BACK TO CONTENTS   |    PDF   |    PREVIOUS   |    NEXT

Title

 

 

 

 

 

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

 

Authors

 

Allan Peter Davis1*, Cynthia G. Murphy1, Cynthia A. Saraceni-Richards1, Michael C. Rosenstein1, Thomas C. Wiegers1, Thomas H. Hampton2 and Carolyn J. Mattingly1

 

Affiliation

 

1Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA; 2Center for Environmental Health Sciences, Dartmouth Medical School, Hanover NH 03755, USA

 

Email

 

apd@mdibl.org

Article Type

 

Database

Date

 

Received September 10, 2009; Accepted October 13, 2009; Published October 15, 2009

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-gene-disease networks.

 

Keywords

gene, chemical, toxicogenomic, database, curation.

Citation

 

Davis et al., Bioinformation 4(4): 173-174 (2009)

Edited by

 

P. Kangueane

 

ISSN

 

0973-2063

 

Publisher

 

Biomedical Informatics

License

 

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.