The SNP ratio test: pathway analysis of genome-wide association datasets | Zendy

Colm Ó'Dúshláine | Zendy; Elaine Kenny | Zendy; Elizabeth A. Heron | Zendy; Ricardo Segurado | Zendy; Michael Gill | Zendy; Derek W. Morris | Zendy; Aiden Corvin | Zendy

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The SNP ratio test: pathway analysis of genome-wide association datasets

Author(s) -

Colm Ó'Dúshláine,

Elaine Kenny,

Elizabeth A. Heron,

Ricardo Segurado,

Michael Gill,

Derek W. Morris,

Aiden Corvin

Publication year - 2009

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/btp448

Subject(s) - genome wide association study , association test , snp , kegg , single nucleotide polymorphism , context (archaeology) , genetic association , computational biology , biology , genetics , gene , genotype , gene ontology , paleontology , gene expression

We present a tool that assesses the enrichment of significant associations from genome-wide association studies (GWAS) in a pathway context. The SNP ratio test (SRT) compares the proportion of significant to all SNPs within genes that are part of a pathway and computes an empirical P-value based on comparisons to ratios in datasets where the assignment of case/control status has been randomized. We applied the SRT to a Parkinson's disease GWAS dataset, using the KEGG database, revealing significance for Parkinson's disease and related pathways.

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