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BioMed Central, BMC Medical Genomics, 1(6), 2013

DOI: 10.1186/1755-8794-6-2

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Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

Journal article published in 2013 by Kristina M. Hettne ORCID, André Boorsma, Dorien A. M. van Dartel, D. A. van Dartel, Jelle J. Goeman, Esther de Jong, Esther de Jong, Aldert H. Piersma, Rob H. Stierum, Jos C. Kleinjans, Jan A. Kors
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

BACKGROUND: Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can be created by next-generation text mining (next-gen TM), and that these can be used with gene set analysis (GSA) methods for chemical treatment identification, for pharmacological mechanism elucidation, and for comparing compound toxicity profiles. METHODS: We created 30,211 chemical response-specific gene sets for human and mouse by next-gen TM, and derived 1,189 (human) and 588 (mouse) gene sets from the Comparative Toxicogenomics Database (CTD). We tested for significant differential expression (SDE) (false discovery rate -corrected p-values