Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data.

ABSTRACT: Identifying enhancers regulating gene expression remains an important and challenging task. While recent sequencing-based methods provide epigenomic characteristics that correlate well with enhancer activity, it remains onerous to comprehensively identify all enhancers across development. Here we introduce a computational framework to identify tissue-specific enhancers evolving under purifying selection. First, we incorporate high-confidence binding site predictions with target gene functional enrichment analysis to identify transcription factors (TFs) likely functioning in a particular context. We then search the genome for clusters of binding sites for these TFs, overcoming previous constraints associated with biased manual curation of TFs or enhancers. Applying our method to the placent

SUBMITTER: Tuteja G 

PROVIDER: S-EPMC3907286 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature