Toxicogenomics and Systems Toxicology

Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals

Volumn , Issue , 2006, Pages 99-150

  Waters, Michael D ^a   Fostel, Jennifer M ^b   Wetmore, Barbara A ^b   Merrick, B Alex ^b  

^a INTEGRATED LABORATORY SYSTEMS   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

Proteomic role in toxicology; Toxicogenomics aims and methods; Toxicogenomics and systems toxicology

Indexed keywords

EID: 37849032722     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470145890.ch5     Document Type: Chapter

References (250)

1. Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD. Database development in toxicogenomics: Issues and efforts. Environ Health Perspect 2004;112(4):495-505.
2. Maunsbach A, Afzelium B. Biomedical electron microscopy: illustrated methods and interpretations. San Diego: Academic Press, 1999.
3. Braga PC, Ricci D. Atomic force microscopy: Biomedical methods and applications, Vol. 242. Totowa, NJ: Humana Press, 2004.
4. Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA. Microarrays and toxicology: The advent of toxicogenomics. Mol Carcinog 1999;24(3):153-9.
5. Shi MM. Technologies for individual genotyping: Detection of genetic polymorphisms in drug targets and disease genes. Am J Pharmacogenomics 2002;2(3):197-205.
6. Wen SY, Wang H, Sun OJ, Wang SQ. Rapid detection of the known SNPs of CYP2C9 using oligonucleotide microarray. World J Gastroenterol 2003;9(6):1342-6.
7. Mandal MN, Heckenlively JR, Burch T, Chen L, Vasireddy V, Koenekoop RK, Sieving PA, Ayyagari R. Sequencing arrays for screening multiple genes associated with early-onset human retinal degenerations on a high-throughput platform. Invest Ophthalmol Vis Sci 2005;46(9):3355-62.
8. Ideker T, Galitski T, Hood L. A new approach to decoding life: Systems biology. An Rev Genomics Hum Genet 2001;2:343-72.
9. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001;292(5518):929-34.
10. Tong W, Cao X, Harris S, Sun H, Fang H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, Shi L, Casciano D. Arraytrack-Supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ Health Perspect 2003;111(15):1819-26.
11. Waters MD, Olden K, Tennant RW. Toxicogenomic approach for assessing toxicant-related disease. Mutat Res 2003;544(2-3):415-24.
12. Waters MD, Fostel JM. Toxicogenomics and systems toxicology: Aims and prospects. Nat Rev Genet 2004;5(12):936-48.
13. Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, Olden K, Paules R, Selkirk J, Stasiewicz S, Weis B, Van Houten B, Walker N, Tennant R. Systems toxicology and the chemical effects in biological systems (CEBS) knowledge base. EHP Toxicogenomics 2003;111(1 T):15-28.
14. Boorman GA, Anderson SP, Casey WM, Brown RH, Crosby LM, Gottschalk K, Easton M, Ni H, Morgan KT. Toxicogenomics, drug discovery, and the pathologist. Toxicol Pathol 2002;30(1):15-27.
15. Storck T, von Brevern MC, Behrens CK, Scheel J, Bach A. Transcriptomics in predictive toxicology. Curr Opin Drug Discov Devel 2002;5(1):90-7.
16. Suter L, Babiss LE, Wheeldon EB. Toxicogenomics in predictive toxicology in drug development. Chem Biol 2004;11(2):161-71.
17. Aardema MJ, MacGregor JT. Toxicology and genetic toxicology in the new era of "toxicogenomics": Impact of "-omics" technologies. Mutat Res 2002;499(1):13-25.
18. Afshari CA. Perspective: Microarray technology, seeing more than spots. Endocrinology 2002;143(6):1983-9.
19. Ulrich R, Friend SH. Toxicogenomics and drug discovery: Will new technologies help us produce better drugs? Nat Rev Drug Discov 2002;1(1):84-8.
20. Fielden MR, Zacharewski TR. Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology. Toxicol Sci 2001;60(1):6-10.
21. Hamadeh HK, Amin RP, Paules RS, Afshari CA. An overview of toxicogenomics. Curr Issues Mol Biol 2002d;4(2):45-56.
22. Tennant RW. The National Center for Toxicogenomics: Using new technologies to inform mechanistic toxicology. Environ Health Perspect 2002;110(1):A8-10.
23. Thomas RS, Rank DR, Penn SG, Zastrow GM, Hayes KR, Pande K, Glover E, Silander T, Craven MW, Reddy JK, Jovanovich SB, Bradfield CA. Identification of toxicologically predictive gene sets using cDNA microarrays. Mol Pharmacol 2001;60(6):1189-94.
24. Olden K, Guthrie J. Genomics: Implications for toxicology. Mutat Res 2001;473(1):3-10.
25. Waters MD, Olden K, Tennant RW. Toxicogenomic approach for assessing toxicant-related disease. Mutat Res 2003a;544(2-3):415-24.
26. Waters MD, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, Olden K, Paules R, Selkirk J, Stasiewicz S, Weis B, Van Houten B, Walker N, Tennant R. Systems toxicology and the chemical effects in biological systems knowledge base. Environ Health Perspect 2003b;111(6):811-24.
27. Lobenhofer EK, Bushel PR, Afshari CA, Hamadeh HK. Progress in the application of DNA microarrays. Environ Health Perspect 2001;109(9):881-91.
28. Burchiel SW, Knall CM, Davis JW, II, Paules RS, Boggs SE, Afshari CA. Analysis of genetic and epigenetic mechanisms of toxicity: Potential roles of toxicoge-nomics and proteomics in toxicology. Toxicol Sci 2001;59(2):193-5.
29. Merrick BA, Tomer KB. Toxicoproteomics: A parallel approach to identifying biomarkers. Environ Health Perspect 2003;111(11):A578-9.
30. Petricoin EF, Rajapaske V, Herman EH, Arekani AM, Ross S, Johann D, Knapton A, Zhang J, Hitt BA, Conrads TP, Veenstra TD, Liotta LA, Sistare FD. Toxicoproteomics: Serum proteomic pattern diagnostics for early detection of drug induced cardiac toxicities and cardioprotection. Toxicol Pathol 2004;32(Suppl 1):122-30.
31. Wilkins MR, Pasquali C, Appel RD, Ou K, Golaz O, Sanchez JC, Yan JX, Gooley AA, Hughes G, Humphery-Smith I, Williams KL, Hochstrasser DF. From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (NY) 1996;14(1):61-5.
32. Griffin JL. Understanding mouse models of disease through metabolomics. Curr Opin Chem Biol 2006;10(4):309-15.
33. Kasper P, Oliver G, Lima BS, Singer T, Tweats D. Joint EFPIA/CHMP SWP workshop: The emerging use of omic technologies for regulatory non-clinical safety testing. Pharmacogenomics 2005;6(2):181-4.
