title: Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Chin
authors.initials: C
authors.lastname: Goi
authors.forename: Peter
authors.initials: P
authors.lastname: Little
authors.forename: Chao
authors.initials: C
authors.lastname: Xie
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002877:Chromosomes, Human; D004247:DNA / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006367:HeLa Cells; D056945:Hep G2 Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020014:K562 Cells; D010641:Phenotype; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
chemical_list: D002843:Chromatin; D014157:Transcription Factors; D004247:DNA