title: GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets.
abstract: 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.
  
  
  
  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.
  
  
  
  GenomeRunner web server is freely available at http://www.integrativegenomics.org/
  
  
  
  mikhail.dozmorov@gmail.com
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Mikhail G
authors.initials: MG
authors.lastname: Dozmorov
authors.affiliation: Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Lukas R
authors.initials: LR
authors.lastname: Cara
authors.affiliation: Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
authors.forename: Cory B
authors.initials: CB
authors.lastname: Giles
authors.affiliation: Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Wren
mesh_terms: D001331:Automation; D003201:Computers; D030541:Databases, Genetic; D023281:Genomics; D020641:Polymorphism, Single Nucleotide; D012984:Software