Advances in toxicogenomics

Chemical Research in Toxicology

Volumn 18, Issue 3, 2005, Pages 403-414

  Hayes, Kevin R ^a   Bradfield, Christopher A ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMIC HYBRIDIZATION; DNA FINGERPRINTING; DNA MICROARRAY; GENE EXPRESSION; GENE MAPPING; GENETIC TRANSCRIPTION; GENOME; PROTEIN INTERACTION; REVIEW; SIGNAL TRANSDUCTION; TOXICOGENETICS;

ANIMALS; DRUG TOXICITY; GENE EXPRESSION PROFILING; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RATS; TOXICOGENETICS;

EID: 15344347753     PISSN: 0893228X     EISSN: None     Source Type: Journal    
DOI: 10.1021/tx0496690     Document Type: Review

References (78)

1. Nuwaysir, E. F., Bittner, M., Trent, J., Barrett, J. C., and Afshari, C. A. (1999) Microarrays and toxicology: The advent of toxicogenomics. Mol. Carcinog. 24, 153-159.
2. Griffin, J. L., and Bollard, M. E. (2004) Metabonomics: Its potential as a tool in toxicology for safety assessment and data integration. Curr. Drug Metab. 5, 389-398.
3. Pognan, F. (2004) Genomics, proteomics and metabonomics in toxicology: Hopefully not "fashionomics". Pharmacogenomics 5, 879-893.
4. Yao, G., Craven, M., Drinkwater, N., and Bradfield, C. A. (2004) Interaction networks in yeast define and enumerate the signaling steps of the vertebrate aryl hydrocarbon receptor. PLoS Biol. 2, E65.
5. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
6. Yang, Y. H., and Speed, T. (2002) Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3, 579-588.
7. Kerr, M. K. (2003) Design considerations for efficient and effective microarray studies. Biometrics 59, 822-828.
8. Churchill, G. A. (2002) Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32, 490-495.
9. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95, 14863-14868.
10. Sherlock, G. (2000) Analysis of large-scale gene expression data. Curr. Opin. Immunol. 12, 201-205.
11. Bleharski, J. R., Li, H., Meinken, C., Graeber, T. G., Ochoa, M. T., Yamamura, M., Burdick, A., Sarno, E. N., Wagner, M., Rollinghoff, M., Rea, T. H., Colonna, M., Stenger, S., Bloom, B. R., Eisenberg, D., and Modlin, R. L. (2003) Use of genetic profiling in leprosy to discriminate clinical forms of the disease. Science 301, 1527-1530.
12. Ueda, A., Hamadeh, H. K., Webb, H. K., Yamamoto, Y., Sueyoshi, T., Afshari, C. A., Lehmann, J. M., and Negishi, M. (2002) Diverse roles of the nuclear orphan receptor CAR in regulating hepatic genes in response to phenobarbital. Mol. Pharmacol. 61, 1-6.
13. Frueh, F. W., Hayashibara, K. C., Brown, P. O., and Whitlock, J. P., Jr. (2001) Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expression. Toxicol. Lett. 122, 189-203.
14. Wei, Y. D., Tepperman, K., Huang, M. Y., Sartor, M. A., and Puga, A. (2004) Chromium inhibits transcription from polycyclic aromatic hydrocarbon-inducible promoters by blocking the release of histone deacetylase and preventing the binding of p300 to chromatin. J. Biol. Chem. 279, 4110-4119.
15. Kramer, J. A., LeDeaux, J., Butteiger, D., Young, T., Crankshaw, C., Harlow, H., Kier, L., and Bhat, B. G. (2003) Transcription profiling in rat liver in response to dietary docosahexaenoic acid implicates stearoyl-coenzyme a desaturase as a nutritional target for lipid lowering. J. Nutr. 133, 57-66.
16. Cherkaoui-Malki, M., Meyer, K., Cao, W. Q., Latruffe, N., Yeldandi, A. V., Rao, M. S., Bradfield, C. A., and Reddy, J. K. (2001) Identification of novel peroxisome proliferator-activated receptor alpha (PPARalpha) target genes in mouse liver using cDNA microarray analysis. Gene Expression 9, 291-304.
