GenomeRunner: automating genome exploration

Motivation: One of the challenges in interpreting high-throughput genomic studies such as a genome-wide associations, microarray or ChIP-seq is their open-ended nature-once a set of experimentally identified regions is identified as statistically significant, at least two questions arise: (i) besides P-value, do any of these significant regions stand out in terms of biological implications? (ii) Does the set of significant regions, as a whole, have anything in common genome wide? These issues are difficult to address because of the growing number of annotated genomic features (e. g. single nucleotide polymorphisms, transcription factor binding sites, methylation peaks, etc.), and it is difficult to know a priori which features would be most fruitful to analyze. Our goal is to provide partial automation of this process to begin examining associations between experimental features and annotated genomic regions in a hypothesis-free, data-driven manner. Results: We created GenomeRunner-a tool for automating annotation and enrichment of genomic features of interest (FOI) with annotated genomic features (GFs), in different organisms. Besides simple association of FOIs with known GFs GenomeRunner tests whether the enriched FOIs, as a group, are statistically associated with a large and growing set of genomic features. Availability: GenomeRunner setup files and source code are freely available at http://sourceforge.net/projects/genomerunner.