EP1220907A2 - Human secretory molecules - Google Patents

Human secretory molecules

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Publication number
EP1220907A2
EP1220907A2 EP00965128A EP00965128A EP1220907A2 EP 1220907 A2 EP1220907 A2 EP 1220907A2 EP 00965128 A EP00965128 A EP 00965128A EP 00965128 A EP00965128 A EP 00965128A EP 1220907 A2 EP1220907 A2 EP 1220907A2
Authority
EP
European Patent Office
Prior art keywords
oct
polynucleotide
sptm
dec
sequence
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP00965128A
Other languages
German (de)
French (fr)
Inventor
David M. Hodgson
Stephen E Lincoln
Frank D Russo
Peter A. Spiro
Steven C Banville
Shawn R Bratcher;
Gerard F Dufour
Howard J Cohen
Bruce H Rosen
Purvi Shah
Michael S Chalup
Jennifer L Hillman
Anissa Lee Jones
Jimmy Y Yu
Lila B Greenawalt
Scott R Panzer
Ann M Roseberry
Rachel J Wright
Wensheng Chen
Tommy F Liu
Pierre E Yap
Theresa K Stockdreher
Stefan Amshey
Willy T Fong
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Incyte Corp
Original Assignee
Incyte Genomics Inc
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Filing date
Publication date
Application filed by Incyte Genomics Inc filed Critical Incyte Genomics Inc
Publication of EP1220907A2 publication Critical patent/EP1220907A2/en
Withdrawn legal-status Critical Current

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Classifications

    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705Receptors; Cell surface antigens; Cell surface determinants
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01KANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00Genetically modified animals
    • A01K2217/05Animals comprising random inserted nucleic acids (transgenic)
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00Medicinal preparations containing peptides

