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Bioinformatics Methods for Interpreting Toxicogenomics Data: The Role of Text-Mining

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Author: Hettne, K.M. · Kleinjans, J. · Stierum, R.H. · Boorsma, A. · Kors, J.A.
Source:Toxicogenomics-Based Cellular Models: Alternatives to Animal Testing for Safety Assessment, 291-304
Identifier: 513332
doi: doi:10.1016/B978012397862200019-X
ISBN: 9780123978622
Keywords: Biology · Bioinformatics · Gene-expression profiling · Gene-set analysis · Text-mining · Biomedical Innovation · Healthy Living · Life · MSB - Microbiology and Systems Biology · ELSS - Earth, Life and Social Sciences


This chapter concerns the application of bioinformatics methods to the analysis of toxicogenomics data. The chapter starts with an introduction covering how bioinformatics has been applied in toxicogenomics data analysis, and continues with a description of the foundations of a specific bioinformatics method called text-mining. Next, the integration of text-mining with toxicogenomics data analysis methods is described. Four different areas in toxicogenomics where conventional bioinformatics solutions can be assisted by text-mining are described: class discovery and separation, connectivity mapping, mechanistic analysis, and identification of early predictors of toxicity. © 2014 Elsevier Inc. All rights reserved.