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This article is part of the supplement: Twelfth International Conference on Bioinformatics (InCoB2013): Computational Biology

Open Access Research

Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data

Chin Lui Goi13, Peter Little123* and Chao Xie23*

Author Affiliations

1 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore

2 Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore

3 Singapore Centre on Environmental Life Sciences Engineering (SCELSE) Nanyang Technological University 60 Nanyang Drive, SBS-01N-27 Singapore 637551, Singapore

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BMC Genomics 2013, 14(Suppl 5):S2  doi:10.1186/1471-2164-14-S5-S2

Published: 16 October 2013



Cell type and TF specific interactions between Transcription Factors (TFs) and cofactors are essential for transcriptional regulation through recruitment of general transcription machinery to gene promoter regions and their identification heavily reliant on protein interaction assays.


Using TF targeted chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) data from Encyclopedia of DNA Elements (ENCODE), we report cell type and TF specific TF-cofactor interactions captured in vivo through enrichments of non target cofactor binding site motifs within ChIP-seq peaks. We observe enrichments in both known and novel cofactor motifs.


Given the regulatory implications which TF and cofactor interactions have on a cell's phenotype, their identification is necessary but challenging. Here we present the findings to our analyses surrounding the investigation of TF-cofactor interactions encoded within TF ChIP-seq peaks. Novel cofactor binding site enrichments observed provides valuable insight into TF and cell type specific interactions driving TF interactions.