Inferring direct DNA binding from ChIP-seq.

ABSTRACT: Genome-wide binding data from transcription factor ChIP-seq experiments is the best source of information for inferring the relative DNA-binding affinity of these proteins in vivo. However, standard motif enrichment analysis and motif discovery approaches sometimes fail to correctly identify the binding motif for the ChIP-ed factor. To overcome this problem, we propose 'central motif enrichment analysis' (CMEA), which is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ChIP-seq peak regions. We describe a novel visualization and statistical analysis tool--CentriMo--that identifies the region of maximum central enrichment in a set of ChIP-seq peak regions

SUBMITTER: Bailey TL 

PROVIDER: S-EPMC3458523 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature