WO2005110460A2 - Diagnosis and treatment methods related to aging, especially in muscle (14.1) - Google Patents

Abstract

Mouse genes differentially expressed in comparisons of gene expression in different ages of mouse muscles have been identified, as have corresponding human genes and proteins. The human molecules, or antagonists thereof, may be used for protection against faster-than-normal biological aging, or to achieve slower-than-normal biological aging. The human molecules may also be used as markers of biological aging.

Description

DIAGNOSIS AND TREATMENT METHODS RELATED. TO AGING, ESPECIALLY IN MUSCLE (14.1)

Cross -Reference to Related Applications Anti -Aging Applications . Mice with a disrupted growth hormone receptor/binding protein gene enjoy an increased lifespan. In U.S. Prov. Appl. 60/485,222, filed July 8, 2003 (Kopchic δ) mouse genes differentially expressed in comparisons of gene expression in growth hormone receptor/binding protein gene-disrupted mouse livers and normal mouse livers were identified, as were corresponding human genes and proteins. It was suggested that the human molecules, or antagonists thereof, could be used for protection against faster-than-normal biological aging, or to achieve slower-than-normal biological aging. It was also taught that the human molecules may also be used as markers of biological aging. In provisional application Ser. No. 60/474,606, filed June 2, 2003 (our docket Kopchick7-USA) , our research group used a gene chip to study the genetic changes in the liver of C57B1/6J mice that occur at frequent intervals of the aging process. Differential hybridization techniques were used to identify mouse genes that are differentially expressed in mice, depending upon their age. The level of gene expression of approximately 10,000 mouse genes (from the Amersham Codelink UniSet Mouse I Bioarray, product code: 300013) in the liver of mice with average ages of 35, 49, 56, 77, 118, 133, 207, 403, 558 and 725 days was determined. In essence, complementary RNA derived from mice of different ages was screened for hybridization with oligonucleotide probes each specific to a particular mouse gene, each gene in turn representative of a particular mouse gene cluster (Unigene) . Mouse genes which were differentially expressed (younger vs. older), as measured by different levels of hybridization of the respective cRNA samples with the particular probe corresponding to that mouse gene, were identified. Related human genes and proteins were identified by sequence comparisons to the mouse gene or protein. In the international appl. Kopchick7A-PCT, filed June 2, 2004, we added some additional studies of CIDE-A (see below) . In a like manner, the effect of aging on the expression of genes in mouse skeletal muscle was studied, see provisional application Ser. No. 60/566,068, filed April 29, 2004 (our docket Kopchickl4-USA) .

Anti -Diabetes Applications . In U.S. Provisional Appl. Ser. No. 60/458,398 (our docket Kelderl-USA) , filed March 31, 2003, members of our research group describe the identification of genes differentially expressed in normal vs. hyperinsulinemic, hyperinsulinemic vs. type II diabetic, or normal vs. type II diabetic mouse liver. Forward- and reverse-substracted cDNA libraries were prepared, clones were isolated_/ and differentially expressed cDNA inserts were sequenced and compared with sequences in publicly available sequence databases. The corresponding mouse and human genes and proteins were identified. The purpose of our research group's provisional application Ser. No. 60/460,415 (our docket: Kopchick6- USA) , filed April 7, 2003, was similar, but complementary RNA, derived from RNA of mouse liver, was screened against a mouse gene chip. See also 60/506,716, filed Sept. 30, 2003 . (Kopchick6.1) . Gene chip analyses have also been used to identify genes differentially expressed in normal vs. hyperinsulinemic, hyperinsulinemic vs. type II diabetic, or normal vs. type II diabetic mouse pancreas, see U.S. Provisional Appl. 60/517,376, filed Nov. 6, 2003 (Kopchickl2) and muscle, see U.S Provisional Appl. 60/547,512, filed Feb. 26, 2004 (Kopchickl5) . Other differential hybridization applications . The use of differential hybridization to identify genes and proteins is also described in our research group's Ser. No. PCT/US00/12145 (Kopchick 3A-PCT) , Ser. No. PCT/USOO/12366 (Kopchick4A-PCT) , and Ser. No. 60/400,052 (Kopchickδ) .

All of the foregoing applications are hereby incorporated by reference in their entirety.

BACKGROUND OF THE INVENTION

Field of the Invention The invention relates to various nucleic acid molecules and proteins, and their use in (1) diagnosing aging, or adverse conditions associated with the aging process, and (2) protecting mammals (including humans) against the aging process or adverse conditions associated with the aging process .

Description of the Background Art The mechanisms that cause aging (the decline in survival and reproductive ability with advancing age) have puzzled our society and scientific community for centuries. The two major theories center on the question of whether normal aging is an evolutionarily-genetically preprogrammed pathway of internal changes or is a normal consequence of existence where there is an accumulation of molecular and cellular damages. Hypotheses of such accumulated damage include free radical-oxidative damage, defective mitochondria, somatic mutations, progressive shortening of telomeres, programmed cell death, impaired cell proliferation and numerous others (1) . The current belief is that aging is not a programmed process in that, to date, no genes are known to have evolved specifically to cause damage and aging. The one factor that has been shown to extend the lifespan in organisms from yeast to mice has been a reduction in caloric intake (2, 3). Recent data suggests that caloric restriction may also be relevant for primates, including humans (4-6) . Unfortunately, it is unlikely that most people will be able to maintain the strict dietary control required to reap the benefits of this finding. Therefore, since the mechanism (s) by which caloric restriction extends lifespan are unknown, the elucidation of such mechanisms could lead to the development of alternative strategies to yield similar benefits. Numerous groups are presently engaged in identifying genes and pathways that are involved in the aging process. A growing list of genes that extend adult longevity have been identified and a large proportion of these genes are involved with hormonal signals . Many of these genes and the corresponding endocrine systems are conserved among a wide variety of eukaryotes . What is becoming clear, at least in lower animal species, is that those pathways that provide advantages to development and growth early in life may impart negative consequences in later life. The clearest example of a genetic pathway affecting adult lifespan has been described in the nematode, Caenorhabdi tis elegans. When food is abundant, C. elegans develops directly to the reproductive adult through four larval stages in three days . Under adverse conditions such as caloric restriction or high population density, C. elegans enters the Dauer diapause, a non-feeding, stress-resistant larval state. Genetic analysis has identified that mutation of single genes involved in dauer formation (Daf) greatly extend the adult lifespan (7) . These genes involve the highly-conserved insulin/lGF-like signal transduction pathway. Ligand binging to the daf -2 insulin-like receptor results in a kinase signaling cascade to phosphorylate the forkhead transcription factor, daf-16. This phosphorylation sequesters daf-16 to the cytoplasm and results in reproductive maturity and aging. In the absence of ligand and signal transduction, the unphosphorylated, daf-16 localizes to the nucleus and regulates the transcription of its target genes that promote dauer formation,, stress resistance and extended longevity (8) . A similar pathway has been described in Drosophilia melanogaster. Mutation of the gene encoding insulin-like receptor (JnR) or the gene encoding insulin-receptor substrate (chico) also extends the normal life-span (9,10). Vertebrate homologues of daf-16 down-regulate genes promoting cell progression, induce genes involved in DNA-damage repair and up-regulate genes that reduce intracellular reactive oxygen species (ROS) (11,12). A second C. elegans gene, clk-1, has also been linked to the reduction of ROS and an extended life-span. While the effect of daf -2 mutants result in a reduction of mitochondrial ROS, clk-1 mutants reduce extramitochondrially produced ROS. Since the majority of cellular ROS is produce in the mitochondria during the process of electron transport, it is not surprising that clk-1 mutants have only a moderately extended life-span. C. eleg'ans containing daf- 2/clk-l double mutations, however, exhibit a very long life- span (13) . Decreased IGF-1 signaling may also extend longevity in mice. Four mouse models with deficiencies in pituitary endocrine action have demonstrated retarded aging. In the Propl and Pit! models, pituitary production of growth hormone (GH) , prolactin (PRL) and thyroid stimulating hormone (TSH) are ablated. These mice have reduced growth rates, reduced adult body size and live 40 to 60% longer than normal mice (14,15). Unfortunately, it is not possible to determine which of the ablated hormones is responsible for the increased longevity of the models . A more straightforward model was developed that targeted the deletion of the growth hormone receptor {GHR- KO) (16) . This mouse line was derived from a founder animal by homologous recombination resulting in deletion and gene substitution of most of the fourth exon and part of the fourth intron of the GHR/BP gene. These mice also exhibit reduced body size and extended life-span and more directly implicates the GH/IGF-1 axis (17, 17a) . Recently, evidence for a direct role of IGF-1 receptor signaling in affecting the aging process was provided by the targeted disruption of the IGR-1 receptor (Igflr) (18) . Heterozygous females, but not males, possess 50% fewer receptors for IGF-1, live 33% longer than wild-type females and also display greater resistance to oxidative stress. Tyrosine phosphorylation of the intracellular signaling molecule, She, was also decreased in the Igflr ^{+ ~} females. Mice containing the targeted deletion of p66shc also have increased resistance to oxidative stress and a 30% increase in life span (19) . While the IGF-1 axis appears to be involved in the aging process, the mechanism by which it does so remains unknown. However, these findings demonstrate that it is possible to identify specific genetic pathways that affect the aging process . The finding that caloric restriction of these mouse models can further extend their life-span suggests that multiple pathways exist that affect the aging process (20) . Therefore, research to identify these pathways and the genes involved in the aging process is of great importance. The role of growth hormone in aging is further discussed in Vance, ML, "Can Growth Hormone Prevent Aging," Ne Engl. J. Med., 348: 779-80 (Feb. 27, 2003).

Gene Chip-Based Identification of genes involved in aging of skeletal muscle Several groups have used DNA microarrays to measure differences in gene expression caused by the aging process. However, these experiments are extremely limited in regards to the number of aging time points or experimental conditions . Weindruch, et al . , "Microarray profiling of gene expression in aging and its alteration by caloric restriction in mice" in Symposium: Calorie Restriction: effects on Body Composition, Insulin Signaling and Aging 918S-923S (2001) (21) compared expression in gastrocnemius muscle from 5- and 30-month old C57BL/6 mice, with and without caloric restriction. In this analysis, the expression of 113 genes was found to be changed by at least two-fold in 5-month old mice compared to 30-month old mice. Caloric restriction of comparable mice caused a reversal of the altered gene expression of 33 genes. Of the 6347 genes surveyed in the oligonucleotide microarray, only 58 (0.9%) displayed a greater than 2 fold increase in gene expression as a function of aging, whereas 55(0.9%) displayed a greater than 2 fold decrease. Of the genes positively correlated with aging, 16% could be assigned to stress responses . The largest differential expression between young and aged animals (3.8 fold) was the mitochondrial sarcomeric creatine kinase. Of the genes negatively correlated with aging, 13% were involved in energy metabolism. A noteworthy number were genes encoding biosynthetic enzymes (cytochrome P450 IIC12, squaelene synthase, stearoyl-CoA desaturase, EF-1-gamma. Another down regulator was a CpG binding protein, MeCP2. Weindruch further reported that age-related changes in gene expression profile were "remarkably attenuated" by caloric restriction. What appears to be the same experiment is discussed in Lee, et al . , "Gene expression profile of aging and its retardation by caloric restriction," Science, 285: 1390 (Aug. 27, 1999) . This papers lists the individual genes which were differentially expressed by more than 2-fold, and classifies them as energy metabolism, neuronal factors, protein metabolism, stress response, biosynthesis, calcium metabolism or DNA repair genes. Welle, et al . , "Skeletal muscle gene expression profiles in 20-29 year old and 65-71 year old women," Exper. Gerontol., 39: 369-77 (2004) and available electronically as doi : 10.1016/j .exger.2003.11.011 studied gene expression and physical condition in seven young and eight older women. With respect to physical condition, the measured or calculated parameters were total body mass, lean body mass, left leg lean mass (by biopsy) , maximum isometric left knee extension force, left knee extension force/left keg lean mass, Peak V0₂/lean body mass, and Peak V0₂/left leg lean mass. There were 1178 "probe sets" (representing 1053 different Unigene clusters) for which differential expression was detected; 550 for which expression was higher in older women, and 628 the inverse effect. The differences ranged from 1.2 to 4 fold; most (78A%) were less than 1.5 fold. The complete list of differentially expressed genes is given in the Rochester Muscle database website, www.urmc.rochester.edu/smd/crc/swindex (".html" omitted, in accordance with USPTO requirements, so that the publication of this application will not create an active hyperlink) . The gene most highly overexpressed in older muscle was p21 (cyclin-dependent kinase inhibitor IA) (4.01 fold). This one of several genes (see Welle Table 2) which are potentially related to DNA damage and repair. Welle also thought it noteworthy how many of the differentially expressed genes were ones that encode proteins which bind to pre-mRNAs or mRNAs (see Welle Table 3) .

Gene-Chip Based Identification of Genes involved in aging of other organs and tissues Microarrays have also been used in the identification of aging-related genes by virtue of differential expression in other organs and tissues, see, e.g., Miller, J. Gerontol., 56A: B52-57 (2001) (liver) ; Lee et al . , Science, 285 : 1390-93 (1999) and Nature Genetics 25: 294-7 ( 2000) (mouse cerebellum and neocortex); Lee et al . , Proc Natl Acad Sci USA 99:14988-14993 (2002) (Ref. 22) (heart) ; Prolla, Chem Senses 27299-306 (2002) (Ref. 23) (brain) . Cao, S.X., et al . , "Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice", Proc. Natl. Acad. Sci. USA, 98:10630-10635 (2001) used Affymetrix microarray technology to study the changes in expression levels of 11,000 genes in liver tissue of 7 month-old mice compared to 27 month-old mice. In this analysis, the expression of 20 genes increased at least 1.7- fold with age while the expression of 26 genes decreased at least 1.7-fold with age. Tollet-Egnell, P., et al., "Gene expression profile of the aging process in rat liver: normalizing effects of growth hormone replacement, Mol. Endocrinol., 15 (2): 308-18 (2001) used microarray technology to study the effect of aging and growth hormone treatment on the expression of 3,000 different genes in the rat liver. The proteins which were over-expressed in the older rat were glucose-6- phosphate isomerase (xl.8), pyruvate kinase (x4.8), hepatic product spot 14 (2.4x), fatty acid synthase (1.9x), staryl CoA desaturase (1.7x), enoyl CoA hyydratase (1.7x), peroxisome proliferator activated receptor-α (1.7x), 3- ketoacyl-CoA thiolase (1.7x), 3-keto-acyl-CoA peroxisomal thiolase (1.9x), CYP4A3 (3.3x), glycerol-3-phosphate dehydrogenase (1.7x), NAPDH-cytochrome P450 oxidoreductase (4.7x) . CUP2C7 (1.9x), CYP3A2 (2.8x), Δ-aminoevulinate synthase (2.3x) . The under-expressed proteins were gluσose- 6-phosphatase (0.3x), farnesyl pyrophosphate synthase (0.5x), carnitine octanoyltransferase (0.5x), mitochrondrial genome (16S ribosomal RNA) (0.3x), mitochondrial cytochrome c oxidase II (0.4x), mitochondrial NADH dehydrogenase SU 5 (0.3x), mitochondrial cytochrome b (0.4x), mitochondrial NADH dhydrogenase SU 3 (0.5x), NADH-ubiquinone oxidoreductase (SU CI-SGDH and SU 39kDa) (both 0.5x), ubiquinol-cytochrome c reductase (Rieske iron-sulfur protein and core 1) (both 0.5x) , CYP2C12 (0.4x), cystathione γ-lyase (0.3x), biphenyl hydrolase-related protein (0.5x), glutathione S-transferase (class pi) (0.3x), α-1 macroglobulin (0.5x), BRAK related protein (0.3x), α-2u- globulin (0.4x), cAMP-dependent transcription factor mATF4 (0.5x), DAP-like kinase (0.5x), PCTAIRE-1 (0.5x), collagen α-1 (0.4x), histone H2A (0.5x), and S-100 protein α (0.5x). See also Dozmorov I, Bartke A, Miller RA. , "Array-based expression analysis of mouse liver genes: effect of age and of the longevity mutant Propldf " , J. Gerontol . , 56A: B52-57 (2001) . Liver mRNA levels were measured in Ames dwarf mice (homozygous for the df allele at the Propl locus; live 40% to 70% longer than nonmutant siblings) and in control mice at ages 5, 13 and 22 months. "The analysis showed seven genes where the effects of age reach p < .01 in normal mice and six others with possible age effects in dwarf mice, but none of these met Bonferroni-adjusted significance thresholds. Thirteen genes showed possible effects of the df/df genotype at p < .01. One of these, insulin-like growth factor 1 (IGF-1) , was statistically significant even after adjustment for multiple comparisons; and genes for two IGF-binding proteins, a cyclin, a heat shock protein, p38 mitogen-activated protein kinase, and an inducible cytochrome P450 were among those implicated by the survey. In young control mice, half of the expressed genes showed SDs that were more than 58% of the mean, and a simulation study showed that genes with this degree of interanimal variation would often produce false-positive findings when conclusions were based on ratio calculations alone (i.e., without formal significance testing) . Many genes in our data et showed apparent young-to-old or normal-to-dwarf ratios above 2, but the large majority of these proved to be genes where high interanimal variation could create high ratios by chance alone, and only a few of the genes with large ratios achieved p < .05. The proportion of genes showing relatively large changes between 5 and 13 months, or from 13 to 22 months of age, was not diminished by the df/df genotype, providing no support for the idea that the dwarf mutation leads to global delay or deceleration of the pace of age-dependent changes in gene expression."

Other Anti -Aging Studies For genes thought to have aging inhibitory activity, see generally International Longevity Center, Workshop Reports, "Longevity Genes :' From Primitive Organisms to Humans," and "Is there an 'Anti-Aging' Medicine?".

Patents of possible interest include the following:

Lin, USP 6,303,768 (2001) ^"'("Methuselah gene")

Lippman, USP 4,695,590 ("Method for retarding aging")

West, USP 6,368,789 (2002) ("Screening methods to identify inhibitors of telomerase activity")

Measurement of Biological Aging Patents of possible interest include the following:

Kojima, USP 5,000,188 (1991) (an apparatus for measuring the physiological age of a subject) . Dimri, USP 5,795,728 (1998) ("Biomarkers of cell senescence")

Jia, USP 6,326,209 (2001) ("Measurement and quantification of 17 ketosteroid -sulfates as a biomarker of biological age")

Articles of interest include Kayo, et al., Proc. nat . Acad. Sci. (USA) 98:5093-98 (2001); Han, et al . , Mch. Ageing Dev. 115:157-74 (2000); Dozmorov, et al . , J. gerontol . A Biol. Sci. Med. Sci. 56:B72-B80 (2001); Dozmorov, et al . , Id., 57: B99-B108 (2002); Miller, et al . , Mol. Endocrinol., 16: 2657-66 (2002) .

Other Studies of Differential Expression in Muscle The papers collected in this section deal principally with type II diabetes, which is an aging-related disease. Sreekumar, et al . , "Gene expression profile in skeletal muscle of type 2 diabetes and the effect of insulin treatment," Diabetes 51: 1913 (June 2002) surveyed 6,451 genes, and identified 85 genes for which there was an alteration in skeletal muscle transcription in diabetic patients after withdrawal of insulin treatment. Subsequent insulin treatment resulted in further changes in transcription of 74 of the 85 genes (15 increased, 59 decreased) , and also resulted in alteration of 29 additional gene transcripts . Mootha, et al . , "PCG-lα responsive genes involved in oxidative phosphorylation are coordinatively downregulated in human diabetes," Nature Genetics 34(3); 267 (July 2003), used D A microarrays to detect changes in the expression of sets of related genes, rather than of individual genes. They classified over 22,000 genes into 149 data sets; some of these data sets overlapped. They looked for a statistical correlation between the overall rank order of the genes in differential expression, and the groups to which the genes belonged. Expression was compared pairwise among three groups: males with normal glucose tolerance; males with impaired glucose tolerance; and males with type 2 diabetes. The set with the highest enrichment score (the one whose members ranked highly most often relative to chance expectation) was an internally curated set of 106 genes involved in oxidative phosphorylation. While the average decrease for the individual genes was modest (-20%) , it was also consistent, being observed in 89% (94/106) of the genes in question. This paper is reviewed by Toye and Gauguier, "Genetics and functional genomics of type 2 diabetes mellitus", Genome Biology, 4: 241 (2003). Patti, et al . , "Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1", Proc. Nat. Acad. SCi. (USA), 100(14): 8466 (July 8, 2003) used microarrays to analyze skeletal muscle expression of genes in nondiabetic insulin-resistant subjects at high risk for diabetes (based on family hisotry of diabetes and Mexican-American ethnicity) and diabetic Mexican-American subjects. Of 7,129 sequences represented on the microarray, 187 were differentially expressed between control and diabetic subjects. However, no single gene remained significantly differentially expressed after controlling for multiple comparison false discovery by using the Benjamin!-Hochberg method, see Benjamini, et al . , J. R. Stat . Soc. Sert . B. 57:289-300 (1995); Dudait, et al . , Stat. Sin. 12: 111-139 (2002). Consequently, Patti et al . sought to identify groups of related genes with similar patterns of differential expression using MAPP FINDER and ONTOEXPRESS. According to MAPP FINDER, the top-ranked cellular component terms were mitochondrion, mitochondrial membrane, mitochondrial inner membrane, and ribosome, and the top- ranked process term was ATP biosynthesis. According to ONTOEXPRESS, the over-represented groups were energy generation, protein biosynthesis/ribosomal proteins, RNA binding, ribosomal structural protein, and ATP synthase complex. Huang, Xudong, "Identification of abnormally expressed genes in skeletal muscle contributing to insulin resistance and type 2 diabetes", Thesis, document id: 9576 Lunds University 2002, reported differential expression of the mitochondrially-encoded ND1 gene in human diabetic patients and of the nuclear-encoded cathepsin L gene in mice. Standaert, et al . , "Skeletal muscle insulin resistance in obesity-associated type 2 diabetes in monkeys is linked to a defect in insulin activation of protein kinase C- zeta/lambda/iota Diabetes 51: 2936 (Oct. 2002). the authors concluded ' that defective activation of atypical PKCs played an important role in the pathogenesis of peripheral insulin resistance in both obese prediabetic and diabetic monkeys. They attributed this linkage to the apparent requirement for aPKCs during insulin-stimulated glucose transport. Srommer, et al . , Am. J. Physiol ., "Skeletal muscle insulin resistance after trauma: insulin signaling and glucose transport", 275(2 Pt . 1): E3518(Aug. 1998) concluded that insulin resistance in skeletal muscle after surgical trauma is associated with reduced glucose transport but not with impaired glucose signaling to PI 3 -kinase or its downstream target, Akt .

Other Differential /Subtractive Hybridization Studies of Interest Zhang, et al . , Kidney International, 56:549-558 (1999) identified genes up-regulated in 5/6 nephrectomized (subtotal renal ablation) mouse kidney by a PCR-based subtraction method. Ten known and nine novel genes were identified. The ultimate goal was to identify genes involved in glomerular hyperfiltration and hypertrophy.Melia, et al . , Endocrinol., 139:688-95 (1998) applied subtractive hybridization methods for the identification of androgen-regulated genes in mouse kidney. The treatment mice were dosed with dihydrotestosterone, an androgen. Kidney androgen-regulated protein gene was used as a positive control, as it is known to be up-regulated by DHT. See also Holland, et al . , Abstract 607, "Identification of Genes Possibly Involved in Nephropathy of Bovine Growth Hormone Transgenic Mice" (Endocrine Society Meeting, June 22, 2000) and Coschigano, et al . , Abstract 333, "Identification of Genes Potentially Involved in Kidney Protection During Diabetes" (Endocrine Society Meeting, June 22, 2000) . The following differential hybridization articles may also be of interest: Wada, et al . , "Gene expression profile > in streptozotocin-induced diabetic mice kidneys undergoing glomerulosclerosis", Kidney Int, 59:1363-73 (2001); Song, et al . , "Cloning of a novel gene in the human kidney homologous to rat muncl3S: its potential role in diabetic nephropathy", Kidney Int., 53:1689-95 (1998); Page, et al . , "Isolation of diabetes-associated kidney genes using differential display", Biochem. Biophys. Res. Comm. , 232:49-53 (1997); Peradi, "Subtractive hybridization claims: An efficient technique to detect overexpressed mRNAs in diabetic nephropathy," Kidney Int. 53:926-31 (1998); Condorelli, EMBO J., 17:3858-66 (1998); See also WOOO/66784 (differential hybridization screening for brown adipose tissue); PCT/US00/12366, filed May 5, 2000 (differential hybridization screening for liver) . Apoptosis and CIDE-A Apoptosis is a form of programmed cell death that occurs in an active and controlled manner to eliminate unwanted cells. Apoptotic cells undergo an orchestrated cascade of morphological changes such as membrane blebbing, nuclear shrinkage, chromatin condensation, and formation of apoptotic bodies which then undergo phagocytosis by neighboring cells. One of the hallmarks of cellular apoptosis is the cleavage of chromosomal DNA into discrete oligonucleosomal size fragments. This orderly removal of unwanted cells minimizes the release of cellular components that may affect neighboring tissue. In contrast, membrane rupture and release of cellular components during necrosis often leads to tissue inflammation. The process of apoptosis is highly conserved and involves the activation of the caspase cascade. Cohen, GM.

(1997) Caspases : the executioners of apoptosis. Biochem. J. 326:1-16; Budihardjo, I., Oliver, H., Lutter, M., Luo, X. , Wang, X. (1999) Biochemical pathways of caspase activation during apoptosis. Annnu. Rev. Cell. Dev. Biol.15:269-290; Jacobson, M.D., Weil, M. , Raff, M.C. (1997) Programmed cell death in animal development. Cell 88:347-354. Caspases are a family of serine proteases that are synthesized as inactive proenzymes . Their activation by apoptotic signals such as CD95 (Fas) death receptor activation or tumor necrosis factor results in the cleavage of specific target proteins and execution of the apoptotic program. Apoptosis may occur by either an extrinsic pathway involving the activation of cell surface death receptors (DR) or by an intrinsic mitochondrial pathway. Yoon, J-H. Gores G.J. (2002) Death receptor-mediated apoptosis and the liver. J. Hepatology 37:400-410. These pathways are not mutually exclusive and some cell types require the activation of both pathways for maximal apoptotic signaling. In type-I cells, death receptor activation leads to the recruitment and activation of caspases-8/10 and the rapid cleavage and activation of caspase-3 in a mitochondrial-independent manner. Hepatocytes are members of the Type-II cells in which mitochondria are essential for DR-mediated apoptosis Scaffidi, C. , Fulda, S., Srinivasan, A., Friesen, C. , Li, F., Tomaselli, K.J., Debatin, K.M., Krammer, P.H., Peter, M.E. (1998) Two CD95 (APO-l/Fas) signaling pathways. EMBO J. 17:1675-1687. In this pathway, the pro-apoptotic protein Bid is truncated by activated caspases-8/10 and translocates to the mitochondria. Luo, X., Budihardjo, I., Zou, H., Slaughter, C, Wang, X. (1998) Bid, a Bcl2 interacting protein, mediates cytochrome c release from mitochondria in response to activation of cell surface death receptors. Cell 94:481-490; Li, H., Zhu, H. , Xu, C.J., Yuan, J. (1998) Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis. Cell 94:491-501. This trans.location leads to mitochondrial cytochrome c release and eventual activation of caspases-3 and 7 via cleavage by activated caspase-9. One of the substrates for activated caspase-3 is the DNA fragmentation factor (DFF) . DFF is composed of a 45 kDa regulatory subunit (DFF45) and a 40 kDA catalytic subunit (DFF40) . Liu, X., Zou, H. , Slaughter, C, Wang, X. (1997) DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis. Cell 89:175-184. DFF45 cleavage by activated caspase-3 results in its dissociation from DFF40 and allows the caspase-activated DNAse (CAD) activity of DFF40 to cleave chromosomal DNA into oligonucleosomal size fragments. Liu, X., Li, P., Widlak, P., Zou, H. , Luo, X., Garrard, W.T., Wang, X. (1998) The 40-kDa subunit of DNA fragmentation factor induces DNA fragmentation and chromatin condensation during apoptosis. Proc. Natl. Acad. Sci. USA. 95:8461-8466; Halenbeck, R. , MacDonald, H., Roulston, A., Chen, T.T., Conroy, L., Williams, L.T. (1998) CPAN, a human nuclease regulated by the caspase-sensitive inhibitor DFF45. Curr Biol. 8:537-540; Nagata, S. (2000) Apoptotic DNA fragmentation. Exp. Cell Res. 256:12-8. Recently, a novel family of cell-death-inducing DFF45-like effectors (CIDEs) have been identified that includes CIDE-A, CIDE-B and CIDE-3/FSP2. Inohara, N. , Koseki, T., Chen, S., Wu, X. , Nunez, G. (1998) CIDE, a novel family of cell death activators with homology to the 45 kDa subunit of the DNA fragmentation factor. EMBO J. 17:2526-2533; Danesch, U. , Hoeck, W. , Ringold, G.M. (1992) Cloning and transcriptional regulation of a novel adipocyte- specific gene, FSP27. CAAT-enhancer-binding protein (C/EBP) and C/EBP-like proteins interact with sequences required for differentiation-dependent expression. J. Biol. Chem. 267:7185-7193; Liang, L. , Zhao, M. , Xu, Z., Yokoyama, K.K., Li, T. (2003) Molecular cloning and characterization of CIDE-3, a novel member of the cell-death-inducing DNA- fragmentation-factor (DFF45) -like effector family. Biochem. J. 370:195-203. The CIDEs contain an N-terminal domain that shares homology with the N-terminal region of DFF45 and may represent a regulatory region via protein interaction. See Inohara, supra; Lugovskoy, A.A. , Zhou, P., Chou, J.J., McCarty, J.S., Li, P., Wagner, G. (1999) Solution structure of the CIDE-N domain of CIDE-B and a model for CIDE-N/CIDE-N interactions in the DNA fragmentation pathway of apoptosis. Cell 9:747-755. The family members also share a C-terminal domain that is necessary and sufficient for inducing cell death and DNA fragmentation; see Inohara supra. The overexpression of CIDE-A induces cell death that can be inhibited by DFF45. However, CIDE-A-induced apoptosis is not inhibited by caspase-8 inhibitors thereby suggesting the presence of additional, caspase-independent, pathway (s) for the induction of apoptosis, see Inohara supra. Previous reports have indicated that human and mouse CIDE-A are expressed in several tissues such as brown adipose tissue (BAT) and heart and are localized to the mitochondria, Zhou, Z., Yon Toh, S., Chen, Z., Guo, K. , Ng, C.P., Ponniah, S., Lin, S.C, Hong, W. , Li, P. (2003) Cidea-deficient mice have lean phenotype and are resistant to obesity. Nat. Genet. 35:49-56. . In addition to the ability to induce apoptosis, CIDE-A can interact and inhibit UCP1 in BAT and may therefore play a role in regulating energy balance, see Zhou supra. Previous reports have indicated that CIDE-A is not expressed in either adult human or mouse liver tissue, see Inohara supra, Zhou supra.

The human protein cell death activator CIDE-A is of particular interest because of its highly dramatic change in liver expression with age, first demonstrated in our Kopchick7 application, supra. CIDE-A expression is elevated in older normal mice. CIDE-A expression was studied for normal C57BI/6J mouse ages 35, 49, 77, 133, 207, 403 and 558 days. Expression is low at the first five data points, then rises sharply at 403 days, and again at 558 days. CIDE-A was therefore classified as an "unfavorable protein", i.e., it was taught that an antagonist to CIDE-A could retard biological aging. In Kopchick7A-PCT we reported that CIDE-A is also prematurely expressed in hyperinsulinemic and type-II diabetic mouse liver tissue. CIDE-A expression also correlates with liver steatosis in diet-induced obesity, hyperinsulinemia and type-II diabetes. These observations suggest an additional pathway of apoptotic cell death in Non-Alcoholic Fatty Liver Disease (NAFLD) and that CIDE-A may play a role in this serious disease and potentially in liver dysfunction associated with type-II diabetes.

SUMMARY OF THE INVENTION Our attention recently has focused on the generation of muscle mRNA expression profiles and the identification of genes involved in the aging process. We have therefore explored the genetic changes in the muscle of C57B1/6 mice that occur during the ageing process, observing the gene expression patterns at many different time points. Nucleic acid hybridization techniques on gene chips have been used to identify mouse genes that are differentially expressed in mice, depending upon their age. We have utilized the Amersham product code: 300013 Codelink UniSet Mouse I Bioarray to determine the level of gene expression of approximately 10,000 mouse genes in the muscle of mice with average ages of 35, 49, 77, 118, 133, 207, 403, 558 and 725 days. In essence, complementary RNA derived from mice of different ages was screened for hybridization with oligonucleotide probes each specific to a particular mouse database DNA, the latter being identified, by database accession number, by the gene manufacturer. Each database DNA in turn was also identified by the gene chip manufacturer as representative of a particular mouse gene cluster (Unigene) . In most cases, this database DNA sequence is a full length genomic DNA or cDNA sequence, and is therefore either identical to, or otherwise encodes the same protein as does, a natural full-length genomic DNA protein coding sequence. Those which don't present at least a partial sequence of a natural gene or its cDNA equivalent . For the sake of simplicity, all of these mouse database DNA sequences, whether full-length or partial, and whether cDNA or genomic DNA, are referred to herein as "mouse genes". When only the genomic sequence is intended, we will refer specifically to "genomic DNA" or "gDNA" . The sequences in the protein databases are determined either by directly sequencing the protein or, more commonly, by sequencing a DNA, and then determining the translated amino acid sequence in accordance with the Genetic Code. All of the mouse sequences in the mouse polypeptide database are referred to herein as "mouse proteins" regardless of whether they are in fact full length sequences. Mouse genes which were differentially expressed (younger vs. older), as measured by different levels of hybridization of the respective cRNA samples with the particular probe corresponding to that mouse gene, were identified. Favorable behavior is when expression decreases with age. Substantially favorable behavior is when the ratio of younger value to older value is at least two fold. Unfavorable behavior is when expression increases with age . Substantially unfavorable behavior is when the ratio of older value to younger value is at least two fold.

A mouse gene is considered to be "favorable" (more precisely, "wholly favorable") for the purpose of Master Table 1 (especially subtable IA) if, for at least one of the time comparisons set forth in the Examples, it exhibited substantially favorable behavior, and if, for all the other comparisons, it at least did not exhibit substantially unfavorable behavior. Note that the classification of a gene as favorable for purpose of the Master Table does not mean that it must have exhibited substantially favorable behavior for all of the comparisons set forth in the Examples . A mouse gene is considered to be "unfavorable" (more precisely, "wholly unfavorable") for the purpose of the Master Table 1 (especially subtable IB) if, for at least one of the time comparisons set forth in the Examples, it exhibited substantially unfavorable behavior, and if, for all the other comparisons, it at least did not exhibit substantially favorable behavior. A mouse gene is considered to be "mixed" (i.e., partially favorable and partially unfavorable) for the purpose of the Master Table, especially subtable IC, if for at least one of the time comparisons set forth in the Examples it exhibited substantially favorable behavior and if for at least one of the other such comparisons it exhibited substantially unfavorable behavior. The expression of a gene may first rise, then fall, with increasing age. Or it may first fall, and then rise. These are just the two simplest of several possible "mixed" expression patterns . Thus, we can subdivide the "favorables" into wholly and partially favorables. Likewise, we can subdivide the unfavorables into wholly and partially unfavorables . The genes/proteins with "mixed" expression patterns are, by definition, both partially favorable and partially unfavorable. In general, use of the wholly favorable or wholly unfavorable genes/proteins is preferred to use of the partially favorable or partially unfavorable ones.

It is evident from the foregoing that mixed genes/proteins are those exhibiting a combination of favorable and unfavorable behavior. A mixed gene/protein can be used as would a favorable gene/protein if its favorable behavior outweighs the unfavorable. It can be used as would an unfavorable gene/protein if its unfavorable behavior outweighs the favorable. Preferably, they are used in conjunction with other agents that affect their balance of favorable and unfavorable behavior. Use of mixed genes/proteins is, in general, less desirable than use of purely f vorable or purely unfavorable genes/proteins . It will be appreciated that the comparisons set forth in the Examples are not exhaustive and that it is possible that a mouse gene which, on the basis of those comparisons, is classified as a "favorable" gene in the Master Table) may turn out, if additional time points are considered, to sometimes exhibit substantially unfavorable behavior. Nonetheless, such a gene will still be considered a "favorable" gene for the purpose of the Master Table and the claims referring to the Master Table. Likewise, a gene which, on the basis of those comparisons, was classified as an "unfavorable" gene in the Master Table may prove, under more detailed examination, to sometimes exhibit substantially favorable behavior. Nonetheless, it will retain "unfavorable" classification for the purpose of the . Master Table and the claims referring thereto. The "favorable", "unfavorable" and "mixed" mouse proteins are thus those listed in the Master Table as encoded by the listed "favorable", "unfavorable" and "mixed" mouse genes, respectively, or which otherwise correspond to those mouse genes .

Related human genes (database DNAs) and proteins were identified by searching a database comprising human DNAs or proteins for sequences corresponding to (i.e., homologous to, i.e., which could be aligned in a statistically significant manner to) the mouse gene or protein. More than one human protein may be identified as corresponding to a particular mouse chip probe and to a particular mouse gene. Note that the terms "human genes" and "human proteins" are used in a manner analogous to that already discussed in the case of "mouse genes" and "mouse proteins". As used herein, the term "corresponding" does not mean identical, but rather implies the existence of a statistically significant sequence similarity, such as one sufficient to qualify the human protein or gene as a homologous protein or DNA as defined below. The greater the degree of relationship as thus defined (i.e., by the statistical significance of each alignment used to connect the mouse chip DNA, and the corresponding mouse gene/cDNA, to the human protein or gene, measured by an E value) , the more close the correspondence. The connection may be direct (mouse gene/cDNA to human protein) or indirect (e.g., mouse gene/cDNA to human gene, human gene to human protein) . In general, the human genes/proteins which most closely correspond, directly or indirectly, to the mouse gene/cDNA are preferred, such as the one(s) with the highest, top two highest, top three highest, top four highest, top five highest, and_. top ten highest E values for the final alignment in the connection process. The human genes/proteins deemed to correspond to our mouse genes are identified in the Master Tables.

Note that it is possible to identify homologous full- length human genes and proteins, if they are present in the database, even if the query mouse DNA or protein sequence is not a full-length sequence. If there is no homologous full-length human gene or protein in the database, but there is a partial one, the latter may nonetheless be useful. For example, a partial protein may still have biological activity, and a molecule which binds the partial protein may also bind the full- length protein so as to antagonize a biological activity of the full-length protein. Likewise, a partial human gene may encode a partial protein which has biological activity, or the gene may be useful in the design of a hybridization probe or in the design of a therapeutic antisense DNA. The partial genes and protein sequences may of course also be used in the design of probes intended to identify the full length gene or protein sequence.

Agents which bind the "favorable" and "unfavorable" nucleic acids (e.g., the agent is a substantially complementary nucleic acid hybridization probe) , or the corresponding proteins (e.g., an antibody vs. the protein) may be used to -estimate the biological age of a human subject, or to predict the rate of biological aging in a human subject (i.e, to evaluate whether a human subject is at increased or decreased risk for faster-than-normal biological aging) . A subject with one or more elevated "unfavorable" and/or one or more depressed "favorable" genes/proteins is at increased risk, and one with one or more elevated "favorable" and/or one or more depressed "unfavorable" genes/proteins is at decreased risk. The assay may be used as a preliminary screening assay to select subjects for further analysis, or as a formal diagnostic assay.

The identification of the related genes and proteins may also be useful in protecting humans against faster-than- normal or even normal aging (hereinafter, "the disorders") . They may be used to reduce a rate of biological aging in the subject, and/or delay the time of onset, or reduce the severity, of an undesirable age-related phenotype in said subject, and/or protect against an age-related disease.

Thus, Applicants contemplate: (1) use of the "favorable" mouse DNAs (or fragments thereof) of the Master Tables (below) to isolate or identify related human DNAs; (2) use of human DNAs, related to favorable mouse DNAs, to express the corresponding human proteins; (3) use of the corresponding human proteins (and mouse proteins, if biologically active in humans) , to protect against the disorder (s) ; . (4) use of the corresponding mouse or human proteins, or nucleic acid probes derived from the mouse or human cDNAs or genes, in diagnostic agents, in assays to measure or predict biological aging or the rate thereof; and (5) use of the corresponding human or mouse genes or cDNAs therapeutically in gene therapy, to protect against the disorder (s) . Moreover Applicants contemplate: (1) use of the "unfavorable" mouse DNAs (or fragments thereof) of the Master Tables to isolate or identify related human DNAs; (2) use of the complement to the "unfavorable" mouse DNAs or related human DNAs, as antisense molecules to inhibit expression of the related human DNAs; (3) use of the mouse or human DNAs to express the corresponding mouse or human proteins; (4) use of the corresponding mouse or human proteins, in diagnostic agents, to measure biological aging or the rate thereof; (5) use of the corresponding mouse or human proteins in assays to determine whether a substance binds to (and hence may neutralize) the protein; and (6) use of the neutralizing substance to protect against the disorder (s).

Thus, DNAs of interest include those which specifically hybridize to the aforementioned mouse or human genes, and are thus of interest as hybridization assay reagents or for antisense therapy. They also include synthetic DNA sequences which encode the same polypeptide as is encoded by the database DNA, and thus are useful for producing the polypeptide in cell culture or in situ (i.e., gene therapy) . Moreover, they include DNA sequences which encode polypeptides which are substantially structurally identical or conservatively identical in amino acid sequence to the mouse and human proteins identified in the Master Table 1, subtables IA or IC. Finally, they include DNA sequences which encode peptide (including antibody) antagonists of the proteins of Master Table 1, subtables IB or IC.

Related human DNAs also may be identified by screening human cDNA or genomic DNA libraries using the mouse gene of the Master Table, or a fragment thereof, as a probe. If the mouse gene of Master Table 1 is not full-length, and there is no closely corresponding full-length mouse gene in the sequence databank, then the mouse DNA may first be used as a hybridization probe to screen a mouse cDNA library to isolate the corresponding full-length sequence. Alternatively, the mouse DNA may be used as a probe to screen a mouse genomic DNA library.

The agents of the present invention may be used alone or in conjunction with each other and/or known anti-aging or anti- age-related disease agents. It is of particular interest to use the agents of the present invention in conjunction with an agent disclosed in one of the related applications cited above, in particular, an antagonist to CIDE-A, the latter having been taught in Kopchick7. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS OF THE

INVENTION

Full-Length vs. Partial Length Genes/Proteins A "full length" gene is here defined as (1) a naturally occurring DNA sequence which begins with an initiation codon (almost always the Met codon, ATG) , and ends with a stop codon in phase with said initiation codon (when introns, if any, are ignored) , and thereby encodes a naturally occurring polypeptide with biological activity, or a naturally occurring precursor thereof, or (2) a synthetic DNA sequence which encodes the same polypeptide as that which is encoded by (1) . The gene may, but need not, include introns . A "full-length" protein is here defined as a naturally occurring protein encoded by a full-length gene, or a protein derived naturally by post-translational modification of such a protein. Thus, it includes mature proteins, proproteins, preproteins and preproproteins . It also includes substitution and extension mutants of such naturally occurring proteins .

Anatomy and Physiology of Muscle Muscle tissue constitutes about 40% of the body mass. Muscles may be classified by location, i.e., skeletal if attached to bone, cardiac if forming the wall of the heart, and visceral if associated with another body organ. Muscles may also be classified as voluntary or involuntary, depending on how their contractions and relaxations are controlled. Skeletal muscles are voluntary, while cardiac and visceral muscles are involuntary. It is also possible to classify muscles morphologically; skeletal and cardiac muscle cells are striated, whereas visceral muscle cells are not . Each skeletal muscle is composed of many individual muscle cells called muscle fibers. The fibers are held together by fibrous connective-tissue membranes called fascia. The fascium which envelops the entire muscle is the epimysium, and the fascia which penetrate the muscle, separating the fibers into bundles (fasciculi) are called perimysium. Very thin fascia (endomysium) sheath each muscle fiber. Skeletal muscles are attached either directly to a bone, or indirectly through a tendon. The individual muscle fibers (cells) comprise threadlike protein structures called myofibrils. There are over 600 muscles in the human body. We will have occasion later to refer to the gastrocnemius . It is a superficial muscle in the posterior compartment of the lower leg, which together with the underlying soleus forms the characteristic bulge of the calf.

Subjects For mice, infancy is defined as the period 0 to 21 days after birth. Sexual maturity is reached, on average, at 42 days after birth. The average lifespan is 832 days. In humans, infancy is defined as the period between birth and two years of age . Sexual maturity in males can occur between 9 and 14 years of age while the average age at first menstrual period for females is 12.6 years. The average human lifespan is 73 years for males and 79 years for females. The maximum verified human lifespan was 122 years, five months and 14 days .

