title: SNPpath: characterizing cattle SNPs by enriched pathway terms.
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.
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, China.
authors.forename: Qishan
authors.initials: Q
authors.lastname: Wang
authors.forename: Minghui
authors.initials: M
authors.lastname: Wang
authors.forename: Yumei
authors.initials: Y
authors.lastname: Yang
authors.forename: Yuchun
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics* / Q000254:growth & development; D055106:Genome-Wide Association Study; D053858:Metabolic Networks and Pathways; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*