Definitions

  • the present invention relates to secretory molecules and to the use of these sequences in the diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, cell signaling and the expression of secretory molecules.
  • Protein transport and secretion are essential for cellular function. Protein transport is mediated by a signal peptide located at the amino terminus of the protein to be transported or secreted.
  • the signal peptide is comprised of about ten to twenty hydrophobic amino acids which target the nascent protein from the ribosome to a particular membrane bound compartment such as the endoplasmic reticulum (ER). Proteins targeted to the ER may either proceed through the secretory pathway or remain in any of the secretory organelles such as the ER, Golgi apparatus, or lysosomes. Proteins that transit through the secretory pathway are either secreted into the extracellular space or retained in the plasma membrane.
  • Proteins that are retained in the plasma membrane contain one or more transmembrane domains, each comprised of about 20 hydrophobic amino acid residues.
  • Proteins that are secreted from the cell are generally synthesized as inactive precursors that are activated by post- translational processing events during transit through the secretory pathway. Such events include glycosylation, proteolysis, and removal of the signal peptide by a signal peptidase.
  • Other events that may occur during protein transport include chaperone-dependent unfolding and folding of the nascent protein and interaction of the protein with a receptor or pore complex. Examples of secretory proteins with amino terminal signal peptides are discussed below and include proteins with important roles in cell-to-cell signaling.
  • Such proteins include transmembrane receptors and cell surface markers, extracellular matrix molecules, cytokines, hormones, growth and differentiation factors, neuropeptides, vasomediators, ion channels, transporters/pumps, and proteases. (Reviewed in Alberts, B. et al. (1994) Molecular Biology of The Cell. Garland Publishing, New York, NY, pp. 557-560, 582-592.)
  • GPCRs G-protein coupled receptors
  • GPCRs comprise a superfamily of integral membrane proteins which transduce extracellular signals. Not all GPCRs contain N-terminal signal peptides. GPCRs include receptors for biogenic amines such as dopamine, epinephrine, histamine, glutamate
  • lipid mediators of inflammation such as prostaglandins, platelet activating factor, and leukotrienes
  • peptide hormones such as calcitonin, C5a anaphylatoxin, follicle stimulating hormone, gonadotropin releasing hormone, neurokinin, oxytocin, and thrombin
  • sensory signal mediators such as retinal photopigments and olfactory stimulatory molecules.
  • the structure of these highly conserved receptors consists of seven hydrophobic transmembrane regions, cysteine disulfide bridges between the second and third extracellular loops, an extracellular N-terminus, and a cytoplasmic C-terminus.
  • the N-terminus interacts with ligands
  • the disulfide bridges interact with agonists and antagonists
  • the large third intracellular loop interacts with G proteins to activate second messengers such as cyclic AMP, 5 phospholipase C, inositol triphosphate, or ion channels.
  • receptors include cell surface antigens identified on leukocytic cells of the immune system. These antigens have been identified using systematic, monoclonal antibody (mAb)- o based "shot gun” techniques. These techniques have resulted in the production of hundreds of mAbs directed against unknown cell surface leukocytic antigens. These antigens have been grouped into "clusters of differentiation” based on common immunocytochemical localization patterns in various differentiated and undifferentiated leukocytic cell types.
  • mAb monoclonal antibody
  • CD antigens in a given cluster are presumed to identify a single cell surface protein and are assigned a "cluster of differentiation" or "CD" 5 designation.
  • Some of the genes encoding proteins identified by CD antigens have been cloned and verified by standard molecular biology techniques.
  • CD antigens have been characterized as both transmembrane proteins and cell surface proteins anchored to the plasma membrane via covalent attachment to fatty acid-containing glycolipids such as glycosylphosphatidylinositol (GPI). (Reviewed in Barclay, A. N. et al. (1995) The Leucocyte Antigen Facts Book. Academic Press, San Diego, CA, 0 pp. 17-20.)
  • MPs Matrix proteins
  • the expression and balance of MPs may be perturbed by biochemical changes that result from congenital, epigenetic, or infectious diseases.
  • MPs affect 5 leukocyte migration, proliferation, differentiation, and activation in the immune response.
  • MPs are frequently characterized by the presence of one or more domains which may include collagen-like domains, EGF-like domains, immunoglobulin-like domains, and fibronectin-like domains.
  • MPs may be heavily glycosylated and may contain an Arginine-Glycine-Aspartate (RGD) tripeptide motif which may play a role in adhesive interactions.
  • MPs include extracellular proteins such as o fibronectin, collagen, galectin, vitronectin and its proteolytic derivative somatomedin B ; and cell adhesion receptors such as cell adhesion molecules (CAMs), cadherins, and integrins.
  • Cytokines are secreted by hematopoietic cells in response to injury or infection. Interleukins, neurotrophins, growth factors, interferons, and chemokines all define cytokine families that work in conjunction with cellular receptors to regulate cell proliferation and differentiation. In addition, cytokines effect activities such as leukocyte migration and function, hematopoietic cell proliferation, temperature regulation, acute response to infection, tissue remodeling, and apoptosis.
  • Chemokines are small chemoattractant cytokines involved in inflammation, leukocyte proliferation and migration, angiogenesis and angiostasis, regulation of hematopoiesis, HIV infectivity, and stimulation of cytokine secretion.
  • Chemokines generally contain 70-100 amino acids and are subdivided into four subfamilies based on the presence of conserved cysteine-based motifs. (Callard, R. and Gearing, A. (1994) The Cytokine Facts Book, Academic Press, New York, NY, pp. 0 181-190, 210-213, 223-227.)
  • Growth and differentiation factors are secreted proteins which function in intercellular communication. Some factors require oligomerization or association with MPs for activity. Complex interactions among these factors and their receptors trigger intracellular signal transduction pathways that stimulate or inhibit cell division, cell differentiation, cell signaling, and cell motility. Most growth 5 and differentiation factors act on cells in their local environment (paracrine signaling).
  • the first class includes the large polypeptide growth factors such as epidermal growth factor, fibroblast growth factor, transforming growth factor, insulin-like growth factor, and platelet-derived growth factor.
  • the second class includes the hematopoietic growth factors such as the colony stimulating factors (CSFs).
  • CSFs colony stimulating factors
  • Hematopoietic growth o factors stimulate the proliferation and differentiation of blood cells such as B-lymphocytes, T- lymphocytes, erythrocytes, platelets, eosinophils, basophils, neutrophils, macrophages, and their stem cell precursors.
  • the third class includes small peptide factors such as bombesin, vasopressin, oxytocin, endothelin, transferrin, angiotensin II, vasoactive intestinal peptide, and bradykinin which function as hormones to regulate cellular functions other than proliferation. 5 Growth and differentiation factors play critical roles in neoplastic transformation of cells in vitro and in tumor progression in vivo.
  • Inappropriate expression of growth factors by tumor cells may contribute to vascularization and metastasis of tumors.
  • growth factor misregulation can result in anemias, leukemias, and lymphomas.
  • Certain growth factors such as interferon are cytotoxic to tumor cells both in vivo and in vitro.
  • some growth factors and o growth factor receptors are related both structurally and functionally to oncoproteins.
  • growth factors affect transcriptional regulation of both proto-oncogenes and oncosuppressor genes. (Reviewed in Pimentel, E. (1994) Handbook of Growth Factors. CRC Press, Ann Arbor, MI, pp.
  • Proteolytic enzymes or proteases either activate or deactivate proteins by hydrolyzing peptide bonds.
  • Proteases are found in the cytosol, in membrane-bound compartments, and in the extracellular 5 space. The major families are the zinc, serine, cysteine, thiol, and carboxyl proteases.
  • Ion channels,, ion pumps, and transport proteins mediate the transport of molecules across cellular -membranes. Transport can occur by a passive, concentration-dependent mechanism or can be linked to an energy source such as ATP hydrolysis.
  • Symporters and antiporters transport ions and small molecules such as amino acids, glucose, and drugs.
  • Symporters transport molecules and ions unidirectionally, and antiporters transport molecules and ions bidirectionally.
  • Transporter superfamilies include facilitative transporters and active ATP-binding cassette transporters which are involved in multiple-drug resistance and the targeting of antigenic peptides to MHC Class I molecules. These transporters bind to a specific ion or other molecule and undergo a conformational change in order to transfer the ion or molecule across the membrane.
  • Ion channels are formed by transmembrane proteins which create a lined passageway across the membrane through which water and ions, such as Na + , K + , Ca 2+ , and CI " , enter and exit the cell.
  • chloride channels are involved in the regulation of the membrane electric potential as well as absorption and secretion of ions across the membrane. Chloride channels also regulate the internal pH of membrane-bound organelles.
  • Ion pumps are ATPases which actively maintain membrane gradients. Ion pumps are classified as P, V, or F according to their structure and function. All have one or more binding sites for ATP in their cytosolic domains.
  • the P-class ion pumps include Ca 2+ ATPase and Na7K + ATPase and function in transporting H + , Na + , K + , and Ca 2+ ions.
  • P-class pumps consist of two ⁇ and two ⁇ transmembrane subunits.
  • the V- and F-class ion pumps have similar structures but transport only H + .
  • F class H + pumps mediate transport across the membranes of mitochondria and chloroplasts, while V-class H + pumps regulate acidity inside lysosomes, endosomes, and plant vacuoles.
  • the proteins in this family contain a highly conserved, large transmembrane domain comprised of 12 ⁇ -helices, and several weakly conserved, cytoplasmic and exoplasmic domains. (Pessin, J. E., and Bell, G.I. (1992) Annu. Rev. Physiol. 54:911-930.)
  • Amino acid transport is mediated by Na + dependent amino acid transporters. These transporters are involved in gastrointestinal and renal uptake of dietary and cellular amino acids and in neuronal reuptake of neurotransmitters. Transport of cationic amino acids is mediated by the system y+ family and the cationic amino acid transporter (CAT) family. Members of the CAT family share a high degree of sequence homology, and each contains 12-14 putative transmembrane domains. (Ito, K. and Groudine, M. (1997) J. Biol. Chem. 272:26780-26786.)
  • Hormones are secreted molecules that travel through the circulation and bind to specific receptors on the surface of, or within, target cells. Although they have diverse biochemical compositions and mechanisms of action, hormones can be grouped into two categories.
  • One category includes small lipophilic hormones that diffuse through the plasma membrane of target cells, bind to cytosolic or nuclear receptors, and form a complex that alters gene expression. Examples of these molecules include retinoic acid, thyroxine, and the cholesterol-derived steroid hormones such as progesterone, estrogen, testosterone, cortisol, and aldosterone.
  • the second category includes hydrophilic hormones that function by binding to cell surface receptors that transduce signals across the plasma membrane.
  • hormones include amino acid derivatives such as catecholamines and peptide hormones such as glucagon, insulin, gastrin, secretin, cholecystokinin, adrenocorticotropic hormone, follicle stimulating hormone, luteinizing hormone, thyroid stimulating hormone, and vasopressin.
  • catecholamines amino acid derivatives
  • peptide hormones such as glucagon, insulin, gastrin, secretin, cholecystokinin, adrenocorticotropic hormone, follicle stimulating hormone, luteinizing hormone, thyroid stimulating hormone, and vasopressin.
  • Neuropeptides and vasomediators comprise a large family of endogenous signaling molecules. Included in this family are neuropeptides and neuropeptide hormones such as bombesin, neuropeptide Y, neurotensin, neuromedin N, melanocortins, opioids, galanin, somatostatin, tachykinins, urotensin II and related peptides involved in smooth muscle stimulation, vasopressin, vasoactive intestinal peptide, and circulatory system-borne signaling molecules such as angiotensin, complement, calcitonin, endothelins, formyl-methionyl peptides, glucagon, cholecystokinin and gastrin.
  • neuropeptides and neuropeptide hormones such as bombesin, neuropeptide Y, neurotensin, neuromedin N, melanocortins, opioids, galanin, somatostatin, tachykinins,
  • NP/VMs can transduce signals directly, modulate the activity or release of other neurotransmitters and hormones, and act as catalytic enzymes in cascades.
  • the effects of NP/VMs range from extremely brief to long- lasting. (Reviewed in Martin, C. R. et al. (1985) Endocrine Physiology. Oxford University Press. New York, NY, pp. 57-62.)
  • the present invention relates to nucleic acid sequences comprising human polynucleotides encoding secretory polypeptides that contain signal peptides and/or transmembrane domains.
  • human polynucleotides as presented in the Sequence Listing uniquely identify partial or full length genes encoding structural, functional, and regulatory polypeptides involved in cell signaling.
  • the invention provides an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63.
  • the polynucleotide comprises at least 60 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • the invention further provides a composition for the detection of expression of secretory polynucleotides comprising at least one isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d); and a detectable label.
  • a composition for the detection of expression of secretory polynucleotides comprising at least one isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleot
  • the invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -63 ; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • the method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.
  • the probe comprises at least 30 contiguous nucleotides.
  • the probe comprises at least 60 contiguous nucleotides.
  • the invention further provides a recombinant polynucleotide comprising a promoter sequence operably linked to an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -
  • the invention provides a cell transformed with the recombinant polynucleotide.
  • the invention provides a transgenic organism comprising the recombinant polynucleotide.
  • the invention provides a method for producing a secretory polypeptide, the method comprising a) culturing a cell under conditions suitable for expression of the secretory polypeptide, wherein said cell is transformed with the recombinant polynucleotide, and b) recovering the secretory polypeptide so expressed.
  • the invention also provides a purified secretory polypeptide (SPTM) encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63. Additionally, the invention provides an isolated antibody which specifically binds to the secretory polypeptide.
  • SPTM purified secretory polypeptide
  • the invention further provides a method of identifying a test compound which specifically binds to the secretory polypeptide, the method comprising the steps of a) providing a test o compound; b) combining the secretory polypeptide with the test compound for a sufficient time and under suitable conditions for binding; and c) detecting binding of the secretory polypeptide to the test compound, thereby identifying the test compound which specifically binds the secretory polypeptide.
  • the invention further provides a microarray wherein at least one element of the microarray is an isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide comprising 5 a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • the invention also provides a method o for generating a transcript image of a sample which contains polynucleotides.
  • the method comprises a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
  • the invention provides a method for screening a compound for effectiveness in 5 altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence o complementary to b); and e) an RNA equivalent of a) through d).
  • the method comprises a) exposing a sample comprising the target polynucleotide to a compound, and b) detecting altered expression of the target polynucleotide.
  • the invention further provides a method for assessing toxicity of a test compound, said method comprising a) treating a biological sample containing nucleic acids with the test compound; b) 5 hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide comprising a polynucleotide sequence selected from the group consisting of i) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1- 63; ii) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; iii) a polynucleotide 5 sequence complementary to i), iv) a polynucleotide sequence complementary to ii), and v) an RNA equivalent of i)-iv).
  • Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of i) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; ii) a naturally o occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; iii) a polynucleotide sequence complementary to i), iv) a polynucleotide sequence complementary to ii), and v) an RNA equivalent of i)-iv), and alternatively, the target polynucleotide comprises a fragment of a polynucleotide sequence selected from the group consisting of i-v above; c) quantifying the amount of hybridization complex; 5 and
  • Table 1 shows the sequence identification numbers (SEQ ID NO:s) and template identification o numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated “start” and “stop” nucleotide positions.
  • the reading frames of the polynucleotide segments are shown, and the polypeptides encoded by the polynucleotide segments constitute either signal peptide (SP) or transmembrane (TM) domains, as indicated.
  • SP signal peptide
  • TM transmembrane
  • Table 2 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with component sequence identification numbers (component IDs) corresponding to each template.
  • the component sequences, which were used to assemble the template sequences, are defined by the indicated “start” and "stop” nucleotide positions along each template.
  • Table 3 shows the tissue distribution profiles for the templates of the invention.
  • Table 4 summarizes the bioinformatics tools which are useful for analysis of the polynucleotides of the present invention.
  • the first column of Table 4 lists analytical tools, programs, and algorithms, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incorporated by reference herein in their entirety, and the fourth 5 column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences).
  • sptm refers to a nucleic acid sequence
  • SPTM amino acid sequence encoded by sptm
  • a “full-length” sptm refers to a nucleic acid sequence containing the entire coding region of a gene endogenously expressed in human tissue.
  • adjuvants are materials such as Freund's adjuvant, mineral gels (aluminum hydroxide), and surface active substances (lysolecithin, pluro ic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol) which may be administered to increase a host's immunological response.
  • Alleles refers to an alternative form of a nucleic acid sequence. Alleles result from a “mutation,” a change or an alternative reading of the genetic code. Any given gene may have none, one, or many allelic forms. Mutations which give rise to alleles include deletions, additions, or substitutions of nucleotides. Each of these changes may occur alone, or in combination with the others, one or more times in a given nucleic acid sequence.
  • the present invention encompasses allelic sptm.
  • amino acid sequence refers to a peptide, a polypeptide, or a protein of either natural or synthetic origin.
  • the amino acid sequence is not limited to the complete, endogenous amino acid sequence and may be a fragment, epitope, variant, or derivative of a protein expressed by a nucleic acid sequence.
  • “Amplification” refers to the production of additional copies of a sequence and is carried out using polymerase chain reaction (PCR) technologies well known in the art.
  • “Antibody” refers to intact molecules as well as to fragments thereof, such as Fab, F(ab') 2> and Fv fragments, which are capable of binding the epitopic determinant.
  • Antibodies that bind SPTM polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen.
  • the polypeptide or peptide used to immunize an animal can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired.
  • a carrier protein e.g., bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH).
  • KLH keyhole limpet hemocyanin
  • Antisense sequence refers to a sequence capable of specifically hybridizing to a target sequence.
  • the antisense sequence may include DNA, RNA, or any nucleic acid mimic or analog such as peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2'-methoxyethyl sugars or 2'-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5 -methyl cytosine, 2'-deoxyuracil, or 7-deaza-2'-deoxyguanosine.
  • PNA peptide nucleic acid
  • Antisense sequence refers to a sequence capable of specifically hybridizing to a target sequence.
  • the antisense sequence can be DNA, RNA, or any nucleic acid mimic or analog.
  • Antisense technology refers to any technology which relies on the specific hybridization of an antisense sequence to a target sequence.
  • a “bin” is a portion of computer memory space used by a computer program for storage of data, and bounded in such a manna- that data stored in a bin may be retrieved by the program.
  • “Biologically active” refers to an amino acid sequence having a structural, regulatory, or biochemical function of a naturally occurring amino acid sequence.
  • “Clone joining” is a process for combining gene bins based upon the bins' containing sequence information from the same clone.
  • the sequences may assemble into a primary gene transcript as well as one or more splice variants.
  • “Complementary” describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing (5'-A-G-T-3' pairs with its complement 3'-T-C-A-5') *
  • a “component sequence” is a nucleic acid sequence selected by a computer program such as
  • a "consensus sequence” or “template sequence” is a nucleic acid sequence which has been assembled from overlapping sequences, using a computer program for fragment assembly such as the
  • GEL VIEW fragment assembly system (Genetics Computer Group (GCG), Madison WT) or using a relational database management system (RDMS).
  • GCG Genetics Computer Group
  • RDMS relational database management system
  • Constant amino acid substitutions are those substitutions that, when made, least interfere with the properties of the original protein, i.e. , the structure and especially the function of the protein is conserved and not significantly changed by such substitutions.
  • the table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.
  • Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
  • “Deletion” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or amino acid residue, respectively, is absent. “Derivative” refers to the chemical modification of a nucleic acid sequence, such as by replacement of hydrogen by an alkyl, acyl, amino, hydroxyl, or other group.
  • array element refers to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray.
  • ⁇ -value refers to the statistical probability that a match between two sequences occurred by chance.
  • a “fragment” is a unique portion of sptm or SPTM which is identical in sequence to but shorter in length than the parent sequence.
  • a fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue.
  • a fragment may comprise from 10 to 1000 contiguous amino acid residues or nucleotides.
  • a fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, may be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous amino acid residues or nucleotides in length. Fragments may be preferentially selected from certain regions of a molecule.
  • a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence.
  • these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing and the 5 figures, may be encompassed by the present embodiments.
  • a fragment of sptm comprises a region of unique polynucleotide sequence that specifically identifies sptm, for example, as distinct from any other sequence in the same genome.
  • a fragment of sptm is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish sptm from related polynucleotide sequences.
  • the precise length of a fragment of sptm o and the region of sptm to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
  • a fragment of SPTM is encoded by a fragment of sptm.
  • a fragment of SPTM comprises a region of unique amino acid sequence that specifically identifies SPTM.
  • a fragment of SPTM is useful as an immunogenic peptide for the development of antibodies that specifically 5 recognize SPTM.
  • the precise length of a fragment of SPTM and the region of SPTM to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
  • a “full length” nucleotide sequence is one containing at least a start site for translation to a protein sequence, followed by an open reading frame and a stop site, and encoding a "full length” 0 polypeptide.
  • “Hit” refers to a sequence whose annotation will be used to describe a given template. Criteria for selecting the top hit are as follows: if the template has one or more exact nucleic acid matches, the top hit is the exact match with highest percent identity. If the template has no exact matches but has significant protein hits, the top hit is the protein hit with the lowest E- value. If the template has no 5 significant protein hits, but does have significant non-exact nucleotide hits, the top hit is the nucleotide hit with the lowest E- value.
  • Homology refers to sequence similarity either between a reference nucleic acid sequence and at least a fragment of an sptm or between a reference amino acid sequence and a fragment of an SPTM.
  • Hybridization refers to the process by which a strand of nucleotides anneals with a o complementary strand through base pairing. Specific hybridization is an indication that two nucleic acid sequences share a high degree of identity. Specific hybridization complexes form under defined annealing conditions, and remain hybridized after the "washing" step.
  • the defined hybridization conditions include the annealing conditions and the washing step(s), the latter of which is particularly important in determining the stringency of the hybridization process, with more stringent conditions 5 allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched.
  • Permissive conditions for annealing of nucleic acid sequences are routinely determinable and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency.
  • stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out.
  • wash temperatures are selected to be about 5°C to 20°C lower than the thermal melting point (T for the specific sequence at a defined ionic strength and pH.
  • T m is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe.
  • High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68°C in the presence of about 0.2 x SSC and about 0.1% SDS, for 1 hour. Alternatively, temperatures of about 65°C, 60°C, or 55°C may be used. SSC concentration may be varied from about 0.2 to 2 x SSC, with SDS being present at about 0.1 %.
  • blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 ⁇ g/ml. Useful variations on these conditions will be readily apparent to those skilled in the art.
  • Hybridization, particularly undo- high stringency conditions may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their resultant proteins.
  • RNA:DNA hybridizations RNA:DNA hybridizations. Appropriate hybridization conditions are routinely determinable by one of ordinary skill in the art. "Immunogenic” describes the potential for a natural, recombinant, or synthetic peptide, epitope, polypeptide, or protein to induce antibody production in appropriate animals, cells, or cell lines.
  • “Insertion” or “addition” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or residue, respectively, is added to the sequence.
  • Labeling refers to the covalent or noncovalent joining of a polynucleotide, polypeptide, or antibody with a reporter molecule capable of producing a detectable or measurable signal.
  • “Microarray” is any arrangement of nucleic acids, amino acids, antibodies, etc., on a substrate.
  • the substrate may be a solid support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.
  • Linkers are short stretches of nucleotide sequence which may be added to a vector or an sptm to create restriction endonuclease sites to facilitate cloning.
  • PolyUnkers are engineered to incorporate multiple restriction enzyme sites and to provide for the use of enzymes which leave 5 ' or 3' overhangs (e.g., BamHI, EcoRI, and Hindlll) and those which provide blunt ends (e.g., EcoRV, SnaBI, and Stul).
  • Nucleic acid sequence refers to the specific order of nucleotides joined by phosphodiester bonds in a linear, polymeric arrangement. Depending on the number of nucleotides, the nucleic acid sequence can be considered an oligomer, ohgonucleotide, or polynucleotide.
  • the nucleic acid can be DNA, RNA, or any nucleic acid analog, such as PNA, may be of genomic or synthetic origin, may be either double-stranded or single-stranded, and can represent either the sense or antisense 0 (complementary) strand.
  • Oligomers refers to a nucleic acid sequence of at least about 6 nucleotides and as many as about 60 nucleotides, preferably about 15 to 40 nucleotides, and most preferably between about 20 and 30 nucleotides, that may be used in hybridization or amplification technologies. Oligomers may be used as, e.g., primers for PCR, and are usually chemically synthesized. 5 "Operably linked” refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence.
  • operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.
  • PNA protein nucleic acid
  • PNAs refers to a DNA mimic in which nucleotide bases are attached to a pseudopeptide backbone to increase stability. PNAs, also designated antigene agents, can prevent gene expression by targeting complementary messenger RNA.
  • percent identity and % identity refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a 5 standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.
  • NCBI National Center for Biotechnology Information
  • BLAST Basic Local Alignment Search 5 Tool
  • NCBI National Center for Biotechnology Information
  • BLAST Basic Local Alignment Search 5 Tool
  • the BLAST software suite includes various sequence analysis programs including "blastn,” that is used to determine alignment between a known polynucleotide sequence and other sequences on a variety of databases.
  • BLAST 2 0 Sequences are used for direct pairwise comparison of two nucleotide sequences.
  • BLAST 2 Sequences can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/bl2/.
  • the "BLAST 2 Sequences” tool can be used for both blastn and blastp (discussed below).
  • BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the "BLAST 2 Sequences" tool Version 5 2.0.9 (May-07-1999) set at default parameters. Such default parameters may be, for example:
  • Percent identity may be measured over the length of an entire defined sequence, for example, as 5 defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides.
  • Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage o identity may be measured.
  • Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.
  • the phrases "percent identity” and "% identity”, as applied to polypeptide sequences refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the hydrophobicity and acidity of the substituted residue, thus preserving the structure (and therefore function) of the folded polypeptide.
  • NCBI BLAST software suite may be used.
  • BLAST 2 Sequences Version 2.0.9 (May-07-1999) with blastp set at default parameters.
  • Such default parameters may be, for example:
  • Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues.
  • Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.
  • Post-translational modification of an SPTM may involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu and the SPTM.
  • Probe refers to sptm or fragments thereof, which are used to detect identical, allelic or related nucleic acid sequences.
  • Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes.
  • Primmers are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification 5 (and identification) of a nucleic acid sequence, e.g Chandler by the polymerase chain reaction (PCR).
  • PCR polymerase chain reaction
  • Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30, 40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may 0 be considerably longer than these examples, and it is understood that any length supported by the specification, including the figures and Sequence Listing, may be used.
  • PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge MA).
  • Oligonucleotides for use as primers are selected using software known in the art for such o purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South 5 West Medical Center, Dallas TX) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope.
  • the Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge MA) allows the user to input a "mispriming library," in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for o microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.)
  • the PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences.
  • this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments.
  • the oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of ohgonucleotide selection are not limited to 5 those described above.
  • “Purified” refers to molecules, either polynucleotides or polypeptides that are isolated or separated from their natural environment and are at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other compounds with which they are naturally associated.
  • a "recombinant nucleic acid” is a sequence that is not naturally occurring or has a sequence o that is made by an artificial combination of two or more otherwise separated segments of sequence.
  • This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra.
  • the term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid.
  • a 5 recombinant nucleic acid may include a nucleic acid sequence operably hnked to a promoter sequence.
  • Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.
  • such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.
  • a viral vector e.g., based on a vaccinia virus
  • regulatory element refers to a nucleic acid sequence from nontranslated regions of a gene, and includes enhancers, promoters, introns, and 3' untranslated regions, which interact with host proteins to carry out or regulate transcription or translation.
  • Reporter molecules are chemical or biochemical moieties used for labeling a nucleic acid, an amino acid, or an antibody. They include radionuclides; enzymes; fluorescent, chemiluminescent, or 5 chromogenic agents; substrates; cof actors; inhibitors; magnetic particles; and other moieties known in the art.
  • RNA equivalent in reference to a DNA sequence, is composed of the same linear sequence of nucleotides as the reference DNA sequence with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose o instead of deoxyribose.
  • Sample is used in its broadest sense. Samples may contain nucleic or amino acids, antibodies, or other materials, and may be derived from any source (e.g., bodily fluids including, but not limited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots 5 or imprints from such cells or tissues).
  • Source e.g., bodily fluids including, but not limited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots 5 or imprints from such cells or tissues.
  • Specific binding or “specifically binding” refers to the interaction between a protein or peptide and its agonist, antibody, antagonist, or other binding partner.
  • the interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope "A,” the presence of a polypeptide containing epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.
  • Substitution refers to the replacement of at least one nucleotide or amino acid by a different nucleotide or amino acid.
  • Substrate refers to any suitable rigid or semi-rigid support including, e.g., membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles or capillaries.
  • the substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.
  • a “transcript image” refers to the collective pattern of gene expression by a particular tissue or cell type under given conditions at a given time.
  • Transformation refers to a process by which exogenous DNA enters a recipient cell. Transformation may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed.
  • Transformants include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as cells which transiently express inserted DNA or RNA.
  • a "transgenic organism,” as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art.
  • the nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus.
  • the term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule.
  • the transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, and plants and animals.
  • the isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), supra.
  • a "variant" of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 25% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07-1999) set at default parameters.
  • Such a pair of nucleic acids may show, for example, at least 30%, at least 5 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or even at least 98% or greater sequence identity over a certain defined length.
  • the variant may result in "conservative" amino acid changes which do not affect structural and/or chemical properties.
  • a variant may be described as, for example, an "allelic” (as defined above), “splice,” “species,” or “polymorphic” variant.
  • a splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser o number of polynucleotides due to alternate splicing of exons during mRNA processing.
  • the corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule.
  • Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other.
  • a polymorphic variant is a variation in the polynucleotide sequence of a particular gene between 5 individuals of a given species.
  • Polymorphic variants also may encompass "single nucleotide polymorphisms" (SNPs) in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
  • variants of the polynucleotides of the present invention may be generated o through recombinant methods.
  • One possible method is a DNA shuffling technique such as
  • MOLECULARBREEDING (Maxygen Inc., Santa Clara CA; described in U.S. Patent Number 5,837,458; Chang, C.-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F.C. et al. (1999) Nat. Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol. 14:315-319) to alter or improve the biological properties of SPTM, such as its biological or enzymatic activity or its ability to bind to 5 other molecules or compounds.
  • DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments.
  • the library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and further subjected to recursive rounds of DNA shuffling and selection/screening.
  • genetic diversity is created through "artificial" breeding and rapid molecular o evolution. For example, fragments of a single gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner.
  • a "variant" of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07- 1999) set at default parameters.
  • Such a pair of polypeptides may show, for example, at least 50%, at 5 least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% or greater sequence identity over a certain defined length of one of the polypeptides.
  • cDNA sequences derived from human tissues and cell lines were aligned based on nucleotide sequence identity and assembled into "consensus” or "template” sequences o which are designated by the template identification numbers (template IDs) in column 2 of Table 1.
  • sequence identification numbers corresponding to the template IDs are shown in column 1. Segments of the template sequences are defined by the "start” and “stop” nucleotide positions listed in columns 3 and 4. These segments, when translated in the reading frames indicated in column 5, have similarity to signal peptide (SP) or transmembrane (TM) domain consensus sequences, 5 as indicated in column 6.
  • the invention incorporates the nucleic acid sequences of these templates as disclosed in the Sequence Listing and the use of these sequences in the diagnosis and treatment of disease states characterized by defects in cell signaling.
  • the invention further utilizes these sequences in hybridization and amplification technologies, and in particular, in technologies which assess gene expression patterns o correlated with specific cells or tissues and their responses in vivo or in vitro to pharmaceutical agents, toxins, and other treatments.
  • the sequences of the present invention are used to develop a transcript image for a particular cell or tissue.
  • Derivation of Nucleic Acid Sequences cDNA was isolated from libraries constructed using RNA derived from normal and diseased 5 human tissues and cell lines.
  • the human tissues and cell lines used for cDNA Ubrary construction were selected from a broad range of sources to provide a diverse population of " cDNAs representative of gene transcription throughout the human body. Descriptions of the human tissues and cell lines used for cDNA Ubrary construction are provided in the LIFESEQ database (Incyte Genomics, Inc. (Incyte), Palo Alto CA). Human tissues were broadly selected from, for example, cardiovascular, dermatologic, 0 endocrine, gastrointestinal, hematopoietic/immune system, musculoskeletal, neural, reproductive, and urologic sources.
  • Cell Unes used for cDNA library construction were derived from, for example, leukemic cells, teratocarcinomas, neuroepitheUomas, cervical carcinoma, lung fibroblasts, and endotheUal cells.
  • Such cell Unes include, for example, THP-1, lurkat, HUVEC, hNT2, WI38, HeLa, and other cell Unes 5 commonly used and available from pubUc depositories (American Type Culture Collection, Manassas VA).
  • cell Unes Prior to mRNA isolation, cell Unes were untreated, treated with a pharmaceutical agent such as 5'-aza-2'-deoxycytidine, treated with an activating agent such as lipopolysaccharide in the case of leukocytic cell Unes, or, in the case of endotheUal cell Unes, subjected to shear stress.
  • Sequencing of the cDNAs Methods for DNA sequencing are well known in the art. Conventional enzymatic methods employ the Klenow fragment of DNA polymerase I, SEQUENASE DNA polymerase (U.S. Biochemical Corporation, Cleveland OH), Taq polymerase (PE Biosystems, Foster City CA), thermostable T7 polymerase (Amersham Pharmacia Biotech, Inc.
  • Chain termination reaction products may be electrophoresed on urea-polyacrylamide gels and detected either by autoradiography (for radioisotope-labeled nucleotides) or by fluorescence (for fluorophore-labeled nucleotides).
  • Machines used to prepare cDNAs for sequencing can include the MICROLAB 2200 Uquid transfer system (Hamilton Company (Hamilton), Reno NV), Peltier thermal cycler (PTC200; MJ Research, Inc. (MJ Research), Watertown MA), and ABI CATALYST 800 thermal cycler (PE Biosystems). Sequencing can be carried out using, for example, the ABI 373 or 377 (PE Biosystems) or MEGABACE 1000 (Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale CA) DNA sequencing systems, or other automated and manual sequencing systems well known in the art.
  • ABI 373 or 377 PE Biosystems
  • MEGABACE 1000 Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale CA
  • nucleotide sequences of the Sequence Listing have been prepared by current, state-of-the- art, automated methods and, as such, may contain occasional sequencing errors or unidentified nucleotides. Such unidentified nucleotides are designated by an N. These infrequent unidentified bases do not represent a hindrance to practicing the invention for those skilled in the art.
  • Several methods employing standard recombinant techniques may be used to correct errors and complete the missing sequence information. (See, e.g., those described in Ausubel, F.M. et al. (1997) Short Protocols in Molecular Biology. John Wiley & Sons, New York NY; and Sambrook, J. et al. (1989) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Press, Plainview NY.)
  • Human polynucleotide sequences may be assembled using programs or algorithms well known in the art. Sequences to be assembled are related, wholly or in part, and may be derived from a single or many different transcripts. Assembly of the sequences can be performed using such programs as PHRAP (Phils Revised Assembly Program) and the GEL VIEW fragment assembly system (GCG), or other methods known in the art.
  • PHRAP Phils Revised Assembly Program
  • GCG GEL VIEW fragment assembly system
  • cDNA sequences are used as "component" sequences that are assembled into “template” or “consensus” sequences as follows. Sequence chromatograms are processed, verified, and quatity scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., the LIFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA). A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) are replaced by "n's", or masked, to prevent spurious matches. Mitochondrial and ribosomal RNA sequences are also removed.
  • Block 1 See, e.g., the LIFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA).
  • a series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleo
  • the processed sequences are then loaded into a relational database management system (RDMS) which assigns edited sequences to existing templates, if available.
  • RDMS relational database management system
  • a process is initiated which modifies existing templates or creates new templates from works in progress (i.e., nonfinal assembled sequences) containing queued sequences or the sequences themselves.
  • the templates can be merged into bins. If multiple templates exist in one bin, the bin can be spUt and the templates reannotated.
  • bins are "clone joined" based upon clone information. Clone joining occurs when the 5' sequence of one clone is present in one bin and the 3' sequence from the same clone is present in a different bin, indicating that the two bins should be merged into a single bin. Only bins which share at least two different clones are merged.
  • a resultant template sequence may contain either a partial or a full length open reading frame, or all or part of a genetic regulatory element. This variation is due in part to the fact that the full length cDNAs of many genes are several hundred, and sometimes several thousand, bases in length.
  • cDNAs comprising the coding regions of large genes cannot be cloned because of vector limitations, incomplete reverse transcription of the mRNA, or incomplete "second strand" synthesis.
  • Template sequences may be extended to include additional contiguous sequences derived from the parent RNA transcript using a variety of methods known to those of skill in the art. Extension may thus be used to achieve the full length coding sequence of a gene. Analysis of the cDNA Sequences
  • cDNA sequences are analyzed using a variety of programs and algorithms which are well known in the art. (See, e.g., Ausubel, 1997, supra, Chapter 7.7; Meyers, R.A. (Ed.) (1995) Molecular Biology and Biotechnology, Wiley VCH, New York NY, pp. 856-853; and Table 4.) These analyses comprise both reading frame determinations, e.g., based on triplet codon periodicity for particular organisms (Fickett, J.W. (1982) Nucleic Acids Res. 10:5303-5318); analyses of potential start and stop codons; and homology searches.
  • BLAST Basic Local AUgnment Search Tool
  • BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose aUgnment is locally maximal and for which the aUgnment score meets or exceeds a threshold or cutoff score set by the user (KarUn, S. et al. (1988) Proc. Natl. Acad. Sci.
  • Protein hierarchies can be assigned to the putative encoded polypeptide based on, e.g., motif, BLAST, or biological analysis. Methods for assigning these hierarchies are described, for example, in "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data," U.S.S.N. 08/812,290, filed March 6, 1997, incorporated herein by reference. Human Secretory Sequences
  • the sptm of the present invention may be used for a variety of diagnostic and therapeutic purposes.
  • an sptm may be used to diagnose a particular condition, disease, or disorder associated with cell signaUng.
  • Such conditions, diseases, and disorders include, but are not limited to, a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, a cancer of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix,
  • the sptm can be used to detect the presence of, or to quantify the amount of, an sptm-related polynucleotide in a sample. This information is then compared to information obtained from appropriate reference samples, and a diagnosis is estabUshed.
  • a polynucleotide complementary to a given sptm can inhibit or inactivate a therapeutically relevant gene related to the sptm Analysis of sptm Expression Patterns
  • the expression of sptm may be routinely assessed by hybridization-based methods to determine, for example, the tissue-specificity, disease-specificity, or developmental stage-specificity of sptm expression.
  • the level of expression of sptm may be compared among different cell types or tissues, among diseased and normal cell types or tissues, among cell types or tissues at different developmental stages, or among cell types or tissues undergoing various treatments.
  • This type of analysis is useful, for example, to assess the relative levels of sptm expression in fully or partially differentiated cells or tissues, to determine if changes in sptm expression levels are correlated with the development or progression of specific disease states, and to assess the response of a cell or tissue to a specific therapy, for example, in pharmacological or toxicological studies.
  • Methods for the analysis of 5 sptm expression are based on hybridization and ampUfication technologies and include membrane-based procedures such as northern blot analysis, high-throughput procedures that utilize, for example, microarrays, and PCR-based procedures.
  • the sptm, their fragments, or complementary sequences may be used to identify the presence of and/or to determine the degree of similarity between two (or more) nucleic acid sequences.
  • the sptm may be hybridized to naturally occurring or recombinant nucleic acid sequences under appropriately selected temperatures and salt concentrations.
  • Hybridization with a probe based on the nucleic acid sequence of at least one of the sptm allows for the detection of nucleic acid sequences, including 5 genomic sequences, which are identical or related to the sptm of the Sequence Listing.
  • Probes may be selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ ID NO: 1 - 63 and tested for their abiUty to identify or ampUfy the target nucleic acid sequence using standard protocols.
  • Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ 0 ID NO:l-63 and fragments thereof, can be identified using various conditions of stringency. (See, e.g., Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A.R. (1987) Methods Enzymol. 152:507-511.) Hybridization conditions are discussed in "Definitions.”
  • a probe for use in Southern or northern hybridization may be derived from a fragment of an sptm sequence, or its complement, that is up to several hundred nucleotides in length and is either 5 single-stranded or double-stranded. Such probes may be hybridized in solution to biological materials such as plasmids, bacterial, yeast, or human artificial chromosomes, cleared or sectioned tissues, or to artificial substrates containing sptm. Microarrays are particularly suitable for identifying the presence of and detecting the level of expression for multiple genes of interest by examining gene expression correlated with, e.g., various stages of development, treatment with a drug or compound, or disease o progression.
  • An array analogous to a dot or slot blot may be used to arrange and Unk polynucleotides to the surface of a substrate using one or more of the following: mechanical (vacuum), chemical, thermal, or UV bonding procedures.
  • Such an array may contain any number of sptm and may be produced by hand or by using available devices, materials, and machines.
  • Microarrays may be prepared, used, and analyzed using methods known in the art.
  • Probes may be labeled by either PCR or enzymatic techniques using a variety of commercially 5 available reporter molecules.
  • commercial kits are available for radioactive and chemiluminescent labeling (Amersham Pharmacia Biotech) and for alkaUne phosphatase labeUng (Life Technologies).
  • sptm may be cloned into commercially available vectors for the production of RNA probes.
  • Such probes may be transcribed in the presence of at least one labeled nucleotide (e.g., 3 P-ATP, Amersham Pharmacia Biotech).
  • polynucleotides of SEQ ID NO:l-63 or suitable fragments thereof can be used to isolate full length cDNA sequences utiUzing hybridization and/or ampUfication procedures well known in the art, e.g., cDNA Ubrary screening, PCR ampUfication, etc.
  • the molecular cloning of such full length cDNA sequences may employ the method of cDNA Ubrary screening with probes using the hybridization, stringency, washing, and probing strategies described above and in Ausubel, supra. 5 Chapters 3, 5, and 6. These procedures may also be employed with genomic libraries to isolate genomic sequences of sptm in order to analyze, e.g., regulatory elements. Genetic Mapping
  • cardiovascular disease may result from malfunctioning receptor molecules that fail to clear cholesterol from the bloodstream
  • diabetes may result when a particular individual's immune system is 5 activated by an infection and attacks the insulin-producing cells of the pancreas.
  • Alzheimer's disease has been Unked to a gene on chromosome 21; other studies predict a different gene and location. Mapping of disease genes is a complex and reiterative process and generally proceeds from genetic linkage analysis to physical mapping.
  • sptm sequences may be used to generate hybridization probes useful in chromosomal mapping of naturally occurring genomic sequences. Either coding or 5 noncoding sequences of sptm may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of an sptm coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping.
  • sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes 0 (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial Pl constructions, or single chromosome cDNA Ubraries.
  • HACs human artificial chromosomes 0
  • YACs yeast artificial chromosomes
  • BACs bacterial artificial chromosomes
  • bacterial Pl constructions or single chromosome cDNA Ubraries.
  • Fluorescent in situ hybridization may be correlated with other physical chromosome 5 mapping techniques and genetic map data.
  • Correlation between the location of sptm on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder may help define the region of DNA associated with that disorder.
  • the sptm sequences may also be used to detect polymo ⁇ hisms that are genetically Unked to the inheritance of a particular condition, disease, or disorder.
  • o In situ hybridization of chromosomal preparations and genetic mapping techniques such as
  • Unkage analysis using estabUshed chromosomal markers may be used for extending existing genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of the corresponding human chromosome is not known. These new marker sequences can be mapped to human chromosomes and 5 may provide valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once a disease or syndrome has been crudely correlated by genetic Unkage with a particular genomic region, e.g., ataxia-telangiectasia to 1 lq22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation.
  • nucleotide sequences of the subject invention may o also be used to detect differences in chromosomal architecture due to translocation, inversion, etc., among normal, carrier, or affected individuals.
  • a disease-associated gene is mapped to a chromosomal region, the gene must be cloned in order to identify mutations or other alterations (e.g., translocations or inversions) that may be correlated with disease.
  • This process requires a physical map of the chromosomal region containing the disease- 5 gene of interest along with associated markers. A physical map is necessary for determining the nucleotide sequence of and order of marker genes on a particular chromosomal region. Physical mapping techniques are well known in the art and require the generation of overlapping sets of cloned DNA fragments from a particular organelle, chromosome, or genome. These clones are analyzed to reconstruct and catalog their order. Once the position of a marker is determined, the DNA from that region is obtained by consulting the catalog and selecting clones from that region. The gene of interest is located through positional cloning techniques using hybridization or similar methods. Diagnostic Uses
  • the sptm of the present invention may be used to design probes useful in diagnostic assays. Such assays, well known to those skilled in the art, may be used to detect or confirm conditions, disorders, or diseases associated with abnormal levels of sptm expression. Labeled probes developed from sptm sequences are added to a sample under hybridizing conditions of desired stringency. In some instances, sptm, or fragments or oUgonucleotides derived from sptm, may be used as primers in ampUfication steps prior to hybridization. The amount of hybridization complex formed is quantified and compared with standards for that cell or tissue. If sptm expression varies significantly from the standard, the assay indicates the presence of the condition, disorder, or disease.
  • QuaUtative or quantitative diagnostic methods may include northern, dot blot, or other membrane or dip-stick based technologies or multiple-sample format technologies such as PCR, enzyme-Unked immunosorbent assay (ELISA)-Uke, pin, or chip-based assays.
  • PCR enzyme-Unked immunosorbent assay
  • the probes described above may also be used to monitor the progress of conditions, disorders, or diseases associated with abnormal levels of sptm expression, or to evaluate the efficacy of a particular therapeutic treatment.
  • the candidate probe may be identified from the sptm that are specific to a given human tissue and have not been observed in GenBank or other genome databases. Such a probe may be used in animal studies, precUnical tests, cUnical trials, or in monitoring the treatment of an individual patient.
  • standard expression is estabUshed by methods well known in the art for use as a basis of comparison, samples from patients affected by the disord ⁇ or disease are combined with the probe to evaluate any deviation from the standard profile, and a therapeutic agent is administered and effects are monitored to generate a treatment profile. Efficacy is evaluated by determining whether the expression progresses toward or returns to the standard normal pattern. Treatment profiles may be generated over a period of several days or several months. Statistical methods well known to those skilled in the art may be use to determine the significance of such therapeutic agents.
  • the polynucleotides are also useful for identifying individuals from minute biological samples, for example, by matching the RFLP pattern of a sample's DNA to that of an individual's DNA.
  • the polynucleotides of the present invention can also be used to determine the actual base-by-base DNA sequence of selected portions of an individual's genome. These sequences can be used to prepare PCR primers for amplifying and isolating such selected DNA, which can then be sequenced. Using this technique, an individual can be identified through a unique set of DNA sequences. Once a unique ID database is established for an individual, positive identification of that individual can be made from extremely small tissue samples.
  • ohgonucleotide primers derived from the sptm of the invention may be used to detect single nucleotide polymo ⁇ hisms (SNPs).
  • SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans.
  • Methods of SNP detection include, but are not Umited to, single-stranded conformation polymo ⁇ hism (SSCP) and fluorescent SSCP (fSSCP) methods.
  • SSCP single-stranded conformation polymo ⁇ hism
  • fSSCP fluorescent SSCP
  • oUgonucleotide primers derived from sptm are used to l o ampUfy DNA using the polymerase chain reaction (PCR).
  • the DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like. SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels. In fSCCP, the oUgonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-
  • siUco SNP sequence database analysis methods
  • sequence database analysis methods termed in siUco SNP (isSNP)
  • siUco SNP are capable of identifying polymo ⁇ hisms by comparing the sequences of individual overlapping DNA fragments which assemble into a common consensus sequence.
  • SNPs may be detected and characterized by mass spectrometry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego CA).
  • DNA-based identification techniques are critical in forensic technology. DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saUva, semen, etc., can be amphfied using, e.g., PCR, to identify individuals. (See, e.g., Erlich, H. (1992)
  • polynucleotides of the present invention can be used as polymo ⁇ hic markers.
  • reagents capable of identifying the source of a particular tissue.
  • Appropriate reagents can comprise, for example, DNA probes or primers prepared from the sequences of the present invention that are specific for particular tissues. Panels of such reagents can identify
  • polynucleotides of the present invention can also be used as molecular weight markers on nucleic acid gels or Southern blots, as diagnostic probes for the presence of a specific mRNA in a particular cell type, in the creation of subtracted cDNA Ubraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oUgomers for attachment to an array or other support, and as an antigen to eUcit an immune response.
  • the polynucleotides encoding SPTM or their mammaUan homologs may be "knocked out” in 5 an animal model system using homologous recombination in embryonic stem (ES) cells.
  • ES embryonic stem
  • Such techniques are well known in the art and are useful for the generation of animal models of human disease.
  • mouse ES cells such as the mouse 129/SvJ cell Une, are derived from the early mouse embryo and grown in culture.
  • the ES cells are transformed with a vector containing the gene of interest disrupted 0 by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M.R. (1989) Science 244: 1288- 1292).
  • the vector integrates into the corresponding region of the host genome by homologous recombination.
  • homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manna- (Marth, J.D. (1996) CUn. Invest. 97:1999-2002; Wagner, KU. et al. (1997) Nucleic Acids Res. 25:4323-4330).
  • Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain.
  • the blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains.
  • Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.
  • Polynucleotides encoding SPTM may also be manipulated in vitro in ES cells derived from o human blastocysts.
  • Human ES cells have the potential to differentiate into at least eight separate cell Uneages including endoderm, mesoderm, and ectodermal cell types. These cell Uneages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J.A. et al. (1998) Science 282:1145-1147).
  • Polynucleotides encoding SPTM can also be used to create "knockin" humanized animals 5 (pigs) or transgenic animals (mice or rats) to model human disease.
  • knockin technology a region of sptm is injected into animal ES cells, and the injected sequence integrates into the animal cell genome.
  • Transformed cells are injected into blastulae, and the blastulae are implanted as described above.
  • Transgenic progeny or inbred Unes are studied and treated with potential pharmaceutical agents to obtain information on treatment of a human disease.
  • a mammal inbred to overexpress o sptm, resulting, e.g. , in the secretion of SPTM in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74). Screening Assays
  • SPTM encoded by polynucleotides of the present invention may be used to screen for molecules that bind to or are bound by the encoded polypeptides.
  • the binding of the polypeptide and the molecule 5 may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the bound molecule.
  • Examples of such molecules include antibodies, oUgonucleotides, proteins (e.g., receptors), or small molecules.
  • the molecule is closely related to the natural Ugand of the polypeptide, e.g., a ligand or fragment thereof, a natural substrate, or a structural or functional mimetic.
  • the molecule can be closely related to the natural receptor to which the polypeptide binds, or to at least a fragment of the receptor, e.g., the active site.
  • the molecule can be rationally designed using known techniques.
  • the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane.
  • Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide or cell membrane fractions which contain the expressed polypeptide are then contacted with a test compound and binding, stimulation, or inhibition of activity of either the polypeptide or the molecule is analyzed.
  • An assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. Alternatively, the assay may assess binding in the presence of a labeled competitor.
  • the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a soUd support, chemical Ubraries, or natural product mixtures.
  • the assay may also simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.
  • an ELISA assay using, e.g., a monoclonal or polyclonal antibody can measure polypeptide level in a sample.
  • the antibody can measure polypeptide level by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.
  • the molecules discovered using these assays can be used to treat disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule.
  • the assays can discover agents which may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues.
  • Transcript Imaging and Toxicological Testing Another embodiment relates to the use of sptm to develop a transcript image of a tissue or cell type.
  • a transcript image represents the global pattern of gene expression by a particular tissue or cell type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at a given time.
  • a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totality of transcripts or reverse transcripts of a particular tissue or cell type.
  • the hybridization takes place in high-throughput format, wherein the polynucleotides of the present invention or their complements comprise a subset of a plurality of elements on a microarray.
  • the resultant transcript image would provide a profile of gene 5 activity pertaining to cell signaUng.
  • Transcript images which profile sptm expression may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples.
  • the transcript image may thus reflect sptm expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell Une.
  • Transcript images which profile sptm expression may also be used in conjunction with in vitro model systems and precUnical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds. All compounds induce characteristic gene expression patterns, frequently termed molecular fingerprints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog.
  • test compound has a signature similar to that of a compound with known toxicity, it is Ukely to share those toxic properties.
  • These finge ⁇ rints or signatures are most useful and refined when they contain expression information from a large number of genes and gene famiUes. Ideally, a genome-wide measurement of expression provides the highest quaUty signature. Even genes o whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normaUze the rest of the expression data.
  • the normaUzation procedure is useful for comparison of expression data after treatment with different compounds. While the assignment of gene function to elements of a toxicant signature aids in inte ⁇ retation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures 5 which leads to prediction of toxicity. (See, for example, Press Release 00-02 from the National
  • the toxicity of a test compound is assessed by treating a biological sample o containing nucleic acids with the test compound.
  • Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be quantified.
  • the transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples 5 are indicative of a toxic response caused by the test compound in the treated sample.
  • Another particular embodiment relates to the use of SPTM encoded by polynucleotides of the present invention to analyze the proteome of a tissue or cell type.
  • proteome refers to the global pattern of protein expression in a particular tissue or cell type. Each protein component of a proteome can be subjected individually to further analysis. Proteome expression patterns, or profiles, 5 are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. A profile of a cell's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type. In one embodiment, the separation is achieved using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl 0 sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra).
  • the proteins are visuaUzed in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains.
  • the optical density of each protein spot is generally proportional to the level of the protein in the sample.
  • the optical densities of equivalently positioned protein spots from different samples, for example, from biological samples either treated or 5 untreated with a test compound or therapeutic agent, are compared to identify any changes in protein spot density related to the treatment.
  • the proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enzymatic cleavage followed by mass spectrometry.
  • the identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of the present invention. In o some cases, further sequence data may be obtained for definitive protein identification.
  • a proteomic profile may also be generated using antibodies specific for SPTM to quantify the levels of SPTM expression.
  • the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and detecting the levels of protein bound to each array element (Lueking, A. et al. (1999) Anal. Biochem. 270:103-11; 5 Mendoze, L. G. et al. (1999) Biotechniques 27:778-88). Detection may be performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol- or amino- reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.
  • Toxicant signatures at the proteome level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level. There is a poor correlation o between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and
  • proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile.
  • the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiling may be more reUable and informative in such cases.
  • the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified. The amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample.
  • a difference 5 in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.
  • Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the SPTM encoded by polynucleotides of the present invention.
  • the toxicity of a test compound is assessed by treating a biological o sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the SPTM encoded by polynucleotides of the present invention. The amount of protein recognized by the antibodies is quantified. The amount of protein in the treated biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated 5 sample.
  • Transcript images may be used to profile sptm expression in distinct tissue types. This process can be used to determine cell signaUng activity in a particular tissue type relative to this activity in a different tissue type. Transcript images may be used to generate a profile of sptm expression characteristic of diseased tissue. Transcript images of tissues before and after treatment may be used o for diagnostic pu ⁇ oses, to monitor the progression of disease, and to monitor the efficacy of drug treatments for diseases which affect cell signaling activity.
  • Transcript images of cell Unes can be used to assess cell signaUng activity and/or to identify cell Unes that lack or misregulate this activity. Such cell Unes may then be treated with pharmaceutical agents, and a transcript image following treatment may indicate the efficacy of these agents in restoring 5 desired levels of this activity. A similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in cell signaling activity. Candidate pharmaceutical agents may be evaluated by comparing their associated transcript images with those of pharmaceutical agents of known effectiveness.
  • Antisense Molecules o The polynucleotides of the present invention are useful in antisense technology.
  • Antisense technology or therapy relies on the modulation of expression of a target protein through the specific binding of an antisense sequence to a target sequence encoding the target protein or directing its expressioa (See, e.g., Agrawal, S., ed. (1996) Antisense Therapeutics, Humana Press Inc., Totawa NJ; Alama, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S.T. (1997) Adv. Pharmacol. 5 40:1-49; Sharma, H.W. and R. Narayanan (1995) Bioessays 17(12):1055-1063; and Lavrosky, Y. et al. (1997) Biochem. Mol. Med.
  • An antisense sequence is a polynucleotide sequence capable of specifically hybridizing to at least a portion of the target sequence. Antisense sequences bind to cellular mRNA and/or genomic DNA, affecting translation and/or transcription. Antisense sequences can be DNA, RNA, or nucleic acid mimics and analogs. (See, e.g., Rossi, J.J. et al. (1991) 5 Antisense Res. Dev. l(3):285-288; Lee, R. et al. (1998) Biochemistry 37(3):900-1010; Pardridge, W.M. et al. (1995) Proc. Natl. Acad. Sci.
  • Antisense sequences can also bind to DNA duplexes through specific interactions in the major groove of the double helix.
  • the polynucleotides of the present invention and fragments thereof can be used as antisense sequences to modify the expression of the polypeptide encoded by sptm.
  • the antisense sequences can be produced ex vivo, such as by using any of the ABI nucleic acid synthesizer series (PE Biosystems) or other automated systems known in the art.
  • Antisense sequences can also be produced biologically, such as by transforming an appropriate host cell with an expression vector containing the sequence of 5 interest. (See, e.g., Agrawal, supra.)
  • Antisense sequences can be deUvered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the cellular sequence encoding the target protein.
  • Slater, J.E., et al. (1998) 0 J. Allergy CUn. Immunol. 102(3):469-475; and Scanlon, K.J., et al. (1995) 9(13):1288-1296.)
  • Antisense sequences can also be introduced intracellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors.
  • viral vectors such as retrovirus and adeno-associated virus vectors.
  • retrovirus vectors See, e.g., Miller, A.D. (1990) Blood 76:271; Ausubel, F.M. et al. (1995) Current Protocols in Molecular Biology. John Wiley & Sons, New York NY; Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63(3):323-347.
  • Other gene delivery mechanisms include 5 Uposome-derived systems, artificial viral envelopes, and other systems known in the art. (See, e.g.,
  • the nucleotide sequences encoding SPTM or o fragments thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host.
  • an appropriate expression vector i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host.
  • Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding SPTM and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, supra. Chapters 4, 8, 16, and 17; and Ausubel, supra. Chapters 9, 10, 13, and 16.)
  • a variety of expression vector/host systems may be utiUzed to contain and express sequences encoding SPTM. These include, but are not Umited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammalian) cell systems.
  • microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors
  • yeast transformed with yeast expression vectors insect cell systems infected with viral expression vectors (e.g., baculovirus)
  • plant cell systems transformed with viral expression vectors
  • Expression vectors derived from retroviruses, adenoviruses, or he ⁇ es or vaccinia viruses, or from various bacterial plasmids may be used for deUvery of nucleotide sequences to the targeted organ, tissue, or cell population.
  • the invention is not Umited by the host cell employed.
  • sequences encoding SPTM can be transformed into cell lines using expression vectors which may contain viral origins of repUcation and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of selection systems may be used to recover transformed cell Unes. (See, e.g., Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.; Wigler, M. et al. (1980) Proc. Natl. Acad. Sci.
  • the polynucleotides encoding SPTM may be used for somatic or germline gene therapy.
  • Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-Xl disease characterized by X-Unked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R.M. et al. (1995) Science 270:475-480; Bordignon, C et al.
  • SCID severe combined immunodeficiency
  • ADA adenosine deaminase
  • sptm 5 expression or regulation causes disease
  • expression of sptm from an appropriate population of transduced cells may alleviate the cUnical manifestations caused by the genetic deficiency.
  • diseases or disorders caused by deficiencies in sptm are treated by constructing mammaUan expression vectors comprising sptm and introducing these vectors by mechanical means into sptm-deficient cells.
  • Mechanical transfer technologies for use with 0 cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (U) balUstic gold particle deUvery, (ui) Uposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R.A. and Anderson, W.F. (1993) Annu. Rev. Biochem. 62:191-217; Ivies, Z. (1997) Cell 91:501-510; Boulay, J-L.
  • Expression vectors that may be effective for the expression of sptm include, but are not Umited to, thePCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad CA), PCMV-SCRIPT, PCMV-TAG, PEGSH PERV (Stratagene, La Jolla CA), and PTET-OFF, PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo Alto CA).
  • the sptm of the invention may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous o sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or ⁇ -actin genes), (ii) an inducible promoter
  • a constitutively active promoter e.g., from cytomegalovirus (CMV), Rous o sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or ⁇ -actin genes
  • an inducible promoter e.g., from cytomegalovirus (CMV), Rous o sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or ⁇ -actin genes
  • Uposome transformation kits e.g., the PERFECT LIPID TRANSFECTION KIT, available from Invitrogen
  • PERFECT LIPID TRANSFECTION KIT available from Invitrogen
  • transformation is performed using the calcium phosphate method (Graham, F.L. and Eb, A.J. (1973) Virology 52:456-467), or by electroporation (Neumann, E. et al. (1982) EMBO J. 1:841-845).
  • the introduction of DNA to primary cells requires modification of these standardized mammaUan transfection protocols.
  • diseases or disorders caused by genetic defects with respect to sptm expression are treated by constructing a retrovirus vector consisting of (i) sptm under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (u) appropriate RNA packaging signals, and (in) a Rev-responsive element (RRE) along with additional retrovirus c ⁇ -acting RNA sequences and coding sequences required for efficient vector propagation.
  • Retrovirus vectors e.g., PFB and PFBNEO
  • the vector is propagated in an appropriate vector producing cell Une (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M.A. et al. (1987) J. Virol. 61:1639-1646; Adam, M.A. and Miller, A.D. (1988) J. Virol. 62:3802-3806; Dull, T. et al. (1998) J. Virol. 72:8463-8471; Zufferey, R. et al.
  • VSVg vector producing cell Une
  • U.S. Patent Number 5,910,434 to Rigg discloses a method for obtaining retrovirus packaging cell lines and is hereby inco ⁇ orated by reference. Propagation of retrovirus vectors, transduction of a population of cells (e.g., CD4 + T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol. 71:7020-7029; Bauer, G. et al.
  • an adenovirus-based gene therapy deUvery system is used to deUver sptm to cells which have one or more genetic abnormaUties with respect to the expression of sptm.
  • the construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art.
  • RepUcation defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M.E. et al. (1995) Transplantation 27:263-268).
  • Potentially useful adenoviral vectors are described in U.S. Patent Number 5,707,618 to Armentano ("Adenovirus vectors for gene therapy"), hereby inco ⁇ orated by reference.
  • Adenovirus vectors for gene therapy For adenoviral vectors, see also Antinozzi, P.A. et al. (1999) Annu. Rev. Nutr. 19:511-544 and Verma, I.M. and Somia, N.
  • he ⁇ es-based, gene therapy deUvery system is used to deUver sptm to target cells which have one or more genetic abnormaUties with respect to the expression of sptm.
  • HSV he ⁇ es simplex virus
  • the use of he ⁇ es simplex virus (HSV)-based vectors may be especially valuable for introducing sptm to cells of the central nervous system, for which HS V has a tropism.
  • the construction and packaging of he ⁇ es-based vectors are well known to those with ordinary skill in the art.
  • HSV he ⁇ es simplex virus
  • Patent Number 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the control of the appropriate promoter for pu ⁇ oses including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W. F. et al. 1999 J. Virol. 73:519-532 andXu, H. et al., (1994) Dev. Biol. 163:152-161, hereby inco ⁇ orated by reference.
  • an alphavirus (positive, single-stranded RNA virus) vector is used to deUver sptm to target cells.
  • SFV SemUki Forest Virus
  • alphavirus RNA repUcation a subgenomic RNA is generated that normally encodes the viral capsid proteins.
  • This subgenomic RNA repUcates to higher levels than the full-length genomic RNA, resulting in the ov ⁇ production of capsid proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase).
  • enzymatic activity e.g., protease and polymerase.
  • inserting sptm into the alphavirus genome in place of the capsid-coding region results in the production of a large number of sptm RNAs and the synthesis of high levels of SPTM in vector transduced cells.
  • alphavirus infection is typically associated with cell lysis within a few days
  • the abiUty to estabUsh a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic repUcation of alphaviruses can be altered to suit the needs of the gene therapy appUcation (Dryga, S.A. et al. (1997) Virology 228:74-83).
  • the wide host range of alphaviruses will allow the introduction of sptm into a variety of cell types.
  • the specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction.
  • the methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA and RNA transfections, and performing alphavirus infections, are well known to those with ordinary skill in the art. 5 Antibodies
  • Anti-SPTM antibodies may be used to analyze protein expression levels. Such antibodies include, but are not Umited to, polyclonal, monoclonal, chimeric, single chain, and Fab fragments. For descriptions of and protocols of antibody technologies, see, e.g., Pound J.D. (1998) Immunochemical Protocols, Humana Press, Totowa, NJ. l o The amino acid sequence encoded by the sptm of the Sequence Listing may be analyzed by appropriate software (e.g., LASERGENE NAVIGATOR software, DNASTAR) to determine regions of high immunogenicity.
  • appropriate software e.g., LASERGENE NAVIGATOR software, DNASTAR
  • the optimal sequences for immunization are selected from the C-terminus, the N-terminus, and those intervening, hydrophiUc regions of the polypeptide which are Ukely to be exposed to the external environment when the polypeptide is in its natural conformation. Analysis used to select
  • Peptides used for antibody induction do not need to have biological activity; however, they must be antigenic.
  • Peptides used to induce specific antibodies may have an amino acid sequence consisting of at five amino acids, preferably at least 10 amino acids, and most preferably 15 amino acids.
  • a peptide which mimics an antigenic fragment of the natural polypeptide may be fused with another protein such as keyhole limpet
  • cyanin 20 cyanin (KLH; Sigma, St. Louis MO) for antibody production.
  • a peptide encompassing an antigenic region may be expressed from an sptm, synthesized as described above, or purified from human cells. Procedures well known in the art may be used for the production of antibodies.
  • Various hosts including mice, goats, and rabbits, may be immunized by injection with a peptide. Depending on the host species, various adjuvants may be used to increase immunological response.
  • peptides about 15 residues in length may be synthesized using an ABI 431 A peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with M-maleimidobenzoyl-N-hydroxysuccinimide ester (Ausubel, 1995, supra). Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity by binding the peptide to plastic, blocking with 1% bovine serum albumin
  • isolated and purified peptide may be used to immunize mice (about 100 ⁇ g of peptide) or rabbits (about 1 mg of peptide). Subsequently, the peptide is radioiodinated and used
  • Clones producing antibodies bind a quantity of labeled peptide that is detectable above background. Such clones are expanded and subjected to 2 cycles of cloning. Cloned hybridomas are o injected into pristane-treated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (Amersham Pharmacia Biotech). Several procedures for the production of monoclonal antibodies, including in vitro production, are described in Pound (supra). Monoclonal antibodies with antipeptide activity are tested for anti-SPTM activity using protocols well known in the art, including ELISA, RIA, and immunoblotting. 5 Antibody fragments containing specific binding sites for an epitope may also be generated.
  • such fragments include, but are not Umited to, the F(ab')2 fragments produced by pepsin digestion of the antibody molecule, and the Fab fragments generated by reducing the disulfide bridges of the F(ab 2 fragments.
  • construction of Fab expression Ubraries in filamentous bacteriophage allows rapid and easy identification of monoclonal fragments with desired specificity 0 (Pound, supra. Chaps. 45-47).
  • Antibodies generated against polypeptide encoded by sptm can be used to purify and characterize full-length SPTM protein and its activity, binding partners, etc. Assays Using Antibodies
  • Anti-SPTM antibodies may be used in assays to quantify the amount of SPTM found in a particular human cell. Such assays include methods utiUzing the antibody and a label to detect 5 expression level under normal or disease conditions.
  • the peptides and antibodies of the invention may be used with or without modification or labeled by joining them, either covalently or noncovalently, with a reporter molecule.
  • Protocols for detecting and measuring protein expression using either polyclonal or monoclonal antibodies are well known in the art. Examples include ELISA, RIA, and fluorescent activated cell o sorting (FACS). Such immunoassays typically involve the formation of complexes between the SPTM and its specific antibody and the measurement of such complexes. These and other assays are described in Pound (supra).
  • RNA was purchased from CLONTECH Laboratories, Inc. (Palo Alto CA) or isolated from various tissues. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life Technologies Inc.).
  • poly(A+) RNA was isolated using oUgo d(T)-coupled paramagnetic particles (Promega Co ⁇ oration (Promega), Madison WI), OLIGOTEX latex particles (QIAGEN, Inc. (QIAGEN), Valencia CA), or an OLIGOTEX mRNA purification kit (QIAGEN).
  • RNA was isolated directly from tissue lysates using other RNA isolation kits, e.g., the POLY(A)PURE mRNA purification kit (Ambion, Inc., Austin TX).
  • Sttatagene was provided with RNA and constructed the corresponding cDNA
  • cDNA Ubraries were synthesized and cDNA Ubraries were constructed with the UNIZAP vector system (Sttatagene Cloning Systems, Inc. (Sttatagene), La Jolla CA) or SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra. Chapters 5.1 through 6.6.) Reverse transcription was initiated using oUgo d(T) or random primers. Synthetic oUgonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes.
  • cDNA was size-selected (300-1000 bp) using SEPHACRYL SI 000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis.
  • cDNAs were Ugated into compatible restriction enzyme sites of the polyUnker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Sttatagene), pSPORTl plasmid (Life Technologies), or pINCY (Incyte).
  • Recombinant plasmids were transformed into competent E. coh cells including XLl-Blue, XLl-BlueMRF, or SOLR from Sttatagene or DH5 ⁇ , DH10B, or ElectroMAX DH10B from Life Technologies.
  • Plasmids were recovered from host cells by in vivo excision using the UNIZAP vector system (Sttatagene) or by cell lysis. Plasmids were purified using at least one of the following: the Magic or WIZARD Minipreps DNA purification system (Promega); the AGTC Miniprep purification kit (Edge BioSystems, Gaithersburg MD); and the QIAWELL 8, QIAWELL 8 Plus, and QIAWELL 8 Ultra 5 plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit (QIAGEN). Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4°C
  • plasmid DNA was ampUfied from host cell lysates using direct Unk PCR in a high-throughput format.
  • Host cell lysis and thermal o cycUng steps were carried out in a single reaction mixture. Samples were processed and stored in 384- well plates, and the concentration of ampUfied plasmid DNA was quantified fluoromefrically using PICOGREEN dye (Molecular Probes, Inc. (Molecular Probes), Eugene OR) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).
  • cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 thermal cycler (PE Biosystems) or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific Co ⁇ ., Sunnyvale CA) or the MICROLAB 2200 Uquid transfer system (Hamilton).
  • cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or suppUed in ABI o sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE
  • Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (PE Biosystems) in conjunction with standard ABI protocols and base calUng software; or other sequence analysis systems known in the art. 5 Reading frames within the cDNA sequences were identified using standard methods (reviewed in
  • sequences from chromatograms were subject to PHRED analysis and assigned a o quality score.
  • the sequences having at least a required quaUty score were subject to various preprocessing editing pathways to eUminate, e.g., low quaUty 3' ends, vector and Unker sequences, polyA tails, Alu repeats, mitochondrial and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs.
  • low-information sequences and repetitive elements e.g., dinucleotide repeats, Alu repeats, etc.
  • sequences were then subject to assembly procedures in which the sequences were assigned to gene bins (bins). Each sequence could only belong to one bin. Sequences in each gene bin were assembled to produce consensus sequences (templates). Subsequent new sequences were added to existing bins using BLASTn (v.1.4 WashU) and CROSSMATCH. Candidate pairs were identified as 5 all BLAST hits having a quality score greater than or equal to 150. AUgnments of at least 82% local identity were accepted into the bin. The component sequences from each bin were assembled using a version of PHRAP. Bins with several overlapping component sequences were assembled using DEEP PHRAP.
  • each assembled template was determined based on the number and orientation of its component sequences. Template sequences as disclosed in the sequence 0 Usting correspond to sense sfrand sequences (the "forward" reading frames), to the best determination. The complementary (antisense) strands are inherently disclosed herein.
  • the component sequences which were used to assemble each template consensus sequence are Usted in Table 2, along with their positions along the template nucleotide sequences.
  • Bins were compared against each other and those having local similarity of at least 82% were 5 combined and reassembled. Reassembled bins having templates of insufficient overlap (less than 95% local identity) were re-spUt. Assembled templates were also subject to analysis by STITCHER/EXON MAPPER algorithms which analyze the probabiUties of the presence of splice variants, alternatively spUced exons, splice junctions, differential expression of alternative spUced genes across tissue types or disease states, etc. These resulting bins were subject to several rounds of the above assembly 0 procedures.
  • bins were clone joined based upon clone information. If the 5' sequence of one clone was present in one bin and the 3' sequence from the same clone was present in a different bin, it was Ukely that the two bins actually belonged together in a single bin. The resulting combined bins underwent assembly procedures to regenerate the 5 consensus sequences.
  • the template sequences were further analyzed by translating each template in all three forward o reading frames and searching each translation against the Pfam database of hidden Markov model- based protein famiUes and domains using the HMMER software package (available to the pubUc from Washington University School of Medicine, St. Louis MO). (See also World Wide Web site http://pfam.wustl.edu/ for detailed descriptions of Pfam protein domains and famiUes.)
  • Template sequences are further analyzed using the bioinformatics tools Usted in Table 4, or using sequence analysis software known in the art such as MACDNASIS PRO software (Hitachi 5 Software Engineering, South San Francisco CA) and LASERGENE software (DNASTAR). Template sequences may be further queried against pubUc databases such as the GenBank rodent, mammaUan, vertebrate, prokaryote, and eukaryote databases. V. Analysis of Polynucleotide Expression
  • Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene o and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; Ausubel, 1995, supra, ch. 4 and 16.)
  • the product score takes into account both the degree of similarity between two sequences and the length of the sequence match.
  • the product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multipUed by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences).
  • the BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and -4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate the product score.
  • the product score represents a balance between fractional overlap and quaUty in a BLAST aUgnment. For example, a product score of 100 is produced only for 100% identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap.
  • polynucleotide sequences encoding SPTM are analyzed with respect to the tissue sources from which they were derived.
  • Polynucleotide sequences encoding SPTM were assembled, at least in part, with overlapping Incyte cDNA sequences.
  • Each cDNA sequence is derived from a cDNA Ubrary constructed from a human tissue.
  • Each human tissue is classified into one of the following organ/tissue categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitaUa, female; genitaUa, male; germ cells; hemic and immune system; Uver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract.
  • the number of Ubraries in each category for each polynucleotide sequence encoding SPTM is counted and divided by the total number of Ubraries across all categories for each polynucleotide sequence encoding SPTM.
  • each human tissue is classified into one of the following disease/condition categories: cancer, cell Une, developmental, inflammation, neurological, frauma, cardiovascular, pooled, and other, and the number of Ubraries in each category for each polynucleotide sequence encoding SPTM is counted and divided by the total number of Ubraries across all categories for each polynucleotide sequence encoding SPTM. The resulting percentages reflect the tissue- and disease-specific expression of cDNA encoding SPTM. Percentage values of tissue-specific and disease-specific expression are reported in Table 3. cDNA sequences and cDNA Ubrary/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto CA).
  • a tissue distribution profile is determined for each template by compiUng the cDNA Ubrary 5 tissue classifications of its component cDNA sequences.
  • Each component sequence is derived from a cDNA Ubrary constructed from a human tissue.
  • Each human tissue is classified into one of the following categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitaUa, female; genitaUa, male; germ cells; hemic and immune system; Uver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; 0 skin; stomatognathic system; unclassified/mixed; or urinary tract.
  • Template sequences, component sequences, and cDNA library/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto CA).
  • Table 3 shows the tissue distribution profile for the templates of the invention. For each template, the three most frequently observed tissue categories are shown in column 3, along with the 5 percentage of component sequences belonging to each category. Only tissue categories with percentage values of > 10% are shown. A tissue distribution of "widely distributed" in column 3 indicates percentage values of ⁇ 10% in all tissue categories.
  • Transcript images are generated as described in Seilhamer et al., "Comparative Gene o Transcript Analysis," U.S. Patent Number 5,840,484, inco ⁇ orated herein by reference.
  • PCR is performed in 96-well plates using the PTC-200 thermal cycler (MJ Research).
  • the reaction mix contains DNA template, 200 nmol of each primer, reaction buffer containing Mg 2+ , (NH 4 ) 2 S0 4 , and ⁇ - mercaptoethanol, Taq DNA polymerase (Amersham Pharmacia Biotech), ELONGASE enzyme (Life 5 Technologies), and Pfu DNA polymerase (Sfratagene), with the following parameters for primer pair PCI A and PCI B: Step 1: 94°C, 3 min; Step 2: 94°C, 15 sec; Step 3: 60°C, 1 min; Step 4: 68°C, 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68 °C, 5 min; Step 7: storage at 4°C
  • the parameters for primer pair T7 and SK+ are as follows: Step 1 : 94°C, 3 min; Step 2:
  • the concentration of DNA in each well is determined by dispensing 100 ⁇ l PICOGREEN quantitation reagent (0.25% (v/v); Molecular Probes) dissolved in IX Tris-EDTA (TE) and 0.5 ⁇ l of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Inco ⁇ orated (Corning), Corning NY), allowing the DNA to bind to the reagent.
  • the plate is scanned in a FLUOROSKAN II o (Labsystems Oy) to measure the fluorescence of the sample and to quantify theconcenfration of DNA.
  • a 5 ⁇ l to 10 ⁇ l ahquot of the reaction mixture is analyzed by electrophoresis on a 1 % agarose mini-gel to determine which reactions are successful in extending the sequence.
  • the extended nucleotides are desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison WI), and 5 sonicated or sheared prior to reUgation into pUC 18 vector (Amersham Pharmacia Biotech).
  • CviJI cholera virus endonuclease Molecular Biology Research, Madison WI
  • 5 sonicated or sheared prior to reUgation into pUC 18 vector
  • the digested nucleotides are separated on low concentration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with AGAR ACE (Promega).
  • Extended clones are religated using T4 Ugase (New England Biolabs, Inc., Beverly MA) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Sfratagene) to fill-in restriction site overhangs, o and transfected into competent E. coli cells. Transformed cells are selected on antibiotic-containing media, individual colonies are picked and cultured overnight at 37 °C in 384-well plates in LB/2x carbenicilUn Uquid media.
  • the cells are lysed, and DNA is ampUfied by PCR using Taq DNA polymerase (Amersham Pharmacia Biotech) and Pfu DNA polymerase (Sttatagene) with the following parameters: Step 1 : 5 94°C, 3 min; Step 2: 94°C, 15 sec; Step 3: 60°C, 1 min; Step 4: 72°C, 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72°C, 5 min; Step 7: storage at 4°C DNA is quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries are reamplified using the same conditions as described above.
  • Samples are diluted with 20% dimethysulfoxide (1 :2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC o DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE Biosystems).
  • the sptm is used to obtain regulatory sequences (promoters, introns, and enhancers) using the procedure above, oUgonucleotides designed for such extension, and an appropriate genomic Ubrary.
  • 5 IX. Labeling of Probes and Southern Hybridization Analyses Hybridization probes derived from the sptm of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA. The labeUng of probe nucleotides between 100 and 1000 nucleotides in length is specifically described, but essentially the same procedure may be used with larger cDNA fragments.
  • Probe sequences are labeled at room temperature for 30 minutes using a 5 T4 polynucleotide kinase, ⁇ P-ATP, and 0.5X One-Phor-All Plus (Amersham Pharmacia Biotech) buffer and purified using a ProbeQuant G-50 Microcolumn (Amersham Pharmacia Biotech).
  • the probe mixture is diluted to 10 7 dpm/ ⁇ g/ml hybridization buffer and used in a typical membrane-based hybridization analysis.
  • the DNA is digested with a restriction endonuclease such as Eco RV and is electrophoresed o through a 0.7% agarose gel.
  • the DNA fragments are transferred from the agarose to nylon membrane
  • blots are sequentially washed at room temperature under increasingly stringent conditions, up to O.lx satine sodium citrate 5 (SSC) and 0.5% sodium dodecyl sulfate. After the blots are placed in a PHOSPHORIMAGER cassette (Molecular Dynamics) or are exposed to autoradiography film, hybridization patterns of standard and experimental lanes are compared. Essentially the same procedure is employed when screening RNA.
  • SSC O.lx satine sodium citrate 5
  • PHOSPHORIMAGER cassette Molecular Dynamics
  • the cDNA sequences which were used to assemble SEQ ID NO: 1-63 are compared with o sequences from the Incyte LIFESEQ database and pubUc domain databases using BLAST and other implementations of the Smith- Waterman algorithm. Sequences from these databases that match SEQ ID NO: 1 -63 are assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as PHRAP (Table 4). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead Institute for Genome 5 Research (WIGR), and Gen ⁇ thon are used to determine if any of the clustered sequences have been previously mapped.
  • SHGC Stanford Human Genome Center
  • WIGR Whitehead Institute for Genome 5 Research
  • Gen ⁇ thon are used to determine if any of the clustered sequences have been previously mapped.
  • a mapped sequence in a cluster will result in the assignment of all sequences of that cluster, including its particular SEQ ID NO:, to that map location.
  • the genetic map locations of SEQ ID NO:l-63 are described as ranges, or intervals, of human chromosomes.
  • the map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p- o arm.
  • centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers.
  • RNA is isolated from tissue samples using the guanidinium thiocyanate method and polyA + RNA is purified using the oligo (dT) cellulose method.
  • Each polyA + RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/ ⁇ l oUgo-dT primer (21mer), IX first strand buffer, 0.03 units/ ⁇ l RNase inhibitor, 500 ⁇ M dATP, 500 ⁇ M dGTP, 500 ⁇ M dTTP, 40 ⁇ M dCTP, 40 ⁇ M dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Pharmacia Biotech).
  • the reverse franscription reaction is performed in a 25 ml volume containing 200 ng polyA + RNA with GEMBRIGHT kits (Incyte).
  • Specific control polyA + RNAs are synthesized by in vitro transcription from non-coding yeast genomic DNA (W. Lei, unpubUshed).
  • the control mRNAs at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse franscription reaction at ratios of 1 : 100,000, 1 : 10,000, 1:1000, 1:100 (w/w) to sample mRNA respectively.
  • the control mRNAs are diluted into reverse transcription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA differential expression patterns.
  • each reaction sample (one with Cy3 and another with Cy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C to the stop the reaction and degrade the RNA. Probes are purified using two successive
  • Sequences of the present invention are used to generate array elements.
  • Each array element is ampUfied from bacterial cells containing vectors with cloned cDNA inserts.
  • PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert.
  • Array elements are ampUfied in thirty cycles of PCR from an initial quantity of 1 -2 ng to a final quantity greater than 5 ⁇ g.
  • AmpUfied array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech).
  • Purified array elements are immobiUzed on polymer-coated glass sUdes.
  • Glass microscope sUdes (Corning) are cleaned by ultrasound in 0.1% SDS and acetone, with extensive distilled water washes between and after treatments.
  • Glass sUdes are etched in 4% hydrofluoric acid (VWR Scientific Products Co ⁇ oration (VWR), West Chester, PA), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol.
  • Coated sUdes are cured in a 110°C oven.
  • Array elements are appUed to the coated glass substrate using a procedure described in US Patent No. 5,807,522, inco ⁇ orated herein by reference.
  • Microarrays are UV-crosslinked using a STRATALINKER UV-crossUnker (Sfratagene). Microarrays are washed at room temperature once in 0.2% SDS and three times in distilled water. Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate buffered saUne (PBS) (Tropix, Inc., Bedford, MA) for 30 minutes at 60° C followed by washes in 0.2% 5 SDS and distilled water as before.
  • PBS phosphate buffered saUne
  • Hybridization reactions contain 9 ⁇ l of probe mixture consisting of 0.2 ⁇ g each of Cy3 and Cy5 labeled cDNA synthesis products in 5X SSC, 0.2% SDS hybridization buffer.
  • the probe mixture is heated to 65° C for 5 minutes and is aUquoted onto the microarray surface and covered with an 1.8 o cm 2 coversUp.
  • the arrays are transferred to a wate ⁇ roof chamber having a cavity just sUghtiy larger than a microscope slide.
  • the chamber is kept at 100% humidity internally by the addition of 140 ⁇ l of 5x SSC in a corner of the chamber.
  • the chamber containing the arrays is incubated for about 6.5 hours at 60° C.
  • the arrays are washed for 10 min at 45° C in a first wash buffer (IX SSC, 0.1% SDS), three times for 10 minutes each at 45° C in a second wash buffer (0. IX SSC), and dried. 5 Detection
  • Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara CA) capable of generating spectral Unes at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5.
  • the excitation laser light is focused on the array using a 20X microscope objective (Nikon, Inc., Melville NY).
  • the sUde o containing the array is placed on a computer-controlled X- Y stage on the microscope and raster- scanned past the objective.
  • the 1.8 cm x 1.8 cm array used in the present example is scanned with a resolution of 20 micrometers.
  • a mixed gas multiUne laser excites the two fluorophores sequentially. Emitted Ught is spUt, based on wavelength, into two photomultipUer tube detectors (PMT R1477, 5 Hamamatsu Photonics Systems, Bridgewater NJ) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultipUer tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5. Each array is typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously.
  • the sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the probe mix at a known concentration.
  • a specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1 : 100,000.
  • the caUbration is done by labeUng samples of the caUbrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.
  • the output of the photomultipUer tube is digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Inc., Norwood, MA) installed in an IBM-compatible PC 5 computer.
  • the digitized data are displayed as an image where the signal intensity is mapped using a Unear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal).
  • the data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.
  • a grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid.
  • the fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal.
  • the software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte).
  • oligonucleotides comprising from about 15 to 30 base pairs is typical in the art. However, smaller or larger sequence fragments can also be used. Appropriate oligonucleotides are designed from the sptm using OLIGO 4.06 software (National Biosciences) or other appropriate programs and are synthesized using methods standard in the art or ordered from a o commercial supplier.
  • OLIGO 4.06 software National Biosciences
  • a complementary oUgonucleotide is designed from the most unique 5 ' sequence and used to prevent transcription factor binding to the promoter sequence.
  • a complementary oUgonucleotide is designed to prevent ribosomal binding and processing of the transcript.
  • SPTM 5 Expression and purification of SPTM is accompUshed using bacterial or virus-based expression systems.
  • cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription.
  • promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator o regulatory element.
  • Recombinant vectors are transformed into suitable bacterial hosts, e.g.,
  • SPTM upon induction with isopropyl beta-D- thiogalactopyranoside (IPTG).
  • IPTG isopropyl beta-D- thiogalactopyranoside
  • Expression of SPTM in eukaryotic cells is achieved by infecting insect or mammaUan cell Unes with recombinant Autographica caUfornica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus.
  • AcMNPV Autographica caUfornica nuclear polyhedrosis virus
  • the nonessential polyhedrin gene of baculovirus is 5 replaced with cDNA encoding SPTM by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription.
  • baculovirus Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases. Infection of the latter requires additional genetic modifications to baculovirus. (See e.g., Engelhard, 5 supra: and Sandig, supra.)
  • SPTM is synthesized as a fusion protein with, e.g., glutathione S- transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates.
  • GST a 26-kilodalton enzyme from Schistosoma iaponicum. enables the purification of fusion proteins on immobiUzed o glutathione undo- conditions that maintain protein activity and antigenicity (Amersham Pharmacia
  • the GST moiety can be proteolytically cleaved from SPTM at specifically engineered sites.
  • FLAG an 8-amino acid peptide
  • 6-His a stretch of six consecutive histidine residues, enables purification on 5 metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra. Chapters 10 and 16). Purified SPTM obtained by these methods can be used directly in the following activity assay.
  • An assay for SPTM activity measures the expression of SPTM on the cell surface.
  • cDNA o encoding SPTM is subcloned into an appropriate mammalian expression vector suitable for high levels of cDNA expression.
  • the resulting construct is transfected into a nonhuman cell Une such as NIH3T3.
  • Cell surface proteins are labeled with biotin using methods known in the art.
  • Immunoprecipitations are performed using SPTM-specific antibodies, and immunoprecipitated samples are analyzed using SDS- PAGE and immunoblotting techniques. The ratio of labeled immunoprecipitant to unlabeled 5 immunoprecipitant is proportional to the amount of SPTM expressed on the cell surface.
  • an assay for SPTM activity measures the amount of SPTM in secretory, membrane-bound organelles.
  • Transfected cells as described above are harvested and lysed.
  • the lysate is fractionated using methods known to those of skill in the art, for example, sucrose gradient ultracentrifugation. Such methods allow the isolation of subcellular components such as the Golgi 0 apparatus, ER, small membrane-bound vesicles, and other secretory organelles.
  • Immunoprecipitations from fractionated and total cell lysates are performed using SPTM-specific antibodies, and immunoprecipitated samples are analyzed using SDS-PAGE and immunoblotting techniques.
  • the concentration of SPTM in secretory organelles relative to SPTM in total cell lysate is proportional to the amount of SPTM in transit through the secretory pathway.
  • 5 XV. Functional Assays SPTM function is assessed by expressing sptm at physiologically elevated levels in mammaUan cell culture systems.
  • cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression.
  • Vectors of choice include pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen Co ⁇ oration, Carlsbad CA), both of which contain the 5 cytomegalovirus promoter.
  • recombinant vector 5-10 ⁇ g of recombinant vector are transiently transfected into a human cell Une, preferably of endotheUal or hematopoietic origin, using either Uposome formulations or electroporation. 1-2 ⁇ g of an additional plasmid containing sequences encoding a marker protein are co-fransfected.
  • Expression of a marker protein provides a means to distinguish transfected cells from o nonttansfected cells and is a reliable predictor of cDNA expression from the recombinant vector.
  • Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; CLONTECH), CD64, or a CD64-GFP fusion protein.
  • Row cytometry an automated laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties. 5 FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death.
  • the influence of SPTM on gene expression can be assessed using highly purified populations 5 of cells transfected with sequences encoding SPTM and either CD64 or CD64-GFP.
  • CD64 and CD64- GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG).
  • Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Inc., Lake Success NY).
  • mRNA can be purified from the cells using methods well known by those of skill in the art. o Expression of mRNA encoding SPTM and other genes of interest can be analyzed by northern analysis or microarray techniques.
  • SPTM substantially purified using polyacrylamide gel electrophoresis PAGE; see, e.g., Harrington, M.G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to 5 immunize rabbits and to produce antibodies using standard protocols.
  • the SPTM amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding peptide is synthesized and used to raise antibodies by means known to those of skill in the art. Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophihc regions are well described in 5 the art. (See, e.g., Ausubel, 1995, supra. Chapter 11.)
  • peptides 15 residues in length are synthesized using an ABI 431 A peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with N- maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity.
  • ABI 431 A peptide synthesizer PE Biosystems
  • KLH Sigma
  • MBS N- maleimidobenzoyl-N-hydroxysuccinimide ester
  • Rabbits are immunized with the peptide- KLH complex in complete Freund's 0 adjuvant.
  • Resulting antisera are tested for antipeptide activity by, for example, binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG.
  • Antisera with antipeptide activity are tested for anti-SPTM activity using protocols well known in the art, including ELISA, RIA, and immunoblotting.
  • XVII Purification of Naturally Occurring SPTM Using Specific Antibodies 5
  • Naturally occurring or recombinant SPTM is substantially purified by immunoaffinity chromatography using antibodies specific for SPTM.
  • An immunoaffinity column is constructed by covalently coupling anti-SPTM antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupUng, the resin is blocked and washed according to the manufacturer's instructions. o Media containing SPTM are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of SPTM (e.g., high ionic strength buffers in the presence of detergent).
  • activated chromatographic resin such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech).
  • the column is eluted under conditions that disrupt antibody/SPTM binding (e.g., a buffer of pH 2 to pH 3, or a high concenfration of a chaofrope, such as urea or thiocyanate ion), and SPTM is collected.
  • a buffer of pH 2 to pH 3 or a high concenfration of a chaofrope, such as urea or thiocyanate ion
  • SPTM or biologically active fragments thereof, are labeled with 125 I Bolton-Hunter reagent.
  • Bolton-Hunter reagent See, e.g., Bolton, A.E. and W.M. Hunter (1973) Biochem. J. 133:529-539.
  • Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled SPTM, washed, and any wells with labeled SPTM complex are assayed. Data obtained using different concentrations of o SPTM are used to calculate values for the number, affinity, and association of SPTM with the candidate molecules.
  • SPTM molecules interacting with SPTM are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989) Nature 340:245-246, or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (CLONTECH).
  • SPTM may also be used in the PATHCALLING process (CuraGen Co ⁇ ., New Haven CT) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions between the proteins encoded by two large libraries of genes (Nandabalan, K. et al. (2000) U.S. Patent No. 6,057,101).

