[CTD-Users] Comparative Toxicogenomics Database (CTD) update

[Carolyn Mattingly]

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. 
0900555.

Coming Soon…
·  Additional integration with other publicly available biological  
databases
·  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.

Sincerely,
The CTD team
_________________________________
Carolyn J. Mattingly, PhD
Investigator
Mount Desert Island Biological Laboratory
PO Box 35
Old Bar Harbor Rd
Salisbury Cove, ME 04672

T: 207.288.9880 ext. 109
F: 207.288.2130
cmattin at mdibl.org
http://ctd.mdibl.org




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