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Bioinformatics. 2013 Aug 15;29(16):2062-3. doi: 10.1093/bioinformatics/btt322. Epub 2013 Jun 5.

DIGEP-Pred: web service for in silico prediction of drug-induced gene expression profiles based on structural formula.

Author information

1
Laboratory for Structure-Function Based Drug Design, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia. alexey.lagunin@ibmc.msk.ru

Abstract

SUMMARY:

Experimentally found gene expression profiles are used to solve different problems in pharmaceutical studies, such as drug repositioning, resistance, toxicity and drug-drug interactions. A special web service, DIGEP-Pred, for prediction of drug-induced changes of gene expression profiles based on structural formulae of chemicals has been developed. Structure-activity relationships for prediction of drug-induced gene expression profiles were determined by Prediction of Activity Spectra for Substances (PASS) software. Comparative Toxicogenomics Database with data on the known drug-induced gene expression profiles of chemicals was used to create mRNA- and protein-based training sets. An average prediction accuracy for the training sets (ROC AUC) calculated by leave-one-out cross-validation on the basis of mRNA data (1385 compounds, 952 genes, 500 up- and 475 down-regulations) and protein data (1451 compounds, 139 genes, 93 up- and 55 down-regulations) exceeded 0.85.

AVAILABILITY:

Freely available on the web at http://www.way2drug.com/GE.

PMID:
23740741
DOI:
10.1093/bioinformatics/btt322
[Indexed for MEDLINE]
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