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Genetics. 2014 May;197(1):285-9. doi: 10.1534/genetics.113.160341. Epub 2014 Feb 21.

SNP2GO: functional analysis of genome-wide association studies.

Author information

1
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria.

Abstract

Genome-wide association studies (GWAS) are designed to identify the portion of single-nucleotide polymorphisms (SNPs) in genome sequences associated with a complex trait. Strategies based on the gene list enrichment concept are currently applied for the functional analysis of GWAS, according to which a significant overrepresentation of candidate genes associated with a biological pathway is used as a proxy to infer overrepresentation of candidate SNPs in the pathway. Here we show that such inference is not always valid and introduce the program SNP2GO, which implements a new method to properly test for the overrepresentation of candidate SNPs in biological pathways.

KEYWORDS:

GWAS; Gene Ontology; SNP; linkage disequilibrium

PMID:
24561481
PMCID:
PMC4012486
DOI:
10.1534/genetics.113.160341
[Indexed for MEDLINE]
Free PMC Article

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