SNPxGE2: a database for human SNP–coexpression associations

AbstractMotivation: Recently, gene–coexpression relationships have been found to be often conditional and dynamic. Many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations.Results: The SNPxGE2 database contains the computationally predicted human SNP–coexpression associations, i.e. the differential coexpression between two genes is associated with the genotypes of an SNP. These data were generated from a large-scale association study that was based on the HapMap phase I data, which covered 269 individuals from 4 human populations, 556 873 SNPs and 15 000 gene expression profiles. In order to reduce the computational cost, the SNP–coexpression associations were assessed using gap/substitution models, proven to have a comparable power to logistic regression models. The results, at a false discovery rate (FDR) cutoff of 0.1, consisted of 44 769 and 50 792 SNP–coexpression associations based on single and pooled populations, respectively, and can be queried in the SNPxGE2 database via either gene symbol or reference SNP ID. For each reported association, a detailed information page is provided.Availability:  http://lambchop.ads.uga.edu/snpxge2/index.phpContact:  wyp1125@uga.edu, rrekaya@uga.edu