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

Pinglang Wang | Zendy; Manhong Dai | Zendy; Weijian Xuan | Zendy; Richard C. McEachin | Zendy; Anne Jackson | Zendy; Laura J. Scott | Zendy; Brian D. Athey | Zendy; Stanley J. Watson | Zendy; Fan Meng | Zendy

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

Author(s) -

Pinglang Wang,

Manhong Dai,

Weijian Xuan,

Richard C. McEachin,

Anne Jackson,

Laura J. Scott,

Brian D. Athey,

Stanley J. Watson,

Fan Meng

Publication year - 2006

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btl241

Subject(s) - snp , tag snp , international hapmap project , single nucleotide polymorphism , dbsnp , biology , computational biology , snp genotyping , genetics , functional genomics , genome wide association study , annotation , function (biology) , genome , human genome , genomics , gene , genotype

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.

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