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Abstract

The present invention provides purified secretory polynucleotides (sptm). Also encompassed are the polypeptides (SPTM) encoded by sptm. The invention also provides for the use of sptm, or complements, oligonucleotides, or fragments thereof in diagnostic assays. The invention further provides for vectors and host cells containing sptm for the expression of SPTM. The invention additionally provides for the use of isolated and purified SPTM to induce antibodies and to screen libraries of compounds and the use of anti-SPTM antibodies in diagnostic assays. Also provided are microarrays containing sptm and methods of use.

Description

SECRETORY MOLECC&ES
TECHNICAL FIELD
The present invention relates to secretory molecules and to the use of these sequences in the diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, cell signaling and the expression of secretory molecules.
BACKGROUND OF THE INVENTION
Protein transport and secretion are essential for cellular function. Protein transport is mediated by a signal peptide located at the amino terminus of the protein to be transported or secreted. The signal peptide is comprised of about ten to twenty hydrophobic amino acids which target the nascent protein from the ribosome to a particular membrane bound compartment such as the endoplasmic reticulum (ER). Proteins targeted to the ER may either proceed through the secretory pathway or remain in any of the secretory organelles such as the ER, Golgi apparatus, or lysosomes. Proteins that transit through the secretory pathway are either secreted into the extracellular space or retained in the plasma membrane. Proteins that are retained in the plasma membrane contain one or more transmembrane domains, each comprised of about 20 hydrophobic amino acid residues. Proteins that are secreted from the cell are generally synthesized as inactive precursors that are activated by post- translational processing events during transit through the secretory pathway. Such events include glycosylation, proteolysis, and removal of the signal peptide by a signal peptidase. Other events that may occur during protein transport include chaperone-dependent unfolding and folding of the nascent protein and interaction of the protein with a receptor or pore complex. Examples of secretory proteins with amino terminal signal peptides are discussed below and include proteins with important roles in cell-to-cell signaling. Such proteins include transmembrane receptors and cell surface markers, extracellular matrix molecules, cytokines, hormones, growth and differentiation factors, neuropeptides, vasomediators, ion channels, transporters/pumps, and proteases. (Reviewed in Alberts, B. et al. (1994) Molecular Biology of The Cell. Garland Publishing, New York, NY, pp. 557-560, 582-592.)
G-protein coupled receptors (GPCRs) comprise a superfamily of integral membrane proteins which transduce extracellular signals. Not all GPCRs contain N-terminal signal peptides. GPCRs include receptors for biogenic amines such as dopamine, epinephrine, histamine, glutamate
(metabotropic-type), acetylcholine (muscarinic-type), and serotonin; for lipid mediators of inflammation such as prostaglandins, platelet activating factor, and leukotrienes; for peptide hormones such as calcitonin, C5a anaphylatoxin, follicle stimulating hormone, gonadotropin releasing hormone, neurokinin, oxytocin, and thrombin; and for sensory signal mediators such as retinal photopigments and olfactory stimulatory molecules. The structure of these highly conserved receptors consists of seven hydrophobic transmembrane regions, cysteine disulfide bridges between the second and third extracellular loops, an extracellular N-terminus, and a cytoplasmic C-terminus. The N-terminus interacts with ligands, the disulfide bridges interact with agonists and antagonists, and the large third intracellular loop interacts with G proteins to activate second messengers such as cyclic AMP, 5 phospholipase C, inositol triphosphate, or ion channels. (Reviewed in Watson, S. and Arkinstall, S. (1994) The G-protein Linked Receptor Facts Book. Academic Press, San Diego, CA, pp. 2-6; and Bolander, F.F. (1994) Molecular Endocrinology. Academic Press, San Diego, CA, pp. 162-176.) Other types of receptors include cell surface antigens identified on leukocytic cells of the immune system. These antigens have been identified using systematic, monoclonal antibody (mAb)- o based "shot gun" techniques. These techniques have resulted in the production of hundreds of mAbs directed against unknown cell surface leukocytic antigens. These antigens have been grouped into "clusters of differentiation" based on common immunocytochemical localization patterns in various differentiated and undifferentiated leukocytic cell types. Antigens in a given cluster are presumed to identify a single cell surface protein and are assigned a "cluster of differentiation" or "CD" 5 designation. Some of the genes encoding proteins identified by CD antigens have been cloned and verified by standard molecular biology techniques. CD antigens have been characterized as both transmembrane proteins and cell surface proteins anchored to the plasma membrane via covalent attachment to fatty acid-containing glycolipids such as glycosylphosphatidylinositol (GPI). (Reviewed in Barclay, A. N. et al. (1995) The Leucocyte Antigen Facts Book. Academic Press, San Diego, CA, 0 pp. 17-20.)
Matrix proteins (MPs) are transmembrane and extracellular proteins which function in formation, growth, remodeling, and maintenance of tissues and as important mediators and regulators of the inflammatory response. The expression and balance of MPs may be perturbed by biochemical changes that result from congenital, epigenetic, or infectious diseases. In addition, MPs affect 5 leukocyte migration, proliferation, differentiation, and activation in the immune response. MPs are frequently characterized by the presence of one or more domains which may include collagen-like domains, EGF-like domains, immunoglobulin-like domains, and fibronectin-like domains. In addition, MPs may be heavily glycosylated and may contain an Arginine-Glycine-Aspartate (RGD) tripeptide motif which may play a role in adhesive interactions. MPs include extracellular proteins such as o fibronectin, collagen, galectin, vitronectin and its proteolytic derivative somatomedin B ; and cell adhesion receptors such as cell adhesion molecules (CAMs), cadherins, and integrins. (Reviewed in Ayad, S. et al. (1994) The Extracellular Matrix Facts Book. Academic Press, San Diego, CA, pp. 2-16; Ruoslahti, E. (1997) Kidney Int. 51 :1413-1417; Sjaastad, M.D. and Nelson, W.J. (1997) BioEssays 19:47-55.) 5 Cytokines are secreted by hematopoietic cells in response to injury or infection. Interleukins, neurotrophins, growth factors, interferons, and chemokines all define cytokine families that work in conjunction with cellular receptors to regulate cell proliferation and differentiation. In addition, cytokines effect activities such as leukocyte migration and function, hematopoietic cell proliferation, temperature regulation, acute response to infection, tissue remodeling, and apoptosis. 5 Chemokines, in particular, are small chemoattractant cytokines involved in inflammation, leukocyte proliferation and migration, angiogenesis and angiostasis, regulation of hematopoiesis, HIV infectivity, and stimulation of cytokine secretion. Chemokines generally contain 70-100 amino acids and are subdivided into four subfamilies based on the presence of conserved cysteine-based motifs. (Callard, R. and Gearing, A. (1994) The Cytokine Facts Book, Academic Press, New York, NY, pp. 0 181-190, 210-213, 223-227.)
Growth and differentiation factors are secreted proteins which function in intercellular communication. Some factors require oligomerization or association with MPs for activity. Complex interactions among these factors and their receptors trigger intracellular signal transduction pathways that stimulate or inhibit cell division, cell differentiation, cell signaling, and cell motility. Most growth 5 and differentiation factors act on cells in their local environment (paracrine signaling). There are three broad classes of growth and differentiation factors. The first class includes the large polypeptide growth factors such as epidermal growth factor, fibroblast growth factor, transforming growth factor, insulin-like growth factor, and platelet-derived growth factor. The second class includes the hematopoietic growth factors such as the colony stimulating factors (CSFs). Hematopoietic growth o factors stimulate the proliferation and differentiation of blood cells such as B-lymphocytes, T- lymphocytes, erythrocytes, platelets, eosinophils, basophils, neutrophils, macrophages, and their stem cell precursors. The third class includes small peptide factors such as bombesin, vasopressin, oxytocin, endothelin, transferrin, angiotensin II, vasoactive intestinal peptide, and bradykinin which function as hormones to regulate cellular functions other than proliferation. 5 Growth and differentiation factors play critical roles in neoplastic transformation of cells in vitro and in tumor progression in vivo. Inappropriate expression of growth factors by tumor cells may contribute to vascularization and metastasis of tumors. During hematopoiesis, growth factor misregulation can result in anemias, leukemias, and lymphomas. Certain growth factors such as interferon are cytotoxic to tumor cells both in vivo and in vitro. Moreover, some growth factors and o growth factor receptors are related both structurally and functionally to oncoproteins. In addition, growth factors affect transcriptional regulation of both proto-oncogenes and oncosuppressor genes. (Reviewed in Pimentel, E. (1994) Handbook of Growth Factors. CRC Press, Ann Arbor, MI, pp. 1-9.) Proteolytic enzymes or proteases either activate or deactivate proteins by hydrolyzing peptide bonds. Proteases are found in the cytosol, in membrane-bound compartments, and in the extracellular 5 space. The major families are the zinc, serine, cysteine, thiol, and carboxyl proteases. Ion channels,, ion pumps, and transport proteins mediate the transport of molecules across cellular -membranes. Transport can occur by a passive, concentration-dependent mechanism or can be linked to an energy source such as ATP hydrolysis. Symporters and antiporters transport ions and small molecules such as amino acids, glucose, and drugs. Symporters transport molecules and ions unidirectionally, and antiporters transport molecules and ions bidirectionally. Transporter superfamilies include facilitative transporters and active ATP-binding cassette transporters which are involved in multiple-drug resistance and the targeting of antigenic peptides to MHC Class I molecules. These transporters bind to a specific ion or other molecule and undergo a conformational change in order to transfer the ion or molecule across the membrane. (Reviewed in Alberts, B. et al. (1994) Molecular Biology of The Cell. Garland Publishing, New York, NY, pp. 523-546.)
Ion channels are formed by transmembrane proteins which create a lined passageway across the membrane through which water and ions, such as Na+, K+, Ca2+, and CI", enter and exit the cell. For example, chloride channels are involved in the regulation of the membrane electric potential as well as absorption and secretion of ions across the membrane. Chloride channels also regulate the internal pH of membrane-bound organelles.
Ion pumps are ATPases which actively maintain membrane gradients. Ion pumps are classified as P, V, or F according to their structure and function. All have one or more binding sites for ATP in their cytosolic domains. The P-class ion pumps include Ca2+ ATPase and Na7K+ ATPase and function in transporting H+, Na+, K+, and Ca2+ ions. P-class pumps consist of two α and two β transmembrane subunits. The V- and F-class ion pumps have similar structures but transport only H+. F class H+ pumps mediate transport across the membranes of mitochondria and chloroplasts, while V-class H+ pumps regulate acidity inside lysosomes, endosomes, and plant vacuoles.
A family of structurally related intrinsic membrane proteins known as facilitative glucose transporters catalyze the movement of glucose and other selected sugars across the plasma membrane. The proteins in this family contain a highly conserved, large transmembrane domain comprised of 12 α-helices, and several weakly conserved, cytoplasmic and exoplasmic domains. (Pessin, J. E., and Bell, G.I. (1992) Annu. Rev. Physiol. 54:911-930.)
Amino acid transport is mediated by Na+ dependent amino acid transporters. These transporters are involved in gastrointestinal and renal uptake of dietary and cellular amino acids and in neuronal reuptake of neurotransmitters. Transport of cationic amino acids is mediated by the system y+ family and the cationic amino acid transporter (CAT) family. Members of the CAT family share a high degree of sequence homology, and each contains 12-14 putative transmembrane domains. (Ito, K. and Groudine, M. (1997) J. Biol. Chem. 272:26780-26786.)
Hormones are secreted molecules that travel through the circulation and bind to specific receptors on the surface of, or within, target cells. Although they have diverse biochemical compositions and mechanisms of action, hormones can be grouped into two categories. One category includes small lipophilic hormones that diffuse through the plasma membrane of target cells, bind to cytosolic or nuclear receptors, and form a complex that alters gene expression. Examples of these molecules include retinoic acid, thyroxine, and the cholesterol-derived steroid hormones such as progesterone, estrogen, testosterone, cortisol, and aldosterone. The second category includes hydrophilic hormones that function by binding to cell surface receptors that transduce signals across the plasma membrane. Examples of such hormones include amino acid derivatives such as catecholamines and peptide hormones such as glucagon, insulin, gastrin, secretin, cholecystokinin, adrenocorticotropic hormone, follicle stimulating hormone, luteinizing hormone, thyroid stimulating hormone, and vasopressin. (See, for example, Lodish et al. (1995) Molecular Cell Biology. Scientific American Books Inc., New York, NY, pp. 856-864.)
Neuropeptides and vasomediators (NP/VM) comprise a large family of endogenous signaling molecules. Included in this family are neuropeptides and neuropeptide hormones such as bombesin, neuropeptide Y, neurotensin, neuromedin N, melanocortins, opioids, galanin, somatostatin, tachykinins, urotensin II and related peptides involved in smooth muscle stimulation, vasopressin, vasoactive intestinal peptide, and circulatory system-borne signaling molecules such as angiotensin, complement, calcitonin, endothelins, formyl-methionyl peptides, glucagon, cholecystokinin and gastrin. NP/VMs can transduce signals directly, modulate the activity or release of other neurotransmitters and hormones, and act as catalytic enzymes in cascades. The effects of NP/VMs range from extremely brief to long- lasting. (Reviewed in Martin, C. R. et al. (1985) Endocrine Physiology. Oxford University Press. New York, NY, pp. 57-62.)
The discovery of new secretory molecules satisfies a need in the art by providing new compositions which are useful in the diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, cell signaling and the expression of secretory molecules.
SUMMARY OF THE INVENTION The present invention relates to nucleic acid sequences comprising human polynucleotides encoding secretory polypeptides that contain signal peptides and/or transmembrane domains. These human polynucleotides (sptm) as presented in the Sequence Listing uniquely identify partial or full length genes encoding structural, functional, and regulatory polypeptides involved in cell signaling. The invention provides an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). In one alternative, the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63. In another alternative, the polynucleotide comprises at least 60 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The invention further provides a composition for the detection of expression of secretory polynucleotides comprising at least one isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d); and a detectable label. The invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -63 ; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof. In one alternative, the probe comprises at least 30 contiguous nucleotides. In another alternative, the probe comprises at least 60 contiguous nucleotides.
The invention further provides a recombinant polynucleotide comprising a promoter sequence operably linked to an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -
63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). In one alternative, the invention provides a cell transformed with the recombinant polynucleotide. In another alternative, the invention provides a transgenic organism comprising the recombinant polynucleotide. In a further alternative, the invention provides a method for producing a secretory polypeptide, the method comprising a) culturing a cell under conditions suitable for expression of the secretory polypeptide, wherein said cell is transformed with the recombinant polynucleotide, and b) recovering the secretory polypeptide so expressed. 5 The invention also provides a purified secretory polypeptide (SPTM) encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63. Additionally, the invention provides an isolated antibody which specifically binds to the secretory polypeptide. The invention further provides a method of identifying a test compound which specifically binds to the secretory polypeptide, the method comprising the steps of a) providing a test o compound; b) combining the secretory polypeptide with the test compound for a sufficient time and under suitable conditions for binding; and c) detecting binding of the secretory polypeptide to the test compound, thereby identifying the test compound which specifically binds the secretory polypeptide. The invention further provides a microarray wherein at least one element of the microarray is an isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide comprising 5 a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The invention also provides a method o for generating a transcript image of a sample which contains polynucleotides. The method comprises a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
Additionally, the invention provides a method for screening a compound for effectiveness in 5 altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence o complementary to b); and e) an RNA equivalent of a) through d). The method comprises a) exposing a sample comprising the target polynucleotide to a compound, and b) detecting altered expression of the target polynucleotide.
The invention further provides a method for assessing toxicity of a test compound, said method comprising a) treating a biological sample containing nucleic acids with the test compound; b) 5 hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide comprising a polynucleotide sequence selected from the group consisting of i) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1- 63; ii) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63; iii) a polynucleotide 5 sequence complementary to i), iv) a polynucleotide sequence complementary to ii), and v) an RNA equivalent of i)-iv). Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of i) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; ii) a naturally o occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63; iii) a polynucleotide sequence complementary to i), iv) a polynucleotide sequence complementary to ii), and v) an RNA equivalent of i)-iv), and alternatively, the target polynucleotide comprises a fragment of a polynucleotide sequence selected from the group consisting of i-v above; c) quantifying the amount of hybridization complex; 5 and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.
DESCRIPTION OF THE TABLES Table 1 shows the sequence identification numbers (SEQ ID NO:s) and template identification o numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated "start" and "stop" nucleotide positions. The reading frames of the polynucleotide segments are shown, and the polypeptides encoded by the polynucleotide segments constitute either signal peptide (SP) or transmembrane (TM) domains, as indicated. 5 Table 2 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with component sequence identification numbers (component IDs) corresponding to each template. The component sequences, which were used to assemble the template sequences, are defined by the indicated "start" and "stop" nucleotide positions along each template. o Table 3 shows the tissue distribution profiles for the templates of the invention.
Table 4 summarizes the bioinformatics tools which are useful for analysis of the polynucleotides of the present invention. The first column of Table 4 lists analytical tools, programs, and algorithms, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incorporated by reference herein in their entirety, and the fourth 5 column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences).
DETAILED DESCRIPTION OF THE INVENTION
Before the nucleic acid sequences and methods are presented, it is to be understood that this invention is not limited to the particular machines, methods, and materials described. Although particular embodiments are described, machines, methods, and materials similar or equivalent to these embodiments may be used to practice the invention. The preferred machines, methods, and materials set forth are not intended to limit the scope of the invention which is limited only by the appended claims. The singular forms "a", "an", and "the" include plural reference unless the context clearly dictates otherwise. All technical and scientific terms have the meanings commonly understood by one of ordinary skill in the art. All publications are incorporated by reference for the purpose of describing and disclosing the cell lines, vectors, and methodologies which are presented and which might be used in connection with the invention. Nothing in the specification is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention. Definitions
As used herein, the lower case "sptm" refers to a nucleic acid sequence, while the upper case "SPTM" refers to an amino acid sequence encoded by sptm. A "full-length" sptm refers to a nucleic acid sequence containing the entire coding region of a gene endogenously expressed in human tissue. "Adjuvants" are materials such as Freund's adjuvant, mineral gels (aluminum hydroxide), and surface active substances (lysolecithin, pluro ic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol) which may be administered to increase a host's immunological response.
"Allele" refers to an alternative form of a nucleic acid sequence. Alleles result from a "mutation," a change or an alternative reading of the genetic code. Any given gene may have none, one, or many allelic forms. Mutations which give rise to alleles include deletions, additions, or substitutions of nucleotides. Each of these changes may occur alone, or in combination with the others, one or more times in a given nucleic acid sequence. The present invention encompasses allelic sptm.
"Amino acid sequence" refers to a peptide, a polypeptide, or a protein of either natural or synthetic origin. The amino acid sequence is not limited to the complete, endogenous amino acid sequence and may be a fragment, epitope, variant, or derivative of a protein expressed by a nucleic acid sequence.
"Amplification" refers to the production of additional copies of a sequence and is carried out using polymerase chain reaction (PCR) technologies well known in the art. "Antibody" refers to intact molecules as well as to fragments thereof, such as Fab, F(ab')2> and Fv fragments, which are capable of binding the epitopic determinant. Antibodies that bind SPTM polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or peptide used to immunize an animal (e.g., a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.
"Antisense sequence" refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence may include DNA, RNA, or any nucleic acid mimic or analog such as peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2'-methoxyethyl sugars or 2'-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5 -methyl cytosine, 2'-deoxyuracil, or 7-deaza-2'-deoxyguanosine.
"Antisense sequence" refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence can be DNA, RNA, or any nucleic acid mimic or analog.
"Antisense technology" refers to any technology which relies on the specific hybridization of an antisense sequence to a target sequence.
A "bin" is a portion of computer memory space used by a computer program for storage of data, and bounded in such a manna- that data stored in a bin may be retrieved by the program. "Biologically active" refers to an amino acid sequence having a structural, regulatory, or biochemical function of a naturally occurring amino acid sequence.
"Clone joining" is a process for combining gene bins based upon the bins' containing sequence information from the same clone. The sequences may assemble into a primary gene transcript as well as one or more splice variants. "Complementary" describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing (5'-A-G-T-3' pairs with its complement 3'-T-C-A-5')*
A "component sequence" is a nucleic acid sequence selected by a computer program such as
PHRED and used to assemble a consensus or template sequence from one or more component sequences. A "consensus sequence" or "template sequence" is a nucleic acid sequence which has been assembled from overlapping sequences, using a computer program for fragment assembly such as the
GEL VIEW fragment assembly system (Genetics Computer Group (GCG), Madison WT) or using a relational database management system (RDMS).
"Conservative amino acid substitutions" are those substitutions that, when made, least interfere with the properties of the original protein, i.e. , the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.
Original Residue Conservative Substitution
Ala Gly, Ser
Arg His, Lys
Asn Asp, Gin, His
Asp Asn, Glu Cys Ala, Ser
Gin Asn, Glu, His
Glu Asp, Gin, His
Gly Ala
His Asn, Arg, Gin, Glu lie Leu, Val
Leu lie, Val
Lys Arg, Gin, Glu
Met Leu, He
Phe His, Met, Leu, Trp, Tyr Ser Cys, Thr
Thr Ser, Val
Tip Phe, Tyr
Tyr His, Phe, Trp Val fie, Leu, Thr Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
"Deletion" refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or amino acid residue, respectively, is absent. "Derivative" refers to the chemical modification of a nucleic acid sequence, such as by replacement of hydrogen by an alkyl, acyl, amino, hydroxyl, or other group.
The terms "element" and "array element" refer to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray.
Ε-value" refers to the statistical probability that a match between two sequences occurred by chance.
A "fragment" is a unique portion of sptm or SPTM which is identical in sequence to but shorter in length than the parent sequence. A fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue. For example, a fragment may comprise from 10 to 1000 contiguous amino acid residues or nucleotides. A fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, may be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous amino acid residues or nucleotides in length. Fragments may be preferentially selected from certain regions of a molecule. For example, a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence. Clearly these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing and the 5 figures, may be encompassed by the present embodiments.
A fragment of sptm comprises a region of unique polynucleotide sequence that specifically identifies sptm, for example, as distinct from any other sequence in the same genome. A fragment of sptm is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish sptm from related polynucleotide sequences. The precise length of a fragment of sptm o and the region of sptm to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
A fragment of SPTM is encoded by a fragment of sptm. A fragment of SPTM comprises a region of unique amino acid sequence that specifically identifies SPTM. For example, a fragment of SPTM is useful as an immunogenic peptide for the development of antibodies that specifically 5 recognize SPTM. The precise length of a fragment of SPTM and the region of SPTM to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
A "full length" nucleotide sequence is one containing at least a start site for translation to a protein sequence, followed by an open reading frame and a stop site, and encoding a "full length" 0 polypeptide.
"Hit" refers to a sequence whose annotation will be used to describe a given template. Criteria for selecting the top hit are as follows: if the template has one or more exact nucleic acid matches, the top hit is the exact match with highest percent identity. If the template has no exact matches but has significant protein hits, the top hit is the protein hit with the lowest E- value. If the template has no 5 significant protein hits, but does have significant non-exact nucleotide hits, the top hit is the nucleotide hit with the lowest E- value.
"Homology" refers to sequence similarity either between a reference nucleic acid sequence and at least a fragment of an sptm or between a reference amino acid sequence and a fragment of an SPTM.
"Hybridization" refers to the process by which a strand of nucleotides anneals with a o complementary strand through base pairing. Specific hybridization is an indication that two nucleic acid sequences share a high degree of identity. Specific hybridization complexes form under defined annealing conditions, and remain hybridized after the "washing" step. The defined hybridization conditions include the annealing conditions and the washing step(s), the latter of which is particularly important in determining the stringency of the hybridization process, with more stringent conditions 5 allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched. Permissive conditions for annealing of nucleic acid sequences are routinely determinable and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency.
Generally, stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out. Generally, such wash temperatures are selected to be about 5°C to 20°C lower than the thermal melting point (T for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating Tm and conditions for nucleic acid hybridization is well known and can be found in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Press, Plainview NY; specifically see volume 2, chapter 9.
High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68°C in the presence of about 0.2 x SSC and about 0.1% SDS, for 1 hour. Alternatively, temperatures of about 65°C, 60°C, or 55°C may be used. SSC concentration may be varied from about 0.2 to 2 x SSC, with SDS being present at about 0.1 %. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 μg/ml. Useful variations on these conditions will be readily apparent to those skilled in the art. Hybridization, particularly undo- high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their resultant proteins.
Other parameters, such as temperature, salt concentration, and detergent concentration may be varied to achieve the desired stringency. Denaturants, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as RNA:DNA hybridizations. Appropriate hybridization conditions are routinely determinable by one of ordinary skill in the art. "Immunogenic" describes the potential for a natural, recombinant, or synthetic peptide, epitope, polypeptide, or protein to induce antibody production in appropriate animals, cells, or cell lines.
"Insertion" or "addition" refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or residue, respectively, is added to the sequence.
"Labeling" refers to the covalent or noncovalent joining of a polynucleotide, polypeptide, or antibody with a reporter molecule capable of producing a detectable or measurable signal.
"Microarray" is any arrangement of nucleic acids, amino acids, antibodies, etc., on a substrate. The substrate may be a solid support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.
"Linkers" are short stretches of nucleotide sequence which may be added to a vector or an sptm to create restriction endonuclease sites to facilitate cloning. "PolyUnkers" are engineered to incorporate multiple restriction enzyme sites and to provide for the use of enzymes which leave 5 ' or 3' overhangs (e.g., BamHI, EcoRI, and Hindlll) and those which provide blunt ends (e.g., EcoRV, SnaBI, and Stul).
"Naturally occurring" refers to an endogenous polynucleotide or polypeptide that may be isolated from viruses or prokaryotic or eukaryotic cells. 5 "Nucleic acid sequence" refers to the specific order of nucleotides joined by phosphodiester bonds in a linear, polymeric arrangement. Depending on the number of nucleotides, the nucleic acid sequence can be considered an oligomer, ohgonucleotide, or polynucleotide. The nucleic acid can be DNA, RNA, or any nucleic acid analog, such as PNA, may be of genomic or synthetic origin, may be either double-stranded or single-stranded, and can represent either the sense or antisense 0 (complementary) strand.
"Oligomer" refers to a nucleic acid sequence of at least about 6 nucleotides and as many as about 60 nucleotides, preferably about 15 to 40 nucleotides, and most preferably between about 20 and 30 nucleotides, that may be used in hybridization or amplification technologies. Oligomers may be used as, e.g., primers for PCR, and are usually chemically synthesized. 5 "Operably linked" refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame. o "Peptide nucleic acid" (PNA) refers to a DNA mimic in which nucleotide bases are attached to a pseudopeptide backbone to increase stability. PNAs, also designated antigene agents, can prevent gene expression by targeting complementary messenger RNA.
The phrases "percent identity" and "% identity", as applied to polynucleotide sequences, refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a 5 standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.
Percent identity between polynucleotide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence o alignment program. This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison WT). CLUSTAL V is described in Higgins, D.G. and Sharp, P.M. (1989) CABIOS 5:151-153 and in Higgins, D.G. et al. (1992) CABIOS 8:189-191. For pairwise alignments of polynucleotide sequences, the default parameters are set as follows: Ktuple=2, gap penalty=5, window=4, and "diagonals saved"=4. The "weighted" residue weight table is selected as the default. Percent identity is reported by CLUSTAL V as the "percent similarity" between aligned polynucleotide sequence pairs.
Alternatively, a suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search 5 Tool (BLAST) (Altschul, S.F. et al. (1990) J. Mol. Biol. 215:403-410), which is available from several sources, including the NCBI, Bethesda, MD, and on the Internet at http://www.ncbi.nlm.nih.gov/BLAST/. The BLAST software suite includes various sequence analysis programs including "blastn," that is used to determine alignment between a known polynucleotide sequence and other sequences on a variety of databases. Also available is a tool called "BLAST 2 0 Sequences" that is used for direct pairwise comparison of two nucleotide sequences. "BLAST 2 Sequences" can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/bl2/. The "BLAST 2 Sequences" tool can be used for both blastn and blastp (discussed below). BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the "BLAST 2 Sequences" tool Version 5 2.0.9 (May-07-1999) set at default parameters. Such default parameters may be, for example:
Matrix: BLOSUM62
Reward for match: 1
Penalty for mismatch: -2
Open Gap: 5 and Extension Gap: 2 penalties o Gap x drop-off: 50
Expect: 10
Word Size: 11
Filter: on
Percent identity may be measured over the length of an entire defined sequence, for example, as 5 defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage o identity may be measured.
Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein. The phrases "percent identity" and "% identity", as applied to polypeptide sequences, refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the hydrophobicity and acidity of the substituted residue, thus preserving the structure (and therefore function) of the folded polypeptide.
Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program (described and referenced above). For pairwise alignments of polypeptide sequences using CLUSTAL V, the default parameters are set as follows: Ktuple=l, gap penalty=3, window=5, and "diagonals saved"=5. The PAM250 matrix is selected as the default residue weight table. As with polynucleotide alignments, the percent identity is reported by CLUSTAL V as the "percent similarity" between aligned polypeptide sequence pairs.
Alternatively the NCBI BLAST software suite may be used. For example, for a pairwise comparison of two polypeptide sequences, one may use the "BLAST 2 Sequences" tool Version 2.0.9 (May-07-1999) with blastp set at default parameters. Such default parameters may be, for example:
Matrix: BLOSUM62
Open Gap: 11 and Extension Gap: 1 penalty
Gap x drop-off: 50 Expect: 10
Word Size: 3
Filter: on
Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured. "Post-translational modification" of an SPTM may involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu and the SPTM.
"Probe" refers to sptm or fragments thereof, which are used to detect identical, allelic or related nucleic acid sequences. Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes. "Primers" are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification 5 (and identification) of a nucleic acid sequence, e.g„ by the polymerase chain reaction (PCR).
Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30, 40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may 0 be considerably longer than these examples, and it is understood that any length supported by the specification, including the figures and Sequence Listing, may be used.
Methods for preparing and using probes and primers are described in the references, for example Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual. 2nd ed., vol. 1-3, Cold Spring Harbor Press, Plainview NY; Ausubel et al.,1987, Current Protocols in Molecular Biology. 5 Greene Publ. Assoc. & Wiley-Intersciences, New York NY; Innis et al., 1990, PCR Protocols. A Guide to Methods and Applications. Academic Press, San Diego CA. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge MA).
Oligonucleotides for use as primers are selected using software known in the art for such o purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South 5 West Medical Center, Dallas TX) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope. The Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge MA) allows the user to input a "mispriming library," in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for o microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.) The PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences. 5 Hence, this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments. The oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of ohgonucleotide selection are not limited to 5 those described above.
"Purified" refers to molecules, either polynucleotides or polypeptides that are isolated or separated from their natural environment and are at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other compounds with which they are naturally associated.
A "recombinant nucleic acid" is a sequence that is not naturally occurring or has a sequence o that is made by an artificial combination of two or more otherwise separated segments of sequence.
This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra. The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a 5 recombinant nucleic acid may include a nucleic acid sequence operably hnked to a promoter sequence. Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.
Alternatively, such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal. o "Regulatory element" refers to a nucleic acid sequence from nontranslated regions of a gene, and includes enhancers, promoters, introns, and 3' untranslated regions, which interact with host proteins to carry out or regulate transcription or translation.
"Reporter" molecules are chemical or biochemical moieties used for labeling a nucleic acid, an amino acid, or an antibody. They include radionuclides; enzymes; fluorescent, chemiluminescent, or 5 chromogenic agents; substrates; cof actors; inhibitors; magnetic particles; and other moieties known in the art.
An "RNA equivalent," in reference to a DNA sequence, is composed of the same linear sequence of nucleotides as the reference DNA sequence with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose o instead of deoxyribose.
"Sample" is used in its broadest sense. Samples may contain nucleic or amino acids, antibodies, or other materials, and may be derived from any source (e.g., bodily fluids including, but not limited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots 5 or imprints from such cells or tissues). "Specific binding" or "specifically binding" refers to the interaction between a protein or peptide and its agonist, antibody, antagonist, or other binding partner. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope "A," the presence of a polypeptide containing epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.
"Substitution" refers to the replacement of at least one nucleotide or amino acid by a different nucleotide or amino acid. "Substrate" refers to any suitable rigid or semi-rigid support including, e.g., membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles or capillaries. The substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.