17. Conney, A. H. (1967) Pharmacological implications of microsomal enzyme induction. Pharmacol. Rev. 19, 317-366.
18. Remmer, H., and Merker, H. J. (1963) Drug-induced changes in the liver endoplasmic reticulum: Association with drug-metabolizing enzymes. Science 142, 1657-1658.
19. Fielden, M. R., and Zacharewski, T. R. (2001) Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology. Toxicol. Sci. 60, 6-10.
20. Hoffmann, K. F., McCarty, T. C., Segal, D. H., Chiaramonte, M., Hesse, M., Davis, E. M., Cheever, A. W., Meltzer, P. S., Morse, H. C., 3rd, and Wynn, T. A. (2001) Disease fingerprinting with cDNA microarrays reveals distinct gene expression profiles in lethal type 1 and type 2 cytokine-mediated inflammatory reactions. FASEB J. 15, 2545-2547.
21. Loertscher, J. A., Sattler, C. A., and Allen-Hoffmann, B. L. (2001) 2,3,7,8-Tetrachlorodibenzo-p-dioxin alters the differentiation pattern of human keratinocytes in organotypic culture. Toxicol. Appl. Pharmacol. 175, 121-129.
22. Nielsen, T. O., West, R. B., Linn, S. C., Alter, O., Knowling, M. A., O'Connell, J. X., Zhu, S., Fero, M., Sherlock, G., Pollack, J. R., Brown, P. O., Botstein, D., and van de Rijn, M. (2002) Molecular characterisation of soft tissue tumours: A gene expression study. Lancet 359, 1301-1307.
23. Ramaswamy, S., Ross, K. N., Lander, E. S., and Golub, T. R. (2003) A molecular signature of metastasis in primary solid tumors. Nat. Genet. 33, 49-54.
24. Scherf, U., Ross, D. T., Waltham, M., Smith, L. H., Lee, J. K., Tanabe, L., Kohn, K. W., Reinhold, W. C., Myers, T. G., Andrews, D. T., Scudiero, D. A., Eisen, M. B., Sausville, E. A., Pommier, Y., Botstein, D., Brown, P. O., and Weinstein, J. N. (2000) A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24, 236-244.
25. Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., Van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J. C., Lashkari, D., Shalon, D., Myers, T. G., Weinstein, J. N., Botstein, D., and Brown, P. O. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet. 24, 227-235.
26. van't Veer, L. J., Dai, H., van de Vijver, M. J., He, Y. D., Hart, A. A., Mao, M., Peterse, H. L., van der Kooy, K., Marton, M. J., Witteveen, A. T., Schreiber, G. J., Kerkhoven, R. M., Roberts, C., Linsley, P. S., Bernards, R., and Friend, S. H. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536.
27. Thomas, R. S., Rank, D. R., Penn, S. G., Zastrow, G. M., Hayes, K. R., Pande, K., Glover, E., Silander, T., Craven, M. W., Reddy, J. K., Jovanovich, S. B., and Bradfield, C. A. (2001) Identification of toxicologically predictive gene sets using cDNA microarrays. Mol. Pharmacol. 60, 1189-1194.
28. Hamadeh, H. K., Bushel, P. R., Jayadev, S., DiSorbo, O., Bennett, L., Li, L., Tennant, R., Stoll, R., Barrett, J. C., Paules, R. S., Blanchard, K., and Afshari, C. A. (2002) Prediction of compound signature using high-density gene expression profiling. Toxicol. Sci. 67, 232-240.
29. Kramer, J. A., Curtiss, S. W., Kolaja, K. L., Alden, C. L., Blomme, E. A., Curtiss, W. C., Davila, J. C., Jackson, C. J., and Bunch, R. T. (2004) Acute molecular markers of rodent hepatic carcinogenesis identified by transcription profiling. Chem. Res. Toxicol. 17, 463-470.
30. Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Vilo, J., Abeygunawardena, N., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G. G., Oezcimen, A., Rocca-Serra, P., and Sansone, S. A. (2003) ArrayExpress-A public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68-71.