Chronological and Biological Aging "Aging" is a process of gradual and spontaneous change, resulting in maturation through childhood, puberty, and young adulthood and then primarily a decline in function through middle and late age. Aging thus has both the positive component of development/maturation and the negative component of decline. "Senescence" refers strictly to the undesirable changes that occur as a result of post-maturation aging. Some of the changes which occur in post-maturation aging are not deleterious to health (e.g., gray hair, baldness), and some may even be desirable (e.g., increased wisdom and experience) . In contrast, the memory impairment that occurs with age is considered senescence. However, we will hereafter use "aging" per se to refer to "senescence", and use "maturation" to refer to pre-maturation development . There is increased mortality with age after maturation. There is also a progressive decrease in physiological capacity with age, but the rate of physiological decline varies from organ to organ and from individual to individual. The physiological decline results in a reduced ability to respond adaptively to environmental stimuli, and increased susceptibility and vulnerability to disease. "Aging is the accumulation of diverse adverse changes that increase the risk of death. These changes can be attributed to development, genetic defects, the environment, disease ,and the inborn aging process. The chance of death at a given age serves as a measure of the number of accumulated changes, that is, of physiologic age, and the rate of change of this measure, as the rate of aging." Harman, Ann. N.Y. Acad. Sci. 854:1-7 (1998). Preferably, the agents of the present invention inhibit aging for at least a subpopulation of mature (post-puberty) adult subjects. The term "healthy aging" (sometimes called "successful aging") refers to post-maturation changes in the body that occur with increasing age even in the absence of an overt disease. However, increased age is a risk factor for many diseases ("age-related diseases") , and hence "total aging" includes both the basal effects of healthy aging and the effects of any age-related disease. (Most literature uses the term "normal aging" as a synonym for "healthy aging", but a minority use it to refer to "total aging". To minimize confusion, we will try to avoid the term "normal aging", but if we use it, it is as a synonym for "healthy aging".) Some, scientists have suggested that normal aging changes should be defined as those which are universal, degenerative, progressive and intrinsic. Preferably, the agents of the present invention inhibit healthy aging for at least a subpopulation of mature (post- puberty) adult subjects. In both aging and senescence, many physiologic functions decline, but normal decline is not usually considered the same as disease. The distinction between normal decline and disease is often but not always clear and may be due only to statistical distribution. Glucose intolerance is considered consistent with healthy aging, but diabetes is considered a disease, although a very common one. Cognitive decline is nearly universal with advanced age and is considered healthy aging; however, cognitive decline consistent with dementia, although common in late life, is considered a disease (as in the case of Alzheimer's, a conclusion supported by analysis of brain tissue at autopsy) . A decline in maximal heart rate is typical of healthy aging. In contrast, coronary heart disease is an age-related disease. A decline in bone density is considered healthy aging, but when it drops to 2.5 SD below the young adult mean, it is called osteoporosis. Generally speaking, the changes typical of healthy aging are gradual, while those typical of a disorder can be rapid. The term average (median) "lifespan" is the chronological age to which 50% of a given population survive. The maximum lifespan potential is the maximum age achievable by a member of the population. As a practical matter, it is estimated as the age reached by the longest lived member (or former member) of the population. The (average) life expectancy is the number of remaining years that an individual of a given age can expect to live, based on the average remaining lifespans of a group of matched individuals . The most widely accepted method of measuring the rate of aging is by reference to the average or the maximum lifespan. If a drug treatment achieves a statistically significant improvement in average or maximum lifespan in the treatment group over the control group, then it is inferred that the rate of aging was retarded in the treatment group. Similarly, one can compare long-term survival between the two groups . Preferably, the agents of the present invention have the effect of increasing the average lifespan and/or the maximum lifespan for at least a subpopulation of mature (post-puberty) adult subjects. This subpopulation may be defined by sex and/or age. If defined in part by age, then it may be defined by a minimum age (e.g., at least 30, at least 40, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 90, etc.) or by a maximum age (not more than 40, not more than 50, not more than 55, not more than 60, not more than 65, not more than 70, not more than 75, not more than 80, not more than 90, not more than 100, etc.), or by a rational combination of a minimum age and a maximum age so as to define a preferred close-ended age range, e.g., 55-75. The subpopulation may additionally be defined by race, e.g., Caucasian, negroid or oriental, and/or by ethnic group, and/or by place of residence (e.g., North America, Europe) . The subpopulation may additionally be defined by nonage risk factors for age-associated diseases, e.g., by blood pressure, body mass index, etc. Preferably, the subpopulation in which an agent of the present invention is reasonably expected to be effective is large, e.g., in the United States, preferably at least 100,000 individuals, more preferably at least 1,000,000 individuals, still more preferably at least 10,000,000, even more preferably at least 20,000,000, most preferably at least 40,000,000. By way of comparison, according to the 2000 U.S. Census, the U.S. population, by age, was

For any given chronological age, statisticians can define the probability of living to a particular later age. These expectancies can be calculated for the entire age cohort, or broken down by sex, race, country of residence, etc. Individuals who live longer than expected can 'be said, after the fact, to have biologically aged more slowly than their peers . One definition of biological age is that it is a measure of one's position in one's life span, i.e., biological age = position in own life span (as fraction in range 0..1) X average life span for species. This simple definition carries with it the implicit assumption that the rate of biological aging is constant. It also has the practical problem of determining one's own life span before death. We will present a more practical definition shortly. The problem with lifespan studies is that they are extremely time-consuming. A maximum lifespan study in mice can take 4-5 years. A maximum lifespan study in dogs or cats would take 15-20 years, in monkeys, 30-40 years, and in humans, over 100 years. Even if the human study group were of sexagenarians, it would take 40-60 years to complete the study. Hence, scientists have sought to identify biological markers (biomarkers) of biological aging, that is, characteristics that can be measured while the subjects are still alive, which correlate to lifespan. These biological markers can be used to calculate a "biological age" (syn. "Physiological age") ; it is the chronological age at which an average member of the population (or relevant subpopulation) would have the same value of a biomarker of biological aging (or the same value of a composite measure of biomarkers of biological aging) as does the subject. This is the definition that will be used in this disclosure, unless otherwise stated. The effect of aging varies from system to system, organ to organ, etc. For example, between ages 30 and 70 years, nerve conduction velocity decreases by only about 10%, but renal function decreases on average by nearly 40%. Thus, there isn't just one biological age for a subject. By a suitable choice of biomarker, one may obtain a whole organism, or a system-, organ- or tissue-specific measure of biological aging, e.g., one can say that a person has the nervous system of a 30 year old but the renal system of a 60 year old. Biomarkers may measure changes at the molecular, cellular, tissue, organ, system or whole organism levels. Generally speaking, in the absence of some form of intervention (drugs, diet, exercise, etc.), biological ages will increase with time. The agents of the present invention preferably reduce the time rate of change of a biological age of the subject. The term "a biological age" could refer to the overall biological age of the subject, to the biological age of a particular system, organ or tissue of that subject, or to some combination of the foregoing. More preferably, the agents of the present cannot only reduce the rate of increase of a biological age of the subject, but can actually reduce a biological age of the subject .

A simple biologic marker (biomarker) is a single biochemical, cellular, structural or functional indicator of an event in a biologic system or sample. A composite biomarker is a mathematical combination of two or more simple biomarkers. (Chronological age may be one of the components of a composite biomarker.) A plausible biomarker of biological age would be a biomarker which shows a cross-sectional and/or longitudinal correlation with chronological age. Nakamura suggests that it is desirable that a biomarker show (a) significant cross- sectional correlation with chronological age, (b) significant longitudinal change in the same direction as the cross-sectional correlation, (c) significant stability of individual differences, and (d) rate of age-related change proportional to differences in life span among related species. Cp. Nakamura, Exp Gerontol . 29(2):151-77 (1994), using desiderata (a) - (c) . A superior biomarker of biological age would be a better predictor of lifespan than is chronological age (preferably for a chronological age at which 90% of the population is still alive) . The biomarker preferably also satisfies one or more of the following desiderata: a statistically significant age- related change is apparent in humans after a period of at most a few years; not affected dramatically by physical conditioning (e.g., exercise), diet, and drug therapy (unless it is possible to discount these confounding influences, e.g., by reference to a second marker which measures them) ; can be tested repeatedly without harming the subject; works in lab animals as well as humans; simple and inexpensive to use; does not alter the result of subsequent tests for other biomarkers if it is to be used in conjunction with them; monitors a basic process that underlies the aging process, not the effects of disease. Preferably, if the biomarker works in lab animals, there is a statistically significant difference in the value of the biomarker between groups of food-restricted and normally-fed animals. It has been shown in some mammalian species that dietary restriction without malnutrition (e.g., caloric decrease of up to 40% from ad libitum feeding) increases lifespan. A biomarker of aging may be used to predict, instead of lifespan, the "Healthy Active Life Expectancy" (HALE) or the "Quality Adjusted Life Years" (QALY) , or a similar measure which takes into account the quality of life before death as well as the time of death itself. For HALE, see Jagger, in Outcomes Assessment for Heal thcare in Elderly People, 67-76 (Farrand Press: 1997) . For QALY, see Rosser RM. A health index and output measure, in Stewart SR and Rosser RM (eds) Quality of Life: Assessment and Application. Lancaster: MTP, 1988. A biomarker of aging may be used to predict, instead of lifespan, the timing and/or severity of a change in one or more age-related phenotypes as described below. A biomarker of aging may be used to estimate, rather than overall biological age for a subject, a biological age for a specific body system or organ. The determination of the biological age of the muscle, and the inhibition of biological aging of the muscle, are of particular interest. Body systems include the nervous system (including the brain, the sensory organs, and the sense receptors of the skin) , the cardiovascular system (includes the heart, the red blood cells and the reticuloendothelial system) , the respiratory system, the gastrointestinal system, the endocrine system (pituitary, thyroid, parathyroid and adrenal glands, gonads, pancreas,^' and parganglia) , the musculoskeletal system, the urinary system (kidneys, bladder, ureters, urethra) , the reproductive system and the immune system (bone marrow, thymus, lymph nodes, spleen, lymphoid tissue, white blood cells, and immunoglobulins) . A biomarker may be useful in estimating the biological age of a system because the biomarker is a chemical produced by that system, because it is a chemical whose activity is primarily exerted within that system, because it is indicative of the morphological character or functional activity of that system, etc. A given biomarker may be thus associated with more than one system. In a like manner, a biomarker may be associated with the biological age, and hence the state, of a particular organ or tissue. The prediction of lifespan, or of duration of system or organ function at or above a particular desired level, may require knowledge of the value of at least one biomarker of aging at two or more times, adequately spaced, rather than of the value at a single time. See McClearn, Biomarkers of Age and Aging, Exp. Gerontol . , 32:87-94 (1997). The levels (or changes in levels) of the human proteins identified in this specification, and their corresponding mRNAs, may be used as simple biomarkers (direct or inverse) of biological aging. They may be used in conjunction with each other, or other simple biomarkers, in a composite biomarker . Once several plausible simple biomarkers have been identified, a composite biomarker may be obtained by standard mathematical techniques, such as multiple regression, principal component analysis, cluster analysis, neural net analysis, and so forth. As a preliminary to such analysis, the values may be standardized, e.g., by converting the raw scores into z-scores based on the distributions for each simple biomarker. For example, principal component analysis can be used to analyze the variation of lifespan with different observables, and the factor score coefficients from the first principal component can be used to derive an equation for estimating a biological age score. Nakamura, Exp Gerontol. 29(2):151-77 (1994). This approach was used to obtain the following BAS (for healthy Japanese women aged 28-80): BAS=-4.37 -0.998FEV_!.,, +0.022SBP +0.133MCH +0.018GLU -1.505 A/G RATIO, where FEV_1-0 is the forced expiratory volume in 1 sec. (Liters), SBP is the systolic blood pressure (mm Hg) , MCH is the mean corpuscular hemoglobin (pg) , GLU is glucose ( g/dl) , and A/G RATIO is the ratio of albumin to globulin. The relative importance of these five biomarkers was 33.7%, 25.1%, 17.1%, 14.8% and 8.9%, respectively. Ueno, et al . , "Biomarkers of Aging in Women and the Rate of Longitudinal Changes," J. Physiol. Anthropol. 22(1): 37-46 (Jan. 2003). It should be noted that particularly when evaluating the overall biological age of the subject, it is not necessarily most desirable to weight all systems or all organs equally. One may find it more desirable to give greater weight to the system or organ with the highest biological age in calculating the overall biological age, because it is presumably more likely to deteriorate or fail, resulting in death. Appropriate statistical analysis can be used to find the weighting scheme resulting in the best prediction of lifespan.

In the H-SCAN (Hoch Company) test, a composite of 12 simple biomarkers is used to measure human aging:

SENSORY

1 . Highest audible pitch (kHz)

2 . Visual accommodation (diopters)

3 . Vibrotactile sensitivity (dB)

MOTOR

4. Muscle Movement time (sec)

5. Muscle Movement time with decision (sec)

6. Alternate button tapping time (sec)

COGNITIVE

7. Memory, length of sequence

8. Auditory reaction time (sec)

9. Visual reaction time (sec)

10. Visual Reaction time with decision (sec)

PULMONARY

11. Forced vital capacity (liters)

12. Forced expiratory Volume- 1 sec (liters)

See Hochschild, R. , Journal of Gerontology [Biological Science] 45 (6) :B187-214 ; 1990).

According to a website discussing the H-SCAN test, "Biomarkers of aging are characteristics of an organism that correlate in large groups with chronological age and mortality. Of particular value in human applications are biomarkers of aging that also correlate with the quality of life in later life in the sense that they involve functions that are crucial to carrying out the activities of daily living.... A single biomarker of aging is limited by the fact that it measures only one isolated characteristic and is hardly representative of the diversity of functional and structural concomitants of aging.... Biological age, in contrast to chronological age, is an individual's hypothetical age calculated from scores obtained on a battery of tests of biomarkers of aging. As a first step in the calculation, the age of which each biomarker score is typical is determined by comparison with scores obtained by a large representative group of persons (or organisms) spanning a range of ages . Then one of a variety of averaging techniques is employed (optionally with standardization steps) to obtain a single index of age, as described in detail by Hochschild. This index varies with, and therefore must be expressed with reference to, the measured biomarkers and the mathematical method of combining scores." http: //www. longevitvinstituteone.com/

Abbo, USP 6,547,729 teaches determining the biological age (he calls it "performance age") of a subject by (1) for a sample population, determining a regression curve relating some set of observed values for an "indicator" of the functionality of a bodily system to the chronological age of the observed individuals, (2) solving the regression equation to obtain a predicted performance age, given the value of the indicator for the subject. The regression can be based on more than one indicator, i.e., it can be a multiple regression. The sample population can be defined by sex, age range, ethnic composition, and geographic location. The bodily system may be a molecular, cellular, tissue or organ system. The following indicators are suggested by Abbo: nervous system (memory tests, reaction time, serial key tapping, digit recall test, letter fluency, category fluency, nerve conduction velocity) , arteries (pulse wave velocity; ankle-brachial index) , skeletal system (bone mineral density) ; lungs (forced vital capacity) , heart (ejection fraction; length of time completed on a treadmill stress test) , kidneys (creatinine clearance) , proteins (glycosylation of hemoglobin) , endocrine glands (load level of bioactive testosterone; level of dehydroepiandrosterone sulfate, ratio of urinary 17-ketosteroids/l7- hydroxycorticosteroids; growth hormone; IGF-1) .

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Preferably, the agents of the invention have a favorable effect on the value of at least one simple biomarker of biological aging, such as any of the plausible biomarkers mentioned anywhere in this specification, other than the level of one of the proteins of the present . invention. More preferably, they have a favorable effect on the value of at least two such simple biomarkers of biological aging. Even more preferably, at least one such pair is of markers which are substantially non-correlated (R² < 0.5) .

Desirably, if more than one simple biomarker is favorably affected, the biomarkers in question reflect different levels of organization, and/or different body components at the same level of organization. For example, a visual reaction time with decision test is on the whole organism level, while a measurement of telomere length is on the cellular level .

A biomarker may, but need not, be an indicator related to one of the postulated causes or contributing factors of aging. It may, but need not, be an indicator of the acute health of a particular body system or organ.

A biomarker may measure behavior, cognitive or sensory function, or motor activity, or some combination thereof. It may measure the level of a type of cell (e.g., a T cell subset, such as CD4, CD4 memory, CD4 naive, and CD4 cells expressing P-glycoprotein) or of a particular molecule (e.g., growth hormone, IGF-1, insulin, DHEAS, an elongation factor, melatonin) or family of structurally or functionally related molecules in a particular body fluid (especially blood) or tissue. For example, lower serum IGF-1 levels are correlated with increasing age, and IGF-1 is produced by many different tissues . On the other hand, growth hormone is produced by the pituitary gland. A biomarker may measure an indicator of stress (particularly oxidative stress) and resistance thereto. It has been theorized that free radicals damage biomolecules, leading to aging. A biomarker may measure protein glycation or other protein modification (e.g., collagen crosslinking) . It has been theorized that such modifications contribute to aging. •

The biomarker may measure changes in the lengths of telomeres or in the rate of cell division. It has been theorized that telomere shortening beyond a critical length leads the cell to stop proliferating. Average telomere length therefore provides a biomarker as to how may divisions the cell as previously undergone and how many divisions the cell can undergo in the future. Suggested biomarkers have also included resting heart rate, resting blood pressure, exercise heart rate, percent body fat, flexibility, grip strength, push strength, abdominal strength, body temperature, and skin temperature. The present invention does not require that all of the biomarkers identified above be validated as indicative of biological age, or that they be equally useful as measures of biological age.

There is an overlap between biomarkers of aging and indicators of functional status. An indicator of functional status is an indicator that defines a functional ability (e.g., physiological, cognitive or physical function). An indicator of functional status may also be related to the increase in morbidity and mortality with chronological age. Such indicators preferably predict physiological, cognitive and physical function in an age-coherent way, and do so better than chronological age. Preferably, they can predict the years of remaining functionality, and the trajectory toward organ-specific illness in the individual. Also, they are preferably minimally invasive. Suggested indicators include anthropometric data (body mass index, body composition, bone density, etc.), functional challenge tests (glucose tolerance, forced vital capacity) , physiological tests (cholesterol/HDL, glycosylated hemoglobin, homocysteine, etc.) and proteomic tests.

A number of mouse models for human aging exist. See Troen, supra, Table 3. The drugs identified by the present invention may be further screened in one or more of these models.

Age-Related Phenotype An age-related phenotype is an observable change which occurs with age. An age-related phenotype may, but need not, also be a biomarker of biological aging.

Preferably, the agent of the present invention favorably affects at least one age-related phenotype. More preferably, it favorably affects at least two age-related phenotypes, more preferably phenotypes of at least two different body systems .

The age-related phenotype may be a system level phenotype, such as a measure of the condition of the nervous system, respiratory system, immune system, circulatory system, endocrine system, reproductive system, gastrointestinal system, or musculoskeletal system. The age-related phenotype may be an organ level phenotype, such as a measure of the condition. of the brain, eyes, ears, lungs, spleen, heart, pancreas, liver, ovaries, testicles, thyroid, prostate, stomach, intestines, or kidney.

The age-related phenotype may be a tissue level phenotype, such as a measure of the condition of the muscle, skin, connective tissue, nerves, or bones.

The age-related phenotype may be a cellular level phenotype, such as a measure of the condition of the cell wall, mitochondria or chromosomes .

The age-related phenotype may be a molecular level phenotype, such as a measure of the condition of nucleic acids, lipids, proteins, oxidants, and anti-oxidants.

The age-related phenotype may be manifested in a biological fluid, such as blood, urine, saliva, lymphatic fluid or cerebrospinal fluid. The biochemical composition of these fluid may be an overall, system level, organ level, tissue level, etc. phenotype, depending on the specific biochemical and fluid involved.

PHYSIOLOGICAL AGING OF THE HUMAN BODY BY SYSTEMS SKIN, HAIR, Loss of subcutaneous fat, Thinning of skin, NAILS Decreased collagen, Nails brittle and flake, Mucous membranes drier, Less sweat glands, Temperature regulation difficult, Hair pigment decreases, Hair thins. Eyelids baggy and wrinkled. EYES AND Eyes deeper in sockets; Conjunctiva thinner VISION and yellow; Quantity of tears decreases; Iris fades; Pupils smaller, let in less light; Night and depth vision less; "Floaters" can appear Lens enlarges; Lens becomes less

Adapted from htt : //ww . texashste .com/html/qer_papl .ppt

The Aging Liver The aging human liver appears to preserve its morphology and function relatively well. The liver appears to progressively decrease in both mass and volume. It also appears browner (a condition called "brown atrophy") , as a result of accumulation of lipofuscin (ceroid) within hepatocytes . Increases occur in the number of macrohepatocytes, and in polyploidy, especially around the terminal hepatic veins. The number of mitochondria declines, and both the rough and smooth endoplasmic recticulum diminish. The number of lysozymes increase. The liver is the premiere metabolic organ of the body. With regard to metabolism, hepatic glycerides and cholesterol levels increase with age, at least up to age 90. On the other hand, phospholipids, aminotransferases, and serum bilirubin appear to remain normal. There are contradictory reports as to the effect of aging on albumin, serum gamma-glutamyltransferase, and hepatic alkaline phosphatase. It is worth noting that it has been shown that the content of cytochrome oxidase exhibits a progressive decline which correlates with age-associated decline in mtRNA synthesis in brain, liver, heart, lungs and skeletal muscle. See generally Anaantharaju, Feller and Chedid, "Aging Liver: A Review," Gerontology, 48: 343-53 (2002).

Aging Skeletal Muscle

Aging affects human skeletal muscle in a number of ways. One of the principal changes in muscle function is that the force-generating capacity (strength) of the muscles is reduced. This, in turn, can lead to problems in performing normal daily activities.

This loss of strength, in turn, is at least in part attributable to muscle atrophy, and alterations in the percentage of contractile tissue within muscle. The atrophy can be characterized as a decrease in the cross- sectional area of the muscle (sarcopenia) . Sarcopenia can result from reductions in fiber size and/or fiber number; the latter appears to be the more important of the two. Also, it appears that the number of both type I (slow) and type II (fast) fibers is reduced, although the changes in the individual fibers are more pronounced in the case of type II fibers. The effects of aging on skeletal muscle may be determined, inter alia, by measurements on whole muscle, or on individual muscle fibers .

Older people have fewer motor units, but this is usually compensated for through increases in the size of the remaining motor units . There is a difference of opinion as to the effect of age on MU firing rates. They may decrease with age, or they may simply become more variable.

Muscle mass also decreases with age. The muscle mass is determined by the relative rates of protein synthesis and breakdown, and it appears that with age, the rate of synthesis of at least some muscle proteins declines. The percentage of muscle mass which is contractile tissue also decreases with age. (Non-contractile tissue includes, e.g., connective tissue) .

There may also be a reduction in intrinsic muscle function (the mechanisms by which a given mass of muscles produces force) , perhaps as a result, at least in part, of an alteration in the sarcoplasmic reticulum.

Muscle performance may be a function of changes, not only in the muscle per se, but also other systems, such as the nervous and circulatory systems. However, Olive et al . did not observe age-related changes in maximal blood flow capacity after exercise, in resting blood flow, or in resting vascular diameter.

For more particulars, see Williams, GN, Higgins, MJ, Lewek, MD, "Aging Skeletal Muscle: Physiologic Changes and the effects of Training, " Physical Therapy 82: 62-68 (2002); Larson L and Ramamurthy B, "Aging-Related Changes in Skeletal Muscle: Mechanisms and Interventions, Drugs and Aging 17: 303-16 (2000); ; Olive et al . , "The effect of aging and activity on muscle blood flow," Dyn. Med. 1(1): 2 (Dec. 19, 2002) .

It is within the contemplation of the invention to address one or more of these age-related changes in skeletal muscle, especially when the "favorable" or "unfavorable" gene/protein in question is one differentially expressed in skeletal muscle as a consequence of age.

Quality of Life

Clinicians are interested, not only in simple prolongation of lifespan, but also in maintenance of a high quality of life (QOL) over as much as possible of that lifespan. QOL can be defined subjectively in terms of the subject's satisfaction with life, or objectively in terms of the subject's physical and mental ability (but not necessarily willingness) to engage in "valued activities", such as those which are pleasurable or financially rewarding.

Flanagan has defined five domains of QOL, capturing 15 dimensions of life quality. The five domains, and their component dimensions, are physical and material well being (Material well-being and financial security; Health and personal safety) , Relations with other people (relations with spouse; Having and rearing children; Relations with parents, siblings, or other relatives ; Relations with friends) Social, community, civic activities (Helping and encouraging others; Participating in local and governmental affairs ) , Personal development, fulfillment (Intellectual development; Understanding and planning; Occupational role career; Creativity and personal expression) , and recreation (Socializing with others; Passive and observational recreational activities; Participating in active recreation) . See Flanagan JC, . "A research approach to improving our quality of life." Am Psychol 33:138-147 (1978).

"Health-related quality of life" (HRQL or HRQOL) is an individual's satisfaction or happiness with domains of life insofar as they affect or are affected by "health" .

In a preferred embodiment, a pharmaceutical agent of the present invention is able to achieve a statistically significant improvement in the expected quality of life, measured according to a commonly accepted measure of QOL, in a treatment group over a control group.

While there is general acceptance of the notion that QOL is important, quantifying QOL is not especially straightforward. Also, QOL can only be measured in humans. Measurements of QOL can be objective (e.g., employment status, marital status, home ownership) or subjective (the subject's opinion of his or her life) , or some combination of the two .

A simple approach to measuring subjective QOL is to simply have the subjects rate their overall quality of life on a scale, e.g., of 7 points. One can also use more elaborate measure, such as the Older Adult Health and Mood Questionaire (a 22 item test for assessing depression) . Objective QOL can be measured by, e.g., an activities checklist .

There is a relationship between QOL assessment and so-called ADL or IADL measures, which assess the need for assistance. The Katz Index of Independence in Activities of Daily Living (Katz ADL) measures adequacy of independent performance of bathing, dressing, toileting, transferring, continence, and feeding. See Katz, S., "Assessing Self-Maintenance : Activities of Daily Living, Mobility and Instrumental Activities of Daily Living, Journal of the American Geriatrics Society, 31(12); 721-726 (1983); Katz S., Down, T.D. , Cash, H.R. et al . Progress in the Development of the Index of ADL. Gerontologist, 10 :20-30 (1970).

Performance of a more sophisticated nature is measured by the "Instrumental Activities of Daily Living" (IADL) scale. This inquires into ability to independently use the telephone, shop, prepare food, carry out housekeeping, do laundry, travel locally, take medication and handle finances. See Lawton, MP and Brody, EM, Gerontologist, 9:179-86 (1969) .

The 36 question Medical Outcomes Study Short Form (SF-36) (Medical Outcomes Trust, Inc., 20 Park Plaza, Suite 1014, Boston, Massachusetts 02116) assesses eight health concepts: 1) limitations in physical activities because of health problems; 2) limitations in social activities because of physical or emotional problems; 3) limitations in usual role activities because of physical health problems; 4) bodily pain; 5) general mental health (psychological distress and well-being) ; 6) limitations in usual role activities because of emotional problems; 7) vitality (energy and fatigue); and 8) general health perceptions.

A low score on an ADL, IADL or SF-36 test is likely to be associated with a low QOL, but a high score does not guarantee a high QOL because these tests do not explore performance of "valued activities", only of more basic activities. Nonetheless, these tests can be considered commonly accepted measures of QOL for the purpose of this invention.

Age-Related Diseases

Age-related (senescent) diseases include certain cancers, atherosclerosis, diabetes (type 2) , osteoporosis, hypertension, depression, Alzheimer's, Parkinson's, glaucoma, certain immune system defects, kidney failure, and liver steatosis. In general, they are diseases for which the relative risk (comparing a subpopulation over age 55 to a suitably matched population under age 55) is at least 1.1. Preferably, the agents of the present invention protect against one or more age-related diseases for at least a subpopulation of mature (post-puberty) adult subjects.

Diabetes Type II diabetes is of particular interest. A deficiency of insulin in the body results in diabetes mellitus, which affects about 18 million individuals in the United States. It is characterized by a high blood glucose (sugar) level and glucose spilling into the urine due to a deficiency of insulin. As more glucose concentrates in the urine, more water is excreted, resulting in extreme thirst, rapid weight loss, drowsiness, fatigue, and possibly dehydration. Because the cells of the diabetic cannot use glucose for fuel, the body uses stored protein and fat for energy, which leads to a buildup of acid (acidosis) in the blood. If this condition is prolonged, the person can fall into a diabetic coma, characterized by deep labored breathing and fruity-odored breath. There are two types of diabetes mellitus, Type I and Type II. Type II diabetes is the predominant form found in the Western world; fewer than 8% of diabetic Americans have the type I disease.

Type I diabetes . In Type I diabetes, formerly called juvenile-onset or insulin-dependent diabetes mellitus, the pancreas cannot produce insulin. People with Type I diabetes must have daily insulin injections. But they need to avoid taking too much insulin because that can lead to insulin shock, which begins with a mild hunger. This is quickly followed by sweating, shallow breathing, dizziness, palpitations, trembling, and mental confusion. As the blood sugar falls, the body tries to compensate by breaking down fat and protein to make more sugar. Eventually, low blood sugar leads to a decrease in the sugar supply to the brain, resulting in a loss of consciousness. Eating a sugary food can prevent insulin shock until appropriate medical measures can be taken. Type I diabetics are often characterized by their low or absent levels of circulating endogenous insulin, i.e., hypoinsulinemia (1) . Islet cell antibodies causing damage to the pancreas are frequently present at diagnosis. Injection of exogenous insulin is required to prevent ketosis and sustain life.

Type II diabetes . Type II diabetes, formerly called adult-onset or non-insulin-dependent diabetes mellitus (NIDDM) , can occur at any age . The pancreas can produce insulin, but the cells do not respond to it . Type II diabetes is a metabolic disorder that affects approximately 17 million Americans. It is estimated that another 10 million individuals are "prone" to becoming diabetic. These vulnerable individuals can become resistant to insulin, a pancreatic hormone that signals glucose (blood sugar) uptake by fat and muscle. In order to maintain normal glucose levels, the islet cells of the pancreas produce more insulin, resulting in a condition called hyperinsulinemi . When the pancreas can no longer produce enough insulin to compensate for the insulin resistance, and thereby maintain normal glucose levels, hyperglycemia (elevated blood glucose) results, and type II diabetes is diagnosed. Eariy Type II diabetics are often characterized by hyperinsulinemia and resistance to insulin. Late Type II diabetics may be nor oinsulinemic or hypoinsulinemic. Type II diabetics are usually not insulin dependent or prone to ketosis under normal circumstances. Little is known about the disease progression from the normoinsulinemic state to the hyperinsulinemic state, and from the hyperinsulinemic state to the Type II diabetic state . As stated above, type II diabetes is a metabolic disorder that is characterized by insulin resistance and impaired glucose-stimulated insulin secretion (2,3,4). However, Type II diabetes and atherosclerotic disease are viewed as consequences of having the insulin resistance syndrome (IRS) for many years (5) . The current theory of the pathogenesis of Type II diabetes is often referred to as the "insulin resistance/islet cell exhaustion" theory. According to this theory, a condition causing insulin resistance compels the pancreatic islet cells to hypersecrete insulin in order to maintain glucose homeostasis. However, after many years of hypersecretion, the islet cells eventually fail and the symptoms of clinical diabetes are manifested. Therefore, this theory implies that, at some point, peripheral hyperinsulinemia will be an antecedent of Type II diabetes. Peripheral hyperinsulinemia can be viewed as the difference between what is produced by the beta cell minus that which is taken up by the liver. Therefore, peripheral hyperinsulinemia can be caused by increased beta cell production, decreased hepatic uptake or some combination of both. It is also important to note that it is not possible to determine the origin of insulin resistance once it is established since the onset of peripheral hyperinsulinemia leads to a condition of global insulin resistance. Multiple environmental and genetic factors are involved in the development of insulin resistance, hyperinsulinemia and type II diabetes. An important risk factor for the development of insulin resistance, hyperinsulinemia and type II diabetes is obesity, particularly visceral obesity (6,7,8). Type II diabetes exists world-wide, but in developed societies, the prevalence has risen as the average age of the population increases and the average individual becomes more obese .

Role of Muscle in Development of Type II Diabetes Muscle, fat and liver tissues are the major contributors to the development of insulin resistance, hyperinsulinemia, and, ultimately, type II diabetes. Muscle cells respond to insulin by increasing glucose uptake from the bloodstream. Muscle tissue can become resistant to insulin, causing the beta cells to initially increase insulin secretion. Eventually, though, the beta cells become "unable to compensate for this increasing insulin resistance from muscle and other cells, and they fail to respond to elevated blood glucose levels. Thus, clinical type 2 diabetes results from the combination- of insulin resistance and impaired beta cell function. Defects in muscle glycogen synthesis are known to play a role in the development of insulin resistance. At least three steps-those mediated by glycogen synthase, hexokinase, and GLUT4-have been reported to be defective in patients with type 2 diabetes . Fatty acids can induce insulin resistance, and it has been suggested that this was a consequence of altered insulin signaling through PI3-kinase. PKC-theata has also been implicated. See generally Petersen, et al . , "Pathogenesis of Skeletal muscle insulin resistance in type 2 diabetes mellitus", in "A Symposium: Evolution of type 2 diabetes mellitus management", at Amer. J. Cardiol . , 90 (5A) : 11G-18G, (Sept. 5, 2002) .

Adverse Effects of Type II Diabetes on Muscle "Myopathy is a general term used to describe any disease of muscles, such as the muscular dystrophies and myopathies associated with thyroid disease. It can be caused by endocrine disorders, including diabetes, metabolic disorders, infection or inflammation of the muscle, certain drugs and mutations in genes. In diabetes, myopathy is thought to be caused by neuropathy, a complication of diabetes . General symptoms of myopathies include muscle weakness of limbs sometimes occurring during exercise although in some cases the symptoms diminish as exercise increases. Depending on the type of myopathy, one muscle group may be more affected than others." See "Joint and Muscle Problems Associated with Diabetes", www, iddtinternational . org/ ointandmuscleproblems .html [Last modified June 12, 2003] .

Diabetic muscle infarction can spontaneously affect patients with a long history of poorly controlled diabetes. "Most affected patients have multiple microvascular complications (neuropathy, nephropathy, and retinopathy) . The clinical presentation is an acute onset of pain and swelling over days to weeks in the affected muscle groups (usually the thigh or calf) , along with varying degrees of tenderness.... Therapy consists of rest and analgesia. Routine daily activities are not deleterious to the condition, but physical therapy may cause exacerbation. Spontaneous diabetic muscle infarction tends to resolve over a period of weeks to months in most cases." See "Musculoskeletal Complications of Diabetes - Part 2", www.diabetic-lifestyle.com/articles/i n02_whats_l .htm [last modified Feb. 9, 2004]. See also Trujillo-Santos, et al . , "Diabetes muscle infarction: an underdiagnosed complication of long-standing diabetes," Diabetes Care, 26(l):211-5 (2003) .

Diseases Characterized by Accelerated Aging Several human diseases display some features of accelerated aging. These include Werner's syndrome (classic early-onset progeria) , Hutchinson-Gilford syndrome (adult progeria) , and Down's syndrome (trisomy 21) . Troen, Biology of Aging, Mt . Sinai J. Med., 70(1): 3 (Jan. 2003). Thus, the present invention may be useful in the treatment (curative or ameliorative) of individuals with these diseases .

Direct and Indirect Utility of Identified Nucleic Acid Sequences and Related Molecules The identified mouse or human genes may be used directly. For diagnostic or screening purposes, they (or specific binding fragments thereof) may be labeled and used as hybridization probes. For therapeutic purposes, they (or specific binding fragments thereof) may be used as antisense reagents to inhibit the expression of the corresponding gene, or of a sufficiently homologous gene of another species . If the database DNA appears to be a full-length cDNA or gDNA, that is, that it encodes an entire, functional, naturally occurring protein, then it may be used in the expression of that protein. Such expression may be in cell culture, with the protein subsequently isolated and administered exogenously to subjects who would benefit therefrom, or in vivo, i.e., administration by gene therapy. Naturally, any DNA encoding the same protein may be used fr the same purpose, and a DNA encoding a protein which a fragment or a mutant of that naturally occurring protein which retains the desired activity, may be used for the purpose of producing the active fragment or mutant. The encoded protein of course has utility therapeutically and, in labeled or immobilized form, diagnostically.

The genes may also be used indirectly, that is, to identify other useful DNAs, proteins, or other molecules. We have attempted to determine whether the mouse genes disclosed herein have significant similarity to any known human DNA, and whether, in any of the six possible combinations of reference frame and strand, they encode a protein similar to a known human protein. If so, then it follows that the known human protein, and DNAs encoding that protein, may be used in a similar manner. In addition, if the known human protein is known to have additional homologues, then those homologous proteins, and DNAs encoding them, may be used in a similar manner. There thus are several ways that a human protein homologue of interest can be identified by database searching, including but not limited to:

1) a DNA->DNA (BlastN) search for human database DNAs closely related to the mouse gene identifies a known human gene, and the sequence of the human protein is deduced by the Genetic Code;

2) a DNA->Protein (BlastX) search for human database proteins closely related to the translated DNA of the mouse gene identifies a known human protein; and

3) the sequence of the mouse protein is known or deduced by the Genetic Code, and a Protein->Protein (BlastP) search for closely related database proteins identifies a known human protein.

Once a known human gene is identified, it may be used in further BlastN or BlastX searches to identify other human genes or proteins . Once a known human protein is identified, it may be used in further BlastP searches to identify other human proteins. Searches may also take cognizance, intermediately, of known genes and proteins other than mouse or human ones, e.g., use the mouse sequence to identify a known rat sequence and then the rat sequence to identify a human one.

If we have identified a mouse gene, and it encodes a mouse protein which appears similar to a human protein, then that human protein may be used (especially in humans) for purposes analogous to the proposed use of the mouse protein in mice. Moreover, a specific binding fragment of an appropriate strand of the corresponding human gene (gDNA or cDNA) could be labeled and used as a hybridization probe (especially against samples of human mRNA or cDNA) . In determining whether the disclosed genes (gDNA or cDNA) have significant similarities to known DNAs (and their translated AA sequences to known proteins) , one would generally use the disclosed gene as a query sequence in a search of a sequence database. The results of several such searches are set forth in the Examples. Such results are dependent, to some degree, on the search parameters. Preferred parameters are set forth in Example 1. The results are also dependent on the content of the database. While the raw similarity score of a particular target (database) sequence will not vary with content (as long as it remains in the database) , its informational value (in bits), expected value, and relative ranking can change. Generally speaking, the changes are small.

It will be appreciated that the nucleic acid and protein databases keep growing. Hence a later search may identify high scoring target sequences which were not uncovered by an earlier search because the target sequences were not previously part of a database .

Hence, in a preferred embodiment, the cognate DNAs and proteins include not only those set forth in the examples, but those which would have been highly ranked (top ten, more preferably top three, even more preferably top two, most preferably the top one) in a search run with the same parameters on the date of filing of this application.

If the mouse or human database DNA appears to be a partial sequence (that is, partial relative to a cDNA or gDNA encoding the whole naturally occurring protein) , it may be used as a hybridization probe to isolate the full-length DNA. If the partial DNA sequence encodes a biologically functional fragment of the cognate protein, it may be used in a manner similar to the full length DNA, i.e., to produce the functional fragment .

If we have indicated that an antagonist of a protein or other molecule is useful, then such an antagonist may be obtained by preparing a combinatorial library, as described below, of potential antagonists, and screening the library members for binding to the protein or other molecule in question. The binding members may then be further screened for the ability to antagonize the biological activity of the target. The antagonists may be used therapeutically, or, in suitably labeled or immobilized form, diagnostically. If the mouse or human database DNA is related to a known protein, then substances known to interact with that protein (e.g., agonists, antagonists, substrates, receptors, second messengers, regulators, and so forth) , and binding molecules which bind them, are also of utility. Such binding molecules can likewise be identified by screening a combinatorial library.

Isolation of Full Length DNAs Using Partial DNAs as probes If it is determined that a DNA of the present invention is a partial DNA, and the cognate full length DNA is not listed in a sequence database, the available DNA may be used as a hybridization probe to isolate the full-length DNA from a suitable DNA library (cDNA or gDNA) . Stringent hybridization conditions are appropriate, that is, conditions in which the hybridization temperature is 5-10 deg. C. below the Tm of the DNA as a perfect duplex. Identification and Isolation of Homologous Genes Using a DNA Probe It may be that the sequence databases available do not include the sequence of any homologous gene (cDNA or gDNA) , or at least of the homologous gene for a species of interest. However, given the DNAs set forth above, one may readily obtain the homologous gene. The possession of one DNA (the "starting DNA") greatly facilitates the isolation of homologous DNAs. If the clone in question only features a partial DNA, this partial DNA may first be used as a probe to isolate the corresponding full length DNA for the same species, and that the latter may be used as the starting DNA in the search for homologous DNAs. The starting DNA, or a fragment thereof, is used as a hybridization probe to screen a cDNA or genomic DNA library for clones containing inserts which encode either the entire homologous protein, or a recognizable fragment thereof. The minimum length of the hybridization probe is dictated by the need for specificity. If the size of the library in bases is L, and the GC content is 50%, then the probe should have a length of at least 1, where L = 4¹. This will yield, on average, a single perfect match in random DNA of L bases. The human cDNA library is about 10^s bases and the human genomic DNA library is about 10^1Q bases. The library is preferably derived from an organism which is known, on biochemical evidence, to produce a homologous protein, and more preferably from the genomic DNA or mRNA of cells of that organism which are likely to be relatively high producers of that protein. A cDNA library (which is derived from an mRNA library) is especially preferred. If the organism in question is known to have substantially different codon preferences from that of the - organism whose relevant cDNA or genomic DNA is known, a synthetic hybridization probe may be used which encodes the same amino acid sequence but whose codon utilization is more similar to that of the DNA of the target organism. Alternatively, the synthetic probe may employ inosine as a substitute for those bases which are most likely to be divergent, or the probe may be a mixed probe which mixes the codons for the source DNA with the preferred codons (encoding the same amino acid) for the target organism. By routine methods, the Tm of a perfect duplex of starting DNA is determined. One may then select a hybridization temperature which is sufficiently lower than the perfect duplex Tm to allow hybridization of the starting DNA (or other probe) to a target DNA which is divergent from the starting DNA. A 1% sequence divergence typically lowers the Tm of a duplex by 1-2 °C, and the DNAs encoding homologous proteins of different species typically have sequence identities of around 50-80%. Preferably, the library is screened under conditions where the temperature is at least 20°C, more preferably at least 50°C, below the , perfect duplex Tm. Since salt reduces the Tm, one ordinarily would carry out the search for DNAs encoding highly homologous proteins under relatively low salt hybridization conditions, e.g., <1M NaCI. The higher the salt concentration, and/or the lower the temperature, the greater the sequence divergence which is tolerated. For the use of probes to identify homologous genes in other species, see, e.g., Schwinn, et al . , J. Biol. Chem., 265:8183-89 (1990) (hamster 67-bp cDNA probe vs. human leukocyte genomic library; human 0.32kb DNA probe vs. bovine brain cDNA library, both with hybridization at 42 °C in 6xSSC) ; Jenkins et al . , J. Biol. Chem., 265:19624-31 (1990) (Chicken 770-bp cDNA probe vs. human genomic libraries; hybridization at 40°C in 50% formamide and 5xSSC) ; Murata et al . , J . Exp . Med . , 175 : 341-51 (1992 ) ( 1 . 2 -kb mouse cDNA probe v. human eosinophil cDNA library; hybridization at

65°C in 6xSSC) ; Guyer et al . , J. Biol. Chem., 265:17307-17

(1990) (2.95-kb human genomic DNA probe vs. porcine genomic

DNA library; hybridization at 42 °C in 5xSSC) . The conditions set forth in these articles may each be considered suitable for the purpose of isolating homologous genes .

Corresponding (Homologous) Proteins and DNAs In the case of a gene chip, the manufacturer of the gene chip determines which DNA to place at each position on the chip. This DNA may correspond in sequence to a genomic DNA, a cDNA, or a fragment of genomic or cDNA, and may be natural, synthetic or partially natural and partially synthetic in origin. The manufacturer of the gene chip will normally identify the DNA for a mouse gene chip as corresponding to a particular mouse gene, in which case it will be assumed that the alignments of chip DNA to mouse gene satisfies the homology criteria of the invention. Usually, the gene chip manufacturer will provide a' sequence database accession number for the mouse DNA. If so, to identify the corresponding mouse protein, we will first inspect the database record for that mouse DNA. Often, the mouse protein accession number will appear in that record or in a linked record. If it doesn't, the corresponding mouse protein can be identified by performing a BlastX search on a mouse protein database with the mouse database DNA sequence as the query sequence. Even if the protein sequence is not in the database, if the DNA sequence comprises a full-length coding sequence, the corresponding protein can be identified by translating the coding sequence in accordance with the Genetic Code. A human protein can be said to be identifiable as corresponding (homologous) to a gene chip DNA if it is identified as corresponding (homologous) to the mouse gene (gDNA or cDNA, whole or partial) identified by the gene chip manufacturer as corresponding to that gene chip DNA.

In turn, it is identifiable as corresponding (homologous) to said identified mouse gene, if

(1) it can be aligned by BlastX directly to that mouse gene, and/or

(2) it is encoded by a human gene, or can be aligned to a human gene by BlastX, which in turn can be aligned by BlastN to said mouse gene and/or

(3) it can be aligned by BlastP to a mouse protein, the latter being encoded by said mouse gene, or aligned to said mouse gene BlastX,

where any alignment by BlastN, BlastP or BlastX is in accordance with the default parameters set forth below, and the expected. value (E) of each alignment (the probability that such an alignment would have occurred by chance alone) is less than e-10. (Note that because this is a negative exponent, a value such as e-50 is less than e-10.)

Desirably, two or all three of these conditions (l)-(3) are satisfied for the corresponding (homologous) human genes and proteins.

A human gene is corresponding (homologous) to a mouse gene chip DNA, and hence to said identified mouse gene (or cDNA) and protein, if it encodes a corresponding (homologous), human protein as defined above, or it can be aligned by BlastN to said mouse gene. Preferably, for at least one of conditions (1) - (3) , the E value is less than e-50, more preferably less than e-60, still more preferably less than e-70, even more preferably less than e-80, considerably more preferably less than e-90, and most preferably less than e-100. Desirably, it is true for two or even all three of these conditions.

In constructing Master table 1, we generally used a BlastX (mouse gene vs. human protein) alignment E value cutoff of e-50. However, if there were no human proteins with that good an alignment to the mouse DNA in question, or if there were other reasons for including a particular human protein (e.g., a known functionality supportive of the observed differential cognate mouse protein expression) , then a human protein with a score worse (i.e., higher) than e-50 may appear in Master Table 1.

If the manufacturer of the gene chip identifies the gene chip DNA as corresponding to an EST, or other DNA which is not a full-length mouse gene or cDNA, a longer (possibly full length) mouse gene or cDNA may be identified by a BlastN search of the mouse DNA database. Alternatively, the identified DNA may be used to conduct a BlastN search of a human DNA database, or a BlastX search of a mouse or human protein database . Thus, more generally, a human protein can be said to be identifiable as corresponding (homologous) to a gene chip DNA, or to a DNA identified by the manufacturer as corresponding to that gene chip DNA, if

(1') it can be aligned directly to the gene chip or corresponding manufacturer identified DNA by BlastX. and/or (2') it can be aligned to a human gene/cDNA by BlastX, whose genomic DNA (gDNA) or cDNA (DNA complementary to messenger RNA) in turn can be aligned to the gene chip or corresponding manufacturer identified DNA by BlastN, and/or

(3') it can be aligned to a mouse gene/cDNA by BlastX, whose gDNA or cDNA in turn can be aligned to the gene chip or corresponding manufacturer identified DNA by BlastN, and/or

(4') it can be aligned to a mouse protein- by BlastP, which in turn can be aligned to the gene chip or corresponding manufacturer identified DNA by BlastX, and/or

(5¹) it can be aligned to a mouse protein by BlastP, which in turn can be aligned to a mouse gene/cDNA by BlastX, whose gDNA or cDNA can in turn be aligned to the gene chip or corresponding manufacturer identified DNA by BlastN;

where any alignment by BlastN, BlastP, or BlastX is in accordance with the default parameters set forth below, and the expected value (E) of each alignment (the probability that such an alignment would have occurred by chance alone) is less than e-10. (Note that because this is a negative exponent, a value such as e-50 is less than e-10.).

Preferably, two, three, four or all five of conditions (l')-(5') are satisfied. Preferably, for at least one of conditions (l')-(5'), for at least the final alignment (i.e., vs. the human protein), the E value is less than e-50, more preferably less than e-60, , still more preferably less than e-70, even more preferably less than e-80, considerably more preferably less than e-90, and most preferably less than e-100. Desirably, one or more of these standards of preference are met for two, three, four or all five of conditions (1')- (5') . In particular, for those conditions in which the gene chip or corresponding manufacturer identified DNA is indirectly connected to the human protein by virtue of two or more successive alignments, the E value is preferably, so limited for all of said alignments in the connecting chain.

A human gene corresponds (is homologous) to a gene chip DNA or manufacturer identified corresponding DNA if it encodes a homologous human protein as defined above, or if it can be aligned either directly to that DNA, or indirectly through a mouse gene which can be aligned to said DNA, according to the conditions set forth above .

Master table 1 assembles a list of human protein corresponding to each of the mouse DNAs/proteins identified as related to the chip DNA. These human proteins form a set and can be given a percentile rank, with respect to E value, within that set . The human proteins of the present invention preferably are those scorers with a percentile rank of at least 50%, more preferably at least 60%, still more preferably at least 70%, even more preferably at least 80%, and most preferably at least 90%.

For each mouse gene/cDNA in Master Table 1, there is a particular human protein which provides the best alignment match as measured by BlastX, i.e., the human protein with the best score (lowest e-value) . These human proteins form a subset of the set above and can be given a percentile rank within that subset, e.g., the human proteins with scores in the top 10% of that subset have a percentile rank of 90% or higher. The human proteins of the present invention preferably are those best scorer subset proteins with a percentile rank within the subset of at least 50%, more preferably at least 60%, still more preferably at least 70%, even more preferably at least 80%, and most preferably at least 90%.

BlastN and BlastX report very low expected values as "0.0". This does not truly mean that the expected value is exactly zero (since any alignment could occur by chance) , but merely that it is so infinitesimal that it is not reported. The documentation does not state the cutoff value, but alignments with explicit E values as low as e-178 (624 bits) have been reported as nonzero values, while a score of 636 bits was reported as "0.0".

Functionally homologous human proteins are also of interest . A human protein may be said to be functionally homologous to the mouse gene if the human protein has at least one biological activity in common with the mouse protein encoded by said mouse gene . The human proteins of interest also include those that are substantially and/or conservatively identical (as defined below) to the homologous and/or functionally homologous human proteins defined above.

