Y44985 Homo SapiensHuman epidermal protein-2.408 65 710 Y16132 Homo SapiensCDT6 1874 100 711 Y68775 Homo SapiensAmino acid sequence 2407 100 of a human phosphorylation effector PHSP-7.

712 X63422 Homo SapiensH(+)-transporting ATP 209 100 synthase 7I3 AF169968Mus musculusDNA binding protein 1467 79 DESRT ' 714 X52563 Bos taurus permability increasing383 29 protein 715 AJ277739Homo SapiensRPBllblalpha protein 480 98 716 AL135791Homo SapiensbA162G10.3 (zinc finger401 98 protein) 717 AF223466Homo SapiensHTO1S protein 1311 97 719 AF117383Homo Sapiensplacental protein 13; 746 100 720 298743 Homo SapiensdJ181C9.2 (Rho GTPase 324 100 activating protein 8 (RhoGAP, p50RhoGAP)) 721 AL163815Arabidopsisputative protein 653 61 thaliana 722 GOI436 Homo SapiensHuman secreted protein,418 96 SEQ ID

WO 01/57190 PCT/USO1/0409&
SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO:

SCORE

NO: 5517.

723 AF282919 Mus musculusZfp228 349 49 724 AB023191 Homo SapiensKIAA0974 protein 2953 100 725 AL03 l Homo SapiensdJ34B21.1 (novel BZRP 920 I00 (benzodiazapine receptor (peripheral) (MBR, PBR, PBKS, IBP, Isoquinoline-binding protein)) LIKE

protein) 726 AL021939 Homo SapiensdJ352A20.2 (aldehyde 1764 100 dehydrogenase family protein) 727 AF 182426Rattus arylacetamide deacetylase791 42 norvegicus 728 Y08565 Homo sapiensUDP-GaINAc:polypeptide3331 99 N-acetylgalactosaminyltransferase 729 AF155135 Homo sapiensnovel retinal pigment 1652 99 epithelial cell protein 730 AL078606 Arabidopsisputative protein 277 55 thaliana 731 Y73352 Homo SapiensHTRM clone 1732368 1720 100 protein sequence.

732 AF178432 Homo SapiensSH3 protein 3302 100 733 Y17832 Human env protein 223 34 endogenous retrovirus K

734 _ Homo SapiensHuman mesoderm induction2067 gg Y28859 early response protein ERl.

735 _ Oryctolagusprotein phosphatase 2352 gg U09355 2A1 B gamma cuniculus subunit 736 Y94922 Homo SapiensHuman secreted protein724 gg clone pv6~1 protein sequence SEQ
ID NO:50.

737 AB027003 Mus musculusprotein phosphatase 378 84 738 AFI12200 Homo SapiensNADH-oxidoreductase 739 100 B18 subunit 739 AF112200 Homo SapiensNADH-oxidoreductase 613 gg B18 subunit 740 AF3021S4 Homo SapiensSPG protein 6556 100 741 B25681 Homo SapiensHuman secreted protein1410 99 sequence encoded by gene 17 SEQ ID NO:70.

742 L27479 Homo SapiensX123 1237 99 743 L27479 Homo SapiensX123 1206 97 744 Y66745 Homo SapiensMembrane-bound protein588 99 PR01186.

745 AJ001019 Homo Sapiensring finger protein 1292 g9 746 X68453 Sus scrofatubulin-tyrosine ligaseI gg2 94 747 Y57897 Homo SapiensHuman transmembrane 1173 100 protein HTMPN-2I.

748 AF151069 Homo sapiensHSPC235 1694 96 749 AF182404 Homo Sapiensmitochondrial uncoupling1674 100 protein 1 750 AL 121993Homo SapiensdJ776P7.1 (Novel protein)2500 99 751 AF149825 Homo SapiensPACSIN3 2253 100 752 AL008635 Homo SapiensdJ510H16.2 (high-mobility3026 gg group protein 2-Like I) 753 Y57914 Homo SapiensHuman transmembrane 1124 100 protein HTMPN-38.

754 AF285109 Homo Sapienseptin 3 isoform B 1766 100 s 755 AF004161 Oryctolagusperoxisomal Ca-dependent2371 95 solute cuniculus arrier c 756 219585 Homo sapienshrombospondin-4 4239 100 t 757 AP001745 Homo Sapiensimilar to zinc forger 1857 100 s S protein 758 AF190664 Mus musculusLMBR2 555 72 759 AF090326 Mus musculusAE-1 binding protein 1540 97 760 AL096677 Homo SapiensJ322G13.3 (novel protein999 94 d similar to SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

bovine and mouse beta-soluble NSF
attachment protein (SNAP-beta) ) 761 AC003007Homo sapiensUnknown gene product 649 96 (partial) 762 U66372 Bos taurusribosomal protein S29 230 73 764 Y90899 Homo SapiensD1-like dopamine receptor1152 100 activity modifying protein SEQ
ID NO:1.

765 U88169 Caenorhabditissimilar to molybdoterin1204 65 . elegans biosynthesis MOEB proteins 766 ALl 18506Homo SapiensdJ591C20.3.1 (novel 1091 100 DnaJ domain protein, similar to mouse and bovine cysteine string protein) 767 AK024693Homo Sapiensunnamed protein product3767 100 768 211518 Homo Sapienshistidyl-tRNA synthetase2582 100 769 X13916 Homo sapiensLDL-receptor related 25529 100 precursor (AA
-19 to 4525) 770 AC009360ArabidopsisContains 3 PF~00400 333 33 thaliana WD40, G-beta repeat domains.

771 AB037685Mus musculusLANP-like protein 1246 91 772 AL161578Arabidopsisputative protein 335 46 thaliana 773 AL161578Arabidopsisputative protein 333 47 thaliana 774 AY008271Homo Sapienshelicase SMARCAD1 5264 99 775 Y21591 Homo SapiensHuman secreted protein 1127 96 -(clone CC332-33).

776 W88853 Homo sapiensPolypeptide fragment 752 100 encoded by gene 89.

777 W88853 Homo SapiensPolypeptide fragment 752 100 encoded by gene 89.

778 W88853 Homo SapiensPolypeptide fragment 752 100 encoded by gene 89.

779 AF196481Homo SapiensRING forger protein; 3644 100 780 AL035427Homo SapiensdJ769N13.1 (KIAA0443 1609 54 protein.) 781 AB026187Homo Sapiensprotocadherin-Xa 5244 100 782 B24458 Homo sapiensHuman secreted protein 1002 100 sequence encoded by gene 22 SEQ
ID N0:83.

783 AB027289Homo sapienscyclin-E binding protein5421 100 784 602916 Homo SapiensHuman secreted protein,627 100 SEQ ID
NO: 6997.

785 AJ245822Homo Sapienstype I transmembrane 4560 100 receptor 786 AJ245820Homo Sapienstype I transmembrane 4624 100 receptor 787 248042 Homo sapiensGPI-anchored protein 3340 99 p137 788 AL031782Homo SapiensdJ708F5.1 (PUTATIVE 2739 100 novel Collagen alpha 1 LIKE
protein) 789 AJ131245Homo sapiensSec24B protein 6602 100 790 AF107203Homo Sapiensataxin 2-binding protein2008 100 791 Y14690 Homo Sapiensprocollagen alpha2(V) 600 34 792 AL031055Homo SapiensdJ28H20.2 (novel protein)1267 100 793 Y36194 787 Human secreted protein 2051 99 794 AB028127Homo Sapiensmannosyltransferase 2138 96 795 AC007228Homo Sapiens831665_2 2738 79 796 AL049482Arabidopsisputative protein 436 47 thaliana 797 AC004528Homo Sapiens832184_3 891 91 798 AB037830Homo SapiensKIAA1409 protein 7532 100 799 X53793 Homo Sapiens5' half of the product 2232 100 is homologues to Bacillus subtiis SAICAR
synthetase, 3' half corresponds to the catalytic subunit of AIR carboxylase SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

800 Y99350 Homo sapiensHuman PR01378 (UNQ715) 1343 I00 amino acid sequence SEQ ID
N0:33.

801 AB042636Homo Sapiensjunctophilin type3 1225 47 802 AB029324Rattus TIP120-family protein 3916 90 norvegicusTIP120B

803 AB029324Rattus TIP120-family protein 4961 90 norvegicusTIP120B

804 AF251040Homo Sapiensputative nuclear protein2119 I00 805 AB033281Homo SapiensF-box and WD-repeats 2879 100 protein beta-TRCP2 isoform C

806 U87305 Rattus transmembrane receptor 3257 90 norvegicusUNC5H1 807 AF118889Rattus b-tomosyn isoform 3155 97 norvegicus 808 AF226993Rattus selective LIM binding 8793 95 norvegicusfactor 809 W19919 Homo SapiensHuman Ksr-1 (kinase 3939 99 suppresser of Ras).

810 AL03I782Homo SapiensdJ708F5.1 (PUTATIVE 1546 I00 novel Collagen alpha 1 LIKE
protein) 811 AC002542Homo Sapienssimilar to C. elegans 2294 100 F11AI0.5; 80%
similarity to 268297 (PID:g1130619) 812 U83246 Homo sapienscopine I 606 52 813 AF242552Gallus retinovin 945 34 gallus 814 X52332 Homo Sapienszinc forger protein 1651 93 815 X52332 Homo Sapienszinc finger protein 2423 99 816 Y09631 Homo SapiensPIBFl protein 2935 99 817 X71997 Rattus myosin I 3883 98 norvegicus 818 AY004877Mus musculuscytoplasmic dynein heavy11105 98 chain 819 Y27196 Homo SapiensHuman cyclic nucleotide3790 100 phosphodiester PDEBB(E) amino acid sequence.

820 AF081947Mus musculustektin 1134 81 821 AL035106Homo SapiensdJ998C11.1 (continues 871 100 in Em:AL445192 as bA269H4.1) 822 AF022795Homo SapiensTGF beta receptor associated3 85 24 protein-823 AF015770Mus musculusradical fringe 1422 82 824 U82695 Homo Sapiensexpressed-Xq28STS protein1444 99 825 X77371 MesocricetusCORl 641 78 auratus 826 AB014576Homo SapiensKIAA0676 protein 296 79 827 AL049733Homo SapiensdJ875H3.1 (APK1 antigen)1584 72 828 AF222980Homo Sapiensdisrupted in Schizophrenia4418 100 1 protein 829 231560 Homo Sapienssox-2 1683 100 830 AF295773Homo Sapiensral guanine nucleotide 4717 99 dissociation stimulator 831 AB041926Homo SapiensGCK family kinase MINK-26866 100 832 L04948 Saccharomycemitochondria) transporter338 35 s cerevisiaeprotein 833 AJ007012Mus musculusFish protein 704 94 834 234289 Homo Sapiensnucleolar phosphoprotein3455 99 p130 835 U10991 Homo SapiensG2 8436 98 836 AF230877Homo SapiensMIP-T3 2945 99 837 X58288 Homo Sapiensprotein-tyrosine phosphatase7734 99 838 X56958 Homo Sapiensankyrin (brank-2) 9631 100 839 AC024791Caenorhabditiscontains similarity 370 24 elegans to beta-lactamases SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER ~ WATERMAN IDENTITY
NO: SCORE

840 D83197 Homo Sapiensankyrin repeat protein802 99 841 AF053711Serinus neurofilament medium 192 31 canaria subunit 842 AF283772Homo Sapienssimilar to Homo Sapiens990 96 ribosomal protein L10 encoded by GenBank Accession Number L25899 843 U76343 Homo SapiensGABA transport protein2992 98 844 Y13645 Homo Sapiensuroplakin II 897 100 845 D21064 Homo Sapienssimilar to rat general2710 99 mitochondrial matrix processing protease mRNA
(RATMPP).

846 AF192522Homo SapiensNiemann-Pick C3 protein;7047 100 847 AF192522Homo SapiensNiemann-Pick C3 protein;5472 100 848 X60489 Homo Sapienselongation factor-i-beta1162 100 849 AC007204Homo SapiensBC273239_1 2277 67 850 AC003682Homo SapiensR28830_I 2401 100 851 AL121583Homo sapiensbA358N2.1 (novel protein)353 61 852 248475 Homo Sapiensglucokinase regulator 3155 99 853 283844 Homo SapiensdJ37E16.2 (SH3-domain 1884 98 binding protein 1) 854 AF233323Homo SapiensFas-associated phosphatase-1390 36 855 AF062741Rattus pyruvate dehydrogenase447 80 norvegicus phosphatase isoenzyme 2 856 Y11411 Homo Sapienspristanoyl-CoA oxidase3595 98 857 M97188 Strongylocentrtektin A 1 290 46 otus purpuratus 858 AB001105Homo Sapienshippocalcin-like protein995 100 859 AF164791Homo sapiensputative 38.3kDa protein1795 100 860 AF298117Homo Sapienshomeobox protein OTX2 1477 93 86I AFOI5264Rattus golgi peripheral membrane1820 8I
norvegicus protein p65 862 X16901 Homo Sapiens30kb subunit of RAB30 1284 100 863 M12140 Homo Sapiensenvelope protein 202 81 864 AF161459Homo SapiensHSPC109 815 98 865 AL109983Homo SapiensdJ718P11.1.1 (novel 444 100 class II
aminotransferase similar to serine palmotyltransferase (isoform I)) 866 M77183 Rattus alpha-1-macroglobulin 227 45 norvegicus 867 AF272663Homo Sapiensgephyrin 3785 100 868 X75285 Mus musculusfibulin-2 3258 87 869 X82494 Homo sapiensfibulin-2 3407 99 870 AJ297743Mus musculustorsinB protein 169 43 871 AJ278313Homo Sapiensphospholipase C-beta-16258 99 a 872 AF073344Homo Sapiensubiquitin-specific 256 43 protease 3 873 Y91955 Homo SapiensHuman cytoskeleton 535 100 associated protein 10 (CYSKP-10).

874 AJ000414Homo SapiensCdc42-interacting protein1136 53 875 AF265555Homo Sapiensubiquitin-conjugating 627 100 BIR-domain enzyme APOLLON

876 Y48586 Homo SapiensHuman breast tumour-associated2537 98 protein 47.

877 AF182198Homo Sapiensintersectin 2 long 8764 99 isoform 878 L17308 Gossypium proline-rich cell wall192 35 hirsutum protein 879 AF177169Homo sapienstropomodulin 2 1769 100 880 W03627 Homo SapiensHuman follicle stimulating210 23 hormone GPR N-terminal sequence.

SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO: SCORE

881 AL021068Homo SapiensdJ206D15.3 2615 99 882 AC005498Homo SapiensR31665_2 318 82 883 AF165518Homo SapiensMAGOH isoform 182 94 884 D21211 Homo Sapiensprotein tyrosine phosphatase368 43 (PTP-I BAS, type 3) 885 U13045 Homo Sapiensnuclear respiratory 869 62 factor-2 subunit beta 1 886 X52836 Homo sapienstryptophan hydroxylase2320 98 (AA 1 - 444) 887 X51466 Homo Sapienselongation factor 2 4460 100 888 AB039903Homo Sapiensinterferon-responsive 1096 98 finger protein 1 long form 889 X51760 Homo Sapienszinc forger protein 3130 100 (583 AA) 890 AJ243396Homo Sapiensvoltage-gated sodium 1024 100 channel beta-3 subunit 891 W67928 Homo sapiensFragment of human secreted391 100 protein encoded by gene 4.

892 AB020598Homo Sapienspeptide transporter 3017 100 893 Y66648 Homo SapiensMembrane-bound protein4722 99 PR01120.

894 Y66648 Homo SapiensMembrane-bound protein3606 96 PR01120.

895 A29218_cdHomo Sapiens19-NOV-1998 DNA encoding2178 100 protein coupled 7 TM
receptor with AXOR15 activity.

896 AJ000332Homo SapiensGlucosidase II 5063 99 897 X98259 Homo SapiensM-phase phosphoprotein1085 100 898 X57110 Homo Sapiensc-cbl protein 4849 99 899 X63652 Homo Sapiensinter-alpha-trypsin 3376 98 inhibitor heavy chain ITIH1 900 X85134 Homo SapiensRB protein binding 2816 99 protein 901 L11672 Homo sapienszinc forger protein 2047 58 902 Y85565 Homo SapiensHuman homologue of 369 83 UNC-53 (Hs-UNC-53/2) sequence.

903 X54871 Homo Sapiensras related protein 1094 100 RabSb 904 298265 Homo Sapiensplakophilin 3 4065 100 905 AL035295Homo Sapienshypothetical protein 959 99 906 AF051782Homo Sapiensdiaphanous 1 801 35 907 AF208536Homo Sapiensnucleotide binding 1372 100 protein; NBP

908 U79240 Homo Sapiensserine/threonine protein2365 98 kinase 909 U79240 Homo Sapiensserine/threonine protein2386 99 kinase 910 AJ132545Homo sapiensprotein kinase 2921 100 911 AJ132545Homo Sapiensprotein kinase 1637 99 912 AL 121733Homo Sapienshypothetical protein 1344 99 913 Y67579 Homo SapiensHuman death inducer-obliterator1586 100 (DIO-1) polypeptide.

914 X87342 Homo SapiensHuman giant larvae 5317 99 homologue 915 X87342 Homo SapiensHuman giant larvae 3495 96 homologue 916 M94362 Homo Sapienslamin B2 2357 93 917 AJ011654Homo Sapienstriple LIM domain protein3432 100 918 AJ131899Rattus proline rich synapse 5776 88 norvegicus associated protein 1 919 AF054986Homo sapiensputative transmembrane1816 100 GTPase 920 U95822 Homo Sapiensputative transmembrane1237 100 GTPase 921 Y11588 Homo Sapiensapoptosis specific 1492 100 protein 922 X84195 Homo Sapiensacylphosphatase 510 100 923 U72882 Homo Sapiensinterferon-induced 1409 99 leucine zipper protein 924 AE000660Homo sapienshADV3651 573 100 925 AF126245Homo Sapiensacyl-Coenzyme A dehydrogenase-82162 100 precursor SEQ ACCESSION SPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO:

SCORE

926 AE001968 Deinococcushypothetical protein 147 27 radiodurans 927 W81576 Homo SapiensEBV-induced G-protein 1778 100 coupled receptor (EBI-2) polypeptide.

928 U01317 Homo sapiensbeta-globin 687 94 929 X98333 Homo Sapiensorganic cation transporter2933 100 930 Y91444 Homo SapiensHuman secreted protein1401 100 sequence encoded by gene 42 SEQ ID

NO: I 65.

931 Y91644 _ Human secreted protein1243 100 Homo Sapienssequence encoded by gene 43 SEQ ID

N0:317.

932 D90279 Homo Sapienscollagen alpha 1(V) S69 39 chain precursor 933 231560 Homo sapienssox-2 1587 96 934 AF147790 .Homo Sapienstransmembrane mucin 3047 99 935 285996 Homo Sapiensmatch: multiple proteins;726 94 match:

1111 Q43554;

match: Q08150 Q40195 Q39222; match: Q40368 ~P40393 Q40723; match:

Q38923 Q40191 Q41022;
match:

Q08146;

match: P10949 P11023 Q20337; match: Q25389 P20336 P05713; match:

Q08I47 PI7609 P22I28;
match:

Q15771 P364i0 P3529I;
GTP-binding 936 AB041S33 Homo Sapienssperm antigen 1054 38 937 X91906 Homo Sapiensvoltage-gated chloride3914 100 ion channel 938 AB032481 Homo Sapienshomeobox transcription1744 100 factor 939 AFl ~ 1106Homo Sapiensprotein serine/threonine4682 99 phosphatase 4 regulatory subunit 940 Y17999 Homo SapiensDyrklB protein kinase 3331 99 941 AF305872 Homo Sapiensthyroglobulin 455 92 942 AF263462 Homo Sapienscingulin 5939 99 943 AK024442 Homo SapiensFLJ00032 protein 1616 61 944 Y35911 Homo SapiensExtended human secreted262 35 protein sequence, SEQ ID NO.
160.

