Dataset Information

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach.

ABSTRACT: The majority of variation identified by genome wide association studies falls in non-coding genomic regions and is hypothesized to impact regulatory elements that modulate gene expression. Here we present a statistically rigorous software tool GREGOR (Genomic Regulatory Elements and Gwas Overlap algoRithm) for evaluating enrichment of any set of genetic variants with any set of regulatory features. Using variants from five phenotypes, we describe a data-driven approach to determine the tissue and cell types most relevant to a trait of interest and to identify the subset of regulatory features likely impacted by these variants. Last, we experimentally evaluate six predicted functional variants at six lipid-associated loci and demonstrate significant evidence for allele-specific impact on expression levels. GREGOR systematically evaluates enrichment of genetic variation with the vast collection of regulatory data available to explore novel biological mechanisms of disease and guide us toward the functional variant at trait-associated loci.GREGOR, including source code, documentation, examples, and executables, is available at http://genome.sph.umich.edu/wiki/GREGOR.cristen@umich.eduSupplementary data are available at Bioinformatics online.

SUBMITTER: Schmidt EM

PROVIDER: S-EPMC4612390 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach.

Schmidt Ellen M EM Zhang Ji J Zhou Wei W Chen Jin J Mohlke Karen L KL Chen Y Eugene YE Willer Cristen J CJ

Bioinformatics (Oxford, England) 20150416 16

<h4>Motivation</h4>The majority of variation identified by genome wide association studies falls in non-coding genomic regions and is hypothesized to impact regulatory elements that modulate gene expression. Here we present a statistically rigorous software tool GREGOR (Genomic Regulatory Elements and Gwas Overlap algoRithm) for evaluating enrichment of any set of genetic variants with any set of regulatory features. Using variants from five phenotypes, we describe a data-driven approach to dete ...[more]

PMID: 25886982

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Dataset Information

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach.

Publications

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach.

Similar Datasets

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