Degree of Differential Expression The degree of differential expression may be expressed as the ratio of the higher expression level to the lower expression level. Preferably, this is at least 2-fold, and more preferably, it is higher, such as at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7- fold, at least 8-fold, at least 9-fold, or at least 10-fold. Most preferably, the human protein of interest corresponds to a mouse gene for which the degree of differential expression places it among the top 10% of the mouse genes in the appropriate subtable .

Relevance of Favorable and Unfavorable Genes If a gene is down-regulated in more favored mammals, or up-regulated in less favored mammals, (i.e., an "unfavorable gene") then several utilities are apparent. First, the complementary strand of the gene, or a portion thereof, may be used in labeled form as a hybridization probe to detect messenger RNA and thereby monitor the level of expression of the gene in a subject. Elevated levels are indicative of progression, or propensity to progression, to a less favored state, and clinicians may take appropriate preventative, curative or ameliorative action. Secondly, the messenger RNA product (or equivalent cDNA) , the protein product, or a binding molecule specific for that product (e.g., an antibody which binds the product) , or a downstream product which mediates the activity (e.g., a signaling intermediate) or a binding molecule (e.g., an antibody) therefor, may be used, preferably in labeled or immobilized form, as an assay reagent in an assay for said nucleic acid product, protein product, or downstream product (e.g., a signaling intermediate) . Again, elevated levels are indicative of a present or future problem. Thirdly, an agent which down-regulates expression of the gene may be used to reduce levels of the corresponding protein and thereby inhibit further damage. This agent could inhibit transcription of the gene in the subject, or translation of the corresponding messenger RNA. Possible inhibitors of transcription and translation include antisense molecules and repressor molecules. The agent could also inhibit a post-translational modification (e.g., glycosylation, phosphorylation, cleavage, GPI attachment) required for activity, or post-translationally modify the protein so as to inactivate it. Or it could be an agent which down- or up-regulated a positive or negative regulatory gene, respectively. Fourthly, an agent which is an antagonist of the messenger RNA product or protein product of the gene, or of a downstream product through which its activity is manifested (e.g., a signaling intermediate), may be used to inhibit its activity. This antagonist could be an antibody, a peptide, a peptoid, a nucleic acid, a peptide nucleic acid (PNA) oligomer, a small organic molecule of a .kind for which a combinatorial library exists (e.g., a benzodiazepine) , etc. An antagonist is simply a binding molecule which, by binding, reduces or abolishes the undesired activity of its target. The antagonist, if not an oligomeric molecule, is preferably less than 1000 daltons, more preferably less than 500 daltons. Fifthly, an agent which degrades, or abets the degradation of, that messenger RNA, its protein product or a downstream product which mediates its activity (e.g., a signaling intermediate) , may be used to curb the effective period of activity of the protein. If a gene is up-regulated in more favored mammals, or down-regulated in less favored animals then the utilities are converse to those stated above. First, the complementary strand of the gene, or a portion thereof, may be used in labeled form as a hybridization probe to detect messenger RNA and thereby monitor the level of expression of the gene in a subject. Depressed levels are indicative of damage, or possibly of a propensity to damage, and clinicians may take appropriate preventative, curative or ameliorative action. Secondly, the messenger RNA product, the equivalent cDNA, protein product, or a binding molecule specific for those products, or a downstream product, or a signaling intermediate, or a binding molecule therefor, may be used, preferably in labeled or immobilized form, as an assay reagent in an assay for said protein product or downstream product. Again, depressed levels are indicative of a present or future problem.

Thirdly, an agent which up-regulates expression of the gene may be used to increase levels of the corresponding protein and thereby inhibit further progression to a less favored state. By way of example, it could be a vector which carries a copy of the gene, but which expresses the gene at higher levels than does the endogenous expression system. Or it could be an agent which up- or down-regulates a positive or negative regulatory gene. Fourthly, an agent which is an agonist of the protein product of the gene, or of a downstream product through which its activity (of inhibition of progression to a less favored state) is manifested, or of a signaling intermediate may be used to foster its activity. Fifthly, an agent which inhibits the degradation of that protein .product or of a downstream product or of a signaling intermediate may be used to increase the effective period of activity of the protein.

Mutant Proteins The present invention also contemplates mutant proteins (peptides) which are substantially identical (as defined below) to the parental protein (peptide) . In general, the fewer the mutations, the more likely the mutant protein is to retain the activity of the parental protein. The effect of mutations is usually (but not always) additive. Certain individual mutations are more likely to be tolerated than others . A protein is more likely to tolerate a mutation which (a) is a substitution rather than an insertion or deletion; (b) is an insertion or deletion at the terminus, rather than internally, or, if internal, is at a domain boundary, or a loop or turn, rather than in an alpha helix or beta strand; (c) affects a surface residue rather than an interior residue; (d) affects a part of the molecule distal to the binding site; (e) is a substitution of one amino acid for another of similar size, charge, and/or hydrophobicity, and does not destroy a disulfide bond or other crosslink; and

(f) is at a site which is subject to substantial variation among a family of homologous proteins to which the protein of interest belongs.

These considerations can be used to design functional mutants .

Surface vs . Interior Residues Charged amino acid residues almost always lie on the surface of the protein. For uncharged residues, there is less certainty, but in general, hydrophilic residues are partitioned to the surface and hydrophobic residues to the interior. Of course, for a membrane protein, the membrane- spanning segments are likely to be rich in hydrophobic residues. Surface residues may be identified experimentally by various labeling techniques, or by 3-D structure mapping techniques like X-ray diffraction and NMR. A 3-D model of a homologous protein can be helpful .

Binding Si te Residues Residues forming the binding site may be identified by (1) comparing the effects of labeling the surface residues before and after complexing the protein to its target, (2) labeling the binding site directly with affinity ligands, (3) fragmenting the protein and testing the fragments for binding activity, and (4) systematic mutagenesis (e.g., alanine-scanning mutagenesis) to determine which mutants destroy binding. If the binding site of a homologous protein is known, the binding site may be postulated by analogy. Protein libraries may be constructed and screened that a large family (e.g., IO⁸) of related mutants may be evaluated simultaneously. Hence, the mutations are preferably conservative modifications as defined below.

"Substantially Identical"

A mutant protein (peptide) is substantially identical to a reference protein (peptide) if (a) it has at least 10% of a specific binding activity or a non-nutritional biological activity of the reference protein, and (b) is at least 50% identical in amino acid sequence to the reference protein (peptide) . It is "substantially structurally identical" if condition (b) applies, regardless of (a) . Percentage amino acid identity is determined by aligning the mutant and reference sequences according to a rigorous dynamic programming algorithm which globally aligns their sequences to maximize their similarity, the similarity being scored as the sum of scores for each aligned pair according to an unbiased PAM250 matrix, and a penalty for each internal gap of -12 for the first null of the gap and - 4 for each additional null of the same gap. The percentage identity is the number of matches expressed as a percentage of the adjusted (i.e., counting inserted nulls) length of the reference sequence . A mutant DNA sequence is substantially identical to a reference DNA sequence if they are structural sequences, and encoding mutant and reference proteins which are substantially identical as described above. If instead they are regulatory sequences, they are substantially identical if the mutant sequence has at least 10% of the regulatory activity of the reference sequence, and is at least 50% identical in nucleotide sequence to the reference sequence. Percentage identity is determined as for proteins except that matches are scored +5, mismatches - 4, the gap open penalty is -12, and the gap extension penalty (per additional null) is -4. More preferably, the sequence is not merely substantially identical, but rather is at least 51%, 66%, 75%, 80%, 85%, 90%, 95%, 96% , 97%, 98% or 99% identical in sequence to the reference sequence.

DNA sequences may also be considered "substantially identical" if they hybridize to each other under stringent conditions, i.e., conditions at which the Tm of the heteroduplex of the one strand of the mutant DNA and the more complementary strand of the reference DNA is not in excess of 10°C. less than the Tm of the reference DNA homoduplex. Typically this will correspond to a percentage identity of 85-90%.

"Conservative Modifications" "Conservative modifications" are defined as (a) conservative substitutions of amino acids as hereafter defined; or (b) single or multiple insertions (extension) or deletions (truncation) of amino acids at the termini . Conservative modifications are preferred to other modifications. Conservative substitutions are preferred to other conservative modifications. "Semi-Conservative Modifications" are modifications which are not conservative, but which are (a) semi- conservative substitutions as hereafter defined; or (b) single or multiple insertions or deletions internally, but at interdomain boundaries, in loops or in other segments of relatively high mobility. Semi-conservative modifications are preferred to nonσonservative modifications. Semi- conservative substitutions are preferred to other semi- conservative modifications. Non-conservative substitutions are preferred to other non-conservative modifications. The term "conservative" is used here in an a priori sense, i.e., modifications which would be expected to preserve 3D structure and activity, based on analysis of the naturally occurring families of homologous proteins and of past experience with the effects of deliberate mutagenesis, rather than post facto, a modification already known to conserve activity. Of course, a modification which is conservative a priori may, and usually is, also conservative post facto. Preferably, except at the termini, no more than about five amino acids are inserted or deleted at a particular locus, and the modifications are outside regions known to contain binding sites important to activity. Preferably, insertions or deletions are limited to the termini . A conservative substitution is a substitution of one amino acid for another of the same exchange group, the exchange groups being defined as follows. I Gly, Pro, Ser, Ala (Cys) (and any nonbiogenic, neutral amino acid with a hydrophobicity not exceeding that of the aforementioned a.a.'s) II Arg, Lys, His (and any nonbiogenic, positively- charged amino acids) III Asp, Glu, Asn, Gin (and any nonbiogenic negatively-charged amino acids) IV Leu, lie, Met, Val (Cys) (and any nonbiogenic, aliphatic, neutral amino acid with a hydrophobicity too high for I above) V Phe, Trp, Tyr (and any nonbiogenic, aromatic neutral amino acid with a hydrophobicity too high for I above) . Note that Cys belongs to both I and IV. Residues Pro, Gly and Cys have special conformational roles. Cys participates in formation of disulfide bonds. Gly imparts flexibility to the chain. Pro imparts rigidity to the chain and disrupts α helices. These residues may be essential in certain regions of the polypeptide, but substitutable elsewhere. One, two or three conservative substitutions are more likely to be tolerated than a larger number. "Semi-conservative substitutions" are defined herein as being substitutions within supergroup i/lI/III or within supergroup IV/V, but not within a single one of groups I-V. They also include replacement of any other amino acid with alanine. If a substitution is not conservative, it preferably is semi-conservative. "Non-conservative substitutions" are substitutions which are not "conservative" or "semi-conservative". "Highly conservative substitutions" are a subset of conservative substitutions, and are exchanges of amino acids within the groups Phe/Tyr/Trp, Met/Leu/lle/Val, His/Arg/Lys, Asp/Glu and Ser/Thr/Ala. They are more likely to be tolerated than other conservative substitutions. Again, the smaller the number of substitutions, the more likely they are to be tolerated.

"Conservatively Identical" A protein (peptide) is conservatively identical to a reference protein (peptide) it differs from the latter, if at all, solely by conservative modi ications, the protein (peptide) remaining at least seven amino acids long if the reference protein (peptide) was at least seven amino acids long. A protein is at least semi-conservatively identical to a reference protein (peptide) if it differs from the latter, if at all, solely by semi-conservative or conservative modifications . A protein (peptide) is nearly conservatively identical to a reference protein (peptide) if it differs from the latter, if at all, solely by one or more conservative modifications and/or a single nonconservative substitution. It is highly conservatively identical if it differs, if at all, solely by highly conservative substitutions. Highly conservatively identical proteins are preferred to those merely conservatively identical. An absolutely identical protein is even more preferred.

The core sequence of a reference protein (peptide) is the largest single fragment which retains at least 10% of a particular specific binding activity, if one is ^"specified, or otherwise of at least one specific binding activity of the referent. If the referent has more than one specific binding activity, it may have more than one core sequence, and these may overlap or not .

If it is taught that a peptide of the present invention may have a particular similarity relationship (e.g., markedly identical) to a reference protein (peptide) , preferred peptides are those which comprise a sequence having that relationship to a core sequence of the reference protein (peptide) , but with internal insertions or deletions in either sequence excluded. Even more preferred peptides are those whose entire sequence has that relationship, with the same exclusion, to a core sequence of that reference protein (peptide) .

Library The term "library" generally refers to a collection of chemical or biological entities which are related in origin, structure, and/or function, and which can be screened simultaneously for a property of interest . Libraries may be classified by how they are constructed (natural vs. artificial diversity; combinatorial vs. noncombinatorial) , how they are screened (hybridization, expression, display) , or by the nature of the screened library members (peptides, nucleic acids, etc.). In a "natural diversity" library, essentially all of the diversity arose without human intervention. This would be true, for example, of messenger RNA extracted from a non- engineered cell. In a "synthetic diversity" library, essentially all of the diversity arose deliberately as a result of human intervention. This would be true for example of a combinatorial library; note that a small level of natural diversity could still arise as a result of spontaneous mutation. It would also be true of a noncombinatorial library of compounds collected from diverse sources, even if they were all natural products . In a "non-natural diversity" library, at least some of the diversity arose deliberately through human intervention.

In a "controlled origin" library, the source of the diversity is limited in some way. A limitation might be to cells of a particular individual, to a particular species, or to a particular genus, or, more complexly, to individuals of a particular species who are of a particular age, sex, physical condition, geographical location, occupation and/or familial relationship. Alternatively or additionally, it might be to cells of a particular tissue or organ. Or it could be cells exposed to particular pharmacological, environmental, or pathogenic conditions. Or the library could be of chemicals, or a particular class of chemicals, produced by such cells. In a "controlled structure" library, the library members are deliberately limited by the production conditions to particular chemical structures. For example, if they are oligomers, they may be limited in length and monomer composition, e.g. hexapeptides composed of the twenty genetically encoded amino acids.

Hybridization Library In a hybridization library, the library members are nucleic acids, and are screened using a nucleic acid hybridization probe. Bound nucleic acids may then be amplified, cloned, and/or sequenced.

Expression Library In an expression library, the screened library members are gene expression products, but one may also speak of an underlying library of genes encoding those products. The library is made by subcloning DNA encoding the library members (or portions thereof) into expression vectors (or into cloning vectors which subsequently are used to construct expression vectors) , each vector comprising an expressible gene encoding a particular library member, introducing the expression vectors into suitable cells, and expressing the genes so the expression products are produced. In one embodiment, the expression products are secreted, so the library can be screened using an affinity reagent, such as an antibody or receptor. The bound expression products may be sequenced directly, or their sequences inferred by, e.g., sequencing at least the variable portion of the encoding DNA.

In a second embodiment, the cells are lysed, thereby exposing the expression products, and the latter are screened with the affinity reagent . In a third embodiment, the cells express the library members in such a manner that they are displayed on the surface of the cells, or on the surface of viral particles produced by the cells. (See display libraries, below) . In a fourth embodiment, the screening is not for the ability of the expression product to bind to an affinity reagent, but rather for its ability to alter the phenotype of the host cell in a particular detectable manner. Here, the screened library members are transformed cells, but there is a first underlying library of expression products which mediate the behavior of the cells, and a second underlying library of genes which encode those products .

Display Library In a display library, the library members are each conjugated to, and displayed upon, a support of some kind. The support may be living (a cell or virus) , or nonliving (e.g., a bead or plate) . If the support is a cell or virus, display will normally be effectuated by expressing a fusion protein which comprises the library member, a carrier moiety allowing integration of the fusion protein into the surface of the cell or virus, and optionally a lining moiety. In a variation on this theme, the cell coexpresses a first fusion comprising the library member and a linking moiety LI, and a second fusion comprising a linking moiety L2 and the carrier moiety. LI and L2 interact to associate the first fusion with the second fusion and hence, indirectly, the library member with the surface of the cell or virus. Soluble Library In a soluble library, the library members are free in solution. A soluble library may be produced directly, or one may first make a display library and then release the library members from their supports.

Encapsulated Library In an encapsulated library, the library members are inside cells or liposomes. Generally speaking, encapsulated libraries are used to store the library members for future use; the members are extracted in some way for screening purposes. However, if they differentially affect the phenotype of the cells, they may be screened indirectly by screening the cells.

cDNA Library A cDNA library is usually prepared by extracting RNA from cells of particular origin, fractionating the RNA to isolate the messenger RNA (mRNA has a poly (A) tail, so this is usually done by oligo-dT affinity chromatography) , synthesizing complementary DNA (cDNA) using reverse transcriptase, DNA polymerase, and other enzymes, subcloning the cDNA into vectors, and introducing the vectors into cells. Often, only mRNAs or cDNAs of particular sizes will be used, to make it more likely that the cDNA encodes a functional polypeptide. A cDNA library explores the natural diversity of the transcribed DNAs of cells from a particular source. It is not a combinatorial library. A cDNA library may be used to make a hybridization library, or it may be used as an (or to make) expression library.

Genomic DNA Library A genomic DNA library is made by extracting DNA from a particular source, fragmenting the DNA, isolating fragments of a particular size range, subcloning the DNA fragments into vectors, and introducing the vectors into cells. Like a cDNA library, a genomic DNA library is a natural diversity library, and not a combinatorial library. A genomic DNA library may be used the same way as a cDNA library.

Synthetic DNA library

A synthetic DNA library may be screened directly (as a hybridization library) , or used in the creation of an expression or display library of peptides/proteins.

Combinatorial Libraries The term "combinatorial library" refers to a library in which the individual members are either systematic or random combinations of a limited set of basic elements, the properties of each member being dependent on the choice and location of the elements incorporated into it. Typically, the members of the library are at least capable of being screened simultaneously. Randomization may be complete or partial; some positions may be randomized and others predetermined, and at random positions, the choices may be limited in a predetermined manner. The members of a combinatorial library may be oligomers or polymers of some kind, in which the variation occurs through the choice of monomeric building block at one or more positions of the oligomer or polymer, and possibly in terms of the connecting linkage, or the length of the oligomer or polymer, too. Or the members may be nonoligomeric molecules with a standard core structure, like the 1,4-benzodiazepine structure, with the variation being introduced by the choice of substituents at particular variable sites on the core structure. Or the members may be nonoligomeric molecules assembled like a jigsaw puzzle, but wherein each piece has both one or more variable moieties (contributing to library diversity) and one or more constant moieties (providing the functionalities for coupling the piece in question to other pieces) . Thus, in a typical combinatorial library, chemical building blocks are at least partially randomly combined into a large number (as high as 10^ls) of different compounds, which are then simultaneously screened for binding (or other) activity against one or more targets .

In a "simple combinatorial library", all of the members belong to the same class of compounds (e.g., peptides) and can be synthesized simultaneously. A "composite combinatorial library" is a mixture of two or more simple libraries, e.g., DNAs and peptides^', or peptides, peptoids, and PNAs, or benzodiazepines and carbamates. The number of component simple libraries in a composite library will, of course, normally be smaller than the average number of members in each simple library, as otherwise the advantage of a library over individual synthesis is small. Libraries of thousands., even millions, of random oligopeptides have been prepared by chemical synthesis (Houghten et al . , Nature, 354:84-6(1991)), or gene expression (Marks et al., J Mol Biol, 222:581-97(1991)), displayed on chromatographic supports (Lam et al . , Nature, 354:82-4(1991)), inside bacterial cells (Colas et al . , Nature, 380:548-550(1996)), on bacterial pili (Lu, Bio/Technology, 13:366-372(1990)), or phage (Smith, Science, 228:1315-7(1985)), and screened for binding to a variety of targets including antibodies (Valadon et al . , J Mol Biol, 261:11-22(1996)), cellular proteins (Schmitz et al . , J Mol Biol, 260:664-677(1996)), viral proteins (Hong and Boulanger, E bo J,^' 14:4714-4727(1995)), bacterial proteins (Jacobsson and Frykberg, Biotechniques, 18:878-885(1995)), nucleic acids (Cheng et al . , Gene, 171:1-8(1996)), and plastic (Siani et al . , J Chem Inf Comput Sci, 34:588- 593 (1994)) . Libraries of proteins (Ladner, USP 4,664,989), peptoids (Simon et al . , Proc Natl Acad Sci U S A, 89:9367-71(1992)), nucleic acids (Ellington and Szostak, Nature, 246:818(1990)), carbohydrates, and small organic molecules

(Eichler et al . , Med Res Rev, 15:481-96(1995)) have also been prepared or suggested for drug screening purposes . The first combinatorial libraries were composed of peptides or proteins, in which all or selected amino acid positions were randomized. Peptides and proteins can exhibit high and specific binding activity, and can act as catalysts. In consequence, they are of great importance in biological systems.

Nucleic acids have also been used in combinatorial libraries. Their great advantage is the ease with which a nucleic acid with appropriate binding activity can be amplified. As a result, combinatorial libraries composed of nucleic acids can be of low redundancy and hence, of high diversity.

There has also been much interest in combinatorial libraries based on small molecules, which are more suited to pharmaceutical use, especially those which, like benzodiazepines, belong to a chemical class which has already yielded useful pharmacological agents. The techniques of combinatorial chemistry have been recognized as the most efficient means for finding small molecules that act on these 'targets. At present, small molecule combinatorial chemistry involves the synthesis of either pooled or discrete molecules that present varying arrays of functionality on a common scaffold. These compounds are grouped in libraries that are then screened against the target of interest either for binding or for inhibition of biological activity.

The size of a library is the number of molecules in it. The simple diversity of a library is the number of unique structures in it . There is no formal minimum or maximum diversity. If the library has a very low diversity, the library has little advantage over just synthesizing and screening the members individually. If the library is of very high diversity, it may be inconvenient to handle, at least without automatizing the process. The simple diversity of a library is preferably at least 10, 10E2, 10E3, 10E4, 10E6, 10E7, 10E8 or 10E9, the higher the better under most circumstances. The simple diversity is usually not more than 10E15, and more usually not more than 10E10. The average sampling level is the size divided by the simple diversity. The expected average sampling level must be high enough to provide a reasonable assurance that, if a given structure were expected, as a consequence of the library design, to be present, that the actual average sampling level will be high enough so that the structure, if satisfying the screening criteria, will yield a positive result when the library is screened. Thus, the preferred average sampling level is a function of the detection limit, which in turn is a function of the strength of the signal to be screened.

There are more complex measures of diversity than simple diversity. These attempt to take into account the degree of structural difference between the various unique sequences. These more complex measures are usually used in the context of small organic compound libraries, see below. The library members may be presented as solutes in solution, or immobilized on some form of support. In the latter case, the support may be living (cell, virus) or nonliving (bead, plate, etc.) . The supports may be separable (cells, virus particles, beads) so that binding and nonbinding members can be separated, or nonseparable (plate) . In the latter case, the members will normally be placed on addressable positions on the support. The advantage of a soluble library is that there is no carrier moiety that could interfere with the binding of the members to the support . The advantage of an immobilized library is that it is easier to identify the structure of the members which were positive. When screening a soluble library, or one with a separable support, the target is usually immobilized. When screening a library on a nonseparable support, the target will usually be labeled. Oligonucleotide Libraries An oligonucleotide library is a combinatorial library, at least some of whose members are single-stranded oligonucleotides having three or more nucleotides connected by phosphodiester or analogous bonds. The oligonucleotides may be linear, cyclic or branched, and may include non- nucleic acid moieties. The nucleotides are not limited to the nucleotides normally found in DNA or RNA. For examples of nucleotides modified to increase nuclease resistance and chemical stability of aptamers, see Chart 1 in Osborne and Ellington, Chem. Rev., 97: 349-70 (1997). For screening of RNA, see Ellington and Szostak, Nature, 346: 818-22 (1990).

There is no formal minimum or maximum size for these oligonucleotides. However, the number of conformations w ich an oligonucleotide can assume increases exponentially with its length in bases. Hence, a longer oligonucleotide is more likely to be able to fold to adapt itself to a protein surface. On the other hand, while very long molecules can be synthesized and screened, unless they provide a much superior affinity to that of shorter molecules, they are not likely to be found in the selected population, for the reasons explained by Osborne and Ellington (1997) . Hence, the libraries of the present invention are preferably composed of oligonucleotides having a length of 3 to 100 bases, more preferably 15 to 35 bases. The oligonucleotides in a given library may be of the same or of different lengths. Oligonucleotide libraries have the advantage that libraries of very high diversity (e.g., 10¹⁵) are feasible, and binding molecules are readily amplified in vitro by polymerase chain reaction (PCR) . Moreover, nucleic acid molecules can have very high specificity and affinity to targets . In a preferred embodiment, this invention prepares and screens oligonucleotide libraries by the SELEX method, as described in King and Famulok, Molec. Biol. Repts., 20: 97- 107 (1994) ; L. Gold, C. Tuerk. Methods of producing nucleic acid ligands, US#5595877; Oliphant et al . Gene 44:177 (1986) . The term "aptamer" is conferred on those oligonucleotides which bind the target protein. Such aptamers may be used to characterize the target protein, both directly (through identification of the aptamer and the points of contact between the aptamer and the protein) and indirectly (by use of the- aptamer as a ligand to modify the chemical reactivity of the protein) . In a classic oligonuclotide, each nucleotide (monomeric unit) is composed of a phosphate group, a sugar moiety, and either a purine or a pyrimidine base. In DNA, the sugar is deoxyribose and in RNA it is ribose. The nucleotides are linked by 5' -3' phosphodiester bonds.

The deoxyribose phosphate backbone of DNA can be modified to increase resistance to nuclease and to increase penetration of cell membranes. Derivatives such as mono- or dithiophosphates, methyl phosphonates, boranophosphates, formacetals, carbamates, siloxanes, and dimethylenethio- - sulfoxideo- and-sulfono- linked species are known in the art .

Peptide Library A peptide is composed of a plurality of amino acid residues joined together by peptidyl (-NHC0-) bonds. A biogenic peptide is a peptide in which the residues are all genetically encoded amino acid residues; it is not necessary that the biogenic peptide actually be produced by gene expression. Amino acids are the basic building blocks with which peptides and proteins are constructed. Amino acids possess both an amino group (-NH₂) and a carboxylic acid group (- COOH) . Many amino acids, but not all, have the alpha amino acid structure NH₂-CHR-COOH, where R is hydrogen, or any of a variety of functional groups. Twenty amino acids are genetically encoded: Alanine, Arginine, Asparagine, Aspartic Acid, Cysteine, Glutamic Acid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine, and Valine. Of these, all save Glycine are optically isomeric, however, only the L- form is found in humans. Nevertheless, the D-forms of these amino acids do have biological significance; D-Phe, for example, is a known analgesic. Many other amino acids are also known, including: 2- Aminoadipic acid; 3-Aminoadipic acid; beta-Aminopropionic acid; 2-Aminobutyric acid; 4-Aminobutyric acid (Piperidinic acid) ;6-Aminocaproic acid; 2-Aminoheptanoic acid; 2- Aminoisobutyric acid, 3-Aminoisobutyric acid; 2-Aminopimelic acid; 2,4-Diaminobutyric acid; Desmosine; 2,2'- Diaminopimelic acid; 2, 3-Diaminopropionic acid; N- Ethylglycine; N-Ethylasparagine; Hydroxylysine; allo- Hydroxylysine; 3-Hydroxyproline; 4-Hydroxyproline; Isodesmosine; allo-Isoleucine; N-Methylglycine (Sarcosine) ; N-Methylisoleucine; N-Methylvaline; Norvaline; Norleucine; and Ornithine. Peptides are constructed by condensation of amino acids and/or smaller peptides. The amino group of one amino acid (or peptide) reacts with the carboxylic acid group of a second amino acid (or peptide)- to form a peptide (-NHCO-) bond, releasing one molecule of water. Therefore, when an amino acid is incorporated into a peptide, it should, technically speaking, be referred to as an amino acid residue. The core of that residue is the moiety which excludes the -NH and -CO linking functionalities which connect it to other residues. This moiety consists of one or more main chain atoms (see below) and the attached side chains . The main chain moiety of each amino acid consists of the -NH and -CO linking functionalities and a core main chain moiety. Usually the latter is a single carbon atom. However, the core main chain moiety may include additional carbon atoms, and may also include nitrogen, oxygen or sulfur atoms, which together form a single chain. In a preferred embodiment, the core main chain atoms consist ' solely of carbon atoms . The side chains are attached to the core main chain atoms. For alpha amino acids, in which the side chain is attached to the alpha carbon, the C-1, C-2 and N-2 of each residue form the repeating unit of the main chain, and the word "side chain" refers to the C-3 and higher numbered carbon atoms and their substituents. It also includes H atoms attached to the main chain atoms .

Amino acids may be classified according to the number of carbon atoms which appear in the main chain between the carbonyl carbon and amino nitrogen atoms which participate in the peptide bonds. Among the 150 or so amino acids which occur in nature, alpha, beta, gamma and delta amino acids are known. These have 1-4 intermediary carbons. Only alpha amino acids occur in proteins. Proline is a special case of an alpha amino acid; its side chain also binds to the peptide bond nitrogen. For beta and higher order amino acids, there is a choice as to which main chain core carbon a side chain other than H is attached to. The preferred attachment site is the C-2 (alpha) carbon, i.e., the one adjacent to the carboxyl carbon of the -CO linking functionality. It is also possible for more than one main chain atom to carry a side chain other than H. However, in a preferred embodiment, only one main chain core atom carries a side chain other than H. A main chain carbon atom may carry either one or two side chains; one is more common. A side chain may be attached to a main chain carbon atom by a single or a double bond; the former is more common. A simple combinatorial peptide library is one whose members are peptides having three or more amino acids connected via peptide bonds. The peptides may be linear, branched, or cyclic, and may covalently or noncovalently include nonpeptidyl moieties. The amino acids are not limited to the naturally occurring or to the genetically encoded amino acids. A biased peptide library is one in which one or more (but not all) residues of the peptides are constant residues .

Cyclic Peptides Many naturally occurring peptides are cyclic. Cyclization is a common mechanism for stabilization of peptide conformation thereby achieving improved association of the peptide with its ligand and hence improved biological activity. Cyclization is usually achieved by intra-chain cystine formation, by formation of peptide bond between side chains or between N- and C- terminals. Cyclization was usually achieved by peptides in solution, but several publications have appeared that describe cyclization of peptides on beads. A peptide library may be an oligopeptide library or a protein library.

Oligopeptides Preferably, the oligopeptides are at least five, six, seven or eight amino acids in length. Preferably, they are composed of less than 50, more preferably less than 20 amino acids. In the case of an oligopeptide library, all or just some of the residues may be variable. The oligopeptide may be unconstrained, or constrained to a particular conformation by, e.g., the participation of constant cysteine residues in the formation of a constraining disulfide bond. Proteins Proteins, like oligopeptides, are composed of a plurality of amino acids, but the term protein is usually reserved for longer peptides, which are able to fold into a stable conformation. A protein may be composed of two or more polypeptide chains, held together by covalent or noncovalent crosslinks. These may occur in a homooligomeric or a heterooligomeric state . A peptide is considered a protein if it (1) is at least 50 amino acids long, or (2) has at least two stabilizing covalent crosslinks (e.g., disulfide bonds). Thus, conotoxins are considered proteins . Usually, the proteins of a protein library will be characterizable as having both constant residues (the same for all proteins in the library) and variable residues (which vary from member to member) . This is simply because, for a given range of variation at each position, the sequence space (simple diversity) grows exponentially with the number of residue positions, so at some point it becomes inconvenient for all residues of a peptide to be variable positions. Since proteins are usually larger than oligopeptides, it is more common for protein libraries than oligopeptide libraries to feature variable positions.

In the case of a protein library, it is desirable to focus the mutations at those sites which are tolerant of mutation. These may be determined by alanine scanning mutagenesis or by comparison of the protein sequence to that of homologous proteins of similar activity. It is also more likely that mutation of surface residues will directly affect binding. Surface residues may be determined by inspecting a 3D structure of the protein, or by labeling the surface and then ascertaining which residues have received labels . They may also be inferred by identifying regions of high hydrophilicity within the protein. Because proteins are often altered at some sites but not others, protein libraries can be considered a special case of the biased peptide library. There are several reasons that one might screen a protein library instead of an oligopeptide library, including (1) a particular protein, mutated in the library, has the desired activity to some degree already, and (2) the oligopeptides are not expected to have a sufficiently high affinity or specificity since they do not have a stable conformation. When the protein library is based on a parental protein which does not have the desired activity, the parental protein will usually be one which is of high stability (melting point >= 50 deg. C.) and/or possessed of hypervariable regions . The variable domains of an antibody possess hypervariable regions and hence, in some embodiments, the protein library comprises members which comprise a mutant of VH or VL chain, or a mutant of an antigen-specific binding fragment of such a chain. VH and VL chains are usually each about 110 amino acid residues, and are held in proximity by a disulfide bond between the adjoing CL and CHI regions to form a variable domain. Together, the VH, VL, CL and CHI form an Fab fragment . In human heavy chains, the hypervariable regions are at 31-35, '49-65, 98-111 and 84-88, but only the first three are involved in antigen binding. There is variation among VH and VL chains at residues outside the hypervariable regions, but to a much lesser degree . A sequence is considered a mutant of a VH or VL chain if it is at least 80% identical to a naturally occurring VH or VL chain at all residues outside the hypervariable region. In a preferred embodiment, such antibody library members comprise both at least one VH chain and at least one VL chain, at least one of which is a mutant chain, and which chains may be derived from the same or different antibodies. The VH and VL chains may be covalently joined by a suitable linker moiety, as in a "single chain antibody", or they may be noncovalently joined, as in a naturally occurring variable domain. If the joining is noncovalent, and the library is displayed on cells or virus, then either the VH or the VL chain may be fused to the carrier surface/coat protein. The complementary chain may be co-expressed, or added exogenously to the library. The members may further comprise some or all of an antibody constant heavy and/or constant light chain, or a mutant thereof .

Peptoid Library A peptoid is an analogue of a peptide in which one or more of the peptide bonds (-NH-CO-) are replaced by pseudopeptide bonds, which may be the same or different. It is not necessary that all of the peptide bonds be replaced, i.e., a peptoid may include one or more conventional amino acid residues, e.g., proline. A peptide bond has two small divalent linker elements, -NH- and -CO-. Thus, a preferred class of psuedopeptide bonds are those which consist of two small divalent linker elements. Each may be chosen independently from the group consisting of amine (-NH-) , substituted amine (-NR-) , carbonyl (-CO-) , thiocarbonyl (-CS-) , methylene (-CH2-) , monosubstituted methylene (-CHR-) , disubstituted methylene (-CR1R2-) , ether (-0-) and thioether (-S-) . The more preferred pseudopeptide bonds include: N-modified -NRCO- Carba Ψ -CH₂-CH₂- Depsi Ψ -CO-0- Hydroxyethylene Ψ -CH0H-CH₂- Ketomethylene Ψ -CO-CH₂- Methylene-Oxy -CH₂-0- Reduced -CH₂-NH- Thiomethylene -CH₂-S- Thiopeptide -CS-NH- Retro-Inverso -CO-NH-

A single peptoid molecule may include more than one kind of pseudopeptide bond. For the purposes of introducing diversity into a peptoid library, one may vary (1) the side chains attached to the core main chain atoms of the monomers linked by the pseudopeptide bonds, and/or (2) the side chains (e.g., the - R of an -NRC0-) of the pseudopeptide bonds. Thus, in one embodiment, the monomeric units which are not amino acid residues are of the structure -NR1-CR2-C0- , where at least one of Rl and R2 are not hydrogen. If there is variability in the pseudopeptide bond, this is most conveniently done by using an -NRCO- or other pseudopeptide bond with an R group, and varying the R group. In this event, the R group will usually be any of the side chains characterizing the amino acids of peptides, as previously discussed. If the R group of the pseudopeptide bond is not variable, it will usually be small, e.g., not more than 10 atoms (e.g., hydroxyl, amino, carboxyl, methyl, ethyl, propyl) . If the conjugation chemistries are compatible, a simple combinatorial library may include both peptides and peptoids .

Peptide Nucleic Acid Library A PNA oligomer is here defined as one comprising a plurality of units, at least one of which is a PNA monomer which comprises a side chain comprising a nucleobase. For nucleobases, see USP 6,077,835.

The classic PNA oligomer is composed of (2- a inoethyl) glycine units, with nucleobases attached by methylene carbonyl linkers. That is, it has the^' structure

H- (-HN-CH₂-CH₂-N(-CO-CH₂-B) -CH₂-CO-)_n -OH

where the outer parenthesized substructure is the PNA monomer.

In this structure, the nucleobase B is separated from the backbone N by three bonds, and the points of attachment of the side chains are separated by six bonds . The nucleobase may be any of the bases included in the nucleotides discussed in connection with oligonucleotide libraries. The bases of nucleotides A, G, T, C and U are preferred. A PNA oligomer may further comprise one or more amino acid residues, especially glycine and proline. One can readily envision related molecules in which (1) the -COCH2- linker is replaced by another linker, especially one composed of two small divalent linkers as defined previously, (2) a side chain is attached to one of the three main chain carbons not participating in the peptide bond (either instead or in addition to the side chain attached to the N of the classic PNA) ; and/or (3) the peptide bonds are replaced by pseudopeptide bonds as disclosed previously in the context of peptoids. PNA oligomer libraries have been made; see e.g. Cook, 6,204,326.

Small Organic Compound Library The small organic compound library ("compound library", for short) is a combinatorial library whose members are suitable for use as drugs if, indeed, they have the ability to mediate a biological activity of the target protein.

Peptides have certain disadvantages as drugs . These include susceptibility to degradation by serum proteases, and difficulty in penetrating cell membranes. Preferably, all or most of the compounds of the compound library avoid, or at least do not suffer to the same degree, one or more of the pharmaceutical disadvantages of peptides . In designing a compound library, it is helpful to bear in mind the methods of molecular modification typically used to obtain new drugs . Three basic kinds of modification may be identified: disjunction, in which a lead drug is simplified to identify its component pharmacophoric moieties; con unction, in which two or more known pharmacophoric moieties, which may be the same or different, are associated, covalently or noncovalently, to form a new drug; and alteration, in which one moiety is replaced by another which may be similar or different, but which is not in effect a disjunction or conjunction. The use of the terms "disjunction", "conjunction" and "alteration" is intended only to connote the structural relationship of the end product to the original leads , and not how the new drugs are actually synthesized, although it is possible that the two are the same . The process of disjunction is illustrated by the evolution of neostigmine (1931) and edrophonium (1952) from physostigmine (1925) . Subsequent conjunction is illustrated by demecarium (1956) and ambenonium (1956) . Alterations may modify the size, polarity, or electron distribution of an original moiety. Alterations include ring closing or opening, formation of lower or higher homologues, introduction or saturation of double bonds, introduction of optically active centers, introduction, removal or replacement of bulky groups, isosteric or bioisosteric substitution, changes in the position or orientation of a group, introduction of alkylating groups, and introduction, removal or replacement of groups with a view toward inhibiting or promoting inductive (electrostatic) or conjugative (resonance) effects. Thus, the substituents may include electron acceptors and/or electron donors. Typical electron donors (+1) include -CH₃, -CH₂R, -CHR₂, -CR₃ and -COO^". Typical electron acceptors (-1) include -NH₃+, -NR₃+, -N0₂, -CN, -COOH, -COOR, -CHO, -COR, -COR, -F, -CI, -Br, -OH, -OR, -SH, -SR, -CH=CH₂, -CR=CR₂, and -C=CH. The substituents may also include those which increase or decrease electronic density in conjugated systems. The former (+R) groups include -CH₃, -CR₃, -F, -CI, -Br, -I, -OH, -OR, -0C0R, -SH, -SR, -NH₂, -NR₂, and -NHCOR. The later (-R) groups include -N0₂, -CN, -CHC, -COR, -COOH, -COOR, -CONH₂, -S0₂R and -CF₃. Synthetically speaking, the modifications may be achieved by a variety of unit processes, including nucleophilic and electrophilic substitution, reduction and oxidation, addition elimination, double bond cleavage, and cyclization. For the purpose of constructing a library, a compound, or a family of compounds, having one or more pharmacological activities (which need not be related to the known or suspected activities of the target protein) , may be disjoined into two or more known or potential pharmacophoric moieties. Analogues of each of these moieties may be identified, and mixtures of these analogues reacted so as to reassemble compounds which have some similarity to the original lead compound. It is not necessary that all members of the library possess moieties analogous to all of the moieties of the lead compound. The design of a library may be illustrated by the example of the benzodiazepines . Several benzodiazepine drugs, including chlordiazepoxide, diazepam and oxazepam, have been used as anti-anxiety drugs. Derivatives of benzodiazepines have widespread biological activities; derivatives have been reported to act not only as anxiolytics, but also as anticonvulsants; cholecystokinin (CCK) receptor subtype A or B, kappa opioid receptor, platelet activating factor, and HIV transactivator Tat antagonists, and GPIIblla, reverse transcriptase and ras farnesyltransferase inhibitors. The benzodiazepine structure has been disjoined into a 2-aminobenzophenone, an amino acid, and an alkylating agent. See Bunin, et al . , Proc. Nat. Acad. Sci. USA, 91:4708 (1994) . Since only a few 2-aminobenzophenone derivatives are commercially available, it was later disjoined into 2- aminoarylstannane, an acid chloride, an amino acid, and an alkylating agent. Bunin, et al . , Meth. Enzymol., 267:448 (1996) . The arylstannane may be considered the core structure upon which the other moieties are substituted, or all four may be considered equals which are conjoined to make each library member. A basic library synthesis plan and member structure is shown in Figure 1 of Fowlkes, et al . , U.S. Serial No. 08/740,671, incorporated by reference in its entirety. The acid chloride building block introduces variability at the R¹ site. The R² site is introduced by the amino acid, and the R³ site by the alkylating agent. The R⁴ site is inherent in the arylstannane. Bunin, et al . generated a 1, 4- benzodiazepine library of 11,200 different derivatives prepared from 20 acid chlorides, 35 amino acids, and 16 alkylating agents. (No diversity was introduced at R⁴; this group was used to couple the molecule to a solid phase.) According to-the Available Chemicals Directory (HDL Information Systems, San Leandro CA) , over 300 acid chlorides, 80 Fmoc-protected amino acids and 800 alkylating agents were available for purchase (and more, of course, could be synthesized) . The particular moieties used were chosen to maximize structural dispersion, while limiting the numbers to those conveniently synthesized in the wells of a microtiter plate. In choosing between structurally similar compounds, preference was given to the least substituted compound. The variable elements included both aliphatic and aromatic groups. Among the aliphatic groups, both acyclic and cyclic (mono- or poly-) structures, substituted or not, were tested. (While all of the acyclic groups were linear, it would have been feasible to introduce a branched aliphatic) . The aromatic groups featured either single and multiple rings, fused or not, substituted or not, and with heteroatoms or not. The secondary substitutents included - NH₂, -OH, -OMe, -CN, -CI, -F, and -COOH. While not used, spacer moieties, such as -0-, -S-, -00-, -CS-, -NH- , and - NR-, could have been incorporated. Bunin et al . suggest that instead of using a 1, 4- benzodiazepine as a core structure, one may instead use a 1, 4-benzodiazepine-2, 5-dione structure. As noted by Bunin et al . , it is advantageous, although not necessary, to use a linkage strategy which leaves no trace of the linking functionality, as this permits construction of a more diverse library. Other combinatorial nonoligomeric compound libraries known or suggested in the art have been based on carbamates, mercaptoacylated pyrrolidines, phenolic agents, aminimides, N-acylamino ethers (made from amino alcohols, aromatic hydroxy acids, and carboxylic acids) , N-alkylamino ethers (made from aromatic hydroxy acids, amino alcohols and aldehydes) 1, 4-piperazines, and 1, 4-piperazine-6-ones. DeWitt, et al . , Proc. Nat. Acad. Sci. (USA), 90:6909-13 (1993) describe the simultaneous but separate, synthesis of 40 discrete hydantoins and 40 discrete benzodiazepines. They carry out their synthesis on a solid support (inside a gas dispersion tube) , in an array format, as opposed to other conventional simultaneous synthesis techniques (e.g., in a well, or on a pin) . The hydantoins were synthesized by first simultaneously deprotecting and then treating each of five amino acid resins with each of eight isocyanates. The benzodiazepines were synthesized by treating each of five deprotected amino acid resins with each of eight 2-amino benzophenone imines. Chen, et al . , J. Am. Chem. Soc, 116:2661-62 (1994) described the preparation of a pilot (9 member) combinatorial library of formate esters. A polymer bead- bound aldehyde preparation was "split" into three aliquots, each reacted with one of three different ylide reagents. The reaction products were combined, and then divided into three new aliquots, each of which was reacted with a different Michael donor. Compound identity was found to be determinable on a single bead basis by gas chromatography/mass spectroscopy analysis. Holmes, USP 5,549,974 (1996) sets forth methodologies for the combinatorial synthesis of libraries of thiazolidinones and metathiazanones . These libraries are made by combination of amines, carbonyl compounds, and thiols under cyclization conditions. Ellman, USP 5,545,568 (1996) describes combinatorial synthesis of benzodiazepines, prostaglandins, beta-turn mimetics, and glycerol-based compounds. See also Ellman, USP 5,288,514. Summerton, USP 5,506,337 (1996) discloses methods of preparing a combinatorial library formed predominantly of morpholino subunit structures. Heterocylic combinatorial libraries are reviewed generally in Nefzi, et al . , Chem. Rev., 97:449-472 (1997).

For pharmacological classes, see, e.g., Goth, Medical Pharmacology: Principles and Concepts (C.V. Mosby Co. : 8th ed. 1976) ; Korolkovas and Burckhalter, Essentials of Medicinal Chemistry (John Wiley & Sons, Inc. : 1976) . For synthetic methods, see, e.g., Warren, Organic Synthesis: The Disconnection Approach (John Wiley & Sons, Ltd. : 1982) ; Fuson, Reactions of Organic Compounds (John Wiley & Sons: 1966) ; Payne and Payne, How to do an Organic Synthesis (Allyn and Bacon, Inc.: 1969); Greene, Protective Groups in Organic Synthesis (Wiley-Interscience) . For selection of substituents, see e.g., Hansch and Leo, Substituent Constants for Correlation Analysis in Chemistry and Biology (John Wiley & Sons: 1979) . The library is preferably synthesized so that the individual members remain identifiable so that, if a member is shown to be active, it is not necessary to analyze it. Several methods of identification have been proposed, including : (1) encoding, i.e., the attachment to each member of an identifier moiety which is more readily identified than the member proper. This has the disadvantage that the tag may itself influence the activity of the conjugate.

(2) spatial addressing, e.g., each member is synthesized only at a particular coordinate on or in a matrix, or in a particular chamber. This might be, for example, the location of a particular pin, or a particular well on a microtiter plate, or inside a "tea bag". The present invention is not limited to any particular form of identification. However, it is possible to simply characterize those members of the library which are found to be active, based on the characteristic spectroscopic indicia of the various • building blocks . Solid phase synthesis permits greater control over which derivatives are formed. However, the solid phase could interfere with activity. To overcome this problem, some or all of the molecules of each member could be liberated, after synthesis but before screening. Examples of candidate simple libraries which might be evaluated include derivatives of the following: Cyclic Compounds Containing One Hetero Atom Heteronitrogen pyrroles pentasubstituted pyrroles pyrrolidines pyrrolines prolines indoles beta-carbolines pyridines dihydropyridines 1,4-dihydropyridines pyrido [2 , 3 -d] pyri idines tetrahydro-3H-imidazo [4,5-c] pyridines Isoquinolines tetrahydroisoquino1ines quinolones beta-lactams azabicyclo [4.3.0] onen-8-one amino acid

Heterooxygen furans tetrahydrofurans 2 , 5-disubstituted tetrahydrofurans pyrans hydroxypyranones tetrahydroxypyranones gamma-butyrolactones Heterosulfur sulfolenes Cyclic Compounds with Two or More Hetero atoms Multiple heteronitrogens imidazoles pyrazoles piperazines diketopiperazines arylpiperazines benzylpiperazines benzodiazepines 1,4 -benzodiazepine- 2, 5-diones hydantoins 5-alkoxyhydantoins dihydropyrimidines

1, 3-disubstituted-5, 6-dihydopyrimidine-2, 4- diones cyclic ureas cyclic thioureas quinazolines chiral 3-substituted-quinazoline-2 , 4- diones triazoles 1,2, 3 -triazoles purines Heteronitrogen and Heterooxygen dikelomorpholines isoxazoles isoxazolines

Heteronitrogen and Heterosulfur thiazolidines N-axylthiazolidines dihydrothiazoles 2-methylene-2, 3-dihydrothiazates 2-aminothiazoles thiophenes 3 -amino thiophenes 4-thiazolidinones 4-melathiazanones benzisothiazolones For details on synthesis of libraries, see Nefzi, et al., Chem. Rev., 97:449-72 (1997), and references cited therein.