945 AB015320 Homo SapienssigmalB subunit of 599 71 AP-1 clathrin adaptor complex 946 282287 CaenorhabditisZK550.2 229 35 elegans 947 D84223 Homo Sapiensleucyl tRNA synthetase6207 99 948 U49057 Rattus rA9 3846 62 norvegicus 949 AK000568 Homo Sapiensunnamed protein product1659 100 950 AL021578 Homo SapiensdJ453C12.6.1 (uncharacterized2S7 42 hypothalamus protein (isoform 1)) 9S1 _ Homosapiensdifferentiation-associatedNa-3063 99 dependent inorganic phosphate cotransporter 952 AF110532 Homo sapiensuncoupling protein 1561 100 9S3 X83587 Mus musculus1A13 protein 1420 59 9S4 AL031665 Homo SapiensdJ545L17.5.1 (novel 386 53 protein) 955 Y87600 Homo SapiensHuman fatty acid synthase-like2377 100 p rotein (HFASLP).

9S6 Y99421 Homo sapiensHuman PR01433 (UNQ738)522 5S
amino a cid sequence SEQ ID
N0:292.

SEQ ACCESSIONSPECIES DESCRIPTION SMITH-ID NUMBER WATERMAN IDENTITY
NO:

SCORE

9S7 U68S35 Mus musculusaldo-keto reductase 4S 1 73 9S8 AC007067 ArabidopsisT10024.10 1594 57 thaliana 959 U72194 Mus muscutusmuskelin 3947 gg 960 AE003661 DrosophilaCG15168 gene product 277 S4 melanogaster 961 X80332 Mus musculusrab20 983 82 962 Y6731S Homo sapiensHuman secreted protein3916 99 BL89_13 amino acid sequence.

963 Y67315 Homo SapiensHuman secreted protein3916 99 BL89_13 amino acid sequence.

964 L32602 Rattus homeodomain 159..341 1821 96 norvegicus 965 297832 Homo SapiensdJ329AS.3 (KIAA06460 3581 99 protein) 966 W8899S Homo sapiensPolypeptide fragment 176 39 encoded by gene 146.

967 U12465 Homo Sapiensribosomal protein L3S 604 100 968 AF151803 Homo SapiensCGI-45 protein 1101 78 969 W7486S Homo SapiensHuman secreted protein1348 98 encoded by gene 137 clone HMWIF35.

970 L21936 Homo Sapienssuccinate dehydrogenase703 100 flavoprotein subunit 971 AJ133S21 Drosophilaprotease, reverse transcriptase,194 23 buzzatii ribonuclease H, integrase 972 AC006017 Homo SapiensN-acetylgalactosaminyltransferase;3271 100 similar to Q10473 (PID:g1709S59) 973 281317 SchizosaccharDNA2-NAM7 helicase 685 3I
family omyces protein pombe 974 M17885 Homo Sapiensacidic ribosomal phosphoprotein792 100 (PO) 97S U22829 Mus musculusP2Y purinoceptor 399 40 976 AL132772 Homo SapiensdJ1013A22.1 (hepatic 2466 99 nuclear factor 4, alpha) 977 AC003973 Homo sapiensZNF91L 1550 43 978 J04031 Homo SapiensMDMCSF (EC 1.5.1.5; 2824 63 EC 3.5.4.9;

EC 6.3.4.3) 979 AF136715 Homo Sapienstaxol resistant associated217 76 protein 980 AF136715 Homo Sapienstaxol resistant associated306 95 protein 981 292822 CaenorhabditisZKS20.1 1109 44 elegans 982 AJ29S Homo Sapiensputative dipeptidase 1 S64 99 983 AL021331 Homo SapiensdJ366N23.3 (KIAA0173 1492 100 and Tubulin-Tyrosine Ligase LIKE) 984 AL161501 Arabidopsisputative adenosine 370 38 deaminase thaliana SEQ ACCESSION DESCRIPTION . RESULTS*
ID NO.
NO:

2 BL00282 Kazal serine protease BL00282 16.88 4.2S9e-14 inhibitors family 97-120 proteins.

3 BL00298 Heat shock hsp90 proteinsBL00298A 10.97 1.000e-40 family 74-proteins. 119 BL00298E 27.30 1.000e-40 321-376 BL00298F 11.21 1.000e-20.50 1.000e-40 553-607 16.40 2.286e-40 186-230 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

BL00298B 15.64 1.290e-39 181 BL00298G 24.57 S.34Se-39 46S-S20 BL00298I 30.07 7.818e-17.97 6.226e-33 242-282 4 PR00237 RHODOPSIN-LIKE GPCR PR00237A 11.48 4.316e-13 SUPERFAMILY SIGNATURE

S PD024S4 ! L I 1 PROTEIN ALU SUBFAMILYPD024S4B 11.61 4.309e-17 PHOSPHO.

6 DM00864 EGF-LIKE DOMAIN. DM00864A 15.217.429e-09 7 PR00237 RHODOPSIN-LIKE GPCR PR00237A 11.48 1.7SOe-11 SUPERFAMILY SIGNATURE PR00237D 8.94 7.000e-09 160 PR00237B 13.50 8.2SOe-09 9 PF008SS PWWP domain proteins. PF008SS 13.75 5.667e-1S

BL00139 Eukaryotic thiol (cysteine)BL00139D 9.24 4.400e-11 proteases 391-cysteine proteins. 408 BL00139A 10.29 7.Slle-09 12 BL01113 Clq domain proteins. BL01113B 18.26 9.294e-19 725 BL01113C 13.18 4.857e-11 757-777 BI,01113D7.472.161e-13 BL01113 Clq domain proteins. BL01113B 18.26 3.813e-14 63S BL01113C 13.18 4.857e-11 667-687 BL01113D 7.47 2.161e-14 BLOOS94 Aromatic amino acids permeasesBLOOS94A 16.75 6.531e-10 proteins.

BL01047 Heavy-metal-associated BL01047B 19.73 4.913e-13 domain proteins. 707-16 PR0062S DNAJ PROTEIN FAMILY PR0062SA 12.84 7.462e-18 SIGNATURE 330 PR0062SB 13.48 3.939e-15 18 BL0061S C-type lectin domain proteins.BL0061SA 16.68 3.700e-09 PR00741 GLYCOSYL HYDROLASE FAMILYPR00741D 16.11 9.082e-21 29 SIGNATURE 195 PR00741F 14.66 9.262e-21 243-265 PR00741B 14.23 1.947e-9.29 2.180e-17 318-340 PR00741C

9.16 7.328e-17 147-166 PR00741 H 10.32 2.141 e-13 3 S 1-374 PR00741A 9.24 3.596e-13 89-lOS PR00741E 13.39 3.535e-22 BLOOI07 Protein kinases ATP-bindingBL00107A 18.39 3.647e-20 region I 17-proteins. 148 BL00107B 13.31 1.000e-16 23 BL00107 Protein kinases ATP-bindingBL00107A 18.39 1.600e-23 region 126-proteins. 1 S7 24 BL00107 Protein kinases ATP-bindingBL00107A 18.39 1.600e-23 region 126-proteins. 1 S7 27 BL00239 Receptor tyrosine kinase BL00239B 25.15 2.324e-16 class II proteins. 91-28 BL00018 EF-hand calcium-binding BL00018 7.41 3.250e-10 domain 681-694 proteins. BL00018 7.41 6.400e-10 29 BL00018 EF-hand calcium-binding BL00018 7.41 3.250e-10 ~ domain 681-694 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

proteins. BL00018 7.41 6.400e-10 30 .BL01113 Clq domain proteins. BLOT 113A 17.99 9.308e-09 33 PD01168 SYNTHETASE LIGASE PROTEINPDOl 168L 9.47 1.667e-09 ALANYL. 416 34 PD01168 SYNTHETASE LIGASE PROTEINPD01168L 9.47 1.667e-09 ALANYL. 426 36 PR00426 CSA-ANAPHYLATOXIN RECEPTORPR00426D 10.59 3.618e-12 37 PF00791 Domain present in ZO-1 PF00791B 28.49 2.049e-10 and UncS-like 1080 netrin receptors. 1135 38 BL003S0 MADS-box domain proteins.BL003S0 20.79 1.000e-40 40 BL00123 Allealine phosphatase BL00123B 19.31 1.000e-40 proteins. 90-133 BL00123C 24.61 1.000e-40 14S-195 BL00123E 22.25 I.OOOe-26.01 1.000e-40 438-488 BL00123F

19.03 8.714e-3S 364-399 BL00123A 10.80 9.000e-24 BL00123D 12.73 1.000e-17 229 ' 44 PD00066 PROTEIN ZINC-FINGER METAL-PD00066 13.92 2.800e-14 BINDI. PD00066 13.92 4.600e-14 PD00066 13.92 1.000e-13 PD00066 13.92 6.000e-13 PD00066 13.92 2,714e-12 PD00066 13.92 3,143e-12 PD00066 13.92 8.714e-12 PD00066 13.92 3,739e-11 PD00066 13.92 2,038e-10 45 DM00973 3 kw RESISTANCE BENOMYL DM00973A 21.17 2.946e-10 YLL028W CYCLOHEXIMIDE. 217 47 BL00649 G-protein coupled receptorsBL00649C 17.82 1.682e-10 family 2 47S-proteins. 501 BL00649B 20.68 7.387e-09 SO PD00066 PROTEIN ZINC-FINGER METAL-PD00066 13.92 8,200e-16 BINDI. PD00066 13.92 5.846e-1S

PD00066 13.92 1.000e-14 PD00066 13.92 1,000e-14 PD00066 13.92 2,800e-14 PD00066 13.92 2.800e-14 PD00066 13.92 8.800e-14 PD00066 13.92 9,400e-14 PD00066 13.92 4.000e-13 PD00066 13.92 6.S71e-12 51 BL00226 Intermediate filaments BL00226D 19.10 1.000e-40 proteins. 417-464 BL00226B 23.86 3.348e-3S

2S 1-299 BL00226C 13.23 1.429e-12.77 1.8S7e-1 S 1 S 1-166 S2 PR00217 43 KD POSTSYNAPTIC PROTEINPR00217C 10.91 5.648e-09 53 BL00232 Cadherins extracellular BL00232B 32.79 1.000e-40 repeat proteins I43-domain proteins. 191 BL00232A 27.72 2.3SOe-28 49-82 BL00232B 32.79 7.OS2e-21 2S2-300 BL00232C 10.65 6.62Se-32.79 1.314e-11367-41S BL00232C

10.65 9.308e-10 470-488 S4 BL00303 S-100/ICaBP type calcium BL00303B 26.15 8.7S9e-23 binding 12S-SEQ ACCESSION DESCRIPTION RESULTS

ID NO.

NO:

protein. 162 BL00303A 21.77 1.000e-21 58 PR00378 INOSITOL PHOSPHATASE PR00378D 16.86 1.000e-15 SIGNATURE 261 PR00378B 13.80 9.250e-13 59 PR00425 BRADYKININ RECEPTOR PR00425C 13.23 9.040e-12 60 BL00280 Pancreatic trypsin inhibitorBL00280 24.61 6.727e-38 (Kunitz) 238-282 family proteins. BL00280 24.61 1.514e-30 65 BL01019 ADP-ribosylation factors BL01019A 13.20 1.222e-11 family proteins. 43-83 68 PR00237 RHODOPSIN-LIKE GPCR PR00237E 13.03 5.091e-13 SUPERFAMILY SIGNATURE 212 PR00237G 19.63 7.207e-13 268-295 PR00237A 11.48 4.375e-11 24-49 PR00237C 15.69 3.057e-10 101-124 PR00237D

8.94 4.750e-10 137-159 PR00237F 13.57 5.364e-10 255 PR002378 13.50 9.438e-10 70 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 7.938e-28 FINGER METAL-BINDING NU.

71 PR00830 ENDOPEPTIDASE LA (LON) PR00830A 8.41 8.759e-12 PROTEASE (S16) SIGNATURE 368 72 BL00120 Lipases, serine proteins.BL00120B 11.37 2.149e-10 77 PR00753 1-AMINOCYCLOPROPANE-1- PR00753E 8.01 3.552e-11 CARBOXYLATE SYNTHASE 216 PR00753D 6.85 2.778e-09 SIGNATURE ' 131-153 78 PR00506 D21 CLASS N6 ADENINE-SPECIFICPR00506C 19.40 8.017e-09 SIGNATURE

82 BL00107 Protein kinases ATP-bindingBL00107A 18.39 3.571e-16 region 436-proteins. 467 84 BL00675 Sigma-54 interaction domainBL00675A 24.86 8.800e-10 proteins 256-ATP-binding region A proteins.300 85 BL00027 'Homeobox' domain proteins.BL00027 26.43 2.286e-30 87 BL00250 TGF-beta family proteins.BL00250A 21.24 6.786e-36 300 BL00250B 27.37 1.450e-26 91 BL00215 Mitochondrial energy transferBL00215A 15.82 9.250e-17 proteins. 10-35 BL00215A 15.82 6.000e-16 246 BL00215A 15.82 7.857e-12 108-133 BL00215B 10.44 9.526e-92 BL00027 'Homeobox' domain proteins.BL00027 26.43 9.526e-24 95 PR00094 ADENYLATE KINASE SIGNATUREPR00094C 12.94 1.000e-08 136 .

96 PD02327 GLYCOPROTEIN ANTIGEN PD02327B 19.84 2.091e-09 PRECURSOR IMMLJNOGLO. 165 97 BL00752 XPA protein. BL00752B 19.17 7.309e-09 98 PR00876 NEMATODE METALLOTHIONEIN PR00876B 7.66 2.268e-10 99 PR00109 TYROSINE KINASE CATALYTICPR00109B 12.27 9.824e-12 100 BL00027 'Homeobox' domain proteins.BL00027 26.43 7.429e-31 101 BL00028 Zinc forger, C2H2 type, BL00028 16.07 6.870e-12 domain proteins. 370-387 BL00028 16.07 6.885e-11 BL00028 16.07 8.269e-11342-359 BL00028 16.07 4.300e-10 SEQ ACCESSION DESCRIPTION RESULTSx ID NO.

NO:

BL00028 16.07 6.100e-10 102 PR00048 C2H2-TYPE ZINC FINGER PR00048A 10.52 7.7SOe-14 SIGNATURE 679 PR00048A 10.52 8.SOOe-14 581-S9S PR00048A 10.52 9.2SOe-10.52 2.OS9e-12 609-623 10.52 2.S88e-12 469-483 PR00048A 10.52 7.353e-12 567 PR00048A 10.52 2.895e-11 S2S-539 PR00048A 10.52 4.316e-10.52 5.263e-11413-427 PR00048B

6.02 2.I2Se-10 569-579 PR00048B 6.02 4.938e-10 523 PR00048A 10.52 5.696e-10 6.02 8.875e-6.02 1.000e-09 457-467 6.02 6.684e-09 485-495 103 PR0019S DYNAMIN SIGNATURE PR0019SA 11.94 5.364e-22 PR0019SB 9.47 1.783e-21 PR0019SC 11.50 3.455e-21 144 PR0019SD 11.76 8.714e-21 175-194 PR00195F 16.20 8.500e-9.82 8.650e-20 194-211 104 BLO1113 C1q domain proteins. BLO1113A 17.99 1.865e-09 12~-148 BL01113A 17.99 5.846e-09 lOS BL00420 Speract receptor repeat BL00420A 20.42 6.400e-11 proteins domain 70-99 proteins. BL00420A 20.42 8.525e-10 102 BL00420A 20.42 5.708e-09 108 PR00860 VERTEBRATE METALLOTHIONEINPR00860B 7.04 2.929e-20 SIGNATURE PR00860A 5.46 S.SOOe-16 PR00860C 9.61 1.474e-14 112 BL01031 Heat shock hsp20 proteins BL01031C 17.68 6.400e-10 family profile. 122-114 DM01840 kw SPAC24B11.09 R07ES.13. DM01840B 22.04 2.688e-40 103 DM01840A 10.95 9.571e-13 11 BLO 1126 Elongation factor Ts proteins.BL01126A 18.48 2.317e-30 BL01126B 13.15 7.387e-19 135 BL01126C 9.20 9.735e-11 116 BL00216 Sugar transport proteins. BL00216B 27.64 4.375e-21 118 BL00437 Catalase proximal heme-ligandBL00437A 18.82 1.000e-40 proteins. 49-101 BL00437B 16.28 1.000e-40 114-168 BL00437C 21.86 1.000e-25.72 1.000e-40 248-301 23.95 1.000e-40 327-379 119 BL00140 Ubiquitin carboxyl-terminalBL00140D 22.64 8.274e-14 hydrolase 164-family 1 cysteine activ. 208 BL00140C 11.80 5.444e-10 120 BL00224 Clathrin light chain proteins.BL00224B 16.94 6.712e-1095-122 BL00203 Vertebrate metallothioneinsBL00203 13.94 1.000e-40 proteins. 16-62 123 PR00041 CAMP RESPONSE ELEMENT PR00041D 7.95 2.906e-09 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

BINDING (CREB) PROTEIN

SIGNATURE

124 PR00041 CAMP RESPONSE ELEMENT PR00041D 7.95 2.906e-09 BINDING (CREB) PROTEIN

SIGNATURE

125 BL00061 Short-chain dehydrogenases/reductasesBL00061C 7.86 3.250e-10 family proteins. 222 126 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 6.400e-25 FINGER METAL-BINDING NU.

127 PR00318 ALPHA G-PROTEIN (TRANSDUCIN)PR00318D 16.28 1.900e-34 SIGNATURE 248 PR00318B 14.79 3.455e-27 168-191 PR00318C 12.09 7.000e-7.84 1.600e-19 35-51 PR00318E
7.23 2.500e-12 265-275 128 PR00927 ADENINE NUCLEOTIDE PR00927E 14.93 9.743e-10 TRANSLOCATOR I SIGNATURE PR00927B 14.66 4.575e-09 130 BL00824 Elongation factor 1 beta/beta'/deltaBL00824B 9.21 7.750e-22 chain 133-proteins. 153 131 BL00824 Elongation factor 1 beta/beta'/deltaBL00824C 14.58 1.000e-40 chain 166-proteins. 204 BL00824D 14.04 1.621e-38 204-239 BL00824B 9.21 7.750e-12.49 1.000e-19 247-263 132 PR00209 ALPHAIBETA GLIADIN FAMILYPR00209B 4.88 9.222e-13 133 PR00209 ALPHA/BETA GLIADIN FAMILYPR00209B 4.88 9.222e-13 134 PR00708 ALPHA-I-ACID GLYCOPROTEINPR00708D 14.67 1.000e-27 SIGNATURE 168 PR00708C 11.77 1.643e-25 98-120 PR00708B 15.15 2.174e-24 73-95 PR00708E 13.33 1.600e-21 189-207 PR00708A

14.40 2.636e-21 51-70 135 PR00109 TYROSINE KINASE CATALYTICPR00109B 12.27 8.468e-13 136 PF00023 Ank repeat proteins. PF00023A 16.03 3.250e-10 137 BL00471 Small cytokines (intercrine/chemokine)BL00471 23.92 7.480e-10 C-x-C subfamily signat.