31. Edgar, R., Domrachev, M., and Lash, A. E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210.
32. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., Gaasterland, T., Glenisson, P., Holstege, F. C., Kim, I. F., Markowitz, V., Matese, J. C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., and Vingron, M. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29, 365-371.
33. Bradfield, C. (2004) Genomics and proteomics. Chem. Res. Toxicol. 17, 2.
34. (2002) Microarray standards at last. Nature 419, 323.
35. Kuo, W. P., Jenssen, T. K., Butte, A. J., Ohno-Machado, L., and Kohane, I. S. (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18, 405-412.
36. Thompson, K. L., Afshari, C. A., Amin, R. P., Bertram, T. A., Car, B., Cunningham, M., Kind, C., Kramer, J. A., Lawton, M., Mirsky, M., Naciff, J. M., Oreffo, V., Pine, P. S., and Sistare, F. D. (2004) Identification of platform-independent gene expression markers of cisplatin nephrotoxicity. Environ. Health Perspect. 112, 488-494.
37. Mah, N., Thelin, A., Lu, T., Nikolaus, S., Kuhbacher, T., Gurbuz, Y., Eickhoff, H., Kloppel, G., Lehrach, H., Mellgard, B., Costello, C. M., and Schreiber, S. (2004) A comparison of oligonucleotide and cDNA-based microarray systems. Physiol. Genomics 16, 361-370.
38. Ghosh, D., Barette, T. R., Rhodes, D., and Chinnaiyan, A. M. (2003) Statistical issues and methods for meta-analysis of microarray data: A case study in prostate cancer. Fund. Integr. Genomics 3, 180-188.
39. Li, J., Pankratz, M., and Johnson, J. A. (2002) Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol. Sci. 69, 383-390.
40. Baker, V. A., Harries, H. M., Waring, J. F., Duggan, C. M., Ni, H. A., Jolly, R. A., Yoon, L. W., De Souza, A. T., Schmid, J. E., Brown, R. H., Ulrich, R. G., and Rockett, J. C. (2004) Clofibrate-induced gene expression changes in rat liver: A cross-laboratory analysis using membrane cDNA arrays. Environ. Health Perspect. 112, 428-438.
41. Irizarry, K., Kustanovich, V., Li, C., Brown, N., Nelson, S., Wong, W., and Lee, C. J. (2000) Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. Nat. Genet. 26, 233-236.
42. Mattes, W. B. (2004) Annotation and cross-indexing of array elements on multiple platforms. Environ. Health Perspect. 112, 506-510.
43. Marshall, E. (2001) DNA arrays. Affymetrix settles suit, fixes mouse chips. Science 291, 2535.
44. Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., Cooke, M. P., Walker, J. R., and Hogenesch, J. B. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U.S.A. 101, 6062-6067.
45. Tennant, R. W. (2002) The National Center for Toxicogenomics: Using new technologies to inform mechanistic toxicology. Environ. Health Perspect. 110, A8-A10.
46. Waters, M., Boorman, G., Bushel, P., Cunningham, M., Irwin, R., Merrick, A., Olden, K., Faules, R., Selkirk, J., Stasiewicz, S., Weis, B., Van Houten, B., Walker, N., and Tennant, R. (2003) Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. EHP Toxicogenomics 111, 15-28.
47. Hayes, K. R., Vollrath, A. L., Zastrow, G. M., B. J., M., Craven, M., Jovanovich, S., Walisser, J. A., Rank, D., Penn, S., Reddy, J. K., Thomas, R., and Bradfield, C. A. (2005) EDGE: A centralized resource for the comparison, analysis and distribution of toxicogenomic information. Mol. Pharmacol. Submitted for publication.
48. Chang, J. T., and Altman, R. B. (2004) Extracting and characterizing gene-drug relationships from the literature. Pharmacogenetics 14, 577-586.
49. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J. P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J. C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R. H., Wilson, R. K., Hillier, L. W., McPherson, J. D., Marra, M. A., Mardis, E. R., Fulton, L. A., Chinwalla, A. T., Pepin, K. H., Gish, W. R., Chissoe, S. L., Wendl, M. C., Delehaunty, K. D., Miner, T. L., Delehaunty, A., Kramer, J. B., Cook, L. L., Fulton, R. S., Johnson, D. L., Minx, P. J., Clifton, S. W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J. F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Gibbs, R. A., Muzny, D. M., Scherer, S. E., Bouck, J. B., Sodergren, E. J., Worley, K. C., Rives, C. M., Gorrell, J. H., Metzker, M. L., Naylor, S. L., Kucherlapati, R. S., Nelson, D. L., Weinstock, G. M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Smith, D. R., Doucette-Stamm, L., Rubenfield, M., Weinstock, K., Lee, H. M., Dubois, J., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H., Yu, J., Wang, J., Huang, G., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S., Davis, R. W., Federspiel, N. A., Abola, A. P., Proctor, M. J., Myers, R. M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D. R., Olson, M. V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G. A., Athanasiou, M., Schultz, R., Roe, B. A., Chen, F., Pan, H., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W. R., de la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J. A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D. G., Burge, C. B., Cerutti, L., Chen, H. C., Church, D., Clamp, M., Copley, R. R., Doerks, T., Eddy, S. R., Eichler, E. E., Furey, T. S., Galagan, J., Gilbert, J. G., Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W., Johnson, L. S., Jones, T. A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W. J., Kitts, P., Koonin, E. V., Korf, I., Kulp, D., Lancet, D., Lowe, T. M., McLysaght, A., Mikkelsen, T., Moran, J. V., Mulder, N., Pollara, V. J., Ponting, C. P., Schuler, G., Schultz, J., Slater, G., Smit, A. F., Stupka, E., Szustakowski, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y. I., Wolfe, K. H., Yang, S. P., Yeh, R. F., Collins, F., Guyer, M. S., Peterson, J., Felsenfeld, A., Wetterstrand, K. A., Patrinos, A., Morgan, M. J., Szustakowki, J., de Jong, P., Catanese, J. J., Osoegawa, K., Shizuya, H., Choi, S., Chen, Y. J., and International Human Genome Sequencing, C. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921.
50. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., Gocayne, J. D., Amanatides, P., Ballew, R. M., Huson, D. H., Wortman, J. R., Zhang, Q., Kodira, C. D., Zheng, X. H., Chen, L., Skupski, M., Subramanian, G., Thomas, P. D., Zhang, J., Gabor Miklos, G. L., Nelson, C., Broder, S., Clark, A. G., Nadeau, J., McKusick, V. A., Zinder, N., Levine, A. J., Roberts, R. J., Simon, M., Slayman, C., Hunkapiller, M., Bolanos, R., Delcher, A., Dew, I., Fasulo, D., Flanigan, M., Florea, L., Halpern, A., Hannenhalli, S., Kravitz, S., Levy, S., Mobarry, C., Reinert, K., Remington, K., Abu-Threideh, J., Beasley, E., Biddick, K., Bonazzi, V., Brandon, R., Cargill, M., Chandramouliswaran, I., Charlab, R., Chaturvedi, K., Deng, Z., Di