2012 Poster Sessions : GREAT Improves Functional Interpretation of CIS-Regulatory Regions

Student Name : Aaron Wenger
Advisor : Gill Bejerano
Research Areas: Artificial Intelligence
We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to analyze the functional significance of /cis/-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. We apply GREAT to ChIP-seq datasets for SRF, REST, GABP, and Stat3 and recover many functions of these factors that are missed by existing gene-based tools in addition to novel, testable hypotheses. The utility of GREAT is not limited to ChIP-seq, as it can be applied to open chromatin, localized epigenomic markers and similar functional data sets, as well as comparative genomics sets. GREAT is available as a web application and has become the de facto standard for functional analysis of ChIP-seq data.

Aaron Wenger is a graduate student in Gill Bejerano's lab interested how regulatory information is encoded in the genome.