140 PR00205 CADHERIN SIGNATURE PR00205B 11.39 5.582e-10 346 PR00205B 11.39 9.018e-10 141 BL00412 Neuromodulin (GAP-43) BL00412D 16.54 7.704e-09 proteins. 976-143 PR00979 TAFAZZIN SIGNATURE PR00979E 10.83 5.950e-26 214 PR00979A 11.91 8.773e-25 63-83 PR00979C 12.16 6.400e-19 108-124 PR00979D 12.38 7.955e-10.14 3.382e-15 230-244 PR00979B

15.59 5.636e-15 94-106 145 DM00686 kw REPLICATION REP 28K DM00686C 14.14 7.720e-09 17.7K. 111-146 PR00604 CLASS IA AND IB CYTOCHROMEPR00604D 15.86 I.OOOe-17 C 8'7-SIGNATURE 104 PR00604B 12.73 9.591e-16 57-73 PR00604C 10.21 8.200e-12 73-84 PR00604E 10.13 1.000e-11 106-117 PR00604A 11.13 8.800e-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

11 44-52 PR00604F 8.60 1.000e-147 BL00107 Protein kinases ATP-bindingBL00107A 18.39 3.864e-15 region 266-proteins. 297 BL00107B 13.31 6.143e-11 148 PD00289 PROTEIN SH3 DOMAIN REPEATPD00289 9.97 8.448e-09 PRESYNA.

149 PR00069 ALDO-KETO REDUCTASE PR00069D 19.36 1.857e-30 SIGNATURE 217 PR00069A 16.01 7.429e-2S

41-66 PR00069E 18.14 3.100e-22 235-260 PR00069C 16.03 7.000e-11.33 8.071 e-19 101-120 150 BL00027 'Homeobox' domain proteins.BL00027 26.43 2.688e-27 151 PD02906 SYNTHASE I PSEUDOURIDYLATEPD02906C 24.17 7.070e-22 PSEUDOURIDINE LYASE TR. 200 PD02906B 15.35 8.393e-15 114-127 PD02906A 10.84 6.500e-153 BL00479 Phorbol esters / diacylglycerolBL00479A 19.86 5.091e-12 binding 891-domain proteins. 914 BL00479B 12.57 1.837e-11 158 BL00027 'Homeobox' domain proteins.BL00027 26.43 6.786e-31 160 BL00422 Granins proteins. BL00422C 16.18 7.750e-12 162 PR00625 DNAJ PROTEIN FAMILY PR00625A 12.84 9.297e-11 SIGNATURE

164 BL01282 BIR repeat proteins. BL01282B 30.49 6.182e-10 166 PR00860 VERTEBRATE METALLOTHIONEINPR00860B 7.04 2.929e-20 SIGNATURE PR00860A 5.46 1.000e-18 PR00860C 9.61 1.900e-15 167 PR00449 TRANSFORMING PROTEIN P21 PR00449A 13.20 7.052e-09 169 BL00514 Fibrinogen beta and gammaBL00514C 17.41 1.346e-39 chains C- 316-terminal domain proteins.353 BL00514G 15.98 2.241e-34 471-501 BL00514H 14.95 6.571e-14.28 1.273e-16 388=405 BL00514D

15.35 9.100e-15 369-382 ' BL00514B 16.42 4.857e-14 276 BL00514F 1 I.65 9.690e-14 416-431 BL00514A 11.68 8.200e-170 BL00514 Fibrinogen beta and gammaBL00514C 17.41 1.346e-39 chains C- 268-terminal domain proteins.305 BL00514G 15.98 2.241e-34 423-453 BL00514H 14.95 6.571e-14.28 1.273e-16 340-357 BL00514D

15.35 9.100e-15 321-334 BL00514B 16.42 4.857e-14 228 BL00514F 11.65 9.690e-14 368-383 BL00514A 11.68 8.200e-171 BL00514 Fibrinogen beta and gammaBL00514G 15.98 2.241e-34 chains C- 38S-terminal domain proteins.415 BL00514H 14.95 6.571e-27 424-449 BL00514C 17.41 4.632e-14.28 1.273e-16 302-319 BL00514D

15.35 9.100e-15 283-296 SEQ ACCESSION DESCRIPTION RESULTSX

ID NO.

NO:

BL00514B 16.42 4.857e-14 228 BL00514F 11.65 9.690e-14 330-345 BL00514A 11.68 8.200e-173 BL00027 'Homeobox' domain proteins.BL00027 26.43 9.400e-29 174 DM01970 0 kw ZK632.12 YDR313C DM01970B 8.60 5.119e-15 ENDOSOMAL III. 1404 176 BL00773 Chitinases family 19 proteins.BL00773C 9.42 8.000e-09 182 PR00109 TYROSINE KINASE CATALYTICPR00109B 12.27 9.163e-14 183 PD01937 DNA PROTEIN POLYMERASE PD01937A 6.68 3.475e-09 ENDONUCLEASE DNA-. 232 185 BL00845 CAP-Gly domain proteins. BL00845 16.43 2.946e-23 BL00845 16.43 1.628e-21 186 PR00452 SH3 DOMAIN SIGNATURE PR00452B 11.65 6.538e-11 187 PR00452 SH3 DOMAIN SIGNATURE PR00452B 11.65 6.538e-11 188 DM01803 1 HERPESVIRUS GLYCOPROTE1NDM01803A 10.51 1.000e-09 H.

189 PF00651 BTB (also known as BR-C/Ttk)PF00651 15.00 5.091e-15 domain 69-82 proteins.

190 PR00194 TROPOMYOSIN SIGNATURE PR00194C 6.38 1.900e-35 174 PR00194E 8.74 3.250e-30 231-257 PR00194D 9.57 1.500e-10.24 5.200e-24120-141 PR00194A

7.86 4.857e-21 84-102 192 PD02042 IRON-SULFUR ELECTRON PD02042B 16.75 5.154e-09 TRANSPORT AROMATIC 146 PD02042A 21.13 5.909e-09 HYDROCARB. 94-121 193 PR0002I SMALL PROLINE-RICH PROTEINPROOOZIA 4.31 2.200e-10 SIGNATURE

195 BL00463 Fungal Zn(2)-Cys(6) binuclearBL00463 8.22 5.071e-09 cluster 111-123 domain proteins.

196 PR00118 BETA-LACTAMASE CLASS A PROO1 f8F 16.42 9.386e-09 197 DM00215 PROLINE-RICH PROTEIN 3. DM00215 19.43 5.424e-09 198 BL00660 Band 4.1 family domain BL00660A 31.50 5.500e-11 proteins. 714-199 BL00282 Kazal serine protease BL00282 16.88 8.820e-13 inhibitors family 70-93 proteins.

202 PR00009 TYPE I EGF SIGNATURE PR00009A 14.15 5.345e-15 987 PR00009C 14.11 8.773e-13 996-1008 PR00009D 16.83 8.000e-11 1008-1018 14.11 1.882e-09 892-904 203 BL00025 P-type'Trefoil' domain BL00025 17.17 4.536e-19 proteins. 38-59 205 BL00018 EF-hand calcium-binding BL00018 7.4I 7.300e-10 domain 165-178 proteins.

206 PR00168 SLOW VOLTAGE-GATED PR00168D 12.88 6.865e-11 POTASSIUM CHANNEL SIGNATURE

207 BL00025 P-type 'Trefoil' domain BL00025 17.1'7 3.423e-20 proteins. 39-60 BL00025 17.17 8.750e-16 209 BL00646 Ribosomal protein 513 BL00646B 21.42 6.100e-30 proteins. 110-143 BL00646A 25.82 6.192e-29 210 PR00138 MATRIXIN SIGNATURE PR00138D 16.56 3.605e-25 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

305 PR00138C 16.41 3.000e-24 2I8-247 PR00138E 6.01 8.714e-13 314-328 1'R00138A
15.14 9.538e-13 134-148 PR00138B

15.82 4.522e-12 188-204 211 DM01206 CORONAVIRUS NUCLEOCAPSID DMOI206B 10.69 8.429e-I2 PROTEIN. 406 DM01206B 10.69 1.247e-10 384-404 DM01206B 10.69 5.068e-10 388-408 212 PD01941 TRANSMEMBRANE PD01941A 14.81 I.OOOe-40 COTRANSPORTER SYMP. 217 PD01941B 15.02 9.705e-30 420-467 PD01941E 15.92 8.714e-19.96 8.200e-20 508-563 PD01941D

27.18 1.600e-16 661-710 PD01941F 28.52 9.645e-15 2I3 BL00362 Ribosomal protein SI5 BL00362 24.67 8.313e-09 proteins. 330-373 214 BL00115 Eukaryotic RNA polymexaseBL00115Z 3.12 2.125e-09 heptapeptide repeat proteins.1227 BL00115Z 3.12 6.096e-09 215 BL00038 Myc-type, 'helix-loop-helix'BL00038B 16.97 7.600e-18 dimerization 125-domain proteins. 146 BL00038A 13.61 1.474e-13 216 BL01108 Ribosomal protein L24 BL01108A 20.33 2.241e-22 proteins. 49-82 BL01108B 11.40 8.457e-10 217 PR00381 KTNESIN LIGHT CHAIN SIGNATUREPR00381A 9.55 1.321e-10 222 BL00514 Fibrinogen beta and gammaBL00514C 17.412.358e-26 chains C- 1166-terminal domain proteins.1203 BL00514G 15.98 9.000e-15 15.35 6.936e-12 1207-1220 11.65 4.288e-10 1253-1268 BL00514H 14.95 8.636e-10 223 BL00325 _ BL00325B 21.66 1.000e-40 Actin-depolymerizing proteins.93-139 BL00325A 24.83 9.333e-24 224 BL00018 EF-hand calcium-binding BL00018 7.41 1.450e-10 domain 231-244 proteins.

225 PF01329 Pterin 4 alpha carbinolaminePF01329B 18.52 1.692e-18 dhydratase. 67-92 228 BL00211 ABC transporters family BL00211B 13.37 6.250e-18 proteins. 1033-1065 BL00211B 13.37 8.875e-18 12.23 1.900e-09 931-943 230 PR00761 BIND1N PRECURSOR SIGNATUREPR00761A 5.81 9.366e-09 23 PR00049 WILM'S TUMOUR PROTEIN PR00049D 0.00 3.500e-10 SIGNATURE

232 BL00412 Neuromodulin (GAP-43) BL00412D 16.541.978e-10 proteins. 109-160 BL00412D 16.54 4.122e-09 233 BL01210 Caveolins proteins. BL012IOB 13.92 8.129e-09 236 BL00939 Ribosomal protein LIe BL00939F 17.27 5.393e-09 proteins. 861-238 BL01252 Endogenous opioids neuropeptidesBL01252D 18.25 3.571e-28 precursors proteins. 233 BL01252B 19.09 5.034e-27 WO O1J57190 PCTlUSOIl04098 SEQ ACCESSION DESCRIPTION RESULTS

ID NO.

NO:

37-67 BL01252C 18.10 1.621e~21 164-190 BL01252A 14.22 7.107e-239 BL00302 Enkaryotic initiation BL00302 14.81 1.000e-40 factor 5A hypusine 25-79 proteins.

240 PR00420 AROMATIC-RING HYDROXYLASEPR00420A 14.78 8.851e-13 (FLAVOPROTEIN

MONOOXYGENASE) SIGNATURE

241 PD02929 ADHESION GLYCOPROTEIN PD02929A 28,27 4.529e-09 PRECURSOR I. 289 243 PD01066 PROTEIN ZINC FINGER ZINC-PDO I066 19.43 8.527e-25 FINGER METAL-BTNDING NU.

244 BL01270 Band 7 protein family BLOI270C 16.91 6.745e-17 proteins. 115-144 BL01270B 18.74 6.857e-17 76-115 BL01270E 13.03 6.016e-20.87 9.160e-13 144-182 24S PF00791 Domain present in ZO-1 PF00791B 28.49 6.305e-12 and UncS-like 253-netrin receptors. 308 PF00791B 28.49 1.909e-11 427-482 PF00791B 28.49 2.651e-28.49 3.890e-09 112-167 246 PD00066 PROTEIN ZINC-FINGER METAL-PD00066 13.92 2.500e-13 BINDI. PD00066 13.92 9.I43e-12 PD00066 13.92 5.304e-11 PD00066 13.92 6.478e-11249-262 PD00066 13.92 3.423e-10 247 BL00406 Actins proteins. BL00406D 12.58 6.400e-20 520 BL00406B 5.47 4.857e-14 249-304 BL00406E 8.44 1.OOOe-6.75 5.449e-11 313-368 248 BL00951 ER lumen protein retainingBL00951C 19.35 1.000e-40 receptor 112-proteins. 161 BL00951A 15.10 7.750e-39 21-57 BL00951D 13.94 6.000e-38 161-196 BL00951B 14.23 3.100e-252 BL01113 Clq domain proteins. BL01113A 17.99 9.129e-15 227 BL01113A 17.99 4.818e-14 194-221 BL01113A 17,99 7.8I8e-17.99 1.730e-13 185-212 BL01113A

17.99 6.595e-13 191-218 BL01113A 17.99 6.077e-12 230 BL01113A 17.99 9.182e-11 179-206 BL01113A 17.99 2.532e-17.99 9.043e-10 2I8-245 BL01113A

17.99 9.426e-10 209-236 BL01113A 17.99 4.115e-09 257 BL0084S CAP-Gly domain proteins. BL00845 16,43 1.837e-21466-491 259 PR00248 IvIETABOTROPIC GLUTAMATE PR00248G 12.67 2.688e-09 GPCR SIGNATURE

260 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 3.400e-10 proteins. 441-452 BL00678 9.67 5.800e-10 BL00678 9.67 8.800e-10 261 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 3.400e-10 proteins, 415-426 BL00678 9.67 5.800e-10 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

BL00678 9.67 8.800e-10 262 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 3.400e-10 proteins. 468-479 BL00678 9.67 5.800e-10 508-519 , BL00678 9.67 8.800e-10 263 BL50002 Src homology 3 (SH3) domainBL50002B 15.18 2.200e-10 proteins 415-profile. 429 264 BL00049 Ribosomal protein L14 BL00049C 17.38 3.040e-12 proteins. 94-265 PD01469 GLYCOPROTEIN PROTEIN PD01469 20.59 2.091e-14 PRECURSOR SA.

266 PD01469 GLYCOPROTEIN PROTEIN PD01469 20.59 2.091e-14 PRECURSOR SA.

267 BL00567 Phosphoribulokinase proteins.BL00567A 10.66 1.161e-12 269 BL00049 Ribosomal protein L14 BL00049C 17.38 2.688e-28 proteins. 92-128 BL00049B 18.42 6.806e-24 54-86 BL00049A 13.86 8.333e-19 19-42 BL00049D 13.47 5.765e-12 272 BLO T 115 GTP-binding nuclear proteinBLO 1115A 10.22 9.735e-12 ran proteins. 14-58 273 PR00021 SMALL PROLINE-RICH PROTEINPR00021A 4.31 1.911e-09 275 PR00179 LIPOCALIN SIGNATURE PR00179B 9.56 2.895e-13 137 PR00179A 13.78 3.250e-11 36-49 PR00179C 19.02 6.040e-11 276 PR00449 TRANSFORMING PROTEIN P21 PR00449A 13.20 8.364e-17 SIGNATURE PR00449C 17.27 1.000e-13 PR00449E 13.50 4.000e-12 195 PR00449B 14.34 5.680e-10 277 BL00140 Ubiquitin carboxyl-terminalBL00140D 22.64 I.OOOe-40 hydrolase 161-family I cysteine activ. 205 BL00140C 11.80 9.053e-30 79-104 BL00140A 15.96 9.400e-28 5-35 BL00140B 12.29 4,649e-278 PD02712 ELEMENT TRANSPOSASE FOR PD02712A 23.03 8.013e-09 TRANSPOSON TRANSPOSABLE.

279 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 1.474e-09 proteins. 100-111 282 DM00892 3 RETROVIRAL PROTEINASE. DM00892C 23.5S 4.767e-21 283 BL00048 Protamine P1 proteins. BL00048 6.39 9.550e-09 286 PR00081 GLUCOSE/RIBITOL PR00081A 10.53 1.878e-11 DEHYDROGENASE FAMILY

SIGNATURE

287 PR00310 ANTI-PROLIFERATIVE PROTEINPR00310B 10.59 4.231e-17 BTG1 FAMILY SIGNATURE PR00310D 9.10 6.679e-16 289 PD01066 PROTEIN ZINC F1NGER ZINC-PD01066 19.43 7.000e-36 FINGER METAL-BINDING NU.

293 BL00979 G-protein coupled receptorsBL00979L 20.63 3.800e-12 family 3 111-proteins. 152 295 PD02411 PROTEIN TRANSCRIPTION PD02411 21.89 7.000e-16195-229 REGULATION NUCLEAR.

296 BL01064 Pyridoxamine 5'-phosphateBL01064A 27.84 8.313e-28 oxidase 77-proteins. 129 BL01064C 15.22 7.136e-25 297 BL00030 Eukaryotic RNA-binding BL00030A 14.39 2.929e-13 region RNP-1 37-56 proteins. BL00030B 7.03 1.900e-11 177 BL00030A 14.39 2.000e-10 SEQ ACCESSION DESCRIPTION RESULTSx ID NO.

NO:

298 BL01183 ubiE/COQS methyltransferaseBL01183B 21.31 6.660e-12 family 143-proteins. 188 299 BL01279 Protein-L-isoaspartate(D-aspartate)BL01279A 24.27 5.862e-11 methyltransferase signa. 105 301 BL00191 Cytochrome b5 family, heme-bindingBL00191K 17.38 4.951e-27 domain proteins. 228 BL00191J 11.37 6.447e-17 302 DM00892 3 RETROVIRAL PROTEINASE. DM00892C 23.55 3.893e-16 306 PF01140 Matrix protein (MA), p15. PF01140D 15.54 2.988e-09 307 PR00245 OLFACTORY RECEPTOR PR00245A 18.03 4.818e-21 SIGNATURE PR00245C 7.84 5.154e-20 254 PR00245D 10.47 4.000e-15 274-286 PR00245B 10.38 8.200e-12.40 5.714e-12 291-306 309 BL00203 Vertebrate metallothioneinsBL00203 13.94 2.245e-10 proteins. 612-658 310 BL00237 G-protein coupled receptorsBL00237A 27.68 7.632e-23 proteins. 119-159 BL00237C 13.19 3.864e-15 251-278 BL00237D 11.23 3.739e-311 BL00380 Rhodanese proteins. BL00380D 15.90 8.200e-28 136 BL00380G 11.26 5.800e-16 267-280 BL00380B 14.77 7.000e-9.76 5.886e-15.67 7.387e-13 82-98 BL00380E
12.44 7.000e-11 181-193 10.48 l .000e-09 10-20 312 BL00227 Tubulin subunits alpha, BL00227B 19.29 1.000e-40 beta, and gamma 50-proteins. 105 BL00227C 25.48 1.000e-40 111-163 BL00227D 18.46 1.000e-21.16 1.000e-40 372-426 24.55 3.250e-39 1-35 24.15 8.500e-34 324-359 327 BL00232 Cadherins extracellular BL00232B 32.79 7.362e-21225-repeat proteins domain proteins. 273 BL00232B 32.79 2.588e-17 435-483 BL00232B 32.79 6.301e-32.79 6.769e-13 330-378 10.65 9.341e-12223-241 BL00232C 10.65 5.696e-11 346 BL00232C 10.65 3.942e-10 329 PD02749 TRANSCRIPTION PROTEIN FACTORPD02749B 12.75 2.241e-37 BTF3 REGULATION NUCL. PD02749C 13.96 4.892e-28 121 PD02749A 9.56 6.000e-15 2-330 PR00391 PHOSPHATIDYLINOSITOL PR00391E 12.50 7.785e-15 TRANSFERPROTEIN SIGNATURE 231 PR00391B 8.39 1.000e-13 83-104 PR00391D 12.21 9.328e-7.83 5.390e-11 16-36 332 BL01030 RNA polymerases M / 15 BL01030 23.44 1.818e-23 Kd subunits 87-125 proteins.