34. Lindon JC, Holmes E, Nicholson JK. Metabonomics techniques and applications to pharmaceutical research & development. Pharm Res 2006;23(6):1075-88.
35. Nurse P. Understanding cells. Nat Biotechnol 2003;424:883.
36. Hamadeh HK, Knight BL, Haugen AC, Sieber S, Amin RP, Bushel PR, Stoll R, Blanchard K, Jayadev S, Tennant RW, Cunningham ML, Afshari CA, Paules RS. Methapyrilene toxicity: Anchorage of pathologic observations to gene expression alterations. Toxicol Pathol 2002c;30:470-482.
37. Zweiger G. Knowledge discovery in gene-expression-microarray data: Mining the information output of the genome. Trends Biotechnol 1999;17(11):429-36.
38. Waring JF, Jolly RA, Ciurlionis R, Lum PY, Praestgaard JT, Morfitt DC, Buratto B, Roberts C, Schadt E, Ulrich RG. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol Appl Pharmacol 2001;175(1):28-42.
39. Mortuza GB, Neville WA, Delaney J, Waterfield CJ, Camilleri P. Characterisation of a potential biomarker of phospholipidosis from amiodarone-treated rats. Biochim Biophys Acta 2003;1631(2):136-46.
40. Kramer JA, Curtiss SW, Kolaja KL, Alden CL, Blomme EAG, Curtiss WC, Davila JC, Jackson CJ, Bunch RT. Acute molecular markers of rodent hepatic carcinogenesis identified by transcription profiling. Chem Res Toxicol 2004;17(4):463-70.
41. Heinloth AN, Irwin RD, Boorman GA, Nettesheim P, Fannin RD, Sieber SO, Snell ML, Tucker CJ, Li L, Travlos GS, Vansant G, Blackshear PE, Tennant RW, Cunningham ML, Paules RS. Gene expression profiling of rat livers reveals indicators of potential adverse effects. Toxicol Sci 2004;80(1):193-202.
42. Hamadeh HK, Bushel PR, Jayadev S, DiSorbo O, Bennett L, Li L, Tennant R, Stoll R, Barrett JC, Paules RS, Blanchard K, Afshari CA. Prediction of compound signature using high density gene expression profiling. Toxicol Sci 2002b;67(2):232-40.
43. Bulera SJ, Eddy SM, Ferguson E, Jatkoe TA, Reindel JF, Bleavins MR, De La Iglesia FA. RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays. Hepatology 2001;33(5):1239-58.
44. Bartosiewicz MJ, Jenkins D, Penn S, Emery J, Buckpitt A. Unique gene expression patterns in liver and kidney associated with exposure to chemical toxicants. J Pharmacol Exp Ther 2001;297(3):895-905.
45. Cutler P, Bell DJ, Birrell HC, Connelly JC, Connor SC, Holmes E, Mitchell BC, Monte SY, Neville BA, Pickford R, Polley S, Schneider K, Skehel JM. An integrated proteomic approach to studying glomerular nephrotoxicity. Electrophoresis 1999;20(18):3647-58.
46. Coen M, Ruepp SU, Lindon JC, Nicholson JK, Pognan F, Lenz EM, Wilson ID. Integrated application of transcriptomics and metabonomics yields new insight into the toxicity due to paracetamol in the mouse. J Pharm Biomed Anal 2004;35(1):93-105.
47. Donald S, Verschoyle RD, Edwards R, Judah DJ, Davies R, Riley J, Dinsdale D, Lopez Lazaro L, Smith AG, Gant TW, Greaves P, Gescher AJ. Hepatobiliary damage and changes in hepatic gene expression caused by the antitumor drug ecteinascidin-743 (ET-743) in the female rat. Cancer Res 2002;62(15):4256-62.
48. Fertuck KC, Eckel JE, Gennings C, Zacharewski TR. Identification of temporal patterns of gene expression in the uteri of immature, ovariectomized mice following exposure to ethynylestradiol. Physiol Genomics 2003;15(2):127-41.
49. Fountoulakis M, de Vera MC, Crameri F, Boess F, Gasser R, Albertini S, Suter L. Modulation of gene and protein expression by carbon tetrachloride in the rat liver. Toxicol Appl Pharmacol 2002;183(1):71-80.
50. Hamadeh HK, Bushel PR, Jayadev S, Martin K, DiSorbo O, Sieber S, Bennett L, Tennant R, Stoll R, Barrett JC, Blanchard K, Paules RS, Afshari CA. Gene expression analysis reveals chemical-specific profiles. Toxicol Sci 2002a;67(2):219-31.
51. Huang Q, Dunn RT, 2nd, Jayadev S, DiSorbo O, Pack FD, Farr SB, Stoll RE, Blanchard KT. Assessment of cisplatin-induced nephrotoxicity by microarray technology. Toxicol Sci 2001;63(2):196-207.
52. Kramer JA, Blomme EA, Bunch RT, Davila JC, Jackson CJ, Jones PF, Kolaja KL, Curtiss SW. Transcription profiling distinguishes dose-dependent effects in the livers of rats treated with clofibrate. Toxicol Pathol 2003;31(4):417-31.
53. Peterson RL, Casciotti L, Block L, Goad ME, Tong Z, Meehan JT, Jordan RA, Vinlove MP, Markiewicz VR, Weed CA, Dorner AJ. Mechanistic toxicogenomic analysis of WAY-144122 administration in Sprague-Dawley rats. Toxicol Appl Pharmacol 2004;196(1):80-94.
54. Ruepp SU, Tonge RP, Shaw J, Wallis N, Pognan F. Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol Sci 2002;65(1):135-50.
55. Waring JF, Gum R, Morfitt D, Jolly RA, Ciurlionis R, Heindel M, Gallenberg L, Buratto B, Ulrich RG. Identifying toxic mechanisms using DNA microarrays: Evidence that an experimental inhibitor of cell adhesion molecule expression signals through the aryl hydrocarbon nuclear receptor. Toxicology 2002;181-182:535-50.
56. Wagenaar GTM, ter Horst SAJ, van Gastelen MA, Leijser LM, Mauad T, van der Velden PA, de Heer E, Hiemstra PS, Poorthuis BJHM, Walther FJ. Gene expression profile and histopathology of experimental bronchopulmonary dysplasia induced by prolonged oxidative stress. Free Rad Biol Med 2004;36(6):782-801.
57. Lu T, Liu J, LeCluyse EL, Zhou YS, Cheng ML, Waalkes MP. Application of cDNA microarray to the study of arsenic-induced liver diseases in the population of Guizhou, China. Toxicol Sci 2001;59(1):185-92.
58. Hamadeh HK, Jayadev S, Gaillard ET, Huang Q, Stoll R, Blanchard K, Chou J, Tucker CJ, Collins J, Maronpot R, Bushel P, Afshari CA. Integration of clinical and gene expression endpoints to explore furan-mediated hepatotoxicity. Mutat Res 2004;549(1-2):169-83.
59. Iida M, Anna CH, Hartis J, Bruno M, Wetmore B, Dubin JR, Sieber S, Bennett L, Cunningham ML, Paules RS, Tomer KB, Houle CD, Merrick AB, Sills RC, Devereux TR. Changes in global gene and protein expression during early mouse liver carcinogenesis induced by non-genotoxic model carcinogens oxazepam and Wyeth-14,643. Carcinogenesis 2003;24(4):757-70.
60. Ellinger-Ziegelbauer H, Stuart B, Wahle B, Bomann W, Ahr HJ. Characteristic expression profiles induced by genotoxic carcinogens in rat liver. Toxicol Sci 2004;77(1):19-34.
61. Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen CF, Nigam R, Kwitek A, Eppig J, Maltais L, Maglott D, Schuler G, Jacob H, Tonellato PJ. Rat Genome Database (RGD): Mapping disease onto the genome. Nucleic Acids Res 2002;30(1):125-8.
62. Higgins MA, Berridge BR, Mills BJ, Schultze AE, Gao H, Searfoss GH, Baker TK, Ryan TP. Gene expression analysis of the acute phase response using a canine microarray. Toxicol Sci 2003;74(2):470-84.
63. Ulrich RG, Rockett JC, Gibson GG, Pettit SD. Overview of an interlaboratory collaboration on evaluating the effects of model hepatotoxicants on hepatic gene expression. Environ Health Perspect 2004;112(4):423-7.
64. Pennie W, Pettit SD, Lord PG. Toxicogenomics in risk assessment: An overview of an HESI collaborative research program. Environ Health Perspect 2004;112(4):417-9.
65. Lindon JC, Nicholson JK, Holmes E, Antti H, Bollard ME, Keun H, Beckonert O, Ebbels TM, Reily MD, Robertson D, Stevens GJ, Luke P, Breau AP, Cantor GH, Bible RH, Niederhauser U, Senn H, Schlotterbeck G, Sidelmann UG, Laursen SM, Tymiak A, Car BD, Lehman-McKeeman L, Colet JM, Loukaci A, Thomas C. Contemporary issues in toxicology the role of metabonomics in toxicology and its evaluation by the COMET project. Toxicol Appl Pharmacol 2003;187(3):137-46.
66. Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA 1997;94(6):2150-5.
67. Merrick BA, Bruno ME. Genomic and proteomic profiling for biomarkers and signature profiles of toxicity. Curr Opin Mol Ther 2004;6(6):600-7.
68. Loeb W, Quimby F, editors. The clinical chemistry of laboratory animals. Philadelphia: Taylor and Francis, 1999.
69. Travlos GS, Morris RW, Elwell MR, Duke A, Rosenblum S, Thompson MB. Frequency and relationships of clinical chemistry and liver and kidney histopathology findings in 13-week toxicity studies in rats. Toxicology 1996;107(1):17-29.
70. Paules R. Phenotypic anchoring: Linking cause and effect. Environ Health Per-spect. 2003;111(6):A338-9.
71. Powell CL, Kosyk O, Ross PK, Schoonhoven R, Boysen G, Swenberg JA, Heinloth AN, Boorman GA, Cunningham ML, Paules RS, Rusyn I. Phenotypic anchoring of acetaminophen-induced oxidative stress with gene expression profiles in rat liver. Toxicol Sci 2006;93:213-22.
72. Guerreiro N, Staedtler F, Grenet O, Kehren J, Chibout SD. Toxicogenomics in drug development. Toxicol Pathol 2003;31(5):471-9.
73. Frank R, Hargreaves R. Clinical biomarkers in drug discovery and development. Nat Rev Drug Discov 2003;2(7):566-80.
74. Kennedy S. The role of proteomics in toxicology: Identification of biomarkers of toxicity by protein expression studies. Biomarkers 2002;7(4):269-90.
75. Gunn L, Smith MT. Emerging biomarker technologies. IARC Sci Publ 2004(157):437-50.
76. Hanash S. Disease proteomics. Nature 2003;422(6928):226-32.
77. Walgren JL, Thompson DC. Application of proteomic technologies in the drug development process. Toxicol Lett 2004;149(1-3):377-85.
78. Wallace KB, Hausner E, Herman E, Holt GD, MacGregor JT, Metz AL, Murphy E, Rosenblum IY, Sistare FD, York MJ. Serum troponins as biomarkers of drug-induced cardiac toxicity. Toxicol Pathol 2004;32(1):106-21.
79. Roberts R, Cain K, Coyle B, Freathy C, Leonard JF, Gautier JC. Early drug safety evaluation: Biomarkers, signatures, and fingerprints. Drug Metab Rev 2003;35(4):269-75.
80. Amacher DE. A toxicologist's guide to biomarkers of hepatic response. Hum Exp Toxicol 2002;21(5):253-62.
81. Lindon JC. Biomarkers: Present concepts and future promise. Preclinica 2003;1(5):221.
82. Bailey WJ, Ulrich R. Molecular profiling approaches for identifying novel biomarkers. Expert Opin Drug Saf 2004;3(2):137-51.
83. Bergmann S, Ihmels J, Barkai N. Iterative signature algorithm for the analysis of large-scale gene expression data. Phys Rev E Stat Nonlin Soft Matter Phys 2003;67(3 Pt 1):031902.
84. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T. Informatics for unveiling hidden genome signatures. Genome Res 2003;13(4):693-702.
85. Choe LH, Dutt MJ, Relkin N, Lee KH. Studies of potential cerebrospinal fluid molecular markers for Alzheimer's disease. Electrophoresis 2002;23(14):2247-51.
86. Bratton SB, Cohen GM. Death receptors leave a caspase footprint that Smacs of XIAP. Cell Death Differ 2003;10(1):4-6.
87. Searfoss GH, Jordan WH, Calligaro DO, Galbreath EJ, Schirtzinger LM, Berridge BR, Gao H, Higgins MA, May PC, Ryan TP. Adipsin, a biomarker of gastrointestinal toxicity mediated by a functional gamma-secretase inhibitor. J Biol Chem 2003;278(46):46107-16.
