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Bioinformatics 2006 22(14):e523-e529; doi:10.1093/bioinformatics/btl241
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

SNP Function Portal: a web database for exploring the function implication of SNP alleles

Pinglang Wang 1, Manhong Dai 1, Weijian Xuan 1, Richard C. McEachin 2, Anne U. Jackson 3, Laura J. Scott 3, Brian Athey 2, Stanley J. Watson 1 and Fan Meng 1,2,*

1 Molecular and Behavioral Neuroscience Institute and Department of Psychiatry, University of Michigan Ann Arbor, MI 48109
2 National Center for Integrative Biomedical Informatics, University of Michigan Ann Arbor, MI 48109
3 Biostatistics Department, School of Public Health, University of Michigan Ann Arbor, MI 48109

*To whom correspondence should be addressed.

Motivation: Finding the potential functional significance of SNPs is a major bottleneck in understanding genome-wide SNP scanning results, as the related functional data are distributed across many different databases. The SNP Function Portal is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, the SNP Function Portal includes a powerful search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, our system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments.

Availability: http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx

Contact: mengf{at}umich.edu


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