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Original

Predictive models of hepatotoxicity using gene expression data from primary rat hepatocytes

, , , , , , & show all
Pages 1122-1139 | Received 05 Apr 2006, Accepted 20 May 2006, Published online: 11 Aug 2009

References

  • Affymetrix. MAS5, Statistical algorithms description document. 2002, (available at: http://www.affymetrix.com/)
  • Ahmad AS, Gogal RM, Jr, Walsh JE. A new rapid and simple non-radioactive assay to monitor and determine the proliferation of lymphocytes: An alternative to 3H-thymidine incorporation assay. Journal of Immunological Methods 1994; 170: 211–224
  • Brown MPS, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M, Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proceedings of the National Academy of Science, USA 2000; 97: 262–267
  • Castle AL, Carver MP, Mendrick DL. Toxicogenomics — a new revolution in drug safety. Drug Discovery Today 2002; 7: 728–737
  • Cleveland WS. Robust locally weighted regression and smoothing scatter plots. Journal of the American Statistical Association 1979; 74: 829–836
  • Dimitriadou E, Hornik K, Leisch F, Meyer D, Weinges A. e1071: Misc functions of the Department of Statistics (e1071). 2006, TU Wien. R package version 1.5-12. 2006
  • Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments. Statistica Sinica 2002; 12(1)111–139
  • 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. Toxicology Science 2002; 67(2)219–231
  • Huby RDJ, Tugwood J. Gene expression profiling for pharmaceutical safety assessment. Expert Opinion on Drug Metabolism and Toxicology 2005; 1(2)247–260
  • Kier LD, Neft R, Tang L, Suizu R, Cook T, Onsurez K, Tiegler K, Sakai Y, Ortiz M, Nolan T, Sankar U, Li AP. Applications of microarrays with toxicologically relevant genes (tox genes) for the evaluation of chemical toxicants in Sprague Dawley rats in vivo and human hepatocytes in vitro. Mutation Research — Fundamental and Molecular Mechanisms of Mutagenesis 2004; 549(1–2)101–113
  • Kim RD, Park PJ. Improving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biology 2004; 5: R70
  • Mukherjee S. Classifying microarray data using support vector machines, understanding and using microarray analysis techniques: A practical guide. Kluwer, Boston, MA 2003
  • Perez-Enciso M, Tenenhaus M. Prediction of clinical outcome with microarray data: A partial least squares discriminant analysis (PLS-DA) approach. Human Genetics 2003; 112(5–6)581–592
  • R Development Core Team. R: A language and environment for statistical computing. Report No. 3-900051-07-0. 2005. R Foundation for Statistical Computing, Vienna
  • Ruepp S, Boess F, Suter L, de Vera MC, Steiner G, Steele T, Weiser T, Albertini S. Assessment of hepatotoxic liabilities by transcript profiling. Toxicology and Applied Pharmacology 2005; 207(2 Suppl.)161–170
  • Ruepp SU, Tonge RP, Shaw J, Wallis N, Pognan F. Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicological Sciences 2002; 65(1)135–150
  • Salter AH. Large-scale databases in toxicogenomics. Pharmacogenomics 2005; 6: 749–754
  • Vapnik V. Statistical learning theory. Wiley, New York, NY 1998
  • 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. Toxicology Letters 2001b; 120(1–3)359–368
  • 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. Toxicology and Applied Pharmacology 2001a; 175(1)28–42
  • Witten I, Frank E. Data mining: Practical machine learning tools and techniques2nd. Morgan Kaufmann, San Francisco, CA 2005

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