88. Newton RK, Aardema M, Aubrecht J. The utility of DNA microarrays for characterizing genotoxicity. Environ Health Perspect 2004;112(4):420-2.
89. Petricoin EF, III. Ornstein DK, Paweletz CP, Ardekani A, Hackett PS, Hitt BA, Velassco A, Trucco C, Wiegand L, Wood K, Simone CB, Levine PJ, Linehan WM, Emmert-Buck MR, Steinberg SM, Kohn EC, Liotta LA. Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 2002;94(20):1576-8.
90. Zhang Z, Bast RC, Jr, Yu Y, Li J, Sokoll LJ, Rai AJ, Rosenzweig JM, Cameron B, Wang YY, Meng XY, Berchuck A, Van Haaften-Day C, Hacker NF, de Bruijn HW, van der Zee AG, Jacobs IJ, Fung ET, Chan DW. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res 2004;64(16):5882-90.
91. Ginsburg GS, Haga SB. Translating genomic biomarkers into clinically useful diagnostics. Expert Rev Mol Diagn 2006;6(2):179-91.
92. Badghisi H, Liebler DC. Sequence mapping of epoxide adducts in human hemoglobin with LC-tandem MS and the SALSA algorithm. Chem Res Toxicol 2002;15(6):799-805.
93. Fennell TR, Snyder RW, Krol WL, Sumner SC. Comparison of the hemoglobin adducts formed by administration of N-methylolacrylamide and acrylamide to rats. Toxicol Sci 2003;71(2):164-75.
94. Gao J, Ann Garulacan L, Storm SM, Hefta SA, Opiteck GJ, Lin JH, Moulin F, Dambach DM. Identification of in vitro protein biomarkers of idiosyncratic liver toxicity. Toxicol In Vitro 2004;18(4):533-41.
95. Nerland DE, Cai J, Benz FW. Selective covalent binding of acrylonitrile to Cys 186 in rat liver carbonic anhydrase III in vivo. Chem Res Toxicol 2003;16(5):583-9.
96. Dare TO, Davies HA, Turton JA, Lomas L, Williams TC, York MJ. Application of surface-enhanced laser desorption/ionization technology to the detection and identification of urinary parvalbumin-alpha: A biomarker of compound-induced skeletal muscle toxicity in the rat. Electrophoresis 2002;23(18):3241-51.
97. Hogstrand C, Balesaria S, Glover CN. Application of genomics and proteomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout. Compar Biochem Physiol Part B: Biochem Mol Biol 2002;133(4):523-35.
98. Hestvik AL, Hmama Z, Av-Gay Y. Kinome analysis of host response to mycobacterial infection: A novel technique in proteomics. Infect Immun 2003;71(10):5514-22.
99. Izzotti A, Bagnasco M, Cartiglia C, Longobardi M, De Flora S. Proteomic analysis as related to transcriptome data in the lung of chromium(VI)-treated rats. Int J Oncol 2004;24(6):1513-22.
100. Hirata A, Masuda S, Tamura T, Kai K, Ojima K, Fukase A, Motoyoshi K, Kamakura K, Miyagoe-Suzuki Y, Takeda S. Expression profiling of cytokines and related genes in regenerating skeletal muscle after cardiotoxin injection: A role for osteopontin. Am J Pathol 2003;163(1):203-15.
101. Lame MW, Jones AD, Wilson DW, Segall HJ. Protein targets of 1,4-benzoquinone and 1,4-naphthoquinone in human bronchial epithelial cells. Proteomics 2003;3(4):479-95.
102. Sorensen M, Autrup H, Moller P, Hertel O, Jensen SS, Vinzents P, Knudsen LE, Loft S. Linking exposure to environmental pollutants with biological effects. Mutat Res 2003;544(2-3):255-71.
103. Castegna A, Thongboonkerd V, Klein JB, Lynn B, Markesbery WR, Butterfield DA. Proteomic identification of nitrated proteins in Alzheimer's disease brain. J Neurochem 2003;85(6):1394-401.
104. Fessler MB, Malcolm KC, Duncan MW, Worthen GS. A genomic and proteomic analysis of activation of the human neutrophil by lipopolysaccharide and its mediation by p38 mitogen-activated protein kinase. J Biol Chem 2002;277(35):31291-302.
105. Heijne WH, Stierum RH, Slijper M, van Bladeren PJ, van Ommen B. Toxicoge-nomics of bromobenzene hepatotoxicity: A combined transcriptomics and pro-teomics approach. Biochem Pharmacol 2003;65(5):857-75.
106. Bandara LR, Kelly MD, Lock EA, Kennedy S. A correlation between a pro-teomic evaluation and conventional measurements in the assessment of renal proximal tubular toxicity. Toxicol Sci 2003;73(1):195-206.
107. Bruno ME, Borchers CH, Dial JM, Walker NJ, Hartis JE, Wetmore BA, Carl Barrett JC, Tomer KB, Merrick BA. Effects of TCDD upon IkappaB and IKK subunits localized in microsomes by proteomics. Arch Biochem Biophys 2002;406(2):153-64.
108. Dapas B, Tell G, Scaloni A, Pines A, Ferrara L, Quadrifoglio F, Scaggiante B. Identification of different isoforms of eEF1A in the nuclear fraction of human T-lymphoblastic cancer cell line specifically binding to aptameric cytotoxic GT oligomers. Eur J Biochem 2003;270(15):3251-62.
109. Mikhailov A, Harmala-Brasken AS, Hellman J, Meriluoto J, Eriksson JE. Identification of ATP-synthase as a novel intracellular target for microcystin-LR. Chem Biol Interact 2003;142(3):223-37.
110. Venkatraman A, Landar A, Davis AJ, Ulasova E, Page G, Murphy MP, Darley-Usmar V, Bailey SM. Oxidative modification of hepatic mitochondria protein thiols: Effect of chronic alcohol consumption. Am J Physiol Gastrointest Liver Physiol 2004;286(4):G521-7.
111. Patterson SD. Proteomics: Evolution of the technology. Biotechniques 2003;35(3):440-4.
112. Pieper R, Su Q, Gatlin CL, Huang ST, Anderson NL, Steiner S. Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 2003;3(4):422-32.
113. Anderson NL, Anderson NG. The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 2002;1(11):845-67.
114. Adkins JN, Varnum SM, Auberry KJ, Moore RJ, Angell NH, Smith RD, Springer DL, Pounds JG. Toward a human blood serum proteome: Analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics 2002;1(12):947-55.
115. Pieper R, Gatlin CL, Makusky AJ, Russo PS, Schatz CR, Miller SS, Su Q, McGrath AM, Estock MA, Parmar PP, Zhao M, Huang ST, Zhou J, Wang F, Esquer-Blasco R, Anderson NL, Taylor J, Steiner S. The human serum proteome: Display of nearly 3700 chromatographically separated protein spots on twodimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 2003;3(7):1345-64.