A "transcript image" refers to the collective pattern of gene expression by a particular tissue or cell type under given conditions at a given time.
"Transformation" refers to a process by which exogenous DNA enters a recipient cell. Transformation may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed.
"Transformants" include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as cells which transiently express inserted DNA or RNA.
A "transgenic organism," as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art. The nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus. The term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule. The transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, and plants and animals. The isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), supra. A "variant" of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 25% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07-1999) set at default parameters. Such a pair of nucleic acids may show, for example, at least 30%, at least 5 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or even at least 98% or greater sequence identity over a certain defined length. The variant may result in "conservative" amino acid changes which do not affect structural and/or chemical properties. A variant may be described as, for example, an "allelic" (as defined above), "splice," "species," or "polymorphic" variant. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser o number of polynucleotides due to alternate splicing of exons during mRNA processing. The corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule. Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other. A polymorphic variant is a variation in the polynucleotide sequence of a particular gene between 5 individuals of a given species. Polymorphic variants also may encompass "single nucleotide polymorphisms" (SNPs) in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
In an alternative, variants of the polynucleotides of the present invention may be generated o through recombinant methods. One possible method is a DNA shuffling technique such as
MOLECULARBREEDING (Maxygen Inc., Santa Clara CA; described in U.S. Patent Number 5,837,458; Chang, C.-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F.C. et al. (1999) Nat. Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol. 14:315-319) to alter or improve the biological properties of SPTM, such as its biological or enzymatic activity or its ability to bind to 5 other molecules or compounds. DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and further subjected to recursive rounds of DNA shuffling and selection/screening. Thus, genetic diversity is created through "artificial" breeding and rapid molecular o evolution. For example, fragments of a single gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner. A "variant" of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07- 1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%, at 5 least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% or greater sequence identity over a certain defined length of one of the polypeptides. THE INVENTION
In a particular embodiment, cDNA sequences derived from human tissues and cell lines were aligned based on nucleotide sequence identity and assembled into "consensus" or "template" sequences o which are designated by the template identification numbers (template IDs) in column 2 of Table 1.
The sequence identification numbers (SEQ ID NO:s) corresponding to the template IDs are shown in column 1. Segments of the template sequences are defined by the "start" and "stop" nucleotide positions listed in columns 3 and 4. These segments, when translated in the reading frames indicated in column 5, have similarity to signal peptide (SP) or transmembrane (TM) domain consensus sequences, 5 as indicated in column 6.
The invention incorporates the nucleic acid sequences of these templates as disclosed in the Sequence Listing and the use of these sequences in the diagnosis and treatment of disease states characterized by defects in cell signaling. The invention further utilizes these sequences in hybridization and amplification technologies, and in particular, in technologies which assess gene expression patterns o correlated with specific cells or tissues and their responses in vivo or in vitro to pharmaceutical agents, toxins, and other treatments. In this manner, the sequences of the present invention are used to develop a transcript image for a particular cell or tissue. Derivation of Nucleic Acid Sequences cDNA was isolated from libraries constructed using RNA derived from normal and diseased 5 human tissues and cell lines. The human tissues and cell lines used for cDNA Ubrary construction were selected from a broad range of sources to provide a diverse population of" cDNAs representative of gene transcription throughout the human body. Descriptions of the human tissues and cell lines used for cDNA Ubrary construction are provided in the LIFESEQ database (Incyte Genomics, Inc. (Incyte), Palo Alto CA). Human tissues were broadly selected from, for example, cardiovascular, dermatologic, 0 endocrine, gastrointestinal, hematopoietic/immune system, musculoskeletal, neural, reproductive, and urologic sources.
Cell Unes used for cDNA library construction were derived from, for example, leukemic cells, teratocarcinomas, neuroepitheUomas, cervical carcinoma, lung fibroblasts, and endotheUal cells. Such cell Unes include, for example, THP-1, lurkat, HUVEC, hNT2, WI38, HeLa, and other cell Unes 5 commonly used and available from pubUc depositories (American Type Culture Collection, Manassas VA). Prior to mRNA isolation, cell Unes were untreated, treated with a pharmaceutical agent such as 5'-aza-2'-deoxycytidine, treated with an activating agent such as lipopolysaccharide in the case of leukocytic cell Unes, or, in the case of endotheUal cell Unes, subjected to shear stress. Sequencing of the cDNAs Methods for DNA sequencing are well known in the art. Conventional enzymatic methods employ the Klenow fragment of DNA polymerase I, SEQUENASE DNA polymerase (U.S. Biochemical Corporation, Cleveland OH), Taq polymerase (PE Biosystems, Foster City CA), thermostable T7 polymerase (Amersham Pharmacia Biotech, Inc. (Amersham Pharmacia Biotech), Piscataway NJ), or combinations of polymer ases and proofreading exonucleases such as those found in the ELONGASE ampUfication system (Life Technologies Inc. (Life Technologies), Gaithersburg MD), to extend the nucleic acid sequence from an oUgonucleotide primer annealed to the DNA template of interest. Methods have been developed for the use of both single-stranded and double-stranded templates. Chain termination reaction products may be electrophoresed on urea-polyacrylamide gels and detected either by autoradiography (for radioisotope-labeled nucleotides) or by fluorescence (for fluorophore-labeled nucleotides). Automated methods for mechanized reaction preparation, sequencing, and analysis using fluorescence detection methods have been developed. Machines used to prepare cDNAs for sequencing can include the MICROLAB 2200 Uquid transfer system (Hamilton Company (Hamilton), Reno NV), Peltier thermal cycler (PTC200; MJ Research, Inc. (MJ Research), Watertown MA), and ABI CATALYST 800 thermal cycler (PE Biosystems). Sequencing can be carried out using, for example, the ABI 373 or 377 (PE Biosystems) or MEGABACE 1000 (Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale CA) DNA sequencing systems, or other automated and manual sequencing systems well known in the art.
The nucleotide sequences of the Sequence Listing have been prepared by current, state-of-the- art, automated methods and, as such, may contain occasional sequencing errors or unidentified nucleotides. Such unidentified nucleotides are designated by an N. These infrequent unidentified bases do not represent a hindrance to practicing the invention for those skilled in the art. Several methods employing standard recombinant techniques may be used to correct errors and complete the missing sequence information. (See, e.g., those described in Ausubel, F.M. et al. (1997) Short Protocols in Molecular Biology. John Wiley & Sons, New York NY; and Sambrook, J. et al. (1989) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Press, Plainview NY.)
Assembly of cDNA Sequences
Human polynucleotide sequences may be assembled using programs or algorithms well known in the art. Sequences to be assembled are related, wholly or in part, and may be derived from a single or many different transcripts. Assembly of the sequences can be performed using such programs as PHRAP (Phils Revised Assembly Program) and the GEL VIEW fragment assembly system (GCG), or other methods known in the art.
Alternatively, cDNA sequences are used as "component" sequences that are assembled into "template" or "consensus" sequences as follows. Sequence chromatograms are processed, verified, and quatity scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., the LIFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA). A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) are replaced by "n's", or masked, to prevent spurious matches. Mitochondrial and ribosomal RNA sequences are also removed. The processed sequences are then loaded into a relational database management system (RDMS) which assigns edited sequences to existing templates, if available. When additional sequences are added into the RDMS, a process is initiated which modifies existing templates or creates new templates from works in progress (i.e., nonfinal assembled sequences) containing queued sequences or the sequences themselves. After the new sequences have been assigned to templates, the templates can be merged into bins. If multiple templates exist in one bin, the bin can be spUt and the templates reannotated.
Once gene bins have been generated based upon sequence aUgnments, bins are "clone joined" based upon clone information. Clone joining occurs when the 5' sequence of one clone is present in one bin and the 3' sequence from the same clone is present in a different bin, indicating that the two bins should be merged into a single bin. Only bins which share at least two different clones are merged. A resultant template sequence may contain either a partial or a full length open reading frame, or all or part of a genetic regulatory element. This variation is due in part to the fact that the full length cDNAs of many genes are several hundred, and sometimes several thousand, bases in length. With current technology, cDNAs comprising the coding regions of large genes cannot be cloned because of vector limitations, incomplete reverse transcription of the mRNA, or incomplete "second strand" synthesis. Template sequences may be extended to include additional contiguous sequences derived from the parent RNA transcript using a variety of methods known to those of skill in the art. Extension may thus be used to achieve the full length coding sequence of a gene. Analysis of the cDNA Sequences
The cDNA sequences are analyzed using a variety of programs and algorithms which are well known in the art. (See, e.g., Ausubel, 1997, supra, Chapter 7.7; Meyers, R.A. (Ed.) (1995) Molecular Biology and Biotechnology, Wiley VCH, New York NY, pp. 856-853; and Table 4.) These analyses comprise both reading frame determinations, e.g., based on triplet codon periodicity for particular organisms (Fickett, J.W. (1982) Nucleic Acids Res. 10:5303-5318); analyses of potential start and stop codons; and homology searches. Computer programs known to those of skill in the art for performing computer-assisted searches for amino acid and nucleic acid sequence similarity, include, for example, Basic Local AUgnment Search Tool (BLAST; Altschul, S.F. (1993) J. Mol. Evol. 36:290-300; Altschul, S.F. et al. (1990) J. Mol. Biol. 215:403-410). BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose aUgnment is locally maximal and for which the aUgnment score meets or exceeds a threshold or cutoff score set by the user (KarUn, S. et al. (1988) Proc. Natl. Acad. Sci. USA 85:841-845). Using an appropriate search tool (e.g., BLAST or HMM), GenBank, SwissProt, BLOCKS, PFAM and other databases may be searched for sequences containing regions of homology to a query sptm or SPTM of the present invention. Other approaches to the identification, assembly, storage, and display of nucleotide and polypeptide sequences are provided in "Relational Database for Storing Biomolecule Information," U.S.S.N. 08/947,845, filed October 9, 1997; "Project-Based Full-Length Biomolecular Sequence Database," U.S.S.N. 08/811,758, filed March 6, 1997; and "Relational Database and System for Storing Information Relating to Biomolecular Sequences," U.S.S.N. 09/034,807, filed March 4, 1998, all of which are incorporated by reference herein in their entirety.
Protein hierarchies can be assigned to the putative encoded polypeptide based on, e.g., motif, BLAST, or biological analysis. Methods for assigning these hierarchies are described, for example, in "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data," U.S.S.N. 08/812,290, filed March 6, 1997, incorporated herein by reference. Human Secretory Sequences
The sptm of the present invention may be used for a variety of diagnostic and therapeutic purposes. For example, an sptm may be used to diagnose a particular condition, disease, or disorder associated with cell signaUng. Such conditions, diseases, and disorders include, but are not limited to, a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, a cancer of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; an immune system disorder such as such as inflammation, actinic keratosis, acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondyUtis, amyloidosis, anemia, arteriosclerosis, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, bronchitis, bursitis, cholecystitis, cirrhosis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, paroxysmal nocturnal hemoglobinuria, hepatitis, hypereosinophilia, irritable bowel syndrome, episodic lymphopenia with lymphocytotoxins, mixed connective tissue disease (MCTD), multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, myelofibrosis, osteoarthritis, osteoporosis, pancreatitis, polycythemia vera, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjogren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, primary thrombocythemia, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, trauma, and hematopoietic cancer including lymphoma, leukemia, and myeloma; and a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyeUnating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myeUtis and radicuUtis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal famiUal insomnia, nutritional and metaboUc diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorder of the central nervous system, cerebral palsy, a neuroskeletal disorder, an autonomic nervous system disorder, a cranial nerve disorder, a spinal cord disease, muscular dystrophy and other neuromuscular disorder, a peripheral nervous system disorder, dermatomyositis and polymyositis, inherited, metaboUc, endocrine, and toxic myopathy, myasthenia gravis, periodic paralysis, a mental disorder including mood, anxiety, and schizophrenic disorder, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postheφetic neuralgia, and Tourette' s disorder. The sptm can be used to detect the presence of, or to quantify the amount of, an sptm-related polynucleotide in a sample. This information is then compared to information obtained from appropriate reference samples, and a diagnosis is estabUshed. Alternatively, a polynucleotide complementary to a given sptm can inhibit or inactivate a therapeutically relevant gene related to the sptm Analysis of sptm Expression Patterns
The expression of sptm may be routinely assessed by hybridization-based methods to determine, for example, the tissue-specificity, disease-specificity, or developmental stage-specificity of sptm expression. For example, the level of expression of sptm may be compared among different cell types or tissues, among diseased and normal cell types or tissues, among cell types or tissues at different developmental stages, or among cell types or tissues undergoing various treatments. This type of analysis is useful, for example, to assess the relative levels of sptm expression in fully or partially differentiated cells or tissues, to determine if changes in sptm expression levels are correlated with the development or progression of specific disease states, and to assess the response of a cell or tissue to a specific therapy, for example, in pharmacological or toxicological studies. Methods for the analysis of 5 sptm expression are based on hybridization and ampUfication technologies and include membrane-based procedures such as northern blot analysis, high-throughput procedures that utilize, for example, microarrays, and PCR-based procedures.
Hybridization and Genetic Analysis 0 The sptm, their fragments, or complementary sequences, may be used to identify the presence of and/or to determine the degree of similarity between two (or more) nucleic acid sequences. The sptm may be hybridized to naturally occurring or recombinant nucleic acid sequences under appropriately selected temperatures and salt concentrations. Hybridization with a probe based on the nucleic acid sequence of at least one of the sptm allows for the detection of nucleic acid sequences, including 5 genomic sequences, which are identical or related to the sptm of the Sequence Listing. Probes may be selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ ID NO: 1 - 63 and tested for their abiUty to identify or ampUfy the target nucleic acid sequence using standard protocols.
Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ 0 ID NO:l-63 and fragments thereof, can be identified using various conditions of stringency. (See, e.g., Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A.R. (1987) Methods Enzymol. 152:507-511.) Hybridization conditions are discussed in "Definitions."
A probe for use in Southern or northern hybridization may be derived from a fragment of an sptm sequence, or its complement, that is up to several hundred nucleotides in length and is either 5 single-stranded or double-stranded. Such probes may be hybridized in solution to biological materials such as plasmids, bacterial, yeast, or human artificial chromosomes, cleared or sectioned tissues, or to artificial substrates containing sptm. Microarrays are particularly suitable for identifying the presence of and detecting the level of expression for multiple genes of interest by examining gene expression correlated with, e.g., various stages of development, treatment with a drug or compound, or disease o progression. An array analogous to a dot or slot blot may be used to arrange and Unk polynucleotides to the surface of a substrate using one or more of the following: mechanical (vacuum), chemical, thermal, or UV bonding procedures. Such an array may contain any number of sptm and may be produced by hand or by using available devices, materials, and machines.
Microarrays may be prepared, used, and analyzed using methods known in the art. (See, e.g., 5 Brennan, T.M. et al. (1995) U.S. Patent No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:10614-10619; Baldeschweiler et al. (1995) PCT appUcation W095/251116; Shalon, D. et al. (1995) PCT appUcation WO95/35505; Heller, R.A. et al. (1997) Proc. Natl. Acad. Sci. USA 94:2150- 2155; and Heller, M.J. et al. (1997) U.S. Patent No. 5,605,662.)
Probes may be labeled by either PCR or enzymatic techniques using a variety of commercially 5 available reporter molecules. For example, commercial kits are available for radioactive and chemiluminescent labeling (Amersham Pharmacia Biotech) and for alkaUne phosphatase labeUng (Life Technologies). Alternatively, sptm may be cloned into commercially available vectors for the production of RNA probes. Such probes may be transcribed in the presence of at least one labeled nucleotide (e.g., 3 P-ATP, Amersham Pharmacia Biotech). 0 Additionally the polynucleotides of SEQ ID NO:l-63 or suitable fragments thereof can be used to isolate full length cDNA sequences utiUzing hybridization and/or ampUfication procedures well known in the art, e.g., cDNA Ubrary screening, PCR ampUfication, etc. The molecular cloning of such full length cDNA sequences may employ the method of cDNA Ubrary screening with probes using the hybridization, stringency, washing, and probing strategies described above and in Ausubel, supra. 5 Chapters 3, 5, and 6. These procedures may also be employed with genomic libraries to isolate genomic sequences of sptm in order to analyze, e.g., regulatory elements. Genetic Mapping
Gene identification and mapping are important in the investigation and treatment of almost all conditions, diseases, and disorders. Cancer, cardiovascular disease, Alzheimer's disease, arthritis, o diabetes, and mental illnesses are of particular interest. Each of these conditions is more complex than the single gene defects of sickle cell anemia or cystic fibrosis, with select groups of genes being predictive of predisposition for a particular condition, disease, or disorder. For example, cardiovascular disease may result from malfunctioning receptor molecules that fail to clear cholesterol from the bloodstream, and diabetes may result when a particular individual's immune system is 5 activated by an infection and attacks the insulin-producing cells of the pancreas. In some studies,
Alzheimer's disease has been Unked to a gene on chromosome 21; other studies predict a different gene and location. Mapping of disease genes is a complex and reiterative process and generally proceeds from genetic linkage analysis to physical mapping.
As a condition is noted among members of a family, a genetic Unkage map traces parts of o chromosomes that are inherited in the same pattern as the condition. Statistics Unk the inheritance of particular conditions to particular regions of chromosomes, as defined by RFLP or other markers. (See, for example, Lander, E. S. and Botstein, D. (1986) Proc. Natl. Acad. Sci. USA 83:7353-7357.) Occasionally, genetic markers and their locations are known from previous studies. More often, however, the markers are simply stretches of DNA that differ among individuals. Examples of genetic linkage maps can be found in various scientific journals or at the OnUne Mendelian Inheritance in Man (OMIM) World Wide Web site.
In another embodiment of the invention, sptm sequences may be used to generate hybridization probes useful in chromosomal mapping of naturally occurring genomic sequences. Either coding or 5 noncoding sequences of sptm may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of an sptm coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping. The sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes 0 (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial Pl constructions, or single chromosome cDNA Ubraries. (See, e.g., Harrington, J.J. et al. (1997) Nat. Genet. 15:345-355; Price, CM. (1993) Blood Rev. 7:127-134; and Trask, B.J. (1991) Trends Genet. 7:149-154.)
Fluorescent in situ hybridization (FISH) may be correlated with other physical chromosome 5 mapping techniques and genetic map data. (See, e.g.. Meyers, supra, pp. 965-968.) Correlation between the location of sptm on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder. The sptm sequences may also be used to detect polymoφhisms that are genetically Unked to the inheritance of a particular condition, disease, or disorder. o In situ hybridization of chromosomal preparations and genetic mapping techniques, such as
Unkage analysis using estabUshed chromosomal markers, may be used for extending existing genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of the corresponding human chromosome is not known. These new marker sequences can be mapped to human chromosomes and 5 may provide valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once a disease or syndrome has been crudely correlated by genetic Unkage with a particular genomic region, e.g., ataxia-telangiectasia to 1 lq22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation. (See, e.g., Gatti, R.A. et al. (1988) Nature 336:577-580.) The nucleotide sequences of the subject invention may o also be used to detect differences in chromosomal architecture due to translocation, inversion, etc., among normal, carrier, or affected individuals.
Once a disease-associated gene is mapped to a chromosomal region, the gene must be cloned in order to identify mutations or other alterations (e.g., translocations or inversions) that may be correlated with disease. This process requires a physical map of the chromosomal region containing the disease- 5 gene of interest along with associated markers. A physical map is necessary for determining the nucleotide sequence of and order of marker genes on a particular chromosomal region. Physical mapping techniques are well known in the art and require the generation of overlapping sets of cloned DNA fragments from a particular organelle, chromosome, or genome. These clones are analyzed to reconstruct and catalog their order. Once the position of a marker is determined, the DNA from that region is obtained by consulting the catalog and selecting clones from that region. The gene of interest is located through positional cloning techniques using hybridization or similar methods. Diagnostic Uses
The sptm of the present invention may be used to design probes useful in diagnostic assays. Such assays, well known to those skilled in the art, may be used to detect or confirm conditions, disorders, or diseases associated with abnormal levels of sptm expression. Labeled probes developed from sptm sequences are added to a sample under hybridizing conditions of desired stringency. In some instances, sptm, or fragments or oUgonucleotides derived from sptm, may be used as primers in ampUfication steps prior to hybridization. The amount of hybridization complex formed is quantified and compared with standards for that cell or tissue. If sptm expression varies significantly from the standard, the assay indicates the presence of the condition, disorder, or disease. QuaUtative or quantitative diagnostic methods may include northern, dot blot, or other membrane or dip-stick based technologies or multiple-sample format technologies such as PCR, enzyme-Unked immunosorbent assay (ELISA)-Uke, pin, or chip-based assays.
The probes described above may also be used to monitor the progress of conditions, disorders, or diseases associated with abnormal levels of sptm expression, or to evaluate the efficacy of a particular therapeutic treatment. The candidate probe may be identified from the sptm that are specific to a given human tissue and have not been observed in GenBank or other genome databases. Such a probe may be used in animal studies, precUnical tests, cUnical trials, or in monitoring the treatment of an individual patient. In a typical process, standard expression is estabUshed by methods well known in the art for use as a basis of comparison, samples from patients affected by the disordα or disease are combined with the probe to evaluate any deviation from the standard profile, and a therapeutic agent is administered and effects are monitored to generate a treatment profile. Efficacy is evaluated by determining whether the expression progresses toward or returns to the standard normal pattern. Treatment profiles may be generated over a period of several days or several months. Statistical methods well known to those skilled in the art may be use to determine the significance of such therapeutic agents.
The polynucleotides are also useful for identifying individuals from minute biological samples, for example, by matching the RFLP pattern of a sample's DNA to that of an individual's DNA. The polynucleotides of the present invention can also be used to determine the actual base-by-base DNA sequence of selected portions of an individual's genome. These sequences can be used to prepare PCR primers for amplifying and isolating such selected DNA, which can then be sequenced. Using this technique, an individual can be identified through a unique set of DNA sequences. Once a unique ID database is established for an individual, positive identification of that individual can be made from extremely small tissue samples. 5 In a particular aspect, ohgonucleotide primers derived from the sptm of the invention may be used to detect single nucleotide polymoφhisms (SNPs). SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans. Methods of SNP detection include, but are not Umited to, single-stranded conformation polymoφhism (SSCP) and fluorescent SSCP (fSSCP) methods. In SSCP, oUgonucleotide primers derived from sptm are used to l o ampUfy DNA using the polymerase chain reaction (PCR). The DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like. SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels. In fSCCP, the oUgonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-
15 throughput equipment such as DNA sequencing machines. Additionally, sequence database analysis methods, termed in siUco SNP (isSNP), are capable of identifying polymoφhisms by comparing the sequences of individual overlapping DNA fragments which assemble into a common consensus sequence. These computer-based methods filter out sequence variations due to laboratory preparation of DNA and sequencing errors using statistical models and automated analyses of DNA sequence
20 chromatograms. In the alternative, SNPs may be detected and characterized by mass spectrometry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego CA).
DNA-based identification techniques are critical in forensic technology. DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saUva, semen, etc., can be amphfied using, e.g., PCR, to identify individuals. (See, e.g., Erlich, H. (1992)
25 PCR Technology. Freeman and Co.. New York. NY). Similarly, polynucleotides of the present invention can be used as polymoφhic markers.
There is also a need for reagents capable of identifying the source of a particular tissue. Appropriate reagents can comprise, for example, DNA probes or primers prepared from the sequences of the present invention that are specific for particular tissues. Panels of such reagents can identify
3 o tissue by species and/or by organ type. In a similar fashion, these reagents can be used to screen tissue cultures for contamination.
The polynucleotides of the present invention can also be used as molecular weight markers on nucleic acid gels or Southern blots, as diagnostic probes for the presence of a specific mRNA in a particular cell type, in the creation of subtracted cDNA Ubraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oUgomers for attachment to an array or other support, and as an antigen to eUcit an immune response. Disease Model Systems Using SPTM
The polynucleotides encoding SPTM or their mammaUan homologs may be "knocked out" in 5 an animal model system using homologous recombination in embryonic stem (ES) cells. Such techniques are well known in the art and are useful for the generation of animal models of human disease. (See, e.g., U.S. Patent Number 5,175,383 and U.S. Patent Number 5,767,337.) For example, mouse ES cells, such as the mouse 129/SvJ cell Une, are derived from the early mouse embryo and grown in culture. The ES cells are transformed with a vector containing the gene of interest disrupted 0 by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M.R. (1989) Science 244: 1288- 1292). The vector integrates into the corresponding region of the host genome by homologous recombination. Alternatively, homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manna- (Marth, J.D. (1996) CUn. Invest. 97:1999-2002; Wagner, KU. et al. (1997) Nucleic Acids Res. 25:4323-4330). 5 Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain. The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains. Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.
Polynucleotides encoding SPTM may also be manipulated in vitro in ES cells derived from o human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell Uneages including endoderm, mesoderm, and ectodermal cell types. These cell Uneages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J.A. et al. (1998) Science 282:1145-1147).
Polynucleotides encoding SPTM can also be used to create "knockin" humanized animals 5 (pigs) or transgenic animals (mice or rats) to model human disease. With knockin technology, a region of sptm is injected into animal ES cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above. Transgenic progeny or inbred Unes are studied and treated with potential pharmaceutical agents to obtain information on treatment of a human disease. Alternatively, a mammal inbred to overexpress o sptm, resulting, e.g. , in the secretion of SPTM in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74). Screening Assays
SPTM encoded by polynucleotides of the present invention may be used to screen for molecules that bind to or are bound by the encoded polypeptides. The binding of the polypeptide and the molecule 5 may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the bound molecule. Examples of such molecules include antibodies, oUgonucleotides, proteins (e.g., receptors), or small molecules.
Preferably, the molecule is closely related to the natural Ugand of the polypeptide, e.g., a ligand or fragment thereof, a natural substrate, or a structural or functional mimetic. (See, CoUgan et al., ( 1991 ) Current Protocols in Immunology 1 (2) : Chapter 5.) Similarly, the molecule can be closely related to the natural receptor to which the polypeptide binds, or to at least a fragment of the receptor, e.g., the active site. In either case, the molecule can be rationally designed using known techniques. Preferably, the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide or cell membrane fractions which contain the expressed polypeptide are then contacted with a test compound and binding, stimulation, or inhibition of activity of either the polypeptide or the molecule is analyzed.
An assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. Alternatively, the assay may assess binding in the presence of a labeled competitor.
Additionally, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a soUd support, chemical Ubraries, or natural product mixtures. The assay may also simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.
Preferably, an ELISA assay using, e.g., a monoclonal or polyclonal antibody, can measure polypeptide level in a sample. The antibody can measure polypeptide level by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.
All of the above assays can be used in a diagnostic or prognostic context. The molecules discovered using these assays can be used to treat disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule. Moreover, the assays can discover agents which may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues. Transcript Imaging and Toxicological Testing Another embodiment relates to the use of sptm to develop a transcript image of a tissue or cell type. A transcript image represents the global pattern of gene expression by a particular tissue or cell type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at a given time. (See Seilhamer et al., "Comparative Gene Transcript Analysis," U.S. Patent Number 5,840,484, expressly incorporated by reference herein.) Thus a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totality of transcripts or reverse transcripts of a particular tissue or cell type. In one embodiment, the hybridization takes place in high-throughput format, wherein the polynucleotides of the present invention or their complements comprise a subset of a plurality of elements on a microarray. The resultant transcript image would provide a profile of gene 5 activity pertaining to cell signaUng.
Transcript images which profile sptm expression may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples. The transcript image may thus reflect sptm expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell Une. o Transcript images which profile sptm expression may also be used in conjunction with in vitro model systems and precUnical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds. All compounds induce characteristic gene expression patterns, frequently termed molecular fingerprints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog. 24:153- 5 159; Steiner, S. and Anderson, N. L. (2000) Toxicol. Lett. 112-113:467-71, expressly incoφorated by reference herein). If a test compound has a signature similar to that of a compound with known toxicity, it is Ukely to share those toxic properties. These fingeφrints or signatures are most useful and refined when they contain expression information from a large number of genes and gene famiUes. Ideally, a genome-wide measurement of expression provides the highest quaUty signature. Even genes o whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normaUze the rest of the expression data. The normaUzation procedure is useful for comparison of expression data after treatment with different compounds. While the assignment of gene function to elements of a toxicant signature aids in inteφretation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures 5 which leads to prediction of toxicity. (See, for example, Press Release 00-02 from the National
Institute of Environmental Health Sciences, released February 29, 2000, available at http://www.niehs.nih.gov/oc/news/toxchip.htm.) Therefore, it is important and desirable in toxicological screening using toxicant signatures to include all expressed gene sequences.
In one embodiment, the toxicity of a test compound is assessed by treating a biological sample o containing nucleic acids with the test compound. Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be quantified. The transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples 5 are indicative of a toxic response caused by the test compound in the treated sample. Another particular embodiment relates to the use of SPTM encoded by polynucleotides of the present invention to analyze the proteome of a tissue or cell type. The term proteome refers to the global pattern of protein expression in a particular tissue or cell type. Each protein component of a proteome can be subjected individually to further analysis. Proteome expression patterns, or profiles, 5 are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. A profile of a cell's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type. In one embodiment, the separation is achieved using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl 0 sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra). The proteins are visuaUzed in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains. The optical density of each protein spot is generally proportional to the level of the protein in the sample. The optical densities of equivalently positioned protein spots from different samples, for example, from biological samples either treated or 5 untreated with a test compound or therapeutic agent, are compared to identify any changes in protein spot density related to the treatment. The proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enzymatic cleavage followed by mass spectrometry. The identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of the present invention. In o some cases, further sequence data may be obtained for definitive protein identification.
A proteomic profile may also be generated using antibodies specific for SPTM to quantify the levels of SPTM expression. In one embodiment, the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and detecting the levels of protein bound to each array element (Lueking, A. et al. (1999) Anal. Biochem. 270:103-11; 5 Mendoze, L. G. et al. (1999) Biotechniques 27:778-88). Detection may be performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol- or amino- reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.
Toxicant signatures at the proteome level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level. There is a poor correlation o between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and
Seilhamer, J. (1997) Electrophoresis 18:533-537), so proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile. In addition, the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiling may be more reUable and informative in such cases. In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified. The amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample. A difference 5 in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample. Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the SPTM encoded by polynucleotides of the present invention.
In another embodiment, the toxicity of a test compound is assessed by treating a biological o sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the SPTM encoded by polynucleotides of the present invention. The amount of protein recognized by the antibodies is quantified. The amount of protein in the treated biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated 5 sample.
Transcript images may be used to profile sptm expression in distinct tissue types. This process can be used to determine cell signaUng activity in a particular tissue type relative to this activity in a different tissue type. Transcript images may be used to generate a profile of sptm expression characteristic of diseased tissue. Transcript images of tissues before and after treatment may be used o for diagnostic puφoses, to monitor the progression of disease, and to monitor the efficacy of drug treatments for diseases which affect cell signaling activity.
