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

[Carolyn Mattingly]

Dear CTD user,
We encourage you to visit the Comparative Toxicogenomics Database  
(CTD; http://ctd.mdibl.org) to take advantage of the significant  
additions we made over the last year, including a large increase in  
manually curated data, integration of new data sets (e.g., KEGG  
pathways) and implementation of data analysis tools.  We highlight  
some of these additions and new publications below.

Curated Data Statistics (October 2008)
·  132,412 curated interactions involving 4,144 unique chemicals and  
14,220 genes and proteins
·  6,985 curated gene-disease relationships
·  3,539 curated chemical-disease relationships
All statistics can be found here: http://ctd.mdibl.org/about/dataStatus.go

New Analysis Tools
·  Data downloads - Download large curated data sets to perform  
analyses with external tools.
·  Batch query - Download data associated with a list of chemicals,  
diseases or genes of interest (e.g., curated chemical-gene  
interactions, gene ontology annotations, pathways).

CTD Publications (2008)
·  Davis AP, Murphy C, Saraceni-Richards CA, Rosenstein MC, Wiegers  
TC, and Mattingly CJ. Comparative Toxicogenomics Database (CTD): a  
knowledgebase and discovery tool for chemical-gene-disease networks.  
Nucleic Acids Research 2008; doi: 10.1093/nar/gkn580.
·  Davis AP, Murphy CG, Rosenstein MC, Wiegers T, Boyer JL and  
Mattingly CJ.  Using the Comparative Toxicogenomics Database to  
explore integrated chemical-gene disease relationships: Arsenic as a  
case study. BMC Medical Genomics 2008, 1:48
·  Mattingly C.J. 2008 Chemical databases for environmental health and  
clinical research.  Toxicological Letters 2008 (TOXLET-D-08-00461R1;  
in press).

Analysis Tools Coming Soon…
·  VennViewer – compare associated data (e.g., interacting genes,  
pathways) for chemicals, genes or diseases
·  ChemProfiler – identify genes with chemical profiles similar to  
your gene of interest.
·  GeneProfiler – identify chemicals with gene profiles similar to  
your chemical of interest.
·  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)

Thank you for your continued support and please send us your feedback  
so that we can help you meet your environmental health research 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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