116. Tirumalai RS, Chan KC, Prieto DA, Issaq HJ, Conrads TP, Veenstra TD. Characterization of the low molecular weight human serum proteome. Mol Cell Proteomics 2003;2(10):1096-103.
117. Merrick BA. The human proteome organization (HUPO) and environmental health. EHP Toxicogenomics 2003;111(1t):1-5.
118. Vitorino R, Lobo MJ, Ferrer-Correira AJ, Dubin JR, Tomer KB, Domingues PM, Amado FM. Identification of human whole saliva protein components using proteomics. Proteomics 2004;4(4):1109-15.
119. Pieper R, Gatlin CL, McGrath AM, Makusky AJ, Mondal M, Seonarain M, Field E, Schatz CR, Estock MA, Ahmed N, Anderson NG, Steiner S. Characterization of the human urinary proteome: A method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 2004;4(4):1159-74.
120. Puchades M, Hansson SF, Nilsson CL, Andreasen N, Blennow K, Davidsson P. Proteomic studies of potential cerebrospinal fluid protein markers for Alzheimer's disease. Brain Res Mol Brain Res 2003;118(1-2):140-6.
121. Jiang L, Lindpaintner K, Li HF, Gu NF, Langen H, He L, Fountoulakis M. Pro-teomic analysis of the cerebrospinal fluid of patients with schizophrenia. Amino Acids 2003;25(1):49-57.
122. Kennedy S. Proteomic profiling from human samples: The body fluid alternative. Toxicol Lett 2001;120(1-3):379-84.
123. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Bio-technol 1999;17(10):994-9.
124. Duan XJ, Xenarios I, Eisenberg D. Describing biological protein interactions in terms of protein states and state transitions: The LiveDIP database. Mol Cell Proteomics 2002;1(2):104-16.
125. Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 2002;1(4):323-33.
126. Washburn MP, Koller A, Oshiro G, Ulaszek RR, Plouffe D, Deciu C, Winzeler E, Yates JR, III. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003;100(6):3107-12.
127. Weinreb O, Mandel S, Youdim MB. cDNA gene expression profile homology of antioxidants and their antiapoptotic and proapoptotic activities in human neuroblastoma cells. FASEB J 2003;17(8):935-7.
128. Kern W, Kohlmann A, Wuchter C, Schnittger S, Schoch C, Mergenthaler S, Ratei R, Ludwig WD, Hiddemann W, Haferlach T. Correlation of protein expression and gene expression in acute leukemia. Cytometry 2003;55B(1):29-36.
129. McRedmond JP, Park SD, Reilly DF, Coppinger JA, Maguire PB, Shields DC, Fitzgerald DJ. Integration of proteomics and genomics in platelets: A profile of platelet proteins and platelet-specific genes. Mol Cell Proteomics 2004;3(2):133-44.
130. Hu Y, Hines LM, Weng H, Zuo D, Rivera M, Richardson A, LaBaer J. Analysis of genomic and proteomic data using advanced literature mining. J Proteome Res 2003;2(4):405-12.
131. Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, Stahl E, Bolouri MS, Ray HN, Sihag S, Kamal M, Patterson N, Lander ES, Mann M. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 2003;115(5):629-40.
132. Thompson KL, Afshari CA, Amin RP, Bertram TA, Car B, Cunningham M, Kind Cl, Kramer JA, Lawton M, Mirsky M, Naciff JM, Oreffo V, Pine PS, Sistare FD. Identification of platform-independent gene expression markers of cisplatin nephrotoxicity. Environ Health Perspect 2004;112(4):488-94.
133. Kramer JA, Pettit SD, Amin RP, Bertram TA, Car B, Cunningham M, Curtiss SW, Davis JW, Kind C, Lawton M, Naciff JM, Oreffo V, Roman RJ, Sistare FD, Stevens J, Thompson K, Vickers AE, Wild S, Afshari CA. Overview on the application of transcription profiling using selected nephrotoxicants for toxicology assessment. Environ Health Perspect 2004;112(4):460-4.
134. Baker VA, Harries HM, Waring JF, Duggan CM, Ni HA, Jolly RA, Yoon LW, De Souza AT, Schmid JE, Brown RH, Ulrich RG, Rockett JC. Clofibrate-induced gene expression changes in rat liver: A cross-laboratory analysis using membrane cDNA arrays. Environ Health Perspect 2004;112(4):428-38.
135. Chu TM, Deng S, Wolfinger R, Paules RS, Hamadeh HK. Cross-site comparison of gene expression data reveals high similarity. Environ Health Perspect 2004;112(4):449-55.
136. Waring JF, Ulrich RG, Flint N, Morfitt D, Kalkuhl A, Staedtler F, Lawton M, Beekman JM, Suter L. Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene. Environ Health Perspect 2004;112(4):439-48.
137. Smith LL. Key challenges for toxicologists in the 21st century. Trends Pharmacol Sci 2001;22(6):281-5.
138. Juan HF, Lin JYC, Chang WH, Wu CY, Pan TL, Tseng MJ, Khoo KH, Chen ST. Biomic study of human meyloid leukemia cells differentiation to macrophages using DNA array, proteomic, and bioinformatic analytical methods. Electrophoresis 2002;23(15):2490-504.
139. Amin RP, Hamadeh HK, Bushel PR, Bennett L, Afshari CA, Paules RS. Genomic interrogation of mechanism(s) underlying cellular responses to toxicants. Toxicology 2002;181-82:555-63.
140. Kita Y, Shiozawa M, Jin W, Majewski RR, Besharse JC, Greene AS, Jacob HJ. Implications of circadian gene expression in kidney, liver and the effects of fasting on pharmacogenomic studies. Pharmacogenetics 2002;12(1):55-65.
141. Kaput J, Rodriguez RL. Nutritional genomics: The next frontier in the post-genomic era. Physiol Genomics 2004;16(2):166-77.
142. Kaput J. Diet-disease gene interactions. Nutrition 2004;20(1):26-31.
143. Klein TE, Altman RB. PharmGKB: The pharmacogenetics nad pharmacogenom-ics knowledge base. Pharmacogenomics J. 2004;4(1):1.
144. Wittliff JL, Erlander MG. Laser capture microdissection and its applications in genomics and proteomics. Meth Enzymol 2002;356:12-25.
145. Jain KK. Application of laser capture microdissection to proteomics. Meth Enzymol 2002;356:157-67.
146. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA. Laser capture microdissection. Science 1996;274(5289):998-1001.
