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ToxSci Advance Access originally published online on May 4, 2006
Toxicological Sciences 2006 92(2):587-595; doi:10.1093/toxsci/kfl008
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© The Author 2006. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The Comparative Toxicogenomics Database: A Cross-Species Resource for Building Chemical-Gene Interaction Networks

Carolyn J. Mattingly*,1, Michael C. Rosenstein*, Allan Peter Davis*, Glenn T. Colby*, John N. Forrest, Jr{dagger} and James L. Boyer{dagger}

* Department of Bioinformatics, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672; and {dagger} Department of Medicine, Yale University School of Medicine, New Haven, Connecticut 06520

Received February 16, 2006; accepted April 29, 2006

Chemicals in the environment play a critical role in the etiology of many human diseases. Despite their prevalence, the molecular mechanisms of action and the effects of chemicals on susceptibility to disease are not well understood. To promote understanding of these mechanisms, the Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org/) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. CTD integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. These comparisons will facilitate understanding of structure-function correlations and the genetic basis of susceptibility. Manual curation and integration of cross-species chemical-gene and chemical-protein interactions from the literature are now underway. These data will provide information for building complex interaction networks. New CTD features include (1) cross-species gene, rather than sequence, query and visualization capabilities; (2) integrated cross-links to microarray data from chemicals, genes, and sequences in CTD; (3) a reference set related to chemical-gene and protein interactions identified by an information retrieval system; and (4) a "Chemicals in the News" initiative that provides links from CTD chemicals to environmental health articles from the popular press. Here we describe these new features and our novel cross-species curation of chemical-gene and chemical-protein interactions.

Key Words: CTD; chemicals; environment; GO; toxicology; pathways; interactions.


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