CoMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data.

ABSTRACT:

Motivation

ChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a coregulator. Biologists are interested in knowing which coregulatory factor motifs may be present in the sequences bound by the protein ChIP'ed.

Results

We present a finite mixture framework with an expectation-maximization algorithm that considers two motifs jointly and simultaneously determines which sequences contain both motifs, either one or neither of them. Tested on 10 simulated ChIP-seq datasets, our method performed better than repeated application of MEME in predicting sequences containing both motifs. When applied to a mouse liver Foxa2 ChIP-seq dataset involving ~ 12 000 400-bp sequences, coMOTIF identified co-occurrence o

SUBMITTER: Xu M 

PROVIDER: S-EPMC3179653 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature