Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions.

ABSTRACT: Multicellular organismal development is controlled by a complex network of transcription factors, promoters and enhancers. Although reliable computational and experimental methods exist for enhancer detection, prediction of their target genes remains a major challenge. On the basis of available literature and ChIP-seq and ChIP-chip data for enhanceosome factor p300 and the transcriptional regulator Gli3, we found that genomic proximity and conserved synteny predict target genes with a relatively low recall of 12-27% within 2 Mb intervals centered at the enhancers. Here, we show that functional similarities between enhancer binding proteins and their transcriptional targets and proximity in the protein-protein interactome improve prediction of target genes. We used all four features to trai

SUBMITTER: Rodelsperger C 

PROVIDER: S-EPMC3074119 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature