Systems toxicology and the chemical effects in biological systems (CEBS) knowledge base

Environmental Health Perspectives

Volumn 111, Issue 1 T, 2003, Pages 15-28

  Waters, Michael D ^a   Boorman, Gary ^a   Bushel, Pierre ^a   Cunningham, Michael ^a   Irwin, Rick ^a   Merrick, Alex ^a   Olden, Kenneth ^a   Paules, Richard ^a   Selkirk, James ^a   Stasiewicz, Stanley ^a   Weis, Brenda ^a   Van Houten, Ben ^a   Walker, Nigel ^a   Tennant, Raymond ^a  

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

Author keywords

Bioinformatics; Compendia; Database; Gene expression; Global query; Heuristic algorithms; Knowledge base; Linkage disequilibrium; Metabonomics; Microarray; Molecular expression; Ontologies; Phenotype; Phenotypic anchoring; Proteomics; Sequence; Single nucleotide polymorphisms; Systems biology; Systems toxicology; Toxicogenomics; Transcription factors

Indexed keywords

CHEMICAL AGENT;

BIOINFORMATICS; BLAST (COMPUTER PROGRAM); CHEMICAL EFFECTS IN BIOLOGICAL SYSTEM KNOWLEDGE BASE; CHEMICAL STRUCTURE; DOSE TIME EFFECT RELATION; DRUG SAFETY; ENVIRONMENTAL DISEASE; ENVIRONMENTAL HEALTH; FACTUAL DATABASE; FUNGAL GENE; GENBANK; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; GENETIC TRANSCRIPTION; GENOMICS; HUMAN; HYPOTHESIS; KNOCKOUT GENE; METABOLISM; METABOLITE; METABONOMICS; MOLECULAR BIOLOGY; NONHUMAN; NUCLEIC ACID DATABASE; PATHOLOGY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; REVIEW; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES; STRESS; TOXICOGENOMICS; TOXICOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES; GENE EXPRESSION PROFILING; HUMANS; KNOWLEDGE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHARMACOGENETICS; PHENOTYPE; PROTEIN ARRAY ANALYSIS; PROTEOMICS;

EID: 0037255214     PISSN: 00916765     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (70)

