The Comparative Toxicogenomics Database: update 2013

被引:317
作者
Davis, Allan Peter [1 ]
Murphy, Cynthia Grondin [1 ]
Johnson, Robin [2 ]
Lay, Jean M. [2 ]
Lennon-Hopkins, Kelley [2 ]
Saraceni-Richards, Cynthia [2 ]
Sciaky, Daniela [2 ]
King, Benjamin L. [2 ]
Rosenstein, Michael C. [2 ]
Wiegers, Thomas C. [1 ]
Mattingly, Carolyn J. [1 ]
机构
[1] N Carolina State Univ, Dept Biol, Raleigh, NC 27695 USA
[2] Mt Desert Isl Biol Lab, Dept Bioinformat, Salsbury Cove, ME 04672 USA
关键词
GENE; VISUALIZATION; ONTOLOGY; TOOL;
D O I
10.1093/nar/gks994
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate expanded networks and predict many novel associations between different data types. CTD now contains over 15 million toxicogenomic relationships. To navigate this sea of data, we added several new features, including DiseaseComps (which finds comparable diseases that share toxicogenomic profiles), statistical scoring for inferred gene-disease and pathway-chemical relationships, filtering options for several tools to refine user analysis and our new Gene Set Enricher (which provides biological annotations that are enriched for gene sets). To improve data visualization, we added a Cytoscape Web view to our ChemComps feature, included color-coded interactions and created a 'slim list' for our MEDIC disease vocabulary (allowing diseases to be grouped for meta-analysis, visualization and better data management). CTD continues to promote interoperability with external databases by providing content and cross-links to their sites. 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.
引用
收藏
页码:D1104 / D1114
页数:11
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