Francesco, V., Dunn, P., Eilbeck, K., Evangelista, C., Gabrielian, A. E., Can, W., Ge, W., Gong, F., Gu, Z., Guan, P., Heiman, T. J., Higgins, M. E., Ji, R. R., Ke, Z., Ketchum, K. A., Lai, Z., Lei, Y., Li, Z., Li, J., Liang, Y., Lin, X., Lu, F., Merkulov, G. V., Milshina, N., Moore, H. M., Naik, A. K., Narayan, V. A., Neelam, B., Nusskern, D., Rusch, D. B., Salzberg, S., Shao, W., Shue, B., Sun, J., Wang, Z., Wang, A., Wang, X., Wang, J., Wei, M., Wides, R., Xiao, C., Yan, C., Yao, A., Ye, J., Zhan, M., Zhang, W., Zhang, H., Zhao, Q., Zheng, L., Zhong, F., Zhong, W., Zhu, S., Zhao, S., Gilbert, D., Baumhueter, S., Spier, G., Carter, C., Cravchik, A., Woodage, T., Ali, F., An, H., Awe, A., Baldwin, D., Baden, H., Barnstead, M., Barrow, I., Beeson, K., Busam, D., Carver, A., Center, A., Cheng, M. L., Curry, L., Danaher, S., Davenport, L., Desilets, R., Dietz, S., Dodson, K., Doup, L., Ferriera, S., Garg, N., Gluecksmann, A., Hart, B., Haynes, J., Haynes, C., Heiner, C., Hladun, S., Hostin, D., Houck, J., Howland, T., Ibegwam, C., Johnson, J., Kalush, F., Kline, L., Koduru, S., Love, A., Mann, F., May, D., McCawley, S., McIntosh, T., McMullen, I., Moy, M., Moy, L., Murphy, B., Nelson, K., Pfannkoch, C., Pratts, E., Puri, V., Qureshi, H., Reardon, M., Rodriguez, R., Rogers, Y. H., Romblad, D., Ruhfel, B., Scott, R., Sitter, C., Smallwood, M., Stewart, E., Strong, R., Suh, E., Thomas, R., Tint, N. N., Tse, S., Vech, C., Wang, G., Wetter, J., Williams, S., Williams, M., Windsor, S., Winn-Deen, E., Wolfe, K., Zaveri, J., Zaveri, K., Abril, J. F., Guigo, R., Campbell, M. J., Sjolander, K. V., Karlak, B., Kejariwal, A., Mi, H., Lazareva, B., Hatton, T., Narechania, A., Diemer, K., Muruganujan, A., Guo, N., Sato, S., Bafna, V., Istrail, S., Lippert, R., Schwartz, R., Walenz, B., Yooseph, S., Allen, D., Basu, A., Baxendale, J., Blick, L., Caminha, M., Carnes-Stine, J., Caulk, P., Chiang, Y. H., Coyne, M., Dahlke, C., Mays, A., Dombroski, M., Donnelly, M., Ely, D., Esparham, S., Fosler, C., Gire, H., Glanowski, S., Glasser, K., Glodek, A., Gorokhov, M., Graham, K., Gropman, B., Harris, M., Heil, J., Henderson, S., Hoover, J., Jennings, D., Jordan, C., Jordan, J., Kasha, J., Kagan, L., Kraft, C., Levitsky, A., Lewis, M., Liu, X., Lopez, J., Ma, D., Majoros, W., McDaniel, J., Murphy, S., Newman, M., Nguyen, T., Nguyen, N., Nodell, M., Pan, S., Peck, J., Peterson, M., Rowe, W., Sanders, R., Scott, J., Simpson, M., Smith, T., Sprague, A., Stockwell, T., Turner, R., Venter, E., Wang, M., Wen, M., Wu, D., Wu, M., Xia, A., Zandieh, A., and Zhu, X. (2001) The sequence of the human genome. Science 291, 1304-1351.
51. Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S. E., Attwood, J., Baertsch, R., Bailey, J., Barlow, K., Beck, S., Berry, E., Birren, B., Bloom, T., Bork, P., Botcherby, M., Bray, N., Brent, M. R., Brown, D. G., Brown, S. D., Bult, C., Burton, J., Butler, J., Campbell, R. D., Carninci, P., Cawley, S., Chiaromonte, F., Chinwalla, A. T., Church, D. M., Clamp, M., Clee, C., Collins, F. S., Cook, L. L., Copley, R. R., Coulson, A., Couronne, O., Cuff, J., Curwen, V., Cutts, T., Daly, M., David, R., Davies, J., Delehaunty, K. D., Deri, J., Dermitzakis, E. T., Dewey, C., Dickens, N. J., Diekhans, M., Dodge, S., Dubchak, I., Dunn, D. M., Eddy, S. R., Elnitski, L., Emes, R. D., Eswara, P., Eyras, E., Felsenfeld, A., Fewell, G. A., Flicek, P., Foley, K., Frankel, W. N., Fulton, L. A., Fulton, R. S., Furey, T. S., Gage, D., Gibbs, R. A., Glusman, G., Gnerre, S., Goldman, N., Goodstadt, L., Grafham, D., Graves, T. A., Green, E. D., Gregory, S., Guigo, R., Guyer, M., Hardison, R. C., Haussler, D., Hayashizaki, Y., Hillier, L. W., Hinrichs, A., Hlavina, W., Holzer, T., Hsu, F., Hua, A., Hubbard, T., Hunt, A., Jackson, I., Jaffe, D. B., Johnson, L. S., Jones, M., Jones, T. A., Joy, A., Kamal, M., Karlsson, E. K., Karolchik, D., Kasprzyk, A., Kawai, J., Keibler, E., Kells, C., Kent, W. J., Kirby, A., Kolbe, D. L., Korf, I., Kucherlapati, R. S., Kulbokas, E. J., Kulp, D., Landers, T., Leger, J. P., Leonard, S., Letunic, I., Levine, R., Li, J., Li, M., Lloyd, C., Lucas, S., Ma, B., Maglott, D. R., Mardis, E. R., Matthews, L., Mauceli, E., Mayer, J. H., McCarthy, M., McCombie, W. R., McLaren, S., McLay, K., McPherson, J. D., Meldrim, J., Meredith, B., Mesirov, J. P., Miller, W., Miner, T. L., Mongin, E., Montgomery, K. T., Morgan, M., Mott, R., Mullikin, J. C., Muzny, D. M., Nash, W. E., Nelson, J. O., Nhan, M. N., Nicol, R., Ning, Z., Nusbaum, C., O'Connor, M. J., Okazaki, Y., Oliver, K., Overton-Larty, E., Pachter, L., Parra, G., Pepin, K. H., Peterson, J., Pevzner, P., Plumb, R., Pohl, C. S., Poliakov, A., Ponce, T. C., Ponting, C. P., Potter, S., Quail, M., Reymond, A., Roe, B. A., Roskin, K. M., Rubin, E. M., Rust, A. G., Santos, R., Sapojnikov, V., Schultz, B., Schultz, J., Schwartz, M. S., Schwartz, S., Scott, C., Seaman, S., Searle, S., Sharpe, T., Sheridan, A., Shownkeen, R., Sims, S., Singer, J. B., Slater, G., Smit, A., Smith, D. R., Spencer, B., Stabenau, A., Stange-Thomann, N., Sugnet, C., Suyama, M., Tesler, G., Thompson, J., Torrents, D., Trevaskis, E., Tromp, J., Ucla, C., Ureta-Vidal, A., Vinson, J. P., Von Niederhausern, A. C., Wade, C. M., Wall, M., Weber, R. J., Weiss, R. B., Wendl, M. C., West, A. P., Wetterstrand, K., Wheeler, R., Whelan, S., Wierzbowski, J., Willey, D., Williams, S., Wilson, R. K., Winter, E., Worley, K. C., Wyman, D., Yang, S., Yang, S. P., Zdobnov, E. M., Zody, M. C., Lander, E. S., and Mouse Genome Sequencing, C. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.
52. Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S., Scott, G., Steffen, D., Worley, K. C., Burch, P. E., Okwuonu, G., Hines, S., Lewis, L., DeRamo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R., Celera, Holt, R. A., Adams, M. D., Amanatides, P. G., Baden-Tillson, H., Barnstead, M., Chin, S., Evans, C. A., Ferriera, S., Fosler, C., Glodek, A., Gu, Z., Jennings, D., Kraft, C. L., Nguyen, T., Pfannkoch, C. M., Sitter, C., Sutton, G. G., Venter, J. C., Woodage, T., Smith, D., Lee, H. M., Gustafson, E., Cahill, P., Kana, A., Doucette-Stamm, L., Weinstock, K., Fechtel, K., Weiss, R. B., Dunn, D. M., Green, E. D., Blakesley, R. W., Bouffard, G. G., De Jong, P. J., Osoegawa, K., Zhu, B., Marra, M., Schein, J., Bosdet, I., Fjell, C., Jones, S., Krzywinski, M., Mathewson, C., Siddiqui, A., Wye, N., McPherson, J., Zhao, S., Fraser, C. M., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, W. C., Havlak, P. H., Chen, R., Durbin, K J., Egan, A., Ren, Y., Song, X. Z., Li, B., Liu, Y., Qin, X., Cawley, S., Cooney, A. J., D'Souza, L. M., Martin, K., Wu, J. Q., Gonzalez-Garay, M. L., Jackson, A. R., Kalafus, K. J., McLeod, M. P., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, D. A., Zhang, Z., Bailey, J. A., Eichler, E. E., Tuzun, E., Birney, E., Mongin, E., Ureta-Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, B. J., Young, J. M., Huang, H., Wang, H., Xing, H., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Mar Alba, M., Abril, J. F., Guigo, R., Smit, A., Dubchak, I., Rubin, E. M., Couronne, O., Poliakov, A., Hubner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y. A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, H. J., Bromberg, S., Gullings-Handley, J., Jensen-Seaman, M. I., Kwitek, A. E., Lazar, J., Pasko, D., Tonellato, P. J., Twigger, S., Ponting, C. P., Duarte, J. M., Rice, S., Goodstadt, L., Beatson, S. A., Emes, R. D., Winter, E. E., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, R. C., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, T. D., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, S. M., Cooper, G. M., Batzoglou, S., Brudno, M., Sidow, A., Stone, E. A., Payseur, B. A., Bourque, G., Lopez-Otin, C., Puente, X. S., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, V. B., Caspi, A., Tesler, G., Pevzner, P. A., Haussler, D., Roskin, K. M., Baertsch, R., Clawson, H., Furey, T. S., Hinrichs, A. S., Karolchik, D., Kent, W. J., Rosenbloom, K. R., Trumbower, H., Weirauch, M., Cooper, D. N., Stenson, P. D., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, R. R., Taylor, M. S., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S., Collins, F., and Rat Genome Sequencing Project, C. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493-521.
53. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J. M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., Gelpke, M. D., Roach, J., Oh, T., Ho, I. Y., Wong, M., Detter, C., Verhoef, F., Predki, P., Tay, A., Lucas, S., Richardson, P., Smith, S. F., Clark, M. S., Edwards, Y. J., Doggett, N., Zharkikh, A., Tavtigian, S. V., Pruss, D., Barnstead, M., Evans, C., Baden, H., Powell, J., Glusman, G., Rowen, L., Hood, L., Tan, Y. H., Elgar, G., Hawkins, T., Venkatesh, B., Rokhsar, D., and Brenner, S. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310.
54. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., and Haussler, D. (2004) Ultraconserved elements in the human genome. Science 304, 1321-1325.
55. Margulies, E. H., Blanchette, M., Haussler, D., Green, E. D., and Program, N. C. S. (2003) Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507-2518.
56. Conkright, M. D., Guzman, E., Flechner, L., Su, A. I., Hogenesch, J. B., and Montminy, M. (2003) Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. [(2003) 11 (5), 1417]. Mol. Cell 11, 1101-1108.
57. Iourgenko, V., Zhang, W., Mickanin, C., Daly, I., Jiang, C., Hexham, J. M., Orth, A. P., Miraglia, L., Meltzer, J., Garza, D., Chirn, G. W., McWhinnie, E., Cohen, D., Skelton, J., Terry, R., Yu, Y., Bodian, D., Buxton, F. P., Zhu, J., Song, C., and Labow, M. A. (2003) Identification of a family of cAMP response element-binding protein coactivators by genome-scale functional analysis in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 100, 12147-12152.
58. Albertson, D. G., and Pinkel, D. (2003) Genomic microarrays in human genetic disease and cancer. Hum. Mol. Genet. 12, R145-R152.
59. Kondo, Y., Shen, L., Van, P. S., Huang, T. H., and Issa, J. P. (2004) Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc. Natl. Acad. Sci. U.S.A. 101, 7398-7403.
60. Lan, H., Stoehr, J. P., Nadler, S. T., Schueler, K. L., Yandell, B. S., and Attie, A. D. (2003) Dimension reduction for mapping mRNA abundance as quantitative traits. Genetics 164, 1607-1614.
61. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29.
62. Doniger, S. W., Salomonis, N., Dahlquist, K. D., Vranizan, K., Lawlor, S. C., and Conklin, B. R. (2003) MAPPFinder: Using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 4, R7.