337 PD01066 PROTEIN ZLNC FINGER ZINC- PD01066 19.43 2.929e-32 FINGER METAL-BINDING NU.

340 PD02711 SYNTHASE PD02711B 14.26 1.973e-20 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

PHOSPHORIBOSYLFORMYLGLY. 968 343 BL00223 Annexins repeat proteins BL00223C 24.79 1.000e-40 domain 245-proteins. 300 BL00223B 28.47 8.714e-38 168-218 BL00223A 15.59 8.250e-15.59 8.750e-27 26-60 BL00223C
24.79 9.438e-16 13-68 BL00223C
24.79 2.735e-15 85-140 BL00223A

15.59 2.253e-11 258-292 346 PR00345 STATHMIN FAMILY SIGNATUREPR00345B 7.12 2.800e-28 PR00345E 8.54 7.652e-28 183 PR00345C 4.54 9.100e-28 110-134 PR00345D 10.97 1.964e-13.46 5.645e-16 52-71 347 BL00586 Ribosomal protein L16 BL00586B 17.00 3.215e-15 proteins. 184-348 PR00388 3',5'-CYCLIC NUCLEOTIDE PR00388A 10.45 2.778e-09 351 BL00018 EF-hand calcium-binding BL00018 7.41 3.118e-11 domain 160-173 proteins. BL00018 7.41 2.350e-10 354 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 1.947e-09 proteins. 256-267 358 DM01206 CORONAVIRUS NUCLEOCAPSID DM01206B 10.69 3.278e-09 PROTEIN. 195 DM01206B 10.69 6.696e-09 183-203 DM01206B 10.69 8.633e-09 132-152 DM01206B

10.69 8.861e-09 181-201 DM01206B 10.69 9.316e-09 361 PD01498 OXIDASE BIOSYNTHESIS PD01498C 24.90 6.880e-14 OXIDOREDUCTASE PORP. 263 362 PD01498 OXIDASE BIOSYNTHESIS PD01498C 24.90 6.880e-14 OXIDOREDUCTASE PORP. 263 365 BL00178 Aminoacyl-transfer RNA BL00178B 7.11 1.000e-11 synthetases 589-class-I proteins. 600 BL00178A 14.23 8.500e-09 366 BL00523 Sulfatases proteins. BL00523E 19.27 1.000e-23 348 BL00523A 13.36 S.SOOe-16 30-47 BL00523B 8.64 1.964e-13 78-90 BL00523C 12.64 9.625e-13 129-140 BL00523G 9.46 S.SOOe-369 BL00107 Protein kinases ATP-bindingBL00107A 18.39 4.818e-09 region 21-52 proteins.

370 BL00880 Acyl-CoA-binding protein.BL00880 17.52 1.000e-40 371 BL00107 Protein kinases ATP-bindingBL00107A 18.39 1.000e-23 region 276-,proteins. 307 BL00107B 13.31 1.692e-12 372 PR00211 GLUTELIN SIGNATURE PR00211B 0.86 6.602e-1 l 326-347 PR00211B 0.86 6.106e-10 320-341 PR00211B 0.86 3.167e-373 BL00279 Membrane attack complex BL00279E 37.11 9.349e-10 components / 749-perforin proteins. 797 375 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 1.231e-33 FINGER METAL-BINDING NU.

377 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 7.563e-28 FINGER METAL-BINDING NU.

379 BL00598 Chromo domain proteins. BL00598 14.45 5.781e-.16 SE ACCESSION DESCRIPTION RESULTS*
Q

ID NO.

NO:

_ 380 PR00413 HALOACID PR00413D 11.28 8.941e-09 ' 864-E FAMILY SIGNATURE
HYDROLAS

383 PR00413 _ PR00413D 11.28 8.941e-09 HYDROLASE FAMILY SIGNATURE

387 BL01060 Flagella transport proteinBL01060A 15.65 1.535e-09 flip family 131-proteins. 174 388 PR00209 ALPHA/BETA GLIADIN FAMILYPR00209B 4.88 6.318e-I

389 PR00837 ALLERGEN VSlTPX-1 FAMILY PR00837B 11.64 1.000e-10 391 BL00240 Receptor tyrosine kinase BL00240B 24.70 7.907e-10 class III 118-pxoteins. 142 392 PR00014 FIBRONECTIN TYPE III REPEATPR00014D 12.04 8.412e-10 393 PR00014 FIBRONECTIN TYPE III REPEATPR00014D 12.04 8.412e-10 394 BL01209 LDL-receptor class A (LDLRA)BL01209 9.313.368e-15 domain 47-60 proteins. BL01209 9.31 5.500e-13 395 BL00634 Ribosomal protein L30 BL00634 34.38 4.090e-13 proteins. 70-121 396 BL01013 Oxysterol-binding proteinBL01013D 26.81 8.000e-26 family 358-proteins. 402 BL01013A 25.14 7.231e-21 45-81 BL01013C 9.97 1.000e-13 132-142 BL01013B 11.33 1.000e-397 BL00930 Peripherin /rom-I proteins.BL00930E 17.80 1.000e-40 BL00930D 9.12 4.632e-37 BL00930F 16.912.800e-36 400 PR00780 LEUSERPIN 2 SIGNATURE PR00780B 4.89 4.491e-09 401 PR008I9 CBXX/CFQX SUPERFAMILY PR00819B 10.83 7.158e-114-20 SIGNATURE

403 BL00381 Endopeptidase Clp serine BL00381C 23.84 1.250e-32 proteins. 150-194 BL00381A 16.48 2.286e-22 74-111 BL00381B 21.42 8.326e-405 BL01105 Ribosomal protein L35Ae BL01105A 17.37 1.000e-40 proteins. 4-49 BL01105B 12.95 1.000e-40 406 BL00344 GATA-type zinc forger BL00344 17.99 7.000e-12 domain proteins. 814-852 407 PR00211 GLUTELIN SIGNATURE PR00211B 0.86 9.750e-09 409 PR00910 LUTEOVIRUS ORF6 PROTEIN PR00910A 2.51 4.321e-09 SIGNATURE

410 BL00762 WHEP-TRS domain proteins.BL00762A 23.43 1.000e-28 789 BL00762A 23.43 4.400e-21 903-940 BL00762A 23.43 5.415e-16.14 8.759e-12 1154-1 168 412 BL00690 DEAN-box subfamily ATP-dependentBL00690B 13.38 5.320e-15 helicases proteins. 280 BL00690A 6.87 1,818e-13 415 BL00227 Tubulin subunits alpha, BL00227B 19.29 1.000e-40 beta, and gamma 52-proteins. 107 BL00227C 25.48 1.000e-40 113-165 BL00227D 18.46 1.000e-21.16 1.000e-40 382-436 BL00227E

24.15 1.7SOe-34 326-361 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

BL00227A 24.55 1.000e-33 416 PF00992 Troponin. PF00992A 16.67 1.71 1e-09 557-418 BL00541 Nuclear transition proteinBL00541 8.44 9.875e-09 1 proteins. 256-310 419 BL00541 Nuclear transition proteinBL00541 8.44 9.875e-09 1 proteins. 197-251 420 PF00856 SET domain proteins. PF00856A 26.14 9.074e-13 938 PF00856B 16.42 2.397e-12 421 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 8.200e-12 proteins. 33-44 423 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 8.600e-30 FINGER METAL-BINDING NU.

424 PF00564 Octicosapeptide repeat PF00564B 24.74 1.305e-17 proteins. 421-426 PR00988 URIDINE KINASE SIGNATURE PR00988A 6.39 4.569e-12 427 PR00988 URIDINE KINASE SIGNATURE PR00988A 6.39 4.569e-12 428 BL00478 LIM domain proteins. BL00478B 14.79 3.250e-13 130 BL00478B 14.79 9.036e-13 431 BL00282 Kazal serine protease BL00282 16.88 8.875e-12 inhibitors family 464-487 proteins.

432 PD00930 PROTEIN GTPASE DOMAIN PD00930B 33.72 7.800e-18 ACTIVATION. 357 PD00930A 25.62 9.617e-12 125-151 PD00930B 33.72 2.521e-433 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 4.649e-34 FINGER METAL-BINDING NU.

434 PR00449 TRANSFORMING PROTEIN P21 PR00449A 13.20 7.563e-11 SIGNATURE

436 PR00120 H+-TRANSPORTING ATPASE PR00120C 9.90 5.800e-19 (PROTON PUMP) SIGNATURE 722 437 BL00115 Eukaryotic RNA polymeriseBLOO115T 8.45 7.273e-29 heptapeptide repeat proteins.1242 BLOO115Q 18.08 2.776e-21 953-983 BLOO115Y 11.86 8.000e-19.19 8.130e-16 731-774 BLOO115H

14.34 9.392e-16 463-496 BLOO115A 15.44 7.414e-15 BLOO115R 6.50 6.128e-14 1010 BLOO115J 16.71 9.289e-14 591-617 BLOO115I 8.33 4.336e-12.25 5.939e-13 662-694 BLOO115G

11.65 6.011e-13 435-463 BLOO115K 15.03 3.417e-10 659 BL001150 16.76 5.805e-10 863-913 BLOO115P 11.54 7.538e-18.24 7.968e-10 1010-1052 10.34 4.475e-09 1242-1265 438 PF00628 PHD-forger. PF00628 15.84 4.536e-10 440 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 6.351 e-34 10-49 FINGER METAL-BINDING NU.

441 PR00309 ARRESTIN SIGNATURE PR00309A 9.68 5.250e-24 PR00309D 7.09 4.938e-23 309 PR00309B 7.81 2.800e-21 69-88 PR00309C 8.22 1.621e-19 165-183 PR00309E 9.82 9.438e-442 BL00600 ~ Aminotransferases class-IIIBL00600B 19.60 7.324e-14 pyridoxal- 103-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

phosphate attachment si. 129 BL00600G 12.43 2.125e-12 306-325 BL00600F 8.77 8.105e-16.43 3.167e-11 228-257 8.71 8.650e-09 207-221 443 BL00972 Ubiquitin carboxyl-terminalBL00972A 11.93 3.160e-18 hydrolases 69-87 family 2 proteins.

444 BL00349 CTF/NF-I proteins. BL00349A 10.07 1.000e-40 BL00349C 9.33 1.000e-40 BL00349E 10.79 1.000e-40 195 BL00349F 11.81 1.000e-40 213-255 BL00349H 15.70 7.387e-10.51 2.227e-34 54-82 BL00349D
11.70 9.100e-34 125-152 19.72 5.781e-30323-356 445 BL00154 EI-E2 ATPases phosphorylationBL00154F 8.23 8.941e-21271-site proteins. 295 BL00154E 20.37 2.620e-15 448 ' DM00215 PROLINE-RICH PROTEIN 3. DM00215 19.43 4.882e-11 DM00215 19.43 6.492e-09 451 BL01283 T-box domain proteins. BL01283A 24.15 3.100e-40 160 BL01283D 11.70 6.000e-39 253-286 BL01283B 23.17 6.538e-13.05 7.750e-19 222-236 452 PR00420 AROMATIC-RING HYDROXYLASE PR00420A 14.78 2.579e-11 (FLAVOPROTEIN

MONOOXYGENASE) SIGNATURE

453 PR00162 RIESKE 2FE-2S SUBUNIT PR00162B 12.77 7.429e-17 SIGNATURE 228 PR00162A 9.35 2.324e-14 193-205 PR00162C 8.10 7.120e-454 PD01066 PROTEIN ZINC FINGER ZINC- PD01066 19.43 7.000e-30 FINGER METAL-BINDING NU.

456 BL00027 'Homeobox' domain proteins.BL00027 26.43 9.333e-18 457 PD01066 PROTEIN ZINC FINGER ZINC- PD01066 19.43 2.737e-24 FINGER METAL-BINDING NU.

459 BL00290 Immunoglobulins and major BL00290A 20.89 1.529e-14 histocompatibility complex177 BL00290B 13.17 proteins. 9.000e-12 460 PR00413 HALOACID PR00413F 14.91 7.333e-11 DEHALOGENASE/EPOXIDE 214 PR00413E 15.78 5.714e-09 463 PR00759 BASIC PROTEASE (KUNITZ-TYPE)PR00759B 11.26 8.385e-09 INHIBITOR FAMILY SIGNATURE

466 BL00019 Actinin-type actin-bindingBL00019D 15.33 4.200e-19 domain 300-proteins. 330 467 BL00019 Actinin-type actin-bindingBL00019D 15.33 4.200e-19 domain 300-proteins. 330 469 PR00153 CYCLOPHILIN PEPTIDYL-PROLYLPR00153D 11.99 3.250e-15 CIS-TRANS ISOMERASE 523 PR00153C 11.014.682e-14 SIGNATURE 495-511 PR00153E 9.10 8.548e-11.57 1.720e-13 452-465 470 BL00491 Aminopeptidase P and prolineBL00491 C 12.15 3.912e-09 dipeptidase proteins. 572 471 PD00289 PROTEIN SH3 DOMAIN REPEAT PD00289 9.97 1.000e-14 ~ 1482-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

PRESYNA. 1496 PD00289 9.97 8.650e-11 474 BL50040 Elongation factor 1 gammaBL50040D 17.41 1.000e-40 chain profile. 279-329 BL50040E 18.79 1.000e-40 333-388 BL50040F 18.99 5.320e-22.62 3.739e-38 141-184 BL50040B

13.65 7.000e-30 59-85 12.98 1.450e-14 10-22 475 BL01144 Ribosomal protein L31 BLO T 144 25.07 1.000e-40 a proteins. 22-74 476 PR00007 COMPLEMENT C1Q DOMAIN PR00007C 15.60 2.421e-21 SIGNATURE 611 PR00007B 14.16 3.500e-21 544-564 PR00007A 19.33 6.897e-9.64 6.571e-12 623-634 477 BL50002 Src homology 3 (SH3) domainBL50002A 14.19 5.846e-10 proteins 170-profile. 189 479 DM01970 0 kw ZK632.12 YDR313C DM01970B 8.60 9.500e-17 ENDOSOMAL III. 980 480 PR00868 DNA-POLYMERASE FAMILY PR00868C 13.76 5.688e-17 A (POL 284-I) SIGNATURE 308 PR00868A 16.33 3.186e-13 224-247 PR00868H 12.51 3.388e-10.87 7.938e-11462-476 PR00868E

13.19 1.608e-10 340-366 481 BL00027 'Homeobox' domain proteins.BL00027 26.43 9.182e-22 482 BL00061 Short-chain dehydrogenases/reductasesBL00061B 25.79 3.647e-21 family proteins. 226 483 BL50002 Src homology 3 (SH3) domainBL50002A 14.19 1.750e-12 proteins 1032-profile. 1051 485 PF00023 Ank repeat proteins. PF00023A 16.03 9.625e-10 776 PF00023A 16.03 3.571e-09 486 PD02870 RECEPTOR INTERLEUKIN-1 PD02870B 18.83 9.262e-20 PRECURSOR. 136 PD02870D 15.74 9.426e-09 487 PR00370 FLAVIN-CONTAINING PR00370G 10.45 3.769e-28 MONOOXYGENASE (FMO) 493 PR00370B 10.91 1.000e-24 SIGNATURE 27-46 PR00370C 12.72 4.000e-21 140-157 PR00370E 11.96 9.229e-16.33 1.750e-20 185-204 PR00370F

17.75 7.395e-20 375-395 PR00370A 3.35 2.038e-18 489 PD01675 GLYCOPROTEIN MAJOR ENVELOPEPD01675C 19.89 2.330e-10 PROBABLE U3.

492 BL00211 ABC transporters family BL00211A 12.23 S.OSOe-09 proteins. 45-57 493 BL00211 ABC transporters family BL00211A 12.23 S.OSOe-09 proteins. 45-57 494 BL00211 ABC transporters family BL00211A 12.23 S.OSOe-09 proteins. 58-70 495 BL00027 'Homeobox' domain proteins.BL00027 26.43 6.786e-12 BL00027 26.43 9.143e-12 BL00027 26.43 2.600e-11 BL00027 26.43 3.625e-10 497 BL00107 Protein kinases ATP-bindingBL00107A 18.39 5.800e-22 region 214-proteins. 245 BL00107B 13.31 1.000e-13 281-297 BL00107A 18.39 3.520e-13.31 8.615e-12 652-668 499 BL00383 ~ Tyrosine specific proteinBL00383E 10.35 1.000e-14 phosphatases 1902-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

proteins. ~ 19I3 BL00383D 11.92 3.077e-14 13.34 5.500e-14 1730-1745 10.10 2.000e-13 1785-1796 BL00383F 15.519.069e-12 1956 BL00383B 7.61 1.692e-11 501 PROOOI9 LEUCINE-RICH REPEAT PR00019B 11.36 i.360e-09 SIGNATURE 150 PR000i9A 11.I9 I.667e-09 91-105 PROOOI9B 11.36 4.600e-503 BL00226 Intermediate filaments BL00226D 19.10 1.000e-40 proteins. 367-414 BL00226B 23.86 6.143e-27 i 95-243 BL00226A 12.?7 7.840e-13.23 2.600e-13 309-340 BL00226C

13.23 6.143e-12 266-297 BL00226B 23.86 1.209e-09 505 PD02407 3-BISPHOSPHOGLYCERATE- PD02407F 7,616.739e-09 INDEPENDENT PHOSPHOGLYCER.930 506 PF00632 HECT-domain (ubiquitin-transferase).PF00632C 20.66 9.830e-19 1023 PF00632B 18.45 1.155e-11 507 BL01082 Ribosomal protein L7Ae BL01082 20.37 4.273e-20 proteins. 76-i I6 508 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 2.421 proteins. e-09 493-504 509 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 2.42Ie-09 proteins. 473-484 5I0 PR00320 G-PROTEIN BETA WD-40 REPEATPR00320B 12.19 4.774e-11 SIGNATURE 582 PR00320B 12.19 5.886e-10 763-778 PR00320C 13.01 6.760e-16.74 7.618e-10 846-861 PR00320A

16,74 3.415e-09 763-778 PR00320A I6.74 6.268e-09 5I BL00479 Phorbol esters / diacylglycerolBI,004?9C I2.01 3.250e-12 1 binding 170-domain proteins. 183 5I2 BL50058 G-protein gamma subunit BL50058 27.23 7.494e-09 profile, ~ I O-58 513 BL00524 Somatomedin B domain proteins.BL00524A 9.65 8.925e-14 515 BL00041 Bacterial regulatory proteins,BL00041 23.99 1.964e-19 araC family 492-524 proteins.

516 PD00066 PROTEIN ZINC-FTNGER METAL-PD00066 13.92 8,500e-13 BINDI.

517 BL0041S Synapsins proteins. BL00415E 4.82 9.291e-09 518 PR00109 TYROSINE KINASE CATALYTICPR00109B 12.27 9,471e-12 5I9 BL00290 Immunoglobulins and majorBL00290B 13.17 4.750e-09 histocompatibility complex proteins.

522 PR00505 D12 CLASS N6 ADENINE-SPECIFICPR00505A 14.15 7.128e-09 SIGNATURE

525 BL00312 Glycophorin A proteins. BL00312B 9.22 5.781e-10 528 PD01066 PROTEIN ,ZINC FINGER ZINC-PD01066 19.43 2.500e-32 FINGER METAL-BINDING NU.

529 PR00254 NICOTINIC ACETYI,CHOLINE PR00254D 15.50 4.OOOe-I7 RECEPTOR SIGNATURE 150 PR00254A 11,23 4.706e-14 6I-78 PR00254C 11.36 4.000e-12 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

113-126 PR00254B 12.97 1.486e.-531 BL00741 Guanine-nucleotide dissociationBL00741B 14.27 6.870e-16 stimulators CDC24 family 810 sign.