Pharmaceutical Methods and Preparations The preferred animal subject of the present invention is a mammal. By the term "mammal" is meant an individual belonging to the class Mammalia. The invention is particularly useful in the treatment of human subjects, although it is intended for veterinary and nutritional uses as well. Preferred nonhuman subjects are of the orders Primata (e.g., apes and monkeys), Artiodactyla or Perissodactyla (e.g., cows, pigs, sheep, horses, ■ goats) , Carnivora (e.g., cats, dogs), Rodenta (e.g., rats, mice, guinea pigs, hamsters), Lagomorpha (e.g., rabbits) or other pet, farm or laboratory mammals. The term "protection", as used herein, is intended to include "prevention," "suppression" and "treatment." "Prevention", strictly speaking, involves administration of the pharmaceutical prior to the induction of the disease (or other adverse clinical condition) . "Suppression" involves administration of the composition prior to the clinical appearance of the disease. "Treatment" involves administration of the protective composition after the appearance of the disease. It will be understood that in human and veterinary medicine, it is not always possible to distinguish between "preventing" and "suppressing" since the ultimate inductive event or events may be unknown, latent, or the patient is not ascertained until well after the occurrence of the event or events. Therefore, unless, qualified, the term "prevention" will be understood to refer to both prevention in the strict sense, and to suppression. The preventative or prophylactic use of a pharmaceutical usually involves identifying subjects who are at higher risk than the general population of contracting the disease, and administering the pharmaceutical to them in advance of the clinical appearance of the disease. The effectiveness of such use is measured by comparing the subsequent incidence or severity of the disease, or of particular symptoms of the disease, in the treated subjects ^• against that in untreated subjects of the same high risk group . While high risk factors vary from disease to disease, in general, these include (1) prior occurrence of the disease in one or more members of the same family, or, in the case of a contagious disease, in individuals with whom the subject has come into potentially contagious contact at a time when the earlier victim was likely to be contagious, (2) a prior occurrence of the disease in the subject, (3) prior occurrence of a related disease, or a condition known to increase the likelihood of the disease, in the subject; (4) appearance of a suspicious level of a marker of the disease, or a related disease or condition; (5) a subject who is immunologically compromised, e.g., by radiation treatment, HIV infection, drug use,, etc., or (6) membership in a particular group (e.g., a particular age, sex, race, ethnic group, etc.) which has been epidemiologically associated with that disease. In some cases, it may be desirable to provide prophylaxis for the general population, and not just a high risk group. This is most likely to be the case when essentially all are at risk of contracting the disease, the effects of the disease are serious, the therapeutic index of the prophylactic agent is high, and the cost of the agent is low. A prophylaxis or treatment may be curative, that is, directed at the underlying cause of a disease, or ameliorative, that is, directed at the symptoms of the disease, especially those which reduce the quality of life. It should also be understood that to be useful, the protection provided need not be absolute, provided that it is sufficient to carry clinical value. An agent which provides protection to a lesser degree than do competitive agents may still be of value if the other agents are ineffective for a particular individual, if it can be used in combination with other agents to enhance the level of protection, or if it is safer than competitive agents. It is desirable that there be a statistically significant (p=0.05 or less) improvement in the treated subject relative to an appropriate untreated control, and it is desirable that this improvement be at least 10%, more preferably at least 25%, still more preferably at least 50%, even more preferably at least 100%, in some indicia of the incidence or severity of the disease or of at least one symptom of the disease . At least one of the drugs of the present invention may be administered, by any means that achieve their intended purpose, to protect a subject against a disease or other adverse condition. The form of administration may be systemic or topical. For example; administration of such a composition may be by various parenteral routes such as subcutaneous, intravenous, intradermal, intramuscular, intraperitoneal, intranasal, transdermal, or buccal routes. Alternatively, or concurrently, administration may be by the oral route. Parenteral administration can be by bolus injection or by gradual perfusion over time. A typical regimen comprises administration of an effective amount of the drug, administered over a period ranging from a single dose, to dosing over a period of hours, days, weeks , months , or years . It is understood that the suitable dosage of a drug of the present invention will be dependent upon the age, sex, health, and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment, and the nature of the effect desired. However, the most preferred dosage can be tailored to the individual subject, as is understood and determinable by one of skill in. the art, without undue experimentation. This will typically involve adjustment of a standard dose, e.g., reduction of the dose if the patient has a low body weight . Prior to use in humans, a drug will first be evaluated for safety and efficacy in laboratory animals. In human clinical studies, one would begin with a dose expected to be safe in humans, based on the preclinical data for the drug in- question, and on customary doses for analogous drugs (if any) . If this dose is effective, the dosage may be decreased, to determine the minimum effective dose, if desired. If this dose is ineffective, it will be cautiously increased, with the patients monitored for signs of side effects. See, e.g., Berkow et al, eds., The Merck Manual, 15th edition, Merck and Co., Rahway, N.J., 1987; Goodman et al . , eds., Goodman and Gil an ' s The Pharmacological Basis of Therapeutics, 8th edition, Pergamon Press, Inc., Elmsford, N.Y., (1990); Avery' s Drug Treatment: Principles and Practice of Clinical Pharmacology and Therapeutics , 3rd edition, ADIS Press, LTD., Williams and Wilkins, Baltimore, MD. (1987), Ebadi, Pharmacology, Little, Brown and Co., Boston, (1985) , which references and references cited therein, are entirely incorporated herein by reference. The total dose required for each treatment may be administered by multiple doses or in a single dose. The protein may be administered alone or in conjunction with other therapeutics directed to the disease or directed to other symptoms thereof . The appropriate dosage form will depend on the disease, the pharmaceutical, and the mode of administration; possibilities include tablets, capsules, lozenges, dental pastes, suppositories, inhalants, solutions, ointments and parenteral depots. See, e.g., Berker, supra, Goodman, supra, Avery, supra and Ebadi, supra, which are entirely incorporated herein by reference, including all references cited therein. In the case of peptide drugs, the drug may be administered in the form of an expression vector comprising a nucleic acid encoding the peptide; such a vector, after incorporation into the genetic complement of a cell of the patient, directs synthesis of the peptide. Suitable vectors include genetically engineered poxviruses (vaccinia) , adenoviruses, adeno-associated viruses, herpesviruses and lentiviruses which are or have been rendered nonpathogenic . In addition to at least one drug as described herein, a pharmaceutical composition may contain suitable pharmaceutically acceptable carriers, such as excipients, carriers and/or auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. See, e.g., Berker, supra, Goodman, supra, Avery, supra and Ebadi, supra, which are entirely incorporated herein by reference, included all references cited therein.

Assay Compositions and Methods

Target Organism The invention contemplates that it may be appropriate to ascertain or to mediate the biological activity of a substance of this invention in a target organism. The target organism may be a plant,^' animal, or microorganism. In the case of a plant, it may be an economic plant, in which case the drug may be intended to increase the disease, weather or pest resistance, alter the growth characteristics, or otherwise improve the useful characteristics or mute undesirable characteristics of the plant. Or it may be a weed, in which case the drug may be intended to kill or otherwise inhibit the growth of the plant, or to alter its characteristics to convert it from a weed to an economic plant. The plant may be a tree, shrub, crop, grass, etc. The plant may be an algae (which are in some cases also microorganisms) , or a vascular plant, especially gymnosperms (particularly conifers) and angiosperms . Angiosperms may be monocots or dicots. The plants of greatest interest are rice, wheat, corn, alfalfa, soybeans, potatoes, peanuts, tomatoes, melons, apples, pears, plums, pineapples, fir, spruce, pine, cedar, and oak. If the target organism is a microorganism, it may be algae, bacteria, fungi, or a virus (although the biological activity of a virus must be determined in a virus-infected cell) . The microorganism may be human or other animal or plant pathogen, or it may be nonpathogenic. It may be a soil or water organism, or one which normally lives inside other living things. If the target organism is an animal, it may be a vertebrate or a nonvertebrate animal . Nonvertebrate animals are chiefly of interest when they act as pathogens or parasites, and the drugs are intended to act as biocidic or biostatic agents. Nonvertebrate animals of interest include worms, mollusks, and arthropods. The target organism may also be a vertebrate animal, i.e., a mammal, bird, reptile, fish or amphibian. Among mammals, the target animal preferably belongs to the order Primata (humans, apes and monkeys), Artiodactyla (e.g., cows, pigs, sheep, goats, horses), Rodenta (e.g., mice, rats) Lagomorpha (e.g., rabbits, hares), or Carnivora (e.g., cats, dogs) . Among birds, the target animals are preferably of the orders Anseriformes (e.g., ducks, geese, swans) or Galliformes (e.g., quails, grouse, pheasants, turkeys and chickens) . Among fish, the target animal is preferably of the order Clupeiformes (e.g., sardines, shad, anchovies, whitefish, salmon) .

Target Tissues The term "target tissue" refers to any whole animal, physiological system, whole organ, part of organ, miscellaneous tissue, cell, or cell component (e.g., the cell membrane) of a target animal in which biological activity may be measured. Routinely in mammals one would choose to compare and contrast the biological impact on virtually any and all tissues which express the subject receptor protein. The main tissues to use are: brain, heart, lung, kidney, liver, pancreas, skin, intestines, adipose, stomach, skeletal muscle, adrenal glands, breast, prostate, vasculature, retina, cornea, thyroid gland, parathyroid glands, thymus, bone marrow, bone, etc. Another classification would be by cell type: B cells, T cells, macrophages, neutrophils, eosinophils, mast cells, platelets, megakaryocytes, erythrocytes, bone marrow stomal cells, fibroblasts, neurons, astrocytes, neuroglia, microglia, epithelial cells (from any organ, e.g. skin, breast, prostate, lung, intestines etc) , cardiac muscle cells, smooth muscle cells, striated muscle cells, osteoblasts, osteocytes, chondroblasts, chondrocytes , keratinocytes, melanocytes, etc. Of course, in the case of a unicellular organism, there is no distinction between the "target organism" and the "target tissue".

Screening Assays Assays intended to determine the binding or the biological activity of a substance are called preliminary screening assays. Screening assays will typically be either in vitro (cell-free) assays (for binding to an immobilized receptor) or cell-based assays (for alterations in the phenotype of the cell) . They will not involve screening of whole multicellular organisms, or isolated organs. The comments on diagnostic biological assays apply mutatis mutandis to screening cell-based assays.

In Vitro vs . In Vivo Assays The term in vivo is descriptive of an event, such as binding or enzymatic action, which occurs within a living organism. The organism in question may, however, be genetically modified. The term in vi tro refers to an event which occurs outside a living organism. Parts of an organism (e.g., a membrane, or an isolated biochemical) are used, together with artificial substrates and/or conditions. For the purpose of the present invention, the term in vitro excludes events occurring inside or on an intact cell, whether of a unicellular or multicellular organism. In vivo assays include both cell-based assays, and organismic assays. The cell-based assays include both assays on unicellular organisms, and assays on isolated cells or cell cultures- derived from multicellular organisms. The cell cultures may be mixed, provided that they are not organized into tissues or organs. The term organismic assay refers to assays on whole multicellular organisms, and assays on isolated organs or tissues of such organisms.

In vitro Diagnostic Methods and Reagents The in vitro assays of the present invention may be applied to any suitable analyte-containing sample, and may be qualitative or quantitative in nature.

Sample The sample will normally be a biological fluid, such as blood, urine, lymph, semen, milk, or cerebrospinal fluid, or a fraction or derivative thereof, or a biological tissue, in the form of, e.g., a tissue section or homogenate. However, the sample conceivably could be (or derived from) a food or beverage, a pharmaceutical or diagnostic composition, soil, or surface or ground water. If a biological fluid or tissue, it may be taken from a human or other mammal, vertebrate or animal, or from a plant. The preferred sample is blood, or a fraction or derivative thereof.

Binding and Reaction Assays The assay may be a binding assay, in which one step involves the binding of a diagnostic reagent to the analyte, or a reaction assay, which involves the reaction of a reagent with the analyte. The reagents used in a binding assay.may be classified as to the nature of their interaction with analyte: (1) analyte analogues, or (2) analyte binding molecules (ABM) . They may be labeled or insolubilized. In a reaction assay, the assay may look for a direct reaction between the analyte and a reagent which is reactive with the analyte, or if the analyte is an enzyme or enzyme inhibitor, for a reaction catalyzed or inhibited by the analyte. The reagent may be a reactant, a catalyst, or an inhibitor for the reaction. An assay may involve a cascade of steps in which the product of one step acts as the target for the next step. These steps may be binding steps, reaction steps, or a combination thereof .

Signal Producing System (SPS) In order to detect the presence, or measure the amount, of an analyte, the assay must provide for a signal producing system (SPS) in which there is a detectable difference in the signal produced, depending on whether the analyte is present or absent (or, in a quantitative assay, on the amount of the analyte) . The detectable signal may be one which is visually detectable, or one detectable only with instruments. Possible signals include production of colored or luminescent products, alteration of the characteristics (including amplitude or polarization) of absorption or emission of radiation by an assay component or product, and precipitation or agglutination of a component or product. The term "signal" is intended to include the discontinuance of an existing signal, or a change in the rate of change of an observable parameter, rather than a change in its absolute value. The signal may be monitored manually or automatically. In a reaction assay, the signal is often a product of the reaction. In a binding assay, it is normally provided by a label borne by a labeled reagent .

Labels The component of the signal producing system which is most intimately associated with the diagnostic reagent is called the "label". A label may be, e.g., a radioisotope, a fluorophore, an enzyme, a co-enzyme, an enzyme substrate, an electron-dense compound, an agglutinable particle. The radioactive isotope can be detected by such means as the use of a gamma counter or a scintillation counter or by autoradiography. Isotopes which are particularly useful for the purpose of the present invention include ³H, ¹²⁵I, ¹³¹I, ³⁵S, ¹⁴C, ³²P and ³³P. ¹²⁵I is preferred for antibody labeling. The label may also be a fluorophore. When the fluorescently labeled reagent is exposed to light of the proper wave length, its presence can then be detected due to fluorescence. Among the most commonly used fluorescent labelling compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o- phthaldehyde and fluorescamine. Alternatively, fluorescence-emitting metals such as ¹²⁵Eu, or others of the lanthanide series, may be incorporated into a diagnostic reagent using such metal chelating groups as diethylenetriaminepentaacetic acid (DTPA) of ethylenediamine-tetraacetic acid (EDTA) . The label may also be a chemiluminescent compound. The presence of the chemilummescently labeled reagent is then determined by detecting the presence of luminescence that arises during the course of a chemical reaction. Examples of particularly useful chemiluminescent labeling compounds are luminol, isolumino, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester. Likewise, a bioluminescent compound may be used for labeling. Bioluminescence is a type of chemiluminescence found in biological systems, in which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence. Important bioluminescent compounds for purposes of labeling are luciferin, luciferase and aequorin. Enzyme labels, such as horseradish peroxidase and alkaline phosphatase, are preferred. When an enzyme label is used, the signal producing system must also include a substrate for the enzyme. If the enzymatic reaction product is not itself detectable, the SPS will include one or more additional reactants so that a detectable product appears. ^• An enzyme analyte may act as its own label if an enzyme inhibitor is used as a diagnostic reagent.

Binding Assay Formats Binding assays may be' divided into two basic types, heterogeneous and homogeneous. In heterogeneous assays, the interaction between the affinity molecule and the analyte does not affect the label, hence, to determine the amount or presence of analyte, bound label must be separated from free label. In homogeneous assays, the interaction does affect the activity of the label, and therefore analyte levels can be deduced without the need for a separation step. In one embodiment, the ABM is insolubilized by coupling it to a macromolecular support, and analyte in the sample is allowed to compete with a known quantity of a labeled or specifically labelable analyte analogue. The "analyte analogue" is a molecule capable of competing with analyte for binding to the ABM, and the term is intended to include analyte itself. It may be labeled already, or it may be labeled subsequently by specifically binding the label to a moiety differentiating the analyte analogue from analyte. The solid and liquid phases are separated, and the labeled analyte analogue in one phase is quantified. The higher the level of analyte analogue in the solid phase, i.e., sticking to the ABM, the lower the level of analyte in the sample . In a "sandwich assay", both an insolubilized ABM, and a labeled ABM are employed. The analyte is captured by the insolubilized ABM and is tagged by the labeled ABM, forming a ternary complex. The reagents may be added to the sample in either order, or simultaneously. The ABMs may be the same or different. The amount of labeled ABM in the ternary complex is directly proportional to the amount of analyte in the sample. The two embodiments described above are both heterogeneous assays. However, homogeneous assays are conceivable. The key is that the label be affected by whether or not the complex is formed.

Conjugation Methods A label may be conjugated, directly or indirectly (e.g., through a labeled anti-ABM antibody), covalently (e.g., with SPDP) or noncovalently, to the ABM, to produce a diagnostic reagent. Similarly, the ABM may be conjugated to a solid phase support to form a solid phase ("capture") diagnostic reagent. Suitable supports include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, agaroses, and magnetite . The nature of the carrier can be either soluble to some extent or insoluble for the purposes of the present invention. The support material may have virtually any possible structural configuration so long as the coupled molecule is capable of binding to its target. Thus the support configuration may be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod. Alternatively, the surface may be flat such as a sheet, test strip, etc.

Biological Assays A biological assay measures or detects a biological response of a biological entity to a substance. The biological entity may be a whole organism, an isolated organ or tissue, freshly isolated cells, an immortalized cell line, or a subcellular component (such as a membrane; this term should not be construed as including an isolated receptor) . The entity may be, or may be derived from, an organism which occurs in nature, or which is modified in some way. Modifications may be genetic (including radiation and chemical mutants, and genetic engineering) or somatic (e.g., surgical, chemical, etc.). In the case of a multicellular entity, the modifications may affect some or all cells. The entity need not be the target organism, or a derivative thereof, if there is a reasonable correlation between bioassay activity in the assay entity and biological activity in the target organism. The entity is placed in a particular environment, which may be more or less natural. For example, a culture medium may, but need not, contain serum or serum substitutes, and it may, but need not, include a support matrix of some kind, it may be still, or agitated. It may contain particular biological or chemical agents, or have particular physical parameters (e.g., temperature), that are intended to nourish or challenge the biological entity. There must also be a detectable biological marker for the response. At the cellular level, the most common markers are cell survival and proliferation, cell behavior (clustering, motility) , cell morphology (shape, color) , and biochemical activity (overall DNA synthesis, overall protein synthesis, and specific metabolic activities, such as utilization of particular nutrients, e.g., consumption of oxygen, production of C0₂, production of organic acids, uptake or discharge of ions) . The direct signal produced by the biological marker may be transformed by a signal producing system into a different signal which is more observable, for example, a fluorescent or colorimetric signal. The entity, environment, marker and signal producing system are chosen to achieve a clinically acceptable level of sensitivity, specificity and accuracy. In some cases, the goal will be to identify substances which mediate the biological activity of a natural biological entity, and the assay is carried out directly with that entity. In other cases, the biological entity is used simply as a model of some more complex (or otherwise inconvenient to work with) biological entity. In that event, the model biological entity is used because activity in the model system is considered more predictive of activity in the ultimate natural biological entity than is simple binding activity in an in vitro system. The model entity is used instead of the ultimate entity because the former is more expensive or slower to work with, or because ethical considerations forbid working with the ultimate entity yet . The model entity may be naturally occurring, if the model entity usefully mpdels the ultimate entity under some conditions. Or it may be non-naturally occurring, with modifications that increase its resemblance to the ultimate entity. Transgenic_. animals, such as transgenic mice, rats, and rabbits, have been found useful as model systems. In cell-based model assays, where the biological activity is mediated by binding to a receptor (target protein) , the receptor may be functionally connected to a signal (biological marker) producing system, which may be endogenous or exogenous to the cell. There are a number of techniques of doing this.

"Zero-Hybrid" Systems In these systems, the binding of a peptide to the target protein results in a screenable or selectable phenotypic change, without resort to fusing the target protein (or a ligand binding moiety thereof) to an endogenous protein. It may be that the target protein is endogenous to the host cell, or is substantially identical to an endogenous receptor so that it can take advantage of the latter' s native signal transduction pathway. Or sufficient elements of the signal transduction pathway normally associated with the target protein may be engineered into the cell so that the cell signals binding to the target protein. "One-Hybrid" Systems In these systems, a chimera receptor, a hybrid of the target protein and an endogenous receptor, is used. The chimeric receptor has the ligand binding characteristics of the target protein and the signal transduction characteristics of the endogenous receptor. Thus, the normal signal transduction pathway of the endogenous receptor is subverted. Preferably, the endogenous receptor is inactivated, or the conditions of the assay avoid activation of the endogenous receptor, to improve the signal-to-noise ratio. See Fowlkes USP 5,789,184 for a yeast system. Another type of "one-hybrid" system combines a peptide: DNA-binding domain fusion with an unfused target receptor that possesses an activation domain.

"Two-Hybrid" System In a preferred embodiment, the cell-based assay is a two hybrid system. This term implies that the ligand is incorporated into a first hybrid protein, and the receptor into a second hybrid protein. The first hybrid also comprises component A of a signal generating system, and the second hybrid comprises component B of that system. Components A and B, by themselves, are insufficient to generate a signal. However, if the ligand binds the receptor, components A and B are brought into sufficiently close proximity so that they can cooperate to generate a signal . Components A and B may naturally occur, or be substantially identical to moieties which naturally occur, as components of a single naturally occurring biomolecule, or they may naturally occur, or be substantially identical to moieties which naturally occur, as separate naturally occurring biomolecules which interact in nature . Two-Hybrid System: Transcription Factor Type In a preferred "two-hybrid" embodiment, one member of a peptide ligand: receptor binding pair is expressed as a fusion to a DNA-binding domain (DBD) from a transcription factor (this fusion protein is called the "bait"), and the other is expressed as a fusion to a transactivation domain (TAD) (this fusion protein is called the "fish", the "prey", or the "catch") . The transactivation domain should be complementary to the DNA-binding domain, i.e., it should interact with the latter so as to activate transcription of a specially designed reporter gene that carries a binding site for the DNA-binding domain. Naturally, the two fusion proteins must likewise be complementary. This complementarity may be achieved by use of the complementary and separable DNA-binding and transcriptional activator domains of a single transcriptional activator protein, or one may use complementary domains derived from different proteins. The domains may be identical to the native domains, or mutants thereof. The assay members may be fused directly to the DBD or TAD, or fused through an intermediated linker. The target DNA operator may be the native operator sequence, or a mutant operator. Mutations in the operator may be coordinated with mutations in the DBD and the TAD. An example of a suitable transcription activation system is one comprising the DNA-binding domain from the bacterial repressor LexA and the activation domain from the yeast transcription factor Gal4, with the reporter gene operably linked to the LexA operator. It is not necessary to employ the intact target receptor; just the ligand-binding moiety is sufficient. The two fusion proteins may be expressed from the same or different vectors. Likewise, the activatable reporter gene may be expressed from the same vector as either fusion protein (or both proteins) , or from a third vector. Potential DNA-binding domains include Gal4 , LexA, and mutant domains substantially identical to the above. Potential activation domains include E. coli B42, Gal4 activation domain II, and HSV VP16, and mutant domains substantially identical to the above. Potential operators include the native operators for the desired activation domain, and mutant domains substantially identical to the native operator. The fusion proteins may comprise nuclear localization signals . ' The assay system will include a signal producing system, too. The first element of this system is a reporter gene operably linked to an operator responsive to the DBD and TAD of choice . The expression of this reporter gene will result, directly or indirectly, in a selectable or screenable phenotype (the signal) . The signal producing system may include, besides the reporter gene, additional genetic or biochemical elements which cooperate in the production of the signal. Such an element could be, for example, a selective agent in the cell growth medium. There may be more than one signal producing system, and the system may include more than one reporter gene . The sensitivity of the system may be adjusted by, e.g., use of competitive inhibitors of any step in the activation or signal production process, increasing or decreasing the number of operators, using a stronger or weaker DBD or TAD, etc. When the signal is the death or survival of the cell in question, or proliferation or nonproliferation of the cell in question, the assay is said to be a selection. When the signal merely results in a detectable phenotype by which the signaling cell may be differentiated from the same cell in a nonsignaling state (either way being a living cell) , the assay is a screen. However, the term "screening assay" may be used in a broader sense to. include a selection. When the narrower sense is intended, we will use the term "nonselective screen" . Various screening and selection systems are discussed in Ladner, USP 5,198,346. Screening and selection may be for or against the peptide: target protein or compound: target protein interaction. Preferred assay cells are microbial (bacterial, yeast, algal, protozooal) , invertebrate, vertebrate (esp. mammalian, particularly human) . The best developed two- hybrid assays are yeast and mammalian systems. Normally, two hybrid assays are used to determine whether a protein X and a protein Y interact, by virtue of their ability to reconstitute the interaction of the DBD and the TAD. However, augmented two-hybrid assays have been used to detect interactions that depend on a third, non- protein ligand. For more guidance on two-hybrid assays, see Brent and Finley, Jr., Ann. Rev. Genet., 31:663-704 (1997); Fremont- Racine, et al., Nature Genetics, 277-281 (16 July 1997); Allen, et al . , TIBS, 511-16 (Dec. 1995); LeCrenier, et al . , BioEssays, 20:1-6 (1998); Xu, et al . , Proc. Nat. Acad. sci. (USA), 94:12473-8 (Nov. 1992); Esotak, et al . , Mol. Cell. Biol., 15:5820-9 (1995); Yang, et al . , Nucleic Acids Res., 23:1152-6 (1995); Bendixen, et al . , Nucleic Acids Res., 22:1778-9 (1994); Fuller, et al . , BioTechniques, 25:85-92 (July 1998); Cohen, et al . , PNAS (USA) 95:14272-7 (1998); Kolonin and Finley, Jr., PNAS (USA) 95:14266-71 (1998). See also Vasavada, et al . , PNAS (USA), 88:10686-90 (1991) (contingent replication assay), and Rehrauer, et al . , J. Biol. Chem., 271:23865-73 91996) (LexA repressor cleavage assay)

Two-Hybrid Systems: reporter Enzyme type In another embodiment, the components A and B reconstitute an enzyme which is not a transcription factor.

As in the last example, the effect of the reconstitution of the enzyme is a phenotypic change which may be a screenable change, a selectable change, or both.

In vivo Diagnostic Uses Radio-labeled ABM may be administered to the human or animal subject. Administration is typically by injection, e.g., intravenous or arterial or other means of administration in a quantity sufficient to permit subsequent dynamic and/or static imaging using suitable radio-detecting devices. The dosage is the smallest amount capable of providing a diagnostically effective image, and may be determined by means conventional in the art, using known radio-imaging agents as a guide. Typically, the imaging is carried out on the whole body of the subject, or on that portion of the body or organ relevant to the condition or disease under study. The amount of radio-labeled ABM accumulated at a given point in time in relevant target organs can then be quantified. A particularly suitable radio-detecting device is a scintillation camera, such as a gamma camera. A scintillation camera is a stationary device that can be used to image distribution of radio-labeled ABM. The detection device in the camera senses the radioactive decay, the distribution of which can be recorded. Data produced by the imaging system can be digitized. The digitized information can be analyzed over time discontinuously or continuously. The digitized data can be processed to produce images, called frames, of the pattern of uptake of the radio- labelled ABM in the target organ at a discrete point in time. In most continuous (dynamic) studies, quantitative data is obtained by observing changes in distributions of radioactive decay in target organs over time. In other words, a time-activity analysis of the data will illustrate uptake through clearance of the radio-labeled binding protein by the target organs with time. Various factors should be taken into consideration in selecting an appropriate radioisotope. The radioisotope must be selected with a view to obtaining good quality resolution upon imaging, should be safe for diagnostic use in humans and animals, and should preferably have a short physical half-life so as to decrease the amount of radiation received by the body. The radioisotope used should preferably be pharmacologically inert, and, in the quantities administered, should not have any substantial physiological effect. The ABM may be radio-labeled with different isotopes of iodine, for example ¹²³I, ¹²⁵I, or ¹³¹I (see for example, U.S. Patent 4,609,725). The extent of radio-labeling must, however be monitored, since it will affect the calculations made based on the imaging results (i.e. a diiodinated ABM will result in twice the radiation count of a similar monoiodinated ABM over the same time frame) . In applications to human subjects, it may be desirable to use radioisotopes other than ¹²⁵I for labeling in order to decrease the total dosimetry exposure of the human body and to optimize the detectability of the labeled molecule (though this radioisotope can be used if circumstances require) . Ready availability for clinical use is also a factor. Accordingly, for human applications, preferred radio-labels are for example, ^99mTc, ^S7Ga, ⁶⁸Ga, ⁹⁰Y, ^11:LIn, ^113raIn, ¹²³I, ^18βRe, ¹⁸⁸Re or ²¹¹At . The radio-labelled ABM may be prepared by various methods. These include radiσ-halogenation by the chloramine - T method or the lactoperoxidase method and subsequent purification by HPLC (high pressure liquid chromatography) , for example as described by J. Gutkowska et al in "Endocrinology and Metabolism Clinics of America: (1987) 16_. (1) :183. Other known methods of radio-labeling can be used, such as IODOBEADS™. There are a number of different methods of delivering the radio-labeled ABM to the end-user. It may be administered by any means that enables the active agent to reach the agent ' s site of action in the body of a mammal . Because proteins are subject to being digested when administered orally, parenteral administration, i.e., intravenous, subcutaneous, intramuscular, would ordinarily be used to optimize absorption of an ABM, such as an antibody, which is a protein.

EXAMPLES Example 1

Differentially expressed mouse genes, and corresponding human genes/proteins, were identified as described in this Example, and compiled into Master Table 1.

Animal Models Upon separation from their mothers (weaning) , C57B1/6J mice (i.e., C57B1/6 mice developed by Jackson Labs) were placed on a normal diet (PMI Nutrition International Inc., Brentwood, MO, Prolab RMH3000) . Two mice were sacrificed at an average of 35, 49, 77, 118, 133, 207, 403, 558 and 725 days of age.

RNA isolation. Total RNA was isolated from muscle (ga trocnemius) using the RNA STAT-60 Total RNA/mRNA Isolation Reagent according to the manufacturer's instructions (Tel-Test, Friendswood, TX) .

Sample Quantification and Quality Assessment Total RNA was quantified and assessed for quality on a Bioanalyzer RNA 6000 Nano chip (Agilent) . Each chip contained an interconnected set of gel-filled channels that allowed for molecular sieving of nucleic acids . Pin- electrodes in the chip were used to create electrokinetic forces capable of driving molecules through these micro- channels to perform electrophoretic separations. Ribosomal peaks were measured by fluorescence signal and displayed in an electropherogram. A successful total RNA sample featured 2 distinct ribosomal peaks (18S and 28S rRNA) .

Biotinylated cRNA Hybridization Target. Total RNA was prepared for use as a hybridization target as described in the manufacturer's instructions for CodeLink Expression Bioarrays (TM) (Amersham Biosciences) . The CodeLink Expression Bioarrays utilize nucleic acid hybridization of a biotin-labeled complementary RNA(cRNA) target with DNA oligonucleotide probes attached to a gel matrix. The biotin-labeled cRNA target is prepared by a linear amplification method. Poly (A) + RNA (within the total RNA population) is primed for reverse transcription by a DNA oligonucleotide containing a T7 RNA polymerase promoter 5¹ to a (dT) 24 sequence. After second-strand cDNA synthesis, the cDNA serves as the template in an in vitro transcription (IVT) reaction to produce the target cRNA. The IVT is performed in the presence of biotinylated nucleotides to label the target cRNA. This procedure results in a 50-200 fold linear amplification of the input poly (A) + RNA.

Hybridization Probes. The oligonucleotide probes were provided by the Codelink Uniset Mouse I Bioarray (Amersham, product code 300013) . Amine-terminated oligonucleotide probes are attached to a three-dimensional polyacrylamide gel matrix. There are 10,000 oligonucleotide probes, each specific to a well-characterized mouse gene. Each mouse gene is representative of a unique gene cluster from the fourth quarter 2001 Genbank Unigene build. There are also 500 control probes . The sequences of the probes are proprietary to Amersham. However, for each probe, Amersham identifies the corresponding mouse gene by NCBI accession number, OGS, LocusLink, Unigene Cluster ID, and description (name) . This information should be available from Amersham. In the case of the differentially expressed probes, this information is duplicated in master table 1. For the complete list, see http : //www4. amershambiosciences . com/aptrix/upp01077. nsf/Cont ent/codelink_literature

Under "Gene Lists", select "Uniset Mouse I", and a gene list, in Excel format, can be downloaded.

Hybridization Using the cRNA target, the hybridization reaction mixture is prepared and loaded into array chambers for bioarray processing as set forth in the manufacturer's instructions for CodeLink Gene Expression BioarraysTM (Amerhsam Biosciences) . Each sample is hybridized to an individual microarray. Hybridization is at 37°C. The hybridization buffer is prepared as set forth in the Motorola instructions. Hybridization to the microarray is detected with an avidinated fluorescent reagent, Streptavidin-Alexa Fluor ® 647 (Amersham) .

Mouse Gene Expression Analysis Processed arrays were scanned using a GenePix 400OB Microarray Scanner (Axon Instruments, Inc.); array images were acquired using the Amersham CodeLink™ Analysis Software (Release 2.2) . The Amersham CodeLink™ Analysis Software gives an integrated optical density (IOD) value for every spot; a unique background value for that spot is subtracted, resulting in "raw" data points. Individual chips are then normalized by the Amersham Codelink™ software according to the median raw intensity for all 10,000 genes. A negative control threshold (0.2) is also calculated according to the control probes. A significant difference in expression between samples was defined as a minimum of 2-fold change in expression values. Genes with expression values below the negative control threshold were eliminated from the analysis and then the expression data was analyzed to identify genes whose expression levels changed significantly with respect to age . The list of genes in the tables is a combination of two analyses. Samples of average age 35, 49, 77 and 133 days were compared pair-wise in all possible combinations (6 comparisons) and genes showing differences in expression greater than 2-fold were listed in the table. The remaining samples were divided into three groups (118 days (2 mice) : young; 207 and 403 (4 mice) averaged together: medium; 558 and 725 (4 mice) averaged together: old) , the three groups were compared in all possible pair-wise combinations (3 comparisons) and genes showing differences in expression greater than 2-fold were added to the table.

Database Searches Nucleotide sequences and predicted amino acid sequences were compared to public domain databases using the Blast 2.0 program (National Center for Biotechnology Information, National Institutes of Health) . Nucleotide database searches were conducted with the then current version of BLASTN 2.0.12, see Altschul, et al . , "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res., 25:3389-3402 (1997) . Searches employed the default parameters, unless otherwise stated. For blastN searches, the default was the blastN matrix (1,-3), with gap penalties of 5 for existence and 2 for extension. Protein database searches were conducted with the then- current version of BLAST X, see Altschul et al . (1997), supra. Searches employed the default parameters, unless otherwise stated. The scoring matrix was BLOSUM62, with gap costs of 11 for existence and 1 for extension. The standard low complexity filter was used. "ref" indicates that NCBI's RefSeq is the source database. The identifier that follows is a RefSeq accession number, not a GenBank accession number. "RefSeq sequences are derived from GenBank and provide non-redundant curated data representing our current knowledge of known genes. Some records include additional sequence information that was never submitted to an archival database but is available in the literature . A small number of sequences are provided through collaboration; the underlying primary sequence data is available in GenBank, but may not be available in any one GenBank record. RefSeq sequences are not submitted primary sequences. RefSeq records are owned by NCBI and therefore can be updated as needed to maintain current annotation or to incorporate additional sequence information." See also htt : //www.ncbi .nlm.nih.gov/LocusLink/refseq. html

It will be appreciated by those in the art that the exact results of a database search will change from day to day, as new sequences are added. Also, if you query with a longer version of the original sequence, the results will change. The results given here were obtained at one time and no guarantee is made that the exact same hits would be obtained in a search on the filing date. However, if an alignment between a particular query sequence and a particular database sequence is discussed, that alignment should not change (if the parameters and sequences remain unchanged) .

Northern Analysis . Northern analysis may be used to confirm the results. Favorable and unfavorable genes, identified as described above, or fragments thereof, will be used as probes in Northern hybridization analyses to confirm their differential expression. Total RNA isolated from subject mice will be resolved by agarose gel electrophoresis through a 1% agarose, 1 % formaldehyde denaturing gel, transferred to positively charged nylon membrane, and hybridized to a probe labeled with [32P] dCTP that was generated from the aforementioned gene or fragment using the Random Primed DNA Labeling Kit (Roche, Palo Alto, CA) , or to a probe labeled with digoxygenin according to the manufacturer's instructions (Roche, Palo Alto, CA) .

Real-Time RNA Analysis. Real-time RNA analysis may also be used for confirmation. For "real-time" RNA analysis, RNA will be converted to cDNA and then probed with gene-specific primers made for each clone. "Real-time" incorporation of fluorescent dye will be measured to determine the amount of specific transcript present in each sample. Sample differences (older vs. younger) of 2-fold or greater (in either direction) will be considered differentially expressed. Confirmation using several independent animals is desirable.

In situ Hybridization Another form of confirmation may be provided by nonisotopic in si tu hybridizations (NISH) on selected human (obtained by Tissue Informatics) and mouse tissues using cRNA probes generated from mouse genes found to be up- or down-regulated during aging. In si tu hybridizations may also be performed on mouse tissues using cRNA probes generated from differentially expressed DNAs. These cRNA's will hybridize to their corresponding messenger RNA's present in cells and will provide information regarding the particular cell types within a tissue that is expressing the particular gene as well as the relative level of gene expression. The cRNA probes may be generated by in vi tro transcription of template cDNA by Sp6 or T7 RNA polymerase in the presence of digoxigenin-11-UTP (Roche Molecular Biochemicals, Mannheim, Germany; Pardue, M.L. 1985. In: In situ hybridization, Nucleic acid hybridization, a practical approach: IRL Press, Oxford, 179-202) .

Transgenic Animals . Transgenic expression may be used to confirm the results. In one embodiment, a mouse is engineered to overexpress the favorable or unfavorable mouse gene in question. In another embodiment, a mouse is engineered to express the corresponding favorable or unfavorable human gene. In a third embodiment, a nonhuman animal other than a mouse, such as a rat, rabbit, goat, sheep or pig, is engineered to express the favorable or unfavorable mouse or human gene.

Hyperquantitative Tissue Analysis In addition to gene expression analysis the tissue sections can also be analyzed using Tissuelnformatics, Inc's TissueAnalytics™ software. A single representative section may be cut from each tissue block, placed on a slide, and stained with H&E. Digital images of each slide may be . acquired using an research microscope and digital camera (Olympus E600 microscope and Sony DKC-ST5) . These images may be acquired at 20x magnification with a resolution of 0.64 mm/pixel. A hyperquantitative analysis may be performed on the resulting images : First a digital image analysis can identify and annotate structural objects in a tissue using machine vision. These objects, that are constituents of the tissue, can be annotated because they are visually identifiable and have a biological meaning. Subsequently a quantification of these structures regarding their geometric properties like area or stain intensities and their relationship to the field of view or per unit area in terms of a % coverage may be performed. Features or parameters for hyper-quantification are specific for each tissue, and may also include relations between features, measures of overall heterogeneity, including orientation, relative locations, and textures.

Correlation Analysis Mathematical statistics provides a rich set of additional tools to analyze time resolved data sets of hyperquantitative and gene expression profiles for similarities, including rank correlation, the calculation of regression and correlation coefficients, and clustering. Continuous functions may also be fitted through the data points of individual gene and tissue feature data. Relation between gene expression and hyper-quantitative tissue data may be linear or non-linear, in synchronous or asynchronous arrangements . The related applications may contain reference to "2-16 week old mice" . In the anti-diabetes series of applications, 3 week old mice were put on a diet to induce obesity, hyperinsulinemia and diabetes. The 2-16 week old mice were more accurately described as mice who had been on that diet for 2-16 weeks, i.e., they were actually 5-19 weeks (35-133 days) old. Even some of the anti-aging series of applications made reference to 2-16 week old mice, even though the mice were in fact 5-19 weeks (35-133 days) old.

ATHUG actin gamma 1 723 0 CAA27723.1 gamma-actin 723 0 AAA51579.1 gamma-actin 723 0 AAH00292.1 actin, gamma 1 723 0 AAH01920.1 actin, gamma 1 723 0 AAH07442.1 actin, gamma 1 723 0 AAH09848.1 actin, gamma 1 723 0 AAH10999.1 Similar to actin, gamma 1 723 0 AAH12050.1 Similar to actin, gamma 1 723 0 AAH15005.1 actin, gamma 1 723 0 AAH15695.1 actin, gamma 1 723 0 AAH15779.1 actin, gamma 1 723 0 AAH18774.1 actin, gamma 1 723 0 NP_001092.1 beta actin; beta cytoskeletal actin 722 0 P02570 ACTBJHUMAN Actin, cytoplasmic 1 (Beta-actin) 722 0 ATHUB actin beta 722 0 CAA25099.1 beta-actin 722 0 AAA51567.1 cytoplasmic beta actin 722 0 AAH01301.1 actin, beta 722 0 AAH02409.1 actin, beta 722 0 AAH04251.1 actin, beta 722 0 AAH13380.1 actin, beta 722 0 AAH14861.1 actin, beta 722 0 AAH16045.1 actin, beta 720 0 CAA45026.1 mutant beta-actin (beta'-actin) 718 0

U08020 AAA88912.1 m.22621 11.16 P02452 CA11 HUMAN Collagen alpha 1(1) chain precursor 486 e -136 alpha 1 type I collagen preproprotein; Collagen I, alpha-1 polypeptide; osteogenesis NPJ300079.1 imperfecta type IV; collagen of skin, tendon and bone, alpha-1 chain 484 e ■136 CAA98968.1 prepro-alphal (I) collagen 484 e -136 CGHU1S collagen alpha 1(1) chain precursor 483 e -136 AAA51995.1 alpha 1 (I) chain propeptide 482 e -135

AAM 10442.1 REDD-1 CAB66603.1 hypothetical protein

NM_009242 secreted protein, acidic, cysteine-rich (osteonectin); Osteonectin (secreted protein, NP 033268.1 Mm.35439 F:4.66 NP_003109.1 acidic, cysteine-rich) SPRC_HUMAN SPARC precursor (Secreted protein acidic and rich in cysteine) P09486 (Osteonectin) (ON) (Basement membrane protein BM-40) GEHUN osteonectin precursor CAA68724.1 extracellular matrix protein BM-40 (AA 1 - 303) AAA60570.1 osteonectin AAH04974.1 secreted protein, acidic, cysteine-rich (osteonectin) AAH08011.1 secreted protein, acidic, cysteine-rich (osteonectin) AAA60993.1 osteonectin 1 BMO A Chain A, Bm-40, FsEC DOMAIN PAIR 1BMO B Chain B, Bm-40, FsEC DOMAIN PAIR 1 NUB A Chain A, Helix C Deletion Mutant Of Bm-40 Fs-Ec Domain Pair 1 NUB B Chain B, Helix C Deletion Mutant Of Bm-40 Fs-Ec Domain Pair

AAH33721.1 Unknown (protein for MGC:45264)

NPJ304675.2 SPARC-like 1; mast9; hevin

CAA60386.1 Hevin-like protein SPL1JHUMAN SPARC-like protein 1 precursor (High endothelial venule protein) Q14515 (Hevin) (MAST 9)

S60062 hevin precursor

CAA57650.1 hevin

AAB663δ3.1 Smadδ _r 515 e-145 AAH09682.1 MAD, mothers against decapentaplegic homolog δ 515 e-145 AAB82665.1 Mad homolog 615 e-145 AAC50791.1 Smadδ 613 e-144 MAD, mothers against decapentaplegic homolog 1; MAD (mothers against decapentaplegic, Drosophila) homolog 1 ; Mothers against NP 005891.1 decapentaplegic, Drosophila, homolog of, 1 δ07 e-143 Q1 δ797Mothers against decapentaplegic homolog 1 (SMAD 1) (Mothers against DPP homolog 1) (Mad-related protein 1) (Transforming Q16797 growth factor-beta signaling protein-1) (BSP-1) (hSMADI) δ07 e-143 S68987 transcription activator Smadl - human 507 e-143 AAC50493.1 mad-related protein MADR1 δ07 e-143 AAB068δ2.1 Smadl 507 e-143 AAC50621.1 transforming growth factor-beta signaling protein-1 δ07 e-143 AAC50790.1 Smadl 507 e-143 AAH01878.1 MAD, mothers against decapentaplegic homolog 1 507 e-143 MAD, mothers against decapentaple gic homolog 1 MAD, mothers against decapentaplegic homolog 1 507 e-143 MAD, mothers against decapentaplegic homolog 9; MAD (mothers against decapentaplegic, Drosophila) homolog 9; Mothers against NP_005896.1 decapentaplegic, drosophila, homolog of, 9 δ05 e-142 BAA21129.1 mother against dpp (Mad) related protein δ05 e-142 AAH 11559.1 MAD , mothers against decapentaplegic homolog 9 505 e-142

NM_009876 Mm.16878 2.00e- NP 034006.1 9 F:3.92 NP_000067.1 cyclin-dependent kinase inhibitor 1C; Beckwith-Wiedemann syndrome 228 59

AAH23620.1 Cyclin D1 253 8e-067 1709366A cyclin PRAD1 253 8e-067 AAA62136.1 cyclin D 250 7e-066 interleukin 6 signal transducer isoform 1 precursor; membrane glycoprotein gp130; oncostatin M receptor; CD130 antigen; interleukin receptor beta chain; gp130 transducer chain;

NM_0 0560 gp130 of the rheumatoid arthritis antigenic I49699 Mm.4364 F:3.4 NP 002175.2 peptide-bearing soluble form 1328 lnterIeukin-6 receptor beta chain precursor (lL-6R-beta) (Interleukin 6 signal transducer) (Membrane glycoprotein 130) (gp130) P40189 (Oncostatin M receptor) (CDw130) (CD130 antigen) 1327 0 A36337 membrane glycoprotein gp130 precursor - human 1327 0 AAA59156.1 membrane glycoprotein 130 1327 0 interleukin 6 signal transducer isoform 2 precursor; membrane glycoprotein gp130; oncostatin M receptor; CD130 antigen; interleukin receptor beta chain; gp130 transducer chain; gp130 of the rheumatoid arthritis antigenic NP_786943.1 peptide-bearing soluble form 467 e-131 gp130 of the rheumatoid arthritis antigenic peptide-bearing soluble BAA78112.1 form (gp130-RAPS) 466 e-130 111 R Chain A, Crystal Structure Of A CytokineRECEPTOR COMPLEX 445 e-124 Chain A, Crystal Structure Of The Hexameric Human II-6IL-6 Alpha 1P9M ReceptorGP130 COMPLEX 436 e-121 pdb|1BQU|A Chain A, Cytokyne-Binding Region Of Gp130 3101e-083 pdb|1BQU|B Chain B, Cytokyne-Binding Region Of Gp130 3101e-083 Chain A, Crystal Structure Of Leukemia Inhibitory Factor In Complex pdb|1PVH|A With Gp130 2893e-077

Chain C, Crystal Structure Of Leukemia Inhibitory Factor In Complex pdb|1PVH|C With Gp130 2893e-077 gp130-like monocyte receptor; soluble type I cytokine receptor CRL3; NP_620586.2 GP130 like receptor 2233e-057 AAM27968.1 gp130-like monocyte receptor 2233e-057 AAQ88484.1 GLM-R 2233e-057 colony stimulating factor 3 receptor isoform a precursor; granulocyte NP_000751.1 colony stimulating factor receptor; CD114 antigen 2102e-053 GCSRJHUMAN Granulocyte colony stimulating factor receptor precursor (G-CSF-R) Q99062 (CD114 antigen) 2102e-053 CAA39263.1 granulocyte colony stimulating factor receptor 26-1 2102e-053 AAA63176.1 granulocyte colony-stimulating factor receptor 2102e-053 AAN05790.1 colony stimulating factor 3 receptor (granulocyte) 2102e-053 ^" AAH53586.1 Colony stimulating factor 3 receptor, isoform a precursor 2102e-053