Transcript images of cell Unes can be used to assess cell signaUng activity and/or to identify cell Unes that lack or misregulate this activity. Such cell Unes may then be treated with pharmaceutical agents, and a transcript image following treatment may indicate the efficacy of these agents in restoring 5 desired levels of this activity. A similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in cell signaling activity. Candidate pharmaceutical agents may be evaluated by comparing their associated transcript images with those of pharmaceutical agents of known effectiveness. Antisense Molecules o The polynucleotides of the present invention are useful in antisense technology. Antisense technology or therapy relies on the modulation of expression of a target protein through the specific binding of an antisense sequence to a target sequence encoding the target protein or directing its expressioa (See, e.g., Agrawal, S., ed. (1996) Antisense Therapeutics, Humana Press Inc., Totawa NJ; Alama, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S.T. (1997) Adv. Pharmacol. 5 40:1-49; Sharma, H.W. and R. Narayanan (1995) Bioessays 17(12):1055-1063; and Lavrosky, Y. et al. (1997) Biochem. Mol. Med. 62(1):11-22.) An antisense sequence is a polynucleotide sequence capable of specifically hybridizing to at least a portion of the target sequence. Antisense sequences bind to cellular mRNA and/or genomic DNA, affecting translation and/or transcription. Antisense sequences can be DNA, RNA, or nucleic acid mimics and analogs. (See, e.g., Rossi, J.J. et al. (1991) 5 Antisense Res. Dev. l(3):285-288; Lee, R. et al. (1998) Biochemistry 37(3):900-1010; Pardridge, W.M. et al. (1995) Proc. Natl. Acad. Sci. USA 92(12):5592-5596; and Nielsen, P. E. and Haaima, G. (1997) Chem. Soc. Rev. 96:73-78.) Typically, the binding which results in modulation of expression occurs through hybridization or binding of complementary base pairs. Antisense sequences can also bind to DNA duplexes through specific interactions in the major groove of the double helix. o The polynucleotides of the present invention and fragments thereof can be used as antisense sequences to modify the expression of the polypeptide encoded by sptm. The antisense sequences can be produced ex vivo, such as by using any of the ABI nucleic acid synthesizer series (PE Biosystems) or other automated systems known in the art. Antisense sequences can also be produced biologically, such as by transforming an appropriate host cell with an expression vector containing the sequence of 5 interest. (See, e.g., Agrawal, supra.)
In therapeutic use, any gene delivery system suitable for introduction of the antisense sequences into appropriate target cells can be used. Antisense sequences can be deUvered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the cellular sequence encoding the target protein. (See, e.g., Slater, J.E., et al. (1998) 0 J. Allergy CUn. Immunol. 102(3):469-475; and Scanlon, K.J., et al. (1995) 9(13):1288-1296.)
Antisense sequences can also be introduced intracellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors. (See, e.g., Miller, A.D. (1990) Blood 76:271; Ausubel, F.M. et al. (1995) Current Protocols in Molecular Biology. John Wiley & Sons, New York NY; Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63(3):323-347.) Other gene delivery mechanisms include 5 Uposome-derived systems, artificial viral envelopes, and other systems known in the art. (See, e.g.,
Rossi, J.J. (1995) Br. Med. Bull. 51(l):217-225; Boado, R.J. et al. (1998) J. Phar Sci. 87(11):1308-
1315; and Morris, M.C. et al. (1997) Nucleic Acids Res. 25(14):2730-2736.)
Expression
In order to express a biologically active SPTM, the nucleotide sequences encoding SPTM or o fragments thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding SPTM and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, supra. Chapters 4, 8, 16, and 17; and Ausubel, supra. Chapters 9, 10, 13, and 16.)
A variety of expression vector/host systems may be utiUzed to contain and express sequences encoding SPTM. These include, but are not Umited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammalian) cell systems. (See, e.g., Sambrook, supra; Ausubel, 1995, supra. Van Heeke, G. and S.M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Bitter, G.A. et al. (1987) Methods Enzymol. 153:516-544; Scorer, CA. et al. (1994) Bio/Technology 12:181-184; Engelhard, E.K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945; Takamatsu, N. (1987) EMBO J. 6:307-311; Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; BrogUe, R. et al. (1984) Science 224:838-843; Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105; The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York NY, pp. 191-196; Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659; and Harrington, J.J. et al. (1997) Nat. Genet. 15:345-355.) Expression vectors derived from retroviruses, adenoviruses, or heφes or vaccinia viruses, or from various bacterial plasmids, may be used for deUvery of nucleotide sequences to the targeted organ, tissue, or cell population. (See, e.g., Di Nicola, M. et al. (1998) Cancer Gen. Ther. 5(6):350-356; Yu, M. et al., (1993) Proc. Natl. Acad. Sci. USA 90(13):6340-6344; Buller, R.M. et al. (1985) Nature 317(6040):813-815; McGregor, D.P. et al. (1994) Mol. Immunol. 31(3):219-226; and Verma, I.M. and N. Somia (1997) Nature 389:239-242.) The invention is not Umited by the host cell employed.
For long term production of recombinant proteins in mammaUan systems, stable expression of SPTM in cell lines is preferred. For example, sequences encoding SPTM can be transformed into cell lines using expression vectors which may contain viral origins of repUcation and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of selection systems may be used to recover transformed cell Unes. (See, e.g., Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.; Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol. 150:1-14; Hartman, S.C. and RCMulligan (1988) Proc. Natl. Acad. Sci. USA 85:8047-8051; Rhodes, CA. (1995) Methods Mol. Biol. 55:121-131.) Therapeutic Uses of sptm
The polynucleotides encoding SPTM may be used for somatic or germline gene therapy. Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-Xl disease characterized by X-Unked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R.M. et al. (1995) Science 270:475-480; Bordignon, C et al. (1995) Science 270:470-475), cystic fibrosis (Zabner, J. et al. (1993) Cell 75:207- 5 216; Crystal, R.G. et al. (1995) Hum. Gene Therapy 6:643-666; Crystal, R.G. et al. (1995) Hum. Gene Therapy 6:667-703), thalassemias, familial hypercholesterolemia, and hemophiUa resulting from Factor VIII or Factor IX deficiencies (Crystal, R.G. (1995) Science 270:404-410; Verma, I.M. and Somia, N. (1997) Nature 389:239-242)), (ii) express a conditionally lethal gene product (e.g., in the case of cancers which result from unregulated cell proUferation), or (Ui) express a protein which affords 0 protection against intracellular parasites (e.g., against human retroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D. (1988) Nature 335:395-396; Poeschla, E. et al. (1996) Proc. Natl. Acad. Sci. USA. 93:11395-11399), hepatitis B or C virus (HBV, HCV); fungal parasites, such as Candida albicans and Paracoccidioides brasihensis; and protozoan parasites such as Plasmodium falciparum and Trvpanosoma cruzi). In the case where a genetic deficiency in sptm 5 expression or regulation causes disease, the expression of sptm from an appropriate population of transduced cells may alleviate the cUnical manifestations caused by the genetic deficiency.
In a further embodiment of the invention, diseases or disorders caused by deficiencies in sptm are treated by constructing mammaUan expression vectors comprising sptm and introducing these vectors by mechanical means into sptm-deficient cells. Mechanical transfer technologies for use with 0 cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (U) balUstic gold particle deUvery, (ui) Uposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R.A. and Anderson, W.F. (1993) Annu. Rev. Biochem. 62:191-217; Ivies, Z. (1997) Cell 91:501-510; Boulay, J-L. and Rέcipon, H. (1998) Curr. Opin. Biotechnol. 9:445- 450). 5 Expression vectors that may be effective for the expression of sptm include, but are not Umited to, thePCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad CA), PCMV-SCRIPT, PCMV-TAG, PEGSH PERV (Stratagene, La Jolla CA), and PTET-OFF, PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo Alto CA). The sptm of the invention may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous o sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or β-actin genes), (ii) an inducible promoter
(e.g., the tetracycUne-regulated promoter (Gossen, M. and Bujard, H. (1992) Proc. Natl. Acad. Sci. U.S.A. 89:5547-5551; Gossen, M. et al., (1995) Science 268:1766-1769; Rossi, F.M.V. and Blau, H.M. (1998) Curr. Opin. Biotechnol. 9:451-456), commercially available in the T-REX plasmid (Invitrogen); the ecdysone-inducible promoter (available in the plasmids PVGRXR and PIND; 5 Invitrogen); the FK506/rapamycin inducible promoter; or the RU486/mifepristone inducible promoter (Rossi, F.M. V. and Blau, H.M. supra), or (ui) a tissue-specific promoter or the native promoter of the endogenous gene encoding SPTM from a normal individual.
Commercially available Uposome transformation kits (e.g., the PERFECT LIPID TRANSFECTION KIT, available from Invitrogen) allow one with ordinary skill in the art to deUver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters. In the alternative, transformation is performed using the calcium phosphate method (Graham, F.L. and Eb, A.J. (1973) Virology 52:456-467), or by electroporation (Neumann, E. et al. (1982) EMBO J. 1:841-845). The introduction of DNA to primary cells requires modification of these standardized mammaUan transfection protocols. In another embodiment of the invention, diseases or disorders caused by genetic defects with respect to sptm expression are treated by constructing a retrovirus vector consisting of (i) sptm under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (u) appropriate RNA packaging signals, and (in) a Rev-responsive element (RRE) along with additional retrovirus cώ-acting RNA sequences and coding sequences required for efficient vector propagation. Retrovirus vectors (e.g., PFB and PFBNEO) are commercially available (Sttatagene) and are based on published data (Riviere, I. et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92:6733-6737), incoφorated by reference herein. The vector is propagated in an appropriate vector producing cell Une (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M.A. et al. (1987) J. Virol. 61:1639-1646; Adam, M.A. and Miller, A.D. (1988) J. Virol. 62:3802-3806; Dull, T. et al. (1998) J. Virol. 72:8463-8471; Zufferey, R. et al. (1998) J. Virol. 72:9873-9880). U.S. Patent Number 5,910,434 to Rigg ("Method for obtaining retrovirus packaging cell Unes producing high transducing efficiency retroviral supernatant") discloses a method for obtaining retrovirus packaging cell lines and is hereby incoφorated by reference. Propagation of retrovirus vectors, transduction of a population of cells (e.g., CD4+ T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol. 71:7020-7029; Bauer, G. et al. (1997) Blood 89:2259-2267; Bonyhadi, M.L. (1997) J. Virol. 71:4707-4716; Ranga, U. et al. (1998) Proc. Natl. Acad. Sci. U.S.A. 95:1201-1206; Su, L. (1997) Blood 89:2283-2290). In the alternative, an adenovirus-based gene therapy deUvery system is used to deUver sptm to cells which have one or more genetic abnormaUties with respect to the expression of sptm. The construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art. RepUcation defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M.E. et al. (1995) Transplantation 27:263-268). Potentially useful adenoviral vectors are described in U.S. Patent Number 5,707,618 to Armentano ("Adenovirus vectors for gene therapy"), hereby incoφorated by reference. For adenoviral vectors, see also Antinozzi, P.A. et al. (1999) Annu. Rev. Nutr. 19:511-544 and Verma, I.M. and Somia, N. (1997) Nature 18:389:239-242, both incoφorated by reference herein. In another alternative, a heφes-based, gene therapy deUvery system is used to deUver sptm to target cells which have one or more genetic abnormaUties with respect to the expression of sptm. The use of heφes simplex virus (HSV)-based vectors may be especially valuable for introducing sptm to cells of the central nervous system, for which HS V has a tropism. The construction and packaging of heφes-based vectors are well known to those with ordinary skill in the art. A replication-competent heφes simplex virus (HSV) type 1 -based vector has been used to deUver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye Res.169:385-395). The construction of a HSV-1 virus vector has also been disclosed in detail in U.S. Patent Number 5,804,413 to DeLuca ("Heφes simplex virus strains for gene transfer"), which is hereby incoφorated by reference. U.S. Patent Number 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the control of the appropriate promoter for puφoses including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W. F. et al. 1999 J. Virol. 73:519-532 andXu, H. et al., (1994) Dev. Biol. 163:152-161, hereby incoφorated by reference. The manipulation of cloned heφesvirus sequences, the generation of recombinant virus following the transfection of multiple plasmids containing different segments of the large heφesvirus genomes, the growth and propagation of heφesvirus, and the infection of cells with heφesvirus are techniques well known to those of ordinary skill in the art.
In another alternative, an alphavirus (positive, single-stranded RNA virus) vector is used to deUver sptm to target cells. The biology of the prototypic alphavirus, SemUki Forest Virus (SFV), has been studied extensively and gene transfer vectors have been based on the SFV genome (Garoff, H. and Li, K-J. (1998) Curr. Opin. Biotech. 9:464-469). During alphavirus RNA repUcation, a subgenomic RNA is generated that normally encodes the viral capsid proteins. This subgenomic RNA repUcates to higher levels than the full-length genomic RNA, resulting in the ovαproduction of capsid proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase). Similarly, inserting sptm into the alphavirus genome in place of the capsid-coding region results in the production of a large number of sptm RNAs and the synthesis of high levels of SPTM in vector transduced cells. While alphavirus infection is typically associated with cell lysis within a few days, the abiUty to estabUsh a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic repUcation of alphaviruses can be altered to suit the needs of the gene therapy appUcation (Dryga, S.A. et al. (1997) Virology 228:74-83). The wide host range of alphaviruses will allow the introduction of sptm into a variety of cell types. The specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction. The methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA and RNA transfections, and performing alphavirus infections, are well known to those with ordinary skill in the art. 5 Antibodies
Anti-SPTM antibodies may be used to analyze protein expression levels. Such antibodies include, but are not Umited to, polyclonal, monoclonal, chimeric, single chain, and Fab fragments. For descriptions of and protocols of antibody technologies, see, e.g., Pound J.D. (1998) Immunochemical Protocols, Humana Press, Totowa, NJ. l o The amino acid sequence encoded by the sptm of the Sequence Listing may be analyzed by appropriate software (e.g., LASERGENE NAVIGATOR software, DNASTAR) to determine regions of high immunogenicity. The optimal sequences for immunization are selected from the C-terminus, the N-terminus, and those intervening, hydrophiUc regions of the polypeptide which are Ukely to be exposed to the external environment when the polypeptide is in its natural conformation. Analysis used to select
15 appropriate epitopes is also described by Ausubel (1997, supra, Chapter 11.7). Peptides used for antibody induction do not need to have biological activity; however, they must be antigenic. Peptides used to induce specific antibodies may have an amino acid sequence consisting of at five amino acids, preferably at least 10 amino acids, and most preferably 15 amino acids. A peptide which mimics an antigenic fragment of the natural polypeptide may be fused with another protein such as keyhole limpet
20 cyanin (KLH; Sigma, St. Louis MO) for antibody production. A peptide encompassing an antigenic region may be expressed from an sptm, synthesized as described above, or purified from human cells. Procedures well known in the art may be used for the production of antibodies. Various hosts including mice, goats, and rabbits, may be immunized by injection with a peptide. Depending on the host species, various adjuvants may be used to increase immunological response.
25 In one procedure, peptides about 15 residues in length may be synthesized using an ABI 431 A peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with M-maleimidobenzoyl-N-hydroxysuccinimide ester (Ausubel, 1995, supra). Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity by binding the peptide to plastic, blocking with 1% bovine serum albumin
3 o (BSA), reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-SPTM activity using protocols well known in the art, including ELISA, radioimmunoassay (RIA), and immunoblotting.
In another procedure, isolated and purified peptide may be used to immunize mice (about 100 μg of peptide) or rabbits (about 1 mg of peptide). Subsequently, the peptide is radioiodinated and used
35 to screen the immunized animals' B-lymphocytes for production of antipeptide antibodies. Positive cells are then used to produce hybridomas using standard techniques. About 20 mg of peptide is sufficient for labeling and screening several thousand clones. Hybridomas of interest are detected by screening with radioiodinated peptide to identify those fusions producing peptide-specific monoclonal antibody. In a typical protocol, wells of a multi-well plate (FAST, Becton-Dickinson, Palo Alto, CA) 5 are coated with affinity-purified, specific rabbit-anti-mouse (or suitable anti-species IgG) antibodies at 10 mg/ml. The coated wells are blocked with 1% BSA and washed and exposed to supernatants from hybridomas. After incubation, the wells are exposed to radiolabeled peptide at 1 mg/ml.
Clones producing antibodies bind a quantity of labeled peptide that is detectable above background. Such clones are expanded and subjected to 2 cycles of cloning. Cloned hybridomas are o injected into pristane-treated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (Amersham Pharmacia Biotech). Several procedures for the production of monoclonal antibodies, including in vitro production, are described in Pound (supra). Monoclonal antibodies with antipeptide activity are tested for anti-SPTM activity using protocols well known in the art, including ELISA, RIA, and immunoblotting. 5 Antibody fragments containing specific binding sites for an epitope may also be generated. For example, such fragments include, but are not Umited to, the F(ab')2 fragments produced by pepsin digestion of the antibody molecule, and the Fab fragments generated by reducing the disulfide bridges of the F(ab 2 fragments. Alternatively, construction of Fab expression Ubraries in filamentous bacteriophage allows rapid and easy identification of monoclonal fragments with desired specificity 0 (Pound, supra. Chaps. 45-47). Antibodies generated against polypeptide encoded by sptm can be used to purify and characterize full-length SPTM protein and its activity, binding partners, etc. Assays Using Antibodies
Anti-SPTM antibodies may be used in assays to quantify the amount of SPTM found in a particular human cell. Such assays include methods utiUzing the antibody and a label to detect 5 expression level under normal or disease conditions. The peptides and antibodies of the invention may be used with or without modification or labeled by joining them, either covalently or noncovalently, with a reporter molecule.
Protocols for detecting and measuring protein expression using either polyclonal or monoclonal antibodies are well known in the art. Examples include ELISA, RIA, and fluorescent activated cell o sorting (FACS). Such immunoassays typically involve the formation of complexes between the SPTM and its specific antibody and the measurement of such complexes. These and other assays are described in Pound (supra).
Without further elaboration, it is beUeved that one skilled in the art can, using the preceding description, utiUze the present invention to its fullest extent. The following preferred specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever.
The disclosures of all patents, applications, and pubUcations mentioned above and below, in particular U.S. Ser. No. 60/156,624, U.S. Ser. No. 60/156,625, U.S. Ser. No. 60/168,614, U.S. Ser. No. 60/168,611, and U.S. Ser. No. 60/168,613 are hereby expressly incoφorated by reference.
EXAMPLES
I. Construction of cDNA Libraries
RNA was purchased from CLONTECH Laboratories, Inc. (Palo Alto CA) or isolated from various tissues. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life
Technologies), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated with either isopropanol or sodium acetate and ethanol, or by other routine methods.
Phenol extraction and precipitation of RNA were repeated as necessary to increase RNA purity. In most cases, RNA was treated with DNase. For most Ubraries, poly(A+) RNA was isolated using oUgo d(T)-coupled paramagnetic particles (Promega Coφoration (Promega), Madison WI), OLIGOTEX latex particles (QIAGEN, Inc. (QIAGEN), Valencia CA), or an OLIGOTEX mRNA purification kit (QIAGEN). Alternatively, RNA was isolated directly from tissue lysates using other RNA isolation kits, e.g., the POLY(A)PURE mRNA purification kit (Ambion, Inc., Austin TX). In some cases, Sttatagene was provided with RNA and constructed the corresponding cDNA
Ubraries. Otherwise, cDNA was synthesized and cDNA Ubraries were constructed with the UNIZAP vector system (Sttatagene Cloning Systems, Inc. (Sttatagene), La Jolla CA) or SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra. Chapters 5.1 through 6.6.) Reverse transcription was initiated using oUgo d(T) or random primers. Synthetic oUgonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes. For most libraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL SI 000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis. cDNAs were Ugated into compatible restriction enzyme sites of the polyUnker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Sttatagene), pSPORTl plasmid (Life Technologies), or pINCY (Incyte). Recombinant plasmids were transformed into competent E. coh cells including XLl-Blue, XLl-BlueMRF, or SOLR from Sttatagene or DH5α, DH10B, or ElectroMAX DH10B from Life Technologies.
II. Isolation of cDNA Clones Plasmids were recovered from host cells by in vivo excision using the UNIZAP vector system (Sttatagene) or by cell lysis. Plasmids were purified using at least one of the following: the Magic or WIZARD Minipreps DNA purification system (Promega); the AGTC Miniprep purification kit (Edge BioSystems, Gaithersburg MD); and the QIAWELL 8, QIAWELL 8 Plus, and QIAWELL 8 Ultra 5 plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit (QIAGEN). Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4°C
Alternatively, plasmid DNA was ampUfied from host cell lysates using direct Unk PCR in a high-throughput format. (Rao, V.B. (1994) Anal. Biochem. 216:1-14.) Host cell lysis and thermal o cycUng steps were carried out in a single reaction mixture. Samples were processed and stored in 384- well plates, and the concentration of ampUfied plasmid DNA was quantified fluoromefrically using PICOGREEN dye (Molecular Probes, Inc. (Molecular Probes), Eugene OR) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).
III. Sequencing and Analysis 5 cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 thermal cycler (PE Biosystems) or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific Coφ., Sunnyvale CA) or the MICROLAB 2200 Uquid transfer system (Hamilton). cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or suppUed in ABI o sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE
Biosystems). Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (PE Biosystems) in conjunction with standard ABI protocols and base calUng software; or other sequence analysis systems known in the art. 5 Reading frames within the cDNA sequences were identified using standard methods (reviewed in
Ausubel, 1997, supra. Chapter 7.7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example VIII.
IV. Assembly and Analysis of Sequences
Component sequences from chromatograms were subject to PHRED analysis and assigned a o quality score. The sequences having at least a required quaUty score were subject to various preprocessing editing pathways to eUminate, e.g., low quaUty 3' ends, vector and Unker sequences, polyA tails, Alu repeats, mitochondrial and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs. In particular, low-information sequences and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) were replaced by "n's", or masked, to prevent spurious 5 matches. Processed sequences were then subject to assembly procedures in which the sequences were assigned to gene bins (bins). Each sequence could only belong to one bin. Sequences in each gene bin were assembled to produce consensus sequences (templates). Subsequent new sequences were added to existing bins using BLASTn (v.1.4 WashU) and CROSSMATCH. Candidate pairs were identified as 5 all BLAST hits having a quality score greater than or equal to 150. AUgnments of at least 82% local identity were accepted into the bin. The component sequences from each bin were assembled using a version of PHRAP. Bins with several overlapping component sequences were assembled using DEEP PHRAP. The orientation (sense or antisense) of each assembled template was determined based on the number and orientation of its component sequences. Template sequences as disclosed in the sequence 0 Usting correspond to sense sfrand sequences (the "forward" reading frames), to the best determination. The complementary (antisense) strands are inherently disclosed herein. The component sequences which were used to assemble each template consensus sequence are Usted in Table 2, along with their positions along the template nucleotide sequences.
Bins were compared against each other and those having local similarity of at least 82% were 5 combined and reassembled. Reassembled bins having templates of insufficient overlap (less than 95% local identity) were re-spUt. Assembled templates were also subject to analysis by STITCHER/EXON MAPPER algorithms which analyze the probabiUties of the presence of splice variants, alternatively spUced exons, splice junctions, differential expression of alternative spUced genes across tissue types or disease states, etc. These resulting bins were subject to several rounds of the above assembly 0 procedures.
Once gene bins were generated based upon sequence aUgnments, bins were clone joined based upon clone information. If the 5' sequence of one clone was present in one bin and the 3' sequence from the same clone was present in a different bin, it was Ukely that the two bins actually belonged together in a single bin. The resulting combined bins underwent assembly procedures to regenerate the 5 consensus sequences.
The final assembled templates were subsequently annotated using the following procedure. Template sequences were analyzed using BLASTn (v2.0, NCBI) versus gbpri (GenBank version 118). "Hits" were defined as an exact match having from 95% local identity over 200 base pairs through 100% local identity over 100 base pairs, or a homolog match having an E- value, i.e. a probabiUty o score, of ≤ 1 x 10"8. The hits were subject to frameshift FASTx versus GENPEPT (GenBank version 118). (See Table 4). In this analysis, a homolog match was defined as having an E- value of < 1 x 10"8. The assembly method used above was described in "System and Methods for Analyzing Biomolecular Sequences," U.S.S.N. 09/276,534, filed March 25, 1999, and the LIFESEQ Gold user manual (Incyte) both incoφorated by reference herein. Following assembly, template sequences were subjected to motif, BLAST, and functional analyses, and categorized in protein hierarchies using methods described in, e.g., "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data," U.S.S.N. 08/812,290, filed March 6, 1997; "Relational Database for Storing Biomolecule Information," 5 U.S.S.N. 08/947,845, filed October 9, 1997; "Project-Based Full-Length Biomolecular Sequence Database," U.S.S.N. 08/811,758, filed March 6, 1997; and "Relational Database and System for Storing Information Relating to Biomolecular Sequences," U.S.S.N. 09/034,807, filed March 4, 1998, all of which are incoφorated by reference herein.
The template sequences were further analyzed by translating each template in all three forward o reading frames and searching each translation against the Pfam database of hidden Markov model- based protein famiUes and domains using the HMMER software package (available to the pubUc from Washington University School of Medicine, St. Louis MO). (See also World Wide Web site http://pfam.wustl.edu/ for detailed descriptions of Pfam protein domains and famiUes.)
Additionally, the template sequences were translated in all three forward reading frames, and 5 each translation was searched against hidden Markov models for signal peptide and transmembrane domains using the HMMER software package. Construction of hidden Markov models and their usage in sequence analysis has been described. (See, for example, Eddy, S.R. (1996) Curr. Opin. Str. Biol. 6:361-365.) Regions of templates which, when translated, contain similarity to signal peptide or transmembrane domain consensus sequences are reported in Table 1. Only those signal peptide or o transmembrane hits with a cutoff score of 11 bits or greater are reported. A cutoff score of 11 bits or greater corresponds to at least about 91-94% true-positives in signal peptide prediction, and at least about 75% true-positives in transmembrane domain prediction.
Template sequences are further analyzed using the bioinformatics tools Usted in Table 4, or using sequence analysis software known in the art such as MACDNASIS PRO software (Hitachi 5 Software Engineering, South San Francisco CA) and LASERGENE software (DNASTAR). Template sequences may be further queried against pubUc databases such as the GenBank rodent, mammaUan, vertebrate, prokaryote, and eukaryote databases. V. Analysis of Polynucleotide Expression
Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene o and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; Ausubel, 1995, supra, ch. 4 and 16.)
Analogous computer techniques applying BLAST were used to search for identical or related molecules in cDNA databases such as GenBank or LIFESEQ (Incyte Genomics). This analysis is 5 much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar. The basis of the search is the product score, which is defined as:
BLAST Score x Percent Identity 5 x minimum {length(Seq. 1), length(Seq. 2)}
The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. The product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multipUed by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences). The BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and -4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate the product score. The product score represents a balance between fractional overlap and quaUty in a BLAST aUgnment. For example, a product score of 100 is produced only for 100% identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap.
Alternatively, polynucleotide sequences encoding SPTM are analyzed with respect to the tissue sources from which they were derived. Polynucleotide sequences encoding SPTM were assembled, at least in part, with overlapping Incyte cDNA sequences. Each cDNA sequence is derived from a cDNA Ubrary constructed from a human tissue. Each human tissue is classified into one of the following organ/tissue categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitaUa, female; genitaUa, male; germ cells; hemic and immune system; Uver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract. The number of Ubraries in each category for each polynucleotide sequence encoding SPTM is counted and divided by the total number of Ubraries across all categories for each polynucleotide sequence encoding SPTM. Similarly, each human tissue is classified into one of the following disease/condition categories: cancer, cell Une, developmental, inflammation, neurological, frauma, cardiovascular, pooled, and other, and the number of Ubraries in each category for each polynucleotide sequence encoding SPTM is counted and divided by the total number of Ubraries across all categories for each polynucleotide sequence encoding SPTM. The resulting percentages reflect the tissue- and disease-specific expression of cDNA encoding SPTM. Percentage values of tissue-specific and disease-specific expression are reported in Table 3. cDNA sequences and cDNA Ubrary/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto CA).
VI. Tissue Distribution Profiling
A tissue distribution profile is determined for each template by compiUng the cDNA Ubrary 5 tissue classifications of its component cDNA sequences. Each component sequence, is derived from a cDNA Ubrary constructed from a human tissue. Each human tissue is classified into one of the following categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitaUa, female; genitaUa, male; germ cells; hemic and immune system; Uver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; 0 skin; stomatognathic system; unclassified/mixed; or urinary tract. Template sequences, component sequences, and cDNA library/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto CA).
Table 3 shows the tissue distribution profile for the templates of the invention. For each template, the three most frequently observed tissue categories are shown in column 3, along with the 5 percentage of component sequences belonging to each category. Only tissue categories with percentage values of > 10% are shown. A tissue distribution of "widely distributed" in column 3 indicates percentage values of <10% in all tissue categories.
VII. Transcript Image Analysis
Transcript images are generated as described in Seilhamer et al., "Comparative Gene o Transcript Analysis," U.S. Patent Number 5,840,484, incoφorated herein by reference.
VIII. Extension of Polynucleotide Sequences and Isolation of a Full-length cDNA OUgonucleotide primers designed using an sptm of the Sequence Listing are used to extend the nucleic acid sequence. One primer is synthesized to initiate 5' extension of the template, and the other primer, to initiate 3' extension of the template. The initial primers may be designed using OLIGO 4.06 5 software (National Biosciences, Inc. (National Biosciences), Plymouth MN), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68 °C to about 72 °C Any stretch of nucleotides which would result in haiφin structures and primer-primer dimerizations are avoided. Selected human cDNA Ubraries are used to extend the sequence. If more than one extension is necessary or desired, o additional or nested sets of primers are designed.
High fidelity ampUfication is obtained by PCR using methods well known in the art. PCR is performed in 96-well plates using the PTC-200 thermal cycler (MJ Research). The reaction mix contains DNA template, 200 nmol of each primer, reaction buffer containing Mg2+, (NH4)2S04, and β- mercaptoethanol, Taq DNA polymerase (Amersham Pharmacia Biotech), ELONGASE enzyme (Life 5 Technologies), and Pfu DNA polymerase (Sfratagene), with the following parameters for primer pair PCI A and PCI B: Step 1: 94°C, 3 min; Step 2: 94°C, 15 sec; Step 3: 60°C, 1 min; Step 4: 68°C, 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68 °C, 5 min; Step 7: storage at 4°C In the alternative, the parameters for primer pair T7 and SK+ are as follows: Step 1 : 94°C, 3 min; Step 2: 94°C, 15 sec; Step 3: 57°C, 1 min; Step 4: 68°C, 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; 5 Step 6: 68 °C, 5 min; Step 7: storage at 4°C
The concentration of DNA in each well is determined by dispensing 100 μl PICOGREEN quantitation reagent (0.25% (v/v); Molecular Probes) dissolved in IX Tris-EDTA (TE) and 0.5 μl of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Incoφorated (Corning), Corning NY), allowing the DNA to bind to the reagent. The plate is scanned in a FLUOROSKAN II o (Labsystems Oy) to measure the fluorescence of the sample and to quantify theconcenfration of DNA.
A 5 μl to 10 μl ahquot of the reaction mixture is analyzed by electrophoresis on a 1 % agarose mini-gel to determine which reactions are successful in extending the sequence.
The extended nucleotides are desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison WI), and 5 sonicated or sheared prior to reUgation into pUC 18 vector (Amersham Pharmacia Biotech). For shotgun sequencing, the digested nucleotides are separated on low concentration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with AGAR ACE (Promega). Extended clones are religated using T4 Ugase (New England Biolabs, Inc., Beverly MA) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Sfratagene) to fill-in restriction site overhangs, o and transfected into competent E. coli cells. Transformed cells are selected on antibiotic-containing media, individual colonies are picked and cultured overnight at 37 °C in 384-well plates in LB/2x carbenicilUn Uquid media.
The cells are lysed, and DNA is ampUfied by PCR using Taq DNA polymerase (Amersham Pharmacia Biotech) and Pfu DNA polymerase (Sttatagene) with the following parameters: Step 1 : 5 94°C, 3 min; Step 2: 94°C, 15 sec; Step 3: 60°C, 1 min; Step 4: 72°C, 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72°C, 5 min; Step 7: storage at 4°C DNA is quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries are reamplified using the same conditions as described above. Samples are diluted with 20% dimethysulfoxide (1 :2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC o DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE Biosystems).
In like manner, the sptm is used to obtain regulatory sequences (promoters, introns, and enhancers) using the procedure above, oUgonucleotides designed for such extension, and an appropriate genomic Ubrary. 5 IX. Labeling of Probes and Southern Hybridization Analyses Hybridization probes derived from the sptm of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA. The labeUng of probe nucleotides between 100 and 1000 nucleotides in length is specifically described, but essentially the same procedure may be used with larger cDNA fragments. Probe sequences are labeled at room temperature for 30 minutes using a 5 T4 polynucleotide kinase, γ^P-ATP, and 0.5X One-Phor-All Plus (Amersham Pharmacia Biotech) buffer and purified using a ProbeQuant G-50 Microcolumn (Amersham Pharmacia Biotech). The probe mixture is diluted to 107 dpm/μg/ml hybridization buffer and used in a typical membrane-based hybridization analysis.
The DNA is digested with a restriction endonuclease such as Eco RV and is electrophoresed o through a 0.7% agarose gel. The DNA fragments are transferred from the agarose to nylon membrane
(NYTRAN Plus, Schleicher & Schuell, Inc., Keene NH) using procedures specified by the manufacturer of the membrane. Prehybridization is carried out for three or more hours at 68 °C, and hybridization is carried out overnight at 68 °C To remove non-specific signals, blots are sequentially washed at room temperature under increasingly stringent conditions, up to O.lx satine sodium citrate 5 (SSC) and 0.5% sodium dodecyl sulfate. After the blots are placed in a PHOSPHORIMAGER cassette (Molecular Dynamics) or are exposed to autoradiography film, hybridization patterns of standard and experimental lanes are compared. Essentially the same procedure is employed when screening RNA. X. Chromosome Mapping of sptm
The cDNA sequences which were used to assemble SEQ ID NO: 1-63 are compared with o sequences from the Incyte LIFESEQ database and pubUc domain databases using BLAST and other implementations of the Smith- Waterman algorithm. Sequences from these databases that match SEQ ID NO: 1 -63 are assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as PHRAP (Table 4). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead Institute for Genome 5 Research (WIGR), and Genόthon are used to determine if any of the clustered sequences have been previously mapped. Inclusion of a mapped sequence in a cluster will result in the assignment of all sequences of that cluster, including its particular SEQ ID NO:, to that map location. The genetic map locations of SEQ ID NO:l-63 are described as ranges, or intervals, of human chromosomes. The map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p- o arm. (The centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers. On average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA in humans, although this can vary widely due to hot and cold spots of recombination.) The cM distances are based on genetic markers mapped by Gέnόthon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters. 5 XI. Microarray Analysis Probe Preparation from Tissue or Cell Samples