532 PR00193 MYOSIN HEAVY CHATN PR00193D 14.36 3.143e-34 SIGNATURE 476 PR00193C 12.60 7.632e-32 216-244 PR00193B 11.69 7.750e-15.41 2.588e-22 111-131 PR00193E

19.47 2.200e-21 501-530 533 PD02870 RECEPTOR INTERLEUKIN-1 PD02870B 18.83 5.596e-09 PRECURSOR. 3 81 535 PR00683 SPECTRIN PLECKSTRIN PR00683D 15.87 2.452e-10 536 BL00027 'Homeobox' domain proteins.BL00027 26.43 6.684e-24 538 PR00239 MOLLUSCAN RHODOPSIN C- PR00239E 1.58 2.739e-09 539 BL00406 Actins proteins. BL00406C 6.75 1.000e-40 212 BL00406B 5.47 6.143e-37 90-145 BL00406D 12.58 4.600e-8.44 2.200e-33 364-414 BL00406A

9.95 4.441e-23 7-42 540 PR00456 RIBOSOMAL PROTEIN P2 PR00456E 3.06 9.625e-10 SIGNATURE

541 PR00456 RIBOSOMAL PROTEIN P2 PR00456E 3.06 9.625e-10 SIGNATURE

542 PF00023 Ank repeat proteins. PF00023A 16.03 7.857e-11 544 PF00642 Zinc finger C-x8-C-x5-C-x3-HPF00642 11.59 9.082e-10 type (and 838-849 similar).

546 BL00383 Tyrosine specific proteinBL00383E 10.35 4.115e-10 phosphatases 104-proteins. 115 547 BL01226 Hydroxymethylglutaryl-coenzymeBL01226A 13.79 1.000e-40 synthase proteins. BL01226C 13.51 1.000e-40 167 BL01226D 11.60 1.000e-40 174-210 BL01226E 13.74 1.000e-17.74 1.000e-40 386-434 BL01226I

25.06 1.000e-40 460-508 BL01226G 15.76 3.483e-32 321 BL01226B 13.35 1.818e-31 95-127 BL01226F 9.78 8.714e-23 549 BL00964 Syndecans proteins. BL00964B 12.05 2.426e-10 551 DM01930 2 kw FINGER SMCX SMCY DM01930E 15.41 1.367e-37 YDR096W. 215 DM01930F 14.16 8.232e-28 267-303 DM01930B 19.86 ' 9.163e-10 37-71 552 BL00195 Glutaredoxin proteins. BL00195B 15.31 7.158e-09 554 BL00383 Tyrosine specific proteinBL00383E 10.35 2.756e-12 phosphatases 436-proteins. 447 555 PR00403 WW DOMAIN SIGNATURE PR00403B 12.19 7.612e-11 137 PR00403A 16.82 3.912e-10 107-121 PR00403B 12.19 2.068e-558 PR00380 KINESIN HEAVY CHAIN PR00380A 14.18 2.714e-26 SIGNATURE PR00380D 9.93 3.000e-24 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

297 PR00380C 13.18 5.154e-20 226-245 PR00380B 12.64 9.400e-559 BL00518 Zinc forger, C3HC4 type BL00518 12.23 5.333e-09 . (RING forger), 522-531 proteins.

561 PD01795 PROTEIN AM1NOPEPTIDASE PD01795B 11.56 2.333e-12 PRECURSOR HYDROLASE SIGNA.172 PD01795A 10.27 1.000e-09 562 PD01795 PROTEIN AMINOPEPTIDASE PD01795B 11.56 2.333e-12 PRECURSOR HYDROLASE SIGNA.123 PDO I795A 10.27 1.000e-09 563 BL00018 EF-hand calcium-binding BL00018 7.41 1.391e-09 domain 41-54 proteins.

565 BL00348 p53 tumor antigen proteins.BL00348F 23.19 4.143e-09 567 PD00301 PROTEIN REPEAT MUSCLE PD00301B 5.49 4.115e-09 CALCIUM-BI. 295 569 PF00850 Histone deacetylase family.PF00850E 8.88 6.553e-21 PF00850D 14.76 1.519e-I6 746 PF00850F 15.70 1.118e-11 794-827 PF00850G 22.75 8.375e-570 PD00289 PROTEIN SH3 DOMAIN REPEATPD00289 9.97 4.960e-10 PRESYNA.

571 BL00518 Zinc finger, C3HC4 type BL00518 12.23 8.800e-11 (RING finger), 44-53 proteins.

573 BL00299 Ubiquitin domain proteins.BL00299 28.84 1.123e-11 574 PF01140 Matrix protein (MA), p15.PF01140D 15.54 3.700e-10 576 BL00284 Serpins proteins. BL00284C 28.56 5.200e-26 242 BL00284A 15.64 4.913e-18 71-95 BL00284B 17.99 7.261e-15 173-194 BL00284D 16.34 5.846e-19.15 7.429e-12 387-412 579 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 6.553e-29 FINGER METAL-BINDING NU.

580 BL50001 Src homology 2 (SH2) domainBL50001B 17.40 4.500e-12 proteins 1010-profile. 1031 581 PD00930 PROTEIN GTPASE DOMAIN PD00930B 33.72 3.189e-22 ACTIVATION. 649 PD00930A 25.62 6.806e-17 584 BL00612 Osteonectin domain proteins.BL00612B 11.35 2.034e-11 585 DM0155I kw OSTEOINDUCTIVE YOPM DM01551C 14.62 8.859e-10 MEMBRANE OUTER. 122 586 PF00628 PHD-forger. PF00628 15.84 3.455e-12 587 BL00027 'Homeobox' domain proteins.BL00027 26.43 6.063e-10 588 PR00326 GTP1/OBG GTP-BINDING PROTEINPR00326A 8.75 7.525e-16 FAMILY SIGNATURE 248 PR00326C 9.79 6.760e-15 276-292 PR00326D 19.09 6.657e-16.74 9.229e-13 248-267 589 BL00422 Granins proteins. BL00422A 28.34 7.429e-09 590 BL00415 Synapsins proteins. BL00415N 4.29 9.794e-10 591 BL00128 Alpha-lactalbumin / lysozymeBL00128A 20.76 3.423e-13 C proteins. 35-65 BL00128C 19.34 2.980e-11 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

596 PR00049 WILM'S TUMOUR PROTEIN PR00049D 0.00 3.136e-09 SIGNATURE

597 DM00547 1 kw CHROMO BROMODOMAIN DM00547C 17.30 1.667e-19 SHADOW GLOBAL. 229 DM00547E 13.94 6.200e-18 319-342 DM00547B 11.28 1.000e-17 179-193 DM00547D

11.60 9.250e-13 289-303 DM00547F 23.43 6.727e-12 726 DM00547A 12.38 4.818e-11 600 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 1.882e-27 FINGER METAL-BINDING NU.

601 BL00192 Cytochrome b/b6 heme-ligandBL00192A 11.90 6.400e-09 proteins. 390-602 BL00936 Ribosomal protein L35 BL00936B 27.27 8.615e-09 proteins. 118-603 BL00936 Ribosomal protein L35 BL00936B 27.27 8.615e-09 proteins. 118-606 PR00019 LEUCINE-RICH REPEAT PR00019B 11.36 7.300e-10 SIGNATURE 306 PR00019A 11.19 5.667e-09 607 PR00019 LEUCINE-RICH REPEAT PR00019B 11.36 7.300e-10 SIGNATURE 306 PR00019A 11.19 5.667e-09 608 PR00320 G-PROTEIN BETA WD-40 REPEATPR00320C I3.OI 9.500e-12 SIGNATURE 183 PR00320A 16.74 2.853e-10 60-75 PR00320A 16.74 4.706e-10 14-29 PR00320C 13.01 5.320e-10 60-75 PR00320C 13.01 5.680e-10 14-29 PR00320A 16.74 6.049e-09 217-232 PR00320B 12.19 8.875e-610 BL00750 Chaperonins TCP-1 proteins.BL00750B 16.17 1.000e-40 120 BL00750A 20.07 6.21 1e-37 26-69 BL00750G 20.12 8.800e-31 43I-471 BL00750F 18.40 S.I25e-24.59 8.650e-29 295-332 BL00750H

21.44 1.000e-27 489-524 BL00750C 25.65 5.345e-17 181 BL00750D 16.16 6.318e-14 613 BL00766 Tetrahydrofolate . BL00766B 24.49 1.000e-40 dehydrogenase/cyclohydrolase190 BL00766E 13.78 proteins. 1.000e-40 322-359 BL00766C 25.86 S.SOOe-17.05 4.536e-26 283-313 BL00766A

21.48 6.063e-24102-132 615 BL00256 Adipokinetic hormone familyBL00256 12.28 3.298e-10 proteins. 746-755 616 BL00319 Amyloidogenic glycoproteinBL00319C 17.12 9.053e-09 extracellular 419-domain proteins. 453 617 BL00030 Eukaryotic RNA-binding BL00030A 14.39 4.429e-09 region RNP-1 44-63 proteins.

618 BL00030 Eukaryotic RNA-binding BL00030A 14.39 4.429e-09 region RNP-1 44-63 proteins.

620 BL00325 Actin-depolymerizing proteins.BL00325B 21.66 5.817e-16 622 BL00972 Ubiquitin carboxyl-terminalBL00972A 11.93 S.SOOe-19 hydrolases 213-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

family 2 proteins. 231 BL00972D 22.55 2.742e-16 501-526 BL00972B 9.45 1,000e-16.48 3.160e-11 370-385 BL00972E

20.72 7.517e-10 526-548 625 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 6.333e-39 FINGER METAL-BINDING NU.

628 BL00039 DEAD-box subfamily ATP-dependentBL00039D 21.67 7.750e-31 helicases proteins. 524 BL00039A 18.44 2.000e-25 198-237 BL00039C 15:63 1.844e-19.19 5.636e-14 242-268 630 PD00306 PROTEIN GLYCOPROTEIN PD00306A 10.26 7.000e-12 PRECURSOR RE. 246 631 PD00306 PROTEIN GLYCOPROTEIN PD00306A 10.26 7.000e-12 PRECURSOR RE. 304 633 BL00785 5'-nucleotidase proteins.BL00785C 9.45 3,625e-16 122 BL00785E 15.85 4.OOOe-I6 279-295 BL00785A 9.73 6.500e-14 29-40 BL00785B 10.65 5.500e-13 72-86 BL00785D
9.89 4.000e-12 135-145 636 PR00832 PAXILLIN SIGNATURE PR00832E 14.43 9.901e-14 637 PR00109 TYROSINE KINASE CATALYTICPR00109B 12.27 6.362e-13 638 PF00635 MSP (Major sperm protein)PF00635B 15.84 4.900e-11 domain 463-proteins. 502 639 PR00860 VERTEBRATE METALLOTHIONEINPR00860B 7.04 1.900e-18 SIGNATURE PR00860C 9.61 1.474e-14 PR00860A 5.46 1.720e-14 641 PD00066 PROTEIN ZINC-FINGER METAL-PD00066 13.92 4,462e-15 B1NDI. PD00066 13.92 4.462e-15 PD00066 13.92 2.800e-14 PD00066 13.92 2,$00e-14 PD00066 13.92 2.800e-14 PD00066 13.92 7.000e-14 PD00066 13.92 8.800e-14 PD00066 13.92 8.800e-14 PD00066 13.92 1,500e-13 PD00066 13.92 7.000e-13 PD00066 13.92 7.000e-13 PD00066 13.92 9.500e-13 PD00066 13.92 9.500e-13 PD00066 13.92 9.500e-13 PD00066 13.92 8.615e-10 PD00066 13.92 1.600e-09 642 BL00961 Ribosomal protein S28e BL0096IB 11.24 7.429e-37 proteins. 67-100 BL0096IA 9.90 4.079e-26 643 BL00585 Ribosomal protein S5 proteins.BL00585A 28.43 1.391e-40 155 BL00585B 18.78 3.250e-30 647 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 9.400e-10 proteins. 181-192 648 PR00876 NEMATODE METALLOTHIONEIN PR00876C 6.15 9.229e-09112-652 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 5.941 e-27 29-68 FINGER METAL-BINDING NU.

653 BL00047 Histone H4 proteins. BL00047A 13.53 1.000e-40 SEQ ACCESSION DESCRIPTION RESULTSx ID NO.

NO:

BL00047B 6.51 I .429e-40 BL00047C 12.18 1.310e-38 ' 104 654 PD01066 PROTEIN ZINC FINGER ZINC- PD01066 19.43 4.109e-25 FINGER METAL-BINDING NU.

655 BL01115 GTP-binding nuclear proteinBL01115A 10.22 3.483e-17 ran proteins. 19-63 657 BL00518 Zinc forger, C3HC4 type BL00518 12.23 8.286e-10 (RING forger), 31-40 proteins.

658 BL00125 Serine/threonine specific BL00125B 21.48 1.OOOe-4089-protein phosphatases proteins. 135 BL00125C 19.97 1.000e-40 153-200 BL00125D 33.11 1.000e-14.83 8.941e-38 47-84 659 PD00066 PROTEIN ZINC-FINGER METAL-PD00066 13.92 8.200e-16 BINDI. PD00066 13.92 9.308e-15,380-393 PD00066 13.92 6.000e-13 PD00066 13.92 7.000e-13 PD00066 13.92 7.500e-13 PD00066 13.92 7.500e-13 PD00066 13.92 2.174e-1 l 464-477 PD00066 13.92 I.OOOe-10 660 PD01066 PROTEIN ZINC FINGER ZINC- PD01066 19.43 2.189e-26 FINGER METAL-BINDING NU.

661 BL00795 Involucrin proteins. BL00795C 17.06 7.882e-15 238 BL00795C 17.06 3.797e-13 187-232 BL00795C 17.06 5.014e-17.06 4.506e-12196-241 BL00795C

17.06 7.896e-12 191-236 BL00795C 17.06 1.667e-11 230 BL00795C 17.06 2.000e-11 198-243 BL00795C 17.06 3.778e-17.06 6.llle-II 197-242 17.06 6.444e-11 194-239 BL00795C 17.06 8.000e-11 234 BL00795C 17.06 8.556e-11 192-237 BL00795C 17.06 1.733e-17.06 2.779e-10 184-229 17.06 4.035e-10 199-244 BL00795C 17.06 5.081e-10 231 BL00795C 17.06 6.965e-10 190-235 BL00795C 17.06 2.700e-17.06 5.800e-09 175-220 17.06 6.500e-09182-227 BL00795C 17.06 6.600e-09 246 BL00795C 17.06 6.600e-09 202-247 BL00795C 17.06 6.600e-662 BL00469 Nucleoside diphosphate BL00469 22.22 1.000e-40 kinases proteins. 149-204 663 BL01160 Kinesin light chain repeatBL01160B 19.54 9.411e-11 proteins. 331-664 BL00601 Tryptophan pentad repeat BL00601A 20.29 5.500e-23 proteins (IRF 7-46 family) proteins. BL00601B 20.92 3.631e-13 665 BL00082 Extradiol ring-cleavage BL00082A 19.07 8.615e-12 dioxygenases 49-72 proteins.

666 DM01537 kw SKI2W SKI2 NUCLEOLAR DM01537B 21.63 4.073e-37 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

HELICASE. 881 DM01537B 21,63 9.750e-21 15.I4 8.650e-I8 698-718 DM01537A

15.14 6.766e-12 1537-1557 667 DM01537 kw SKI2W SI~I2 NUCLEOLAR DM01537B 21.63 7.923e-38 HELICASE. 867 DM01537B 21.63 9.750e-21 15.14 8.650e-18 684-704 DM01537A

15.14 6.766e-12 1523-1543 669 BL00107 Protein kinases ATP-bindingBL00107A 18.39 6.786e-24 region 849-proteins. 880 BL00107B 13.31 6.727e-13 670 BL00299 Ubiquitin domain proteins.BL00299 28.84 9.735e-27 671 BL00027 'Homeobox' domain proteins.BL00027 26.43 6.571e-12 432-4?5 676 PR00861 ALPHA-LYTIC ENDOPEPTIDASEPR00861E 9.88 2.385e-09 SERINE PROTEASE (52A) 221 SIGNATURE

678 BL00225 Crystallins beta and gammaBL002258 18.06 7.517e-24 'Greek key' 1805-motif proteins. 1840 BL00225B 18.06 8.297e-20 18.06 2.575e-191896-1931 18.06 8.200e-19175-210 BL00225B 18.06 8.200e-19 1733 BL00225B 18.06 4.808e-14 73-I08 BL00225B I8.06 4.808e-18.06 5.500e-14 2077-2I 12 13.82 5.829e-12 2043-2064 BL00225A 13.82 3.127e-09 679 PR00320 G-PROTEIN BETA WD-40 REPEATPR00320C 13.01 4.240e-10 SIGNATURE ' 184 PR00320A 16.74 6.294e-10 680 BL00243 Integrins beta chain cysteine-richBL0024313I.77 I.143e-I
domain 1 172-proteins. 215 681 PR00852 XERODERMA PIGMENTOSUM PR00852H 5.90 1.000e-29 GROUP D PROTEIN SIGNATURE635 PR00852E 8.14 3.769e-27 348-371 PR00852D 11.38 8.875e-11.08 2.800e-2S 249-269 PR00852I

17.26 3.500e-2S 683-?04 PR00852F 11.85 5.909e-24 398 PR00852G 16.19 4.462e-23 468-486 PR00852C 8,81 9,143e-682 BL50058 G-protein gamma subunit BL50058 27.23 1.375e-35 profile. I5-d3 685 BL00972 Ubiquitin carboxyl-terminalBL00972A I 1.93 7.500e-20 hydrolases 40-58 family 2 proteins. BL00972D 22.55 3.903e-16 325 BL00972B 9.45 1,000e-13 120-130 BL00972E 20.72 5.500e-687 BL00237 G-protein coupled receptorsBL00237A 27.68 4.273e-14 proteins. 98-688 BL00388 Proteasome A-type subunitsBL00388A 23.14 I.OOOe-40 proteins. 8-54 BL00388B 31.38 3.864e-33 108 BL00388D 20.71 1.000e-21 153-184 BL00388C 18.79 8.147e-X689 PD02796 PROTEIN STEROL CARRIER PD0279bB 20.92 1.105e-15 ~ LIPID- 347-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

TRAN. 394 691 PDO1S72 PHOTOSYSTEM II REACTION PDOiS72 8.77 4.083e-09 1 ~ 1 CENTRE T PROTEIN PHOTOS.

692 BL00028 Zinc forger, C2H2 type, BL00028 16.07 7.600e-10 domain proteins. 488-SOS

694 BL01013 Oxysterol-binding proteinBL01013A 25.14 9.3S7e-33 family S27-proteins. S63 BL01013D 26.81 8.23Se-23 814-8S8 BL01013C 9.97 6.211e-11.33 3.60Se-13 S92-603 69S PD00289 PROTEIN SH3 DOMAIN REPEATPD00289 9,97 3.S71e-13 PRESYNA. PD00289 9.97 8.6SOe-11 2161 PD00289 9.97 2.SS2e-09 698 PR00161 NICKEL-DEPENDENT PR00161C 9.S 1 4.930e-09 CYTOCHROME SIGNATURE

700 PR00749 LYSOZYME G SIGNATURE PR00749F 13.63 8.636e-13 156 PR00749H 8.22 3.681e-12 173-194 PR00749B 16.54 1.419e-7.26 3.060e-11 72-91 PR00749A 10.33 4.815e-10 24-4S

703 PR00704 CALPAIN CYSTEINE PROTEASEPR00704I 9.52 1.000e-29 (C2) 476-SOS

FAMILY SIGNATURE PR00704D 11.05 2.500e-27 158 PR00704E 12.55 S.SOOe-27 162-186 PR00704F 13.61 1.000e-13.87 1.237e-21 317-339 PR00704H

13.38 8.138e-21 367-385 PR00704A 14.68 2.125e-19 PR00704C 11.88 1.257e-17 113 PR00704B 17.94 1.833e-15 705 PR008S9 PROKARYOTE METALLOTHIONEINPR008S9C 7.06 2.776e-09 SIGNATURE

706 BL00226 Intermediate filaments BL00226D 19.10 9.581e-26 proteins, 369-416 BL00226B 23.86 3.250e-24 203-2S 1 BL00226C 13.23 8.269e-12.77 8.200e-14 103-118 707 PR00021 SMALL PROLINE-RICH PROTEINPR00021A 4.31 2.440e-10 SIGNATURE

708 BL00361 Ribosomal protein 510 BL00361B 18.34 S.lOle-10 proteins. 82-lOS

709 PR00021 SMALL PROLINE-RICH PROTEINPR00021A 4.31 2.200e-10 SIGNATURE

710 BLOOS 14 Fibrinogen beta and gammaBLOOS 14C 17.41 8.412e-27 chains C- 160-terminal domain proteins.197 BLOOS14E 14.28 8.909e-16 219-236 BLOOS14H 14.95 l.SSle-15.98 7.7SOe-1S 284-314 BLOOS14D

15.35 4.789e-10201-214 711 PD00930 PROTEIN GTPASE DOMAIN PD00930B 33.72 8.714e-12 ACTIVATION.

