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

Abstract

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.

Semantics based approach for analyzing disease-target associations

“…Comparative Toxicogenomics Database (CTD) provides a centralized platform for toxico-genomic research by integrating information on chemicals, relevant genes and proteins, and their interactions associated with a disease [41]. OMIM is a high quality and authoritative resource for relationships between human genes and genetic phenotypes [42].…”

Public Databases Supporting Computational Toxicology

“…CTD (Comparative Toxicogenomics Database) (Mattingly et al, 2006;Davis et al, 2009;Gohlke et al, 2009) is a knowledgebase combining information on three classes of interactions: chemical-disease, chemicalgene, and gene-disease. All information is taken from the open literature and is handcurated to insure data quality.…”

Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events

“…For instance, clinical and pathology data along with proteomic and gene expression experiments studying the toxic effects of acetaminophen on liver is stored within CEBS. The Comparative Toxicogenomics Database (CTD) is another curated knowledge-base that captures the relationships between chemicals, genes and diseases with over 4,000 chemicals, 14,000 genes and 3,000 diseases (45). For example, sirolimus has 75 known interacting genes, associations with 236 diseases, and 162 pathways associations.…”