147. Bonner RF, Emmert-Buck M, Cole K, Pohida T, Chuaqui R, Goldstein S, Liotta LA. Laser capture microdissection: Molecular analysis of tissue. Science 1997;278(5342):1481,1483.
148. Karsten SL, Van Deerlin VM, Sabatti C, Gill LH, Geschwind DH. An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res 2002;30(2):E4.
149. Hamadeh HK, Bushel P, Tucker CJ, Martin K, Paules R, Afshari CA. Detection of diluted gene expression alterations using cDNA microarrays. Biotechniques 2002e;32(2):322,324,326-9.
150. Huang RP. Detection of multiple proteins in an antibody-based protein microarray system. J Immunol Meth 2001;255(1-2):1-13.
151. Merchant M, Weinberger SR. Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis 2000;21(6):1164-77.
152. Liotta L, Petricoin E. Molecular profiling of human cancer. Nat Rev Genet 2000;1(1):48-56.
153. Herbert A. The four Rs of RNA-directed evolution. Nat Genet 2004;36(1):19-25.
154. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, 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 AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, et al. The sequence of the human genome. Science 2001;291(5507):1304-51.
155. McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, et al. A physical map of the human genome. Nature 2001;409(6822):934-41.
156. Shearstone JR, Wang YE, Clement A, Allaire NE, Yang C, Worley DS, Carulli JP, Perrin S. Application of functional genomic technologies in a mouse model of retinal degeneration. Genomics 2005;85(3):309-21.
157. Benard J, Douc-Rasy S, Ahomadegbe JC. TP53 family members and human cancers. Hum Mutat 2003;21(3):182-91.
158. Courtois S, de Fromentel CC, Hainaut P. p53 protein variants: Structural and functional similarities with p63 and p73 isoforms. Oncogene 2004;23(3):631-8.
159. Demonacos C, La Thangue NB. Drug discovery and the p53 family. Prog Cell Cycle Res 2003;5:375-82.
160. Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M. A question of size: The eukaryotic proteome and the problems in defining it. Nucleic Acids Res 2002;30(5):1083-90.
161. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI. Directed proteomic analysis of the human nucleolus. Curr Biol 2002;12(1):1-11.
162. Wu CC, MacCoss MJ, Mardones G, Finnigan C, Mogelsvang S, Yates JR III, Howell KE. Organellar proteomics reveals Golgi arginine dimethylation. Mol Biol Cell 2004;15(6):2907-19.
163. Liu ZX, Kaplowitz N. Immune-mediated drug-induced liver disease. Clin Liver Dis 2002;6(3):467-86.
164. Ju C, Pohl LR. Immunohistochemical detection of protein adducts of 2,4-dinitrochlorobenzene in antigen presenting cells and lymphocytes after oral administration to mice: Lack of a role of Kupffer cells in oral tolerance. Chem Res Toxicol 2001;14(9):1209-17.
165. Ju C, Uetrecht JP. Mechanism of idiosyncratic drug reactions: Reactive metabolite formation, protein binding and the regulation of the immune system. Curr Drug Metab 2002;3(4):367-77.
166. Quackenbush J. Computational analysis of microarray data. Nat Rev Genet 2001;2(6):418-27.
167. Farland WH. The U.S. Environmental Protection Agency's Risk Assessment Guidelines: Current status and future directions. Toxicol Ind Health 1992;8(3):205-12.
168. Farland WH. Cancer risk assessment: Evolution of the process. Prev Med 1996;25(1):24-5.
169. Larsen JC, Farland W, Winters D. Current risk assessment approaches in different countries. Food Addit Contam 2000;17(4):359-69.
170. Begley TJ, Rosenbach AS, Ideker T, Samson LD. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res 2002;1(2):103-12.
171. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH. Functional discovery via a compendium of expression profiles. Cell 2000;102(1):109-26.
172. Lewis F, Maughan NJ, Smith V, Hillan K, Quirke P. Unlocking the archive-Gene expression in paraffin-embedded tissue. J Pathol 2001;195(1):66-71.
173. Wetmore B, Merrick BA. Toxicoproteomics: Proteomics applied to toxicology and pathology. Toxicol Pathol 2004;32:619-42.
174. Stuart GW, Berry MW. A comprehensive whole genome bacterial phylogeny using correlated peptide motifs defined in a high dimensional vector space. J Bioinform Comput Biol 2003;1(3):475-93.
175. Chaussabel D, Sher A. Mining microarray expression data by literature profiling. Genome Biol 2002;3(10):RESEARCH0055.
176. Sluka JP. Extracting knowledge from genomic experiments by incorporating the biomedical literature. In: Lin SM, Johnson KF, editors, Methods of microarray data analysis II Boston: Kluwer Academics, 2002.
177. Patterson SD, Aebersold RH. Proteomics: The first decade and beyond. Nat Genet 2003;33(Suppl):311-23.
178. Davis TN. Protein localization in proteomics. Curr Opin Chem Biol 2004;8(1):49-53.
179. Zhu H, Bilgin M, Snyder M. Proteomics. An Rev Biochem 2003;72:783-812.
180. Wolters DA, Washburn MP, Yates JR, III. An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 2001;73(23):5683-90.
181. MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI, Yates JR, III. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci USA 2002;99(12):7900-5.
182. Dongre AR, Opiteck G, Cosand WL, Hefta SA. Proteomics in the postgenome age. Biopolymers 2001;60(3):206-11.
183. Cordwell SJ, Nouwens AS, Verrills NM, Basseal DJ, Walsh BJ. Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels. Electrophoresis 2000;21(6):1094-103.
184. Dreger M. Subcellular proteomics. Mass Spectrom Rev 2003;22(1):27-56.
185. Schirmer EC, Florens L, Guan T, Yates JR, III, Gerace L. Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science 2003;301(5638):1380-2.
186. Ping P. Identification of novel signaling complexes by functional proteomics. Circ Res 2003;93(7):595-603.
187. Lee CL, Hsiao HH, Lin CW, Wu SP, Huang SY, Wu CY, Wang AH, Khoo KH. Strategic shotgun proteomics approach for efficient construction of an expression map of targeted protein families in hepatoma cell lines. Proteomics 2003;3(12):2472-86.
188. Nicholson JK, Connelly J, Lindon JC, Holmes E. Metabonomics: A platform for studying drug toxicity and gene function. Nat Rev Drug Discov 2002;1(2):153-61.
189. Xirasagar S, Gustafson S, Merrick BA, Tomer KB, Stasiewicz S, Chan DD, Yost KJ, III, Yates JR, III, Sumner S, Xiao N, Waters MD. CEBS object model for systems biology data, SysBio-OM. Bioinformatics 2004;20(13):2004-15.
190. Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ, III, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD. Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: Design and application. Bioinformatics 2006;22(7):874-82.
191. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215(3):403-10.
192. Petricoin EF, III, Hackett JL, Lesko LJ, Puri RK, Gutman SI, Chumakov K, Woodcock J, Feigal DW, Jr, Zoon KC, Sistare FD. Medical applications of microarray technologies: A regulatory science perspective. Nat Genet 2002;32(Suppl):474-9.
193. Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002;30(1):207-10.
194. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Jr, Boyer JL. Promoting comparative molecular studies in environmental health research: An overview of the comparative toxicogenomics database (CTD). Pharmacogenomics J 2004;4(1):5-8.
195. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress-A public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003;31(1):68-71.
196. Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J. Standards for microarray data. Science 2002;298(5593):539.
197. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-Toward standards for microarray data. Nat Genet 2001;29(4):365-71.
198. Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y. CIBEX: Center for information biology gene expression database. CR Biol 2003;326(10-11):1079-82.
199. Bartosiewicz M, Trounstine M, Barker D, Johnston R, Buckpitt A. Development of a toxicological gene array and quantitative assessment of this technology. Arch Biochem Biophys 2000;376(1):66-73.
200. Jiang XS, Zhou H, Zhang L, Sheng QH, Li SJ, Li L, Hao P, Li YX, Xia QC, Wu JR, Zeng R. A high-throughput approach for subcellular proteome: Identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis. Mol Cell Proteomics 2004;3(5):441-55.
201. Talamo F, D'Ambrosio C, Arena S, Del Vecchio P, Ledda L, Zehender G, Ferrara L, Scaloni A. Proteins from bovine tissues and biological fluids: Defining a reference electrophoresis map for liver, kidney, muscle, plasma and red blood cells. Proteomics 2003;3(4):440-60.
202. Reddy PH, McWeeney S, Park BS, Manczak M, Gutala RV, Partovi D, Jung J, Yau V, Searles R, Mori M, Quinn J. Gene expression profiles of transcripts in amyloid precursor protein transgenic mice: Up-regulation of mitochondrial metabolism and apoptotic genes is an early cellular change in Alzheimer's disease. Hum Mol Genet 2004;13(12):1225-40.
203. Weiss A, Delproposto J, Giroux CN. High-throughput phenotypic profiling of gene-environment interactions by quantitative growth curve analysis in Saccha-romyces cerevisiae. Anal Biochem 2004;327(1):23-34.
204. Fountoulakis M, Berndt P, Boelsterli UA, Crameri F, Winter M, Albertini S, Suter L. Two-dimensional database of mouse liver proteins: Changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioiso-mer 3-acetamidophenol. Electrophoresis 2000;21(11):2148-61.
205. Lee WM. Drug-induced hepatotoxicity. N Engl J Med 2003;349(5):474-85.
206. Xie T, Tong L, Barrett T, Yuan J, Hatzidimitriou G, McCann UD, Becker KG, Donovan DM, Ricaurte GA. Changes in gene expression linked to methamphet-amine-induced dopaminergic neurotoxicity. J Neurosci 2002;22(1):274-83.
207. Dam K, Seidler FJ, Slotkin TA. Transcriptional biomarkers distinguish between vulnerable periods for developmental neurotoxicity of chlorpyrifos: Implications for toxicogenomics. Brain Res Bull 2003;59(4):261-5.
208. Hamadeh HK, Trouba KJ, Amin RP, Afshari CA, Germolec D. Coordination of altered DNA repair and damage pathways in arsenite-exposed keratinocytes. Toxicol Sci 2002;69(2):306-16.
209. Hu D, Cao K, Peterson-Wakeman R, Wang R. Altered profile of gene expression in rat hearts induced by chronic nicotine consumption. Biochem Biophys Res Commun 2002;297(4):729-36.
210. Waring JF, Ciurlionis R, Jolly RA, Heindel M, Ulrich RG. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett 2001;120(1-3):359-68.
211. Hamadeh HK, Bushel P, Paules R, Afshari CA. Discovery in toxicology: Mediation by gene expression array technology. J Biochem Mol Toxicol 2001;15(5):231-42.
212. Witzmann FA, Bobb A, Briggs GB, Coppage HN, Hess RA, Li J, Pedrick NM, Ritchie GD, Iii JR, Still KR. Analysis of rat testicular protein expression following 91-day exposure to JP-8 jet fuel vapor. Proteomics 2003;3(6):1016-27.
213. Huang Q, Jin X, Gaillard ET, Knight BL, Pack FD, Stoltz JH, Jayadev S, Blanchard KT. Gene expression profiling reveals multiple toxicity endpoints induced by hepatotoxicants. Mutat Res 2004;549(1-2):147-67.
214. Adachi T, Koh KB, Tainaka H, Matsuno Y, Ono Y, Sakurai K, Fukata H, Iguchi T, Komiyama M, Mori C. Toxicogenomic difference between diethylstilbestrol and 17beta-estradiol in mouse testicular gene expression by neonatal exposure. Mol Reprod Dev 2004;67(1):19-25.
215. Nadadur SS, Schladweiler MC, Kodavanti UP. A pulmonary rat gene array for screening altered expression profiles in air pollutant-induced lung injury. Inhal Toxicol 2000;12(12):1239-54.
216. Akhtar RA, Reddy AB, Maywood ES, Clayton JD, King VM, Smith AG, Gant TW, Hastings MH, Kyriacou CP. Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr Biol 2002;12(7):540-50.
217. Heijne WH, Slitt AL, Van Bladeren PJ, Groten JP, Klaassen CD, Stierum RH, Van Ommen B. Bromobenzene-induced hepatotoxicity at the transcriptome level. Toxicol Sci 2004;79(2):411-22.
218. Bajzer Z, Randic M, Plavsic D, Basak SC. Novel map descriptors for characterization of toxic effects in proteomics maps. J Mol Graph Model 2003;22(1):1-9.
219. Bandara LR, Kelly MD, Lock EA, Kennedy S. A potential biomarker of kidney damage identified by proteomics: Preliminary findings. Biomarkers 2003;8(3-4):272-86.
220. Charlwood J, Skehel JM, King N, Camilleri P, Lord P, Bugelski P, Atif U. Proteomic analysis of rat kidney cortex following treatment with gentamicin. J Proteome Res 2002;1(1):73-82.
221. Drake MG, Witzmann FA, Hyde J, Witten ML. JP-8 jet fuel exposure alters protein expression in the lung. Toxicology 2003;191(2-3):199-210.