Total RNA is isolated from tissue samples using the guanidinium thiocyanate method and polyA+ RNA is purified using the oligo (dT) cellulose method. Each polyA+ RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/μl oUgo-dT primer (21mer), IX first strand buffer, 0.03 units/μl RNase inhibitor, 500 μM dATP, 500 μM dGTP, 500 μM dTTP, 40 μM dCTP, 40 μM dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Pharmacia Biotech). The reverse franscription reaction is performed in a 25 ml volume containing 200 ng polyA+ RNA with GEMBRIGHT kits (Incyte). Specific control polyA+ RNAs are synthesized by in vitro transcription from non-coding yeast genomic DNA (W. Lei, unpubUshed). As quantitative controls, the control mRNAs at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse franscription reaction at ratios of 1 : 100,000, 1 : 10,000, 1:1000, 1:100 (w/w) to sample mRNA respectively. The control mRNAs are diluted into reverse transcription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA differential expression patterns. After incubation at 37° C for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C to the stop the reaction and degrade the RNA. Probes are purified using two successive
CHROMA SPIN 30 gel filtration spin columns (CLONTECH Laboratories, Inc. (CLONTECH), Palo Alto CA) and after combining, both reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol. The probe is then dried to completion using a SpeedVAC (Savant Instruments Inc., Holbrook NY) and resuspended in 14 μl 5X SSC/0.2% SDS.
Microarray Preparation
Sequences of the present invention are used to generate array elements. Each array element is ampUfied from bacterial cells containing vectors with cloned cDNA inserts. PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert. Array elements are ampUfied in thirty cycles of PCR from an initial quantity of 1 -2 ng to a final quantity greater than 5 μg.
AmpUfied array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech).
Purified array elements are immobiUzed on polymer-coated glass sUdes. Glass microscope sUdes (Corning) are cleaned by ultrasound in 0.1% SDS and acetone, with extensive distilled water washes between and after treatments. Glass sUdes are etched in 4% hydrofluoric acid (VWR Scientific Products Coφoration (VWR), West Chester, PA), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol. Coated sUdes are cured in a 110°C oven. Array elements are appUed to the coated glass substrate using a procedure described in US Patent No. 5,807,522, incoφorated herein by reference. 1 μl of the array element DNA, at an average concentration of 100 ng/μl, is loaded into the open capillary printing element by a high-speed robotic apparatus. The apparatus then deposits about 5 nl of array element sample per slide. Microarrays are UV-crosslinked using a STRATALINKER UV-crossUnker (Sfratagene). Microarrays are washed at room temperature once in 0.2% SDS and three times in distilled water. Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate buffered saUne (PBS) (Tropix, Inc., Bedford, MA) for 30 minutes at 60° C followed by washes in 0.2% 5 SDS and distilled water as before. Hybridization
Hybridization reactions contain 9 μl of probe mixture consisting of 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in 5X SSC, 0.2% SDS hybridization buffer. The probe mixture is heated to 65° C for 5 minutes and is aUquoted onto the microarray surface and covered with an 1.8 o cm2 coversUp. The arrays are transferred to a wateφroof chamber having a cavity just sUghtiy larger than a microscope slide. The chamber is kept at 100% humidity internally by the addition of 140 μl of 5x SSC in a corner of the chamber. The chamber containing the arrays is incubated for about 6.5 hours at 60° C. The arrays are washed for 10 min at 45° C in a first wash buffer (IX SSC, 0.1% SDS), three times for 10 minutes each at 45° C in a second wash buffer (0. IX SSC), and dried. 5 Detection
Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara CA) capable of generating spectral Unes at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5. The excitation laser light is focused on the array using a 20X microscope objective (Nikon, Inc., Melville NY). The sUde o containing the array is placed on a computer-controlled X- Y stage on the microscope and raster- scanned past the objective. The 1.8 cm x 1.8 cm array used in the present example is scanned with a resolution of 20 micrometers.
In two separate scans, a mixed gas multiUne laser excites the two fluorophores sequentially. Emitted Ught is spUt, based on wavelength, into two photomultipUer tube detectors (PMT R1477, 5 Hamamatsu Photonics Systems, Bridgewater NJ) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultipUer tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5. Each array is typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously. o The sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the probe mix at a known concentration. A specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1 : 100,000. When two probes from different sources (e.g., representing test and control cells), each labeled with a different fluorophore, are 5 hybridized to a single array for the puφose of identifying genes that are differentially expressed, the caUbration is done by labeUng samples of the caUbrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.
The output of the photomultipUer tube is digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Inc., Norwood, MA) installed in an IBM-compatible PC 5 computer. The digitized data are displayed as an image where the signal intensity is mapped using a Unear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum. 0 A grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid. The fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte).
XII. Complementary Nucleic Acids 5 Sequences complementary to the sptm are used to detect, decrease, or inhibit expression of the naturally occurring nucleotide. The use of oligonucleotides comprising from about 15 to 30 base pairs is typical in the art. However, smaller or larger sequence fragments can also be used. Appropriate oligonucleotides are designed from the sptm using OLIGO 4.06 software (National Biosciences) or other appropriate programs and are synthesized using methods standard in the art or ordered from a o commercial supplier. To inhibit transcription, a complementary oUgonucleotide is designed from the most unique 5 ' sequence and used to prevent transcription factor binding to the promoter sequence. To inhibit translation, a complementary oUgonucleotide is designed to prevent ribosomal binding and processing of the transcript.
XIII. Expression of SPTM 5 Expression and purification of SPTM is accompUshed using bacterial or virus-based expression systems. For expression of SPTM in bacteria, cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator o regulatory element. Recombinant vectors are transformed into suitable bacterial hosts, e.g.,
BL21(DE3). Antibiotic resistant bacteria express SPTM upon induction with isopropyl beta-D- thiogalactopyranoside (IPTG). Expression of SPTM in eukaryotic cells is achieved by infecting insect or mammaUan cell Unes with recombinant Autographica caUfornica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is 5 replaced with cDNA encoding SPTM by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription. Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases. Infection of the latter requires additional genetic modifications to baculovirus. (See e.g., Engelhard, 5 supra: and Sandig, supra.)
In most expression systems, SPTM is synthesized as a fusion protein with, e.g., glutathione S- transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates. GST, a 26-kilodalton enzyme from Schistosoma iaponicum. enables the purification of fusion proteins on immobiUzed o glutathione undo- conditions that maintain protein activity and antigenicity (Amersham Pharmacia
Biotech). Following purification, the GST moiety can be proteolytically cleaved from SPTM at specifically engineered sites. FLAG, an 8-amino acid peptide, enables immunoaffinity purification using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak Company, Rochester NY). 6-His, a stretch of six consecutive histidine residues, enables purification on 5 metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra. Chapters 10 and 16). Purified SPTM obtained by these methods can be used directly in the following activity assay. XIV. Demonstration of SPTM Activity
An assay for SPTM activity measures the expression of SPTM on the cell surface. cDNA o encoding SPTM is subcloned into an appropriate mammalian expression vector suitable for high levels of cDNA expression. The resulting construct is transfected into a nonhuman cell Une such as NIH3T3. Cell surface proteins are labeled with biotin using methods known in the art. Immunoprecipitations are performed using SPTM-specific antibodies, and immunoprecipitated samples are analyzed using SDS- PAGE and immunoblotting techniques. The ratio of labeled immunoprecipitant to unlabeled 5 immunoprecipitant is proportional to the amount of SPTM expressed on the cell surface.
Alternatively, an assay for SPTM activity measures the amount of SPTM in secretory, membrane-bound organelles. Transfected cells as described above are harvested and lysed. The lysate is fractionated using methods known to those of skill in the art, for example, sucrose gradient ultracentrifugation. Such methods allow the isolation of subcellular components such as the Golgi 0 apparatus, ER, small membrane-bound vesicles, and other secretory organelles. Immunoprecipitations from fractionated and total cell lysates are performed using SPTM-specific antibodies, and immunoprecipitated samples are analyzed using SDS-PAGE and immunoblotting techniques. The concentration of SPTM in secretory organelles relative to SPTM in total cell lysate is proportional to the amount of SPTM in transit through the secretory pathway. 5 XV. Functional Assays SPTM function is assessed by expressing sptm at physiologically elevated levels in mammaUan cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen Coφoration, Carlsbad CA), both of which contain the 5 cytomegalovirus promoter. 5-10 μg of recombinant vector are transiently transfected into a human cell Une, preferably of endotheUal or hematopoietic origin, using either Uposome formulations or electroporation. 1-2 μg of an additional plasmid containing sequences encoding a marker protein are co-fransfected.
Expression of a marker protein provides a means to distinguish transfected cells from o nonttansfected cells and is a reliable predictor of cDNA expression from the recombinant vector.
Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; CLONTECH), CD64, or a CD64-GFP fusion protein. Row cytometry (FCM), an automated laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties. 5 FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward Ught scatter and 90 degree side Ught scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular o proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994) Flow Cytometry. Oxford, New York NY.
The influence of SPTM on gene expression can be assessed using highly purified populations 5 of cells transfected with sequences encoding SPTM and either CD64 or CD64-GFP. CD64 and CD64- GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Inc., Lake Success NY). mRNA can be purified from the cells using methods well known by those of skill in the art. o Expression of mRNA encoding SPTM and other genes of interest can be analyzed by northern analysis or microarray techniques.
XVI. Production of Antibodies
SPTM substantially purified using polyacrylamide gel electrophoresis (PAGE; see, e.g., Harrington, M.G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to 5 immunize rabbits and to produce antibodies using standard protocols. Alternatively, the SPTM amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding peptide is synthesized and used to raise antibodies by means known to those of skill in the art. Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophihc regions are well described in 5 the art. (See, e.g., Ausubel, 1995, supra. Chapter 11.)
Typically, peptides 15 residues in length are synthesized using an ABI 431 A peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with N- maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity. (See, e.g., Ausubel, supra.) Rabbits are immunized with the peptide- KLH complex in complete Freund's 0 adjuvant. Resulting antisera are tested for antipeptide activity by, for example, binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-SPTM activity using protocols well known in the art, including ELISA, RIA, and immunoblotting. XVII. Purification of Naturally Occurring SPTM Using Specific Antibodies 5 Naturally occurring or recombinant SPTM is substantially purified by immunoaffinity chromatography using antibodies specific for SPTM. An immunoaffinity column is constructed by covalently coupling anti-SPTM antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupUng, the resin is blocked and washed according to the manufacturer's instructions. o Media containing SPTM are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of SPTM (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/SPTM binding (e.g., a buffer of pH 2 to pH 3, or a high concenfration of a chaofrope, such as urea or thiocyanate ion), and SPTM is collected. 5 XVIII. Identification of Molecules Which Interact with SPTM
SPTM, or biologically active fragments thereof, are labeled with 125I Bolton-Hunter reagent. (See, e.g., Bolton, A.E. and W.M. Hunter (1973) Biochem. J. 133:529-539.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled SPTM, washed, and any wells with labeled SPTM complex are assayed. Data obtained using different concentrations of o SPTM are used to calculate values for the number, affinity, and association of SPTM with the candidate molecules.
Alternatively, molecules interacting with SPTM are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989) Nature 340:245-246, or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (CLONTECH). SPTM may also be used in the PATHCALLING process (CuraGen Coφ., New Haven CT) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions between the proteins encoded by two large libraries of genes (Nandabalan, K. et al. (2000) U.S. Patent No. 6,057,101).
All pubhcations and patents mentioned in the above specification are herein incoφorated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly Umited to such specific embodiments. Indeed, various modifications of the above-described modes for carrying out the invention which are obvious to those skilled in the field of molecular biology or related fields are intended to be within the scope of the following claims.
Table 1
SEQ Template ID Start Stop Frame Domain SEQ Template ID Start Stop Frame Domain
ID NO Type ID NO Type
1 198450.6.oct 272 343 forward 2 TM 26 231583.3.dec 1159 1239 forward 1 TM
1 198450.6.oct 269 334 forward 2 SP 26 231583.3.dec 1165 1233 forward 1 SP
1 198450.6.oct 263 346 forward 2 TM 26 231583.3.dec 1188 1238 forward 3 TM
2 475178.1.oct 1233 1292 forward 3 SP 26 231583.3.dec 1195 1257 forward 1 TM
2 475178.1.oct 95 172 forward 2 SP 26 231583.3.dec 1162 1233 forward 1 TM
2 475178.1.oct 1221 1274 forward 3 SP 26 231δ83.3.dec 1165 1227 forward 1 SP
2 475178.1.oct 95 157 forward 2 SP 26 231583.3.dec 571 618 forward 1 SP
3 231793.2.oct 739 801 forward 1 SP 26 231583.3.dec 1195 1251 forward 1 TM
3 231793.2.oct 739 810 forward 1 SP 26 231583.3.dec 1184 1243 forward 2 TM
3 231793.2.oct 86δ 930 forward 1 SP 26 231583.3.dec 1170 1232 forward 3 TM
3 231793.2.oct 739 810 forward 1 SP 26 231583.3.dec 1182 1238 forward 3 TM
3 231793.2.oct 730 810 forward 1 SP 27 215051.δ.dec 975 1031 forward 3 TM
4 000010.4.oct 1637 1684 forward 2 SP 27 21δ0δ1.δ.dec 1428 1 87 forward 3 TM
4 000010.4.oct 1637 1696 forward 2 SP 27 216051.5.dec 1424 1492 forward 2 SP
5 412959.6.oct 329 409 forward 2 TM 27 215051.5.dec 960 1034 forward 3 SP
5 412959.6.oct 586 642 forward 1 SP 27 2150δ1.5.dec 1394 1456 forward 2 TM
5 412959.6.0Ct 350 406 forward 2 TM 27 215051.5.dec 1424 1480 forward 2 SP
6 331521.5.oct 807 860 forward 3 TM 27 215051. δ.dec 861 920 forward 3 TM
6 331521.5.oct 840 902 forward 3 SP 27 215051.5.dec 51 140 forward 3 SP
7 902114.1.oct 288 341 forward 3 SP 27 215051. δ.dec 506 577 forward 2 SP
7 902114.1.oct 288 338 forward 3 SP 27 215051.δ.dec 1421 1501 forward 2 TM
7 902114.1.oct 288 353 forward 3 SP 27 215061. δ.dec 1424 1480 forward 2 TM
7 902114.1.oct 288 347 forward 3 SP 27 21δ0δ1.δ.dec 1412 1462 forward 2 TM
8 481382.1.oct 730 798 forward 1 SP 27 21δ0δ1.δ.dec 1424 1471 forward 2 SP
8 481382.1.oct 730 789 forward 1 SP 27 215051.δ.dec 1424 1480 forward 2 SP
9 903849. Loot 1361 1414 forward 2 TM 28 277726.5.dec 655 711 forward 1 TM
9 903849.1.oct 1338 1403 forward 3 SP 28 277726.5.dec 853 918 forward 1 TM
10 433776.4.oct 737 802 forward 2 SP 28 277726.5.dec 826 900 forward 1 TM
10 433776.4.oct 797 892 forward 2 SP 28 277726.δ.dec 370 426 forward 1 TM
11 407607.4.oct 1634 1687 forward 2 TM 28 277726.5.dec 652 729 forward 1 TM
11 407607.4.oct 1429 1500 forward 1 SP 28 277726.5.dec 832 894 forward 1 TM
12 234828.6.oct 1091 1180 forward 2 SP 28 277726.5.dec 1377 1430 forward 3 TM
12 234828.6.oct 1115 1189 forward 2 SP 28 277726.5.dec 832 903 forward 1 TM
13 336430.2.dec 1290 1355 forward 3 SP 28 277726.5.dec 844 894 forward 1 TM
13 336430.2.dec 857 931 forward 2 SP 29 978637.1. dec 19 123 forward 1 SP
13 336430.2.dec 749 850 forward 2 SP 30 240518.12.dec 61 114 forward 1 TM
14 242269.2.dec 769 837 forward 1 TM 30 240518.12.dec 64 126 forward 1 TM
15 432120.2.dec 503 559 forward 2 TM 30 240518.12.dec 868 978 forward 1 SP
16 198060.6.dec 40 126 forward 1 SP 30 240518.12.dec 931 978 forward 1 SP
17 460295.5.dec 369 449 forward 3 TM 31 413231.8.dec 1182 1244 forward 3 SP
18 235983.6.dec 3319 3375 forward 1 TM 31 413231.8.dec 2531 2593 forward 2 TM
18 235983.6.dec 900 953 forward 3 SP 31 413231.8.dec 1188 1256 forward 3 SP
18 235983.6.dec 34883δ6δ forward 2 SP 31 413231.8.dec 1741 1803 forward 1 TM
18 235983.6.dec 33283390 forward 1 TM 31 413231.8.dec 1182 1235 forward 3 SP
18 235983.6.dec 4361 4414 forward 2 SP 31 413231.8.dec 1188 1262 forward 3 SP
18 235983.6.dec 21682236 forward 2 TM 31 413231.8.dec 1182 1262 forward 3 SP
18 235983.6.dec 43404420 forward 2 SP 32 334406.5.dec 886 969 forward 1 SP
18 235983.6.dec 4361 4435 forward 2 SP 33 411429.8.dec 468 630 forward 3 TM
18 235983.6.dec 43794426 forward 2 SP 34 320674.7.dec 1649 1717 forward 2 TM
18 235983.6.dec 4361 4426 forward 2 SP 36 197267.1. dec δ 76 forward 2 SP
18 235983.6.dec 4361 4420 forward 2 SP 35 197267.1. dec 14 68 forward 2 SP
19 238703.2.dec 1067 1140 forward 1 SP 35 197267.1. dec 5 67 forward 2 SP
20 038751.5.dec 744 809 forward 3 TM 35 197267.1. dec 2 67 forward 2 SP
20 038751.δ.dec 167 238 forward 2 TM 35 197267.1. dec 11 67 forward 2 SP
20 038751.5.dec 729 803 forward 3 SP 35 197267.1. dec 723 803 forward 3 SP
20 038751.δ.dec 464 526 forward 2 TM 36 332335.1. dec 785 883 forward 2 SP
21 236099.4.dec 1254 1352 forward 3 SP 37 238992.13.dec 905 994 forward 2 SP
22 350875.2.dec 479 535 forward 2 TM 38 199736.1. dec 157 219 forward 1 TM
23 466521. δ.dec 598 666 forward 1 SP 38 199736.1. dec 145 204 forward 1 TM
24 466521.6.dec 719 787 forward 2 SP 38 199736.1. dec 166 228 forward 1 TM
25 474522.8.dec 483 666 forward 3 SP 39 228864.5.dec 562 642 forward 1 SP
25 474522.8.dec 483 δδ7 forward 3 SP 39 228864.5.dec 26 139 forward 2 SP
25 474522.8.dec 607 666 forward 3 SP 40 986539.1. dec 3 95 forward 3 SP
25 474522.8.dec 507 572 forward 3 SP 41 481454.4.dec 561 647 forward 3 SP
26 231583.3.dec 1186 1230 forward 1 TM 41 481454.4.dec 1239 1298 forward 3 SP Table 1 cont.
41 481454.4.dec 1206 1298 forward 3 SP 69 480961.δ.dec 964 1011 forward 1 SP
41 481454.4.dec 456 520 forward 2 SP 59 480951.δ.dec 1479 1538 forward 3 TM
41 481454.4.dec 422 602 forward 2 SP 60 350399.5.dec 1080 1127 forward 3 SP
41 4814δ4.4.dec 446 505 forward 2 SP 60 350399.5.dec 1697 1759 forward 2 TM
41 4814δ4.4.dec 4δδ 502 forward 2 SP 60 350399.5.dec 37423801 forward 1 SP
41 481454.4.dec 446 502 forward 2 SP 60 350399.5.dec 1856 1918 forward 2 TM
41 481454.4.dec 422 502 forward 2 SP 60 350399.5.dec 1703 1750 forward 2 TM
42 474800.7.dec 337 420 forward 1 SP 60 350399.5.dec 21692234 forward 3 SP
43 427883.13.dec 36 89 forward 3 TM 60 350399.5.dec 21832239 forward 2 TM
44 018945.1. dec 518 571 forward 2 TM 60 350399.δ.dec 2169 2228 forward 3 TM
4δ 353271.2.dec 982 1062 forward 1 SP 60 3δ0399.δ.dec 1173 1223 forward 3 TM
46 221686.2.dec 728 793 forward 2 SP 60 3δ0399.δ.dec 1709 1765 forward 2 TM
46 221686.2.dec 728 781 forward 2 SP 60 3δ0399.δ.dec 3751 3804 forward 1 TM
46 221686.2.dec 728 799 forward 2 SP 60 350399.6.dec 1697 1768 forward 2 TM
47 233347.7.dec 972 1046 forward 3 SP 61 085713.2.dec 24692528 forward 3 SP
47 233347.7.dec 387 473 forward 3 SP 61 085713.2.dec 1792 1848 forward 1 SP
47 233347.7.dec 998 1069 forward 2 SP 61 085713.2.dec 2481 2540 forward 3 TM
47 233347.7.dec 998 1066 forward 2 SP 61 085713.2.dec 24472500 forward 2 TM
47 233347.7.dec 228 326 forward 3 SP 61 085713.2.dec 24562527 forward 2 TM
47 233347.7.dec 273 335 forward 3 TM 61 085713.2.dec 24562518 forward 2 TM
47 233347.7.dec 998 1051 forward 2 SP 61 085713.2.dec 23442400 forward 1 SP
47 233347.7.dec 264 317 forward 3 TM 61 085713.2.dec 24642523 forward 1 TM
47 233347.7.dec 264 323 forward 3 TM 61 085713.2.dec 125 175 forward 2 SP
47 233347.7.dec 273 338 forward 3 TM 61 085713.2.dec 24562612 forward 2 TM
47 233347.7.dec 273 344 forward 3 TM 61 085713.2.dec 24582611 forward 1 TM
47 233347.7.dec 264 326 forward 3 SP 61 085713.2.dec 25402596 forward 2 SP
47 233347.7.dec 264 335 forward 3 SP 62 246014.1. dec 791 865 forward 2 SP
48 230631.3.dec 1675 1737 forward 1 TM 62 245014.1. dec 770 823 forward 2 TM
48 230631.3.dec 524 577 forward 2 SP 62 245014.1. dec 785 850 forward 2 TM
48 230631.3.dec 524 674 forward 2 SP 62 245014.1. dec 785 866 forward 2 TM
48 230631.3.dec 1675 1734 forward 1 TM 63 117464.7.dec 1411 1458 forward 1 SP
49 336146.1. dec 218 271 forward 2 TM 63 117464.7.dec 1399 1473 forward 1 SP
49 335146.1. dec 203 268 forward 2 TM 63 117464.7.dec 1408 1470 forward 1 SP
49 335146.1. dec 218 274 forward 2 TM 63 117464.7.dec 1921 1983 forward 1 SP
50 337160.1. dec 281 386 forward 2 SP 63 117464.7.dec 231 278 forward 3 SP
51 346341.12.dec 1434 1520 forward 3 SP 63 117464.7.dec 574 633 forward 1 SP
61 346341.12.dec 25892654 forward 3 SP 63 117464.7.dec 1909 1992 forward 1 SP
51 346341.12.dec 1208 1291 forward 2 SP 63 117464.7.dec 1664 1720 forward 2 TM
51 346341.12.dec 25892660 forward 3 SP 63 117464.7.dec 1939 1992 forward 1 SP
51 346341.12.dec 26892648 forward 3 SP 63 117464.7.dec 29763040 forward 2 SP
61 346341.12.dec 25172591 forward 3 TM 63 117464.7.dec 27402808 forward 1 SP
51 346341.12.dec 3712 3762 forward 1 TM 63 117464.7.dec 29663052 forward 2 SP
51 346341.12.dec 25892642 forward 3 SP 63 117464.7.dec 1906 1983 forward 1 TM
51 346341.12.dec 982 1068 forward 1 SP 63 117464.7.dec 1918 1968 forward 1 SP
51 346341.12.dec 3712 3768 forward 1 TM 63 117464.7.dec 1930 1989 forward 1 TM
52 428745.2.dec 113 181 forward 2 SP 63 117464.7.dec 1918 1986 forward 1 SP
53 444839.17.dec 265 312 forward 1 TM 63 117464.7.dec 1921 1992 forward 1 SP
54 245000.6.dec 797 868 forward 2 TM 63 117464.7.dec 231 302 forward 3 SP
54 245000.6.dec 806 868 forward 2 SP 63 117464.7.dec 1423 1494 forward 1 TM
54 245000.6.dec 806 874 forward 2 SP 63 117464.7.dec 1933 1983 forward 1 TM
54 245000.6.dec 251 367 forward 2 SP 63 117464.7.dec 1933 1995 forward 1 TM
54 245000.6.dec 563 619 forward 2 SP
54 245000.6.dec 572 634 forward 2 TM
54 245000.6.dec 806 866 forward 2 TM
54 245000.6.dec 767 841 forward 2 SP
54 245000.6.dec 812 865 forward 2 TM
54 245000.6.dec 806 850 forward 2 SP
54 245000.6.dec 773 862 forward 2 SP
64 245000.6.dec 806 862 forward 2 SP
56 428362.36.dec 270 326 forward 3 TM
56 480710.12.dec 878 931 forward 2 TM
56 480710.12.dec 2216 2266 forward 2 TM
56 480710.12.dec 22 126 forward 1 SP
57 234137.10.dec 548 646 forward 2 SP
58 480630.4.dec 881 931 forward 2 TM
59 480951.δ.dec 964 1023 forward 1 SP m m in h- i- o co i- i- io cM CM in oO ' *^ ιn .. ιn.. ω._ c.M. in.. c.o. c.o. c.θ. '*. *ι- c .. c .o. o .o_ o_ c_o c,M. τ- oo -
CM CM CM CM 1- 1- C σ> *- *- '* β ω <o o M cM N *- *- -- *- o *- CM CM <M CM CM C\I *ι- τ- CM CM CN CM *>- '- C
IPNIII σ> c» co c» co cM i"- 3- ι ._ _ _ . ι- 00 ffl Mn 0. C0 (00 o co co co cθ '<3- co θ ' i*- O S θ ω N O) MO CM '* σ> O) co oo CO CM ' CO CO O CO lO C co * in row •* *< CM in ro rocθ *ι— oiiot ** o q o o o o q q o q q o o q q q q q q q q q ι-- ιnιnw
OJ Z
^ o o - Oi r- i— *^* ιn oo cOi- in-< coo o>coo)^ O)i- coo>o)mcoc3 i-oo o)CMi- ocj)o> 0 '< O)0) o (O N O) 0) <o <o o> s co 't (oc in ifl (o w *- in o) oo *- (O oO '* - t- '* s s cii N '* ιn*»tooιncMco cMcθ'<t ιoι--cocococoσ ι~-o coθ) inθ'< '*cocθ ' coι-co -< S Is- N CO Iβ O(M 't β 0110N 'tlβ O) a SS 010in θ *- O NβO O *-(M OO O *- *- ι- *^ w *ι- M *ι- CM CM CM < ^ '* co c co co co co *< o *« ι^ t-- ι-. rs. h- r>- -< ιn r^ t« t/3 *- N Cϋ iΛ ιO in ιn θ) (O 00 β MOU5S S CO (O CO O)O)O) '- O) O) *- *- *- ι- *- *- CO O - m ω C_M. C_O. C_O. C_O. C_O. C_. c co r_ 1- JO 1- 1- o o α> H- X X U. X X xxxr-.xxcoXmr-.xx X X X X X U- X X iNiiroiniiiii- O O l h o co cn -tf in X X co i c oo co r~- O co in OI θ ι- 1- ι- r -^ o ιn o o cD ι- ιn r-. co co -tf co cM cO 'tf i- in cM i-- in co i- in in co co co cD oo -* in X oo in o) co i- CM co 00 CM * X *r- s c -t n r- oin oj - o inns co co o co co co co r-- *ι- ι- '< oo σ> co cM oo ιo J MJl O N J O lOO r r-lO CM '* o oo '* oo oo m cM θ> r^ oρ oo c» ι- -<j* co ι- r^ co oo in in o) co N toon -* (θ τ- ιo o. oo o> co in in co m lo cΛ Oi i- rj- ^j- oo in oo in o co o 0) W *- eθ N (O Λ N CO M)D O θ) co -* o ιn o o oo i-. co h- σ σ> w o o i- i- '-t o co r a CM co in ι- i- CM CM ι- '«t *>* *^ oo oo oi σ> h- iN~ co m '< *- β θ)Mnτ* **- s w σ> (θ co o oo ιn m oo oo co σ) co co cθ '< co CM en in t ιn σ> j* ι-. <M *^ -<t *rf c
5 T- CO CD CO 00 OS T— in ->- i- ->- cj> cj) o o c3) 0) co o c» 00) ( N ^ t O (D ^ * 0 (0 coβiowmoo-- (D ^ OO B -t i- Ol - W CO W O co CM m oo ι- N n m n Oi N 'i c Λ cθ - N 00 OO (O CM j- tO CO CM τ- τ- τ- 1- oθ OO ι- in oθ σ) co *ι- *ι- σ> c» '* ι- ι- ιs- r^ co *ι- m co cD -* co m co co co oo ι- ** oo in co CO '« CM ι- CO '< O -^ C s roco co CM CM CO -a- co cM CM roro roco co *ι- τ- W '<* m minco rococo roin ro w o * CM rocM ι- * ro rocM co * co CM ro rocM Is- CM ro ro ro ro roin co σi
Q — 1 * o- —o• o oo oo oo o o υ υ o u o o o o o o o o o o o o o o o o o o o υ υ o o υ υ υ o o υ υ υ o o o o o o o o o o o o o o o CJ o o
" oo oo o oo oo oo o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o
-3 o co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co o co co co co co co co C
,ό ό ό ό ό ύ ό i c> O O ό ό ό ό ci ό ό o ό ύ ώ ό ό ό ό ό ό ό ό ύ ε in in in in in tn in tn in in in in in in in in in in in in in in in in in in Ln tn in in in in in tn in in in in in in in in in in n in in in in in in i^ ώ inόmύincmiώinciniciniύin t ^ ^ ** ** ** ** ** ** ** ** -* -* -* ^ ^ ^ ** ** ** ** ** ** ** *^ *^ ** *^ <!l- '>!l- »* ^* *< *< *< -< oo oo oo oo oo oo oO αo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo oo o
Cn θ> 0) 0> 0> 0> 0> 0> 0> 0> 0> 0> 0) 0) 0> 0> 0> 0) 0> 0> Φ O) 0 0) 0) Φ O> 0> C O> 0) 0> ^ 0> 0> 0> 0> 0> 0> 0) 0> 0> 0> 0> 0> 0> 0> 0) 0> 0) 0) 0) 0> 0) O) O> O) G) 0) O) O) 0 o
W Q
984506. 984506. 984506. 840956. (0<Bi ιnN(i
ffl oso N'*' ι-* *
i-rixx xx N l N o m o o o -< ^- τ- σ5 C f- co cD i- in m c r-- 05 *< i- m in o ι- CO CO C0 00 '* C ro-* -< i- co * i- *< υ υ υ c> o υ υ υ υ O o υ υ υ υ υ υ υ υ υ o o o υ υ υ υ υ υ υ o o o o o υ υ o o o o o o o o o o o o o o o o o o o O o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o υ o o
CM CM CM ^^^^ t**************-******^**-* *^-* ^** f*<t t^ *****^**-**^ cocococococooo όό όόόόόόόόόόό iόόόόόόoόόόoόόόόόόόόό
Oi O) 050505 05 Oi 05 05 α> CD i . r^. f- i— r~- t ^ «—- ι ^~-— I-- r ^--— I-- r-- o o o o δ OδOδOδOδOδOδOδOδOδQδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδQδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδOδO
CO O CO O CO O o o OOOOOOOQOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
CM CM CM CM o o OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO c O CO CO O CO O CO CO CO O CO ^ ^ ^ ^ ^ ^ t ** ** ** ** ** *^ ** ** *^ ** ^ *^ ** ** ** ^ ^ ^ o υ c
8
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90 o o o o o o υ υ υ υ υ υ υ υ o o υ o o u o o o o o o o o o o o o o o o o υ o o o o o o o o o o o o o o o o o o o o o o υ υ υ υ o υ υ υ IΛ o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o IΛ CM CM CM CM CM CM CO f CO CO CO CO CO O cόcococococococo cococόcόcocόcococόcococo cόcόcoco cόcόcόcoco cόcocow o'cocόcόcoc 050505050505 CA ) 05 0505050505 Oi 0i O) 050i 05050505050505 050i 0i O) O> 0i 0i O) Oi 0i 0i 05050505 O505 O505 O5 O505 050505 050505 05 05 O5 0505 cococ c
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r^ o oo CD θ Cβ C0 CO _ . σι τf* ιn ιn ιn ιn co N S N in ιn ιo
'«t Oi 05 CM co - o oo co '<t m X co o CM θ ιn o oi co *ir '* '<j- CM ι- σι co m σι oo σi ι- w ιs. r-- ιs- ι- ,* cM CM in oo σι co cM c ι- co co o5 CM '* co co m cD CD ι- ιn co o co ιn cM CM -* ro ro ro *<j- * * roin cM Oi CM CM CM ro o o o o o o o o o o o o o o o o o o o o o o o o o o o υ o υ o υ o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o
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X X X X X ::* CM X I CM H X I- X IX X X X X DC X X X I X X I I I I I I X X X X X I U. X co σi i--. oo o X 0-0X t--X I"*-r DC: X:i1--x1-icolσi *<* r«- r-- CM θ o σι co * σi in * co oi in o o σι co co σι co σι i"- θ! ι- ι- o cM W o> co co ι-> o O x 01xC0xl--rI:xOιOxOxCMx01x01iODi-cxi-αi-:xC0rX;0 o co in oo in CO CO I-- CO CO CO 00 Oi O h- σi cM w σi oi w oo co co oo in o co co σi 0101 C001 ' O C0 CM Is- r-- 00 CM CJl l-- C0 co co T— T- σi σi S co r-. ι-- ιn ι- ι- cM m ι- oo co oo oo cM CM
MO O O N co co m co CM CM CO O * f- σι oo ιn σι r-- θ '* r^ o co co o o in * N - Oi Oi eO IΛ N CO CO OO Λ O CO oo co *— oo o co cM is- co ιs- oo ιn oo co oι co co cθ '* co
•* ■■* in ι- CM CM O CO CO O) oi T- oo oi in C0 t"- C0 τl- O *ι- CM I-- oo co 00 I*- r«- co oo ooc n o 't N 't- io oi o. mω N O) oo oo ■■* ι- r- is. '<< oo σσι> σcjιι ccoo oo ccMM imn cooo σσιι rr-- ιι-- **>'--- *'ι-- ''3*- ccoo ι oo σi * o in M in CM CM * -*(0*---*- * ιn ι- ιn co cM θ σι 05 -tf 1- in in ι- in to ιo o o) S Mn s o> w n w o) ω *- oo ιn ιn oo ι-- σι ι-- σι -ι- co o co co co ι- r-- c oi in o -•* m i— 00 CO CO 0000 CM 0000 * ι- co oθ f- σι co ιo cvι CM oo in in in oo i-- OI OI I-- *>- CO CO O! CD CO I"- CM CO CM CO O> ι~- σi w co w w co CO CM Is- CM CM oi i— co co co σ><f co rot- in CM "•* •* f- rocM CM ι- co ι- ι- cM CM M o co c ι '< *^ M in '* CM in in co * ι- ι- ^*-*- -*ιn( iow* i*o*- *-*-w^ υ υ υ υ υ υ o o o o o o o o o o o o o o o o o o o o o o o o o o o o o υ o υ υ υ υ υ υ o o o o υ υ υ υ υ υ υ υ o o υ υ υ o o υ o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o t -t "•* < t •*** * * -•* * t * * t * •****<t*<t^-* t * * t -* -• t -•* " o o o o o o o o o o o o o o o o o o o o o o o o ooooooooooo ooooooooo o o o oooooooo o o o o o o o o o o o o oooooooooooooooooooooooooooooooooooooooooooooooooooooo ooooo ooooo ooo ooooooooooooooooooooooooooooooooooooooooooo ooooooooooooooooooooooooooooooooooooooo o ooooooooooooooooooooooo ooooooooooooooooooo ooooooo ooooo ooooo oooooooo ooooo oooooooooooooooooooooooooooooooooooooooooooooo
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Table 2 cont.
5 412959.6.oct 2470746H1 416 614 5 412959.6.0Ct 2763336H1 14 249
5 412959.6.0Ct 6363δ89T6 422 966 5 412959.6.0Ct 1703741 H1 7 225
5 412959.6.oct g4189438 430 815 5 412959.6.oct 1632693H1 14 225
5 412969.6.oct g4188920 430 815 5 412959.6.oct 4296049H1 14 268
5 412959.6.oct g4188326 437 815 5 412959.6.oct 5074132H1 14 297
5 412959.6.0Ct g4302701 439 815 5 412959.6.oct 2599392H1 1 268
5 412959.6.0Ct g3539347 444 815 5 412959.6.oct 3846287H1 2 234
5 412959.6.oct 776186H1 445 673 5 412959.6.oct g1157175 1 358 δ 412959.6.oct g3048416 448 815 5 412959.6.0Ct 1253994H1 1 212 δ 4129δ9.6.0Ct g2782788 447 815 5 412959.6.oct 4527929H1 1 264
6 412959.6.0Ct g2901391 464 815 5 412959.6.0Ct g2029372 1 177
5 412959.6.0Ct g3801639 471 815 5 412969.6.0Ct 776186H1 2 217
5 412959.6.oct g2874031 480 889 5 412959.6.oct 6353589F6 2 480
5 4129δ9.6.0Ct g2741867 489 979 5 412959.6.0Ct 2586285H1 1 218
5 412959.6.oct g2675057 493 815 5 412959.6.0Ct 3206565H1 2 177
5 412959.6.oct g3038162 493 970 δ 412959.6.oct 3269334H1 3 233 δ 412959.6.0Ct g1639027 501 715 δ 412959.6.0Ct 3495688H1 14 298 δ 412959.6.0Ct g4373288 506 973 δ 412969.6.0Ct 4655833H1 16 264
6 412959.6.oct g3988967 509 815 5 412959.6.0Ct 496681 H1 23 259
5 412959.6.0Ct g3961978 522 816 5 412959.6.0Ct 3679041 H1 26 206
5 412959.6.0Ct g3869490 625 968 5 412959.6.0Ct 496697H1 23 248
5 4129δ9.6.0Ct g4004707 525 977 5 412959.6.oct 5209034H1 27 292
5 412959.6.0Ct g3086363 530 815 5 412969.6.0Ct 6110991 H1 29 247
5 412959.6.0Ct g3897838 533 967 5 412959.6.0Ct g1745450 29 322
5 412959.6.oct g2115818 534 973 δ 412959.6.oct 3879459H1 3δ 312
5 412959.6.oct g3281206 537 970 δ 412959.6.oct 3752872H1 39 256
5 4129δ9.6.0Ct g4070114 540 971 δ 412959.6.oct 4756963H1 69 311
5 412959.6.oct g4069838 543 980 δ 412959.6.oct 5644885H1 60 188
5 412959.6.oct g2934294 545 982 5 412959.6.0Ct g1940430 73 532
5 412959.6.oct g1331787 545 973 5 4129δ9.6.0Ct 2904488H1 130 412
5 4129δ9.6.0Ct g2626614 546 976 5 4129δ9.6.0Ct g1987165 144 469
5 412959.6.0Ct g2932297 548 974 5 412959.6.oct g1237710 146 287 δ 4129δ9.6.oct 5608040H1 568 805 5 412959.6.0Ct 2120694H1 166 337 δ 412959.6.oct g2264793 563 967 5 412959.6.0Ct 308151 OH 1 165 470 δ 412959.6.oct g3281079 573 973 5 412959.6.oct g786906 173 499 δ 412959.6.0Ct 2672133H1 581 814 5 412959.6.oct 981383H1 191 432 δ 4129δ9.6.oct 1772941 H1 581 855 5 412959.6.0Ct 3705428H1 201 468
5 412959.6.0Ct g3038169 584 970 5 412959.6.0Ct g1745306 206 502
5 412959.6.oct g3968916 591 976 5 412959.6.0Ct g1981799 245 508
5 412959.6.oct g2876891 597 970 6 4129δ9.6.oct 2581268H1 339 583
5 412959.6.oct g1741463 597 949 δ 412959.6.oct 5909478H1 340 621
6 412959.6.θct g1882898 598 967 δ 412959.6.oct 1781627T6 346 929
5 412959.6.0Ct 4624368H1 3 240 5 412959.6.oct 4129041 H1 348 631
5 412959.6.oct 2654578H1 3 303 5 412959.6.oct 5029110H1 347 611
5 412959.6.oct 4460844H1 4 197 5 4129δ9.6.oct 3771103H1 357 530
5 412959.6.oct 2644911 H1 4 269 5 412959.6.0Ct 1781527H1 360 619
5 412959.6.oct g2159460 4 460 δ 4129δ9.6.oct 1781527R6 360 826
5 4129δ9.6.0Ct 4065681 H1 4 276 6 4129δ9.6.oct 3029101 T6 372 931
5 4129δ9.6.oct 686032H1 7 225 δ 4129δ9.6.0Ct 2956192H1 372 645
5 412959.6.oct 3988406H1 7 195 δ 4129δ9.6.oct g1319510 377 893 δ 412959.6.oct 041056H1 9 275 δ 412959.6.oct g1447775 254 598
5 412959.6.0Ct g1745820 11 208 5 4129δ9.6.0Ct g1882897 259 612
5 412959.6.oct 4164076H1 6 267 5 412959.6.oct g828247 261 526
5 412959.6.0Ct 3156341 H1 10 285 5 4129δ9.6.oct 2350937H1 272 467
5 412959.6.0Ct 2561686H1 10 255 5 4129δ9.6.0Ct 1307384H1 275 507
5 412959.6.oct g1996909 10 311 5 412959.6.0Ct 1541305H1 288 497
5 412959.6.oct 034375H1 12 226 δ 412959.6.oct 4744668H1 392 660
5 412959.6.oct g1618697 13 306 5 412959.6.oct 5435925H1 300 532
5 4129δ9.6.oct 5374474H1 13 185 5 4129δ9.6.oct g2838960 866 972
5 412959.6.oct 5152582H1 14 277 5 412959.6.oct g1745821 866 967
5 412959.6.oct 5069232H1 14 271 5 412959.6.0Ct 721875H1 866 958 δ 412959.6.oct 3706309H1 7 290 5 412959.6.0Ct 721352H1 866 958
6 412959.6.oct 1333267H1 14 298 5 412959.6.0Ct g3041378 866 970
5 412959.6.oct 2764864H1 14 255 5 412959.6.0Ct g1193527 907 979
5 412969.6.oct 4888767H1 14 282 δ 412959.6.0Ct g2185358 599 971
5 412959.6.oct 3479540H1 14 247 δ 412959.6.oct g3785891 609 995
5 412959.6.θct 2912750H1 14 286 5 412959.6.0Ct g3016900 610 970
5 412969.6.oct 4295435H1 14 234 5 412959.6.oct 1918481 H1 614 815 Mn *- o o (o co co *- co co i- co w σi σi i- in in CM co oo σi co ό t- o ιo oo m o) θ) θ ω n Nθ ^ θ) w o>n ω ffl θJ θ N θ (» N θι- s o o s o N θ '- ω >θι- ffl cθN in c w *- so ιn co ιή '* '* '^- '^t- '<t co cM c —o ι- co o cM c —o ι-. σ} co cM o —o *< ιn co ι ι "- n — ιo n * " o —) i —oN θ —) Mn ιo tt " *^ ιβ co o ιn - "s ) θ '* " in o oo σι σι rs. oo ιs- ι-- ι-. σi h- ι-- *^ ι- '> F i- i- *r N M0 N i- *r *r i- *r i- B C M0 - N 01 (
JS i- co oo cM -a- o o o in i- co σι σi f<τ oθ '<a- r«- oo -<t * _ c_o c_o_ r.- CM
CM CM co * ^ ιn ιn ιn co ^ ^ * cM θ5 θ5 co co ιs- ι-- ιn co oo oo o *ι- -ι- ^ ιn 5 oo - cM θ -- ιn o -- co co j* " σi oo oo j- i rrrrrrr rOθnβOIO Oι-IOIOOOOOOrrr OOOOOI(l)fflOlll)« NNe. N σi σi σi σi o σ -τ- ---^ι-----τ-*-to<o(oιnιni()inu.oιnm*---*---*-*-*-*---^*'t't^--------ι- cM M -* '* '*- '^- ιn ^
H U α. -* X i- CO N in i-- co H- <t ι- oιnι'>ocl-iCOiI-.rXucO)i*ι-iCMnCMiι- C_5*ι*r-ιCMιI-«iOoCONOOiO JrOOϊCOiMoϊΛ'tϊinϊOXϊOrl;I • C*M σCOi xIs- IC-M TCO-CO CM CO iCOiCθjDCrIocθ C
CONCMS co co co cM oo co o5 '«!j* o co cO '<i- co '>cr co is- co oo *r- oo i- i-- CM cO '* i i- cM CM Oi r^ ι- ι- w co ιs- co cθ '* σι ^ w ιn co co in o T- ι-«. o .-- ιn '* co τ- ι-- o cD co ιn α5 o rs. '*-_- cM w co cM O '- O 'Ϊ O CO IO - O S'f <t co co o cM '* r,-- i- co co w w i- c co oo r»- co CM CM i- '* C r-- OO OO s CO OO CM CO CO O in 0505 '« 05 W C Oi O '* CM "-J- '<-|- i- i- 00 cM co o o oo o in i- in co oo oo oo c
I-- 01 CM Is- CM CM '* r-- '< oo oo ι- co ι- σι co cM ι- oι ι-. τj- ιn ι- ι-- CM '* CM "-I- '* - CJl t"- Oi r-- CM CM CM CO ι- 00 » ts. cO l- CM ι- ι- CM C co in CM CM σι σι cθ co oι rs. co *^ co τ— *ι— I-* **— ιn *f— co *ι— co co oi CO CO CO CO -* CM 01 in O I-- CM CM CM I-*. m CM W C000 ι- ι- 0000 ι- " rom rooi ro ro ro roco *•— co ro* co rocM roco co cM co ro ro^ σi roco roco i- in in n o -* ro roin co ro rororo't * r-- ι-- roi
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 o o o o o o o o o o q q q q q q o o o o o o q q q q q q q q q q q q q q q q q q q q q q q q q q i iri iri iri iri iri iri iri in iή iri in iri iri iri iri iri in iri iri in iΛ in iri iri ιnιnιnιnιnιn ιnιnιnιn ιnιnιnιnιnιnιnιn ιnιnιnιn ιnιnιnιnιnιnιnιn ιnιnιnιniΛiΛinιnιn ιnιnιnιn ιniΛinιn ιnι ι- ι- ι- τ- ι- ι- ι- ι- ι- ι- ι- ι- ι- - ι- *r- ι- ι- **- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- **- *ι- ι- **- ι- ι- ι- ι- ι- **- ι- ι- ι- ι- ι- ι- ι- *ι- ι- ι co co co co co co co co co co co co co co co co o co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co c co co co co co co co co co co co co co co c o co c co co co c co co co co co co o o co co co co co co co co c co co co co co co co o co c e CO CD CO CO CO CO CD CD CD CO CD CO CO CO CO CO CO CO CD CO CO CO CD CO CO CO CO CO CO CO CO CO CO CO CO CD CO CO CO CO CO CO CO CD CD CO CO CD C o u
co m ι-- co *- io * 0) N (ooo(o t σι r^ » ω o *ι- CM σι co cM CM '^ cM oo co ** o t co σι ιn cM σι co o ιn oo co co ιn ι,s co o *ι- ι- 'i- r-- oo o cM in ιn co co ι- oo o
■ i oM CcoMωCOιCoOιo(θi!nθC<θ00(θ1(0θ10NSi-SinNCOs-s01c0oi-)cCoM - *r
(i-θ(θ-(CθM C( cCOooθ'lc. O*O l^» CθO)© 010 τ- '-O»-*----- 0ω1 CoM)iθn)ωco5ιCM-*C-M^CO-C-O C*-O CO-CrO-CO*-'*- l^ l ι- ι- to CO CO o : to •- ι- to r- co in cM co oo o i- i- o X r- X m X H- CM rs. Is- co X _= co in X X X I— lO LL CM CO H X X u. X r-- co I := f- X i_ X in i- co σi σi cM in σi in σi NMOWOCO CM in co co o X CM 05 i o * co ->- co ιn oo rs. ι- cM N SN MJ1--I S S l-- CO OO "<* i- cM oo ^ o i- co m in oo r«- oo CM co w * fs. o CM CO ι- ι- 05 ι- CM co in CM -51- op co σi τ- oo co t- i- co cM i- co -' in in in in i- w i in in oo co co o in oo oo in oo co co Is- o O o σi w in in co σi co Is- oo co i- CM '* '<t l- CM C001 CM CM τ- ι- τ- 0 -* CO CO Φ O> CO T
CO -* 1000) * N r* ^* r- i- Is- in I-- in <* co co -< co T- * "* -< ι- CO CM 1— r-* c cθ oι co co co co co o i- co cM W in in lO O N N W MO -* O in iO τ- (M CM 00011- CM Is- oo ι- i- CM r- oo T- o ι- in o CO 00 00 *ι- CO I-- CO co ioco -ct to a c o o o co o ι- σ CM ι- CM CM ι- C CM ι- 1- 00 - I-. CO CM f» CO ι- i- CO ι- I"*- I"-* CO CO CM * CM co co σi co i- co co m (O IO C W 100 U. S ι-- oo σι cM ro ro rorororo ro ro rocM ro σ>ι- rocM CM ro ro ro ro** r*- ro rocM co CM CM roco ro ro**-!- * in <* -* roro σico oo cM CM CM ro σiι-
90 o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o q q q q q o o o o o o o q q q q q q q q q q q q q q q q q q q q q q q q q (ό cό to d d cό cq cό cό c co co cq c c c c cq cό cq cq oi σ) σi (Jϊ θi oi θ) θ) θ) σ> θϊ ϊJ) θ) Φ θ) θ) θi oi φ θ θ) σ) θ) θ) '- '- -- '- *- -- '- *- *- *- *- *- *- - -- *- *- τ- τ- τ- τ- -- -- *- i cn>iioniioniioniioniioniicn»iOniicnnicn_icinnioniioniioniionioinici»n ion}OiniiOniiOniian>ioniionicinM CinM CinM CinM CinM CinM CnM CinM CinM CtnM CinM CinM CinM CiMnCiMnCinM CinM CinM CinM CinM CiMnCiMnCtnMini
1- 1— 1- 1- 1— i— — - T- 1— -I— 1— i— 1— 1— 1— i— 1— i— ι— i— 1— ■■— *- — - co co co co co co co co co co co co co co co co co co co co co co co co c t ** ** ** * * ** ** ** ** ** ** ** ** * * ** ** ** co co co co n co co co co co co co co co co co co co co c
ιn ιn ιn ιn ιn ιn ιn ιn ιn ιn ιn Ln ιn ιn ιn ιn ιn ιn ιn ιn ιn ιn ιn ιn co co co Φ co co co co co co co co co co co co co co co co co co co co c
Table 2 cont.
481382." .oct 2444372H1 129 370 9 903849.1 .oct 2624665H1 1394 1608
481382." .oct 3344969H1 179 422 9 903849.1 .oct g2695471 1408 1620
481382." .oct 4043328H1 206 389 9 903849." .oct g2988037 1413 1610
481382." .oct 2508704H1 252 489 9 903849." .oct g2875731 1418 1612
481382. .oct 2370123H1 285 508 9 903849." .oct 2120483H1 1423 1602
481382." .oct 2370123F6 286 610 9 903849.1 .oct 899503T1 1431 1572
481382." .oct 2803027H1 308 418 9 903849.1 .oct 899503H1 1431 1610
481382." .oct 5336386F6 326 822 9 903849.1 .oct 2680380H2 1439 1589
481382." .oct 6381667H1 334 534 9 903849.1 .oct g1331532 1452 1617
481382." .oct 1431535H1 378 650 9 903849." .oct g2806322 1462 1610
481382." .oct 2755583H1 396 656 9 903849." .oct g3093063 1468 1616
481382. .oct 4665103H1 586 848 9 903849." .oct g3041606 1471 1618
481382." .oct 2680942H1 1 285 9 903849." .oct g920645 1481 1617
903849. .oct g3961274 1180 1621 9 903849." .oct 2325791 H1 1511 1615
903849. I .oct 1380812H1 1191 1421 9 903849." .oct 2325782H1 1511 1608
903849. I .oct g3017243 1195 1610 9 903849." .oct g4087654 1542 1610
903849. I .oct 2448407T6 1200 1567 9 903849." .oct 3165133H1 594 874
903849. I .oct 5062263T6 1203 1592 9 903849."l.oct 2507856H1 619 878
903849. I .oct g1803794 1209 1608 9 903849. l.oct g1670047 644 1015
903849. I .oct 1697502H1 1209 1417 9 903849. .oct g890906 646 862
903849. I .oct g3366973 1210 1614 9 903849. .oct g751221 653 865
903849. I .oct g3245013 1219 1611 9 903849. .oct 1255114F6 657 1157
903849. .oct g4078415 1223 1614 9 903849. .oct 1255114H1 657 897
903849. l.oct g2740706 1225 1614 9 903849. .oct 3953586H1 670 893
903849. t.oct g2463862 1227 1612 9 903849. .oct 2912329H1 676 855