714 BL00400 LBP / BPI / CETP family BL00400C 24.53 6.029e-17 proteins. 158-202 BL00400D 23.26 2.080e-14 222-259 BL00400A 21.59 1.600e-715 BLOT IS4 RNA polymerases L / 13 BLO11S4B 24.55 S.SOOe-36 to 16 Kd 40-76 SEQ ACCESSION DESCRIPTION RESULTSX

ID NO.

NO:

subunits proteins. BLOT 154A 18.70 3.000e-22 716 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 9.786e-32 FINGER METAL-BINDING NU.

717 BL0021 S Mitochondrial energy transferBL0021 SA 15.82 9.206e-14 proteins. 77-102 BL00215A 15.82 8.412e-10 719 BL00309 Vertebrate galactoside-bindingBL00309C 18.65 2.241e-09 lectin 62-87 proteins.

726 BL00687 Aldehyde dehydrogenases BL00687E 25.37 7.136e-33 glutamic acid 266-proteins. 316 BL00687D 26.00 5.333e-28 151-198 BL00687B 17.54 3.647e-26 39-81 BL00687C 24.13 6.087e-22 96-133 BL00687F
9.5S

2.500e-11 352-363 727 DM01354 kw TRANSCRIPTASE REVERSE DM013S4N 13.17 1.000e-40 ORF2. 174 DM013540 8.73 6.60Se-1S

734 PD00301 PROTEIN REPEAT MUSCLE PD00301A 10.24 6.400e-09 CALCIUM-BI. 112 735 BL01024 Protein phosphatase 2A BL01024A 10.26 1.000e-40 regulatory 22-69 subunit PRSS proteins. BL01024B 8.91 1.000e-40 BL01024C 7.80 1.000e-40 185 BL01024D 13.22 1.000e-40 185-222 BL01024E 11.96 1.000e-9.42 1.000e-40 266-317 BL01024G

11.09 1.000e-40 317-349 BL01024H 13.88 1.000e-40 736 PF00913 Trypanosome variant surfacePF00913D 11.90 7.130e-10 glycoprotein.

737 PR00700 PROTEIN TYROSINE PHOSPHATASEPR00700D 12.47 2.200e-09 740 PR00320 G-PROTEIN BETA WD-40 REPEATPR00320C 13.01 1.600e-09 SIGNATURE PR00320A 16.74 7.366e-09 743 PR00871 DNA PR00871 G 14.48 8.000e-09 (TDT) SIGNATURE

745 BL00518 Zinc forger, C3HC4 type BL00518 12.23 2.286e-10 (RING forger), 33-42 proteins.

749 BL0021S Mitochondrial energy transferBL0021SA 15.82 5.200e-15 proteins. 221-246 BL0021SA 15.82 7.618e-14 20-45 BL002ISA 15.82 8.851e-11 123-148 BL0021SB 10.44 9.526e-10.44 7.300e-09 272-285 BL0021SB

10.44 8.500e-09165-178 7S BLS0002 Src homology 3 (5H3) domainBLS0002A 14.19 1.000e-14 1 proteins 370-profile. 389 BLS0002B 15.18 2.200e-10 752 BL00353 HMG1/2 proteins. BL003S3B 11.47 3.089e-12 753 PF00622 Domain in SPIa and the PF00622B 21.00 4.214e-14 RYanodine 47-69 Receptor.

754 BL00211 ABC transporters family BL00211A 12.23 8.941e-10 proteins. 66-78 755 PR00926 MITOCHONDRIAL CARRIER PR00926F 17.75 7.750e-19 PROTEIN SIGNATURE 415 PR00926C 16.07 5.935e-17 253-274 PR00926D 10.53 2.059e-11.70 SEQ ACCESSION DESCRIPTION RESULTS' ID NO.

NO:

4.971e-15 344-363 PR00926B

16.07 9.526e-13 210-225 PR00926A 10.41 1.514e-12 756 BL01187 Calcium-binding EGF-Like BL01187A 9.98 2.125e-12 domain 324-proteins pattern proteins.336 BL01187A 9.98 4.789e-11 377-389 BLOI 187B 12.04 3.057e-7S7 PF00651 BTB (also known as BR-C/Ttk)PF00651 15.00 4.429e-10 domain 43-56 .proteins.

758 PR00055 HIV TAT DOMAIN SIGNATURE PR00055A 8.13 8.855e-09 759 PD00066 PROTEIN ZINC-FINGER METAL-PD00066 13.92 5.304e-11 BINDI.

760 PR00448 NSF ATTACHMENT PROTEIN PR00448D 12.42 3.455e-27 SIGNATURE 186 PR00448A 10.74 1.273e-22 37-57 PR00448B 16.01 9.379e-21 100-118 PR00448C 11.46 1,000e-765 BL01042 Homoserine dehydrogenase BL01042A 13.29 5.909e-11 proteins. 74-95 766 PR00625 DNAJ PROTEIN FAMILY PR0062SA 12.84 2.154e-18 SIGNATURE PR00625B 13,48 9.000e-16 768 BL00762 WHEP-TRS domain proteins.BL00762A 23.43 B.SOOe-28 149 BL007628 16.14 3.793e-12 64-78 BL00762A 23.43 6.625e-12 6-43 BL00762C 15.58 4.176e-09 459-472 BL00762D 11.15 9.667e-769 PR00709 AVIDIN SIGNATURE PR00709A 4.60 1.934e-09 770 PR00320 G-PROTEIN BETA WD-40 REPEATPR00320C 13.01 1.720e-10 SIGNATURE 277 PR00320A 16.74 2.853e-10 262-277 PR00320C 13.01 4.300e-12.19 5.500e-09 262-277 PR00320A

16.74 6.268e-09 SS-70 771 PR00019 LEUCINE-RICH REPEAT PR00019B 11.36 8.714e-12 SIGNATURE 101 PR00019A 11.191.000e-10 772 PD02807 APOLIPOPROTEIN E PRECURSORPD02807C 8.91 6.308e-10 APO-E GLYCOPROTEIN PLAS. 159 773 PD02807 APOLIPOPROTEIN E PRECURSORPD02807C 8.91 6.308e-10 APO-E GLYCOPROTE1N PLAS. 204 774 DM00547 1 kw CHROMO BROMODOMAIN DM00547F 23.43 3.942e-28 SHADOW GLOBAL. 990 DM00547E 13.94 9.750e-21 652-675 DM00547B 11.28 1.818e-18 518-532 DM00547C

17.30 3.531 e-17 S46-568 DM00547A 12.38 1.273e-II

509 DMOOS47D 11.60 9.200e-11 776 PR00?79 INOSITOL 1,4,5-TRISPHOSpHATE-PR00779F 14.51 5.147e-09 SIGNATURE

777 PR00779 INOSITOL 1,4,5-TRISPHOSPHATE-PR00779F 14:51 5.147e-09 SIGNATURE

778 PR00779 INOSITOL 1,4,5-TRISPH05PHATE-PR00779F 14.51 5.147e-09 SIGNATURE

SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

779 BL01282 BIR repeat proteins. BL01282B 30.49 2.543e-09 781 PR00205 CADHERIN SIGNATURE PR00205B 11.39 3.118e-11 672 PR00205B 11.39 8.588e-2 1 230-248 PR00205B 11.39 8.527e-11.39 4.203e-09 336-354 783 BL00625 Regulator of chromosome BL00625B 17.69 2.167e-19 condensation 193-(RCC1) proteins. 227 BL00625A 16.21 5.500e-17 199-228 BL00625B 17.69 1.885e-17.69 2.770e-16 245-279 BL00625A

16.21 9.115e-16 251-280 BL00625A 16.21 6.507e-I4 785 PF00084 Sushi domain proteins PF00084B 9.45 7.188e-10 (SCR repeat 595-607 proteins. PF00084B 9.45 6.400e-09 786 PF00084 Sushi domain proteins PF00084B 9.45 7.188e-10 (SCR repeat 595-607 proteins. PF00084B 9.45 6.400e-09 787 BL00826 MARCKS family proteins. BL00826C 7.63 6.738e-09 788 PR00453 VON WILLEBRAND FACTOR PR00453A 12.79 1.310e-I4 A DOMAIN SIGNATURE PR00453B 14.65 8.568e-10 789 PR00102 ORNITHINE PR00102B 14.82 5.418e-09 SIGNATURE

790 BL00030 Eukaryotic RNA-binding BL00030B 7.03 5.500e-11 region RNP-1 199-proteins. 209 791 BL00415 Synapsins proteins. BL00415N 4.29 9.519e-10 437 BL00415N 4.29 2.117e-09 103-147 BL00415N 4.29 3.628e-0997-141 BL00415N4.29 5.664e-09 387-431 795 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 2.091 e-36 105-144 FINGER METAL-BINDING NU.

799 PF00731 AIR carboxylase. PF00731C 23.16 7.333e-35 380 PF00731B 19.47 7.429e-28 299-336 PF00731A 19.32 6.333e-804 BL00170 Cyclophilin-type peptidyl-prolylBL00170B 20.97 8.071e-09 cis-trans 297-isomerase signatur. 337 805 BL00678 Trp-Asp (WD) repeat proteinsBL00678 9.67 3.400e-10 proteins. 378-389 BL00678 9.67 5.800e-10 BL00678 9.67 8.800e-10 806 PD01719 PRECURSOR GLYCOPROTEIN PD01719A 12.89 7.571e-14 SIGNAL RE. 318 807 PR00320 G-PROTEIN BETA WD-40 REPEATPR00320B 12.19 9.I
OOe-09 451-809 BL00107 Protein kinases ATP-bindingBL00107A 18.39 4.462e-12 region 564-proteins. 595 810 PR00453 VON WILLEBRAND FACTOR PR00453A 12.79 1.310e-14 A DOMAIN SIGNATURE PR00453B 14.65 8.568e-10 814 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 2.047e-31 FINGER METAL-BINDING NU.

8I5 PDO 1066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 2.047e-3 FINGER METAL-BINDING NU.

817 PR00193 MYOSIN HEAVY CHAIN PR00193D 14.36 5.154e-36 SIGNATURE 154 PR00193E 19.47 3.919e-18 ~18 PR00830 ENDOPEPTIDASE LA (LON) PR00830A 8.41 9.571e-11 ~ SERINE 115-SEQ ACCESSION DESCRIPTION RESULTS'' ID NO.

NO:

PROTEASE (516) SIGNATURE 135 819 BL00126 3'S'-cyclic nucleotide BL00126C 22.07 7.857e-24 phosphodiesterases 528-proteins. 569 BL00126E 35.22 3.714e-15 669-724 BLOOI26D 25.50 1.173e-15.20 1.000e-12 502-514 BL00126A

27.56 3.361e-09 461-498 820 PR005I1 TEKTIN SIGNATURE PR00511B 12.25 8.826e-22 195 PR00511A 13.59 7.723e-11' 821 BL00741 Guanine-nucleotide dissociationBL00741B 14.27 2.800e-15 stimulators CDC24 family sign.

822 PF00780 Domain found in NIKl-likePF00780I 14.69 4.825e-09 kinases, 231-mouse citron and yeast 261 ROM.

827 BL00030 Eukaryotic RNA-binding BL00030A 14.39 5.235e-11 region RNP-1 144-proteins. 163 828 BL00326 Tropomyosins proteins. BL00326D 8.76 9.357e-11 829 PD02448 TRANSCRIPTION PROTEIN PD02448A 9.37 1.000e-40 BINDIN. PD02448B 10.17 1.000e-40 133 PD02448C 13.62 1.000e-40 152-189 PD02448E 11.33 9.000e-14.22 9.654e-25 279-303 PD02448D

11.48 3.659e-18 197-211 PD02448G 10.73 7.857e-16 830 BL00720 Guanine-nucleotide dissociationBL00720B 16.57 4.500e-23 stimulators CDC25 family 507 sign.

831 BL00107 Protein kinases ATP-bindingBL00107A 18.39 6.625e-21 region 143-proteins. 174 BL00107B 13.31 4.214e-10 832 BL00215 Mitochondrial energy transferBL00215A 15.82 5.787e-11 proteins. 32-57 833 PR00497 NEUTROPHIL CYTOSOL FACTORPR00497A 6.92 4.375e-09 834 BL00229 Tau and MAP proteins tubulin-bindingBL00229A 23.57 9.565e-10 domain proteins. 138 835 BL00421 Transmembrane 4 family BL00421E 20.97 2.216e-09 proteins. 1053-836 BL00795 Involucrin proteins. BL00795B 12.41 7.931e-09 837 PR00020 MAM DOMAIN SIGNATURE PR00020A 18.17 1.000e-17 PR00020B 15.52 5.846e-16 PR00020D 12.70 2.543e-15 162 PR00020C 13.66 3.483e-13 95-107 PR00020E 8.64 6.586e-13 838 BL50017 Death domain proteins BL50017B 17.60 6.897e-13 profile. 1499-839 PF00850 Histone deacetylase family.PF00850C 14.55 9.542e-09 840 PF00023 Ank repeat proteins. PF00023A 16.03 4.500e-12 PF00023B 14.20 7.923e-11 PF00023B 14.20 9.OOOe-IO

149 PF00023B 14.20 5.500e-09 842 BL01194 Ribosomal protein LlSe BL01194B 13.66 1.000e-40 proteins. 37-85 BL01194C 12.35 9.250e-40 138 BL01194A 18.70 7.632e-38 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

2-37 BLOT 194D 19.02 2.658e-36 843 BL00610 Sodium:neurotransmitter BL00610A 17.73 1.000e-40 symporter 40-90 family proteins. BL00610B 23.65 1.000e-40 154 BL00610C 12.94 1.000e-40 206-258 BL00610E 20.34 1.000e-29.02 1.000e-40 454-509 20.97 6.063e-35 272-325 BL00610G 12.89 8.588e-13 845 BL00143 Insulinase family, zinc-bindingBL00143A 20.914.300e-20 region 94-proteins. 121 BL00143C 14.16 5.500e-13 245-258 BL00143B 14.41 9.053e-846 PR00543 OESTROGEN RECEPTOR PR00543D 10.87 1.355e-09 847 PR00543 OESTROGEN RECEPTOR PR00543D 10.87 1.355e-09 SIGNATURE . 914 848 BL00824 Elongation factor 1 beta/beta'/deltaBL00824C 14.58 1.000e-40 chain 129-proteins. 167 BL00824D 14.04 6.192e-39 167-202 BL00824B 9.21 2.080e-12.49 3.333e-19 210-226 13.78 8.650e-14 19-34 849 PD01066 PROTEIN ZINC FINGER ZINC- PD01066 19.43 1.000e-40 FINGER METAL-BINDING NU.

850 PD01066 PROTEIN ZINC FINGER ZINC- PD01066 19.43 7.316e-24 FINGER METAL-BINDING NU.

852 BL01272 Glucokinase regulatory BL01272B 19.61 6.870e-30 protein family 136-proteins. 171 BL01272C 11.68 3.314e-25 249-274 BL01272A 6.49 1.231e-853 PD00930 PROTEIN GTPASE DOMAIN PD00930B 33.72 9.341e-20 ACTIVATION. 106 854 PD00289 PROTEIN SH3 DOMAIN REPEAT PD00289 9.97 6.850e-11 PRESYNA.

858 PR00450 RECOVERIN FAMILY SIGNATUREPR00450C 12.22 3.250e-25 PR00450B 11.76 8.125e-23 PR00450D 16.58 8.920e-22 112 PR00450E 12.14 1.58Ie-19 114-133 PR00450G 15.33 5.500e-. 19 166-187 PR00450F
12.30 4.375e-15 140-156 13.58 1.857e-14 8-23 860 BL00027 'Homeobox' domain proteins.BL00027 26.43 7.188e-27 866 BL00477 Alpha-2-macroglobulin familyBL00477L 23.51 7.480e-20 thiolester 54-87 region proteins.

867 BL01078 Molybdenum cofactor biosynthesisBL01078B 14.20 1.621e-20 proteins. 429 BL01078A 10.16 2.000e-13 366-379 BL01078D 5.99 3.455e-10.52 3.793e-11 501-513 868 BLOT 177 Anaphylatoxin domain proteins.BL01177E 20.64 5.800e-24 489 BL01177C 17.39 5.333e-19 416-435 BL01177B 13.61 7.840e-17.50 1.900e-15 441-459 L 869 BL01177 Anaphylatoxin domain proteins.BLO1177E 20.64 5.800e-24 ~ ~ ~ 415-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

442 BL01177C 17.39 5.333e-19 369-388 BL01177B 13.61 7.840e-17.50 1.900e-15 394-412 871 BL50007 Phosphatidylinositol-specificBL50007A 19.61 1.000e-40 phospholipase X-box domain368 BL50007D 19.54 proteins 1.000e-40 prof. 589-631 BL50007B 20.90 6.700e-25.63 9.053e-33 748-785 BL50007C

8.97 5.200e-19 452-469 872 BL00972 Ubiquitin carboxyl-terminalBL00972D 22.55 3.250e-17 hydrolases 90-family 2 proteins. 115 874 PR00452 SH3 DOMAIN SIGNATURE PR00452B 11.65 4.250e-09 877 BL00741 Guanine-nucleotide dissociationBL00741B 14.27 5.500e-13 stimulators CDC24 family 1366 sign.

878 DM00215 PROLINE-RICH PROTEIN 3. DM00215 19.43 2.525e-09 881 PD02807 APOLIPOPROTEIN E PRECURSORPD02807E 10.90 4.702e-09 APO-E GLYCOPROTEIN PLAS. 407 882 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 7.1 ~8e-37 FINGER METAL-BINDING NU.

885 PF00023 Ank repeat proteins. PF00023A 16.03 8.071e-09 886 PR00372 BIOPTERIN-DEPENDENT PR00372B 10.30 9.308e-27 AROMATIC AMINO ACID 248 PR00372A 13.39 7.000e-24 HYDROXYLASE SIGNATURE 134-154 PR00372E 12.62 2.125e-7.90 3.025e-22 289-309 PR00372F

13.09 6.333e-21 395-414 PR00372D 10.22 1.000e-19 887 BL00301 GTP-binding elongation BL00301B 20.09 2.800e-24 factors proteins. 103-135 BL00301A 12.41 4.316e-13 888 BL00518 Zinc forger, C3HC4 type BL00518 12.23 1.667e-09 (RING finger), 30-39 proteins.

889 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 4.906e-26 FINGER METAL-BINDING NU.

890 DM00179 w KINASE ALPHA ADHESION DM00179 13.97 7.652e-09 CELL. 123 892 BL01022 PTR2 family proton/oligopeptideBL01022B 22.19 6.016e-14 symporters proteins. 118 BL01022E 23.51 1.173e-12 472-508 BL01022A 11.58 9.135e-12 42-61 BL01022D 9.42 3.455e-893 PD02407 3-BISPHOSPHOGLYCERATE- PD02407K 12.59 6.529e-10 INDEPENDENT PHOSPHOGLYCER.383 894 PD02407 3-BISPHOSPHOGLYCERATE- PD02407K 12.59 6.S29e-10 INDEPENDENT PHOSPHOGLYCER.383 895 PR00237 RHODOPSIN-LIKE GPCR PR00237B 13.50 9.100e-14116-SUPERFAMILY SIGNATURE 138 PR00237F 13.57 1.360e-13 312-337 PR00237G 19.63 9.069e-13.03 7.120e-12 243-267 PR00237D

8.94 4.150e-11 194-216 PR00237A 11.48 4.375e-11 ~

896 BL00129 Glycosyl hydrolases familyBL00129D 16.76 8.258e-26 31 proteins. 634-678 BL00129A 26.21 1.720e-25 384-430 BL00229E 22.60 4.857e-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

15.12 1.750e-22 596-624 BL00129B

19.19 5.891 e-18 495-522 BL00129F 26.19 7.545e-I5 897 BL00598 Chromo domain proteins. BL00598 14.45 1.220e-13 898 BL00518 Zinc finger, C3HC4 type BL00518 12.23 6.000e-09 (RING forger), 396-405 proteins.

