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PolyDoms


NAR Molecular Biology Database Collection entry number 973
Jegga A.G.1,2, Gowrisankar S.1,3, Chen J.1,3 and Aronow B.J.1,2,3
1Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 2Department of Pediatrics, College of Medicine, 3Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45229, USA

Database Description

PolyDoms is an integrated database of human coding SNPs and related data. Unlike other databases of similar nature, apart from integrating several cSNP and protein-related information resources, we predict the implications of the non-synonymous SNPs using two well known algorithms (SIFT and PolyPhen). All these results are presented in an intuitive visualization that depicts the cSNPs mapped onto protein domains and highlights those nsSNPs that are potentially damaging/deleterious or have been reported as disease allelic variants (based on OMIM). The query interface also supports searching for a list of proteins associated with any gene ontology term, pathway, disease term, or gene family. Results can also be downloaded as a spreadsheet. The visualization page also provides links to several other related sources and dynamic links to literature references. We strongly believe that the nsSNPs that are predicted to be functional upon evolutionary conservation analysis and are located in functional protein domains and/or motifs constitute an excellent resource for specific molecular studies to elucidate the direct consequences of these variations on protein function and interaction, which could also eventually help the molecular epidemiology and genetic studies aiming to reveal the genetic variationdisease risk association.

Acknowledgements

The authors would like to thank Drs. Deb Nickerson, Robert Livingston, and RobertWeiss for super discussions and the Ohio Supercomputer Center for the assistance inusing their supercomputing clusters to run whole genome SIFT and PolyPhen analyses.This work was supported by grants NCI UO1 CA84291-07 (Mouse Models of HumanCancer Consortium), NIH R24 DK 064403 (Digestive Diseases Research DevelopmentCenter - DDRDC), NIEHS ES-00-005 (Comparative Mouse Genome CentersConsortium) and NIEHS P30-ES06096 (Center for Environmental Genetics).


Go to the abstract in the NAR 2007 Database Issue.
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