The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks.

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.

[1]  M. E. Hahn.  The aryl hydrocarbon receptor: a comparative perspective. , 1998, Comparative biochemistry and physiology. Part C, Pharmacology, toxicology & endocrinology.

[2]  C E Lipscomb,et al.  Medical Subject Headings (MeSH). , 2000, Bulletin of the Medical Library Association.

[3]  Samuel H. Wilson,et al.  Environmental health and genomics: visions and implications , 2000, Nature Reviews Genetics.

[4]  M. E. Hahn,et al.  The evolution of aryl hydrocarbon signaling proteins: diversity of ARNT isoforms among fish species. , 2000, Marine environmental research.

[5]  R. Pohjanvirta,et al.  The AH receptor of the most dioxin-sensitive species, guinea pig, is highly homologous to the human AH receptor. , 2001, Biochemical and biophysical research communications.

[6]  Carol A. Bean,et al.  Relationships in the Organization of Knowledge , 2001, Information Science and Knowledge Management.

[7]  Betsy L. Humphreys,et al.  Relationships in Medical Subject Headings (MeSH) , 2001 .

[8]  Jennifer E. Rowley,et al.  Relationships in the Organization of Knowledge , 2002, J. Documentation.

[9]  M. E. Hahn,et al.  Aryl hydrocarbon receptors: diversity and evolution. , 2002, Chemico-biological interactions.

[10]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: 2002 update , 2002, Nucleic Acids Res..

[11]  Tsviya Olender,et al.  GeneCardsTM 2002: towards a complete, object-oriented, human gene compendium , 2002, Bioinform..

[12]  J. Wakefield.  Toxicogenomics: roadblocks and new directions. , 2003, Environmental health perspectives.

[13]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[14]  M Waters,et al.  Systems Toxicology and the Chemical Effects in Biological Systems (CEBS) Knowledge Base , 2003, EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences.

[15]  Carl G. Figdor,et al.  Different Faces of the Heme-Heme Oxygenase System in Inflammation , 2003, Pharmacological Reviews.

[16]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[17]  Michael Krauthammer,et al.  GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data , 2004, J. Biomed. Informatics.

[18]  E. Linney,et al.  Environmental genomics: a key to understanding biology, pathophysiology and disease. , 2004, Human molecular genetics.

[19]  G. Colby,et al.  Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD) , 2004, The Pharmacogenomics Journal.

[20]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

[21]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2005, Nucleic Acids Res..

[22]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[23]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[24]  Mark Craven,et al.  EDGE: A Centralized Resource for the Comparison, Analysis, and Distribution of Toxicogenomic Information , 2005, Molecular Pharmacology.

[25]  Marc Vidal,et al.  Interactome modeling , 2005, FEBS letters.

[26]  William A. Toscano,et al.  Systems Biology: New Approaches to Old Environmental Health Problems , 2005, International journal of environmental research and public health.

[27]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[28]  J. van Loon.  Network , 2006 .

[29]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[30]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..