222. Imanishi S, Harada K. Proteomics approach on microcystin binding proteins in mouse liver for investigation of microcystin toxicity. Toxicon 2004;43(6):651-9.
223. Jin J, Yang J, Gao Z, Yu Y. Proteomic analysis of cellular responses to low concentration N-methyl-N'-nitro-N-nitrosoguanidine in human amnion FL cells. Environ Mol Mutagen 2004;43(2):93-9.
224. Keightley JA, Shang L, Kinter M. Proteomic analysis of oxidative stres-resistant cells: A specific role for aldose reductase overexpression in cytoprotection. Mol Cell Proteomics 2004;3(2):167-75.
225. Kleno TG, Leonardsen LR, Kjeldal HO, Laursen SM, Jensen ON, Baunsgaard D. Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis. Proteomics 2004;4(3):868-80.
226. Krapfenbauer K, Berger M, Lubec G, Fountoulakis M. Changes in the brain protein levels following administration of kainic acid. Electrophoresis 2001;22(10):2086-91.
227. Krayl M, Benndorf D, Loffhagen N, Babel W. Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyl tert-butyl ether in Pseudomonas putida KT2440. Proteomics 2003;3(8):1544-52.
228. Kristensen DB, Kawada N, Imamura K, Miyamoto Y, Tateno C, Seki S, Kuroki T, Yoshizato K. Proteome analysis of rat hepatic stellate cells. Hepatology 2000;32(2):268-77.
229. Lee YM, Park SH, Chung KC, Oh YJ. Proteomic analysis reveals upregulation of calreticulin in murine dopaminergic neuronal cells after treatment with 6-hydroxydopamine. Neurosci Lett 2003;352(1):17-20.
230. Macdonald N, Chevalier S, Tonge R, Davison M, Rowlinson R, Young J, Rayner S, Roberts R. Quantitative proteomic analysis of mouse liver response to the peroxisome proliferator diethylhexylphthalate (DEHP). Arch Toxicol 2001;75(7):415-24.
231. Man WJ, White IR, Bryant D, Bugelski P, Camilleri P, Cutler P, Heald G, Lord PG, Wood J, Kramer K. Protein expression analysis of drug-mediated hepatotox-icity in the Sprague-Dawley rat. Proteomics 2002;2(11):1577-85.
232. Marengo E, Robotti E, Gianotti V, Righetti PG, Cecconi D, Domenici E. A new integrated statistical approach to the diagnostic use of two-dimensional maps. Electrophoresis 2003;24(1-2):225-36.
233. Meneses-Lorente G, Guest PC, Lawrence J, Muniappa N, Knowles MR, Skynner HA, Salim K, Cristea I, Mortishire-Smith R, Gaskell SJ, Watt A. A proteomic investigation of drug-induced steatosis in rat liver. Chem Res Toxicol 2004;17(5):605-12.
234. Moller A, Soldan M, Volker U, Maser E. Two-dimensional gel electrophoresis: A powerful method to elucidate cellular responses to toxic compounds. Toxicology 2001;160(1-3):129-38.
235. Sharma R, Komatsu S, Noda H. Proteomic analysis of brown planthopper: Application to the study of carbamate toxicity. Insect Biochem Mol Biol 2004;34(5):425-32.
236. Shepard JL, Olsson B, Tedengren M, Bradley BP. Protein expression signatures identified in Mytilus edulis exposed to PCBs, copper and salinity stress. Mar Environ Res 2000;50(1-5):337-40.
237. Shrader EA, Henry TR, Greeley MS, Jr, Bradley BP. Proteomics in zebrafish exposed to endocrine disrupting chemicals. Ecotoxicology 2003;12(6):485-8.
238. Son WK, Lee DY, Lee SH, Joo WA, Kim CW. Analysis of proteins expressed in rat plasma exposed to dioxin using 2-dimensional gel electrophoresis. Proteomics 2003;3(12):2393-401.
239. Steiner S, Gatlin CL, Lennon JJ, McGrath AM, Seonarain MD, Makusky AJ, Aponte AM, Esquer-Blasco R, Anderson NL. Cholesterol biosynthesis regulation and protein changes in rat liver following treatment with fluvastatin. Toxicol Lett 2001;120(1-3):369-77.
240. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Pro-teomics 2001;1(3):377-96.
241. Toussaint O, Dumont P, Dierick JF, Pascal T, Frippiat C, Chainiaux F, Magalhaes JP, Eliaers F, Remacle J. Stress-induced premature senescence as alternative toxicological method for testing the long-term effects of molecules under development in the industry. Biogerontology 2000;1(2):179-83.
242. Vido K, Spector D, Lagniel G, Lopez S, Toledano MB, Labarre J. A proteome analysis of the cadmium response in Saccharomyces cerevisiae. J Biol Chem 2001;276(11):8469-74.
243. Wattiez R, Noel-Georis I, Cruyt C, Broeckaert F, Bernard A, Falmagne P. Susceptibility to oxidative stress: Proteomic analysis of bronchoalveolar lavage from ozone-sensitive and ozone-resistant strains of mice. Proteomics 2003;3(5):658-65.
244. Wheelock AM, Zhang L, Tran MU, Morin D, Penn S, Buckpitt AR, Plopper CG. Isolation of rodent airway epithelial cell proteins facilitates in vivo proteomics studies of lung toxicity. Am J Physiol Lung Cell Mol Physiol 2004;286(2):L399-410.
245. Witzmann FA, Bauer MD, Fieno AM, Grant RA, Keough TW, Kornguth SE, Lacey MP, Siegel FL, Sun Y, Wright LS, Young RS, Witten ML. Proteomic analysis of simulated occupational jet fuel exposure in the lung. Electrophoresis 1999;20(18):3659-69.
246. Witzmann FA, Bauer MD, Fieno AM, Grant RA, Keough TW, Lacey MP, Sun Y, Witten ML, Young RS. Proteomic analysis of the renal effects of simulated occupational jet fuel exposure. Electrophoresis 2000;21(5):976-84.
247. Zhang Y, Champagne N, Beitel LK, Goodyer CG, Trifiro M, LeBlanc A. Estrogen and androgen protection of human neurons against intracellular amyloid beta1-42 toxicity through heat shock protein 70. J Neurosci 2004;24(23):5315-21.
248. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. The HUPO PSI's molecular interaction format-A community standard for the representation of protein interaction data. Nat Biotechnol 2004;22(2):177-83.
249. Jones A, Hunt E, Wastling J, Pizarro A, Stoeckert CJ, Jr. An object model and database for functional genomics. Bioinformatics 2004;20(10):1583-90.
250. Orchard S, Hermjakob H, Julian RK, Jr, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R. Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics 2004;4(2):490-1.