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CTD - Comparative Toxicogenomics Database


NAR Molecular Biology Database Collection entry number 1188
Davis, A.P.1, Murphy, C.1, Johnson, R.2, Lay, J.2, Lennon-Hopkins, K.2, Saraceni-Richards, C.2, Sciaky, D.2, King, B.2, Rosenstein, M.2, Wiegers, T.1, and Mattingly, C.1
1Department of Biology, North Carolina State University, Raleigh, NC 27695-7617

2Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672

Database Description

Exposure to environmental chemicals may influence human health; however, the molecular mechanisms of action between chemicals and gene products are not well understood. Towards that end, the Comparative Toxicogenomics Database (CTD; http://ctdbase.org) provides information about interactions between environmental chemicals and gene products, and their relationships to diseases. Biocurators manually curate chemical-gene, chemical-disease, and gene-disease relationships from the scientific literature (1). This core data is then internally integrated to generate inferred chemical-gene-disease networks. Additionally, the core data is integrated with external data sets (such as Gene Ontology and pathway annotations) to predict many novel associations between different data types. A unique and powerful feature of CTD is the inferred relationships generated by data integration: if chemical A interacts with gene B, and independently gene B is directly associated with disease C, then chemical A has an inferred relationship to disease C (inferred via gene B). Thus, via integration, CTD helps turn knowledge into discoveries by identifying novel connections between chemicals, genes, diseases, pathways, and GO annotations that might not otherwise be apparent using other biological resources. These inferences are powerful data sets for generating testable hypotheses. CTD evaluates these inferred relationships and assigns statistical scores and p-values, which allow users to sort and rank the inferred relationships to help prioritize hypothesis testing. As of August 2012, CTD contains over 15 million toxicogenomic relationships (http://ctdbase.org/about/dataStatus.go). All CTD data files are freely available from either individual web pages or from our “Downloads” tab (http://ctdbase.org/downloads/) in multiple formats (CSV, TSV, XML, Excel, and OBO). New users of CTD should consult our “Help” (http://ctdbase.org/help/) and “FAQ” (http://ctdbase.org/help/faq/) guides.

Recent Developments

CTD provides users with several analysis and visualization tools (http://ctdbase.org/tools/), including:

1. Batch Query: downloads custom data associated with a set of chemicals, diseases, genes, Gene Ontology terms, pathways, or references (2).

2. VennViewer: compares associated data sets for up to three chemicals, diseases, or genes (2). 3. Gene Set Enricher: finds Gene Ontology and pathway annotations that are enriched for sets of genes.

4. GeneComps and ChemComps: finds comparable genes and chemicals (respectively) that share toxicogenomic profiles, allowing users to explore gene and chemical sets from a new perspective (3).

5. DiseaseComps: finds comparable diseases that share toxicogenomic profiles, allowing users to explore diseases based upon common genes and chemicals, instead of shared physiology or tissue (4).

To improve data visualization, we have also added a Cytoscape Web view to our ChemComps feature, included color-coded interactions, and created a ‘slim list’ for our MEDIC disease vocabulary (5), allowing diseases to be grouped for meta-analysis, visualization, and better data management.

Together, this wealth of expanded chemical-gene-disease data, combined with novel ways to analyze and view content, continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases.

Acknowledgements

CTD is supported by the National Institute of Environmental Health Sciences (NIEHS) grants “Comparative Toxicogenomics Database” [grant number R01-ES014065] and “Generation of a centralized and integrated resource for exposure data” [grant number R01-ES019604].

References

1. Davis, A.P., Wiegers, T.C., Rosenstein, M.C., Murphy, C.G., and Mattingly, C.J. (2011) The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database. Database, Sep 20;2011:bar034.

2. Davis, A.P., King, B.L., Mockus, S., Murphy, C.G., Saraceni-Richards, C., Rosenstein, M. Wiegers, T., and Mattingly, C.J. (2011) The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res., 39, D1067-1072.

3. Davis, A.P., Murphy, C.G., Saraceni-Richards, C.A., Rosenstein, M.C., Wiegers, T.C., Hampton, T.H., and Mattingly, C.J. (2009) GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles. Bioinformation, 4, 173-174.

4. Davis, A.P., Rosenstein, M.C., Wiegers, T.C., and Mattingly, C.J. (2011) DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomics profiles at CTD. Bioinformation, 7, 154-156.

5. Davis, A.P., Wiegers, T.C., Rosenstein, M.C. and Mattingly, C.J. (2012) MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database. Database, Mar 20;2012:bar065.


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