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The Comparative Toxicogenomics Database: update 2013.

Allan Peter Davis1, Cynthia Grondin Murphy, Robin Johnson

  • 1Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA. apdavis3@ncsu.edu

Nucleic Acids Research
|October 25, 2012
PubMed
Summary
This summary is machine-generated.

The Comparative Toxicogenomics Database (CTD) now offers enhanced tools for exploring over 15 million chemical-gene-disease interactions. New features aid in discovering relationships and generating hypotheses about environmental health impacts.

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Area of Science:

  • Toxicogenomics
  • Environmental Health
  • Bioinformatics

Background:

  • The Comparative Toxicogenomics Database (CTD) integrates manually curated literature data on chemical-gene and chemical-disease interactions.
  • Existing data integration facilitates network generation and prediction of novel associations.

Purpose of the Study:

  • To enhance the CTD with new features for improved data navigation, analysis, and visualization.
  • To facilitate hypothesis generation regarding the molecular mechanisms of environmentally linked diseases.

Main Methods:

  • Integration of chemical-gene, chemical-disease, and gene-disease interactions.
  • Development of new tools: DiseaseComps, statistical scoring for inferred relationships, filtering options, and Gene Set Enricher.
  • Implementation of improved data visualization: Cytoscape Web view, color-coded interactions, and a 'slim list' for the MEDIC disease vocabulary.

Main Results:

  • CTD now contains over 15 million toxicogenomic relationships.
  • New features enable identification of comparable diseases based on toxicogenomic profiles.
  • Enhanced visualization and data management tools improve user analysis and interoperability.

Conclusions:

  • The expanded CTD with novel analytical and visualization tools supports hypothesis generation on environmental disease mechanisms.
  • CTD promotes data interoperability and serves as a valuable resource for toxicogenomic research.