903849. l.oct g265744δ 1228 1610 9 903849. l.oct 6181226H1 676 946
903849. l.oct 197091OH1 1232 1493 9 903849. l.oct g2459206 684 1109
903849. l.oct gδ19042 1234 1610 9 903849. l.oct 295δ53δH1 696 948
903849. .oct g3739697 1238 1614 9 903849. l.oct 059142H1 738 937
903849. l.oct g3306909 1240 1614 9 903849."l.oct 1226685H1 746 994
903849. l.oct g2526781 1243 1438 9 903849. .oct 042939H1 749 1024
903849. l.oct g1368047 1253 1599 9 903849. .oct 4797142H1 783 1048
903849. l.oct gδ64656 1260 1614 9 903849. l.oct 6072193H1 796 1058
903849. l.oct 1696378H1 1261 1440 9 903849. l.oct g3166808 838 1077
903849. .oct 2807436F6 1275 1614 9 903849. l.oct 4167804H1 845 926
903849. l.oct 2807436H1 1275 1518 9 903849. .oct 2252617H1 845 1076
903849. l.oct g1689946 1281 1582 9 903849. l.oct 4716926H1 845 960
903849. l.oct g1669936 1283 1608 9 903849. .oct 6372420H1 845 1094
903849. l.oct g2207021 1284 1614 9 903849. l.oct 4157804F8 845 1339
903849. l.oct g751861 1286 1602 9 903849. l.oct 4375829H1 861 1128
903849. l.oct g1140272 1290 1618 9 903849. l.oct 2881017H1 863 1082
903849. l.oct g1136826 1296 1614 9 903849. l.oct 032587H1 871 1016
903849. l.oct g1801343 1308 1614 9 903849. l.oct 2448064F6 871 1320
903849. l.oct 761194H1 1316 1398 9 903849. l.oct g488666 871 1098
903849. l.oct g3179612 1328 1617 9 903849. l.oct 2448062H1 871 1110
903849. l.oct g1231798 1329 1614 9 903849. l.oct 5863686H1 873 1147
903849. l.oct g1124676 1331 1610 9 903849. l.oct 184041H1 876 1090
903849. l.oct g1648331 1332 1610 9 903849. l.oct 4723163H1 878 1074
903849. t.oct g1241547 1338 1610 9 903849. l.oct 4004305H1 907 1163
903849. l.oct g2945487 1339 1610 9 903849. l.oct 3219576H1 930 1275
903849. l.oct g1693991 1339 1611 9 903849. l.oct 3073390H1 937 1208
903849. l.oct g1229235 1342 1616 9 903849. .oct 466399H1 939 1165
903849. .oct g1018304 1346 1690 9 903849. .oct 1929780H1 940 1226
903849. l.oct 2045971H1 1351 1614 9 903849. l.oct 1929780F6 940 1397
903849. l.oct g1124543 1358 1630 9 903849. l.oct 674013H1 948 1205
903849. l.oct g1226701 1361 1610 9 903849. l.oct 1845763H1 972 1239
903849. .oct g2882614 1363 1614 9 903849. l.oct 1929780T6 977 1565
903849. l.oct 568980H1 1365 1610 9 903849. .oct 760376R1 986 1465
903849. l.oct g890854 1365 1605 9 903849. l.oct 760376H1 986 1258
903849. l.oct g3644590 1156 1608 9 903849. .oct g1146796 1006 1435
903849. l.oct 2467148H1 1157 1381 9 903849. l.oct g1162478 1006 1263
903849. .oct g3666122 1157 1610 9 903849. l.oct 6698908H1 1013 1286
903849. l.oct 5099110H1 1161 1424 9 903849. l.oct 3623694H1 1014 1339
903849. .oct g3076029 1366 1617 9 903849. l.oct 5698808H1 1014 1278
903849. .oct g3117308 1366 1614 9 903849. l.oct 4466790H1 1017 1280
903849. l.oct g750565 1369 1615 9 903849. l.oct 2344474T6 1019 1571
903849. l.oct gδ18777 1370 1614 9 903849. l.oct 507835H1 1022 1113
903849. l.oct g1368048 1379 1611 9 903849. l.oct 3925430H1 1024 1224 -'-** ''** *'* *
oo X X σi X X r-. to co i- o o x- xin xco Xr: c oo ι— o 00 i— ι— CM ι- σi σi * LO M T- CO o (MOOffl - oo o rs. oo CM I* 00 CO CO 0 CM co co CM in σi σi o o in o ι- r-- •* ι- CM co oo oi * σi rocM T- rocM co * CM CM * c υo υ o υυ oooooooυooooυooooooυυ υoooooooooυ oo oooooυoo υo oo ooooooo o ooυoυoυoooυoυoooooooooooooooooooooooooooooooooooooooooooυo ooooooυoυoυoυoυo
0101 0505 ^ 010101 0101 05050) 05 01050505 050505 050505010101010101 0101010101 01050505 050501010101010101010101 01010101 0101010101010101 01010101
* co*oo*oo*oo^oo*oo*oo*oo co*oo*co*αo*oo*oo*oo co αo oo*oo oo oo*co*co*oύ^oo*oo^oo oo oo*oo oo*co*oo oo co c*o*co*co co o ** *** **^*^^ co co co co co co co co co co co co co cO cO co co co co co co o co co co co co cO cO co cO co co co co co co co co co co co co co cO co o
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c Oi Oi 01010i 010i 010i i i Oi Oi Oi 0101010i Oi i > 010101010i 010i Oi Oi 05010i i Oi 01010i 010505050505010i 01010i 01010i 010i Oi 050505050505050505050505 o υ
CS ι--cθ ι- c_ιcocMmoι-cM τ-coθ'<t moocoι-σισιcoco σi'*
(θ^ o)t- Mn*- -wwN*- ιnnω'* tθτ- -t- *-osN*-offl 'tθ CMS N I- IO ON o * ι- **co ι-- ι--r-- t-- co ι- cM ,« rs-ooc '< coco m coιnσιcM i cMCM incoinin incococo co*coco coco* io in coco* incocM coooin ino5*coo505co cM r--^^* is-cM inoi*i- * oo*i- r^
■■- •- ■■- ■■- •- •- τ- **- *ι- **- **- ***- ***- **- **- **- *ι- *ι- **- *ι- *ι- **- *ι- **- CM CM CO CO C W co oo m "* ι-- oo - τ ** co ιn ιn ι-- ι- *>- oo cjo σi '<t m oι cM co o
CM CM C CO * * CO I- rs. oO C_001010000 ι- CM CO CO '* * ιn 00 - * |S.
P P P O O O O P P P P O O ι- ι- *r- *r- ι- ι- ι- ι- ι- ι- ι- * tO CO <O S CO S CO O) 0 » 00 {0 (θ n {O CO CO '* (O W '* W O CVl - CO W UD -- M_) N OJ
■- τ- ^ ^ *- *-τ- τ- r *- *- *- *- ι- *- *- *- *- *- ^ τ-*- *r *r *-*- τ- *- n n nffl -- -- -- *- '- --*- CJ '- N τ- W NW W W ϊ coϊcoh*ϊιnh-^hσιfco;XjDCϊoϊcolc-oH*oϊ*ϊσιϊι-.fcβ2h*fflρ**ι-*phco-ιjnffl^ϊ*ϊ*ϊσιϊCMϊcoHcoιnϊ-^ϊcoϊc»;XH* ρϊρHcococΛi-- ιnc_ιcoιs- ooea*^co »
00* O00 -^00 CMCJlC_lCMC0C0CMCM CMC0^00 ^CMC0h- C0inc0CM O*^010i 01CM* inO C0CMCM C00)r 00in* 00t-- O ra co oco* **^ *ι- *^coco cooc» co* s ω '*- ιn-r- fflc» ιs. -r-coιnιnτ-co p*ι-rs.* » cMoo ai ιnιn*ι- * » θBso onΦ«moo)fflo»θτ-ooιn inι-oιnoeonnoN N*-*-N^fflwηθN nffl^BθU)ooiΛθ Nθc\ιc.ιθ'i-βιβaiΛθiι_)(o^N ω*-ιnωu)N-*ωooooιn'-wι)u. U) ) -oocooω().lff ω--*-ιncow(S'-Φ f fflNcoN*ω ι-N SN(\ιo*N .^sooswθ)ωm*^
CM co *ι- ι- ιn *^ ιn * * ι-- - r-- co r rs. o o oo cM CM co *ι- ι-- cM *ι- - co cθ τ- co co co co ιn o σι rs. |s. *^ ιn co *ι- ιn co *ι-
CO ι- '* CO '* CM * l- ls- CM ι- ι- CM CM CM C0 C0 ι- ι- O) O) OI *r- ro ro* C0 CO * CO C0 C0 CO * * * C0 C0 C0 * C0 CM CM CO CM CO CO *ι- *ι- CO CM CO in *ι- '< C0 in cO CM CM C0 ro o ro CM *
90 oqoqoqoqoqoqoqoqoqoqoqoqoqoqoqoqoqoqoqqooqoqoqoqoqoqoqoqoqoqoqoqoqoqoqoqqoqooqoqoqoqoqqooqoqoqoqoqoqoqoqoqoqoq oqoqqooqoqoqoqqoqooqqoo IΛ q IΛ
0_ d d d d θi θi θi d d θ- 01 050505 d d d θ5 θi θi d θ5 050505 05 0505 G! 0101 0! 01010! 0! 01010! 01010101 01010! 0! 010! 01 0 fS * oo*oo*oo*oo*oo*oo*oO*oo*oo o*o o*o*oo*oo*oo*oo*oo*oo*cO*c*o*o*O*ao*oo*oo*oo*oo*oo*oo*oo*oo*oo*ao*oo*oo*oO*GO*co*oo*oo*co*oo*oo*oo*oo*oo*oo*oo*oo*oo*cio*oo*oo*oo*oo*oo*oo*oo*oo*oo*oo*oo*oo*oo*oo*φ*** c co co co co co co co co co co cO cO cO cO cO co co co co co co co co co co cO co cO cO cO cO cO cO cO cO co cO co co co co co co co co co co co co co w
O O O O O O O O O O O O O O O P O P P P P P O O O O O O O O P P P P P P P P P O O O O O O O O O O O O O O O O O O O O O O O O O O O O 01010101010i 01 C_O Oi C 010101 01 0101010i 0505 05050) i 01050101010i 010i C_O i i Oi Oi 01 0i 01010010101 0i 01010} 0101 Cb 010101 0i 010101 0101 010i i 010i O>
0101 0i Oi 01 010i Oi 010i 010i 010i i i l Oi 0101010i Oi i i i 01010101010101010i 010i 010i Oi Oi Oi 050i 05050i Oi Oi 010i i Oi 010i 010i Oi Oi Oi Oi 010i i 010i Oi
* co co co co in * cM -i- oi * co - co rs co co co oo cM co in c_5 in o cM r-- oo co r^ cM O) co *^ in i^ cM co *^ -^ in cD in rs. o co i- in co n in 0 _).0 _5.0.5. C .M. CO C_5 CM CO in CO in *ι- in cθ CO CM OO * C C_5 CM CM * l-- C» r-- l-O I^ CM in l-- CO C I-- O CO ->- 0 ->- O CO O O *ι- * CO CM co irs-.. |ιs->. | rs->. ^ * -φ *<t * co * * * ιn * ιn * co * co co ι^ * ιn ιn ιn ιn ιn ιn ιn ι^ ιn ιn Ln ιn ιn c» ιn oo co co co co co ιn co co ιn co ι-- oo oo ∞ IΛ JS
© © CM CM co * co co ιn cM CM * * cM io ø) ι- o cM co co *^ ι- σι o o cM co o o o cM CJ CM *ι- *ι- ιn ιn * ιn - σι ιn co θ5 τ- o o ι-- ι-- θ) CM co ι co ω !__ CM CM * * l-- OO OO O5 O505 Ol Ol Ol Ol O -i- *i- CM CM CO I-- CO I-- r-* l-- Ol O O CJ CM CM CM CO CO CO CO CO CO * * in cO CO OO OO OO OO CD O> O O O s |^ rs. r^ - ι- ι- *ι- ι- *ι- ι- ι- ι- ι- CM CM CM CM CM CM N C CM CM CM CM C C e CO CO CO CO CO CO CO CO CO CO C CO Cθ m
H U 1- 1- ι- 1- to ι- •- α. i I I I DC X IIIDCIIXX CM l I CO CM CM lO ^ ^ I I I— (O S * I I W (0 (0 ml *xoo x* ri-nxr-- o * CM 05 in ι I-iO1rI--iPρCMOιncCoiT-ι0)ι05ιW-_Ir_I=_I=ι*_I= rs. CM 0) Oi co i- i-- oo IDC oo(- ls- l-* l-CM * * co oi -* in o * CM l I i- co i- co i- o cM Oi cM in * in T- i CM in co 1- * in M 00 P CM ooo*cococoι-oι*rs.σιcoι--*ι--ι- Cf MO CO CO i- ω S cM w ω cj o w in s co io ω σι r * is. co σι o o co co co σι ιn oo ι- t-- CM m ι- co 0 o m co co 1- Is- CM •>- 1- CO 1- 00 C0 C0 O O C0 * 00 00 s CM 01 * *i- C000 i- Ol l-- ls- 0} * CO CO in in oo in cM O CM co h- co co ιs. cM - co co co co * co cM CM ø) * co σi ι- co ιs- m o 01 * ι
CO * 0) * i- co T- * * co σι * ι-- * * ιn m co co o * o cM co co ι- co rs co co τ- 1- p oo SNO BOOO-tβB oo m i-- i-- in m o5 i-- co o oo co co oo co co in * cM - r.05
CM CM in oo in OS--ON IO O CO O O) IO . IO (C U) N S CO N O) 0) P CM CM CM ι- ι- * l"- * * ι- -* r-- co co ιn oo cM CM σι ι-- co cM ι- t-- ιn rs oo cM co ι- ι-- p p σi P oo * cM CO 1- 1
I"- I-- * CO * co in o o 05010 *- -0 *- (M N M\i n MO O O O B o * σ> σι * ιn ιn o CO CO O C CM ι- * OO ι- CM CM ι- CM OO CM * CO CO P P OO CM CO C -* '* * O ι- CO ι- O CO C
1- 1- CM roin CO CO CO 1- 1- co 1- σii- ro ro ro* * * ι- w co co co σι ι- W ι- ι- CM * CM CO oi 05 CM Oi in * CM * roi- i- roin i— ro roro rooo oo * co — ro ro ro**— CM ro ro cj o o o υ o o o o o o o o o ϋ o o o o o o o o o o υ υ o υ υ υ o o o o o o o o o o o o o o o o o o o o o o o o o o υ o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o
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CO CO όrcsό.|csd.crsό.tcs.|c^o|csD.|CsD. c rso.c|so.|csD.|csø.|cso.cr sό.|csø.|sό.tcsb.|csb.cros.|cso.|cso.c|sø.c|so. | csό.rcos.c|sό.rcbs.|-b.rcόs.|so.|csό.|csø.|csø.c| CO CO
Is- ι-- | t^ sό.|c c c c ^o|cso.fcøs.crsό.|csø.^cb c|s. r tos |cSd. |cSD. C|SD. |cSd. c|Sd. c|So. rcsd. c|Sd. c|sd» |cSό. |cSd. CO CO CO CO CO S. |S. |S. |S. |S. |. I-- r~- e- I-- r» - is. CsO. o CO to CO rs. i r-- f»- |S. |S. |S. |. |S. |S. |S. |S. ι. rs. r . |s. rs. ι« |. |s. ps |s. rs. |s. |s. *s. |s. rs. is. r . r . rs. i-. rs. i~. is. is. rs. r . rs. is. r . ts. ts. is. h- r . |S. rs. r |S. | I-- t-- Is- i-*- r-- r. r-. is. r-- * r~- I-- ι~-* r- ι-» i o o o co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co co CO O co co co pj 3cp co c co co co o co c c
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* * * * *o c*o*co c*o c*O c*o c**o c*o c*o c*o co c 3o3co c3o c *o c*o c*ό c*o c c*o c*o c*o c*o c*o c*o c J *o cJ*oC c*Jo c*o c*o c*o c*o c*o c*o c*o*co c*o C *O C*O C*O 33 333 33 C *O *O
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C 1- 1- 1- 1- 1- 1- 1- T- 1- T- 1— 1— 1— 1- 1— 1— 1— 1- 1- 1— 1— T- - 1- 1- 1- — 1- 1— 1— 1- 1- 1- 1— 1— 1- 1- 1- 1— 1- 1- 1- 1- 1- 1- 1- 1- -1— 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1- 1 o υ S
,Λ co co oι ιn ι- co cM co cM CM i-- cβ *^ o ιn ι- oo ι-- * ι- r-- ιn * co cM co * co co ι- * co co co co co co * ι- co ιn co cD co co co co co co co ιn oo ω co w r-1 oo * oo * CΛ ι- cM i^ ιn c_5 ι- o co ro * * ιn co ιn - θ ι- ιn ι-» * co co σι cM CM in σι σ} σι σι σ5 σι oι co σι ι-- * σ> σ) σι σι ro σι σ} σ5 i-- co cΛ σ5 ι- σ5 ro ι- co cM CM * co co cM CM CM CM CM co co ι- co co t-- TO i-- ιs- ιs- ω is- i- ιs- ω ιs- co oo ω ιs- . ι-. ι-. ι-. t-- ι-- t-- ιs- ca « θ5 CM - ι- ι- ι- * * * ω co co co co t-- eβ o o ι-- r-- cΛ i-. p ι-« σ) co co cβ co * co ι- - ι-- ι^ * CM cθ (» cΛ σ) in ι- co ι^ cM co ι- ι- p c ^ c in ^ c ^ ^ Φ w σi f-^ ^ c i^ ^ i^ ^ ^ ^ ^ t g g OT OT φ P D -i^ ^ i^ i^ -^
* -* * * *- * * * ** ** * ^ ** in ιή u5 iθ ιt * * * * * * * * * * * * * in in in in m in in m in in m co co co co co co co co co co co co co co co t ι- 1- 1- i- to ι- : co
I I I I U- I Ϊ Ϊ Ϊ Ϊ ; O N X x I CM CO W i— Ol OO CO CO l ^ CO CM σi * -* 0!_*1. ι 1-— σi _ i-_ _=_ -_- X X loll— COlOlcoIIi-I σi in i- co co p τ- oo oo ιn l co co co ι- i σ> θ iι- ι cno 1cM c 1o xι-- icio.c xoX r: ico oX := ι-- l— oo in * co o co co o X co co r-- CM i- co co co co DC X co oo oo r-- co co 0) co co co co r-- in o in * O5 o σi co h- co * 0O CM * O5 CO CO CM * τ- rs- OO CO OO CO CM CM CM O CM lO OO in CM in o co co * * i- 05 co o o i- i- co co co in co * co co co m o5 io rs. 5 -- O5 CO - σi * P CM M 05 ** O CM O 00 00 O * ι-- ιn co t-- CM C_i ι- σ5 in co * * ι- 0) M0Nωu. SONO OW*-l000Oι-010)(θnθτ-τ- * CO 00 in CM * CO CO O
* ι- σι σι co ιn o o co * o cD
00 * ι- I-- CM CM σι σ> rs. cM ι- * co σi ρ r-. CM co co co * w * o o co r-. co 05 co cM cD in co in * o oi co oo co in co co oo in co cM in in o cM - co co co cM oo co co co rs- in oi i-s co cM t in co * CM co I"- w * CM co co co cθ - ιn r-. CM C C005 W CO in c0005 i- CO OO CO CM CM in CM I~- O * CM CO O * i- C - |*s 0> 0) CO in in CM I"- CO - * w oo co in o 1- σι ιn ιn o ιn - - ιn ιn l-- CM O ι- CM CO * CO C001 CO CO O) CM 05 i- * CM CM C CM C005 CO CO CM CO * CO CO CM CO CM in in oO m m s O CO - O CO * - * * CM CO C CO
* in 1- m * co * ι- ιn cvι rororo* * co m rocM 1- * 1- co co 1- rooo i— oo rororo ro ro roroco * ro ro ro ro ro ro roro rors- r*- oii— OI* CM 1- rocM 1- ro* ro rocM co rocM
Table 2 cont.
433776.4.oct 4618315H1 448 711 11 407607.4.oct 488730H1 129 369
433776.4.0Ct g3277674 456 863 11 407607.4.oct 488730R1 129 504
433776.4.oct g3596734 458 854 11 407607.4.oct 2697915H1 130 430
433776.4.0Ct 1794582H1 461 741 11 407607.4.oct 492452H1 133 356
433776.4.oct g1521528 465 633 11 407607.4.oct g758924 146 455
433776.4.oct g1686055 466 848 11 407607.4.oct 3384932H1 154 402
433776.4.0Ct g1242116 1 486 11 407607.4.oct 2724183H1 168 400
433776.4.oct 2968496H1 1 231 11 407607.4.oct 4776138H1 168 424
433776.4.oct 6180815H1 3 302 12 234828.6.0Ct 754031 H1 421 672
433776.4.oct 3537661 H1 8 232 12 234828.6.0Ct 754031 R1 421 865
433776.4.oct 1395263H1 11 280 12 234828.6.oct 3872540H1 421 681
433776.4.oct 2724869H1 11 269 12 234828.6.oct 1606048H1 423 642
433776.4.oct 1616991 H1 11 218 12 234828.6.oct 5δ838δ5H1 424 664
433776.4.oct 1616966H1 11 224 12 234828.6.oct 4931209H1 424 680
433776.4.oct 3106763H1 15 306 12 234828.6.0Ct 2079883H1 424 689
433776.4.oct 4921156H1 20 263 12 234828.6.0Ct 2382770H1 426 561
433776.4.oct 1619551H1 20 228 12 234828.6.θct 2765895H1 432 676
433776.4.oct 5284327H1 21 266 12 234828.6.0Ct 474122H1 436 525
433776.4.oct 3325136H1 24 296 12 234828.6.0Ct 6318333H1 457 700
433776.4.oct g2035324 32 235 12 234828.6.oct 2759116H1 470 737
433776.4.oct g1277594 35 625 12 234828.6.0Ct g2343422 479 890
433776.4.oct 3370603H1 52 339 12 234828.6.0Ct 2252236H1 494 718
433776.4.oct 2819668H1 57 311 12 234828.6.oct 3272534H1 495 682
433776.4.oct 1208864H1 75 323 12 234828.6.0Ct 2874450H1 495 790
433776.4.oct g2037990 123 445 12 234828.6.oct 3467554H1 495 766
433776.4.oct 5485307H1 128 406 12 234828.6.oct 6433753H1 519 954
433776.4.oct 5485506H1 127 388 12 234828.6.0Ct 882889H1 527 759
433776.4.oct 3570542H1 133 403 12 234828.6.oct 878619H1 527 755
433776.4.oct 6426991 H1 134 393 12 234828.6.0Ct 4787945H1 554 810
433776.4.oct 5614090H1 166 430 12 234828.6.oct 2470206H1 569 815
433776.4.oct 966762H1 173 448 12 234828.6.0Ct g1646982 572 925
407607.4.oct g3040496 424 758 12 234828.6.oct g1629292 572 925
407607.4.oct g3804220 492 758 12 234828.6.oct 1856323H1 583 834
407607.4.oct 638371OH1 685 884 12 234828.6.θct 2961901 H1 685 875
407607.4.oct 2653689H1 695 920 12 234828.6.oct 583034H1 608 847
407607.4.oct 2653689F6 696 1081 12 234828.6.oct 4913286H1 623 914
407607.4.oct 2704443H1 743 1018 12 234828.6.oct 5579641 H1 632 892
407607.4.oct 273964H1 821 1112 12 234828.6.oct 147644T6 632 934
407607.4.oct 4630477H1 1020 1279 12 234828.6.0Ct 2018051 H1 638 919
407607.4.oct 2170060T6 1137 1693 12 234828.6.0Ct 4696590H1 648 856
407607.4.oct 3567607H1 1160 1456 12 234828.6.oct 4089780H1 652 939
407607.4.oct 488730F1 1187 1728 12 234828.6.oct 6844923H1 662 896
407607.4.oct g2931185 1236 1731 12 234828.6.θct 479038H1 670 908
407607.4.oct g2804896 1271 1731 12 234828.6.oct 2234295H1 718 883
407607.4.oct 678335H1 1299 1562 12 234828.6.oct 4839363H1 735 1003
407607.4.oct g4522930 1324 1730 12 234828.6.0Ct 1260912T6 860 1148
407607.4.oct g2825971 1344 1728 12 234828.6.0Ct 1260912H1 909 1124
407607.4.oct g3418650 1350 1729 12 234828.6.oct g2354133 1049 1528
407607.4.oct 534448H1 1473 1715 12 234828.6.0Ct 1369950R6 1062 1501
407607.4.oct g761634 1475 1731 12 234828.6.0Ct 1369942H1 1255 1501
407607.4.oct 2600372H1 173 414 12 234828.6.oct 1369950H1 1265 1501
407607.4.oct 2731329H1 187 360 12 234828.6.θct 2227669H1 31 285
407607.4.oct 3664068H1 187 394 12 234828.6.0Ct 2514489H1 32 330
407607.4.oct 6262965H1 213 390 12 234828.6.θct 3574863H1 32 316
407607.4.oct g311811δ 368 756 12 234828.6.0Ct 3421549H1 33 232
407607.4.oct 1756214H1 421 650 12 234828.6.oct 2821346H1 35 316
407607.4.oct 1336835F6 1530 1728 12 234828.6.0Ct 2219014H1 37 288
407607.4.oct 1336835H1 1530 1728 12 234828.6.0Ct 2698914H1 37 343
407607.4.oct 1336836T6 1533 1683 12 234828.6.oct 3513638H1 38 214
407607.4.oct 2698094H1 1612 1736 12 234828.6.0Ct 1865052H1 37 296
407607.4.oct g3034065 1645 1728 12 234828.6.θct 1865052F6 37 455
407607.4.oct 4041804H1 1 286 12 234828.6.θct g1958966 41 498
407607.4.oct 6015486H1 97 359 12 234828.6.oct 1402025H1 39 305
407607.4.oct 6098079H1 102 317 12 234828.6.0Ct 3110477H1 39 344
407607.4.oct 4067739H1 110 383 12 234828.6.oct 3127973H1 39 306
407607.4.oct 2865608H1 112 393 12 234828.6.oct 551414H1 39 306
407607.4.oct 2170060H1 118 382 12 234828.6.θct 3238033H1 39 287
407607.4.oct 2170060F6 118 568 12 234828.6.0Ct 2456375F6 39 431 c in r-- o co co σι co co ι- o ι-. co co σi ι- cjo co ι- σι oo co rs. oo cM co ι-- co ι-- σi - ι-- * ι-- ι- o o ιn ιn co cM CM o OoO cCoO ιι-- cCoO cCoO oOoO cC o oi r>- co i- in cM in in cM co oo oi o co oi cM co CM rs. CO O Ol CO * 05 * ** * CM OO CM CD |s. in CM CO CM CM OO O i- O O55 CCMM CCOO CCOO CCMM hh-- IΛ i- CM CM CO CM i- CM CM CO i- CM CM - CM i- CM CM in cO * l>s in 00 in 00 I^. CO in i-. CO i JS
© © m is- p 05 i- in * cD co co cM co i- c !__ in ts. |s. C0 fs. * l-- l>s 00 e0 00050101 O1010101 O 0505 O 05 0505050505 i- * in in o in * co oo o * 0) i- cM in oo i- CM CM CM CM CM i- CM CM CM CM CM CM CM CM CM CM CM CM CO CM CM CO CM i- ιs- ι- ι- CM CM CM <n co co * τ- ι- cM CM CM co co co * * * * ιn c
H U α. IIXXXIIXXXXXXXXXXXXXXXXXXXXXXl£xXXXXoooXrs.XXIIcoIII L ιncMcorocococΛco -ιn^ooor--ι-ιncMσιc h-coσιcoooc_ιcoιnoo«)coh-ιnι-coιnιnσιoocooιaι-*-*ιncMc
OCO*CDOOι-*CMOCMncβ*CθσiσiCM - -CM*θσ}CθσiCOCOC ι-ι-COOO*ι-OCOι-OOI--ωθCΛCMCJlCDI--*^CMC CO CM h- CM CO CO I- l-- in cO * O C_O CD O} * i- ei_i CM CO * CM - l- * CO « i- * * CM in O *^ CM O i- O O I-- in *i- P 01 * OO CO Ol C o ιn * o co cM ι- co * ιn co co * ι- σ α_ co ι-- ι- cM in oo ca co *^ cM θ * oι σ) co c» ιn ι-- ιn o ι- ιs- ι- - * cvι cM θ ι- ι- ι-- o * ι-- « co r^ ι-- o σι * θ - co σι * co ι-- cΛ P CΛ P oo cM i-- p σι oo oo cM is- ιn ιn co cΛ * CM co co ι- eo cM co * co co * * ι-- cr) p * co co co co ι- ιn ιn *- cM θ i-- ι- * cΛ ι- ι- σ) Csi σι r co ι- CM io rs. oo ιn ιn ιn ιn cM CM θ CM in ι- CM co cM i- ιn o co cM θ CM ω CM CO 1- CO CO 1- C CM CO CM CM CM 1- CM CD M CM CO M CM 1- CO O CO CM CO CO CO 1- 1- M 1- CO 1- 1- rorocM roco co * co roιn ιn * *
O O O O O O O O O O O O O O O O O O O O O O O Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ
0 0 0 0 0 0 0 0 0 0 0 0 q q 0 q q q q q q q O Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό Ό d cq co cό cό cq co cό cό cq cό cq cq co c cό cό c
(XJ ad ad cό eό co eό co oό cό cό aό eθ GO cό co oό co ao cό eό oO GO d d d d d d d d d d d d
CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CO CO CO CO CO CO CO CO CO n cO CO CO CO CO CO CO CO CO CO t-O ro cO CO OO W CO OO OO OO OO OO OO TO OO OO OO W CO W W TO W * * * * * * * * * * * * * * * * * * **** * * *- * * *
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CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO rø
C CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO W c CM CM CM CM CM CM CM CM CM Cvl CM CM CM CM CM CJ CM W CM CM CM CM CM CO CO CO CO CO CO CO CO CO CO CO CO W o υ S o cM in σι * o o o τ- co o) CM CM oo * co co ιn ι- ι-- * ιn co ι- oo ι- ι- θ ι- σ> ι cM in co oo - m i- co io co o co i- oo i- 0) * c
O C001 l-- 01 ca |s. r^ 00010 CM * - OO OO C005 CM I- i- i- O CM h- CO CM '* 05 in CO CO i- CM rs. in CM CO |-s CO CO C0 0500000 - C CO CO CM CM CM CM CM CM CO i- CO CM CM CO CM CM CM CM CO CO * CD * * ** * * * CO * * * Ln in * * * m in * in in in in co in in ' ι- θ) co ιθ ι- ι- CM '* * r co ιn σi N (j) θ) θ o θ τ- τ- 1- ιn ifl in co (θ (θ _ co ι- o ιn i-) S S S N S ι- cϋ
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i 1111111 01;1 iOx10 1- l-« co X DC * I*- 00 CM CM O 00 ϊ *ϊooϊmϊi-ϊoooo)ϊCMϊ*ϊcoϊcMϊi-ϊooϊoorIrIϊcMϊinϊ*ϊoϊcoι*ϊis-ϊi--ϊin?XϊooϊorXrXΪoΞIΪoi rs r- o r- Is- NOΦNS CM co co I-- h- co 00 o co r-- o * ιn cM in ι- oo ι-- oo o co cΛ i-. c» co co ιn co * ιn σι co cM co co co ι-- oo ι- c
1- CM Is- o 1— CO * CO CO CO CO CO 001— 0) 00 CM ι- * * co ι-- co co r^ * o « * cM c_ι co o ιn co co o co co co ι-- - CM co co ω t-- cΛ σ
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* σ> 00 * * * * CM CM 0O I-. * - T- - CO CM CO 00 * * * O) P * 00 CO CO r-- l-- CO * CO 00 i- CO in i- CO i- CO C co 01 CM CM 1- CM CM Is- Is- ι- CM in ιn co rocM CM co ιn ιn ιn ι- p ιn cM co cM * ι- - ι- ι- ι- oo cM CM i-- ι-- co co *
90 o o o o o o o o 0 0 O O O O O υ o o o o o IΛ o o o o o o o o 9 9 9 O O o o o o o o IΛ co co co co co co co co co co co co co co co co co co co co co co co co e 999 CO CO tq O CO CO fS 00 CO 0000 CO 00 000000 0000 0000 0000 CO 00 0000 000000 000000 CO CO 000000 0000 000000 0000 CO 00 OO 0000 000000 CO CO 000 CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM C 000000000000 00000000000000 *000 0000 CO 000000 CO 0 0 CO 0 0 00 CO 00 CO 00 00 00 0 OO 00 CO CO CO
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CO CO CO CO CO O CO CO CO CO cό cό cό to cό tό to cό cό CO CO CO CO CO CO CO CO cό cό cό cό cό cό CO CO CO CO CO CO CO O CO cό CD CO cό ό cό cό cό to cό cό cό cό cό cό cό CD oi oi CM oi oi oi oi oi rt rt co co co co co co CO CO CO O CO CO CO co co co co CO CO CO rt rt O CO O O CO CO rt O rt co co co co co co co co co rt rt rt rt CO cocococococococococococo
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90 TJJI TTJJ T TJJ TTJJ TJ TJ TJ TJ TJ TJ IΛ CO CO CO CO to cό cό cό cό cό CO CO cό cό cό cό cό cό to to CO CO CO CO IΛ CO CD CO CO CO CO co co co co co rt co co co co rt co rt rt CO rt O rt co co co co co co co co rt co CO d P P P di P P P P ' oi oi CM CM oi oi oi oi i oi CM CM cvi oi oi oi oi oi oi oi CM CM CM CM fS PP dPP dP P Pι_ dP dP P P P P co co CO O co co co co CO CO CO CO co co CO CO co co CO CO CO CO CO CO
PP PP P P PP Pi P P P P P co co CO CO co co CO rt co co rt CO CO O rt O CO O CO CO rt O O rt ww ww w W wW wI w w w w w oo ao CO ao 00000000 0000 00 000000 000000 oo 0000 00 CO CO 00
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TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ T3 TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ T ' J TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ
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Is- CO 0 01 CO fs rt P CO CM CO Is- CO 0 ^ 01 0100 * 01- 0001 rt OO * W CO O) * O OO CO * CO CO P 0> -- O) rt * O) CM OO C i- Ol W OO fs W CM O) CM OO W aO CM OO P P CO rt f
Is- w Is- w co rt O) 01 00 w w w Is- 00 CM O 0) CO * CD CO CD P ι- αo αo cD θo co co w * ι- αo σ) w O) * CO CO * rt O i- P - CM Is- O5 fs W P f~ * CO OO I- CO OO CO 0) CO Ol i- ls co αo p co p 00 CO 00 * ^^^^— f~ P ^^— * øJ OO CO OJ CO CO CO * l- W * W CO O0 P CM 0O W τ- τ- CM rt O CO CO CO O) * i- OO CO rs. * 0) OI * CJ) CM CO W * W f- OO O W * CO O Ol C
CO fs CO w P ^— CO CO CO w w w Is- ^- Is- Is- w 05 CM T- W CM CO W P W i- t^ W W CJl i- P αO CM CD * ^ 01 CM OJ CO W * CO i- C0000005 CM i- 0001 W 01 * i- CO fs O * i- CM CM i- w CO * * 0505 00 rt 00 co co co rt CO 01 01 05 W * 00 * ι- fs 05 ι- CO fs i- CM CD - i- i- CJl OO CO fs * W CM OJ W W - |- i- * * CM 0 05 CO CO i- 05 * OO fs O * 05 CO * W OI 05 ro ro ro rooi roco ro * rooi CM * w ro ro ro ro ro row rororo ro ro* * row * oι co cM * ro roro roro roco w w w cM roco co ro row ao row co co i- ro roco roc
0 0 0 0 0 0 C) C) 0 υ υ 0 υ υ υ υ υ υ o υ υ υ υ υ υ o υ υ o υ o o o o o υ o o υ υ
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TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ T) TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ
90 IΛ CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM CM 01 IΛ CM CM CM OJ CM CM CM CM CM CM OJ CM CM CM oi oi oi oi oi CM CM CM CM Oi oi oi w
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Table 2 cont.
480710.12.dec g1968577 2420 2694 56 480710.12.dec 2732286H1 3906 4120
480710.12.dec 3450783H1 2443 2689 56 480710.12.dec 465744H1 3945 4176
480710.12.dec 427384H1 2501 2606 56 480710.12.dec 1840923T6 3948 4432
480710.12.dec 4358866H1 2568 2831 56 480710.12.dec 2722361T6 3953 4443
480710.12.dec 6649881 H1 2604 3093 56 480710.12.dec 2722361H1 34 293
480710.12.dec 1444544H1 2637 2908 56 480710.12.dec6482171H1 155 615
480710.12.dec g1358409 2736 3179 56 480710.12.dec g2219055 236 491
480710.12.dec 1436708F1 2737 3258 56 480710.12.dec g4327833 345 695
480710.12.dec 1436708H1 2737 3006 56 480710.12.dec g1985324 386 601
480710.12.dec 1438425H1 2737 2979 56 480710.12.dec 4677757H1 402 671
480710.12.dec 1627631 F6 2757 3064 56 480710.12.dec 3592515H1 429 742
480710.12.dec 1627631 H1 2757 2951 56 480710.12.dec 3322162F6 469 987
480710.12.dec 197491 H1 2785 2977 66 480710.12.dec 3322162H1 469 751
480710.12.dec 2830313H1 2798 3035 66 480710.12.dec 3281467H1 505 759
480710.12.dec g1383816 2839 3174 56 480710.12.dec 3281459H1 506 656
480710.12.dec4319982H1 2847 3123 56 480710.12.dec 3824991 H1 588 863
480710.12.dec 494817T7 2899 3448 56 480710.12.dec 574866H1 595 823
480710.12.dec 2070657H1 2904 3179 56 480710.12.dec 4186145H1 798 1131
480710.12.dec 751662H1 2923 3156 56 480710.12.dec 3373301 H1 849 1100
480710.12.dec 1911471 F6 2925 3484 56 480710.12.dec 2968518H1 948 1257
480710.12.dec 1911471H1 2925 3200 56 480710.12.dec 6378908H1 978 1160
480710.12.dec 4254047H1 2933 3208 56 480710.12.dec 494817R6 1099 1499
480710.12.dec 2234211T6 2941 3468 56 480710.12.dec 494817R7 1099 1316
480710.12.dec 494817T6 2943 3449 56 480710.12.dec 4158239H1 1179 1426
480710.12.dec 2797596F6 2948 3425 56 480710.12.dec 5218041H1 1363 1621
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CO CM CTOI rt 1- CO W 00 CO CM 1- CM ro row CM CM ro ro ro ro row co oi rooi CM OJ 1- * * rooo * row w w w w co CM w OJ roco ro rooi co w co co * CM roco CM w rorocø ro roco υ υ υ o υ υ υ υ υ υ υ υ υ υ υ υ υ o υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ o υ υ o o υ υ o υ o υ υ υ υ υ υ υ υ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ rt cό cό cό cό w cό cό rt rt cό cό cό cό cό cό cό cό cό cό cό w rt OT rt cό rt rt OT rt rt rt rt OT rt rt rt OT OT OT OT rt f^ ^ ^ ^ ^ |s- |s. |s. |s. fs |s. |s. |s. fs |s. fs |s- |s. fs fs |s. fs fs fs fs |s. |s. |s. |-s rs- fs |s- ls. |s- ls. f^ wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww rt OT rt rt rt rt rt rt OO rt rt rt rt rt rt rt rt rt OT OT rt rt OT rt rt rt rt rt rt rt rt rt CO CO CO OO OO OO OO OO CO CO OO OO GO OO OO OO OO OO OO OO CO CO CO OO αO CO OO OO OO OO GO OO OO OO OO O O P P P P P P P P O O O O O O P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P P O O O O O O O O O O O O
C CO CO CD CO CD CO CO CO CO CO CO CO CO CD CD CO CD CD CD CD CO CD CD CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CD CO CO CD CD CO CD CD CO CD CO CD CD CO CO CO CO CO CO CO CO CO CO C o υ S
8 W 1- 1- O O) CO CO O * O5 CO W fs fs CM O5 OO * W P CO P Is- 05 * C0 OI CO - 00 CM P 0500 C0 O l- O * Ol l- W CM Is- C0 C0 CM O 00 O CM * rs CO
Φ n o -5-* c w © cι ω ω sMo ω n o Φ ω ω N Φ Φ (θ θΦ <-o oo N -3S t- ffloo * β S '. ffl * SΦ in ιθ N w oo Φ^ Φ co Φ c. N '* n 't Φ Φ c ci N ι- c
CO CD P * W CM i- l- ls- CO W rt CO rt ro i- 0) OO P i- *r- i- 0) 0) rt rt CM rt rt CM rt rt CM OT rt * P CM ro CM rt i- i- rt rt i- CM OJ OJ * OJ OJ rt -i- rt rt W W I^ oo oo σι co oo w oι oι w w ι- co * oι co w co * - w co co co αo ρ cM CM i- * σι oo rt P CM θi co i- ιs- - CM τ- σι oo oθ τ- ι- oι cθ ι- co w co αo p ι- ι- co * co p p * * * oj o * fs * σ> rt co co o - - τ- co co w σι co co rt ι- ι- ι- θ5 co co * * * ιs- ιs- ι- ι- ι- rs- ιs- oo ιs- ιs- ι- p p p ι- ι- ι- * co 0> O CO CO CO CO 0> 0) 01 01 Ol Ol O O O i- i- CO CO OT Ol O CM OT OT OT * * * * O O i - OJ W W W CO W W W ι- ι- -^ ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- '»- ι- ι- ι- - rt * * W i- i- i- i- i- i- i- i- i- i- CM CM OI CM CM 0101 O101 - CM OI OJ OJ OI OI OJ CM i- CO CO C
I I I X X fs LL X 1- I I Oi rt I I 05 * X X X X X TZ Ό co o is--ai oo fs JXO.IZ Ioi Ioi CO Is- CM Is- OT OO O OT OT 1- CO 0) * rt * W CM W I σ)wχioooσ)i ix 01 rt W * Is- W OT OT CO * o 00 Is- o O CO 1- 00 Is- CO W 011- CM 01 CM 01 00 fs 00 co σi CO oo CO OO 000) fs * O * 00 * CM 0) CM CO CO Is- W CM W co co CM CO 05 * CM CO
* oo o r-s P CO CO Is- W OT CO CM CO OO Is- fs O 00 CM 1- 00 W CM
CO * rt CM * rt W 00 * W W OT OT OT CM CO CO OO Is- * * w w CM - ι- ι- * ι- CM fs co oj ao ao ao rt * ro ro ro roi— i— co CM w co ro - co ro* 1- ro row w ro row CM W roco CM w ro roco CM ro ro root CM roco CM CM c υ υ υ υ o o υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ o o o υ o υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ φ φ φ φ φ φ φ φ φ φ φ φ φ φ φ φ φ φ φ φ φ φ Φ Φ Φ Φ φ φ φ Φ Φ υ φ υ
Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ
90 TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ i w w w w w w w w w w w w w w w w ui ui ui ui ui w w ui ui w w w w w w w w w W CM oi oi CM CM Oj oi oJ oJ oJ oj cM oi oJ oi oj oj oi oi oj cM oj cM cvi cvi cM oi oi σ> σ> 05 OO 05 OO 05 OO σi σi σi σi oi σi σ> o) σi σi ø) oo oo σ> σ> σi σi ø> oo 0) rt cό cό co co co co rt co co co co co co co co co co co ao co co co co co rt co rt co rt co c
0505 σ> oo OO Ol 0) 0) O) oo O) 05 oo 05 oo oo O) 0505 05 OO σ> oo σ> ø) oo co co co co rt CO rt rt CO rt rt O rt rt co co o co CO rt OT rt OT co co co co co r- r- rs- rs- r-s r^ fs fs is- fs i- fs fs s rs- f- f~ fs fs |s. fs fs |s. |s. fs fs fs rs. fs fs fs f
P P P P P P P P P P P P rt P rt P P P o o p p P P P o o o o o o o w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w oo oo oo ao ao oo oo oo oo oo oo oo oo ao oo ao oo oo oo oo oo oo oo oo oo oo oo oo oo ao oo o
CO rt rt w rt rt CO CO rt O rt rt rt w w
CO rt rt rt w w w w co co CO CO co o OOOOOOOOOOOOOOOOOOOOOOOOOPPPPP
P P P P P P P P P P P P O O O O O O O O O P P P P P P P P P P P P P P P ι- ι- ι- *r- - ι- -^ ι- τ- ι- *^ ι- ι- *^ ι- *ι- *^ τ- -ι- -r- *I- - -^ ι- -^ *ι- *ι- ι- ι- *r- ι- ι CO CO CO CO CO CO CO CO CO CO CO CO CO CD CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO P CO CO CO CO CO CO CO CO P CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO CD CO CO CO CO C
αo - OJ Oj σ> OT C0 ι- CM W W OT W C0 on*ι-rtC wιs-«OT ι-BBOWNΦBB-- Ortθ 0 O5 O5 COaCM θCO OCO OOTOOT-C-O-rt--C-
CM C0 OI W 00 W 0 ONCMWCM C JS
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CM i- i- i- OJ OT W CO I- « CJ) O5 05 O505 i- i- i- i- i- i- i- i- i- i- -^ i- i- -^ i- *^ -^ -^ i- i- -^ T- CM CM OJ -i- - CM -^ i- *r- -^ u H α. 1- 1- 1- CM CO
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* s- W CO CM CO OO CO 1- 1- W * - I I— CO CO I OJ Ol w If- αooowι-σι Wι-ιs- Wι- * PCM iI rtI c
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Ol CO * 1- w OT W 1- * Is- σ> 01 σ> 1- 1- OT fs W * * fs σi w oi i- w cΛ co w cD co co cn co o i- i- o o co w * co σi w co Is- p CO P f~ O0 p T- CM OJ fs W * * CM CO i- i- 00 CM OJ
OT Is- CO CM f- co Is- Is- 1- 00 CO Is- CO CO OT 00 Ol 00 CO CO p oι oj rs- τ- * co * is- ι- co co w w p øι σι * P ι- ιs- co 1- o oi w αo co oo σι w o 0o0 ** ** ** cCo0 wW oιl C CM CO C0 CM OJ W ι- C0 l
CO * 00 CO 1- CO 1- Is- * CM CO CO CO * * 00 co 1— r-» 01 I CO OO ι- W * CO ι- ι- ι- W W P CM CO * * 01 t- P ι- OO 1- W 0) Is- o o OT CO CO — CO "O-5 —i- O"»5 -O-0 —i- "CO- * i- CO O0 i- i- CM a0 rt w 01 αo * w * rt CO w o 01010100 00 OO W W 0005 O| T- i- W fs p 0) W W * W W P CO * P P W OO OJ W αo co f- f co co 1— 1- * Ol 00 W ι- CM CM - * CM * CM 0000 00 O 05 * ι roco co co 00 w ro* w * rt rt rt 1— 1- W rt CO OT 1- fs co ro* row co co co co * * cM rorooι oι * w rooo co w rofs rooi w 0101 ro w * ro ro ro rooj ro ro* CM 1- 1- CM * co c o υ φ φ
TJ TJ i-s" f-:
CO S
*fs *fs a co co rt rt rt rt rt rt rt rt rt rt CO CO CO rt CO CO CO rt rt CO CO CO rt CO CO CO CO CO CO rt CO rt CO rt CO rt CO rt CO CO CO CO CO CO CO CO CO CO rt CO CO CO OT CO CO CO CO CO CO CO CO CO CO CO CO C o Φ Φ < <0 <0 <D (O ^D O fD < fD f <D D <D <O iD <D (O iD D (O iD <D (0 <D (0 <D <D iD D i iD D (D iD D fD D <0 <O f <O tO fD ( iO <D <D (D <D iD (D iD (D iD iD <D (D (D <D iD (D iD D < υ
<s o w fs ι- * co * Φ r » σ) fs fs ι- fs * cM W ι- w σι rs 00 o O ι- * oo * ι-
Φ τ- -- * o Φ CM CM rt « rt * « rt Φ Φ θ * * w o * w * Φ » c5 P » rt « p cM ι- Φ n Φ Φ Φ CM P rt W Φ -r- oι oi Φ oι r- cM ι- σi P W ι- ι- * ι- σj * fs fs σi Φ σi P ι
H w w w * w rt i- w ι- fs is- φ is- ιs- φ is- Φ w w ιs- ι- p ffl Φ (-o ι- Φ r- ι- » ι- p p c5θ cM ι- ι- W ι- OT ι- CM ι- τ- oι * w w P rt Φ θ cn o w » ι- ι- w σ) θ Φ θ σ) ι- c» φ ι- ι- ι- ι- ι- ι- ι- ι- CM CM CM θ o oj cM Φ Φ is- * * Φ Φ W rø cn Φ ro ro ι- « ι- τ- - cn ι- ι- -^ σ) -^ w oι n * n * rt * Φ W Φ Φ Φ Φ ι- » » » ι- φ rø τ- . cM θj oj oj oj co p p σι p i- co φ oo * w w w rs- co * co o 1- 1- 1- rt σ) ro « cn θ) * σ) co fs » » P ι- CM ι- p w oo ι- ι- - Φ ι- oι * P θJ OT co ι- w oι t- τ- * τ- Φ * Φ * rs. ι- w oι co σι σi Φ rt u5 CM C_θ ι- Φ Φ * σi Φ σι w
OT *ι- ι- ι- ι- ι- CM θj * * * * w w w ι- ι- ω w ∞ ω rt rt ι- oι co co co co co * W Φ w rs. ιs- cM θi P co oθ - ι- * p ρ p * w Φ Φ * ι- n * Φ ao σ) P P P oo fs oo fs CM
--•--rrι-rr«NN(\INNNB**^ι-ι---BΦSΦΦNSSS Nffle0fflfflfflτ-φι-ΦCOβaι-NNBnBB*ΦΦΦΦin-)ΦΦΦ--C|--«(.-
o υ υ υ υ o o o o υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ o o υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ υ o o υ o o o o υ 0 o υ υ υ υ υ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ Φ o υ o Φ Φ Φ Φ Φ Φ Φ φ φ φ φ φ φ φ
90 Ό TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ TJ IΛ IΛ oi oJ oi oi cM CM cvi oJ oJ oJ c cM oJ oJ oJ cvi cvi oJ oi cM oi w r-- Is- 1-. I CO cό cό cό cό cό co rt rt co rt rt rt rt rt co rt rt co co co co co co ************************************ fS S" * Φ *CO fws fws fws fws fwswfs fws fws fws fws fws fws fws fws fws fws fws fws fws fws fws fws fws PwPwPw 0w0w0w0w0w0w0w0w0w0w0w0w0w0w0w0w O O O P o 00 φφφφφφφφφφφφφφφφ*** w00 00000000 OOOOPPPPPPPPPPPPPOCMCMOJ * M*OJ*OJ*OJ C*M*CM*OJ* * w w O *w w w w w 00* w w w w w w w W W W Is- * Is- *f- *fs φφφφφφφ PPPPO * *******
OJ*OJ C OJ*OJ OJ*OI*OI*OJ*CM * CM*CM Ol*CM O*J*OJ * CM * w w Ol *OJ *OJ CM OJ CM Ol CM CM CM 01 Ol OJ 1- ι- *^ ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- ι- τ- -*- ι- ι- CM OJ OJ OJ OJ CM CM OJ OJ CM OJ OJ OJ CM OJ OJ OJ OJ CM CM OJ OJ OJ OJ OJ OJ CM W i iD KD 0 <D iD Ω <0 <0 <0 <O iO 0 <O fD < iD fD D fD ^ Φ ^D <O iD iD fD <D iD ^D f <D (D SO fO <0 D ^D iD D D ^D iD <D iD fO iD <0 <0 <O iD <0 0 D D D D iD O fD (D <O tO <O fD D f
Table 3
SEQ Template ID Tissue Distribution
ID NO
1 198450.6.oct Embryonic Structures - 17%, Germ Cells - 16%, Cardiovascular System - 13%
2 475178.1.oct Sense Organs - 44%, Unclassified/Mixed - 20%, Connective Tissue - 11 %
3 231793.2.oct Germ Cells - 29%, Digestive System - 12%, Embryonic Structures - 11%
4 000010.4.oct Stomatognathic System - 21%, Germ Cells - 15%
5 412959.6.oct Unclassified/Mixed - 24%, Stomatognathic System - 20%
6 331521.5.oct Embryonic Structures - 21%
7 902114.l.oct Skin - 41 %, Musculoskeletal System - 20%, Female Genitalia - 17%, Hemic and Immune System - 17%
8 481382.1.oct Exocrine Glands - 22%, Connective Tissue - 15%, Musculoskeletal System - 14%, Hemic and Immune System - 14%
9 903849.l.oct Skin - 14%, Cardiovascular System - 11%
10 433776.4.oct Male Genitalia - 15%, Endocrine System - 10%
11 407607.4.oct Unclassified/Mixed - 19%, Pancreas - 14%, Female Genitalia - 10%
12 234828.6.oct Liver - 16%, Endocrine System - 12%
14 242269.2.dec Stomatognathic System - 54%, Musculoskeletal System - 18%
16 198060.6.dec Hemic and Immune System - 100%
18 235983.6.dec Nervous System - 100%
20 038751.δ.dec Pancreas - 100%
21 236099.4.dec Unclassified/Mixed - 10%
23 466521.δ.dec Female Genitalia - 50%, Hemic and Immune System - 50%
24 466521.6.dec Urinary Tract - 32%, Exocrine Glands - 14%, Cardiovascular System - 14%
25 474522.8.dec Exocrine Glands - 31 %, Urinary Tract - 31%, Digestive System - 23%
26 231583.3.dec Sense Organs - 19%
28 277726.5.dec Nervous System - 50%, Digestive System - 50%
29 978637.1.dec Embryonic Structures - 29%, Nervous System - 24%, Connective Tissue - 19%
31 413231.8.dec Female Genitalia - 16%, Respiratory System - 15%, Connective Tissue - 14%
32 334406.5.dec Urinary Tract - 100%
33 411429.8.dec Urinary Tract - 100%
34 320674.7.dec Endocrine System - 32%, Skin - 25%, Connective Tissue - 12%, Cardiovascular System - 12%, Exocrine Glands - 12%
36 332335.1.dec Digestive System - 24%, Skin - 21%, Liver - 17%
37 238992.13.dec Digestive System - 100%
38 199736.1.dec Urinary Tract - 25%, Pancreas - 22%, Male Genitalia - 14%
39 228864.5.dec Nervous System - 100%
40 986539.1.dec Skin - 24%, Embryonic Structures - 17%, Hemic and Immune System - 16%, Unclassified/Mixed - 16%
41 481454.4.dec Musculoskeletal System - 53%, Sense Organs - 42%
42 474800.7.dec Male Genitalia - 100%
45 353271.2.dec Female Genitalia - 25%, Digestive System - 25%, Hemic and Immune System - 25%
46 221686.2.dec Embryonic Structures - 12%, Endocrine System - 11%, Unclassified/Mixed - 10%
47 233347.7.dec Stomatognathic System - 73%
48 230631.3.dec Embryonic Structures - 100%
50 337160.1.dec Embryonic Structures - 22%, Unclassified/Mixed - 20%, Urinary Tract - 19%
51 346341.12.dec Embryonic Structures - 11%, Germ Cells - 11%
Table 3 cont.
SEQ Template ID Tissue Distribution
ID NO
52 428745.2.dec Hemic and Immune System - 100%
53 444839.17.dec Musculoskeletal System - 70%, Female Genitalia - 30%
55 428362.36.dec Embryonic Structures - 34%, Connective Tissue - 24%, Liver - 18%
56 480710.12.dec Urinary Tract - 33%, Nervous System - 25%, Digestive System - 25%
57 234137.10.dec Skin - 59%, Endocrine System - 21%, Digestive System - 10%, Hemic and Immune System - 10%
58 480630.4.dec Hemic and Immune System - 67%, Nervous System - 33%
60 350399.5.dec Unclassified/Mixed - 100%
61 085713.2.dec Cardiovascular System - 29%, Urinary Tract - 29%, Female Genitalia - 21%
63 117464.7.dec Skin - 25%, Endocrine System - 13%
Table 4
Program Description Reference Parameter Threshold
ABI FACTURA A program that removes vector sequences and PE Biosystems, Foster City, CA. masks ambiguous bases in nucleic acid sequences.
ABI/PARACEL FDF A Fast Data Finder useful in comparing and PE Biosystems, Foster City, CA; Mismatch <50% annotating amino acid or nucleic acid sequences. Paracel Inc., Pasadena, CA.
ABI AutoAssembler A program that assembles nucleic acid sequences. PE Biosystems, Foster City, CA.
BLAST A Basic Local Alignment Search Tool useful in Altschul, S.F. et al. (1990) J. Mol. Biol. ESTs: Probability value= 1.0E-8 sequence similarity search for amino acid and 215:403-410; Altschul, S.F. et al. (1997) or less nucleic acid sequences. BLAST includes five Nucleic Acids Res. 25:3389-3402. Full Length sequences: Probabilit functions: blastp, blastn, blastx, tblastn, and tblastx. value= 1.OE-10 or less
FASTA A Pearson and Lipman algorithm that searches for Pearson, W.R. and D.J. Lipman (1988) Proc. ESTs: fasta E value=1.06E-6 similarity between a query sequence and a group of Natl. Acad Sci. USA 85:2444-2448; Pearson, Assembled ESTs: fasta Identity= sequences of the same type. FASTA comprises as W.R. (1990) Methods Enzymol. 183:63-98; 95% or greater and least five functions: fasta, tfasta, fastx, tfastx, and and Smith, T.F. and M.S. Waterman (1981) Match length=200 bases or greate ssearch. Adv. Appl. Math. 2:482-489. fastx E value=1.0E-8 or less
Full Length sequences: fastx score=100 or greater
BLIMPS A BLocks IMProved Searcher that matches a Henikoff, S. and J.G. Henikoff (1991) Nucleic Score=1000 or greater; sequence against those in BLOCKS, PRINTS, Acids Res. 19:6565-6572; Henikoff, J.G. and Ratio of Score/Strength = 0.75 or DOMO, PRODOM, and PFAM databases to search S. Henikoff (1996) Methods Enzymol. larger; and, if applicable, for gene families, sequence homology, and structural 266:88-105; and Attwood, T.K. et al. (1997) J. Probability value= 1.0E-3 or less fingerprint regions. Chem. Inf. Comput. Sci. 37:417-424.
HMMER An algorithm for searching a query sequence against Krogh, A. et al. (1994) J. Mol. Biol. Score= 10-50 bits for PFAM hits, hidden Markov model (HMM)-based databases of 235:1501-1531 ; Sonnhammer, E.L.L. et al. depending on individual protein protein family consensus sequences, such as PFAM. (1988) Nucleic Acids Res. 26:320-322. families
Table 4 (cont.)
Program Description Reference Parameter Threshold
ProfileScan An algorithm that searches for structural and Gribskov, M. et al. (1988) CABIOS 4:61-66; Normalized quality score≥GCG- sequence motifs in protein sequences that match Gribskov, M. et al. (1989) Methods Enzymol. specified "HIGH" value for that sequence patterns defined in Prosite. 183:146-159; Bairoch, A. et al. (1997) particular Prosite motif. Nucleic Acids Res. 25:217-221. Generally, score= 1.4-2.1.
Phred A base-calling algorithm that examines automated Ewing, B. et al. (1998) Genome Res. sequencer traces with high sensitivity and 8:175-185; Ewing, B. and P. Green probability. (1998) Genome Res. 8:186-194.
Phrap A Phils Revised Assembly Program including Smith, T.F. and M.S. Waterman (1981) Adv. Score= 120 or greater; SWAT and CrossMatch, programs based on Appl. Math. 2:482-489; Smith, T.F. and M.S. Match length= 56 or greater efficient implementation of the Smith- Waterman Waterman (1981) J. Mol. Biol. 147:195-197; algorithm, useful in searching sequence homology and Green, P., University of Washington, and assembling DNA sequences. Seattle, WA. σ-*
Consed A graphical tool for viewing and editing Phrap Gordon, D. et al. (1998) Genome assemblies. Res. 8: 195-202.
SPScan A weight matrix analysis program that scans protein Nielson, H. et al. (1997) Protein Engineering Score=3.5 or greater sequences for the presence of secretory signal 10:1-6; Claverie, J.M. and S. Audic (1997) peptides. CABIOS 12:431-439.
Motifs A program that searches amino acid sequences for Bairoch, A. et al. (1997) Nucleic Acids Res. patterns that matched those defined in Prosite. 25:217-221 ; Wisconsin Package Program Manual, version 9, page M51-59, Genetics Computer Group, Madison, WI.

