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Bioinformation. 2009 Oct 15;4(4):173-4.

GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles.

Author information

  • 1Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA. apd@mdibl.org

Abstract

The Comparative Toxicogenomics Database is a public resource that promotes understanding about the effects of environmental chemicals on human health. Currently, CTD describes over 184,000 molecular interactions for more than 5,100 chemicals and 16,300 genes/proteins. We have leveraged this dataset of chemical-gene relationships to compute similarity indices following the statistical method of the Jaccard index. These scores are used to produce lists of comparable genes ("GeneComps") or chemicals ("ChemComps") based on shared toxicogenomic profiles. GeneComps and ChemComps are now provided for every curated gene and chemical in CTD. ChemComps are particularly significant because they provide a way to group chemicals based upon their biological effects, instead of their physical or structural properties. These metrics provide a novel way to view and classify genes and chemicals and will help advance testable hypotheses about environmental chemical-genedisease networks.

AVAILABILITY:

CTD is freely available at http://ctd.mdibl.org/

KEYWORDS:

chemical; curation; database; gene; toxicogenomic

PMID:
20198196
[PubMed]
PMCID:
PMC2825594
Free PMC Article
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