1. Aardema MJ, MacGregor JT. 2002. Toxicology and genetic toxicology in the new era of "toxicogenomics": impact of "-omics" technologies. Mutat Res 499(1):13-25.
2. Afshari CA. 2002. Perspective: microarray technology, seeing more than spots. Endocrinology 143(6):1983-1989.
3. Alaiya AA, Franzen B, Hagman A, Dysvik B, Roblick UJ, Becker S, et al. 2002. Molecular classification of borderline ovarian tumors using hierarchical cluster analysis of protein expression profiles. Int J Cancer 98(6):895-899.
4. Alizadeh Aa, Ross DT, Perou CM, van de Rijn M. 2001. Towards a novel classification of human malignancies based on gene expression patterns. J Pathol 195(1):41-52.
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3):403-410.
6. Bartosiewicz MJ, Jenkins D, Penn S, Emery J, Buckpitt A. 2001. Unique gene expression patterns in liver and kidney associated with exposure to chemical toxicants. J Pharmacol Exp Ther 297(3):895-905.
7. Bessems JG, Vermeulen NP. 2001. Paracetamol (acetaminophen)-induced toxicity: molecular and biochemical mechanisms, analogues and protective approaches. Crit Rev Toxicol 31(1):55-138.
8. Boorman GA, Anderson SP, Casey WM, Brown RH, Crosby LM, Gottschalk K, et al. 2002. Toxicogenomics, drug discovery, and the pathologist. Toxicol Pathol 30(1):15-27.
9. Brazman a, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, et al. 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365-371.
10. Bundy JG, Spurgeon DJ, Svendsen C, Hankard PK, Osborn D, Lindon JC, et al. 2002. Earthworm species of the genus Eisenia can be phenotypically differentiated by metabolic profiling. FEBS Lett 521(1-3):115-120.
11. Burchiel SW, Knall CM, Davis JW II, Paules RS, Boggs SE, Afshari CA. 2001. Analysis of genetic and epigenetic mechanisms of toxicity: potential roles of toxicogenomics and proteomics in toxicology. Toxicol Sci 59(2):193-195.
12. Bushel PR, Hamadeh H, Bennett L, Sieber S, Martin K, Nuwaysir EF, et al. 2001. MAPS: a microarray project system for gene expression experiment information and data validation. Bioinformatics 17(6):564-565.
13. Castle AL, Carver MP, Mendrick DL. 2002. Toxicogenomics: a new revolution in drug safety. Drug Discov Today 7(13):728-736.
14. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, et al. 1998. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282(5396):2022-2028.
15. Culetto E, Sattelle DB. 2000. A role for Caenorhabditis elegans in understanding the function and interactions of human disease genes. Hum Mol Genet 9(6):869-877.
16. Cunningham MJ, Liang S, Fuhrman S, Seilhamer JJ, Somogyi R. 2000. Gene expression microarray data analysis for toxicology profiling. Ann NY Acad Sci 919:52-67.
17. Dudley AM, Aach J, Steffen MA, Church GM. 2002. Measuring absolute expression with microarrays with a calibrated reference sample and in extended signal intensity range. Proc Natl Acad Sci U S A 99(11):7554-7559.
18. Edgar R, Domrachev M, Lash AE. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acid Res 20(1):207-210.
19. Ermolaeva O, Rastogi M, Pruitt KD, Schuler GD, Bittner ML, Chen Y, et al. 1998. Data management and analysis for gene expression arrays. Nat Genet 29(1):19-23.
20. Farland WH. 1992. The U.S. Environmental Protection Agency's Risk Assessment Guidelines: current status and future directions. Toxicol Ind Health 8(3):205-212.
21. Farland WH. 1996. Cancer risk assessment: evolution of the process. Prev Med 25(1):24-25.
22. Fielden MR, Zacharewski TR. 2001. Challenges and limitations of gene expression profiling in mechanistics and predictive toxicology. Toxicol Sci 60(1):6-10.
23. Forde CE, Gonzales AD, Smessaert JM, Murphy GA, Shields SJ, Fitch JP, et al. 2002. A rapid method to capture and screen for transcription factors by SELDI mass spectrometry. Biochem Biophys Res Commun 290(4):1328-1335.
24. Gibas C, Jambeck P. 2001. Developing Bioinformatics Computer Skills. Sebastopol, CA:O'Reilly & Associates, Inc.
25. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, et al. 1999. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439):531-537.
26. Hamadeh HK, Amin RP, Paules RS, Afshari CA. 2002a. An overview of toxicogenomics. Curr Issues Mol Biol 4(2):45-56.
27. Hamadeh HK, Bushel PR, Jayadev S, DiSorbo O, Bennett L, Li L, et al. 2002b. Prediction of compound signature using high density gene expression profiling. Toxicol Sci 67(2):232-240.
28. Hamadeh HK, Bushel PR, Jayadev S, Martin K, DiSorbo O, Sieber S, et al. 2002c. Gene expression analysis reveals chemical-specific profiles. Toxicol Sci 67(2):219-231.
29. Hamadeh HK, Knight BL, Haugen AC, Sieber S, Amin RP, Bushel PR, et al. 2002d. Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations. Toxicol Pathol 30:470-482.
30. Holmes E, Nicholls AW, Lindon JC, Connor SC, Connelly JC, Haselden JN, et al 2000. Chemometric models for toxicity classification based on NMR spectra of biofluids. Chem Res Toxicol 13(6):471-478.
31. Holmes E, Nicholson JK, Tranter G. 2001. Metabonomic characterization of genetic variations in toxicological and metabolic responses using probabilistic neural networks. Chem Res Toxicol 14(2):182-191.
32. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, et al. 2000. Functional discovery via a compendium of expression profiles. Cell 102(1):109-126.
33. Ideker T, Galitski T, Hood L. 2001. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2:343-372.
34. Issaq HJ, Veenstra TD, Conrads TP, Felschow D. 2002. The SELDI-TOF MS approach to proteomics:protein profiling and biomarker identification. Biochem Biophys Res Commun 292(3):587-592.
