GenomeRunner is accessible at http://www.integrativegenomics.org/
The release version of GenomeRunner is maintained at https://github.com/mdozmorov/genomerunner_web.
GenomeRunner is currently developed in shiny branch.
See the main documentation on https://mdozmorov.github.io/grdocs/index.html
GenomeRunner web is a tool for investigation of potential regulatoy impact of sets of single nucleotide polymorphisms (SNPs) by considering their co-localization with functional/regulatory genome annotation data (regulatory datasets). It is particularly useful for the interpretation of functional roles of sets of rare variants and SNPs in non-protein coding regions. An example of GenomeRunner’s results can be found in the analysis of Sjogren’s syndrome GWAS (Nature Genetics ), where it identified RFX5 transcription factor binding site as the most statistically significantly co-localized with the set of disease-associated SNPs.
GenomeRunner web calculates enrichment p-values (Chi-squared test) by evaluating whether a set of SNPs co-localizes with regulatory datasets more often that could happen by chance. For three or more sets of SNPs, GenomeRunner web performs the ‘regulatory similarity’ analysis by correlating SNP set-specific regulatory enrichment profiles. Downloadable results are visualized as interactive heatmaps and tables.