Claims

CLAIMS What is claimed is:
1. An isolated polynucleotide comprising a polynucleotide sequence selected from the group 5 consisting of: a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63, b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-63, c) a polynucleotide sequence complementary to a), 0 d) a polynucleotide sequence complementary to b), and e) an RNA equivalent of a) through d).
2. An isolated polynucleotide of claim 1 , comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-63. 5
3. An isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide of claim 1.
4. A composition for the detection of expression of secretory polynucleotides comprising at o least one of the polynucleotides of claim 1 and a detectable label.
5. A method for detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 1, the method comprising: a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction 5 ampUfication, and b) detecting the presence or absence of said ampUfied target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.
6. A method for detecting a target polynucleotide in a sample, said target polynucleotide o comprising a sequence of a polynucleotide of claim 1 , the method comprising: a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide or fragments thereof, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.
7. A method of claim 5, wherein the probe comprises at least 30 contiguous nucleotides.
5
8. A method of claim 5, wherein the probe comprises at least 60 contiguous nucleotides.
9. A recombinant polynucleotide comprising a promoter sequence operably hnked to a polynucleotide of claim 1. 0
10. A cell transformed with a recombinant polynucleotide of claim 9.
11. A transgenic organism comprising a recombinant polynucleotide of claim 9.
5 12. A method for producing a secretory polypeptide, the method comprising: a) culturing a cell under conditions suitable for expression of the secretory polypeptide, wherein said cell is transformed with a recombinant polynucleotide of claim 9, and b) recovering the secretory polypeptide so expressed.
0 13. A purified secretory polypeptide encoded by at least one of the polynucleotides of claim 2.
14. An isolated antibody which specifically binds to a secretory polypeptide of claim 13.
15. A method of identifying a test compound which specifically binds to the secretory 5 polypeptide of claim 13, the method comprising the steps of: a) providing a test compound; b) combining the secretory polypeptide with the test compound for a sufficient time and under suitable conditions for binding; and c) detecting binding of the secretory polypeptide to the test compound, thereby identifying the o test compound which specifically binds the secretory polypeptide.
16. A microarray wherein at least one element of the microarray is a polynucleotide of claim 3.
17. A method for generating a transcript image of a sample which contains polynucleotides, the method comprising the steps of: a) labeUng the polynucleotides of the sample, b) contacting the elements of the microarray of claim 16 with the labeled polynucleotides of the 5 sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
18. A method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence of claim 1 , the o method comprising : a) exposing a sample comprising the target polynucleotide to a compound, under conditions suitable for the expression of the target polynucleotide, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of 5 the compound and in the absence of the compound.
19. A method for assessing toxicity of a test compound, said method comprising: a) treating a biological sample containing nucleic acids with the test compound; b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at o least 20 contiguous nucleotides of a polynucleotide of claim 1 under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence of a polynucleotide of claim 1 or fragment thereof; c) quantifying the amount of hybridization complex; and 5 d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.
EP00965128A 1999-09-28 2000-09-19 Human secretory molecules Withdrawn EP1220907A2 (en)

Applications Claiming Priority (11)

Application Number Priority Date Filing Date Title
US15662499P 1999-09-28 1999-09-28
US15662599P 1999-09-28 1999-09-28
US156624P 1999-09-28
US156625P 1999-09-28
US16861499P 1999-12-02 1999-12-02
US16861399P 1999-12-02 1999-12-02
US16861199P 1999-12-02 1999-12-02
US168611P 1999-12-02
US168614P 1999-12-02
US168613P 1999-12-02
PCT/US2000/025610 WO2001023558A2 (en) 1999-09-28 2000-09-19 Human secretory molecules

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GB0027905D0 (en) * 2000-11-15 2000-12-27 Glaxo Group Ltd New protein

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WO1999003990A1 (en) * 1997-07-16 1999-01-28 Human Genome Sciences, Inc. 64 human secreted proteins
WO1999018204A2 (en) * 1997-10-08 1999-04-15 Sagami Chemical Research Center HUMAN PROTEINS HAVING SECRETORY SIGNAL SEQUENCES AND cDNAS ENCODING THESE PROTEINS
AU758004B2 (en) * 1997-12-17 2003-03-13 Genset S.A. Extended cDNAs for secreted proteins

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Title
See references of WO0123558A3 *

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