NM_018871 Mm.28498 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation P35214 4 F:3.3δ NP_036611.2 protein, gamma polypeptide; 14-3-3 gamma 462 e- 29 14-3-3 protein gamma (Protein kinase C inhibitor protein-1) P36214 (KCIP-1) 462 e-129 BAA85184.1 14-3-3gamma 462 e-129 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation AAH20963.1 protein, gamma polypeptide 462 e-129 AAD48408.1 14-3-3 gamma protein 422 e-117 tyrosine 3/tryptophan 5 -monooxygenase activation protein, eta NP_003396.1 polypeptide; 14-3-3 eta 407 e-113 Q04917 14-3-3 protein eta (Protein AS1) 407 e-113 S38609 14-3-3 protein eta chain - human 407 e-113 CAA65017.1 14-3-3 eta subtype 407 e-113 CAA66676.1 14-3-3 protein 407 e-113 AAB36036.1 14.3.3 eta chain 407 e-113

BAA1 418.1 14-3-3 protein eta chain 407 e-113 CN44A4.1 (tyrosine 3-monooxygenase/tryptophan δ-monooxygenase activation protein, eta polypeptide (14-3-3 protein CAB05112.1 ETA)) 407 e-113 Tyrosine 3/tryptophan 5 -monooxygenase activation protein, eta AAH03047.1 polypeptide 407 e-113 AAA35483.1 14-3-3n 406 e-112 S38532 protein 14-3-3 eta chain - human 401 e-111 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide; 14-3-3 protein beta/alpha; protein kinase C inhibitor protein-1; protein 1064; NP_003395.1 brain protein 14-3-3, beta isoform 3484e-09δ dJ148E22.1 (Tyrosine 3-monooxygenase/tryptophan δ-monooxygenase CAA15497.1 activation protein, beta polypeptide, isoform 1) 3484e-095 CAA40620.1 AS1 3478e-095 AAH63824.1 Unknown (protein for IMAGE:6180974) 3461e-094 AAH51814.1 YWHAZ protein 3461e-094 AAH03623.2 YWHAZ protein 3461e-094

NM_011489 signal transducer and activator of transcription 6B; transcription I49274 Mm.34064 F:3.26 NPJ336580.2 factor STAT5B 1510 0 P51692 Signal transducer and activator of transcription δB 1510 0 AAC60485.2 transcription factor Statδb 1610 0 CAD 19638.1 STAT5B_CDS 1610 0 AAH66227.1 Unknown (protein for MGC:74606) 1510 0 AAC50491.1 signal transducer and activator of transcription StatδB 1508 0 NP_003143.2 signal transducer and activator of transcription 6A 1405 0 P42229 Signal transducer and activator of transcription δA 1405 0 AAA73962.1 signal transducer and activator of transcrption 1405 0 AAH27036.1 Signal transducer and activator of transcription δA 1406 0

Mm.19111 F:2.92

NM_010271 Mm.25239 P13707 1 F:2.9

P0 344 IGF2_HUMAN Insulin-like growth factor II precursor (IGF-II) (Somatomedin A) 255

IGHU2 insulin-like growth factor II precursor 255

CAA25426.1 IGF-ll precursor 255

CAA29616.1 precursor polypeptide (AA -24 to 156) 265

AAA52442.1 preproinsulin-like growth factor II, domains A-E 255

AAA52535.1 insulin-like growth factor 255

AAA52545.1 insulin-like growth factor II precursor 255

AAA60088.1 insulin-like growth factor II 255

AAB34155.1 insulin-like growth factor II; IGF-II 255

AAG17220.1 AF217977 1 unknown 255

AAH00531.1 insulin-like growth factor 2 (somatomedin A) 255

AAM51825.1 AF517226_1 insulin-like growth factor 2 (somatomedin A) 255

1009249A insulin-like growth factor II precursor 265

1203258B insulin-like growth factor II 255

AAA52544.1 insulin-like growth factor II precursor 264

167610 insulin-like growth factor II, domains A-E 250

AAA52443.1 preproinsulin-like growth factor II, domains A-E 250

S02423 insulin-like growth factor II precursor, splice form II 249

CAA27249.1 put. IGF-II 249

CAA29517.1 precursor polypeptide (AA -24 to 140) 223

Mm.19080 F:2.86 NP_004277.1 GTP binding protein 1; G-protein 1 984 000178 GTP-binding protein 1 (G-protein 1) (GP-1) (GP1) 984 AAB51273.1 putative G-protein 984 CAB42864.1 dJ508H5.3 (GTP binding protein 1) 984 AAH 14075.1 GTP binding protein 1 984 JC5291 GTP-binding protein GP-1 - human 984 PC7084 GTP-binding protein 2 - human (fragment) 441 AAF78884.1 putative GTP-binding protein 441 CAC36269.1 bA22l24.2.1 (GTP binding protein 2) 441 AAH64968.1 GTPBP2 protein 441 AAH28347.2 GTPBP2 protein 440 CAD38999.1 hypothetical protein 427 NP_061969.2 GTP binding protein 2 424 BAB12431.1 GTP-binding like protein 2 424

AAH20980.2 GTPBP2 protein 380

U08378 Mm.24993 ignal transducer and activator of transcription 3 isoform 2;

1BG1 4 F:2.85 NP_003141.2 acute-phase response factor; DNA-binding protein APRF 1499 0 AAH00627.1 Signal transducer and activator of transcription 3, isoform 2 1499 0 signal transducer and activator of transcription 3 isoform 1 ; NP_644805.1 acute-phase response factor; DNA-binding protein APRF 1494 0 CAA10032.1 transcription factor 1494 0 AAH14482.1 Signal transducer and activator of transcription 3, isoform 1 1494 0 Signal transducer and activator of transcription 3 (Acute-phase P40763 response factor) 1485 0 A54444 DNA-binding protein APRF - human 1485 0 AAA58374.1 DNA-binding protein 1485 0 signal transducer and activator of transcription 1 isoform alpha; signal transducer and activator of transcription-1; transcription factor ISGF-3; transcription factor ISGF-3 NP_009330:1 components p91/p84 748 Signal transducer and activator of transcription 1 -alpha/beta P42224 (Transcription factor ISGF-3 components p91/p84) 748 AAB64012.1 transcription factor ISGF-3 748 signal transducer and activator of transcription 1 isoform beta; signal transducer and activator of transcription-1 ; transcription factor ISGF-3; transcription factor ISGF-3 NP_644671.1 components p91/p84 742 0 AAH02704.1 Signal transducer and activator of transcription 1 , isoform beta 742 0 AAP35905.1 signal transducer and activator of transcription 1 , 91 kDa 742 0 interferon-dependent positive-acting transcription factor ISGF-3 91 K A46159 chain - human 728 0 NP_003142.1 signal transducer and activator of transcription 4 674 0 Q14765 Signal transducer and activator of transcription 4 674 0

MFA2_HUMAN Microfibrillar-associated protein 2 precursor (MFAP-2) P56001 (Microfibril-associated glycoprotein) (MAGP) (MAGP-1) 288

138923 microfibril-associated glycoprotein MFAP2 288

AAA79920.1 microfibril-associated glycoprotein 288 dJ37C 0.4 (microfibrillar-associated protein 2 (microfibril-associated glycoprotein CAB96824.1 precursor, MGAP1)) 288

AAH15039.1 microfibrillar-associated protein 2 288 PC01_HUMAN Procollagen C-proteinase enhancer protein precursor (PCPE) (Type l

NM_008788 procollagen COOH-terminal proteinase enhancer) (Type 1 procollagen C-proteinase NP 032814.1 Mm.18808 F:2.7 Q15113 enhancer protein) 588 BAA23281.1 type 1 procollagen C-proteinase enhancer protein 588 AAC78800.1 PCOLCE 588 AAD16041.1 procollagen C-proteinase enhancer protein 688 AAH00574.1 procollagen C-endopeptidase enhancer 588 AAH33205.1 procollagen C-endopeptidase enhancer 588 procollagen C-endopeptidase enhancer; procollagen, type 1, COOH-terminal NP_002δ84.1 proteinase enhancer 585 A55362 procollagen l C-proteinase enhancer protein precursor 686 AAA61949.1 procollagen C-proteinase enhancer protein 585

NP_037495.1 procollagen C-endopeptidase enhancer 2 332266

AAF04621.1 AF098269_1 procollagen C-terminal proteinase enhancer protein 2 332266

AAK63128.1 procollagen C-proteinase enhancer protein 2 332266

NP_002014.1 fibromodulin precursor 237

S55275 fibromodulin precursor 237

CAA53233.1 fibromodulin 237

NP_005005.1 osteomodulin 229 OMD_HUMAN Osteomodulin precursor (Osteoadherin) (OSAD) (Keratan sulfate

Q99983 proteoglycan osteomodulin) (KSPG osteomodulin) 229

BAA19055.1 osteomodulin 229

BAA23982.1 Osteomodulin 229

AAH46356.1 osteomodulin 229

AAA85268.1 lumican 227

NP_002336.1 lumican 227 LUMJHUMAN Lumican precursor (Keratan sulfate proteoglycan lumican) (KSPG

P51884 lumican) 227

AAA91639.1 lumican 227

AAH07038.1 lumican 227

AAH35997.1 lumican 227

AAH32953.1 Unknown (protein for MGC:33476) ficolin 2 isoform a precursor; ficolin (collagen/fibrinogen domain-containing lectin) 2;

NPJD04099.1 ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin); hucolin FCN2JHUMAN Ficolin 2 precursor (Collagen/fibrinogen domain-containing protein 2) Q15486 (Ficolin-B) (Ficolin B) (Serum lectin p35) (EBP-37) (Hucolin) (L-Ficolin)

BAA08362.1 serum lectin P35

BAA09636.1 lectin P3δ ficolin 2 isoform b precursor; ficolin (collagen/fibrinogen domain-containing lectin) 2;

NP_0566δ2.1 ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin); hucolin

NP_001994.2 ficolin 1 precursor; ficolin (collagen/fibrinogen domain-containing) 1 FCN1_HUMAN Ficolin 1 precursor (Collagen/fibrinogen domain-containing protein 1)

000602 (Ficolin-A) (Ficolin A) (M-Ficolin)

AAH20635.1 ficolin (collagen/fibrinogen domain-containing) 1

BAA12120.1 ficolin

S61617 ficoiin-1 precursor

AAB50706.1 ficolin ficolin 3 isoform 1 precursor; ficolin-3; collagen/fibrinogen domain-containing lectin 3 NP_0036δ6.2 p35; collagen/fibrinogen domain-containing protein 3; Hakata antigen; H-ficolin FCN3JHUMAN Ficolin 3 precursor (Collagen/fibrinogen domain-containing protein 3) 076636 (Collagen/fibrinogen domain-containing lectin 3 p35) (Hakata antigen)

NM_011340 NP 035470.1 Mm.2044 F:2.62

NM_01136δ 2211430A Mm.δ6595 F:2.62

Mm.30191 F:2.59

Mm.709 F:2.59

BAA11928.1 ER-60 protease δδ2

AAC51518.1 ER-60 protein 880

S55507 protein disulfide-isomerase (EC 5.3.4.1) ER60 precursor 880

CAA39996.1 protein disulfide isomerase 880

2209333A protein disulfide isomerase 880

BAA03759.1 phospholipase C-alpha 871

S63994 protein disulfide-isomerase (EC 5.3.4.1) ER60 precursor 867

2201353A glucose-regulated protein ERp57/GRP5δ 863

NP_004902.1 protein disulfide isomerase related protein (calcium-binding protein, intestinal-related) 340

P13667 PDA4JHUMAN Protein disulfide isomerase A4 precursor (Protein ERp-72) (ERp72) 340

A23723 protein disulfide-isomerase (EC 5.3.4.1 ) ERp72 precursor 340

AAA53460.1 protein disulfide isomerase-related protein 340

AAH00425.1 protein disulfide isomerase related protein (calcium-binding protein, intestinal-related) 340

AAH0192δ.1 protein disulfide isomerase related protein (calcium-binding protein, intestinal-related) 340

AAH06344.1 protein disulfide isomerase related protein (calcium-binding protein, intestinal-related) 340 Similar to protein disulfide isomerase related protein (calcium-binding protein,

AAH11764.1 intestinal-related) 340 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein pδδ);

NP_000909.2 v-erb-a avian erythroblastic leukemia viral oncogene homolog 2-like 260

Rho guanine nucleotide exchange factor 7 isoform b; SH3 domain-containing proline-rich protein; PAK-interacting NP_663788.1 exchange factor beta 333 e-111 AAH50521.1 Rho guanine nucleotide exchange factor (GEF) 7 333 e-111

NM_009075 ribose δ-phosphate isomerase A (ribose δ-phosphate epimerase);

P4796δ Mm.17905 F:2.4δ NP_653164.1 RIBOSE 5-PHOSPHATE ISOMERASE 450 e-126 P49247 Ribose δ-phosphate isomerase (Phosphoriboisomerase) 450 e-126 AAK95569.1 ribose 5-phosphate isomerase 450 e-126

NMJ307788 casein kinase II alpha 1 subunit isoform a; CK2 catalytic subunit

149141 Mm.23692 F:2.48 NP_001886.1 alpha 730 casein kinase II alpha 1 subunit isoform a; CK2 catalytic subunit NP_80δ227.1 alpha 730 0 P19138 Casein kinase II, alpha chain (CK II) 730 0 A30319 casein kinase II (EC 2.7.1.-) alpha chain - human 730 0 AAA35503.1 casein kinase II alpha subunit 730 0 AAA56821.1 casein kinase II alpha subunit 730 0 CAB65624.1 dJδ63C7.1.1 (casein kinase 2, alpha 1 polypeptide (EC 2.7.1.37)) 730 0 AAH11668.1 Casein kinase II alpha 1 subunit, isoform a 730 0 AAH53632.1 Casein kinase II alpha 1 subunit, isoform a 730 0 CAA49758.1 casein kinase II alpha subunit 722 0 AAM62224.1 casein kinase II alpha subunit 719 0 1JWH|A Chain A, Crystal Structure Of Human Protein Kinase Ck2 Holoenzyme 652 0 1JWH1B Chain B, Crystal Structure Of Human Protein Kinase Ck2 Holoenzyme 652 0 Chain A, Crystal Structure Of A C-Terminal Deletion Mutant Of Human 1PJK|A Protein Kinase Ck2 Catalytic Subunit 648 0 1NA7|A Chain A, Crystal Structure Of The Catalytic Subunit Of Human Protein 638 0 NP_001δδ7.1 casein kinase 2, alpha prime polypeptide 558 e-158 P19784 Casein kinase II, alpha' chain (CK II) 558 e-158 B35833 casein kinase II (EC 2.7.1.-) alpha' chain - human 568 e-158

NM_008028 Mm.13022 O06917 7 F:2.4δ

NM_016670 Mm.25929 070477 5 F:2.47

AAF61404.1 NF-E2-reIated factor 3 2993e-080 AAF61415.1 NF-E2-related factor 3 2993e-0δ0 AAG43276.1 NF-E2-related factor 3 2993e-030 AAH56142.1 NFE2L3 protein 251 9e-066 AAH49219.1 NFE2L3 protein 2424e-063 BAA7623δ.1 NF-E2-related factor 3 2424e-063 AAP22344.1 UNKNOWN 2424e-063 NP 006165.2 nuclear factor (erythroid-derived 2)-like 2 241 7e-063 Nuclear factor erythroid 2 related factor 2 (NF-E2 related factor 2) (NFE2-related factor 2) (Nuclear factor, erythroid Q16236 derived 2, like 2) (HEBP1) 241 7e-063 AAH11558.1 Nuclear factor (erythroid-derived 2)-like 2 241 7e-063 AAF17228.1 NFE2-related factor 1 2362e-061

NM_016357 T03722 Mm.22530 F:2.45 BAA83019.1 KIAA1067 protein 1231 0 CAD38992.1 hypothetical protein 1231 0 AAH11045.1 EXOC7 protein 1231 0 Q9UPT5 Exocyst complex component Exo70 1207 0 AAH18466.1 EXOC7 protein 1204 0 NP_0δ6034.1 exocyst complex component 7 1146 0 BAB14694.1 unnamed protein product 1146 0 BAB14095.1 unnamed protein product 47δ e-134 BAB14026.1 unnamed protein product 47δ e-134

BC016102 DNA-directed RNA polymerase III 47 kDa polypeptide (RNA polymerase C AAH16102.1 Mm.20420 F:2.4δ P06423 subunit 4) (RPC4) (RPC53) (BN61 protein) 562 e-165 AAH02603.1 POLR3D protein 582 e-165 AAH04434.1 POLR3D protein 582 e-165 AAM16216.1 RNA polymerase III 53 kDa subunit RPC4 678 e-164

RNA polymerase III 63 kDa subunit RPC4; temperature sensitive complementation, cell cycle specific, tsBN51; BN61 NP_001713.1 (BHK21) temperature sensitivity complementing 5δδ e-158 A43700 BN51 protein - human 55δ e-158 AAA51833.1 BN61 protein 558 e-158 AAH03039.1 POLR3D protein 2192e-067

NM_009926 NP 034056.1 Mm.20230 F:2.44 NP_542412.1 alpha 2 type XI collagen isoform 2 preproprotein 1099 0 AAC50213.1 Pro-a2(XI) 1092 0 NP_542410.1 alpha 2 type XI collagen isoform 3 preproprotein 1068 0 AAC60215.1 Pro-a2(XI) 1052 0 NP_642411.1 alpha 2 type XI collagen isoform 1 preproprotein 998 0 P13942 CA2B_HUMAN Collagen alpha 2(XI) chain precursor 997 0 CAA20240.1 dJ1033B10.12 (collagen, type XI, alpha 2) 996 0 CGHU2E collagen alpha 2(XI) chain precursor 994 0 AAC50214.1 Pro-a2(XI) 991 0 2123363A collagen:SUBUNIT=alpha2:ISOTYPE=XI 991 0 AAA35498.-1 alpha-2 type XI collagen 811 0 191721 OA Pro/Arg-rich protein (alpha-2 type XI collagen) 811 0

NM_018δ62 1-acylglycerol-3-phosphate O-acyltransferase 1; lysophosphatidic acid acyltransferase 035083 Mm.δ6δ4 2.44 NP 006402.1 alpha; 1 -AGP acyltransferase 1 ; lysophospholipid acyltransferase 496 e-140 1-acylglycerol-3-phosphate O-acyltransferase 1; lysophosphatidic acid acyltransferase NP 116130.2 alpha; 1-AGP acyltransferase 1 ; lysophospholipid acyltransferase 496 e-140 PLCAJHUMAN 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (1-AGP acyltransferase 1) (1-AGPAT 1) (Lysophosphatidic acid acyltransferase-alpha) Q99943 (LPAAT-alpha) (1-acyIglyceroI-3-phosphate O-acyltransferase 1) (G15 protein) 496 e-140 AAB53776.1 lysophosphatidic acid acyltransferase-alpha 496 e-140 AAB96373.1 putative lysophospholipid acyltransferase 496 e-140 CAA7075δ.1 1 -acylglycerol-3-phosphate O-acyltransferase 496 e-140

AAH02402.1 1-acylglycerol-3-phosphate O-acyltransferase 1 496 e-140 AAH03007.1 1-acylglycerol-3-phosphate O-acyltransferase 1 496 e-140 AAH04310.1 1-acylglycerol-3-phosphate O-acyltransferase 1 496 e-140 AAB47493.1 LPAAT 4δ7 e-137 AAC19153.1 unknown 456 e-128 AAG17276.1 unknown 3262e-0δ8 AAB64299.1 lysophosphatidic acid acyltransferase 2352e-061 1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid AAH19292.1 acyltransferase, beta) 2343e-061 1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta); lysophosphatidic acid acyltransferase beta; Berardinelli-Seip NP_006403.2 congenital lipodsytrophy 2343e-061 PLCB_HUMAN 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (1-AGP acyltransferase 2) (1-AGPAT 2) (Lysophosphatidic acid acyltransferase-beta) 015120 (LPAAT-beta) (1-acylglycerol-3-phosphate O-acyltransferase 2) 2343e-061 AAC51649.1 lysophosphatidic acid acyltransferase 2343e-061 AAB53776.2 lysophosphatidic acid acyltransferase-beta 2343e-061 1-acylglycero!-3-phosphate O-acyltransferase 2 (lysophosphatidic acid AAH00026.1 acyltransferase, beta) 2337e-061 mitogen-activated protein kinase kinase 7; dual specificity mitogen-activated protein kinase kinase 7; c-Jun

NM_011944 N-terminal kinase kinase 2; MAP kinase kinase 7; NP 036074 Mm.3906 F:2.44 NP 660136.1 JNK-activating kinase 2; JNK kinase 2 710 Dual specificity mitogen-activated protein kinase kinase 7 (MAP kinase kinase 7) (MAPKK 7) (MAPK/ERK kinase 7) (JNK activating kinase 2) (c-Jun N-terminal kinase kinase 2) 014733 (JNK kinase 2) (JNKK 2) 710 AAC26142.1 c-Jun N-terminal kinase kinase 2 710

NP__00884δ.1 retinoid X receptor, gamma 590 e-168

P48443 Retinoic acid receptor RXR-gamma 590 e-168

AAA806δ1.1 retinoid X receptor-gamma 590 e-168

CAC00596.1 bA280O1.2 (retinoid X receptor, gamma (NR2B3)) 590 e-168

AAH12063.1 Retinoid X receptor, gamma 590 e-68

AAA60293.1 retinoid X receptor beta 574 e-163

NP_068811.1 retinoid X receptor, beta; MHC class I promoter binding protein 574 e-163

P28702 Retinoic acid receptor RXR-beta 574 e-163

CAA45087.1 retinoic acid X receptor b 574 e-163

AAC18599.1 retinoic X receptor B 574 e-163

CAA20239.1 dJ1033B10.11 (retinoid X receptor beta) 574 e-163

AAD13794.1 retinoic X receptor beta 574 e-163

AAH01167.1 Retinoid X receptor, beta 574 e-163

AAP35944.1 Retinoid X receptor, beta 574 e-163

S37781 retinoid X receptor beta - human 574 e-163

1LBD Ligand-Binding Domain Of The Human Nuclear Receptor Rxr-Alpha 518 e-146 Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding Domain Bound To The Eicosanoid Dha (Docosa Hexaenoic

1MV9|A Acid) And A Coactivator Peptide 476 e-134 Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding Domain Bound To The Synthetic Agonist Compound Bms 649

1MVC|A And A Coactivator Peptide 476 e-134 Chain A, Crystal Structure At 1.9 Angstroems Resolution Of The Homodimer Of Human Rxr Alpha Ligand Binding Domain Bound To The Synthetic Agonist Compound Bms 649 And A

1MZN|A Coactivator Peptide 476 e-134

Chain C, Crystal Structure At 1.9 Angstroems Resolution Of The Homodimer Of Human Rxr Alpha Ligand Binding Domain Bound To The Synthetic Agonist Compound Bms 649 And A 1 MZN [C Coactivator Peptide 476 e-134 Chain E, Crystal Structure At 1.9 Angstroems Resolution Of The Homodimer Of Human Rxr Alpha Ligand Binding Domain Bound To The Synthetic Agonist Compound Bms 649 And A 1MZN|E Coactivator Peptide 476 e-134 Chain G, Crystal Structure At 1.9 Angstroems Resolution Of The Homodimer Of Human Rxr Alpha Ligand Binding Domain Bound To The Synthetic Agonist Compound Bms 649 And A 1MZN|G Coactivator Peptide 476 e-134 Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding

1 FBY|A Domain Bound To 9-Cis Retinoic Acid 474 e-133 Chain B, Crystal Structure Of The Human Rxr Alpha Ligand Binding

1 FBY|B Domain Bound To 9-Cis Retinoic Acid 474 e-133 Chain A, The 2.1 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Rxralpha And Ppargamma Ligand Binding Domains Respectively Bound With 9-Cis Retinoic 1 FM6|A Acid And Rosigiitazone And Co-Activator Peptides. 473 e-133 Chain U, The 2.1 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Rxralpha And Ppargamma Ligand Binding Domains Respectively Bound With 9-Cis Retinoic 1 FM6|U Acid And Rosigiitazone And Co-Activator Peptides. 473 e-133

Chain A, The 2.1 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Rxralpha And Ppargamma Ligand Binding Domains Respectively Bound With 9-Cis Retinoic 1 FM9|A Acid And Gi262570 And Co-Activator Peptides. 473 e-133 Chain A, The 2.0 Angstrom Resolution Crystal Structure Of The

Rxralpha Ligand Binding Domain Tetramer In The Presence 1 G5Y|A Of A Non-Activating Retinoic Acid Isomer. 473 e-133 Chain B, The 2.0 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain Tetramer In The Presence 1 G5Y]B Of A Non-Activating Retinoic Acid Isomer. 473 e-133 Chain C, The 2.0 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain Tetramer In The Presence 1 G5Y|C Of A Non-Activating Retinoic Acid Isomer. 473 e-133 Chain D, The 2.0 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain Tetramer In The Presence 1 G5YJD Of A Non-Activating Retinoic Acid Isomer. 473 e-133 Chain A, The 2.5 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain In Tetramer In The Absence

1G1UJA Of Ligand 473 e-133 Chain B, The 2.5 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain In Tetramer In The Absence 1G1U|B Of Ligand 473 e-133 Chain C, The 2.5 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain In Tetramer In The Absence 1G1U)C Of Ligand 473 e-133

BAA09715.1 aquaporin 521 e-148

AAB26_.957.1 aquaporin 4 521 e-148

AAH22286.1 Aquaporin 4, isoform a 621 e-148

139173 aquaporin 4, long splice form - human 516 e-146

AAC62112.1 mercurial-insensitive water channel 516 e-146

NP_004019.1 aquaporin 4 isoform b; mercurial-insensitive water channel 506 e-143

AAB26953.1 aquaporin 4 506 e-143

AAC60284.1 mercurial-insensitive water channel 500 e-141

NP_001642.1 aquaporin 5; Aquaporin-δ 2212e-057

P56064 Aquaporin 5 2212e-057

AAC50474.1 aquaporin-δ 2212e-057

AAH32946.1 aquaporin-δ 2212e-057

NP_036196.1 major intrinsic protein of lens fiber; aquaporin 2151e-055

P30301 Lens fiber major intrinsic protein (MIP26) (MP26) (Aquaporin 0) 2151e-055

A65279 major intrinsic protein - human 2151e-055

AAC02794.2 lens major intrinsic protein 2151e-055

AAB30268.1 hAQP-CD=coliecting duct aquaporin [human, kidney, Peptide, 271 aa] 2151e-055

NP 000477.1 aquaporin 2; collecting duct water channel protein; aquaporin-CD 2142e-055 Aquaporin-CD (AQP-CD) (Water channel protein for renal collecting duct) (ADH water channel) (Aquaporin 2) (Collecting duct

P41181 water channel protein) (WCH-CD) 214 2e-055

A63442 aquaporin 2 - human 214 2e-055

CAA82627.1 water channel aquaporin-2 214 2e-055

BAA06632.1 human aquaporin-2 water channel 214 2e-055

AAD36692.1 aquaporin 2 214 2e-055

AAH42496.1 aquaporin 2 214 2e-055

I52366 uterine water channel - human 212 9e-055

AAB31193.1 uterine water channel; hUWC 212 9e-055

AAL37136.1 aquaporin 1 211 1e-054

BAA91176.1 unnamed protein product 352 0 BAA99557.1 mitochondrial seryl-tRNA synthetase δ52 0 AAH42912.1 Seryl-tRNA synthetase 2 δ52 0 AAH01020.2 SARS2 protein 268 3e-071 sialyltransferase 4B; sialyltransferase 4B (beta-galactoside aipha-2,3-sialytransferase); alpha 2,3-ST; Gal-beta-1 ,3-GalNAc-aipha-2,3-sialyltransferase;

NM_009179 Mm.20038 CMP-N-acetylneuraminate-beta-galactosamide-alpha-2, A54420 8 F:2.38 NP_008858.1 3-sialyltransferase 702 CMP-N-acetylneuraminate-beta-gaIactosamide-alpha-2, 3-sialyltransferase (Beta-galactoside alpha-2,3-sialyltransferase) (Alpha 2,3-ST) (Gal-NAc6S) (Gal-beta-1,3-GalNAc-alpha-2,3-sialyltransferase) Q16842 (ST3GalA.2) (SIAT4-B) (ST3Gal II) 702 0 JC5251 beta-galactoside alpha-2,3-sialyltransferase (EC 2.4.99.4) - human 702 0 CAA65447.1 beta-galactoside alpha-2,3-sialyltransferase 702 0 AAB40389.1 Gal beta-1 ,3 GalNAc alpha-2,3 sialyltransferase 702 0 AAH36777.1 Sialyltransferase 4B 702 0 sialyltransferase 4A; CMP-N-acetylneuraminate-beta-galactosamide-alpha-2, 3-sialyltransferase; sialyltransferase 4A (beta-galactoside alpha-2,3-sialytransferase); alpha NP_003024.1 2,3-ST; Gal-beta-1 ,3-GalNAc-alpha-2,3-sialyltransferase 357 3e-098 sialyltransferase 4A; CMP-N-acetylneuraminate-beta-galactosamide-alpha-2, 3-sialyltransferase; sialyltransferase 4A (beta-galactoside alpha-2,3-sialytransferase); alpha NP_775479.1 2,3-ST; Gal-beta-1 ,3-GaINAc-alpha-2,3-sialyltransferase 357 3e-098

NM_016973 NP 058669.1 Mm.8δ831 R2.36

sialyltransferase 7D isoform a; NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc-alpha-2, 6-sialyltransferase alpha2,6-sialyltransferase; sialyltransferase 3C; NeuAc-alpha-2,3-Gal-beta-1 ,3-GalNAc-alpha-2, NP_05521δ.3 6-sialyltransferase IV 203 1e-053 sialyltransferase 7D isoform a; NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc-alpha-2, 6-sialyltransferase alpha2,6-sialyltransferase; sialyltransferase 3C; NeuAc-alpha-2,3-Gal-beta-1,3-GaiNAc-alpha-2, NP_773204.1 6-sialyltransferase IV 2081e-053 Alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1 , 3-N-acetyl-gaIactosaminide alpha-2,6-sialyltransferase (NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc-alpha-2, 6-sialyltransferase) (STβGalNAc IV) (Sialyltransferase Q9H4F1 7D) (Sialyltransferase 3C) 2081e-053 BAA67034.1 N-acetylgalactosaminide alpha2,6-sialyltransferase 2081e-053 AAH36705.1 SIAT7D protein 2081e-053

AK009218 Mm.22809 SKI-interacting protein; nuclear receptor coactivator, 62-kD; BX42, BAB26144.1 5 F:2.36 NPJ336377.1 Drosophila, homolog of 587 e-167 Nuclear protein SkiP (Ski-interacting protein) (SNW1 protein) Q13573 (Nuclear receptor coactivator NCoA-62) 587 e-167 AAC15912.1 nuclear protein Skip 587 e-167 AAC31697.1 nuclear receptor coactivator NCoA-62 587 e-167 AAF23325.1 nuclear receptor coactivator NCoA-62 587 e-167 AAH40112.1 SNW1 protein 587 e-167

AAH46105.2 SNW1 protein similar to Nuclear protein SkiP (Ski-interacting protein) (SNW1 XP_291504.2 protein) (Nuclear receptor coactivator NCoA-62) AAF01479.1 nuclear receptor coactivator NCOA-62 AAB48δ57.1 unknown serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1 ; protease inhibitor 2 (anti-elastase), monocyte/neutrophil; protease inhibitor 2 (anti-elastase), AK018226 Mm.9268δ F:2.35 NPJ09591.1 monocyte/neutrophil derived ILEUJHUMAN Leukocyte elastase inhibitor (LEI) (Monocyte/neutrophil elastase P30740 inhibitor) (M/NEI) (El) S27383 elastase inhibitor AAC31394.1 monocyte/neutrophil elastase inhibitor AAH09015.1 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 9; protease NP_004146.1 inhibitor 9 (ovalbumin type) SPB9_HUMAN Cytoplasmic antiproteinase 3 (CAP3) (CAP-3) (Protease inhibitor 9) P50453 (Serpin B9)

B59273 proteinase inhibitor 9

AAC41940.1 cytoplasmic antiproteinase 3

AAC50793.1 serine proteinase inhibitor

AAH02533.1 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 9

BAB91078.1 serine protease inhibitor 9

serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8; protease

NP_002631.1 inhibitor 8 (ovalbumin type) 207 SPB8_HUMAN Cytoplasmic antiproteinase 2 (CAP2) (CAP-2) (Protease inhibitor 8)

P50452 (Serpin B8) 207

A59273 proteinase inhibitor 8 207

AAC41939.1 cytoplasmic antiproteinase 2 207 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10; protease NPJD05015.1 inhibitor 10 (ovalbumin type, bomapin) 179

P48595 SB10_HUMAN Bomapin (Protease inhibitor 10) (Serpin B10) 179

139184 bomapin 179

AAC50282.1 bomapin 179 PTI6_HUMAN Placental thrombin inhibitor (Cytoplasmic antiproteinase) (CAP) P35237 (Protease inhibitor 6) (PI-6) 192

AAB30320.1 cytoplasmic antiproteinase; CAP 192

AAH01394.1 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6 192

1 BY7 A Chain A, Human Plasminogen Activator lnhibitor-2. Loop (66-9δ) Deletion Mutant 199 A Chain A, Human Plasminogen Activator lnhibitor-2.[loop (66-9δ) Deletionmutant]

1 JRR Complexed With Peptide Mimicking The Reactive Center Loop 199 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6; protease NP_004559.3 inhibitor 6 (placental thrombin inhibitor) 190

AAH44672.1 solute carrier family 15 (H+/peptide transporter), member 2 1128 Oligopeptide transporter, kidney isoform (Peptide transporter 2) (Kidney H+/peptide cotransporter) (Solute carrier family Q16348 15, member 2) 1122 152481 PEPT 2 - human 1122 AAB34388.1 PEPT 2 1122 2113193A H/peptide cotransporter 1122 AAC15477.1 Caco-2 oligopeptide transporter 561 solute carrier family 15 (oligopeptide transporter), member 1; NP 005064.1 peptide transporter HPEPT1 561 Oligopeptide transporter, small intestine isoform (Peptide transporter 1) (Intestinal H+/peptide cotransporter) P46059 (Solute carrier family 15, member 1) 561 A56163 peptide transport protein hPEPTI - human 561 AAA63797.1 peptide transporter 561 AAB61693.1 intestinal H+/peptide cotransporter 561 bA5δ1 18.1.1 (solute carrier family 16 (oligopeptide transporter) CAC27442.1 member 1 ) 502 JC5638 pH-sensing regulatory factor - human 231 BAA22632.1 pH-sensing regulatory factor of peptide transporter 231 heat shock transcription factor 1 [Homo sapiens] sp|Q00613|HSF1_HUMAN Heat shock factor protein 1 (HSF 1) (Heat shock

X61753 Mm.18401 transcription factor A40583 9 F:2.35 NP_005517.1 1) (HSTF 1) 837 A41137 heat shock transcription factor 1 - human 837 AAA52695.1 heat shock factor 1 837 AAH14638.1 Heat shock transcription factor 1 837 AAP36015.1 heat shock transcription factor 1 837 2102266A heat shock factor 835

BAA14323.1 collagen alpha 1(V) chain precursor 257

CGHU1V collagen alpha 1(V) chain precursor 257

AAA59993.1 pro-alpha-1 type V collagen 257

NP_000084.2 alpha 1 type V collagen preproprotein 257

AAF04726.1 collagen type XI aipha-a isoform B 257

NP_542196.1 alpha 1 type XI collagen isoform B preproprotein; collagen XI, alpha-1 polypeptide 257 cytoplasmic nuclear factor of activated T-cells 3 isoform 1 ; nuclear D86612 Mm.27600 factor of activated T-cells, cytoplasmic 3; T cell

P97305 0 F:2.32 NP_77δ1δ8.1 transcription factor NFAT4 1643 Nuclear factor of activated T-cells, cytoplasmic 3 (T cell Q12968 transcription factor NFAT4) (NF-ATc3) (NF-AT4) (NFATx) 1643 A57377 transcription factor NFATx - human 1643 AAA86308.1 NFATx 1643 AAH01050.1 Cytoplasmic nuclear factor of activated T-cells 3, isoform 1 1643 cytoplasmic nuclear factor of activated T-cells 3 isoform 3; nuclear factor of activated T-cells, cytoplasmic 3; T cell NP_775186.1 transcription factor NFAT4 1598 cytoplasmic nuclear factor of activated T-cells 3 isoform 2; nuclear factor of activated T-cells, cytoplasmic 3; T cell NP_004δ46.1 transcription factor NFAT4 1598 AAA79174.1 alternative splicing form 1698

NM_013699 149257 Mm.28052 F:2.31

NM_011638 NP 035768.1 Mm.28683 F:2.31

AAH01188.1 TFRC protein 1195 0 Chain C, Hemochromatosis Protein Hfe Complexed With Transferrin 1DE4|C Receptor 1023 0 Chain F, Hemochromatosis Protein Hfe Complexed With Transferrin 1DE4|F Receptor 1023 0 Chainl, Hemochromatosis Protein Hfe Complexed With Transferrin 1DE4|I Receptor 1023 0 Chain A, Crytal Structure Of The Ectodomain Of Human Transferrin 1CX8|A Receptor 1020 0 Chain B, Crytal Structure Of The Ectodomain Of Human Transferrin 1CX8|B Receptor 1020 0 Chain C, Crytal Structure Of The Ectodomain Of Human Transferrin 1CX8|C Receptor 1020 0 Chain D, Crytal Structure Of The Ectodomain Of Human Transferrin 1CXδ|D Receptor 1020 0 Chain E Crytal Structure Of The Ectodomain Of Human Transferrin 1CX8(E Receptor 1020 0 Chain F, Crytal Structure Of The Ectodomain Of Human Transferrin 1CX8|F Receptor 1020 0 Chain G Crytal Structure Of The Ectodomain Of Human Transferrin 1CXδ|G Receptor 1020 Chain H, Crytal Structure Of The Ectodomain Of Human Transferrin 1CX8|H Receptor 1020 0

NP_003218.2 transferrin receptor 2 545 e-164 Q9UP52 Transferrin receptor protein 2 (TfR2) 545 e-154

AAD45561.1 transferrin receptor 2 alpha 545 e-154 AAC78796.1 transferrin-receptor2 493 e-140 BAA91153.1 unnamed protein product 3155e-035

BAA01995.1 PMP-22(PAS-II/SR13/Gas-3) 246

AAB26811.1 peripheral myelin protein 244

Mm.8385 F:2.28 CAA77754.1 44kDa protein kinase 699 1813206C mitogen-activated protein kinase 699 Mitogen-activated protein kinase 3 (Extracellular signal-regulated kinase 1) (ERK-1) (Insulin-stimulated MAP2 kinase) (MAP kinase 1) (MAPK 1) (p44-ERK1) (ERT2) (p44-MAPK) P27361 (Microtubule-associated protein-2 kinase) 699 AAH13992.1 Mitogen-activated protein kinase 3 699 AAA36142.1 kinase 1 699 mitogen-activated protein kinase 3; p44erk1; p44mapk; protein kinase, NP_002737.1 mitogen-activated 3 (MAP kinase 3; p44) 697 A48082 MAP kinase 3 (EC 2.7.1.-) - human 697 CAA42744.1 protein serine/threonine kinase 697 CAD97δδ8.1 hypothetical protein 646 mitogen-activated protein kinase ; extracellular signal-regulated kinase 2; protein tyrosine kinase ERK2; mitogen-activated NP 620407.1 protein kinase 2 639 Mitogen-activated protein kinase 1 (Extracellular signal-regulated kinase 2) (ERK-2) (Mitogen-activated protein kinase 2) P28482 (MAP kinase 2) (MAPK 2) (p42-MAPK) (ERT1) 639 JQ1400 MAP kinase 1 (EC 2.7.1.-) - human 639 AAA58459.1 protein kinase 2 639 AAH 17332.1 Mitogen-activated protein kinase 1 639

CAA77763.1 40kDa protein kinase 639

NM_010233 NP 034368 Mm.3444 F:2.27

ARP1 actin-related protein 1 homolog A, centractin alpha; ARP1 (actin-related protein 1 , yeast) homolog A (centractin alpha); centractin alpha; actin-RPV;

NM_016860 Mm.13276 centrosome-associated actin homolog; ARP1, yeast homolog

P42024 4 F:2.27 NP_005727.1 A 756 Alpha-centractin (Centractin) (Centrosome-associated actin homolog) P42024 (Actin-RPV) (ARP1) 755 0 S29089 alpha-centractin - human 75δ 0 CAA78701.1 actin-related protein 756 0 actin-related protein, actin-RPV=dynactin complex major component AAB23391.1 [human, N-Tera teratocarcinoma, Peptide, 376 aa] 766 0 CAA57690.1 alpha-centractin 75δ 0 CAC08404.1 bA13114.9 (novel protein similar to beta-centracin (ACRTR1B)) 75δ 0 AAH00693.1 ARP1 actin-related protein 1 homolog A, centractin alpha 756 0 AAH26016.1 ACTR1A protein 755 0 1818368A actin-related protein 753 0 ARP1 actin-related protein 1 homolog B, centractin beta; centractin beta; ARP1 (actin-related protein 1, yeast) homolog B NP_005726.1 (centractin beta); PC3; ARP1 , yeast homolog B 709 0 P42026 Beta-centractin (Actin-related protein 1B) (ARP1B) 709 0 CAA67691.1 beta-centracetin 709 0 AAH04374.1 ARP1 actin-related protein 1 homolog B, centractin beta 709 0 AAH10090.1 ARP1 actin-related protein 1 homolog B, centractin beta 709 0 AAH10090.1 ARP1 actin-related protein 1 homolog B, centractin beta 703 0 CAA57692.1 beta-centractin 616 e-176 actin, gamma 1 propeptide; cytoskeletal gamma-actin; actin, NP_001605.1 cytoplasmic 2 425 e-11δ P02571 Actin, cytoplasmic 2 (Gamma-actin) 425 e-118 ATHUG actin gamma 1 - human 425 e-118

CAA27723.1 gamma-actin 426 e- 18

AAA51579.1 gamma-actin 425 e-' 18

AAH00292.1 Actin, gamma 1 425 e-' 18

AAH01920.1 ACTG1 protein 425 e-118

AAH07442.1 Actin, gamma 1 425 e-' 18

AAH09848.1 Actin, gamma 1 425 e- 18

AAH10999.1 ACTG1 protein 426 e- 18

AAH 12050.1 Actin, gamma 1 425 e- 18

AAH15005.1 ACTG1 protein 425 e- 18

AAH15695.1 Actin, gamma 1 425 e- 18

AAH15779.1 ACTG1 protein 425 e- 18

AAH18774.1 ACTG1 protein 425 e-' 18

AAH53572.1 Actin, gamma 1 425 e- 18

NPJ005160.1 actin, alpha, cardiac muscle precursor 425 e-' 18

P04270 Actin, alpha cardiac 425 e-' 18

ATHUC actin, cardiac muscle - human 425 e- 18

AAB59619.1 alpha-cardiac actin 425 e- 18

AAH09978.1 Actin, alpha, cardiac muscle precursor 425 e- 18

JC5818 gamma-actin - human 425 e-' 18

NP_001092.1 beta actin; beta cytoskeletal actin 424 e-' 18

P02570 Actin, cytoplasmic 1 (Beta-actin) 424 e- 18

ATHUB actin beta - human 424 e- 18

CAA26099.1 unnamed protein product 424 e- 18

AAA61667.1 cytoplasmic beta actin 424 e- 18

AAH01301.1 Beta actin 424 e- 18

AAH02409.1 Beta actin 424 e-' 18

AAH04251.1 Beta actin 424 e- 18

AAH13380.1 Beta actin 424 e-' 18

AAH14861.1 Beta actin 424 e-118

AAP22343.1 unknown 424 e-

Q15756 Inward rectifying K+ channel negative regulator Kir2.2v 756 0

S71341 inward rectifier potassium Ghannel chain Kir2.2 - human 756 0

AAC50615.1 inward rectifying K+ channel negative regulator Kir2.2v 756 0 potassium inwardly-rectifying channel J2; inward rectifier potassium channel 2; inward rectifier K+ channel KIR2.1; cardiac

NP 000382.1 inward rectifier potassium channel 593 e-169 Inward rectifier potassium channel 2 (Potassium channel, inwardly rectifying, subfamily J, member 2) (Inward rectifier K+ channel Kir2.1) (Cardiac inward rectifier potassium

P48049 channel) (IRK1) 693 e-169

I38727 cardiac inward rectifier potassium channel - human 693 e-169

AAA91781.1 inward rectifying potassium channel 593 e-169

AAC50072.1 cardiac inward rectifier potassium channel 593 e-169

AAA64282.1 inward rectifier potassium channel 593 e-169

AAB50277.1 inward rectifier K+ channel protein 593 e-169

AABδδ797.1 inward rectifier potassium channel 593 e-169

AAF73241.1 inwardly-rectifying potassium channel Kir2.1 593 e-169

AAF73242.1 inwardly-rectifying potassium channel Kir2.1 593 e-169

2105159A inward rectifier K channel 593 e-169

AAC39555.1 inwardly rectifying potassium channel Kir 2.1 590 e-168 potassium inwardly-rectifying channel J4; inward rectifier K+ channel

NP_004972.1 Kir2.3; hippocampal inward rectifier potassium channel 523 e-148 potassium inwardly-rectifying channel J4; inward rectifier K+ channel

NP 690607.1 Kir2.3; hippocampal inward rectifier potassium channel 523 e-148 Inward rectifier potassium channel 4 (Potassium channel, inwardly rectifying, subfamily J, member 4) (Inward rectifier K+ channel Kir2.3) (Hippocampal inward rectifier) (HIR)

P43050 (HRK1) (HIRK2) 523 e-148 136521 inwardly rectifying potassium channel, hippocampal - human 523 e-148

AAA19962.1 inwardly rectifying potassium channel; inward rectifier 523 e-148 AAA66076.1 inward rectifier K+ channel protein 523 e-148 A54862 potassium rectifier protein, brain - human 521 e-147 AAC60632.1 HRK1 521 e-147 AAC01951.1 inward rectifying K+ channel negative regulator 493 e-139 potassium inwardly-rectifying channel J14; inwardly rectifying NP_0374δ0.1 potassium channel KIR2.4 454 e-127 potassium inwardly-rectifying channel J14; inwardly rectifying NP_73333δ.1 potassium channel K1R2.4 454 e-127 AAD51376.1 inward rectifier potassium channel 454 e-127 AAF97619.1 inwardly rectifying potassium channel Kir2.4; IRK4 454 e-127 AAH35918.1 Potassium inwardly-rectifying channel J14 454 e-127

NM_007δ02 NP 031628.1 Mm.3109 F:2.2δ NP_000387.1 cathepsin K preproprotein; cathepsin X; cathepsin 01; cathepsin 02 60δ e-174 P43235 CATK_HUMAN Cathepsin K precursor (Cathepsin O) (Cathepsin X) (Cathepsin 02) 608 e-174 JC2476 cathepsin K (EC 3.4.22.-) precursor 608 e-174 CAA57649.1 Cathepsin O 608 e-174 AAA65233.1 cathepsin O 608 e-174 AAB35521.1 cathepsin 02 60δ e-174 AAA95998.1 cathepsin X 605 e-173 7PCK A Chain A, Crystal Structure Of Wild Type Human Procathepsin 530 e-165 7PCK B Chain B, Crystal Structure Of Wild Type Human Procathepsin K 5δ0 e-165 7PCK C Chain C, Crystal Structure Of Wild Type Human Procathepsin K 5δ0 e-165 7PCK D Chain D, Crystal Structure Of Wild Type Human Procathepsin K 580 e-165 1BYδ A Chain A, The Crystal Structure Of Human Procathepsin K 580 e-165 Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With The 1ATK Covalent Inhibitor E-64 402 e-112 A Chain A, Crystal Structure Of Cathepsin K Complexed With A Potent Vinyl Sulfone 1MEM Inhibitor 402 e-112

Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A

1AU4 Covalent Pyrrolidinone Inhibitor Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A

1 AUO Covalent Symmetric Diacylaminomethyl Ketone Inhibitor Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A 1AU2 Covalent Propanone Inhibitor Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A 1AU3 Covalent Pyrrolidinone Inhibitor Crystal Structure Of Cysteine Protease Human Cathepsin K In Complex With A

1AYU Covalent Symmetric Biscarbohydrazide Inhibitor Crystal Structure Of Cysteine Protease Human Cathepsin K In Complex With A

1AYV Covalent Thiazolhydrazide Inhibitor Crystal Structure Of Cysteine Protease Human Cathepsin K In Complex With A

1AYW Covalent Benzyloxybenzoylcarbohydrazide Inhibitor Crystal Structure Of Cysteine Protease Human Cathepsin K In Complex With A 1BGO Covalent Peptidomimetic Inhibitor A Chain A, Crystal Structure Of The Cysteine Protease Human Cathepsin K In 1 NL6 Complex With A Covalent Azepanone Inhibitor B Chain B, Crystal Structure Of The Cysteine Protease Human Cathepsin K In 1 NL6 Complex With A Covalent Azepanone Inhibitor A Chain A, Crystal Structure Of The Cysteine Protease Human Cathepsin K In 1 NLJ Complex With A Covalent Azepanone Inhibitor B Chain B, Crystal Structure Of The Cysteine Protease Human Cathepsin K In 1 NLJ Complex With A Covalent Azepanone Inhibitor

AAH02642.1 cathepsin NP_004070.3 cathepsin S preproprotein

P25774 CATS_HUMAN Cathepsin S precursor

138972 hypoxia-inducible factor 1 alpha - human 551 e-156 AAC50152.1 hypoxia-inducible factor 1 alpha 551 e-156 AAC51210.1 ARNT interacting protein 551 e-156 AAF20139.1 hypoxia-inducible factor 1 alpha 561 e-156 AAF20140.1 hypoxia-inducible factor 1 alpha 551 e-156 AAF20149.1 hypoxia-inducible factor 1 alpha 551 e-156 AAG43026.1 hypoxia-inducible factor 1 alpha subunit 551 e-156 AAH12527.1 Hypoxia-inducible factor 1 , alpha subunit, isoform 1 561 e-156 hypoxia-inducible factor 1 , alpha subunit (basic helix-loop-helix AAP86778.1 transcription factor) 551 e-156 2114407A hypoxia-inducible factor 1 551 e-156 AAC68568.1 hypoxia-inducible factor 1 alpha subunit 549 e-165 hypoxia-inducible factor-3 alpha isoform c; inhibitory PAS domain NP_69000δ.1 protein 363 e-100 AAL69947.1 inhibitory PAS domain protein 363 e-100 hypoxia-inducible factor-3 alpha isoform a; inhibitory PAS domain NP_690007.1 protein 363 e-100 JC7771 hypoxia inducible factor-3 alpha - human 363 e-100 AAD2266δ.1 Putative homolog of hypoxia inducible factor three alpha 363 e-100 BAB696δ9.1 hypoxia-inducible factor-3 alpha 363 e-100 BAB55324.1 unnamed protein product 3631e-099 hypoxia-inducible factor-3 alpha isoform b; inhibitory PAS domain NP_071907.2 protein 3284e-089

AF378762 tumor endothelial marker 8 isoform 1 precursor; anthrax toxin receptor; tumor AAL11999.1 Mm.29636 F:2.23 NP_115534.1 endothelial marker 8, isoform 3 precursor 881 0 Q9H6X2 ATR_HUMAN Anthrax toxin receptor precursor (Tumor endothelial marker δ) 8δ1 0 AAK52094.1 tumor endothelial marker δ precursor 881 0 tumor endothelial marker 8 isoform 2 precursor; anthrax toxin receptor; tumor NP 444262.1 endothelial marker 8, isoform 3 precursor 600 3-171

AACδ1735.1 uncoupling protein 3 NP_073714.1 uncoupling protein 3 isoform UCP3S; Uncoupling protein-3 AAC51356.1 UCP3S AAB46411.1 uncoupling protein-2 NP_003346.2 uncoupling protein 2; Uncoupling protein-2 P55851 UCP2_HUMAN Mitochondrial uncoupling protein 2 (UCP 2) (UCPH) AAC51336.1 UCP2 AAC39690.1 uncoupling protein 2 AAD21151.1 uncoupling protein-2 AAH11737.1 uncoupling protein 2 (mitochondrial, proton carrier) AAB53091.1 uncoupling protein homolog CAA11402.1 uncoupling protein 2

NP_068605.1 uncoupling protein 1 ; mitochondrial brown fat uncoupling protein

G0185δ uncoupling protein 1, mitochondrial

AAAδ5271.1 uncoupling protein

P25374 UCP1JHUMAN Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)

CAA36214.1 uncoupling protein

AAH03392.1 Similar to uncoupling protein 3 (mitochondrial, proton carrier) Mm.8033 F:2.21 AAK61566.1 AF371328 chondroadherin AAH36360.1 Similar to chondroadherin NP_001253.1 chondroadherin precursor

015335 CHAD_HUMAN Chondroadherin precursor (Cartilage leucine-rich protein)

AAH14095.1 RELA protein 457 e-128 AAH11603.1 RELA protein 446 e-124 v-rel reticuloendotheliosis viral oncogene homolog; oncogene REL, NP_002899.1 avian reticuloendotheliosis; C-Rel proto-oncogene protein 375 e-103 Q04864 C-Rel proto-oncogene protein (C-Rel protein) 375 e-103 A60646 transforming protein (c-rel) - human 375 e-103 CAA52954.1 c-rel 375 e-103 reticuloendotheliosis viral oncogene homolog B; v-rel avian reticuloendotheliosis viral oncogene homolog B (nuclear factor of kappa light polypeptide gene enhancer in NP_006500.2 B-cells 3) 3121e-084 AAC82346.1 I-REL 321e-0δ4 AAH28013.1 Reticuloendotheliosis viral oncogene homolog B 3121e-084 Q01201 Transcription factor RelB (l-Rel) 3075e-083 A42617 66K rel-related protein l-rel - human 3075e-083 AAA36127.1 l-Rel 307 δe-0δ3 ATP-binding cassette, sub-family C, member 1 isoform 1 ; multiple drug

NMJ308576 Mm.19663 resistance-associated protein; multiple drug resistance NP 032602.1 4 F:2.21 NP_004987.1 protein 1; multidrug resistance protein 2623 0 P33527 Multidrug resistance-associated protein 1 2623 0 AAB46616.1 multidrug resistance-associated protein 2623 0 DVHUAR multidrug resistance protein (cell line H69AR) - human 2619 0 AAB33979.1 multidrug resistance protein 2590 0 ATP-binding cassette, sub-family C, member 1 isoform 6; multiple drug resistance-associated protein; multiple drug resistance NP 063956.1 protein 1 ; multidrug resistance protein 2536

P10253 Lysosomal alpha-glucosidase precursor (Acid maltase) 1559 CAA68763.1 glucan 1 , 4-alpha-glucosidase 1559 CAA68764.1 70 kD alpha-glucosidase 1302 MGAJHUMAN Maltase-glucoamylase, intestinal [Includes: Maltase (Alpha-glucosidase); Glucoamylase (Glucan 043451 1 ,4-alpha-giucosidase)] 747 AAC39568.2 maltase-glucoamylase 747 NP_0046δ9.1 maltase-glucoamylase; brush border hydrolase; alpha-glucosidase 745 AAL83560.1 maltase-glucoamylase 724 NP_001032.1 sucrase-isomaltase 717 P14410 Sucrase-isomaltase, intestinal [Contains: Sucrase ; Isomaltase ] 717 sucrose alpha-glucosidase (EC 3.2.1.48) / oligo-1, 6-glucosidase (EC UUHU 3.2.1.10) [validated] - human 717 CAA45140.1 prosucrose-isomaitase 717 XP_374541.1 similar to maltase-glucoamylase 589 AAA60551.1 sucrase-isomaltase 531

NM_009727 Mm.15323 ATPase, aminophospholipid transporter (APLT), class I, type 8A, NP 033857.1 0 F:2.2 NP_006086.1 member 1 ; ATPase II; aminophospholipid translocase 2206 Potential phospholipid-transporting ATPase IA (Chromaffin granule Q9Y2Q0 ATPase II) (ATPase class I type δA member 1) 2206 AAD34706.1 ATPase II 2206 BAA77248.1 ATPasell 2197 BAC86905.1 unnamed protein product 1576 Potential phospholipid-transporting ATPase IB (ATPase class 1 type δA Q9NTI2 member 2) (ML-1) 1568 CAD97δ48.1 hypothetical protein 1357 BAC86402.1 unnamed protein product 1285 BAC04396.1 unnamed protein product 1062

probable adenosinetriphosphatase (EC 3.6.1.3) DKFZp434B1913.1 T46328 [similarity] - human (fragment) 984 0 CAB7065δ.1 hypothetical protein 984 0 Potential phospholipid-transporting ATPase ID (ATPase class I type 3B P9δ19δ member 2) δ22 0 NP_065185.1 ATPase, Class I, type δB, member 2 δ21 0 AAQ19027.1 possible aminophospholipid translocase ATP6B2 621 0

NM_019547 RNA-binding region containing protein 1 isoform a; ssDNA binding S33384 Mm.3865 F:2.2 NP_059965.2 protein SEB4; CLL-associated antigen KW-5 3529e-097 S38382 SEB4D protein - human (fragment) 3273e-0δ9 CAA53063.1 SEB4D 3273e-089 RNA-binding region containing protein 1 (HSRNASEB) (ssDNA binding Q9H0Z9 protein SEB4) (CLL-associated antigen KW-5) 3267e-089 CAC21462.1 dJδOOJ21.2.1 (ssDNA binding protein SEB4D (HSRNASEB), isoform 1) 3267e-089 AAH18711.1 RNPC1 protein 3267e-089 AAL99924.1 CLL-associated antigen KW-5 3267e-0δ9 S3δ3δ3 SEB4B protein - human (fragment) 3121e-084 CAA53064.1 SEB4B 3121e-084 CAC36889.1 dJ259A10.1 (ssDNA binding protein (SEB4D)) 2391e-062 BAC04474.1 unnamed protein product 2231e-057 CAC322δ1.1 dJδOOJ21.2.3 (ssDNA binding protein SEB4D (HSRNASEB), isoform 3) 2192e-0δ6 CAC32282.1 dJδ00J21.2.2 (ssDNA binding protein SEB4D (HSRNASEB), isoform 2) 2091e-053

NM_011607 tenascin C (hexabrachion); Hexabrachion (tenascin); hexabrachion

NP 035737.1 Mm.980 F:2.2 NP 002161.1 (tenascin C, cytofactin) 2695 0 Tenascin precursor (TN) (Hexabrachion) (Cytotactin) (Neuronectin) (GMEM) (Jl) (Miotendinous antigen) (Glioma-associated-extracellular matrix antigen) (GP P24621 150-226) (Tenascin-C) (TN-C) 2595 0 A32160 tenascin-C - human 2595 . 0

AAG23737.1 fer-1 like protein 3 2013 0 AAF27177.1 myoferlin 1983 0 T12449 hypothetical protein DKFZp564E1616.1 - human (fragments) 1696 0 CAB46370.1 hypothetical protein 1696 0 AAH52617λ FER1 L3 protein 867 0 XP_031009.3 similar to Fer113 protein 686 0

NM_016749 Mm.26962 P70402 1 F:2.18 AAH44226.1 ^' Myosin binding protein H 793 0 Q13203 Myosin-binding protein H (MyBP-H) (H-protein) 793 0 AAB36737.1 myosin binding protein H 784 0 NP_0049δδ.1 myosin binding protein H; myosin-binding protein H 775 0 A46118 myosin-binding protein H - human 775 0 fibronectin type III domains, aa 70-170 and aa 265-365; immunoglobulin C2 domains, aa 185-264 and aa 391-473; 86 AAA36339.1 kD protein 775 0 XP_291485.3 similar to Myosin-binding protein H (MyBP-H) (H-protein) 469 e-132 myosin binding protein C, fast type; myosin-binding protein C, NP_004524.1 fast-type; fast-type muscle myosin-binding-protein C 562 e-130 Myosin-binding protein C, fast-type (Fast MyBP-C) (C-protein, Q14324 skeletal muscle fast-isoform) 562 e-130 S36845 myosin-binding protein C, fast-type muscle - human 562 e-130 CAA51544.1 fast MyBP-C 562 e-130 myosin binding protein C, slow type; myosin-binding protein C, NP_002456.1 slow-type; skeletal muscle C-protein 459 e-129 S36846 myosin-binding protein C, slow-type muscle - human 459 e-129 CAA51545.1 slow MyBP-C 459 e-129

CAD33625.1 hypothetical protein 458 e-128 CAD91144.1 hypothetical protein 458 e-128 CAD33925.1 hypothetical protein 457 e-128

AAA60170.1 cAMP-dependent protein kinase catalytic subunit 694

AAH360δδ.1 PRKACB protein 6δ8

NP_δ91993.1 protein kinase, cAMP-dependent, catalytic, beta isoform a 671

CAD9731 δ .1 hypothetical protein 671

CAE46017.1 hypothetical protein 671

NP_002721.1 protein kinase, cAMP-dependent, catalytic, alpha 661

P17612 cAMP-dependent protein kinase, alpha-catalytic subunit (PKA C-alpha) 661 protein kinase (EC 2.7.1.37), cAMP-dependent, alpha catalytic chain - OKHU2C human 661

CAA30697.1 unnamed protein product 661 AAH39846.1 Protein kinase, cAMP-dependent, catalytic, alpha 661 protein kinase (EC 2.7.1.37), cAMP-dependent, gamma catalytic chain -

OKHUCG human

AAC41690.1 protein kinase A gamma-subunit 578 e-164 protein kinase, cAMP-dependent, catalytic, gamma; PKA C-gamma; NP_002723.2 serine(threonine) protein kinase 576 e-163

P22612 cAMP-dependent protein kinase, gamma-catalytic subunit (PKA C-gamma) 575 e-163

CAA04863.1 cAMP-dependent protein kinase gamma isoform 575 e-163 AAH398δδ.1 Protein kinase, cAMP-dependent, catalytic, gamma 574 e-163 AAH162δδ.1 PRKACB protein 504 e-142 NP_00503δ.1 protein kinase, X-linked 375 e-103

P51817 Serine/threonine protein kinase PRKX (Protein kinase PKX1) 375 e-103

138121 protein kinase - human 375 e-103

CAA69733.1 protein kinase 375 e-103 AAH41073.1 Protein kinase, X-linked 376 e-103 protein kinase (EC 2.7.1.37), cAMP-dependent, alpha catalytic

A38143 chain, short splice form - human (fragment) 363 1e-099

AAA60094.1 protein kinase A-alpha 363 1e-099

decorin isoform a preproprotein; dermatan sulphate proteoglycans II; bone NPJD01911.1 proteoglycan II; proteoglycan core protein 395 decorin isoform a preproprotein; dermatan sulphate proteoglycans II; bone NP_59δ010.1 proteoglycan II; proteoglycan core protein 395 P07585 PGS2_HUMAN Decorin precursor (Bone proteoglycan II) (PG-S2) (PG40) 395 NBHUC8 decorin precursor 395 AAB00774.1 proteoglycan core protein 395 AAD44713.1 decorin variant A 395 AAH05322.1 decorin 395 AAL92176.1 AF491944 decori 395 AAA52301.1 decorin 375

BAA90967.1 unnamed protein product 244 decorin isoform b precursor; dermatan sulphate proteoglycans II; bone proteoglycan NP_598011.1 Ii; proteoglycan core protein 213

AAF61437.1 decorin B 21δ

BAB55060.1 unnamed protein produc 209

NM_007682 centromere protein B; centromere protein B (80kD); centromere P27790 Mm.41454 R2.15 NP_001801.1 autoantigen B 828 P07199 Major centromere autoantigen B (Centromere protein B) (CENP-B) 828 S18736 centromere protein B - human 828 CAA33879.1 centromere autoantigen B (CENP-B) 82δ CAC17547.1 dJ1009E24.5 (Centromere protein B (80KDa)) δ2δ AAH53847.1 Centromere protein B δ28 AAB21673.1 major centromere protein, CENP-B [human, Peptide, 594 aa] 82δ CAA2391δ.1 CENP-B 822

Mm.7919 R2.13

Mm.41557 R2.12

Mm.27366 2 F:2.12

Mm.34533 R2.1

sialyltransferase 4A; CMP-N-acetylneuraminate-beta-galactosamide-alpha-2, 3-sialyltransferase; sialyltransferase 4A (beta-galactoside alpha-2,3-sialytransferase); alpha NP_775479.1 2,3-ST; Gal-beta-1 ,3-GalNAc-alpha-2,3-sialyItransferase 562 e-160 CMP-N-acetylneuraminate-beta-galactosamide-aipha-2, 3-sialyltransferase (Beta-galactoside alpha-2,3-sialyltransferase) (Alpha 2,3-ST) (Gal-NAc6S) (Gal-beta-1 ,3-GalNAc-alpha-2,3-sialyltransferase) (ST3GallA) (ST30) (ST3GalA.1) (SIAT4-A) (ST3Gal I)

Q11201 (SIATFL) 562 e-160

I54229 beta-galactoside alpha-2,3-sialyltransferase (EC 2.4.99.4) - human 562 e-160

AAC37574.1 beta-galactoside alpha-2,3-sialyltransferase 562 e-160

AAH 18357.1 Sialyltransferase 4A 562 e-160

AAA36612.1 sialyltransferase 562 e-160

AAC17874.1 alpha-2,3-sialyltransferase 559 e-159 sialyltransferase 4B; sialyltransferase 4B (beta-galactoside alpha-2,3-sialytransferase); alpha 2,3-ST; Gal-beta-1 ,3-GalNAc-alpha-2,3-sialyltransferase; CMP-N-acetylneuraminate-beta-galactosamide-alpha-2, NP_00δδ5δ.1 3-siaiyltransferase 332 2e-090 CMP-N-acetylneuraminate-beta-galactosamide-alpha-2, 3-sialyltransferase (Beta-galactoside alpha-2,3-sialyltransferase) (Alpha 2,3-ST) (Gal-NAc6S) (Gal-beta-1,3-GalNAc-alpha-2,3-sialyltransferase)

Q16642 (ST3GalA.2) (SIAT4-B) (ST3GaI II) 332 2e-090

JC5251 beta-galactoside alpha-2,3-sialyltransferase (EC 2.4.99.4) - human 332 2e-090

AAF05834.1 AF196571 Delta-like-1 protein 226

Mm.28δ64 F:2.07 AAF21976.1 AF114494_1 putative tyrosine phosphatase 478 AAG10713.1 PTPLA 474 NP_055056.2 protein tyrosine phosphatase-like, member a; proline instead of catalytic arginine 472 Similar to protein tyrosine phosphatase-like (proline instead of catalytic arginine), AAH10353.1 member a 472

XP_114343.2 similar to protein tyrosine phosphatase-like protein PTPLB [Mus musculus] 322

Mm.17403 F:2.07 AAL12161.1 AF418272_1 coagulation factor XIII, A1 polypeptide 482 A Chain A, Coagulation Factor Xiii (A-Subunit Zymogen) (E.C.2.3.2.13) 1GGT (Protein-Glutamine Gamma-GIutamyltransferase A Chain) 482 B Chain B, Coagulation Factor Xiii (A-Subunit Zymogen) (E.C.2.3.2.13) 1GGT (Protein-Glutamine Gamma-GIutamyltransferase A Chain) 482 1F13 A Chain A, Recombinant Human Cellular Coagulation Factor Xiii 482 1F13 B Chain B, Recombinant Human Cellular Coagulation Factor Xiii 482 1GGU A Chain A, Human Factor Xiii With Calcium Bound In The Ion Site 482 1GGY A Chain A, Human Factor Xiii With Ytterbium Bound In The Ion Site 482 1GGY B Chain B, Human Factor Xiii With Ytterbium Bound In The Ion Site 482 1QRK A Chain A, Human Factor Xiii With Strontium Bound In The Ion Site 482 1QRK B Chain B, Human Factor Xiii With Strontium Bound In The Ion Site 482 1GGU B Chain B, Human Factor Xiii With Calcium Bound In The Ion Site 482 CAC368δ6.1 bA526021.1 (coagulation factor XIII, A1 polypeptide) 4δ2 AAA52415.1 factor XIII a subunit 4δ1 coagulation factor XIII A1 subunit precursor; Coagulation factor XIII, A polypeptide; NP__000120.1 TGase 4δ1

AAA62488.1 clotting factor Xllla precursor (EC 2.3.2.13) 4δ1

F13A_HUMAN Coagulation factor XIII A chain precursor (Protein-glutamine P00488 gamma-glutamyltransferase A chain) (Transglutaminase A chain) 481 EKHUX protein-glutamine gamma-glutamyltransferase (EC 2.3.2.13), plasma 4δ1 1 EVU A Chain A, Human Factor Xiii With Calcium Bound In The Ion Site 431 1EVU B Chain B, Human Factor Xiii With Calcium Bound In The Ion Site 431 AAA524δ9.1 factor XIII precursor 431 1FIE A Chain A, Recombinant Human Coagulation Factor Xiii 431 1FIE B Chain B, Recombinant Human Coagulation Factor Xiii 4δ1 AAH27963.1 coagulation factor XIII, A1 polypeptide 430

NM_009425 tumor necrosis factor (ligand) superfamily, member 10; Apo-2 ligand; TNF-related NP 033461.1 Mm.1062 F:2.06 NP_003δ01.1 apoptosis inducing ligand TRAIL 345 TN10_HUMAN Tumor necrosis factor ligand superfamily member 10 (TNF-related P60591 apoptosis inducing ligand) (TRAIL protein) (Apo-2 ligand) (Apo-2L) 345

AAC50332.1 TNF-related apoptosis inducing ligand TRAIL 345

AAB01233.1 Apo-2 ligand 345

AAH32722.1 tumor necrosis factor (ligand) superfamily, member 10 345

1 DG6 A Chain A, Crystal Structure Of Apo2ITRAIL 266

1 DOG A Chain A, Crystal Structure Of Death Receptor δ (Drδ) Bound To Apo2ITRAIL 248

1 DOG B Chain B, Crystal Structure Of Death Receptor 5 (Dr5) Bound To Apo2ITRAIL 248

1 DOG D Chain D, Crystal Structure Of Death Receptor 5 (Drδ) Bound To Apo2ITRAIL 248

1 DU3 D Chain D, Crystal Structure Of Trail-Sdrδ 248

1 DU3 E Chain E, Crystal Structure Of Trail-Sdr5 248

1 DU3 F Chain F, Crystal Structure Of Trail-Sdrδ 248

1 DU3 J Chain J, Crystal Structure Of Trail-Sdrδ 248

1 DU3 K Chain K, Crystal Structure Of Trail-Sdrδ 248

1 DU3 L Chain L, Crystal Structure Of Trail-Sdrδ 248

1 D4V B Chain B, Crystal Structure Of Trail-Dr5 Complex 248 Mm.41573 F:2.05 AAH35281.1 Similar to fibromodulin 610 NP_002014.1 fibromodulin precursor 604 S65275 fibromodulin precursor 604 CAA53233.1 fibromodulin 604 FMOD_HUMAN Fibromodulin precursor (FM) (Collagen-binding 59 kDa protein) Q06828 (Keratan sulfate proteoglycan fibromodulin) (KSPG fibromodulin) 602 CAA51418.1 fibromodulin 602

AAA8526δ.1 lumican 291

NP_002336.1 lumican 291 LUM HUMAN Lumican precursor (Keratan sulfate proteoglycan lumican) (KSPG

P513δ4 lumican) 291

AAA91639.1 lumican 291

AAH0703δ.1 lumican 291

AAH35997.1- lumican 291

NPJD02716.1 proline arginine-rich end leucine-rich repeat protein 235 PRLP_HUMAN Prolargin precursor (Proline-arginine-rich end leucine-rich repeat P61388 protein) 235

I39068 proline- arginine-rich end leucine-rich repeat protein PRELP precursor 235

AAC50230.1 proline- arginine-rich end leucine-rich repeat protein 235

AAC18782.1 prolargin 235

AAH32498.1 proline arginine-rich end leucine-rich repeat protein 235

NP_008966.1 keratocan; cornea plana 2 (autosomal recessive) 233

060938 KERA_HUMAN Keratocan precursor (KTN) (Keratan sulfate proteoglycan keratocan) 233

AAC16390.1 keratan sulfate proteoglycan 233

AAC17741.1 keratocan; kera; corneal keratan sulfate proteoglycan 233

AAF69126.1 keratocan 233

Q9BR76 Coronin 1B (Coronin 2) 650 0 AAH06449.1 Coronin, actin binding protein, 1B 650 0 T47172 hypothetical protein DKFZp762H186.1 - human (fragment) 633 0 CABδ2406.1 hypothetical protein 633 0 coronin, actin binding protein, 1C; coronin, actin-binding protein, NP_055140.1 1 C; coronin 1 C 638 0 Q9ULV4 Coronin 1C (Coronin 3) (hCRNN4) 638 0 BAAδ3077.1 hCRNN4 638 0 AAH02342.1 Coronin, actin binding protein, 1C 638 0 BAA76769.1 KIAA0925 protein 406 e- 13 coronin, actin binding protein, 2B; clipin C; coronin, actin-binding, NPJ306082.1 2B; coronin, actin-binding protein, 2B 405 e-112 AAH26335.1 Coronin, actin binding protein, 2B 405 e-112 Q9UQ03 Coronin 2B (Coronin-like protein C) (ClipinC) (Protein FC96) 404 e-112 BAA36341.1 ClipinC 404 e-112 coronin, actin binding protein, 2A; coronin, actin-binding protein, 2A; coronin 2A; coronin-like protein B; WD-repeat protein NP_433171.1 2; WD protein IR10 395 e-109 Q92δ28 Coronin 2A (WD-repeat protein 2) (IR10) 395 e-109 AAH00010.1 Coronin, actin binding protein, 2A 395 e- 09 AAH11690.1 Coronin, actin binding protein, 2A 395 e- 09 coronin, actin binding protein, 2A; coronin, actin-binding protein, 2A; coronin 2A; coronin-like protein B; WD-repeat protein NP 003380.2 2; WD protein IR10 394 e-109 endothelial differentiation, sphingolipid G-protein-coupled receptor,

NM_007901 1 ; edg-1 ; G protein-coupled sphingolipid receptor; 006530 Mm .982 F:2.04 NP_001391.2 sphingosine 1 -phosphate receptor EDG1 683 0 AAF43420.1 G protein-coupled sphingolipid receptor 683 0 AAH18650.1 EDG1 protein 683 0

P21463 Probable G protein-coupled receptor EDG-1 674 0 A35300 G protein-coupled receptor edg-1 - human 674 0 AAA62336.1 endothelial differentiation protein (edg-1 ) 674 0 AAC51906.1 G protein-coupled receptor 674 0 AAK01993.1 EDG1 596 e-170 endothelial differentiation, sphingolipid G-protein-coupled receptor, 3; G protein-coupled receptor, endothelial differentiation gene-3; S1P receptor EDG3; sphingosine 1 -phosphate receptor 3; chromosome 9 open reading frame

NP_005217.2 47 369 e-101 AAP84353.1 endothelial differentiation sphingolipid G-protein-coupled receptor 3 369 e-101 Endothelial differentiation, sphingolipid G-protein-coupled receptor,

AAH60827.1 3 369 e-101 Sphingosine 1-phosphate receptor Edg-3 (S1P receptor Edg-3) (Endothelial differentiation G-protein-coupled receptor

Q99500 3) 368 e-101 JC5245 G protein-coupled receptor - human 368 e-101 CAA58744.1 G-protein coupled receptor (putative) 368 e-101 AAC51906.1 lysosphingolipid receptor 363 e-101 endothelial differentiation, sphingolipid G-protein-coupled receptor, 8; sphingosine 1-phosphate receptor Edg-8; sphingosine

NP_110387.1 1-phosphate receptor 5 317 1e-035 AAG3δ113.1 sphingosine 1-phosphate receptor Edg-8 317 1e-035 AAL57041.1 SPPR 317 1e-0δ5 BAB89315.1 putative G-protein coupled receptor 317 1e-085 Endothelial differentiation, sphingolipid G-protein-coupled receptor,

AAH34703.1 8 317 1e-0δ5 BAC11119.1 unnamed protein product 317 1e-035

Mm .30978 F:2.04

AAD02640.1 multiple exostoses-like 1 975 AAF73172.1 exostoses-like protein 1 975 Exostosin-1 (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N- acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase) (Putative tumor Q16394 suppressor protein EXT1 ) (Multiple exostoses protein 1 ) 530 0 AAH01174.1 Exostoses (multiple) 1 530 0 NP_000118.1 exostoses (multiple) 1 526 e-149 putative tumour suppressor/hereditary multiple exostoses candidate AAB62283.1 gene 526 e-149 2204384A EXT1 gene 526 e-149 NP_000392.1 exostoses (multiple) 2 2715e-072 Exostosin-2 (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N- acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase) (Putative tumor Q93063 suppressor protein EXT2) (Multiple exostoses protein 2) 2715e-072 AAB07008.1 EXT2 271 δe-072 AAC51219.1 multiple exostosis 2 2715e-072 AAC60764.1 hereditary multiple exostoses gene 2 protein 271 δe-072 AAH10058.1 EXT2 protein 271 5e-072 AAB62718.1 multiple exostoses type II protein EXT2.I 2471e-064

AAδ32579 a disintegrin and metalloprotease with thrombospondin motifs-2 isoform 1 ; procollagen δ.OOe- XP 109630.2 Mm.δ9δ63 F:2.03 NP_055059.1 I N-proteinase; Procollagen N-endopeptidase 240 64 ATS2_HUMAN ADAMTS-2 precursor (A disintegrin and metalloproteinase with thrombospondin motifs 2) (ADAM-TS 2) (ADAM-TS2) Procollagen l/ll amino-propeptide processing enzyme) (Procollagen I N-proteinase) (PC l-NP) δ.OOe- 095450 (Procollagen N-endopeptidase) (pNPl) 240 64

CAA05δδ0.1 procollagen I N-proteinase 240

AAH16461.1 AAH16461 Unknown (protein for IMAGE:34δ1933) 160 Mm.42δδ F:2.03 NP_0δ4776.1 osteoglycin preproprotein; osteoinductive factor; mimecan 495 NP_077727.1 osteoglycin preproprotein; osteoinductive factor; mimecan 495 NP_143935.1 osteoglycin preproprotein; osteoinductive factor; mimecan 495 P20774 MIME_HUMAN Mimecan precursor (Osteoglycin) (Osteoinductive factor) (OIF) 495 B36272 osteoinductive factor 495 AAD43022.1 osteoinductive factor OIF 496 CAB53706.1 hypothetical protein 495 AAF19364.1 mimecan 495 AAF69109.1 AF202167_1 mimecan 495 AAH37273.1 osteoglycin (osteoinductive factor, mimecan) 495

CAB61417.1 hypothetical protein 241 PGLB_HUMAN Dermatan sulfate proteoglycan 3 precursor (Epiphycan) (Small Q99646 chondroitin/dermatan sulfate proteoglycan) (Proteoglycan-Lb) (PG-Lb) 215

AAH30958.1 dermatan sulfate proteoglycan 3 216

NP_004941.1 dermatan sulfate proteoglycan 3; Pg-Lb; dermatan sulphate proteoglycan 3 210

AAC50945.1 dermatan sulfate proteoglycan 3 210

NP 355174.1 opticin; oculoglycan; opticin, oculoglycan 204

Q9UBM4 OPT_HUMAN Opticin precursor (Oculoglycan) 204

AAD45900.1 AF161702_1 oculoglycan

CAB53459.1 opticin

AAL78286.1 opticin cartilage oligomeric matrix protein presursor; epiphyseal dysplasia, multiple 1 ;

NM_016635 pseudoachondroplasia (epiphyseal dysplasia 1 , multiple); cartilage oligomeric matrix NP 057694.1 Mm.45071 F:2.03 NP_0000δ6.1 protein(pseudoachondroplasia, epiphyseal dysplasia 1 , multiple) P49747 COMP_HUMAN Cartilage oligomeric matrix protein precursor (COMP) AAA57253.1 matrix protein BAC533δ8.1 cartilage oligomeric matrix protein AAB86501.1 COMP_HUMAN Similar to cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal AAH33676.1 dysplasia 1, multiple) NP_003239.1 thrombospondin 4 P35443 TSP4_HUMAN Thrombospondin 4 precursor TSHUP4 thrombospondin 4 precursor CAA79635.1 thrombospondin-4 NP_009043.1 thrombospondin 3 P49746 TSP3_HUMAN Thrombospondin 3 precursor A57121 thrombospondin 3 precursor AAC41762.1 thrombospondin 3 AAH1δ766.1 Similar to thrombospondin 3 NP_003237.1 thrombospondin 1 CAA32δδ9.1 precursor polypeptide (AA -31 to 1139) P07996 TSP1_HUMAN Thrombospondin 1 precursor TSHUP1 thrombospondin 1 precursor CAA2δ370.1 precursor polypeptide (AA -1δ to 1152)

1304281 A throm bospondin 567 e- 61 NP_003238.1 thrombospondin 2 560 e-156 P35442 TSP2_HUMAN Thrombospondin 2 precursor 560 e-156 TSHUP2 thrombospondin 2 precursor 560 e-156 AAA03703.1 thrombospondin 2 550 e-156 AAC51818.1 thrombospondin3 467 e-131

NM_009762 Mm.23427 SET and MYND domain containing 1; CD8 beta opposite; zinc finger, NP 033692.1 4 F:2.03 NP_938015.1 MYND domain containing 1δ 935 0 QδNB12 SET and MYND domain containing protein 1 935 0 BAC03732.1 unnamed protein product 935 0 SET and MYND domain containing 2; HSKM-B protein; zinc finger, MYND NP_064532.1 domain containing 14 2437e-064 AAFδ6953.1 HSKM-B 2437e-064 SET and MYND domain containing protein 3 (Zinc finger MYND domain Q9H7B4 containing protein 1) 2339e-061

AAH31010.1 SMYD3 protein 2339e-061 AAH49367.1 SMYD2 protein 2244e-053 SET and MYND domain containing 3; zinc finger protein, subfamily 3A (MYND domain containing), 1 ; zinc finger, MYND domain NP_073530.1 containing 1 2106e-054 BAB149δ1.1 unnamed protein product 2106e-054

U61363 Mm.10363 transducin-Iike enhancer protein 4; transducin-like enhancer of split S35681 8 F:2.03 NP_00δ936.2 4; enhancer of split groucho 4; B lymphocyte gene 1 1043 0 Q04727 Transducin-like enhancer protein 4 1043 0 T47149 hypothetical protein DKFZp547P103.1 - human (fragment) 1043 0 CABδ2397.1 hypothetical protein 1043 0 BAAδ657δ.1 KIAA1261 protein 1043 0 AAH59406.1 TLE4 protein 1026 0

I38596 calcium-activated potassium channel - human (fragment) 1155 0 AAA60216.1 calcium-activated potassium channel 1155 0

NM_009673 Annexin V (Lipocortin V, Endonexin li, Placental Anticoagulant Protein) (Calcium Ions NP 033803.1 Mm.1620 F:2.02 1HVD Are Visible) Mutation With Glu 17 Replaced By Gly (E17g) 566 e-161 Annexin V (Lipocortin V, Endonexin li, Placental Anticoagulant Protein) Mutant With Glu 17 Replaced By Gly, Glu 7δ Replaced By Gin (E17g,E78q) Complexed With 1HVF Calcium 665 e-161 1A W A Chain A, Annexin V 563 e-160 1ANW B Chain B, Annexin V 563 e-160 1ANX A Chain A, Annexin V 563 e-160 1ANX B Chain B, Annexin V 563 e-160 1ANX C Chain C, Annexin V 563 e-160 NP_001145.1 annexin V; endonexin ll; anchorin CH; lipocortin V; placental anticoagulant. protein I 663 e-160 ANX5_HUMAN Annexin V (Lipocortin V) (Endonexin II) (Calphobindin I) (CBP-I) (Placental anticoagulant protein I) (PAP-I) (PP4) (Thromboplastin inhibitor) (Vascular P0875δ anticoagulant-alpha) (VAC-alpha) (Anchorin Cll) 663 e-160 AQHUP annexin V 663 e-160 1AVH A Chain A, Annexin V (Hexagonal Crystal Form) 563 e-160 1AVH B Chain B, AnnexinV (Hexagonal Crystal Form) 563 e-160 1AVR Annexin V (Rhombohedra! Crystal Form) 563 e-160 B Chain B, Crystal Structure Of Recombinant Human Placental Annexin V Complexed 1HAK With K-201 As A Calcium Channel Activity Inhibitor 563 e-160 A Chain A, Crystal Structure Of Recombinant Human Placental Annexin V Complexed 1HAK With K-201 As A Calcium Channel Activity lnhibitor563 563 e-160 CAA30935.1 VAC protein (AA 1-320) 563 e-160 AAA35570.1 anticoagulant precursor (5' end put.); putative 563 e-160 AAA52336.1 endonexin II 563 e-160 AAB59545.1 anticoagulant protein 4 563 e-160 BAA00122.1 blood coagulation inhibitor 563 e-160

folate hydrolase (prostate-specific membrane antigen) 1 ; folate hydrolase 1 NP_004467.1 (prostate-specific membrane antigen) 228 FOH1_HUMAN Glutamate carboxypeptidase II (Membrane glutamate carboxypeptidase) (mGCP) (N-acetylated-alpha-iinked acidic dipeptidase I) (NAALADase I) (Pteroylpoly-gamma-glutamate carboxypeptidase) (Folylpoly-gamma-glutamate carboxypeptidase) (FGCP) (Folate hydrolase 1) Q04609 (Prostate-specific membrane antigen) (PSMA) (PSM) 228

A56δδ1 prostate-specific membrane antigen 228

AAA60209.1 prostate- specific membrane antigen 228

AAD51121.1 AF176574_1 folylpoly-gamma-glutamate carboxypeptidase 228

AAM34479.1 prostate-specific membrane antigen 228 N-acetylated alpha-linked acidic dipeptidase 2; N-acetylated alpha-linked acidic NP_00545δ.1 dipeptidase II 216

Q9Y3Q0 NLD2_HUMAN N-acetylated-alpha-linked acidic dipeptidase II (NAALADase II) 216

CAB39967.1 NAALADase II protein 216 Mm.25157 F:2.02 NP_057491.1 chromosome 20 open reading frame 43 393 AAF2912δ.1 HSPC164 393 Q9BY42 Protein C20orf43 (HSPC164/HSPC169) (AD-007) (CDAOδ) 393 AAF29133.1 HSPC169 393 AAH03369.1 C20orf43 protein 393

CAC03740.1 dJ1153D9.1.1 (novel protein) 392

BAA91193.1 unnamed protein product 390 e-108 AAF17212.1 protein x 0001 389 e-108 AAK14929.1 CDAOδ 389 e-108

U67327 Mm.29619 T-box 1 isoform A; brachyury; T-box 1 transcription factor C; P70323 4 F:2.02 NP_δ42377.1 Testis-specific T-box protein 350 6e-097 T-box transcription factor TBX1 (T-box protein 1 ) (Testis-specific 043435 T-box protein) 3506e-097 AAB9401δ.1 brachyury 3506e-097 T-box 1 isoform C; brachyury; T-box 1 transcription factor C; NP_542378.1 Testis-specific T-box protein 3506e-097 AAKδ8955.1 T-box 1 transcription factor C 3506e-097 T-box 1 isoform B; brachyury; T-box 1 transcription factor C; NP_005983.1 Testis-specific T-box protein 3506e-097 AAB94019.1 brachyury 3506e-097 NP_005936.2 T-box 10 3101e-084 AA073463.1 transcription factor TBX10 3101e-084 NP_0651δ0.1 T-box transcription factor TBX20; T-box protein 20 2245e-059 CAB51916.1 T-box transcription factor 2245e-059 Q9UMR3 T-box transcription factor TBX20 (T-box protein 20) 2245e-059 AAD21787.1 similar to fly T-box protein H1 δ; similar to Q94890 (PID:g2δ01131) 2245e-059 075333 T-box transcription factor TBX10 (T-box protein 10) 2132e-055 AAC23481.1 T-box-containing transcriptional activator 2132e-055 NP_06095δ.2 T-box 4 2101e-054 Pδ70δ2 T-box transcription factor TBX4 (T-box protein 4) 2101e-054 ras homolog gene family, member C; Aplysia RAS-related homolog 9

NM_007484 (oncogene RHO H9); Aplysia ras-related homolog 9; RhoC; Q62159 Mm.262 F:2.02 NP_7δ6δδ6.1 RAS homolog gene family, member C (oncogene RHO H9) 394 e-109 P0δ134 Transforming protein RhoC (H9) 394 e-109 TVHURC GTP-binding protein rhoC - human 394 e-109

CAA29969.1 unnamed protein product 394 AAC33179.1 GTPase [ 394 AAH07245.1 Ras homolog gene family, member C 394 AAH09177.1 Ras homolog gene family, member C 394 AAM21119.1 small GTP binding protein RhoC 394 AAH52808.1 Ras homolog gene family, member C 394 ras homolog gene family, member A; Aplysia ras-related homolog 12;

NP_001655.1 oncogene RHO H12 369 P06749 Transforming protein RhoA (H12) 369 TVHU12 GTP-binding protein rhoA - human 369 CAA28690.1 unnamed protein product 369 AAC33173.1 GTP-binding protein 369 AAH01360.1 ARHA protein 369 AAH05976.1 ARHA protein 369 AAM21117.1 small GTP binding protein RhoA 369 CAE46190.1 hypothetical protein 369 Chain B, Crystal Structure Of The Dbl And Pleckstrin Homology

1LB1 |B Domains Of Dbs In Complex With Rhoa 365 Chain D, Crystal Structure Of The Dbl And Pleckstrin Homology

1LB1 |D Domains Of Dbs In Complex With Rhoa 365 Chain F, Crystal Structure Of The Dbl And Pleckstrin Homology

1LB1 |F Domains Of Dbs In Complex With Rhoa 365 Chain H, Crystal Structure Of The Dbl And Pleckstrin Homology

1LB1 |H Domains Of Dbs In Complex With Rhoa 366

1 FTN Crystal Structure Of The Human RhoaGDP COMPLEX 365

10W3|B Chain B, Crystal Structure Of Rhoa.Gdp.Mgf3-ln Complex With Rhogap 365

1CC0|A Chain A, Crystal Structure Of The Rhoa.Gdp-Rhogdi Complex 363

1CC0|C Chain C, Crystal Structure Of The Rhoa.Gdp-Rhogdi Complex 363

AAA50612.1 multidrug resistance protein 362

NP_008966.1 keratocan; cornea plana 2 (autosomal recessive) 220

060933 KERA_HUMAN Keratocan precursor (KTN) (Keratan sulfate proteoglycan keratocan) 220

AAC16390.1 keratan sulfate proteoglycan 220

AAC17741.1 keratocan; kera; corneal keratan sulfate proteoglycan 220

AAF69126.1 keratocan 220

AAH32667.1 keratocan 220

NP_002716.1 proline arginine-rich end leucine-rich repeat protein 21δ PRLP_HUMAN Prolargin precursor (Proline-arginine-rich end leucine-rich repeat

P51δδδ protein) 218

I39063 proline- arginine-rich end leucine-rich repeat protein PRELP precursor 21 δ

AAC60230.1 proline- arginine-rich end leucine-rich repeat protein 21 δ

AAC18782.1 prolargin 21 δ

AAH32498.1 proline arginine-rich end leucine-rich repeat protein 21 δ

NP_005005.1 osteomodulin 211 OMD_HUMAN Osteomodulin precursor (Osteoadherin) (OSAD) (Keratan sulfate

Q99983 proteoglycan osteomodulin) (KSPG osteomodulin) 211

NM_00δ594 A55182 Mm.2759 F:2.01

Mm.34118 F:2

AAH02805.1 gap junction protein, beta 1 , 32kD (connexin 32) 319 gap junction protein, beta 1 , 32kD (connexin 32, Charcot-Marie-Tooth neuropathy,

AAH22426.1 X-linked) 319 gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy,

AAH39198.1 X-linked) 319 gap junction protein, beta 3, 31 kDa (connexin 31); gap junction protein, beta 3, 31 kD

NP_076372.1 (connexin 31) 256

075712 CXB3_HUMAN Gap junction beta-3 protein (Connexin 31 ) (Cx31 ) 266

JE0274 connexin 31 266

CAA06165.1 connexin31 266

AAD11616.1 connexin 31; gap junctional protein cx31 266

AAC95471.1 connexin 31 266

CAB90269.1 dJ34M23.2 (gap junction protein, beta 3, 31 kD (connexin 31 )) 256

AAH12913.1 gap junction protein, beta 3, 31 kD (connexin 31) 256

NP_694944.1 gap junction protein, beta 4; connexin 30.3 254

Q9NTQ9 CXB4JHUMAN Gap junction beta-4 protein (Connexin 30.3) (Cx30.3) 264

CAB90270.1 dJ34M23.3 (gap junction protein, beta 4 (connexin 30.3)) 254

AAH34709.1 similar to Gap junction beta-4 protein (Connexin 30.3) (Cx30.3) 254

NP_0052δ9.1 gap junction protein, beta 5 (connexin 31.1) 241

095377 CXB5_HUMAN Gap junction beta-5 protein (Connexin 31.1) (Cx31.1) 241

AAD13005.1 connexin 31.1 ; gap junctional protein cx31.1 241

CAB90271.1 dJ34M23.4 (gap junction protein, beta 5 (connexin 31.1 )) 241

AAH04379.1 gap junction protein, beta 5 (connexin 31.1) 241

AAC95472.1 connexin 31.1 241 gap junction protein, alpha 8, δOkDa (connexin 50); gap junction membrane channel protein alpha-8; connexin 50; Gap junction membrane channel protein alpha-8 NP_00δ258.1 (connexin δO); gap junction protein, alpha 8, 50kD (connexin 50) 241

139176 intrinsic membrane protein MP70 241

AAA77062.1 gap junction membrane channel protein alpha-8 241 Mm.2770 F:2 AAA961δ2.1 insulin-like growth factor-l 248

P05019 IGFB_HUMAN Insulin-like growth factor IB precursor (IGF-IB) (Somatomedin C) 237

IGHU1 B insulin-like growth faGtor I precursor, splice form B 237

AAA52543.1 insulin-like growth factor I precursor

1203253A insulin-like growth factor I cytochrome P450, family 2, subfamily E, polypeptide 1; cytochrome P450, subfamily HE (ethanol-inducible), polypeptide 1; microsomal monooxygenase; xenobiotic

NM_021282 monooxygenase; flavoprotein-linked monooxygenase; cytochrome P450, subfamily

NP 067257.1 Mm.21758 F:2 NP_000764.1 HE (ethanol-inducible) P05131 CPE1_HUMAN Cytochrome P4602E1 (CYPIIE1) (P450-J) A31949 cytochrome P450 2E1 AAAδ215δ.1 cytochrome P450IIE1 AAA35743.1 cytochrome P450J AAF13601.1 AF132276_1 cytochrome P450-2E1 AAD13753.1 cytochrome P4502E1 cytochrome P460, family 2, subfamily C, polypeptide 19; cytochrome P460, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19; mephenytoin 4'-hydroxylase; microsomal monooxygenase; xenobiotic monooxygenase; flavoprotein-linked NP_000760.1 monooxygenase CPCJ_HUMAN Cytochrome P4502C19 (CYPHC19) (P460-11A) (Mephenytoin P33261 4-hydroxylase) (CYPIIC17) (P450-264C) AAB59426.1 cytochrome cytochrome P4δO, family 2, subfamily C, polypeptide 16; cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 17; cytochrome P460, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 1δ; microsomal monooxygenase; NP_000763.1 flavoprotein-linked monooxygenase AAB59356.1 cytochrome P33260 CPCIJHUMAN Cytochrome P460 2C1 δ (CYPIIC1 δ) (P450-6B/29C) A61269 cytochrome P4502C18

AAH19610. 1 Somatostatin receptor 2 326 4e-089 BAC06126.1 seven transmembrane helix receptor 326 4e-089 AAO92064. 1 somatostatin receptor 2 326 4e-039 AAF42810.1 somatostatin receptor 2B 326 4e-0δ9

U89434 Mm.24776 NP_004740.