35. Karp PD. 2000. An ontology for biological function based on molecular interactions. Bioinformatics 16(3):269-285.
36. Larsen JC, Farland W, Winders D. 2000. Current risk assessment approaches in different countries. Food Addit Contam 17(4):359-369.
37. Li H. 2001. A permutation procedure for the haplotype method for identification of disease-predisposing variants. Ann Hum Genet 65:189-196.
38. Nebert DW, McKinnon RA. 1994. Cytochrome P450: evolution and functional diversity. Prog Liver Dis 12:63-97.
39. Nelson DR. 1999a. Cytochrome P450 and the individuality of species. Arch Biochem Biophys 369(1):1-10.
40. Nelson DR. 1999b. A second CYP26 P450 in humans and zebrafish: CYP26B1. Arch Biochem Biophys 371(2):345-347.
41. Nelson DR, Koymans L, Kamataki T, Stegeman JJ, Feyereisen R, Waxman DJ, et al. 1996. P450 superfamily: update of new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6(1):1-42.
42. Nicholson JK, Connelly J, Lindon JC, Holmes E. 2002. Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov 1(2):153-161.
43. Nicholson JK, Lindon JC, Holmes E. 1000. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biologica NMR spectroscopic data. Xenobiotica 29(1):1181-1189.
44. Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA. 1999. Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog 24(3):153-159.
45. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. 1999. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27(1):29-34.
46. Olden K. 2002. New opportunities in toxicology in the post-genomic era. Drug Discov Today 7(5):273-276.
47. Pennie WD, Kimber I. 2002. Toxicogenomics; transcript profiling and potential application to chemical allergy. Toxicol In Vitro 16(3):319-326.
48. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, et al. 2000. Molecular portraits of human breast tumours. Nature 406(6797):747-752.
49. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, et al. 2001. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 29(1):159-164.
50. Reilly TP, Bourdi M, Brady JN, Pise-Masison CA, Radonovich MF, George JW, et al. 2001a. Expressing profiling of acetaminophen liver toxicity in mice using microarray technology. Biochem Biophys Res Commun 282(1):321-328.
51. Reilly TP, Brady JN, Marchick MR, Bourdi M, George JW, Radonovich MF, et al. 2001b. A protective role for cyclooxgenase-2 in drug-induced liver injury in mice. Chem Res Toxicol 14(12):1620-1628.
52. Richard AM, Williams CR. 2002. Distributed structure-searchable toxicity (DSSTox) public database network: a proposal. Mutat Res 499(1):27-52.
53. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, et al. 2000. Comparative genomics of the eukaryotes. Science 287(5461):2204-2215.
54. Rubin RB, Merchant M. 2000. A rapid protein profiling system that speeds study of cancer and other diseases. Am Clin Lab 19(8):28-29.
55. Ruepp SU, Tonge RP, Shaw J, Wallis N, Pognan F. 2002. Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol Sci 65(1):135-150.
56. Schrem H, Klempnauer J, Borlak J. 2002. Liver-enriched transcription factors in liver function and development. Part I: The hepatocyte nuclear factor network and liver-specific gene expression. Pharmacology Rev 54(1):129-158.
57. Selkov E Jr., Grechkin Y, Mikhailova N, Selkov E. 1998. MPW: the Metabolic Pathways Database. Nucleic Acids Res 26(1):43-45.
58. Simmons PT, Portier CJ. 2002. Toxicogenomics: the new frontier in risk analysis. Carcinogenesis 23(6):903-905.
59. Sluka JP. 2002. Extracting knowledge from genomic experiments by incorporating the biomedical literature. In: Methods of Microarray Data Analysis, II (Lin SM, Johnson KF, eds). Boston:Kluwer.
60. Tennant RW. 2002. The National Center for Toxicogenomics: using new technologies to inform mechanistic toxicology. Environ Health Perspect 110(1):A8-A10.
61. Thomas RS, Rank DR, Penn SG, Zastrow GM, Hayes KR, Pande K, et al. 2001. Identification of toxicologically predictive gene sets using cDNA microarrays. Mol Pharmacol 60(6):1189-1194.
62. Ulrich R, Friend SH. 2002. Toxicogenomics and drug discovery: will new technologies help us produce better drug? Nat Rev Drug Discov 1(1):84-88.
63. Waring JF, Cavet G, Jolly RA, McDowell J, Dai H, Ciurlionis R, Zhang C, Stoughton R, Lum P, Ferguson A, et al. Development of a DNA microarray for oxicology based on hepatotoxin-regulated sequences. Environ Health Perspect Toxicogenomics 111(1T):53-60(2003).
64. Waring JF, Jolly RA, Ciurlionis R, Lum PY, Praestgaard JT, Morfitt DC, et al. 2001. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol Apply Pharmacol 175(1):28-42.
65. Waters MD, Stack HF, Garret NE, Jackson MA. 1991. The Genetic Activity Profile database. Environ Health Perspect 96:41-45.
66. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, et al. 2001. The TRANSFAC system on gene expression regulation. Nucleic Acids Res 29(1):281-283.
67. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, et al. 2000. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28(1):316-319.
68. Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, et al. 2001. Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8(6):625-637.
69. Yamazaki K, Kuromitsu J, Tanaka I. 2002. Microarray analysis of gene expression changes in mouse liver induced by peroxisome proliferator-activated receptor alpha agonists. Biochem Biophys Res Commun 290(3):1114-1122.
70. Zweiger G. 1000. Knowledge discovery in gene-expression-microarray data: mining the information output of the genome. Trends Biotechnol 17(11):429-436.