899 PDO1101 INHIBITOR HEAVY CHAIN PDO1101B 21.53 1.000e-40 CHANNEL IN. 327 PDO1101D 24.45 1.000e-40 457-512 PDOl lOlA 18.25 6.268e-12.69 1.237e-16 366-386 PDO1101E

6.73 7.750e-12 566-576 900 PR00600 PROTEIN PHOSPHATASE PP2A PR00600A 11.61 5.979e-09 REGULATORY SUBUNIT

SIGNATURE

901 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 8.116e-31 FINGER METAL-BINDING NU.

903 BL01115 GTP-binding nuclear proteinBLO 1115A 10.22 1.509e-1 ran proteins. I 21-65 906 DM00215 PROLINE-RICH PROTEIN 3. DM00215 19.43 2.174e-13 572 DM00215 19.43 4.750e-12 549-582 DM00215 19.43 9.824e-19.43 2.929e-I O 548-581 19.43 4.054e-10 550-583 DM00215 19.43 5.339e-10 585 DM00215 19.43 7.107e-10 907 PR00988 URIDINE KINASE SIGNATURE PR00988A 6.39 6.276e-12 908 BL00107 Protein kinases ATP-bindingBL00107A 18.39 5.950e-17 region 1125-proteins. 1156 909 BL00107 Protein kinases ATP-bindingBL00107A 18.39 5.950e-17 region 1118-proteins. 1149 910 BL00107 Protein kinases ATP-bindingBL00107A 18.39 8.560e-13 region 150-proteins. 181 911 BL00107 Protein kinases ATP-bindingBL00107A 18.39 8.560e-13 region 150-proteins. 181 912 PF00856 SET domain proteins. PF00856A 26.14 4.553e-11 913 PF00628 PHD-forger. PF00628 15.84 6.400e-13 914 PR00962 LETHAL(2) GIANT LARVAE PR00962D 10.40 1.000e-27 PROTEIN SIGNATURE 459 PR00962G 15.714.086e-26 593-618 PR00962B 11.98 9.122e-13.28 6.143e-22 15-34 PR00962C
8.00 4.000e-21 348-369 PR00962F

12.39 9.769e-21 552-572 PR00962H 13.32 2.636e-20 643 PR00962I 11.68 9.786e-20 692-712 PR00962E 8.812.915e-915 PR00962 LETHAL(2) GIANT LARVAE PR00962D 10.40 1.000e-27 PROTEIN SIGNATURE 389 PR00962G 15.71 4.086e-26 523-548 PR00962A 13.28 6.143e-22 15-34 PR00962C 8.00 4.000e-12.39 9.769e-21 482-502 PR00962H

SEQ ACCESSION ~ DESCRIPTION RESULTS*

ID NO.

NO:

13.32 2.636e-20 553-573 PR00962I 11.68 9.786e-20 642 PR00962E 8.81 2.915e-18 916 BL00134 Serine proteases, trypsinBL00134A 11.96 5.886e-14 family, histidine 90-proteins. 107 917 BL00478 LIM domain proteins. BL00478B 14.79 8.393e-13 226 BL00478B 14.79 6.712e-10 918 PR00049 WILM'S TUMOUR PROTEIN PR00049D 0.00 5.729e-09 922 BL00150 Acylphosphatase proteins.BL00150 25.33 1.000e-40 924 DM00031 IMMLJNOGLOBULIN V REGION.DM00031B 15.41 8.063e-09 925 BL00072 Acyl-CoA dehydrogenases BL00072D 30.08 2.837e-24 proteins. 280-331 BL00072E 24.12 8.200e-24 368-411 BL00072C 25.30 7.873e-9.48 6.049e-12 183-196 927 BL00237 G-protein coupled receptorsBL00237C 13.19 1.692e-13 proteins. 229-256 BL00237A 27.68 6.657e-13 90-130 BL00237D 11.23 9.571e-928 BL01033 Globins profile. BL01033A 16.94 7.923e-18 BL01033B 13.81 1.000e-15 929 BL00216 Sugar transport proteins.BL00216B 27.64 8.714e-13 932 BL00415 Synapsins proteins. BL00415N 4.29 9.519e-10 397 BL00415N 4.29 2.117e-09 63-107 BL00415N 4.29 3.628e-09 57-101 BL00415N 4.29 5.664e-09 933 PD02448 TRANSCRIPTION PROTEIN PD02448A 9.37 1.000e-40 BINDIN. PD02448B 10.17 1.000e-40 133 PD02448C 13.62 1.000e-40 152-189 PD02448E 11.33 9.000e-14.22 9.654e-25 267-291 PD02448D

11.48 3.659e-18 197-211 PD02448G 10.73 7.857e-16 934 DM00191 w SPAC8A4.04C RESISTANCE DM00191D 13.94 9.083e-10 SPAC8A4.OSC DAUNORUBICIN.175 935 BLO1115 GTP-binding nuclear proteinBLO1115A 10.22 4.696e-10 ran proteins. 67-936 BL00019 Actinin-type actin-bindingBL00019D 15.33 8.138e-14 domain 865-proteins. 895 937 PR00762 CHLORIDE CHANNEL SIGNATUREPR00762A 14.22 4.000e-22 201 PR00762C 9.29 1.000e-21 268-288 PR00762E 12.07 3.250e-11.29 1.000e-19 470-491 PR00762F

15.12 1.429e-19 538-558 PR00762B 12.12 1.818e-18 234 PR00762G 14.13 3.455e-17 938 BL00027 'Homeobox' domain proteins.BL00027 26.43 9.500e-25 L 939 ~ DMO1111 4 kw PHOSPHATASE DMO1111E 17.28 1.568e-10 ~ 248-SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

TRANSFORMING 61K PDF1. 297 DMO1111E 17.28 5.168e-10 659-708 DMO1111D 16.76 5.263e-09 279-325 DMO1111M

10.67 8.674e-09 911-935 940 BL00107 Protein kinases ATP-bindingBL00I07B 13.31 1.000e-14 region 293-proteins. 309 BL00107A 18,39 6.760e-13 942 BL01160 Kinesin Iight chain repeatBL01160B 19.54 9.832e-11 proteins. 543-943 PD01066 PROTEIN ZINC FINGER ZINC-PD01066 19.43 3.500e-35 FINGER METAL-BINDING NU.

945 BL00989 Clathrin adaptor complexesBL00989B 26.51 I.000e-40 small chain 66-proteins. 117 BL00989A 11.66 1.000e-13 946 PROOI78 FATTY ACID-BINDING PROTEINPR00178D 13.52 9.571e-09 947 BL00178 Aminoacyl-transfer RNA BL00178B 7.11 4.857e-09 synthetases 713-class-I proteins. 724 948 PF00628 PHD-forger. PF00628 15.84 8.412e-14 951 BL002I6 Sugar transport proteins.BL00216B 27.64 2.050e-10 952 PR00926 MITOCHONDRIAL CARRIER PR00926F 17.75 4.300e-11 PROTEIN SIGNATURE PR00926F 17.75 6.348e-09 955 PF00109 Beta-ketoacyl synthase. PF00109 13.08 2.846e-12 9S7 PR00069 ALDO-KETO REDUCTASE PR00069A 16.01 8.826e-24 SIGNATURE PR00069B 11.33 1.S14e-17 105 PR00069C 16.03 8.816e-14 958 PF00583 Acetyltransferase (GNAT) PF00583A 12.53 5.500e-10 family. 631-961 PR00328 GTP-BINDING SARI PROTEIN PR00328A 10.62 8.740e-I0 SIGNATURE

962 BL00354 HMG-I and HMG-Y DNA-bindingBL00354A 3.83 9.438e-10 domain proteins (A+T-hook).1499 963 BL00354 HMG-I and HMG-Y DNA-bindingBL00354A 3.83 9.438e-10 domain proteins (A+T-hook).1499 964 BL00027 'Homeobox' domain proteins.BL00027 26.43 7.188e-27 965 PF00992 Troponin. PF00992A16.672.42Ie-09581-966 PR00515 5-HYDROXYTRYPTAMINE 1F PROOSISD 7.91 5.741e-09 RECEPTOR SIGNATURE

967 BL00579 Ribosomal protein L29 BL00579B 21.99 5.065e-21 proteins. 164-970 BL00504 Fumarate reductase / succinateBL00504C 18.68 2.227e-24 dehydrogenase FAD-bindingBL00504D 10.43 7.261e-21 site 75-93 proteins.

973 PFOOS80 UvrDIREP helicase. PF00580A 13.37 4.720e-09 974 PR00456 RIBOSOMAL PROTEIN P2 PR004S6F 5.86 1.000e-10 SIGNATURE

975 BL00237 G-protein coupled receptorsBL00237A 27.68 4.429e-22 pxoteins. 99-976 BL00031 Nuclear hormones receptorsBL00031A 19.55 7.158e-33 binding region proteins. BL00031B 22.25 S.SOOe-28 977 PD00066 PROTEIN ZINC-FINGER METAL-PD00066 13.92 8.200e-16 BINDI. PD00066 13.92 8.200e-16 pPD00066 13.92 2.385e-15 SEQ ACCESSION DESCRIPTION RESULTS*

ID NO.

NO:

PD00066 13.92 9.308e-15 PD00066 13.92 2.800e-14 PD00066 13.92 4.600e-14 PD00066 13.92 5.200e-14 PD00066 13.92 4.000e-13 PD00066 13.92 4.429e-12 PD00066 13.92 9.571e-12 PD00066 13.92 6.870e-11 978 BL00721 Formate--tetrahydrofolateBL00721B 13.21 1.000e-40 ligase proteins. 346-401 BL00721D 13.90 1.000e-40 538-592 BL00721E 13.46 1.000e-18.79 2.500e-40 814-860 BL00721H

21.20 8.239e-39 763-814 BL00721A 15.31 9.719e-32 321 BL00721C 16.924.000e-30 498-535 BL00721F 15.96 8.232e-27 660-702 BL0072fG
7.97 3.017e-10 721-734 981 PD00126 PROTEIN REPEAT DOMAIN PD00126A 22.53 2.552e-09 NUCLEA. 201 982 BL00869 Renal dipeptidase proteins.BL00869C 12.58 3.172e-19 BL00869E 13.12 9.129e-18 157 BL00869J 15.60 6.032e-17 270-310 BL00869H 11.08 1.840e-13.55 2.543e-16 192-214 BL00869F

12.77 7.031e-14 157-192 BL00869I 12.92 3.274e-12 270 BL00869D 14.02 5.282e-10 95-124 BL00869B 15.55 9.382e-983 PR00196 ANNEX1N FAMILY SIGNATURE PR00196F 13.89 2.125e-09 984 BL00485 Adenosine and AMP deaminaseBL00485D 30.82 2.427e-10 proteins. 154-* Results include in order: accession number subtype; raw score; p-value;
position of signature in amino acid sequence SEQ PFAM NAME DESCRIPTION p-value PFAM
ID SCORE
NO:

2 ig Immunoglobulin domain 3.9e-17 60.3 3 HSP90 Hsp90 protein 0 1548.4 6 tsp_l Thrombospondin type 0.002 22.1 1 domain 7 7tm-1 7 transmembrane receptor6.7e-08 27.3 (rhodopsin family) 9 PWWP PVWVP domain 8.1e-16 66.0 12 Clq Clq domain 1.7e-26 101.5 13 CIq CIq domain 2e-20 81.3 14 Aa_trans Transmembrane amino 2.7e-42 153.9 acid transporter protein 15 E1-E2 ATPaseEI-E2 ATPase 6.3e-124 412.2 16 trypsin Trypsin 1.2e-87 278.6 17 ig Immunoglobulin domain 7.6e-12 43.2 18 lectin_c Lectin C-type domain 0.0003 21.2 20 Alpha L Alpha-L-fucosidase 1.2e-217 736.5 fucos SEQ PFAM NAME DESCRIPTION p-value PFAM
ID SCORE
NO:

22 pkinase Eukaryotic protein kinase3.3e-87 303.1 domain 23 pkinase Eukaryotic protein kinase2.7e-85 296.8 domain 24 pkinase Eukaryotic protein kinase2.7e-85 296.8 domain 25 ank Ank repeat 5.5e-14 59.9 27 pkinase Eukaryotic protein kinase1.5e-100 347.4 domain 28 spectrin Spectrin repeat 4e-57 203.2 29 spectrin Spectrin repeat 4e-57 203.2 30 WD40 WD domain, G-beta repeat1.2e-07 38.8 33 rrm RNA recognition motif. 1.1e-17 72.2 34 rnn RNA recognition motif. 1.1e-17 72.2 36 7tm~1 7 transmembrane receptor3e-36 117.3 (rhodopsin family) 37 ank Ank repeat 5.9e-25 96.3 38 SRF-TF SRF-type transcription 1.4e-36 133.9 factor 40 alk-phosphataseAllcaline phosphatase 0 1034.9 44 zf C2H2 Zinc forger, C2H2 type 8.6e-103 354.9 45 sugar_tr Sugar (and other) transporter3. I e-0840.3 47 7tm 2 7 transmembrane receptor6.4e-79 275.6 (Secretin family) 50 zf C2H2 Zinc forger, C2H2 type 1.3e-98 341.0 51 filament Intermediate filament 1.2e-176 600.3 proteins 52 zf C3HC4 Zinc forger, C3HC4 type2.7e-10 37.7 (RING
forger) 53 Cadherin Cadherin cytoplasmic 1.9e-94 327.2 C ter region m 54 S_100 S-100/ICaBP type calcium5.2e-18 73.3 binding domain 58 inositol_P Inositol monophosphatase5e-13 49.8 family 59 7tm_1 7 transmembrane receptor8.8e-46 147.6 (rhodopsin family) 60 Kunitz_BPTIKunitz/Bovine pancreatic3.7e-47 148.6 trypsin inhibito 62 DAD DAD family 2.5e-74 260.3 63 MOZ_SAS MOZ/SAS family 5.9e-133 455.1 64 MOZ SAS MOZ/SAS family 1.7e-123 423.6 65 ras Ras family 9.3e-89 308.3 67 Hamlp like Haml family 3.7e-49 176.7 68 7tm~1 7 transmembrane receptor5.2e-39 126.1 (rhodopsin family) 70 zf C2H2 Zinc forger, C2H2 type 1.5e-112 387.3 71 Peptidase_M41Peptidase family M41 1.2e-110 381.0 72 abhydrolasealpha/beta hydrolase 9.8e-05 26.5 fold 81 K_tetra K+ channel tetramerisation0.022 -16.8 domain 82 pkinase Eukaryotic protein kinase5e-49 176.3 domain 84 AAA ATPases associated with1.3e-77 271.3 various cellular act 85 homeobox Homeobox domain 1.4e-28 108.3 87 TGF-beta Transforming growth 6.7e-68 210.2 factor beta like 91 mito_carr Mitochondrial carrier 4.6e-57 198.5 proteins 95 adenylatekinaseAdenylate kinase 1.1e-15 60.0 96 ig Immunoglobulin domain 4.1e-20 69.8 99 CNH CNH domain 3.4e-120 412.7 100 homeobox Homeobox domain 7.4e-32 119.3 101 zf C2H2 Zinc forger, C2H2 type 2.2e-47 170.8 102 zf C2H2 Zinc forger, C2H2 type 4.4e-89 309.4 ~

103 dynamin Dynamin family 1.4e-150 513.6 104 lectin c Lectin C-type domain 4.2e-15 63.6 105 lectin_c Lectin C-type domain 4.2e-15 63.6 ' 108 metalthio Metallothionein 2e-25 97.9 SEQ PFAM NAME DESCRIPTION p-value PFAM
ID SCORE
NO:

112 HSP20 Hsp20/alpha crystallin 2.6e-20 77.7 family 115 EF_TS Elongation factor TS 3.8e-63 221.1 116 sugar_tr Sugar (and other) transporter4e-63 223.1 118 catalase Catalase 0 1158.9 119 UCH Ubiquitin carboxyl-terminal1e-10 24.4 hydrolase, famil 122 metalthio Metallothionein 2.8e-25 97.4 125 adh_short short chain dehydrogenase1.6e-45 164.6 126 KRAB KRAB box 7.9e-25 95.9 127 G-alpha G-protein alpha subunit1e-249 843.0 128 mito_carr Mitochondrial carrier 2e-65 227.2 proteins 131 EF1BD EF-1 guanine nucleotide4.9e-53 189.6 exchange domain 132 GYF GYF domain 4.9e-28 106.6 133 GYF GYF domain 4.9e-28 106.6 134 lipocalin Lipocalin / cytosolic 2.1e-33 119.1 fatty-acid binding pr 135 pkinase Eukaryotic protein kinase3.3e-86 299.8 domain 136 ank Ank repeat 2.2e-29 111.1 137 IL8 Small cytokines 3.1e-18 65.2 (intecrine/chemokine), inter 139 pyridoxal Pyridoxal-dependent 0.00011 19.0 deC decarboxylase conse 140 cadherin Cadherin domain 1.3e-88 307.8 142 efhand EF hand 5.7e-33 123.0 143 AcyltransferaseAcyltransferase 2e-29 111.2 146 cytochrome Cytochrome c 1.7e-33 124.7 c 147 pkinase Eukaryotic protein kinase2.3e-86 300.3 domain 148 PDZ PDZ domain (Also known 1.7e-09 45.0 as DHR or GLGF).

149 aldo_ket_redAldo/keto reductase 7.4e-189 640.8 family 150 homeobox Homeobox domain 3.2e-08 38.7 151 PseudoU_synth-tRNA pseudouridine synthase4.7e-57 203.0 152 abhydrolasealpha/beta hydrolase 1.7e-31 118.0 fold 153 PDZ PDZ domain (Also known 1.1e-09 45.6 as DHR or GLGF).