NP_075713.1 1 F:2 2 cell cycle progression 2 protein isoform 1 243 1e-064 AAH14918. 1 Cell cycle progression 2 protein, isoform 1 243 1e-064 AAH17235. 1 Cell cycle progression 2 protein, isoform 1 243 1e-064 CAD33700.1 hypothetical protein 243 1e-064 AAH02732.2 CPR2 protein 243 1e-064 AAB69312.1 ell cycle progression 2 protein 230 6e-061

MASTER TABLE 1. Subtable 1B Unfavorable Genes/Proteins

Mouse

Gene Human Score E-valu

Protein Unigene Behavior Proteins Human Protein Name (bits) e

AK015750 Chain A, Crystal Structure Of Human Estrogen Sulfotransferase V269e Mutant In

NP_075624 Mm.39655 U:+7.39 pdb|1HY3|A The Presence Of Paps 497 e-140 Chain B, Crystal Structure Of Human Estrogen Sulfotransferase V269e Mutant In pdb|1HY3]B The Presence Of Paps 497 e-140 sulfotransferase, estrogen-preferring; estrogen sulfotransferase; estrone NP_005411.1 sulfotransferase 494 e-139 P49888 Estrogen sulfotransferase (Sulfotransferase, estrogen-preferring) (EST-1) 494 e-139 JC2229 estrogen sulfotransferase (EC 2.8.2.-) - human 494 e-139 Chain A, Crystal Structure Of Human Estrogen Sulfotransferase In Complex With pdb(1G3M|A In-Active Cofactor Pap And 3,5,3',5'- Tetrachloro-Biphenyl-4,4'-Diol 494 e-139 Chain B, Crystal Structure Of Human Estrogen Sulfotransferase In Complex With pdb|1G3M|B In-Active Cofactor Pap And 3,5,3',δ'- Tetrachloro-Biphenyl-4,4'-Diol 494 e-139 AAA82125.1 estrogen sulfotransferase 494 e-139 AAB34601.1 estrogen sulfotransferase; hEST-1 494 e-139 AAC50286.1 estrogen sulfotransferase 494 e-139 CAA72079.1 estrogen sulfotransferase 494 e-139 AAQ97179.1 sulfotransferase, estrogen-preferring 494 e-139 AAH27956.1 Sulfotransferase, estrogen-preferring 492 e-139 sulfotransferase family, cytosolic, 1B, member 1; thyroid hormone sulfotransferase; NP_055280.2 sulfotransferase 1B1; sulfotransferase 1B2 323 δe-08δ AAB65154.1 thyroid hormone sulfotransferase 323 5e-0δδ JC5δδ5 thyroid hormone sulfotransferase (EC 2.8.2.-) B2 - human 323 5e-088 BAA24647.1 ST1B2 323 5e-088 AAH10δ95.1 Sulfotransferase family, cytosolic, 1B, member 1 322 1e-087 JC2623 aryl sulfotransferase (EC 2.8.2.1) brain isoform - human 315 1e-0δ5 AAA67896.1 phenol sulfotransferase 315 1e-0δ5

AAH22016.1 Protein kinase C, iota 871 0 NP_005391.1 protein kinase C, epsilon 399 e-110 Q02156 Protein kinase C, epsilon type (nPKC-epsilon) 399 e-110 S28942 protein kinase C (EC 2.7.1.-) epsilon - human 399 e-110 CAA463δδ.1 protein kinase C epsilon 399 e-110 NP_006246.2 protein kinase C, eta 384 e-106 AAH37263.1 Protein kinase C, eta 384 e-106 P24723 Protein kinase C, eta type (nPKC-eta) (PKC-L) 382 e-105 A39666 protein kinase C (EC 2.7.1.-) eta - human 382 e-105 AAA60100.1 protein kinase C-L 382 e-105 P05771 Protein kinase C, beta type (PKC-beta) (PKC-B) 367 e-101 IHUC1 protein kinase C (EC 2.7.1.-) beta-l - human 367 e-101 CAA29634.1 PKC beta 1 (AA 1 -671 ) 367 e-101

NM 013737

NP 038765 phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma);

.1 Mm .9277 U.-+3.16 NP_00δ075.1 Platelet-activating factor acetylhydrolase 58δ e-168 PAFA_HUMAN Platelet-activating factor acetylhydrolase precursor (PAF acetylhydrolase) (PAF 2-acylhydrolase) (LDL-associated phospholipase A2) (LDL-PLA(2)) (2-acetyl-1-alkylglycerophosphocholine esterase) Q13093 (1-alkyl-2-acetylglycerophosphocholine esterase) 58δ e-168 S60247 platelet-activating factor acetylhydrolase precursor 588 e-168 AAC50126.1 platelet-activating factor acetylhydrolase 588 e-168 2109334A platelet-activating factor acetylhydrolase 588 e-168 AAB04170.1 LDL-phospholipase A2 587 e-167 AAH38452.1 phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma) 587 e-167 platelet-activating factor acetylhydrolase 2; platelet-activating factor acetylhydrolase 3.000e NP_000428.2 2 (40kD) 287 -77

M74752

NP_542766

.1 Mm.155714 U:+2.δ3 CAC20413.1 beta-myosin heavy chain 662 0 NP_00024δ.1 myosin, heavy polypeptide 7, cardiac muscle, beta 6δ2 0 P12δδ3 MYH7_HUMAN Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta) 6δ2 0 A37102 myosin beta heavy chain, cardiac and skeletal muscle 6δ2 0 AAA51δ37.1 beta-myosin heavy chain 6δ2 0 AAA62830.1 beta-myosin heavy chain 6δ2 0 CAA35940.1 beta-myosin heavy chain (1151 AA) 679 0 CAA37068.1 cardiac beta myosin heavy chai 673 0 P13633 MYH6_HUMAN Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha) 667 0 NP_002462.1 myosin heavy chain 6; myosin heavy chain, cardiac muscle alpha isoform 665 0 CAA79675.1 cardiac alpha-myosin heavy chai 665 0 XP_033377.7 similar to cardiac alpha-myosin heavy chain 665 0 A46762 myosin alpha heavy chain, cardiac muscle 664 0 BAA00791.1 cardiac alpha-myosin heavy chain 664 0 NP_005954.2 myosin, heavy polypeptide 1, skeletal muscle, adult; myosin heavy chain llx/d 660 0 MYH1_HUMAN Myosin heavy chain, skeletal muscle, adult 1 (Myosin heavy chain P12882 llx/d) (MyHC-llx/d) 660 0 AAD29951.1 myosin heavy chain ilx/d 560 0 NP_060004.1 myosin, heavy polypeptide 2, skeletal muscle, adult 560 0 MYH2JHUMAN Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain Q9UKX2 lla) (MyHC-lla) 560 0 AAD29950.1 myosin heavy chain lla 560 0

AK016750

BAB29966. A Chain A, Crystal Structure Of Human Estrogen Sulfotransferase V269e Mutant In

1 Mm.896δδ U:+2.δ2 1HY3 The Presence Of Paps 497 e-140

CAA55089.1 aryl sulfotransferase 313

CAA07495.1 phenol sulfotransferase 313

20212δOC ary) sulfotransferase 313

S52791 aryl sulfotransferase (EC 2.8.2.1) 313

AAB31316.1 aryl sulfotransferase ST1 A2 [human, liver, Peptide, 295 aa] 313

CAA5δ088.1 aryl sulfotransferase 313

2021280B ary! sulfotransferase 313

I57945 phenol-sulfating phenol sulfotransferase 313

AAA99892.1 phenol-sulfating phenol sulfotransferase 313

AAC50430.1 phenol sulfotransferase 313 cytochrome P450, family 1 , subfamily B, polypeptide 1; aryl hydrocarbon

NM 009994 hydroxylase; cytochrome P450, subfamily l (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile); microsomal monooxygenase; xenobiotic

NP 034124 Mm.214016 U:+2.73 NP_00009δ.1 monooxygenase; flavoprotein-linked monooxygenase 785 Q1667δ Cytochrome P450 1 B1 (CYPIB1 ) 785 A54116 cytochrome P450 1 B1 - human 785 AAA19567.1 cytochrome P460 785 AAH12049.1 Cytochrome P450, family 1, subfamily B, polypeptide 1 785

AAC50δ09.1 cytochrome P460 CYP1B1 735 0

AAM50612.1 cytochrome P450 CYP1 B1 7δ5 0

AAQ87875.1 cytochrome P4δ0, family 1 , subfamily B, polypeptide 1 7δ5 0 cytochrome P450, family 1 , subfamily A, polypeptide 1 ; aryl hydrocarbon hydroxylase; cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1; flavoprotein-linked monooxygenase; cytochrome P1-450, dioxin-inducible; P450 form 6; xenobiotic monooxygenase; microsomal

NP_000490.1 monooxygenase 324 8e-088

P0479δ Cytochrome P450 1A1 (CYPIA1) (P450-P1) (P450 form 6) (P450-C) 324 8e-08δ aryl hydrocarbon (benzo[a]pyrene) hydroxylase (EC 1.14.14.-) cytochrome P450

04HU6 1A1 - human 324 δe-088

CAA27643.1 P-450 c 324 8e-088

AAK25727.1 cytochrome P450 324 8e-088

AAH23019.1 Cytochrome P450, family 1, subfamily A, polypeptide 1 324 8e-088

AAA62139.1 cytochrome P-450-1 322 3e-0δ7

CAA2645δ.1 cytochrome P(1)-460 322 5e-037 cytochrome P450, family 1, subfamily A, polypeptide 2; cytochrome P450, subfamily l (aromatic compound-inducible), polypeptide 2; dioxin-inducible P3-450; P450 form 4; xenobiotic monooxygenase; aryl hydrocarbon hydroxylase; microsomal

NP_000752.1 monooxygenase; flavoprotein-linked monooxygenase 310 1e-083

P05177 Cytochrome P460 1A2 (CYPIA2) (P460-P3) (P(3)450) (P4604) 310 1e-083

04HU4 cytochrome P4δ0 1A2 - human 310 1e-083

CAA77335.1 unnamed protein product 310 1e-083

AAA62146.1 cytochrome P3-450 ^' 310 1e-063

AAA52163.1 cytochrome P450 310 1e-0δ3

1916405A cytochrome P450 1A2 310 1e-083

AAK25728.1 cytochrome P450 310 1e-0δ3

AAF13599.1 cytochrome P450-1A2 309 4e-033

AAA35738.1 cytochrome P450 4 308 6e-083

AAH14074.1 PRAME protein 404 e-112 AAH39731.1 PRAME protein 404 e-112 XP_372764.1 similar to Hypothetical protein DJ845024.2 399 e-110 XP_372761.1 similar to Hypothetical protein DJδ45024.2 399 e-110 O60613 Hypothetical protein DJ645024.5 372 e-102 dJ846024.5 (Melanoma Preferentially Expressed Antigen PRAME and KIAA0014 CAA178δ0.1 LIKE) 372 e-102 CAB41252.1 hypothetical protein 372 e-102 XP_291394.2 similar to Hypothetical protein DJ845024.5 372 e-102

NM 021347

NP_067322 .1 Mm.86870 U:+2.44 AAL14426.1 gastric cancer-related protein FKSG9 651 0 NP_835465.1 gasdermin 651 0 BAC04790.1 unnamed protein product 651 0 BAC75636.1 gasdermin 650 0

NM 008161

NP 032187 Mm.7156 U:+2.43 BAA00626.1 glutathione peroxidase 397 e-110 CAA41223.1 glutathione peroxidase 397 e-110 GSHPJHUMAN Plasma glutathione peroxidase precursor (GSHPx-P) (Extracellular P22352 glutathione peroxidase) (GPx-P) 397 e-110 JQ0476 glutathione peroxidase (EC 1.11.1.9) 3, precursor 397 e-110 NP_00207δ.2 plasma glutathione peroxidase 3 precursor 390 e-108 AAF43006.1 extracellular glutathione peroxidase 390 e-108 LOOOe NPJ301500.1 glutathione peroxidase 5 precursor isoform 1 ; epididymal androgen-related protein 301 -81

NM__024283

NP_077245 .1 Mm.274301 U:+2.4 NP_115787.1 esophageal cancer related gene 4 protein 236 3e-062 AAG42321.1 esophageal cancer related gene 4 protein 236 3e-062 AAH21742.1 ECRG4 protein 236 3e-062 AAQ8δ964.1 ECRG4 236 3e-062

NM_008706 NAD(P)H menadione oxidoreductase 1 , dioxin-inducible; diaphorase-4; diaphorase

NP_032732 (NADH/NADPH); NAD(P)H:menadione oxidoreductase 1, dioxin-inducible 1; .1 U:+2.37 NP 000394.1 diaphorase (NADH/NADPH) (cytochrome b-5 reductase) 472 e-133 NQ01_HUMAN NAD(P)H dehydrogenase [quinone] 1 (Quinone reductase 1) (QR1) (DT-diaphorase) (DTD) (Azoreductase) (Phylloquinone reductase) (Menadione P15559 reductase) 472 e-133 A30679 NAD(P)H2 dehydrogenase (quinone) (EC 1.6.99.2) 1 472 e-133 AAA59940.1 NAD(P)H:menadione oxidoreductase ^' " 472 e-133 AAB60701.1 NAD(P)H:quinone oxireductase 472 e-133 AAH07659.1 diaphorase (NADH/NADPH) (cytochrome b-5 reductase) 472 e-133 A Chain A, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With 1H66 2,5-Diaziridinyl-3-Hydroxyl-6-Methyl-1 ,4-Benzoquinone 471 e-132 B Chain B, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With 1H66 2,5-Diaziridinyl-3-Hydroxyl-6-Methyl-1 ,4-Benzoquinone 471 e-132 C Chain C, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With 1H66 2,5-Diaziridinyl-3-Hydroxyl-6-Methyl-1 ,4-Benzoquinone 471 e-132 D Chain D, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With 1 H66 2,5-Diaziridinyl-3-Hydroxyl-6-Methyl-1 ,4-Benzoquinone 471 e-132 A Chain A, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With 1H69 2,3,5,6,Tetramethyl-P-Benzoquinone (Duroquinone) At 2.5 Angstrom Resolution 471 e-132

B Chain B, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With

1H69 2,3,5,6,Tetramethyl-P-Benzoquinone (Duroquinone) At 2.5 Angstrom Resolution 471 e-132 C Chain C, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With

1H69 2,3,5,6,Tetramethyl-P-Benzoquinone (Duroquinone) At 2.6 Angstrom Resolution 471 e-132 D Chain D, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With

1 H69 2,3,δ,6,Tetramethyl-P-Benzoquinone (Duroquinone) At 2.5 Angstrom Resolution 471 e-132

1 QBG A Chain A, Crystal Structure Of Human Dt-Diaphorase (Nad(P)h Oxidoreductase) 470 e-132

1 QBG B Chain B, Crystal Structure Of Human Dt-Diaphorase (Nad(P)h Oxidoreductase) 470 e-132

1QBG C Chain C, Crystal Structure Of Human Dt-Diaphorase (Nad(P)h Oxidoreductase) 470 e-132

1QBG D Chain D, Crystal Structure Of Human Dt-Diaphorase (Nad(P)h Oxidoreductase) 470 e-132 A Chain A, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase At 1.7 A

1D4A Resolution 470 e-132 B Chain B, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase At 1.7 A

1D4A Resolution 470 e-132 C Chain C, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase At 1.7 A

1D4A Resolution 470 e-132 D Chain D, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase At 1.7 A

1D4A Resolution 470 e-132 A Chain A, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With

1 DXO 2,3,δ,6,Tetramethy!-P-Benzoquinone (Duroquinone) At 2.5 Angstrom Resolution 470 e-132 B Chain B, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With

1 DXO 2,3,5,6,Tetramethyl-P-Benzoquinone (Duroquinone) At 2.5 Angstrom Resolution 470 e-132 C Chain C, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With

1 DXO 2,3,5,6,Tetramethyl-P-Benzoquinone (Duroquinone) At 2.5 Angstrom Resolution 470 e-132 D Chain D, Crystal Structure Of Human Nad[p]h-Quinone Oxidoreductase Co With

1 DXO 2,3,5,6,Tetramethyl-P-Benzoquinone (Duroquinone) At 2.5 Angstrom Resolution 470 e-132 A Chain A, Crystal Structure Of A Complex Of Human Nad[p]h-Quinone

1 GG5 Oxidoreductase And A Che otherapeutic Drug (E09) At 2.6 A Resolution 470 e-132

B Chain B, Crystal Structure Of A Complex Of Human Nad[p]h-Quinone

1 GG5 Oxidoreductase And A Chemotherapeutic Drug (E09) At 2.5 A Resolution 470 C Chain C, Crystal Structure Of A Complex Of Human Nad[p]h-Quinone

1 GG5 Oxidoreductase And A Chemotherapeutic Drug (E09) At 2.5 A Resolution 470 D Chain D, Crystal Structure Of A Complex Of Human Nad[p]h-Quinone

1 GG5 Oxidoreductase And A Chemotherapeutic Drug (E09) At 2.5 A Resolution 470 A Chain A, Complex Of Human Recombinant Nad(P)h:quinone Oxide Reductase

1 KBO Type 1 With 5-Methoxy-1 ,2-Dimethyl-3-(Phenoxymethyl)indole-4,7-Dione (Es1340) 470 B Chain B, Complex Of Human Recombinant Nad(P)h:quinone Oxide Reductase

1 KBO Type 1 With 5-Methoxy-1 ,2-Dimethyl-3-(Phenoxymethyl)indole-4,7-Dione (Es1340) 470 C Chain C, Complex Of Human Recombinant Nad(P)h:quinone Oxide Reductase 1 KBO Type 1 With 5-Methoxy-1 ,2-Dimethyl-3-(Phenoxymethyl)indole-4,7-Dione (Es1340) 470 D Chain D, Complex Of Human Recombinant Nad(P)h:quinone Oxide Reductase 1 KBO Type 1 With 5-Methoxy-1 ,2-Dimethyl-3-(Pheπoxymethyl)indole-4,7-Dione (Es1340) 470 A Chain A, Complex Of Human Nad(P)h Quinone Oxidoreductase With 1 KBQ δ-Methoxy-1 ,2-Dimethyl-3-(4-NitrophenoxymethyI)indole-4,7-Dione (Es936) 470 B Chain B, Complex Of Human Nad(P)h Quinone Oxidoreductase With 1 KBQ δ-Methoxy-1 ,2-Dimethyl-3-(4-Nitrophenoxymethyl)indole-4,7-Dione (Es936) 470 C Chain C, Complex Of Human Nad(P)h Quinone Oxidoreductase With 5- 1 KBQ Methoxy-1 ,2-Dimethyl-3-(4-Nitrophenoxymethyl)indole-4,7-Dione (Es936) 470 D Chain D, Complex Of Human Nad(P)h Quinone Oxidoreductase With 1 KBQ δ-Methoxy-1 ,2-Dimethyl-3-(4-Nitrophenoxymethyl)indole-4,7-Dione (Es936) 470 NAD(P)H dehydrogenase, quinone 2; NAD(P)H menadione oxidoreductase-1, NP_00089δ.1 dioxin-inducible-2; NAD(P)H menadione oxidoreductase 2, dioxin-inducible 224 NQ02_HUMAN NRH dehydrogenase [quinone] 2 (Quinone reductase 2) (QR2) P16083 (NRH:quinone oxidoreductase 2) 224

A32667 NAD(P)H2 dehydrogenase (quinone) (EC 1.6.99.2) 2 224

Dermatan sulfate proteoglycan 3 precursor (Epiphycan) (Small Q99645 chondroitin/dermatan sulfate proteoglycan) (Proteoglycan-Lb) (PG-Lb) 215 3e-055 AAH30958.1 Dermatan sulfate proteoglycan 3 215 3e-055 NP_004941.1 dermatan sulfate proteoglycan 3; Pg-Lb; dermatan sulphate proteoglycan 3 210 8e-054 AAC50946.1 dermatan sulfate proteoglycan 3 210 8e-054 NP_055174.1 opticin; oculoglycan; opticin, oculoglycan 204 8e-052 Q9UBM4 Opticin precursor (Oculoglycan) 204 δe-052 AAD45900.1 oculoglycan 204 δe-052 CAB53459.1 opticin 204 8e-052 AAL78286.1 opticin 204 8e-052

NM_007570 - B-cell translocation gene 2; pheochromacytoma cell-3; NGF-inducible

Q04211 Mm.239605 U.-+2.31 NP_006754.1 anti-proliferative protein PC3; nerve growth factor-inducible anti-proliferative 304 5e-082 P78543 BTG2 protein (NGF-inducible anti-proliferative protein PC3) 304 5e-082 AAB37580.1 BTG2 304 5e-082 CAA71074.1 NGF-inducible PC3 304 56-082 AAL05626.1 BTG2 304 δe-082 NP_001722.1 B-cell translocation protein 1 211 6e-054 P31607 BTG1 protein (B-cell translocation gene 1 protein) 211 6e-054 S20947 BTG1 protein - human 211 6e-0δ4 CAA43436.1 BTG1 211 6e-0δ4 AAH16769.1 B-cell translocation protein 1 211 6e-054 AAH64953.1 B-cell translocation protein 1 211 6e-054

NMJD19662

NP_062636

.1 Mm.29467 U:+2.3 NP_004156.1 Ras-related associated with diabetes 486 e-137 AAA36540.1 Rad 486 e-137 AAH11645.1 Similar to Ras-related associated with diabetes 486 e-137 AAB17064.1 Rad GTPase 478 e-135

NM_007483 P01121 Mm.687 U:+2.26

DAA01912.1 TPA: Ras-related small GTPase 402 e-111 D AA01133.1 TPA: Ras-related small GTPase 400 e-111 AAA36565.1 AAA36565.1 347 4e-09δ ras homolog gene family, member A; Aplysia ras-related homolog 12; oncogene

NP_001656.1 RHO H12 337 4e-092

P06749 Transforming protein RhoA (H12) 337 4e-092

TVHU12 GTP-binding protein rhoA - human 337 4e-092

CAA23690.1 unnamed protein product 337 4e-092

AAC33173.1 GTP-binding protein 337 4e-092

AAH01360.1 ARHA protein 337 4e-092

AAH05976.1 ARHA protein 337 4e-092

AAM21117.1 small GTP binding protein RhoA 337 4e-092

CAE46190.1 CAE46190.1 337 4e-092 ras homolog gene family, member C; Aplysia RAS-related homolog 9 (oncogene RHO H9); Aplysia ras-related homolog 9; RhoC; RAS homolog gene family, NP_7δ6δδ6.1 member C (oncogene RHO H9) 336 1e-091 P0δ134 Transforming protein RhoC (H9) 336 1e-091

TVHURC GTP-binding protein rhoC - human 336 1e-091

CAA29969.1 unnamed protein product 336 1e-091 AAC33179.1 GTPase 336 16-091

AAH07246.1 Ras homolog gene family, member C 336 16-091 AAH09177.1 Ras homolog gene family, member C 336 1e-091 AAM21119.1 small GTP binding protein RhoC 336 1e-091 AAHδ2δ0δ.1 Ras homolog gene family, member C 336 1e-091 Chain B, Crystal Structure Of The Dbl And Pleckstrin Homology Domains Of Dbs In pdb)1LB1 )B Complex With Rhoa 335 2e-091 Chain D, Crystal Structure Of The Dbl And Pleckstrin Homology Domains Of Dbs In pdb|1 LB1 |D Complex With Rhoa 335 2e-091

Chain F, Crystal Structure Of The Dbl And Pleckstrin Homology Domains Of Dbs In pdb|1LB1 |F Complex With Rhoa 3362e-091 Chain H, Crystal Structure Of The Dbl And Pleckstrin Homology Domains Of Dbs In pdb|1 LB1 |H Complex With Rhoa 3352e-091 1 FTN Crystal Structure Of The Human RhoaGDP COMPLEX 3344e-091 10W3 Chain B, Crystal Structure Of Rhoa.Gdp.Mgf3-ln Complex With Rhogap 3344e-091 pdb|1 CC0|A Chain A, Crystal Structure Of The Rhoa.Gdp-Rhogdi Complex 3337e-091 pdb|1 CC0|C Chain C, Crystal Structure Of The Rhoa.Gdp-Rhogdi Complex 3337e-091 AAA60612.1 multidrug resistance protein 331 4e-090 1A2B Human Rhoa Complexed With Gtp Analogue 3282e-089 Chain A, Crystal Structure Of Human Rhoa Complexed With The Effector Domain 1 CXZ Of The Protein Kinase PknPRKI 323 2e-0δ9

NM 023603

NP_076097 osteoblast differentiation promoting factor protein; lycerophosphodiester .1 Mm.233495 U:+2.26 NP_060181.2 phosphodiesterase 3 756 0 BAB13350.1 osteoblast differentiation promoting factor 755 0 AAH32009.1 Osteoblast differentiation promoting factor protein 755 0 AAQ89345.1 AESP1936 755 0 BAA91014.1 unnamed protein product 545 e-166 NP_110419.4 hypothetical protein PP1665 3482e-095 AAL5δ85δ.1 unknown 3482e-095 AALδ5δδ4.1 unknown 3482e-095 AAH30626.1 PP1665 protein 3483e-095 CAD36796.1 hypothetical protein 331 4e-090 AAQ88841.1 PP1665 3178e-0δ6 BAC11242.1 BAC11242.1 2906e-07δ AAP97686.1 unknown 2δ44e-076 AAH1δ771.1 PP1666 protein 2645e-070

AAQ72549.1 glycerophosphoryldiester phosphodiesterase UgpQ 252 2e-066

AK010249 Q61398 Mm.46016 U:+2.26 NP_037495.1 procollagen C-endopeptidase enhancer 2 709 0 AAF04621.1 procollagen C-terminal proteinase enhancer protein 2 709 0 AAK63128.1 procollagen C-proteinase enhancer protein 2 709 0 AAQ8δ921.1 PCOLCE2 709 0 AAH06265.1 PCOLCE2 protein 603 e-142 Procollagen C-proteinase enhancer protein precursor (PCPE) (Type I procollagen COOH-terminal proteinase enhancer) (Type 1 procollagen C-proteinase enhancer Q15113 protein) 383 e-106 BAA23281.1 type 1 procollagen C-proteinase enhancer protein 383 e-106 AAC78δ00.1 PCOLCE 3δ3 e-106 AAD 16041.1 procollagen C-proteinase enhancer protein 383 e-106 AAH00574.1 Procollagen C-endopeptidase enhancer 383 e-106 AAH33205.1 Procollagen C-endopeptidase enhancer 383 e-106 procollagen C-endopeptidase enhancer; procollagen, type 1, COOH-terminal NP_0025δ4.1 proteinase enhancer 382 e-105 A55362 procollagen I C-proteinase enhancer protein precursor - human 382 e-105 AAA61949.1 procollagen C-proteinase enhancer protein 382 e-105

NM 013556

NP 038584 Mm.1867δ U:+2.22 NP_000185.1 hypoxanthine phosphoribosyltransferase 1 428 e-120 HPRT HUMAN Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) P00492 (HGPRTase) 428 e-120 RTHUG hypoxanthine phosphoribosyltransferase (EC 2.4.2.3) 428 e-120

CAA23789.1 coding sequence 428 e-120 AAA36012.1 hypoxanthine phosphoribosyltransferase 428 e-120 AAA52690.1 hypoxanthine phosphoribosyltransferase 428 e-120

AAH20635.1 Ficolin 1 precursor 3δ6 e-107 S61517 ficolin-1 precursor - human 382 e-106 AAB60706.1 ficolin 382 e-106 ficolin 2 isoform a precursor; ficolin (collagen/fibrinogen domain-containing lectin) 2; NP_004099.1 ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin); hucolin 379 e-105 FCN2JHUMAN Ficolin 2 precursor (Collagen/fibrinogen domain-containing protein Q 5485 2) (Ficolin-B) (Ficolin B) (Serum lectin p35) (EBP-37) (Hucolin) (L-Ficolin) 379 e-105 BAA08352.1 serum lectin P35 379 e-105 BAA09636.1 lectin P3δ 379 e-105 ficolin 2 isoform b precursor; ficolin (collagen/fibrinogen domain-containing lectin) 2; NP_0566δ2.1 ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin); hucolin 3528e-097 ficolin 3 isoform 1 precursor; ficolin-3; collagen/fibrinogen domain-containing lectin 3 NP_003656.2 p35; collagen/fibrinogen domain-containing protein 3; Hakata antigen; H-ficolin 2896e-078 Ficolin 3 precursor (Collagen/fibrinogen domain-containing protein 3) 075636 (Collagen/fibrinogen domain-containing lectin 3 p35) (Hakata antigen) 2δ96e-07δ ficolin 3 isoform 2 precursor; ficolin-3; collagen/fibrinogen domain-containing lectin 3 NP_775628.1 p35; collagen/fibrinogen domain-containing protein 3; Hakata antigen; H-ficolin 281 2e-075 AAQ88448.1 NL3 2682e-068 AAQ88678.1 NL7 2368e-062

NM 008302

NP 032328 heat shock 90kDa protein 1, beta; heat shock 90kD protein 1, beta; Heat-shock

.1 Mm.2180 U:+2.19 NP_0313δL2 90kD protein-1, beta 1202 0 P08238 HS9B_HUMAN Heat shock protein HSP 90-beta (HSP 84) (HSP 90) 1202 0 AAA36026.1 90 kD heat shock protein 1202 0

AAH04928.1 Unknown (protein for MGC:10493) 1202 0 AAH12807.1 Unknown (protein for MGC:3433) 1202 0 AAH 14486.1 Unknown (protein for MGC:23206) 1202 0 AAH16753.1 Unknown (protein for MGC:113δ) 1202 0

HHHU84 heat shock protein 90-beta 1197 0 AAA36025.1 90kDa heat shock protein 1197 0 1307197A heat shock protein 90kD 1197 0 T46243 hypothetical protein DKFZp761 K0511.1 1170 0 CAB66473.1 hypothetical protein 1170 0 NP_005339.1 heat shock 90kDa protein 1 , alpha; heat shock 90kD protein 1 , alpha 1099 0 HHHU36 heat shock protein 90-alpha 1099 0 AAA63194.1 heat shock protein 1099 0 P07900 HS9A_HUMAN Heat shock protein HSP 90-alpha (HSP 86) 109δ 0 CAA33259.1 90 kDa heat-shock protein (AA 1-732) 109δ 0 AAF82792.1 AF27δ719_1 chaperone protein HSP90 beta 1052 0 AAH09206.1 heat shock 90kD protein 1 , beta 1052 0 AAH23006.1 Unknown (protein for MGC:30059) 961 0 AAH00987.1 Unknown (protein for !MAGE:3446372) 600 0 AAC25497.1 Hsp89-alpha-delta-N 750 0 AAH079δ9.1 Similar to heat shock 90kD protein 1 , alpha 696 0

K027δ2 P01027 Mm.19131 U:+2.19 AARδ9906.1 complement component 3 2550 0 NP_00005δ.1 complement component 3 precursor; acylation-stimulating protein cleavage product 2550 0 P01024 Complement C3 precursor [Contains: C3a anaphylatoxin] 2550 0 C3HU complement C3 precursor [validated] - human 2550 0 AAA65332.1 complement component C3 2550 0 XP_3δ1177.1 similar to Complement C3 precursor 709 0 NP_001726.2 complement component 5 65δ 0 P01031 Complement Cδ precursor [Contains: Cδa anaphylatoxin] 65δ 0 C5HU complement Cδ precursor [validated] - human 65δ 0 AAA51926.1 complement component Cδ 6δδ 0 NPJ300583.1 complement component 4B proprotein 618 e-176 AAB67930.1 complement component C4 618 e-176 CAB69302.1 dJ34F7.4 (complement component 4A) 616 e-175

NM 011569

NP 035699 Mm.42257 U:+2.14 NP_444515.1 tektin 1 633 0 Q969V4 Tektin 1 633 0 AAH14599.1 Tektin 1 663 0 AAL27695.1 tektin protein 683 0 NP_114104.1 tektin 3; testicular microtubules-related protein 291 2e-078 Q9BXF9 Tektin 3 291 2e-078 AAK15340.1 testicular microtubules-related protein TEKTIN3 291 2e-07δ BAB71464.1 unnamed protein product 2903e-078 AAH31688.1 TEKT3 protein 2897e-078 NP_653306.1 hypothetical protein MGC27019 2734e-073 AAH21716.1 Hypothetical protein MGC27019 2734e-073 NP_6δ3275.1 hypothetical protein FLJ32871 2674e-071 BAB71484.1 unnamed protein product 2674e-071 NP_0δ52δ1.2 tektin 2; testicular tektin B1 -like protein 2197e-057 Q9UIF3 Tektin 2 (Tektin-t) (Testicular tektin Bl-like protein) 2197e-057 BAAδ9350.1 h-TEKTIN-t 2197e-057 CAC21454.1 dJ665N4.3 (novel tektin) 2197e-057 AAH35620.1 Tektin 2 2197e-057 AAC09343.1 testicular tektin B1-like protein 2182e-056

D32δ66

BAA11614. LOOOe

1 Mm.16347 U:+2.13 NPJ006219.1 prepronociceptin; propronociceptin 248 -65 LOOOe Q13519 PNOCJHUMAN Nociceptin precursor (Orphanin FQ) (PPNOC) 24δ -65 LOOOe JC6152 orphanin FQ precursor 24δ -65

NM_010780

S26043 Mm.12δ2 U:+2.13

CYP4F2; LEUKOTRIENE-B420-MONOOXYGENASE; YTOCHROME

AAC27730.1 P450-LTB-OMEGA; LEUKOTRIENE-B4 OMEGA-HYDROXYLASE 863 0 AAL67578.1 cytochrome P450, subfamily lVF, polypeptide 2 853 0 Q9HBI6 CPFBJHUMAN Cytochrome P4504F11 (CYP1VF11) 846 0 AAH16853.1 cytochrome P450, subfamily IVF, polypeptide 11 δ46 0 cytochrome P450, family 4, subfamily F, polypeptide 11 ; cytochrome P450,

NP 367010.1 subfamily IVF, polypeptide 11 δ4δ 0 AAG15889.1 AF236035J CYP4F11 84δ 0 AAC50052.2 cytochrome P450 4F2 645 0 cytochrome P450, family 4, subfamily F, polypeptide 3; cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase); leukotriene B4 omega

NP 0008δ7.1 hydroxylase; leukotriene-B420-monooxygenase; cytochrome P450-LTB-omega δOδ CPF3_HUMAN Cytochrome P450 4F3 (CYP1VF3) (Leukotriene-B4 omega-hydroxylase) (Leukotriene-B420-monooxygenase) (Cytochrome

Q06477 P450-LTB-omega) δOδ 0

A46661 leukotriene B4 omega-hydroxylase (EC 1.14.15.-) cytochrome P450 δOδ 0

BAA02144.1 cytochrome P-450LTBV δθδ 0

BAA25990.1 leukotriene B4 omega-hydroxylase 608 0

BAA25991.1 leukotriene B4 omega-hydroxylase 808 0

Q9HCS2 CPFC_HUMAN Cytochrome P4504F12 (CYPIVF12) 807 0

JC7594 cytochrome P450 enzyme, CYP4F12 isoform, liver 807 0

JC759δ cytochrome P450 enzyme, CYP4F12 isoform, small intestine 807 0

BAB16269.1 cytochrome P450 807 0

AAG33247.1 cytochrome P460 isoform 4F12 607 0 cytochrome P450, family 4, subfamily F, polypeptide 3; cytochrome P460, subfamily IVF, polypeptide δ; microsomal monooxygenase; flavoprotein-linked

NP_009134.1 monooxygenase 604 0

P9δ1δ7 CPFδ_HUMAN Cytochrome P450 4Fδ (CYPIVF8) δ04 0

AAD49566.1 AF133298_1 cytochrome P450 604 0

ITHUC alpha-1 -antichymotrypsin precursor - human 476 e-134 AAA51560.1 alpha-1 -antichymotrypsin precursor 470 e-132 Chain A, Alphal -Antichymotrypsin Serpin In The Delta Conformation (Partial Loop 1QMN Insertion) 460 e-129 1313184C chymotrypsin inhibitor 441 e-123 NP_001076.1 alpha-1-antichymotrypsin, precursor; alpha-1 -antichymotrypsin; antichymotrypsin 439 e-123 antichymotryp sin alpha-1 -antichymotrypsin 439 e-123 2ACH Chain A, Alphal Antichymotrypsin 434 e-121

NM 011513

NP_03564δ .1 Mm .4708 U:+2.02 NP_003168.2 spleen tyrosine kinase 1198 0 P43405 KSYK_HUMAN Tyrosine-protein kinase SYK (Spleen tyrosine kinase) 1198 0 A53596 protein-tyrosine kinase (εc 2.7.1.112) syk 1198 0 AAA36526.1 protein tyrosine kinase 1198 0 AAH02962.1 Similar to spleen tyrosine kinase 1198 0 AAH01645.1 Similar to spleen tyrosine kinase 1198 0 191δ215A protein Tyr kinase 1197 0 CAA51970.1 protein tyrosin kinase 1191 0 CAAδ2737.1 protein-tyrosine kinas 1140 0 AAH11399.1 Similar to spleen tyrosine kinase 1140 0 similar to Tyrosine-protein kinase ZAP-70 (70 kDa zeta-associated protein) XP_047776.3 (Syk-related tyrosine kinase) 679 ZA70_HUMAN Tyrosine-protein kinase ZAP-70 (70 kDa zeta-associated protein) P43403 (Syk-related tyrosine kinase) 679 0

A44266 protein-tyrosine kinase (EC 2.7.1.112) ZAP-70 677 0 2101280A p72syk protein 658 0 AAH39039.1 Similar to zeta-chain (TCR) associated protein kinase (70kD) 519 e-146

A Chain A, Crystal Structure Of The Tandem Sh2 Domain Of The Syk Kinase 1A81 Bound To A Dually Tyrosine-Phosphorylated Itam 498 e-140 C Chain C, Crystal Structure Of The Tandem Sh2 Domain Of The Syk Kinase 1A81 Bound To A Dually Tyrosine-Phosphorylated Itam 498 e-140 E Chain E, Crystal Structure Of The Tandem Sh2 Domain Of The Syk Kinase 1Aδ1 Bound To A Dually Tyrosine-Phosphorylated Itam 49δ e-140 G Chain G, Crystal Structure Of The Tandem Sh2 Domain Of The Syk Kinase 1Aδ1 Bound To A Dually Tyrosine-Phosphorylated Itam 49δ e-140 I Chain I, Crystal Structure Of The Tandem Sh2 Domain Of The Syk Kinase Bound 1A81 To A Dually Tyrosine-Phosphorylated Itam 49δ e-140 K Chain K, Crystal Structure Of The Tandem Sh2 Domain Of The Syk Kinase 1Aδ1 Bound To A Dually Tyrosine-Phosphorylated Itam 49δ e-140 BAC43747.1 truncated ZAP kinase 334 e-106

NM_011236

NP_035366 AD52 homolog isoform alpha; recombination protein RAD52; DNA repair protein

.1 Mm.149 U:+2.01 NP_002370.2 RAD52 50δ e-143 P43331 RA52_HUMAN DNA repair protein RAD62 homolog 506 e-143 AAB06203.1 homolgue of yeast DNA repair and recombination enzyme (RAD62) gene 505 e-143 AAA86793.1 RAD62 505 e-143 AAA87564.1 recombination protein RAD52 503 e-142 A67518 DNA repair protein RAD62 503 e-142 1 KNO A Chain A, Crystal Structure Of The Human Rad52 Protein 3δ4 e-106 1KN0 B Chain B, Crystal Structure Of The Human Radδ2 Protein 384 e-106 1 KNO C Chain C, Crystal Structure Of The Human Radδ2 Protein 384 e-106 1 KNO D Chain D, Crystal Structure Of The Human Rad52 Protein 384 e-106 1 KNO E Chain E, Crystal Structure Of The Human Radδ2 Protein 384 e-106 1 KNO F Chain F, Crystal Structure Of The Human Rad52 Protein 384 e-106 1 KNO G Chain G, Crystal Structure Of The Human Radδ2 Protein 384 e-106

B Chain B, Crystal Structure Of Human Serum Albumin Complexed With The

1E7B General Anesthetic Halothane 276 1.00e-74 A Chain A, Human Serum Albumin Complexed With Myristic Acid And The General

1E7C Anesthetic Halothane 276 1.00e-74

1 E73 A Chain A, Crystal Structure Of Human Serum Albumin 276 1.00e-74

1 E7δ B Chain B, Crystal Structure Of Human Serum Albumin 276 1.00e-74 A Chain A, Human Serum Albumin Complexed With Myristic Acid And The R-(+)

1H9Z Enantiomer Of Warfarin 276 1.00e-74 A Chain A, Human Serum Albumin Complexed With Myristic Acid And The S- (-)

1HA2 Enantiomer Of Warfarin 276 1.00e-74 A Chain A, Human Serum Albumin Complexed With Cis-9-Octadecenoic Acid

1GN1 (Oleic Acid) 276 1.00e-74 A Chain A, Human Serum Albumin Complexed With

1GNJ Cis-5,δ,11,14-Eicosatetraenoic Acid (Arachidonic Acid) 276 1.00e-74 similar to human albumin, Swiss-Prot Accession Number P02768; Method:

AAA64922.1 conceptual translation supplied by author 276 1.00e-74

AAA9879δ.1 alloalbumin Venezia 276 1.00e-74

AAF01333.1 AF19016δ_1 serum albumin precursor 276 1.00e-74

CAA23753.1 reading frame HSA 276 L00e-74

CAA23754.1 serum albumin 276 1.00e-74

AAN17δ25.1 serum albumin 276 1.00e-74 NP_00046δ.

1 albumin precursor; PRO0δδ3 protein 276 1.00e-74

P0276δ ALBUJHUMAN Serum albumin precursor 276 1.00e-74

ABHUS serum albumin precursor 276 1.00e-74

AAA9δ797.1 albumin 276 1.00e-74

AAF69594.1 AF119917_2 PRO0903 276 1.00e-74

AAH34023.1 albumin 276 1.00e-74

AAH36003.1 similar to serum albumin 276 1.00e-74

Mm.22126

_.

NM_010234 U:+5.37 P01101 Mm.246513 F:2.35

NM_021462 U:+3.6

NP 067437 Mm.42126 F:7.17

Chain B, Three-Dimensional Structure Of The Human Transglutaminase 3 Enzyme: Binding Of Calcium Ions Change Structure For pdb|1L9N|B Activation 510 e-144 Chain A, Role Of Calcium Ions In The Activation And Activity Of The pdb|1 NUD|A Transglutaminase 3 Enzyme (3 Calciums, Active Form) 510 e-144 Chain B, Role Of Calcium Ions In The Activation And Activity Of The pdb|1NUD|B Transglutaminase 3 Enzyme (3 Calciums, Active Form) 510 e-144 Chain A, Role Of Calcium ions In The Activation And Activity Of The pdb|1 NUF|A Transglutaminase 3 Enzyme 510 e-144 Chain A, Role Of Calcium Ions In The Activation And Activity Of The Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive pdb|1NUG|A Form) 510 e-144 Chain B, Role Of Calcium Ions In The Activation And Activity Of The Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive pdb|1NUG|B Form) 510 e-144 Chain A, Structural Basis For The Coordinated Regulation Of Transglutaminase 3 By Guanine Nucleotides And pdb|1RLE|A CalciumMAGNESIUM 510 e-144 Chain B, Structural Basis For The Coordinated Regulation Of Transglutaminase 3 By Guanine Nucleotides And pdb|1RLE|B CalciumMAGNESIUM 510 e-144 Chain A, Structural Basis For The Coordinated Regulation Of Transglutaminase 3 By Guanine Nucleotides And pdb|1RLL|A CalciumMAGNESIUM 510 e-144 Chain B, Structural Basis For The Coordinated Regulation Of Transglutaminase 3 By Guanine Nucleotides And pdb|1RLL|B CalciumMAGNESIUM 510 e-144

v-maf musculoaponeurotic fibrosarcoma oncogene homolog; Avian NP_0053δ1. musculoaponeurotic fibrosarcoma (MAF) protooncogene; v-maf 2 musculoaponeurotic fibrosarcoma (avian) oncogene homolog 228 3e-059 075444 Transcription factor Maf (Proto-oncogene c-maf) 228 3e-059 AAC27038.1 long form transcription factor C-MAF 22δ 3e-059 NM_011930 U:+2.84 NP_00127δ.

