Toxygates: Interactive toxicity analysis on a hybrid microarray and linked data platform

Bioinformatics

Volumn 29, Issue 23, 2013, Pages 3080-3086

  Nyström Persson, Johan ^a   Igarashi, Yoshinobu ^a   Ito, Maori ^a   Morita, Mizuki ^a,b   Nakatsu, Noriyuki ^a   Yamada, Hiroshi ^a   Mizuguchi, Kenji ^a  

^a NATIONAL INSTITUTE OF BIOMEDICAL INNOVATION   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; GLUTATHIONE;

ANIMAL; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA MICROARRAY; DOSE RESPONSE; DRUG EFFECTS; FACTUAL DATABASE; GENE EXPRESSION REGULATION; HUMAN; KIDNEY; LIVER; LIVER CELL; METABOLISM; PROCEDURES; RAT; TOXICOGENETICS; ARTICLE; DRUG EFFECT; METHODOLOGY;

ANIMALS; BIOLOGICAL MARKERS; DATABASES, FACTUAL; DOSE-RESPONSE RELATIONSHIP, DRUG; GENE EXPRESSION REGULATION; GLUTATHIONE; HEPATOCYTES; HUMANS; KIDNEY; LIVER; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RATS; SOFTWARE; TOXICOGENETICS; USER-COMPUTER INTERFACE;

EID: 84890017620     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt531     Document Type: Article

References (32)

1. Banerjee, A. et al. (1998) Induction of an ATPase inhibitor protein by propylthiouracil and protection against paracetamol (acetaminophen) hepatotoxicity in the rat. Br. J. Pharmacol., 124, 1041-1047.
2. Barrett, T. et al. (2011) NCBI GEO: archive for functional genomics data sets - 10 years on. Nucleic Acids Res., 39, D1005-D1010.
3. Beddowes, E.J. et al. (2003) Chloroform, carbon tetrachloride and glutathione depletion induce secondary genotoxicity in liver cells via oxidative stress. Toxicology, 187, 101-115.
4. Berners-Lee, T. et al. (2001) The semantic web. Scie. Am., 284, 34-43.
5. Borroz, K.I. et al. (1994) Modulation of gamma-glutamylcysteine synthetase large subunit mRNA expression by butylated hydroxyanisole. Toxicol. Appl. Pharmacol., 126, 150-155.
6. Boyland, E. and Chasseaud, L.F. (1967) Enzyme-catalysed conjugations of glutathione with unsaturated compounds. Biochem. J., 104, 95-102.
7. Chen, Y.A. et al. (2011) Targetmine, an integrated data warehouse for candidate gene prioritisation and target discovery. PLoS One, 6, e17844.
8. Comporti, M. et al. (1991) Glutathione depletion: its effects on other antioxidant systems and hepatocellular damage. Xenobiotica, 21, 1067-1076.
9. Davis, A.P. et al. (2013) The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res., 41, D1104-D1114.
10. Fielden, M.R. et al. (2007) A gene expression biomarker provides early prediction and mechanistic assessment of hepatic tumor induction by nongenotoxic chemicals. Toxicol. Sci., 99, 90-100.
11. Ganter, B. et al. (2005) Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action. J. Biotechnol., 119, 219-244.
12. Gao, W. et al. (2010) Mechanism-based biomarker gene sets for glutathione depletion- related hepatotoxicity in rats. Toxicol. Appl. Pharmacol., 247, 211-221.
13. Gaulton, A. et al. (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic acids Res., 40, D1100-D1107.
14. Gene Ontology Consortium. (2000) Gene ontology: tool for the unification of biology. Nat. Genetics, 25, 25-29.
15. Goble, C. and Stevens, R. (2008) State of the nation in data integration for bioinformatics. J. Biomed. Inform., 41, 687-693.
16. Hinson, J.A. (1983) Reactive metabolites of phenacetin and acetaminophen: a review. Environ. Health Perspect., 49, 71-79.
17. Kanehisa, M. et al. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
18. Knox, C. et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res., 39, D1035-D1041.
19. Kohonen, P. et al. (2013) The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Mol. Inform., 32, 47-63.
20. Lamb, J. et al. (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science, 313, 1929-1935.
21. Lotkova, H. et al. (2007) S-adenosylmethionine exerts a protective effect against thioacetamide-induced injury in primary cultures of rat hepatocytes. Altern. Lab. Anim., 35, 363-371.
22. Luchini, A.C. et al. (2008) Intestinal anti-inflammatory activity of coumarin and 4-hydroxycoumarin in the trinitrobenzenesulphonic acid model of rat colitis. Biol. Pharm. Bull., 31, 1343-1350.
23. Lyne, R. et al. (2007) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol., 8, R129.
24. Mizutani, T. et al. (1999) Metabolism-dependent hepatotoxicity of methimazole in mice depleted of glutathione. J. Appl. Toxicol., 19, 193-198.
25. Monks, T.J. et al. (1982) Stereoselective formation of bromobenzene glutathione conjugates. Chem. Biol. Interact., 41, 203-216.
26. Nerini-Molteni, S. et al. (2008) Redox homeostasis modulates the sensitivity of myeloma cells to bortezomib. Br. J. Haematol., 141, 494-503.
27. Powell, S. et al. (2012) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res., 40, D284-D289.
28. Rustici, G. et al. (2013) ArrayExpress update - trends in database growth and links to data analysis tools. Nucleic Acids Res., 41, D987-D990.
29. Uehara, T. et al. (2008) A toxicogenomics approach for early assessment of potential non-genotoxic hepatocarcinogenicity of chemicals in rats. Toxicology, 250, 15-26.
30. Uehara, T. et al. (2010) The Japanese toxicogenomics project: application of toxicogenomics. Mol. Nutr. Food Res., 54, 218-227.
31. van Doorn, R. et al. (1978) Synergistic effects of phorone on the hepatotoxicity of bromobenzene and paracetamol in mice. Toxicology, 11, 225-233.
32. Weidolf, L. et al. (1992) A metabolic route of omeprazole involving conjugation with glutathione identified in the rat. Drug Metab. Dispos., 20, 262-267.