156 PHD PHD-finger 7.6e-15 62.8 157 fn3 Fibronectin type III 0.015 21.9 domain 158 homeobox Homeobox domain 2.7e-27 104.1 160 PWI PWI domain 3.9e-24 93.6 162 DnaJ DnaJ domain 2e-06 34.8 164 Cbl_N CBL proto-oncogene N-terminal8e-117 401.5 domain 166 metalthio Metallothionein 3.1e-26 100.6 167 LRR Leucine Rich Repeat 0.00069 26.3 169 fibrinogen Fibrinogen beta and 5.3e-180 611.4 C gamma chains, C-term 170 fibrinogen_CFibrinogen beta and 5.3e-180 611.4 gamma chains, C-term 171 fibrinogen_CFibrinogen beta and 1e-149 510.8 gamma chains, C-term 173 homeobox Homeobox domain 1.5e-29 111.6 174 FYVE FYVE zinc finger 7.4e-28 103.8 175 GRIP GRIP domain 3.9e-08 40.5 182 pkinase Eukaryotic protein kinase3.4e-71 250.0 domain 185 CAP_GLY CAP-Gly domain 5.6e-51 182.8 186 TBC TBC domain 2.2e-50 180.8 187 TBC TBC domain 2.2e-50 180.8 SEQ PFAM NAME DESCRIPTION p-value PFAM
ID SCORE
NO:

188 PDZ PDZ domain (Also known 4e-13 57.0 as DHR or GLGF).

189 Kelch Kelch motif 5.2e-106 365.6 190 TropomyosinTropomyosins 3.8e-171 535.4 192 Rieske Rieske [2Fe-2S] domain 0.0016 18.5 199 ig Immunoglobulin domain 5.9e-19 66.1 202 EGF EGF-like domain 3.4e-54 193.5 203 trefoil Trefoil (P-type) domain1e-24 95.5 ~

204 TBC TBC domain 8.5e-38 139.0 205 ethand EF hand 0.0096 22.6 206 ISK_ChannelSlow voltage-gated potassium0.0031 8.1 channel 207 trefoil Trefoil (P-type) domain2.9e-48 173.7 209 Ribosomal Ribosomal protein S13/S181.2e-78 274.7 210 hemopexin Hemopexin 1.3e-62 221.5 213 TBC ~ TBC domain 2.5e-48 174.0 215 Basic Myogenic Basic domain 4.3e-50 I79.8 216 Ribosomal KOW motif 8.2e-23 89.2 222 fn3 Fibronectin type III 7.3e-141 481.4 domain 223 cofilin_ADFCofilin/tropomyosin-type9.3e-47 168.8 actin-binding pr 224 efhand EF hand 6.1e-06 33.2 225 Pterin_4a Pterin 4 alpha carbinolamine9.3e-42 152.1 dehydratase 228 ABC_tran ABC transporter 4.1e-110 379.2 234 E1_DerP2_DerFE1 family 3.7e-90 312.9 235 E1_DerP2_DerFE1 family 1.6e-48 174.6 237 PMP22_ClaudinPMP-22/EMP/MP20/Claudin1.7e-25 98.1 family 238 Opiods neuropeVertebrate endogenous 1.8e-159 543.2 p opioids neurope 239 eIF-5a Eukaryotic initiation 5.9e-104 358.8 factor 5A
hypusine 240 Amino_oxidaseFlavin containing amine2.5e-1 37.8 oxidase l 243 zf C2H2 Zinc finger, C2H2 type 2.1e-99 343.6 244 Band_7 SPFH domain / Band 7 2.3e-53 190.7 family 245 ank Ank repeat I.6e-88 307.5 246 zf C2H2 Zinc finger, C2H2 type 6.7e-49 175.9 247 actin Actin 2.3e-42 140.3 248 ER_lumen_recepER lumen protein retaining2.4e-155 529.5 t receptor 250 PMP22_ClaudinPMP-22/EMP/MP20/Claudin2.2e-38 140.9 family 252 Collagen Collagen triple helix 1.4e-13 58.6 repeat (20 copies) 255 C2 C2 domain 0.052 7.8 257 CAP_GLY CAP-Gly domain 1.4e-20 8I.8 260 WD40 WD domain, G-beta repeat9.9e-62 218.5 261 WD40 WD domain, G-beta repeat9.9e-62 218.5 262 WD40 WD domain, G-beta repeat9.9e-62 218.5 263 cofilin_ADFCofilin/tropomyosin-type7.8e-21 82.6 actin-binding pr 264 Ribosomal Ribosomal protein Ll4p/L23e9.2e-10 40.6 265 SAPA Saposin A-type domain 4.4e-27 103.4 266 SAPA Saposin A-type domain 4.4e-27 103.4 267 ABC_tran ABC transporter 9.5e-39 142.2 269 Ribosomal_L14Ribosomal protein Ll4p/L23e6.2e-62 219.2 270 abhydrolasealpha/beta hydrolase 0.042 -3.3 fold 272 ras Ras family 4.3e-87 302.8 SEQ PFAM NAME DESCRIPTION p-value PFAM
ID SCORE
NO:

273 mn RNA recognition motif. 0.074 14.6 275 Iipocalin Lipocalin l cytosolic 2.5e-41 146.4 fatty-acid binding pr 276 ras Ras family 1.1e-67 238.3 277 UCH Ubiquitin carboxyl-terminal1.2e-147 503.9 hydrolase, famil 278 START START domain 3.2e-09 44.1 279 WD40 WD domain, G-betaxepeat1,8e-27 104.7 282 G-patch G-patch domain - 7.$e-2286.0 287 Anti_proliferatBTGl family 1.2e-101 351.0 289 KRAB KKAB box 7.1e-21 82.8 293 7tm 3 7 transmembrane receptor3.3e-73 256.6 295 SET SET domain Se-30 113.2 296 Pyridox Pyridoxamine 5'-phosphateI.3e-76 268.0 oxidase oxidase 297 rrm RNA recognition motif. 5.4e-45 162.9 298 Ubie_methyltranubiE/COQS methyltransferase6.3e-05 -96.3 family 299 Ubie_methyltranubiEfCOQS methyltransferase0.0024 -118.1 family 301 Cyt reductaseFAD/NAD-binding Cytochrome7.7e-61 215.5 reductase 302 G-patch G-patch domain 3.1e-14 60 .7 307 7tm 1 7 transmembrane receptor7.7e-43 _ (rhodopsin 138.2 family) 308 PH PH domain 0.0015 17.8 310 7tm_1 7 transmembrane receptor1.4e-84 270.8 (rhodopsin family) 31 Rhodanese Rhodanese-lilee domain 3.3e-64 226.7 I

312 tubulin Tubulin/FtsZ family 4.9e-286 963.6 314 SURF4 SURF4 family 1.2e-19 676.6 325 IMS impB/mucB/samB family _ 207.5 2e-58 327 cadherin Cadherin domain 4.3e-9I 316.0 329 NAC NAC domain 2.1e- 107.8 330 IP_trans Phosphatidylinositol 6.5e-98 338.7 transfer protein 332 TFIIS Transcription factor 8.8e-05 29.3 S-II (TFIIS) 337 zf C2H2 Zinc forger, C2H2 type 3.6e-61 216.6 340 AIRS AIR synthase related 4e-32 120.2 protein 343 annexin Annexin 4.6e-80 279.4 346 Stathmin Stathmin family I .8e-90 314.0 347 Ribosomal_L16Ribosomal protein L16 4.6e-09 34.9 348 lactamase Metallo-beta-lactamase 0.012 -6.0 B superfamily 351 ethand EF hand 2.5e-14 61.0 353 lectin_c Lectin C-type domain 1.3e-05 32.1 354 WD40 WD domain, G-beta repeat2.2e-18 74.5 360 lipocalin Lipocalin / cytosolic 6.3e-10 38.3 fatty-acid binding pr 362 AcetyltransfAcetyltransferase (GNAT)0.0019 24.9 family 365 tRNA-synt tRNA synthetases class 4.6e-I85 628.2 1 I (I, L, M and V ) 366 Sulfatase Suifatase 6.1 e-228770.6 368 START START domain 3.8e-11 50.5 369 pkinase Eukaryotic protein kinase2.4e-10 41.3 domain 370 ACBP Acyl CoA binding protein4.4e-56 199.7 371 pkinase Eukaryotic protein kinase1.6e-94 327.5 domain 373 EGF EGF-like domain 2.6e-12 54.3 375 zf C2H2 Zinc forger, C2H2 type 8.2e-64 225.4 377 KRAB DRAB box 3.7e-27 103.7 379 SET SET domain 7.3e-61 215.6 380 Glyco_transfGlycosyl transferase 0.0028 -40.1 8 family 8 381 zf C2H2 Zinc forger, C2H2 type 4.3e-06 33.7 383 Glyco transfGlycosyl transferase 0.0028 -40.1 8 family 8 SEQ PFAM NAME DESCRIPTION p-value PFAM
ID SCORE
NO:

384 RasGEF RasGEF domain 8.1 e-43 l 55.7 385 TBC TBC domain 0.017 -66.6 389 Glycos_transfGlycosyl transferases 1.3e-15 65.3 390 Na_Ca Ex Sodium/calcium exchanger3.9e-105 362.7 protein 391 fn3 Fibronectin type III 4.1e-102 352.6 domain 392 fn3 Fibronectin type III 3.4e-45 163.6 domain 393 fn3 Fibronectin type III 3.4e-45 163.6 domain 394 ldl_recept Low-density lipoprotein7.1e-49 175.8 b receptor repeat 395 Ribosomal_L30Ribosomal protein L30p/L7e0.0023 16.0 396 Oxysterol_BPOxysterol-binding protein1.5e-94 327.5 397 RDS_ROMl Peripherin/rom-1 2.9e-33 123.9 399 lactamase Metallo-beta-lactamase 3.4e-39 143.6 B superfamily 402 F-box F-box domain. 0.0002 28.1 403 CLP'proteaseClp protease 4.8e-64 226.2 405 Ribosomal_L35Ribosomal protein L35Ae6e-77 269.0 Ae 406 LIM LIM domain containing 0.00021 20.7 proteins 410 tRNA-synt_lctRNA synthetases class 1e-236 799.8 I (E and Q) 411 NTP_transf Nucleotidyltransferase 3.9e-16 67.0 2 domain 412 DEAD DEAD/DEAH box helicase 0.00016 17.2 414 DUF94 Domain of unknown function0.00011 26.9 415 tubulin Tubulin/FtsZ family 4.5e-289 973.7 420 SET SET domain 3.3e-57 203.5 421 WD40 WD domain, G-beta repeat6.1 e-29 109.6 423 zf C2H2 Zinc forger, C2H2 type 1.5e-39 144.9 424 pkinase Eukaryotic protein kinase8.9e-75 261.8 domain 428 LIM LIM domain containing 1.8e-34 126.7 proteins 431 kazal I~azal-type serine protease3.7e-18 73.8 inhibitor domain 432 SH2 Src homology domain 1.4e-67 198.4 433 zf C2H2 Zinc forger, C2H2 type 2.8e-144 492.7 434 ras Ras family 0.012 -106.8 436 El-E2_ATPaseE1-E2 ATPase 1.6e-117 391.0 437 RNA_pol RNA polymerase alpha 0 1077.7 A subunit 438 PHD PHD-forger 1.6e-11 51.7 439 lectin_c Lectin C-type domain 4.7e-30 113.3 440 zf C2H2 Zinc forger, C2H2 type 1.1 e-65 231.6 441 arrestin Arrestin (or S-antigen)2.9e-254 858.1 442 aminotran_3Aminotransferases class-III8.2e-80 231.1 pyridoxal-pho 443 UCH-1 Ubiquitin carboxyl-terminal8.5e-12 52.6 hydrolases famil 444 CTF_NFI CTF/NF-I family 2.6e-277 934.6 451 T-box T-box 3.8e-117 402.6 453 Rieske Rieske [2Fe-2S] domain 2.6e-13 57.7 454 zf C2H2 Zinc forger, C2H2 type 3.9e-64 226.5 456 homeobox Homeobox domain 2.8e-08 38.9 459 ig Immunoglobulin domain 2.6e-20 70.5 460 Hydrolase haloacid dehalogenase-like4e-25 96.9 " hydrolase 462 rve Integrase core domain 1.6e-13 50.7 466 CH Calponin homology (CH) 2.4e-17 71.1 domain 467 CH Calponin homology (CH) 2.4e-17 71.1 domain 468 Sterol_desatSterol desaturase 7.5e-38 139.2 469 pro isomeraseCyclophilin type peptidyl-prolyl2.6e-63 220.9 cis-470 Peptidase metallopeptidase family6e-08 28.1 471 PDZ PDZ domain (Also known 5.4e-129 441.9 as DHR or GLGF).

SEQ PFAM NAME DESCRIPTION p-value PFAM
ID SCORE
NO:

472 myb DNA- Myb-like DNA-binding 3.6e-06 33.9 binding domain 473 ZZ Zinc finger present 0.012 20.0 in dystrophin, CB

474 EF1G_domainElongation factor 1 6.3e-88 305.5 gamma, conserved doma 475 Ribosomal Ribosomal protein L3le 6.1e-66 232.5 L3le 476 Clq Clq domain 2.5e-75 263.7 477 SH3 SH3 domain 1.1e-12 55.6 478 MoaA_NifB_PqmoaA / nifB / pqqE family0.002 -17.7 qE

479 FYVE FYVE zinc forger 9.3e-21 78.6 480 DNA_pol_A DNA polymerase family 2.3e-46 167.4 A

482 adh_short short chain dehydrogenase1.2e-62 221.6 483 ank Ank repeat 1.3e-17 71.9 484 IMS impB/mucB/samB family 2.2e-83 290.5 486 TIR TIR domain 3.2e-19 67.8 487 FMO-like Flavin-binding monooxygenase-like0 1425.5 488 I_LWEQ I/LWEQ domain 9.5e-101 341.0 495 homeobox Homeobox domain 3.6e-06 30.8 497 pkinase Eukaryotic protein kinase2.3e-166 566.1 domain 499 fn3 Fibronectin type III 2.5e-237 801.8 domain 501 LRR Leucine Rich Repeat 9.3e-31 115.6 502 RGS Regulator of G protein 0.041 11.9 signaling domain 503 filament Intermediate filament 1e-142 487.5 proteins 505 fn3 Fibronectin type III 1.3e-100 347.7 domain 506 HECT HECT-domain (ubiquitin-1e-13 59.0 transferase).

507 Ribosomal_L7ARibosomal protein L7Ae 5.7e-26 99.7 a 508 WD40 WD domain, G-beta repeat0.063 19.8 509 WD40 WD domain, G-beta repeat0.063 19.8 510 WD40 WD domain, G-beta repeat2.1 e-42 154.3 511 pkinase Eukaryotic protein kinase2.3e-86 300.4 domain 512 G-gamma GGL domain 1.9e-08 34.3 513 SH3 SH3 domain 3e-06 34.2 515 HTH_AraC Bacterial regulatory 3.9e-27 103.6 helix-turn-helix protei 516 zf C2H2 Zinc forger, C2H2 type 1.7e-34 128.0 517 S 1 S 1 RNA binding domain 6.1 e-58 205.9 518 pkinase Eukaryotic protein kinase1.8e-75 264.2 domain 525 cadherin Cadherin domain 2e-80 280.6 528 zf C2H2 Zinc finger, C2H2 type 4e-70 246.4 529 neur_chan Neurotransmitter-gated 5.8e-222 750.8 ion-channel 531 RhoGEF RhoGEF domain 3.5e-44 160.2 532 myosin headMyosin head (motor domain)0 1494.5 533 LRR Leucine Rich Repeat 8.3e-15 62.6 535 Sec7 Sec7 domain 5.1e-92 319.1 536 homeobox Homeobox domain 4.8e-05 26.4 539 actin Actin 2.4e-100 330.6 542 ank Ank repeat 1.9e-35 131.2 544 zf CCCH Zinc forger C-x8-C-x5-C-x3-H2.8e-10 41.7 type 546 DSPc Dual specificity phosphatase,2.4e-40 147.4 catalytic doma 547 HMG CoA_syntHydroxymethylglutaryl-coenzyme0 1250.8 A
synthas 549 laminin Laminin G domain 3.3e-76 266.6 G

551 PHD PHD-forger 0.008 9.3 552 PDZ PDZ domain (Also known 0.0017 25.0 as DHR or 89 1073 2057 3041 787CIP2 9,1 7896 176. 1160 2144 3128 787CIP2 178 8157 ' l ~

' ~

~

618 1602 2586 3570 _269 7686 ~

620 1604 2588 3572 _271 7697 ~

~

624 1608 2592 3576 _275 7751 ~

~

~

629 1613 2597 3581 ' _280 7783 ~

631 1615 2599 3583 _282 7800 632 1616 2600 3584 787CIP2B~283 7801 ~

635 1619 2603 3587 _286 7821 641 1625 2609 3593 ~ 787CIP2B 293 7936 648 1632 2616 3600 787CIP2B 301 8029' jig 1703 687 3 671 787CIP2B 372 8698 735 1720 2704 3688 ?87CIP2B 389 9260 743 1727 2712 3696 _ 9382 , ?8? CIP2B

747 1?31 2716 3700 _ 9663 74g 1732 2717 3701 ' 787CIP2B 402 9715 749 1733 2718 3702 787CI1'2B 9755 787CIP2B~

764 1748 2732 _ 10246 767 175I 2735 3719 787CI1'2C_i 886 76g 1752 2736 3720 787CIP2C 2 1028 ' l ~

' ~

~

618 1602 2586 3570 _269 7686 ~

620 1604 2588 3572 _271 7697 ~

~

624 1608 2592 3576 _275 7751 ~

~

~

629 1613 2597 3581 ' _280 7783 ~

631 1615 2599 3583 _282 7800 632 1616 2600 3584 787CIP2B~283 7801 ~

635 1619 2603 3587 _286 7821 641 1625 2609 3593 ~ 787CIP2B 293 7936 648 1632 2616 3600 787CIP2B 301 8029' DEMANDE OU BREVET VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVET COMPREND
PLUS D'UN TOME.

~~ TTENANT LES PAGES 1 A 208 NOTE : Pour les tomes additionels, veuillez contacter 1e Bureau canadien des brevets JUMBO APPLICATIONS/PATENTS
THIS SECTION OF THE APPLICATION/PATENT CONTAINS MORE THAN ONE
VOLUME

NOTE: For additional volumes, please contact the Canadian Patent Office NOM DU FICHIER / FILE NAME
NOTE POUR LE TOME / VOLUME NOTE:

Claims (28)

WHAT IS CLAIMED IS:

1. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of SEQ ID N0:1-984, 1969-2952, 3937-3942 or 3949-3954, a full length protein coding portion of SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954, a mature protein coding portion of SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954, an active domain coding portion of SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954, 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: 1-984,1969-2952, 3937-3942 or 3949-3954.

11. A composition comprising the polypeptide of claim 10 and a carrier.

12. An antibody directed against the polypeptide of claim 10.

13. A method for detecting the polynucleotide of claim 1 in a sample, comprising:

a) contacting the sample with a compound that binds to and forms a complex with the polynucleotide of claim 1 for a period sufficient to form the complex; and b) detecting the complex, so that if a complex is detected, the polynucleotide of claim 1 is detected.

14. A method for detecting the polynucleotide of claim 1 in a sample, comprising:

a) contacting the sample under stringent hybridization conditions with nucleic acid primers that anneal to the polynucleotide of claim 1 under such conditions;

b) amplifying a product comprising at least a portion of the polynucleotide of claim 1; and c) detecting said product and thereby the polynucleotide of claim 1 in the sample.

15. The method of claim 14, wherein the polynucleotide is an RNA molecule and the method further comprises reverse transcribing an annealed RNA molecule into a cDNA
polynucleotide.

16. A method for detecting the polypeptide of claim 10 in a sample, comprising:

a) contacting the sample with a compound that binds to and forms a complex with the polypeptide under conditions and for a period sufficient to form the complex; and b) detecting formation of the complex, so that if a complex formation is detected, the polypeptide of claim 10 is detected.

17. A method for identifying a compound that binds to the polypeptide of claim 10, comprising:

a) contacting the compound with the polypeptide of claim 10 under conditions sufficient to form a polypeptide/compound complex; and b) detecting the complex, so that if the polypeptide/compound complex is detected, a compound that binds to the polypeptide of claim 10 is identified.

18. A method for identifying a compound that binds to the polypeptide of claim 10, comprising:

a) contacting the compound with the polypeptide of claim 10, in a cell, under conditions sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a reporter gene sequence in the cell; and b) detecting the complex by detecting reporter gene sequence expression, so that if the polypeptide/compound complex is detected, a compound that binds to the polypeptide of claim 10 is identified.

19. A method of producing the polypeptide of claim 10, comprising, a) culturing a host cell comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-984; 1969-2952, 3937-3942 or 3949-3954, a mature protein coding portion of SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954, an active domain coding portion of SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954, complementary sequences thereof and a polynucleotide sequence hybridizing under stringent conditions to SEQ ID NO: 1-984, 1969-2952, 3937-3942 or 3949-3954, 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: 985-1968, 2953-3936, 3943-3948 or 3955-3960, 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: 1-984, 1969-2952, 3937-3942 or 3949-3954.

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.