070496 Mm.270δδ7 F:4 1 chloride channel 7; CIC-7 1395 0 P5179δ Chloride channel protein 7 (CIC-7) 1395 0 AAF34711.1 chloride channel protein 7 1395 0 AAH12737.1 Chloride channel 7 1395 0 AAK61232.1 putative chloride channel protein 7 13δδ 0 S6δ427 chloride channel protein 7 (CIC-7) - human (fragment) 1359 0 CAA91656.1 CLC-7 chloride channel protein 1359 0 AAH0615δ.1 CLCN7 protein 864 0 AAH04946.1 Unknown (protein for IMAGE:3615790) 499 e-140 BAA05836.4 KIAA0046 447 e-125 NP_001277. 1 chloride channel 6 isoform ClC-6a 447 e-125 P51797 Chloride channel protein 6 (CIC-6) 447 e-125 S6842δ probable chloride channel CIC-6 - human 447 e-125 CAA5δ292.1 putative chloride channel 447 e-125 AAB692δ7.1 putative chloride channel 447 e-125 CAA15951.1 dJ934G17.1.1 (chloride chanel protein CLC-6A (KIAA0046)) 442 e-123 CAA67δ36.1 chloride channel 257 1e-067 CAA05033.1 CIC-7 chloride channel 250 1e-065

NM_016906 U:+2.79 NP_037463. Sec61 alpha form 1; sec61 homolog; protein transport protein SEC61

P3δ378 Mm.28375 F:3.89 1 alpha subunit isoform 1 931 Protein transport protein Sec61 alpha subunit isoform 1 (Sec61 P38378 alpha-1) 931

AAD39647.1 sec61 homolog 931 0 AAK290δ3.1 Sec61 alpha form 1 931 0 Protein transport protein Sec61 alpha subunit isoform 2 (Secδl Q9Y2R3 alpha-2) 909 0 AAD27765.1 sec61 homolog 909 0 NP_060614. 2 Sec61 alpha form 2 891 0 AAK29084.1 Sec61 alpha form 2 891 0 AAH02951.1 SEC61A1 protein 828 0 AAH26179.1 SEC61A2 protein 778 0 BAB14148.1 unnamed protein product 775 0 BAC1129δ.1 unnamed protein product 696 0 BAA91692.1 unnamed protein product 432 e-120 BAB13955.1 unnamed protein product 432 e-120 CAD38592.1 hypothetical protein 425 e-118 BAC112δ3.1 unnamed protein product 338 3e-092 BAC11434.1 unnamed protein product 338 3e-092

NM_011180 - U:^'+2.73 NP_004753. pleckstrin homology, Sec7 and coiled/coil domains 1 isoform 1 ; homolog of

Q9QX11 Mm .86413 F:5.98 1 secretory protein SEC7; cytoadhesin 1; cytohesin 1 802 0 Q15438 Cytohesin 1 (SEC7 homolog B2-1) 802 0 S24168 SEC7 homolog - human 802 0 AAA36602.1 yeast sec7 gene homologue 802 0 AAH50452.1 Pleckstrin homology, Sec7 and coiled/coil domains 1, isoform 1 802 0 NP_059430. pleckstrin homology, Sec7 and coiled/coil domains 1 isoform 2; homolog of 1 secretory protein SEC7; cytoadhesin 1; cytohesin 1 773 0 AAF37733.1 cytohesin 1 765 0 AAF37737.1 cytohesin 1 758 0 NPJ359431. pleckstrin homology, Sec7 and coiled/coil domains 2 isoform 1; pleckstrin 1 homology, Sec7 and coiled/coil domains 2; cytohesin 2 689

Mm.276298

NM_017376 NP_059072. U:+2.41 NP_003207. 1 Mm.27027δ F:4.33 1 thyrotrophic embryonic factor; thyrotroph embryonic factor 446 e-124 G02360 thyrotroph embryonic factor - human 446 e-124 AAB06497.1 thyrotroph embryonic factor 446 e-124 AAH39258.1 Thyrotrophic embryonic factor 446 e-124 AAH42476.1 Thyrotrophic embryonic factor 446 e-124 Q10587 Thyrotroph embryonic factor 410 e-114 dJ979N1.5.1 (thyrotrophic embryonic factor (ortholog of chicken vitellogenin gene-binding protein VBP alpha/alpha CAB62498.1 variant) (variant 1 )) 410 e-114 AAA61373.1 thyrotroph embryonic factor 410 e-114 dJ979N1.5.2 (thyrotrophic embryonic factor (orthlog of chicken vitellogenin gene-binding protein VBP beta/beta variant) CAB62497.1 (variant 2)) 403 e-111 CAD97856.1 hypothetical protein 273 5e-074 NP_002117. 1 hepatic leukemia factor 259 3e-06δ Q16534 Hepatic leukemia factor 259 3e-068 A44064 hepatic leukemia factor - human 259 3e-068 AAA52675.1 hepatic leukemia factor 259 3e-06δ CAA48777.1 hepatic leukemia factor 259 3e-06δ AAH36093.1 hepatic leukemia factor 259 3e-068 NP_001343. D site of albumin promoter (albumin D-box) binding protein; D site of 2 albumin promoter binding protein 209 2e-0δ3 Q105δ6 D-site-binding protein (Albumin D box-binding protein) (TAXREB302) 209 2e-0δ3 AAB1366δ.1 D-site binding protein 209 2e-053 AAB50219.1 albumin D-box binding protein 209 2e-053 AAH11965.1 D site of albumin promoter (albumin D-box) binding protein 209 2e-053

JC4898 Down-syndrome-critical-region protein - human 612 e-175

BAA12866.1 MNB protein kinase 612 e-175

BAA13110.1 serine/threonine protein kinase 612 e-175 dual-specificity tyrosine-(Y)-phosphoryIation regulated kinase 1A isoform 1; minibrain (Drosophila) homolog; protein kinase minibrain homolog; dual specificity YAK1 -related kinase; serine/threonine-specific protein kinase; mnb protein

NP_001387. kinase homolog hp86; serine/threonine kinase MNB; MNB 2 protein kinase; MNB/DYRK protein kinase 612 e-175 Dual-specificity tyrosine-phosphorylation regulated kinase 1A (Protein kinase minibrain homolog) (MNBH) (HP86) (Dual

Q13627 specificity YAK1 -related kinase) 612 e-175 AAB18639.1 MNB 612 . e-175 AAC50939.1 hpδ6 610 e-174 dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A isoform 3; minibrain (Drosophila) homolog; protein kinase minibrain homolog; dual specificity YAK1 -related kinase; serine/threonine-specific protein kinase; mnb protein NP_567δ24. kinase homolog hpδ6; serine/threonine kinase MNB; MNB

1 protein kinase; MNB/DYRK protein kinase 603 e-173

AAD31169.1 serine-threonine protein kinase 603 e-173 dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A isoform 5; minibrain (Drosophila) homolog; protein kinase minibrain homojog; dual specificity YAK1 -related kinase; serine/threonine-specific protein kinase; mnb protein

NP_δ69122. kinase homolog hp86; serine/threonine kinase MNB; MNB

1 protein kinase; MNB/DYRK protein kinase 603 e-172

NM_01678δ U.-+2.32

NP 053068 Mm.251115 F:3.3δ

NP_776297. 1 chloride channel 3 isoform e; CIC-3 10δ4 0 BAC54560.1 clcn3e 10δ4 0 NP_000075. 1 chloride channel 5 1074 0 P51795 Chloride channel protein δ (CIC-5) 1074 0 CAA63000.1 voltage-gated chloride ion channel 1074 0 I37277 chloride channel protein, kidney - human (fragment) 417 e-116 CAA57430.1 Dents disease candidate 417 e-116

NM_011329 U:+2.31 NP_399066.

P50096 Mm.260707 F:4.3δ 1 inosine monophosphate dehydrogenase 1 isoform b; sWSS260δ 996 0 NP_000δ74. 2 inosine monophosphate dehydrogenase 1 isoform a; sWSS260δ 993 0 lnosine-5'-monophosphate dehydrogenase 1 (IMP dehydrogenase 1) P20839 (IMPDH-I) (IMPD 1) 991 0 AAH33622.1 IMPDH1 protein 991 0 A35566 IMP dehydrogenase (EC 1.1.1.205) I - human 986 0 Chain A, Binary Complex Of Human Type-I Inosine Monophosphate pdb|1JCN|A Dehydrogenase With 6-CI-lmp 9δ6 Chain B, Binary Complex Of Human Type-I Inosine Monophosphate pdb|1JCN|B Dehydrogenase With 6-CI-lmp 9δ6 0 AAA36114.1 IMP dehydrogenase type 1 (EC 1.1.1.205) 97δ 0 BAB70780.1 unnamed protein product 924 0 XP_093044. 2 similar to IMP dehydrogenase (EC 1.1.1.205) I - human 905 0 XP_294562. 2 similar to inosine monophosphate dehydrogenase 1 isoform b; sWSS2608 683 0

IMD2JHUMAN lnosine-5'-monophosphate dehydrogenase 2 (IMP dehydrogenase 2) P1226δ (IMPDH-tl) (IMPD 2) δ68 A31997 IMP dehydrogenase (EC 1.1.1.205) II - human 86δ Chain A, Ternary Complex Of Human Type-li Inosine Monophosphate Dehydrogenase With 6-CI-lmp And Selenazole Adenine pdb|1B30|A Dinucleotide 668 Chain B, Ternary Complex Of Human Type-li Inosine Monophosphate Dehydrogenase With 6-CI-lmp And Selenazole Adenine pdb|1B30|B Dinucleotide 868 0 AAA67054.1 inosine monophosphate dehydrogenase type II 868 0 AAB70699.1 inosine monophosphate dehydrogenase type (I 868 0 AAH06 24.1 IMP (inosine monophosphate) dehydrogenase 2 86δ 0 AAH12840.1 IMP (inosine monophosphate) dehydrogenase 2 δ6δ 0 AAH15567.1 IMP (inosine monophosphate) dehydrogenase 2 δδδ 0 XPJ)69325. 4 similar to Impdhl protein 865

NM_00δ773 U:+2.30 P2Y purinoceptor 2 (P2Y2) (P2U purinoceptor 1) (P2U1) (ATP receptor)

A47556 Mm.3000 F:3.29 P41231 (Purinergic receptor) 578 e-164 AAH28136.1 Purinergic receptor P2Y2 678 e-164 AAN01279.1 purinergic receptor P2RY2 578 e-164 NPJ302555. purinergic receptor P2Y2; purinoceptor_P2Y2; P2U nucleotide receptor; 2 P2Y purinoceptor 2; P2U purinoceptor 1 ; ATP receptor 578 e-164 NP_788085. purinergic receptor P2Y2; purinoceptor P2Y2; P2U nucleotide receptor; 1 P2Y purinoceptor 2; P2U purinoceptor 1 ; ATP receptor 578 e-164 NP_7δ8086. purinergic receptor P2Y2; purinoceptor P2Y2; P2U nucleotide receptor; 1 P2Y purinoceptor 2; P2U purinoceptor 1 ; ATP receptor 578 e-164 AAC04923.1 P2U nucleotide receptor 576 e-164

AAA76236.1 myotonin-protein kinase, Form I 884 0.0 AAA76239.1 myotonin-protein kinase, Form VI 867 0.0 AAA648δ4.1 protein kinase 627 0.0 AAA75240.1 myotonin-protein kinase, Form II.III V δ22 0.0 AAB31300.1 myotonin protein kinase; MtPK δ20 0.0

NM_007333 U:+2.14 NP_00000δ. 149605 Mm.18759 F:2.δ1 1 acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain precursor 6δ0 Acyl-CoA dehydrogenase, short-chain specific, mitochondrial precursor P16219 (SCAD) (Butyryl-CoA dehydrogenase) 660 acyl-CoA dehydrogenase (EC 1.3.99.3) precursor, short-chain-specific A30605 - human 660 0 AAA60307.1 short chain acyl-CoA dehydrogenase precursor (EC 1.3.99.2) 6δ0 0 CAB02492.1 acyl-CoA dehydrogenase 6δ0 0 AAD00562.1 short chain acyl CoA dehydrogenase 6δ0 0 1704375A short chain acyl-CoA dehydrogenase 660 0 AAH25963.1 Acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain precursor 67δ 0 CAD33535.2 hypothetical protein 273 7e-073 acyl-Coenzyme A dehydrogenase, short/branched chain precursor; NP_001600. 2-methyl branched chain acyl-CoA dehydrogenase; 1 2-methylbutyryl-CoA dehydrogenase 273 7e-073 Acyl-CoA dehydrogenase, short/branched chain specific, mitochondrial precursor (SBCAD) (2-methyl branched chain acyl-CoA dehydrogenase) (2-MEBCAD) (2-methyIbutyryl-coenzyme A P45964 dehydrogenase) (2-methylbutyryl-CoA dehydrogenase) 273 7e-073 acyl-CoA dehydrogenase (EC 1.3.99.-) short/branched chain specific A5δ6δ0 precursor - human 273 7e-073 AAA74424.1 acyl-CoA dehydrogenase 273 7e-073 AAF97921.1 short/branched chain acyl-CoA dehydrogenase 273 7e-073 AAH13756.1 Acyl-Coenzyme A dehydrogenase, short/branched chain precursor 273 7e-073

AAF63626.1 medium-chain acyl-CoA dehydrogenase 25δ 2e-06δ

NP_000007. acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain;

1 medium-chain acyl-CoA dehydrogenase 2δδ 2e-06δ ACDMJHUMAN Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial P11310 precursor (MCAD) 253 2e-06δ acyl-CoA dehydrogenase (EC 1.3.99.3) precursor, DEHUCM medium-chain-specific, mitochondrial [validated] - human 258 2e-068

AAA51566.1 medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3) 258 2e-068

AAA59667.1 medium-chain acyl-CoA dehydrogenase 258 2e-068

AAH05377.1 Acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain 233 2e-06δ Chain A, Structure Of T25δe, E376g Mutant Of Human Medium Chain 1EGE|A Acyl-Coa Dehydrogenase 257 5e-06δ Chain B, Structure Of T2δ5e, E376g Mutant Of Human Medium Chain

1EGE|B Acyl-Coa Dehydrogenase 267 5e-06δ Chain C, Structure Of T265e, E376g Mutant Of Human Medium Chain

1EGE|C Acyl-Coa Dehydrogenase 267 5e-063 Chain D, Structure Of T2δ5e, E376g Mutant Of Human Medium Chain 1EGE|D Acyl-Coa Dehydrogenase 267 5e-068 Chain A, Structure Of T2δ5e, E376g Mutant Of Human Medium Chain 1EGD|A Acyl-Coa Dehydrogenase 254 3e-067 Chain B, Structure Of T255e, E376g Mutant Of Human Medium Chain 1EGD|B Acyl-Coa Dehydrogenase 254 3e-067 Chain C, Structure Of T255e, E376g Mutant Of Human Medium Chain

1EGD|C Acyl-Coa Dehydrogenase 254 3e-067 Chain D, Structure Of T255e, E376g Mutant Of Human Medium Chain

1EGD|D Acyl-Coa Dehydrogenase 254 3e-067 Chain A, Structure Of T255e, E376g Mutant Of Human Medium Chain 1 EGC|A Acyl-Coa Dehydrogenase Complexed With Octanoyl-Coa 254 3e-067

S09692 retinoid X receptor alpha [validated] - human 526 e-149

CAA36982.1 unnamed protein product 526 e-149

1609194A retinoic acid receptor RXRalpha 526 e-149

NP_00δδ4δ.

1 retinoid X receptor, gamma 494 e-139

P4δ443 Retinoic acid receptor RXR-gamma 494 e-139

AAA806δ1.1 retinoid X receptor-gamma 494 e-139

CAC00596.1 bA2δ0O1.2 (retinoid X receptor, gamma (NR2B3)) 494 e-139

AAH12063.1 Retinoid X receptor, gamma 494 e-139

1LBD Ligand-Binding Domain Of The Human Nuclear Receptor Rxr-Alpha 419 e-117 Chain A, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic

1 H9U|A Agonist Lg 100263 416 e-115 Chain B, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic

1 H9U|B Agonist Lg10026δ 416 e-115 Chain C, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic

1H9U|C Agonist Lg10026δ 416 e-116 Chain D, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic

1 H9U|D Agonist Lg10026δ 416 e-115

136104 MHC class I promoter binding protein - human (fragment) 415 e-115

CAA46456.1 MHC class I promoter binding protein 415 e-115 Chain A, The 2.1 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Rxralpha And Ppargamma Ligand Binding Domains Respectively Bound With 9-Cis Retinoic

1FM6|A Acid And Rosigiitazone And Co-Activator Peptides. 406 e-113

Chain U, The 2.1 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Rxralpha And Ppargamma Ligand Binding Domains Respectively Bound With 9-Cis Retinoic 1 FM6JU Acid And Rosigiitazone And Co-Activator Peptides. Chain A, The 2.1 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Rxralpha And Ppargamma Ligand Binding Domains Respectively Bound With 9-Cis Retinoic 1 FM9[A Acid And Gi262570 And Co-Activator Peptides. Chain A, The 2.0 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain Tetramer In The Presence 1 G5YJA Of A Non-Activating Retinoic Acid Isomer. Chain B, The 2.0 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain Tetramer In The Presence 1 G5Y|B Of A Non-Activating Retinoic Acid Isomer. Chain C, The 2.0 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain Tetramer In The Presence 1 G5Y|C Of A Non-Activating Retinoic Acid Isomer. Chain D, The 2.0 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain Tetramer In The Presence 1 GδY|D Of A Non-Activating Retinoic Acid Isomer. Chain A, The 2.5 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain In Tetramer In The Absence G1U|A Of Ligand Chain B, The 2.5 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain In Tetramer In The Absence G1U]B Of Ligand

Chain C, The 2.5 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain In Tetramer In The Absence G1U|C Of Ligand Chain D, The 2.5 Angstrom Resolution Crystal Structure Of The Rxralpha Ligand Binding Domain In Tetramer In The Absence G1U|D Of Ligand Chain A, The 2.3 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Ppargamma And Rxralpha Ligand Binding Domains Respectively Bound With Gw409544 And 1K74|A 9-Cis Retinoic Acid And Co-Activator Peptides. v-ets erythroblastosis virus E26 oncogene homolog 2; Oncogene ETS-2; v-ets avian erythroblastosis virus E2 oncogene homolog 2;

NM_011δ09 U.-+2.02 NP_005230. v-ets avian erythroblastosis virus E26 oncogene homolog

P15037 Mm.290207 F:2.δ 1 2; human erythroblastosis virus oncogene homolog 2 P15036 C-ets-2 protein TVHUE2 transcription factor ets-2 - human AAA52412.1 ets2 protein AAB94057.1 erythroblastosis virus oncogene homolog 2 protein AAH17040.1 V-ets erythroblastosis virus E26 oncogene homolog 2 AAH42954.1 V-ets erythroblastosis virus E26 oncogene homolog 2 AAP35484.1 V-ets erythroblastosis virus E26 oncogene homolog 2 CAB9046δ.1 human erythroblastosis retrovirus oncogene homologue 2 CAE457δ3.1 hypothetical protein

v-ets erythroblastosis virus E26 oncogene homolog 1 ; Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1 ; v-ets avian erythroblastosis virus E2 oncogene homolog 1; v-ets avian erythroblastosis virus E26 oncogene homolog NP_005229. 1; v-ets erythroblastosis virus E26 oncogene homolog 1 1 (avian) 420 e-117 P14921 C-ets-1 protein (p54) 420 e-117 TVHUET transcription factor ets-1 , splice form a - human 420 e-117 CAA32904.1 unnamed protein product 420 e-117 AAA52410.1 ets-1 protein 420 e-117 BAA95514.1 erythroblastosis retrovirus oncogene homologue 2 335 3e-091 AAA52411.1 ets protein 302 2e-081 CAA32903.1 alternate cets-1 b protein 222 .3e-057

NM_011714 bromodomain adjacent to zinc finger domain, 1 B; transcription factor

NP_035344. U:+2.01 NP_115764. WSTF; Williams-Beuren syndrome chromosome region 10;

1 Mm.40331 F:3.72 1 Williams-Beuren syndrome chromosome region 9 2211 Bromodomain adjacent to zinc finger domain protein 1 B (Williams-Beuren syndrome chromosome region 9 protein) Q9UIG0 (WBRS9) (Williams syndrome transcription factor) (hWALP2) 22,11 0 AAD08675.1 Williams-Beuren syndrome deletion transcript 9 2209 0 bromodomain adjacent to zinc finger domain, 1 B; transcription factor NP_075331. WSTF; Williams-Beuren syndrome chromosome region 10; 2 Williams-Beuren syndrome chromosome region 9 2203 0 BAAδ9210.1 bromodomain adjacent to zinc finger domain 1B 2203 0 AAC97879.1 transcription factor WSTF 2116 0 AAP22332.1 unknown 1403 0 AAH65029.1 BAZ1B protein 1222 0 AAD04720.1 similar to U47321 (PID:g1245146) 734 0

NMJD09599 U:+2.01 NP_000656.

JH0314 Mm.255464 F:3.16 1 acetylcholinesterase hydrophilic form precursor 1065 0 P22303 Acetylcholinesterase precursor (AChE) 1065 0 acetylcholinesterase (EC 3.1.1.7) precursor, brain splice form - A39256 human 1065 0 AAA66 51.1 acetylcholinesterase 1065 0 AAP22365.1 unknown 1065 0 Chain A, Crystal Structure Of Mutant E202q Of Human Acetylcholinesterase Complexed With Green Mamba Venom 1 F8U Peptide Fasciculin-li 1057 NP_056646. 1 acetylcholinesterase Pl-linked form precursor 978 0 AAP22364.1 unknown 976 0 Chain A, Human Acetylcholinesterase Complexed With Fasciculin-li, 1B41 Glycosylated Protein 963 0 NP_000046. 1 butyrylcholinesterase precursor 627 e-179 Choiinesterase precursor (Acylcholine acylhydroiase) (Choline esterase li) (Butyrylcholine esterase) P06276 (Pseudocholinesterase) 627 e-179 ACHU choiinesterase (EC 3.1.1.δ) precursor [validated] - human 627 e-179 AAA9δ113.1 choiinesterase (EC 3.1.1.8) 627 e-179 AAA5201 δ.1 butyrylcholinesterase (EC 3.1.1.8) 627 e-179 AAA99296.1 butyrylcholinesterase 627 e-179 AAH1 δ141.1 Butyrylcholinesterase precursor 627 e-179 AA032946.1 apoptosis-related acetylcholinesterase 600 e-171 1 POI Chain A, Crystal Structure Of Human Butyryl Choiinesterase 56δ e-161 Chain A, Crystal Structure Of Human Butyryl Choiinesterase In Complex 1 POM With A Choline Molecule 56δ e-161

CAA460δ7.1 insulin-like growth factor binding protein 3 233 2e-060 AAH00013.1 Insulin-like growth factor binding protein 3 233 2e-060 AAH18962.1 Insulin-like growth factor binding protein 3 233 2e-060 BAC37023.1 unnamed protein product 213 2e-054

NM_021601 U:+2.01 NP_0569δ1.

NP 067476 Mm.3442δ F:3.07 2 protein inhibitor of activated STAT protein PIASy 344 Protein inhibitor of activated STAT protein gamma (PIAS-gamma) Q8N2W9 (PIASy) δ44 0 AAH29δ74.1 Protein inhibitor of activated STAT protein PIASy 644 0 AAH10047.2 PIASY protein 637 0 AAC36703.1 protein inhibitor of activated STAT protein PIASy 835 0 AAD46156.1 protein inhibitor of activated STAT 819 0 protein inhibitor of activated STAT, 1; protein inhibitor of NP_057250. activated STAT-1 ; AR interacting protein; DEAD/H 1 (Asp-Glu-Ala-Asp/His) box binding protein 1 412 e-114 Protein inhibitor of activated STAT protein 1 (Gu binding protein) (GBP) (RNA helicase II binding protein) (DEAD/H 075925 box-binding protein 1) 412 e-114 AAD49722.1 protein inhibitor of activated STAT-1 412 e-114 AAC36702.1 protein inhibitor of activated STAT protein PIAS1 410 e-114 JC5517 Gu/RNA helicase II binding protein - human 409 e-114 AAB58488.1 Gu binding protein 409 e-114 NP_006090. 1 protein inhibitor of activated STAT3 406 e-113 Q9Y6X2 Protein inhibitor of activated STAT protein 3 406 e-113 BAA7δ533.1 protein inhibitor of activatied STAT3 406 e-113 AAH01154.1 protein inhibitor of activatied STAT3 406 e-113 AAH30556.1 protein inhibitor of activatied STAT3 406 e-113 AAP35634.1 protein inhibitor of activatied STAT3 406 e-113

NP_004662.

1 protein inhibitor of activated STAT X isoform beta 403 e-112

AAC36705.1 protein inhibitor of activated STAT protein PIASx-beta 403 e-112

NP_77529δ.

1 protein inhibitor of activated STAT X isoform alpha 403 e-112

AAC36704.1 protein inhibitor of activated STAT protein PIASx-alpha 403 e-112

AAH15190.1 Protein inhibitor of activated STAT X, isoform alpha 403 e-112

Master Tables 101-199

In the related applications set forth at the beginning of the specification, we have looked at differential expression of genes in various organs and tissue with respect to (1) aging, (2) hyperinsulinemia and/or type II diabetes. Master Tables 101-199 (note that some of these table numbers are reserved for future use) tabulate those mouse genes which appear both in Master Table 1 of this application, and in the corresponding table of. at least one of the related applications .

The following human proteins are considered to be of particular interest :

Human proteins corresponding to mouse genes listed as favorable both in Master Table 1 and in at least one of Master Tables 101-199, which are not listed as unfavorable in any of Master Tables 101-199; and

Human proteins corresponding to mouse genes listed as unfavorable both in Master Table 1 and in at least one of Master Tables 101-199, which are not listed as favorable in any of Master Tables 101-199.

415

References Cited by Reference Number:

1. Se sei I. (2000) On the nature of aging. ech Aging Dev 117:93-108.

2. Sohal, RS, eindruch, R. (1998) Oxidative stress, caloric restriction, and aging. Science 273:59-63.

3. Finch, CE, Revkun, G. (2001) The genetics of aging. Annu. Rev. Genom. Hum. Genet. 2:435-462.

4. Roth, GS, Lasnikov, V, Lesnikov, M, Ingram, DK, Land, MA (2001) Dietary caloric restriction prevents the age-related decline in plasma melatonin levels of rhesus monkeys. J Clin Endocrinol Metab. 86:3292-5.

5. Roth GS, Lane MA, Ingram DK, Mattison JA, Elahi D, Tobin JD, Muller D, Metter EJ (2002) Biomarkers of caloric restriction may predict longevity in humans. Science. 297:811-813.

6. Walford RL, Mock D, Verdery R, MacCallum T. (2002) Calorie restriction in biosphere 2: alterations in physiologic, hematologic, hormonal, and biochemical parameters in humans restricted for a 2-year period. J Gerontol A Biol Sci Med Sci 57:211-24.

7. Kenyon C, Chang J, Gensch E, Rudner A, Tabtiang R. (1993) A C. elegans mutant that lives twice as long as wild type. Nature 366:461-464.

8. Lin, K, Dorman, JB, Rodan, A, Kenyon, C. (1997). daf-16: an HNF-3/Forkhead family member that can function to double the life-span of Caenorhabditis elegans . Science 278, 1319- 1322. 9. Clancy DJ, Gems D, Harshman LG, Oldham S, Stocker H, Hafen E, Leevers SJ, Partridge L. (2001) Extension of life-span by loss of CHICO, a Drosophila insulin receptor substrate protein. Science 292:104-106.

10. Tatar, M, Bartke, A, Antebi . (2003) The endocrine regulation of aging by insulin-like signals. Science 299:1346-1351.

11. Tran H, Brunet A, Grenier JM, Datta SR, Fornace AJ Jr, DiStefano PS, Chiang LW, Greenberg ME. (2002) DNA repair pathway stimulated by the forkhead transcription factor FOX03a through the Gadd45 protein. Science 296:530-

534.

12. Ramaswamy S, Nakamura N, Sansal I, Bergeron L, Sellers WR. (2002) A novel mechanism of gene regulation and tumor suppression by the transcription factor FKHR. Cancer Cell 2002 2:81-91.

13. Hekimi, S, Guarente, L. (2003) Genetics and the specificity of the aging process. Science 299:1351-1354.

14. Brown-Borg, HM, Borg, KE, Meliska, CJ, Bartke, A. (1996) Dwarf mice and the aging process. Nature 384:33.

15. Flurkey K, Papaconstantinou J, Miller RA, Harrison DE. (2001) Lifespan extension and delayed immune and collagen aging in mutant mice with defects in growth hormone production. Proc Natl Acad Sci USA 98:6736-6741.

16. Zhou, Y, Xu, BC, Maheshwari, HG, He, L, Reed, M, Lozykowski, M, Okada, S, Cataldo, L, Coschigano,- K, Wagner, TE, Baumann, G, Kopchick, JJ. (1997) A mammalian model for Laron syndrome produced by targeted disruption of the mouse growth hormone receptor/binding protein gene (the Laron mouse). Proc. Nat. Acad. Sci. USA 94:13215-13220.

17. Coschigano, K, Clemmons, D, Bellush, LL, Kopchick, JJ. (2000) Assessment of growth parameters and life-span of GHR/BP gene-disrupted mice. Endocrinology 141:2608- 2613.

17a. Coschigano, KT, Holland, AN, Riders, ME, List, EO, Fl vberg, A, Kopchick, JJ, Deletion, but not antagonism, of the mouse growth hormone receptor results in .severely decreased body weights, insulin and IGF-1 levels and increased lifespan, Endocrinology (electronically published May 30, 2003 as doi : 10.1210/en.2003-0374) .

18. Holzenberger M, Dupont J, Ducos B, Leneuve P, Geloen A, Even PC, Cervera P, Le Bouc Y. (2003) IGF-1 receptor regulates lifespan and resistance to oxidative stress in mice. Nature 421:182-187.

19. Migliaccio E, Giorgio M, Mele S, Pelicci G, Reboldi P, Pandolfi PP, Lanfrancone L, Pelicci PG. (1999) The p66shc adaptor protein controls oxidative stress response and life span in mammals. Nature 402:309-313.

20. Bartke A, Wright JC, Mattison JA, Ingram DK, Miller RA, Roth GS. (2001) Extending the lifespan of long-lived mice. Nature 414:412.

21. Weindruch R, Kayo T, Lee CK, Prolla TA. (2002) Gene expression profiling of aging using DNA microarrays. Mech Aging Dev 123:177-193.

22. Lee CK, Allison DB, Brand J, Weindruch R, Prolla TA. (2002) Transcriptional profiles associated with aging and middle age-onset caloric restriction in mouse hearts. Proc Natl Acad Sci USA 99:14988-14993. 23. Prolla TA. (2002) DNA microarray analysis of the aging brain. Chem Senses 27299-306.

Ci tation of documents herein is not intended as an admission that any of the documents ci ted herein is pertinent prior art, or an admission that the ci ted documents is considered material to the patentabili ty of any of the claims of the present application . All statements as to the date or representation as to the contents of these documents is based on the information available to the applicant and does not consti tute any admission as to the correctness of the dates or contents of these documents . The appended claims are to be treated as a non-limi ting reci tation of preferred embodiments .

In addi tion to those set forth elsewhere, the following references are hereby incorporated by reference, in their most recent editions as of the time of filing of this application: Kay, Phage Display of Peptides and Proteins : A Laboratory Manual; the John Wiley and Sons Current Protocols series, including Ausubel, Current Protocols in Molecular Biology; Coligan, Current Protocols in Protein Science; Coligan, Current Protocols in Immunology; Current Protocols in Human Genetics ; Current Protocols in Cytometry; Current Protocols in Pharmacology; Current Protocols in Neuroscience; Current Protocols in Cell Biology; Current Protocols in Toxicology; Current Protocols in Field Analytical Chemistry; Current Protocols in Nucleic Acid Chemistry; and Current Protocols in Human Genetics; and the following Cold Spring Harbor Laboratory publications : Sambrook, Molecular Cloning: A Laboratory Manual ; Harlow, Antibodies : A Laboratory Manual ; Manipulating the Mouse Embryo : A Laboratory Manual ; Methods in Yeast Genetics : A Cold Spring Harbor Laboratory Course Manual ; Drosophila Protocols; Imaging Neurons : A Laboratory Manual ; Early

Development of Xenopus laevis : A Laboratory Manual ; Using Antibodies : A Laboratory Manual ; At the Bench : A Laboratory Navigator; Cells : A Laboratory Manual ; Methods in Yeast Genetics : A Laboratory Course Manual; Discovering Neurons : The Experimental Basis of Neuroscience; Genome Analysis : A Laboratory Manual Series ; Laboratory DNA Science; Strategies for Protein Purification and Characterization: A Laboratory Course Manual ; Genetic Analysis of Pathogenic Bacteria : A Laboratory Manual; PCR Primer: A Laboratory Manual ; Methods in Plant Molecular Biology: A Laboratory Course Manual ; Manipulating the Mouse Embryo : A Laboratory Manual; Molecular Probes of the Nervous System; Experiments with Fission Yeast: A Laboratory Course Manual; A Short Course in Bacterial Genetics : A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria; DNA Science : A First Course in Recombinant DNA Technology; Methods in Yeast Genetics : A Laboratory Course Manual ; Molecular Biology of Plants: A Laboratory Course Manual . All references ci ted herein, including journal articles or abstracts, published, corresponding, prior or otherwise related U. S. or foreign patent applications, issued U. S. or foreign patents, or any other references, are entirely incorporated by reference herein, including all data, tables, figures, and ex presented in the ci ted references . Addi tionally, the entire contents of the references ci ted wi thin the references ci ted herein are also entirely incorporated by reference . Reference to known method steps, conventional methods steps, known methods or conventional methods is not in any way an admission that any aspect, description or embodiment of the present invention is disclosed, taught or suggested in the relevant art . The foregoing description of the specific embodiments will so fully reveal the general nature of the invention that others can, by applying knowledge wi thin the skill of the art (including the contents of the references cited herein) , readily modify and/or adapt for various applications such specific embodiments, wi thout undue experimentation, wi thout departing from the general concept of the present invention . Therefore, such adaptations and modifications are intended to be wi thin the meaning and range of equivalents of the disclosed embodiments, based on the teaching and guidance presented herein . It is to be understood that the phraseology or terminology herein is for the purpose of description and not of limi tation, such that the terminology or phraseology of the present specification is to be interpreted by the skilled artisan in light of the teachings and guidance presented herein, in combination wi th the knowledge of one of ordinary skill in the art.

Any description of a class or range as being useful or preferred in the practice of the invention shall be deemed a description of any subclass (e. g. , a disclosed class wi th one or more disclosed members omitted) or subrange contained therein, as well as a separate description of each individual member or value in said class or range. The description of preferred embodiments individually shall be deemed a description of any possible combination of such preferred embodiments, except for combinations which are impossible (e.g, mutually exclusive choices for an element of the invention) or which are expressly excluded by this specification .

If an embodiment of this invention is disclosed in the prior art, the description of the invention shall be deemed to include the invention as herein disclosed wi th such embodi en t exci sed . Introduction to Master Tables

The master tables reflect applicants' analysis of the gene chip data.

For each probe corresponding to a differentially expressed mouse gene, Master Table 1 identifies

Col. 1: The mouse gene (upper) and mouse protein (lower) database accession #s.

Col. 2: The corresponding mouse Unigene Cluster, as of the 4^th Quarter 2001 build.

Col. 3: The behavior (differential expression) observed for the mouse gene. This column identifies the gene as favorable (F) or unfavorable (U) on the basis of its differential behavior in the comparisons (older vs. younger) . As more than one older vs. younger comparison is made, only the result of the comparison yielding the greatest differential is listed. In the case of a gene with mixed behavior, both the result of the comparison yielding the greatest favorable differential and the result of the comparison yielding the greatest unfavorable differential are listed.

One possible way of characterizing the degree of differential expression for a particular comparison would be to take the ratio of older to younger. If that ratio is at least 2:1, the behavior is considered unfavorable, and if it is not more than 0.5:1, it is unfavorable.

Use of an older/younger ratio is awkward when one wants to compare the degree of differential expression without regard to the direction of change. Consequently, in the Master Table, the numerical value is the ratio of the greater value to the lesser value. If this ratio is at least two fold, the degree of differential expression is considered significant.

In some of the related applications cited above, and perhaps occasionally in this application, a ratio may be given as a negative number. This does not have its usual mathematical meaning; it is merely a flag that in the comparison, the older value was less than the younger one, i.e., the gene was favorable. For the purpose of applying the teachings of the specification concerning desired ratios, any negative value should be converted to a positive one by taking its absolute value.

Col. 4: A related human protein, identified by its database accession number. Usually, several such proteins are identified relative to each mouse gene. These proteins have been identified by BLAST searches, as explained in cols. 6- 7.

Col. 5: The name of the related human protein.

Col. 6: The score (in bits) for the alignment performed by the BLAST program.

Col. 7: The E-value for the alignment performed by the BLAST program. It is worth noting that Unigene considers a Blastx E Value of less than le-6 to be a "match" to the reference sequence of a cluster.

Unless otherwise indicated, the bit score and E-value for the alignment is with respect to the alignment of the mouse DNA of col. 1 to the human protein of col. 4 by BlastX, according to the default parameters .

Master Table 1 is divided into three subtables on the basis of the Behavior" in col. 3. If a gene has at least one favorable behavior, and no unfavorable ones, it is put into Subtable IA. In the opposite case, it is put into Subtable IB. If its behavior is mixed, i.e., at least one favorable and at least one unfavorable, it is put into Subtable IC.

(If no subtable IC appears below, then no genes had mixed behavior which satisfied the minimum two-fold difference requirement . )

The corresponding human gene clusters are also of interest. These may be obtained in a number of ways . First , one may search on Unigene

(http: //www.ncbi .nlm.nih.gov/entrez/query. fcgi?db=unigene) for the identified human protein. Review the "hits" (each of which is a Unigene record) for those prefixed by "Hs." Secondly, one may access the Unigene record for the mouse gene cluster (which is given in Master Table 1) , and then click on "Homologene". This will bring up a new page which includes the section "Possible Homologous Genes". One of the entries should be a Homo sapiens gene (considered by Unigene to be the most related human gene) ,- click on its Unigene record link. Additional information of interest may be accessed by searching with the mouse gene accession # in the Mouse Gene Informatics database, at http: //www. informatics . iax.org/ . The related applications may contain reference to "2-16 week old mice". In the anti-diabetes series of applications, 3 week mice were put on a diet to induce obesity, hyperinsulinemia and diabetes. The 2-16 week old mice were more accurately described as mice who had been on that diet for 2-16 weeks, i.e., they were actually 5-19 weeks (35-133 days) oid. Even some of the anti-aging series of applications made reference to 2-16 week old mice, even though the mice were in fact 5-19 weeks (35-133 days) old.

Claims

CLAIMS i/We hereby claim:

1. A method of (I) reducing a rate of biological aging in a human subject, and/or (II) delaying the time of onset, or reducing the severity, of an undesirable age-related phenotype, and/or (III) protecting against an age-related (senescent) disease, which comprises

administering to the, subject a protective amount of an agent which is (1) a polypeptide which is substantially structurally identical or conservatively identical in sequence to a reference protein which is selected from the group consisting of mouse and human proteins set forth in master table 1, subtables IA or IC,

or

(2) an expression vector encoding the polypeptide of (1) above and expressible in a human cell, under conditions conducive to expression of the polypeptide of (1) ;

where said agent reduces a rate of biological aging in said subject, and/or delays the time of onset, or reduces the severity, of an undesirable age-related phenotype in said subject, and/or protects against an age-related disease.

2. A method of (I) reducing a rate of biological aging in a human subject, and/or (II) delaying the time of onset, or reducing the severity, of an undesirable age-related phenotype, and/or (III) protecting against an age-related (senescent) disease, which comprises administering to the subject a protective amount of an agent which is (1) an antagonist of a polypeptide, occurring in said subject, which is substantially structurally identical or conservatively identical in sequence to a reference protein which is selected from the group consisting of mouse and human proteins set forth in master table 1, subtables IB or IC,

(2) an anti-sense vector which inhibits¹ expression of said polypeptide in said subject,

where said agent reduces a rate of biological aging in said subject, and/or delays the time of onset, or reduces the severity, of an undesirable age-related phenotype in said subject, and/or protects against an age-related disease.

3. A method of determining a biological age of a human subject, or a rate of biological aging of a human subject, which comprises

assaying tissue or body fluid samples from said subjects to determine the level of expression of a "favorable" human marker gene, said human marker gene encoding a human protein which is substantially structurally identical or conservatively identical in sequence to a reference protein which is selected from the group consisting of mouse and human proteins set forth in master table 1, subtables IA or IC ,

and inversely correlating the level of expression of said marker gene with a biological age or a rate of biological aging of said patient.

4. A method of determining a biological age of a human subject, or a rate of biological aging of a human subject, which comprises assaying tissue or body fluid samples from said subjects to determine the level of expression of an "unfavorable" human marker gene, said human marker gene encoding a human protein which is substantially structurally identical or conservatively identical in sequence to a reference protein which is selected from the group consisting of mouse and human proteins set forth in master table 1, subtables IB or

IC,

and directly correlating the level of expression of said marker gene with a biological age or a rate of biological aging of said subject.

5. The method of claims 1 or 2 in which (I) applies.

6. The method of claims 1 or 2 in which (II) applies.

7. The method of claims 1 or 2 in which (III) applies

8. The method of claims 3 or 4 in which the level of expression of the marker gene is ascertained by measuring the level of the corresponding messenger RNA.

9. The method of claims 3 or 4 in which the level of expression is ascertained by measuring the level of a protein encoded by said marker gene .

10. The method of any one of claims 1-9 in which the reference protein is a human protein.

11. The method of claim 10 in which the E-value cited for the BlastX alignment of the reference human protein in Master Table 1 to the corresponding reference mouse DNA in Master Table 1 is not more than e-60.

12. The method of claim 10 in which the E-value cited for the BlastX alignment of the reference human protein in Master Table 1 to the corresponding reference mouse DNA in Master Table 1 is not more than e-70.

13. The method of claim 10 in which the E-value cited for the BlastX alignment of the reference human protein in Master Table 1 to the corresponding reference mouse DNA in Master Table 1 is not more than e-80.

14. The method of any one of claims 1-9 in which the reference protein is a mouse protein.

15. The method of any one of claims 1-14 in which said polypeptide is at least 80% identical or at least highly conservatively identical to said reference protein.

16. The method of any one of claims 1-14 in which said polypeptide is at least 90% identical to said reference protein.

17. The method of any one of claims 1-14 in which said polypeptide is at least 95% identical to said reference protein.

18. The method of any one of claims 1-14 in which said polypeptide is identical to said reference protein, or differs from it by not more than a single amino acid substitution.

19. The method of claim 18 in which said polypeptide is identical to said reference protein.

20. The method of claims 2 or 4, or of any of claims 5-19 to the extent dependent on 2 or 4, in which the antagonist is an , antibody, or an antigen-specific binding fragment of an antibody.

21. The method of claims 2 or 4, or of any of claims 5-19 to the extent dependent on 2 or 4, in which the antagonist is a peptide, peptoid, nucleic acid, or peptide nucleic acid oligomer.

22. The method of claims 2 or 4, or of any of claims 5-19 to the extent dependent on 2 or 4 , in which the antagonist is an organic molecule with a molecular weight of less than 500 daltons.

23. The method of claim 22 in which said organic molecule is identifiable as a molecule which binds said polypeptide by screening a combinatorial library.

24. The method of claims 1 or 2 , or of any one of claims 5-23 to the extent dependent on 1 or 2, which further comprises administration of an antagonist of CIDE-A.

25. The method of claim 5 in which biological age is measured by a biomarker.

26. The method of claim 25 in which at least one marker is the level of a biochemical in the blood of the subject.

27. The method of claim 26 in which the biochemical is growth hormone or IGF-1.

28. The method of claim 25 in which the marker is a simple biomarker.

29. The method of claim 25 in which the marker is a composite biomarker .

30. The method of claim 5 in which the affected biological age is the overall biological age of the subject.

31. The method of claim 5 in which the affected biological age is the biological age of a body system of the subject.

32. The method of claim 5 in which the affected biological age is the biological age of an organ or tissue of the subject.

33. The method of claim 32 in which the organ or tissue is a muscle.

34. The method of claim 32 in which the organ or tissue is a skeletal muscle.

35. The method of claim 32 in which the organ or tissue is the gastrocnemius muscle.

36. The method of claims 1 or 3 , or of any of the other preceding claims to the extent dependent on 1 or 3 , where the reference protein is listed in subtable IA.

37. The method of claims 2 or 4, or of any of the other preceding claims to the extent dependent on 1 or 3 , where the reference protein is listed in subtable IB.

38. Use of a protective amount of an agent which is (1) a polypeptide which is substantially structurally identical or conservatively identical in sequence to a reference protein which is selected from the group consisting of mouse and human proteins set forth in master table 1, subtables IA or IC, or (2) an expression vector encoding the polypeptide of (1) above and expressible in a human cell, under conditions conducive to expression of the polypeptide of (1) ; where said agent reduces a rate of biological aging in a subject, and/or delays the time of onset, or reduces the severity, of an undesirable age-related phenotype in said subject, and/or protects against an age-related disease, in the manufacture of a composition for (I) reducing a rate of biological aging in a human subject, and/or (II) delaying the time of onset, or reducing the severity, of an undesirable age-related phenotype, and/or (III) protecting against an age- related (senescent) disease.

39. Use of a protective amount of an agent which is

(1) an antagonist of a polypeptide, occurring in said subject, which is substantially structurally identical or conservatively identical in sequence to a reference protein which is selected from the group consisting of mouse and human proteins set forth in master table 1, subtables IB or IC,

(2) an anti-sense vector which inhibits expression of said polypeptide in said subject, where said agent reduces a rate of biological aging in said subject, and/or delays the time of onset, or reduces the severity, of an undesirable age-related phenotype in said subject, and/or protects against an age-related disease, in the manufacture of a composition for (I) reducing a rate of biological aging in a human subject, and/or (II) delaying the time of onset, or reducing the severity, of an undesirable age-related phenotype, and/or (III) protecting against an age- related (senescent) disease.

40. A method of determining a biological age of a human subject, or a rate of biological aging of a human subject, which comprises

assaying tissue or body fluid samples from said subjects to determine the level of expression of a "favorable" human marker gene, said human marker gene encoding a human protein which is substantially structurally identical or conservatively identical in sequence to a reference protein which is selected from the group consisting of mouse and human proteins set forth in master table 1, subtables IA or IC ,

and inversely correlating the level of expression of said marker gene with a biological age or a rate of biological aging of said patient.

41. A method of determining a biological age of a human subject, or a rate of biological aging of a human subject, which comprises assaying tissue or body fluid samples from said subjects to determine the level of expression of an "unfavorable" human marker gene, said human marker gene encoding a human protein which is substantially structurally identical or conservatively identical in sequence to a reference protein which is selected from the group consisting of mouse and human proteins set forth in master table 1, subtables IB or

IC,

and directly correlating the level of expression of said marker gene with a biological age or a rate of biological aging of said subject.

42. The use of claims 38 or 39 in which (I) applies.

43. The use of claims 38 or 39 in which (II) applies.

44. The use of claims 38 or 39 in which (III) applies,

45. The method of claims 40 or 41 in which the level of expression of the marker gene is ascertained by measuring the level of the corresponding messenger RNA.

46. The method of claims 40 or 41 in which the level of expression is ascertained by measuring the level of a protein encoded by said marker gene .

47. The use or method of any one of claims 38-46 in which the reference protein is a human protein.

48. The use or method of claim 47 in which the E-value cited for the BlastX alignment of the reference human protein in Master Table 1 to the corresponding reference mouse DNA in Master Table 1 is not more than e-60.

49. The method of claim 47 in which the E-value cited for the

BlastX alignment of the reference human protein in Master

Table 1 to the corresponding reference mouse DNA in Master

Table 1 is not more than e-70.

50. The method of claim 47 in which the E-value cited for the BlastX alignment of the reference human protein in Master Table 1 to the corresponding reference mouse DNA in Master Table 1 is not more than e-80.

51. The use or method of any one of claims 38-46 in which the reference protein is a mouse protein.

52. The use or method of any one of claims 38-51 in which said polypeptide is at least 80% identical or at least highly conservatively identical to said reference protein.

53. The use or method of any one of claims 38-51 in which said polypeptide is at least 90% identical to said reference protein.

54. The use or method of any one of claims 38-51 in which said polypeptide is at least 95% identical to said reference protein.

55. The use or method of any one of claims 38-51 in which said polypeptide is identical to said reference protein, or differs from it by not more than a single amino acid substitution.

56. The use or method of claim 55 in which said polypeptide is identical to said reference protein.

57. The use or method of claims 38 or 40, or of any of claims 42-56 to the extent dependent on 38 or 40, in which the antagonist is an antibody, or an antigen-specific binding fragment of an antibody.

58. The use or method of claims 38 or 40, or of any of claims 42-56 to the extent dependent on 38 or 40, in which the antagonist is a peptide, peptoid, nucleic acid, or peptide nucleic acid oligomer.

59. The use or method of claims 38 or 40, or of any of claims 42-56 to the extent dependent on 38 or 40, in which the antagonist is an organic molecule with a molecular weight of less than 500 daltons.

60. The use or method of claim 59 in which said organic molecule is identifiable as a molecule which binds said polypeptide by screening a combinatorial library.

61. The use of claims 38 or 39, or of any one of claims 42-60 to the extent dependent on 38 or 39, which further comprises administration of an antagonist of CIDE-A.

62. The method of claim 41 in which biological age is measured by a biomarker .

63. The method of claim 62 in which at least one marker is the level of a biochemical in the blood of the subject.

64. The method of claim 63 in which the biochemical is growth hormone or IGF-1.

65. The method of claim 62 in which the marker is a simple biomarker.

66 . The method of claim 62 in which the marker is a composite biomarker.

67. The method of claim 42 in which the affected biological age is the overall biological age of the subject.

68. The method of claim 42 in which the affected biological age is the biological age of a body system of the subject.

69. The method of claim 42 in which the affected biological age is the biological age of an organ or tissue of the subject .

70. The method of claim 69 in which the organ or tissue is a muscle.

71. The method of claim 70 in which the organ or tissue is a skeletal muscle.

72. The method of claim 71 in which the organ or tissue is the gastrocnemius muscle .

73. The use or method of claims 38 or 40, or of any of the other preceding claims to the extent dependent on 38 or 40, where the reference protein is listed in subtable IA.

74. The use or method of claims 39 or 41, or of any of the other preceding claims to the extent dependent on 39 or 41, where the reference protein is listed in subtable IB.