63. Dahlquist, K. D., Salomonis, N., Vranizan, K., Lawlor, S. C., and Conklin, B. R. (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet. 31, 19-20.
64. Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E., Houstis, N., Daly, M. J., Patterson, N., Mesirov, J. P., Golub, T. R., Tamayo, P., Spiegelman, B., Lander, E. S., Hirschhorn, J. N., Altshuler, D., and Groop, L. C. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267-273.
65. Salwinski, L., Miller, C. S., Smith, A. J., Pettit, F. K., Bowie, J. U., and Eisenberg, D. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res. 32, D449-D451.
66. Chaussabel, D., and Sher, A. (2002) Mining microarray expression data by literature profiling. Genome Biol. 3, RESEARCH0055.
67. Pandey, R., Guru, R. K., and Mount, D. W. (2004) Pathway Miner: Extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics 20, 2156-2158.
68. Hu, Y., Hines, L. M., Weng, H., Zuo, D., Rivera, M., Richardson, A., and LaBaer, J. (2003) Analysis of genomic and proteomic data using advanced literature mining. J. Proteome Res. 2, 405-412.
69. Masys, D. R., Welsh, J. B., Lynn Fink, J., Gribskov, M., Klacansky, I., and Corbeil, J. (2001) Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics 17, 319-326.
70. Basik, M., Mousses, S., and Trent, J. (2003) Integration of genomic technologies for accelerated cancer drug development. Biotechniques 35, 580-582, 584, 586 passim.
71. Guerreiro, N., Staedtler, F., Grenet, O., Kehren, J., and Chibout, S. D. (2003) Toxicogenomics in drug development. Toxicol. Pathol. 31, 471-479.
72. Chang, J. C., Wooten, E. C., Tsimelzon, A., Hilsenbeck, S. G., Gutierrez, M. C., Elledge, R., Mohsin, S., Osborne, C. K., Chamness, G. C., Allred, D. C., and O'Connell, P. (2003) Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. Lancet 362, 362-369.
73. Sotiriou, C., Powles, T. J., Dowsett, M., Jazaeri, A. A., Feldman, A. L., Assersohn, L., Gadisetti, C., Libutti, S. K., and Liu, E. T. (2002) Gene expression profiles derived from fine needle aspiration correlate with response to systemic chemotherapy in breast cancer. Breast Cancer Res. 4, R3.
74. van de Vijver, M. J., He, Y. D., van't Veer, L. J., Dai, H., Hart, A. A., Voskuil, D. W., Schreiber, G. J., Peterse, J. L., Roberts, C., Marton, M. J., Parrish, M., Atsma, D., Witteveen, A., Glas, A., Delahaye, L., van der Velde, T., Bartelink, H., Rodenhuis, S., Rutgers, E. T., Friend, S. H., and Bernards, R. (2002) A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347, 1999-2009.
75. Hackett, J. L., and Lesko, L. J. (2003) Microarray data-the US FDA, industry and academia. Nat. Biotechnol. 21, 742-743.
76. van den Berg, M., Peterson, R. E., and Schrenk, D. (2000) Human risk assessment and TEFs. Food Addit. Contam. 17, 347-358.
77. Van den Berg, M., Birnbaum, L., Bosveld, A. T., Brunstrom, B., Cook, P., Feeley, M., Giesy, J. P., Hanberg, A., Hasegawa, R., Kennedy, S. W., Kubiak, T., Larsen, J. C., van Leeuwen, F. X., Liem, A. K., Nolt, C., Peterson, R. E., Poellinger, L., Safe, S., Schrenk, D., Tillitt, D., Tysklind, M., Younes, M., Waern, F., and Zacharewski, T. (1998) Toxic equivalency factors (TEFs) for PCBs, PCDDs, PCDFs for humans and wildlife. Environ. Health Perspect. 106, 775-792.
78. Finley, B. L., Connor, K. T., and Scott, P. K. (2003) The use of toxic equivalency factor distributions in probabilistic risk assessments for dioxins, furans, and PCBs. J. Toxicol. Environ. Health A 66, 533-550.