Mapping drug physico-chemical features to pathway activity reveals molecular networks linked to toxicity outcome

PLoS ONE

Volumn 5, Issue 8, 2010, Pages

  Antczak, Philipp ^a   Ortega, Fernando ^a   Chipman, J Kevin ^a   Falciani, Francesco ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TOXIC SUBSTANCE; DRUG;

ARTICLE; CELL COMMUNICATION; CONTROLLED STUDY; MATHEMATICAL MODEL; NEPHROTOXICITY; PHYSICAL CHEMISTRY; PREDICTION; SIGNAL TRANSDUCTION; ANIMAL; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; CYTOLOGY; DRUG DEVELOPMENT; DRUG EFFECT; DRUG TOXICITY; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; KIDNEY TUBULE; METABOLISM; PHENOTYPE; RAT; REPRODUCIBILITY;

ANIMALS; CELL COMMUNICATION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DRUG DISCOVERY; DRUG TOXICITY; GENE EXPRESSION PROFILING; KIDNEY TUBULES; PHARMACEUTICAL PREPARATIONS; PHENOTYPE; PHYSICOCHEMICAL PROCESSES; RATS; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 77957925228     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012385     Document Type: Article

References (33)

1. Mayr L, Bojanic D (2009) Novel trends in high-throughput screening. Current Opinion in Pharmacology 9: 580-588.
2. Vedani A, Dobler M, Lill M (2006) The challenge of predicting drug toxicity in silico. Basic and Clinical Pharmacology and Toxicology 99: 195.
3. Merlot C (2009) Computational toxicology-a tool for early safety evaluation. Drug Discovery Today 15: 16-22.
4. Vayer P, Arrault A, Lesur B, Bertrand M, Walther B (2009) Chemoinformatics and virtual screening of molecules for therapeutic use. Me ́decine Sciences: M/S 25: 871.
5. Conesa A, Bro R, García-García F, Prats J, Götz S, et al. (2008) Direct functional assessment of the composite phenotype through multivariate projection strategies. Genomics 92: 373-383.
6. Thomas R, Rank D, Penn S, Zastrow G, Hayes K, et al. (2001) Identification of toxicologically predictive gene sets using cDNA microarrays. Molecular Pharmacology 60: 1189.
7. Amin R, Hamadeh H, Bushel P, Bennett L, Afshari C, et al. (2002) Genomic interrogation of mechanism (s) underlying cellular responses to toxicants. Toxicology 181: 555-563.
8. Waring J, Gum R, Morfitt D, Jolly R, Ciurlionis R, et al. (2002) Identifying toxic mechanisms using DNA microarrays: evidence that an experimental inhibitor of cell adhesion molecule expression signals through the aryl hydrocarbon nuclear receptor. Toxicology 181: 537-550.
9. Lobenhofer E, Auman J, Blackshear P, Boorman G, Bushel P, et al. (2008) Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype. Genome Biology 9: R100.
10. Bushel P, Hamadeh H, Bennett L, Green J, Ableson A, et al. (2002) Computational selection of distinct class-and subclass-specific gene expression signatures. Journal of Biomedical Informatics 35: 160-170.
11. Steiner G, Suter L, Boess F, Gasser R, de Vera M, et al. (2004) Discriminating different classes of toxicants by transcript profiling. Environmental Health Perspectives 112: 1236.
12. Dieterle F, Marrer E, Suzuki E, Grenet O, Cordier A, et al. (2008) Monitoring kidney safety in drug development: emerging technologies and their implications. Current Opinion in Drug Discovery and Development 11: 60.
13. Fielden M, Eynon B, Natsoulis G, Jarnagin K, Banas D, et al. (2005) A gene expression signature that predicts the future onset of drug-induced renal tubular toxicity. Toxicologic Pathology 33: 675.
14. Gower J (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53: 325-338.
15. Schoeppe W (1977) Effects of dopamine on kidney function. Proceedings of the Royal Society of Medicine 70: 36.
16. Freeman J, DeArmond D, Lake M, Huang W, Venkatasubbarao K, et al. (2004) Alterations of cell signaling pathways in pancreatic cancer. Front Biosci 9: 1889-98.
17. Geng H, Lan R, Wang G, Siddiqi A, Naski M, et al. (2009) Inhibition of Autoregulated TGF {beta} Signaling Simultaneously Enhances Proliferation and Differentiation of Kidney Epithelium and Promotes Repair Following Renal Ischemia. American Journal of Pathology 174: 1291.
18. Chipman J, Mally A, Edwards G (2003) Disruption of gap junctions in toxicity and carcinogenicity. Toxicological Sciences 71: 146.
19. Pereira C, Moreira A, Pereira S, Machado N, Carvalho F, et al. (2009) Investigating Drug-induced Mitochondrial Toxicity: A Biosensor to Increase Drug Safety? Current Drug Safety 4: 34-54.
20. Klaassen C, Amdur M, et al. (1993) Casarett and Doull's toxicology: the basic science of poisons. Journal of Occupational and Environmental Medicine 35: 76.
21. Doi A, Hill G, Seely J, Hailey J, Kissling G, et al. (2007) a2u-Globulin Nephropathy and Renal Tumors in National Toxicology Program Studies. Toxicologic Pathology 35: 533-540.
22. Cariello N, Wilson J, Britt B, Wedd D, Burlinson B, et al. (2002) Comparison of the computer programs DEREK and TOPKAT to predict bacterial mutagenicity. Mutagenesis 17: 321.
23. Dix D, Houck K, Martin M, Richard A, Setzer R, et al. (2007) The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicological Sciences 95: 5.
24. Judson R, Richard A, Dix D, Houck K, Martin M, et al. (2009) The toxicity data landscape for environmental chemicals. Environmental Health Perspectives 117: 685.
25. Raychaudhuri S, Stuart J, Altman R (2000) Principal components analysis to summarize microarray experiments: application to sporulation time series. In: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing NIH Public Access. 455 p.
26. Sameith K, Antczak P, Marston E, Turan N, Maier D, et al. (2008) Functional Modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage. Bioinformatics 24: 2602.
27. Team RDC (2005) R: A language and environment for statistical computing. Vienna, Austria: Foundation for Statistical Computing.
28. Kong S, Pu W, Park P (2006) A multivariate approach for integrating genomewide expression data and biological knowledge. Bioinformatics 22: 2373.
29. Song S, Black M (2006) Principal coordinates and hotelling's t2 method. URL http://bioconductor.org/packages/bioc/html/pcot2.html (last accessed 2010).
30. Song S, Black M (2008) Microarray-based gene set analysis: a comparison of current methods. BMC Bioinformatics 9: 502.
31. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological). pp 289-300.
32. Tetko I, Gasteiger J, Todeschini R, Mauri A, Livingstone D, et al. (2005) Virtual computational chemistry laboratory-design and description. Journal of Computer- Aided Molecular Design 19: 453-463.
33. Trevino V, Falciani F (2006) GALGO: an R package for multivariate variable selection using genetic algorithms. Bioinformatics 22: 1154.