Dataset Information
GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets.
Ontology highlight
ABSTRACT: Motivation
The growing amount of regulatory data from the ENCODE, Roadmap Epigenomics and other consortia provides a wealth of opportunities to investigate the functional impact of single nucleotide polymorphisms (SNPs). Yet, given the large number of regulatory datasets, researchers are posed with a challenge of how to efficiently utilize them to interpret the functional impact of SNP sets.Results
We developed the GenomeRunner web server to automate systematic statistical analysis of SNP sets within a regulatory context. Besides defining the functional impact of SNP sets, GenomeRunner implements novel regulatory similarity/differential analyses, and cell type-specific regulatory enrichment analysis. Validated against literature- and disease ontology-based approaches, analysis of 39 disease/trait-associated SNP sets demonstrated that the functional impact of SNP sets corresponds to known disease relationships. We identified a group of autoimmune diseases with SNPs distinctly enriched in the enhancers of T helper cell subpopulations, and demonstrated relevant cell type-specificity of the functional impact of other SNP sets. In summary, we show how systematic analysis of genomic data within a regulatory context can help interpreting the functional impact of SNP sets.Availability and implementation
GenomeRunner web server is freely available at http://www.integrativegenomics.org/Contact
mikhail.dozmorov@gmail.comSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Dozmorov MG
PROVIDER: S-EPMC4965636 | biostudies-literature | 2016 Aug
REPOSITORIES: biostudies-literature
Publications
GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets.
Bioinformatics (Oxford, England) 20160401 15
<h4>Motivation</h4>The growing amount of regulatory data from the ENCODE, Roadmap Epigenomics and other consortia provides a wealth of opportunities to investigate the functional impact of single nucleotide polymorphisms (SNPs). Yet, given the large number of regulatory datasets, researchers are posed with a challenge of how to efficiently utilize them to interpret the functional impact of SNP sets.<h4>Results</h4>We developed the GenomeRunner web server to automate systematic statistical analys ...[more]