[CTD-Users] Comparative Toxicogenomics Database (CTD) update
cmattin at mdibl.org
Tue Jun 2 12:00:31 EDT 2009
Dear CTD user,
We invite you to visit the Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org
) to explore hypotheses about chemical-gene-disease connections and to
take advantage of the significant additions we made over the last 6
months. We highlight some of these additions below.
Curated Data Statistics (May 2008)
· 167,235 curated interactions involving 4,770 unique chemicals and
15,910 genes and proteins
· 8,102 curated gene-disease relationships
· 5,070 curated chemical-disease relationships
Detailed statistics can be found here: http://ctd.mdibl.org/about/dataStatus.go
New Analysis Tools
· VennViewer – compare associated data (e.g., interacting genes,
pathways, GO annotations) for up to 3 chemicals, genes or diseases (http://ctd.mdibl.org/tools/
· ChemComps – identify chemicals with gene interaction profiles
similar to your chemical of interest (accessible via Chemical pages).
· GeneComps – identify genes with chemical interaction profiles
similar to your gene of interest (accessible via Gene pages).
· Additional query options – identifying curated chemical-gene
interactions by degree (e.g., increased expression) or aspect of an
interacting gene or protein (e.g., promoter)
CTD-related Publications (2009)
· Davis, A.P., Murphy, C.G., Saraceni-Richards, C.A., et al. (2009)
Comparative Toxicogenomics Database: a knowledgebase and discovery
tool for chemical-gene-disease networks. Nucleic Acids Res. 37, D786-92.
· Gohlke, J.M., Thomas, R., Zhang, Y., et al. (2009) Genetic and
environmental pathways to complex diseases. BMC Syst Biol. 3, 46.
· Mattingly, C. J., T. Hampton, K. Brothers, N. E. Griffin and A. J.
Planchart (2009). Perturbation of defense pathways by low-dose arsenic
exposure in zebrafish embryos. Environ Health Perspect doi:10.1289/ehp.
· Additional integration with other publicly available biological
· Integration of text mining with our manual curation workflow
Recently we started contacting authors for whom we have email
information, requesting that they review data we curated from their
published articles. We are particularly grateful to those of you that
have responded to this request.
Thank you for your continued support and use of CTD. Please send us
your feedback so that we can help you meet your environmental health
research and education goals.
The CTD team
Carolyn J. Mattingly, PhD
Mount Desert Island Biological Laboratory
PO Box 35
Old Bar Harbor Rd
Salisbury Cove, ME 04672
T: 207.288.9880 ext. 109
cmattin at mdibl.org
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