Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells.

ABSTRACT:

Background

To facilitate deciphering underlying transcriptional regulatory circuits in mouse embryonic stem (ES) cells, recent ChIP-seq data provided genome-wide binding locations of several key transcription factors (TFs); meanwhile, existing efforts profiled gene expression in ES cells and in their early differentiated state. It has been shown that the gene expression profiles are correlated with the binding of these TFs. However, it remains unclear whether other TFs, referred to as cofactors, participate the gene regulation by collaborating with the ChIP-seq TFs.

Results

Based on our analyses of the ES gene expression profiles and binding sites of potential cofactors in vicinity of the ChIP-seq TF binding locations, we identified a list of co-binding features that show si

SUBMITTER: Chen G 

PROVIDER: S-EPMC3265564 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature