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Anim Sci J. 2012 Apr;83(4):279-83. doi: 10.1111/j.1740-0929.2011.00952.x. Epub 2011 Sep 12.

SNPpath: characterizing cattle SNPs by enriched pathway terms.

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  • 1School of Agriculture and Biology, Shanghai Jiao Tong University, China.

Abstract

High-density single nucleotide polymorphism (SNP) microarrays have made large-scale genome-wide association studies (GWAS) and genomic selection (GS) feasible. Valuable insight into the genetic basis underlying complex polygenic traits will likely be gained by considering functionally related sets of genes simultaneously. SNPpath, a suite of computer-generated imagery-based web servers has been developed to automatically annotate and characterize cattle SNPs by enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway terms. The SNPpath allows users to navigate and analysis large SNP sets and is the only web server currently providing pathway annotations of cattle SNPs in National Center for Biotechnology Information's dbSNP database and three commercial platforms. Hence, we describe SNPpath and provide details of the query options, as well as biological examples of use. The SNPpath may be favorable for the analysis of combining SNP association analysis with pathway-driven gene set enrichment analysis and is freely available at http://klab.sjtu.edu.cn/SNPpath.

© 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.

PMID:
22515686
[PubMed - indexed for MEDLINE]
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