title: Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.
abstract: BACKGROUND
  Chromatin immunoprecipitation (ChIP) coupled to high-throughput sequencing (ChIP-Seq) techniques can reveal DNA regions bound by transcription factors (TF). Analysis of the ChIP-Seq regions is now a central component in gene regulation studies. The need remains strong for methods to improve the interpretation of ChIP-Seq data and the study of specific TF binding sites (TFBS).
  
  
  RESULTS
  We introduce a set of methods to improve the interpretation of ChIP-Seq data, including the inference of mediating TFs based on TFBS motif over-representation analysis and the subsequent study of spatial distribution of TFBSs. TFBS over-representation analysis applied to ChIP-Seq data is used to detect which TFBSs arise more frequently than expected by chance. Visualization of over-representation analysis results with new composition-bias plots reveals systematic bias in over-representation scores. We introduce the BiasAway background generating software to resolve the problem. A heuristic procedure based on topological motif enrichment relative to the ChIP-Seq peaks' local maximums highlights peaks likely to be directly bound by a TF of interest. The results suggest that on average two-thirds of a ChIP-Seq dataset's peaks are bound by the ChIP'd TF; the origin of the remaining peaks remaining undetermined. Additional visualization methods allow for the study of both inter-TFBS spatial relationships and motif-flanking sequence properties, as demonstrated in case studies for TBP and ZNF143/THAP11.
  
  
  CONCLUSIONS
  Topological properties of TFBS within ChIP-Seq datasets can be harnessed to better interpret regulatory sequences. Using GC content corrected TFBS over-representation analysis, combined with visualization techniques and analysis of the topological distribution of TFBS, we can distinguish peaks likely to be directly bound by a TF. The new methods will empower researchers for exploration of gene regulation and TF binding.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Worsley Hunt
authors.forename: Anthony
authors.initials: A
authors.lastname: Mathelier
authors.forename: Luis
authors.initials: L
authors.lastname: Del Peso
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. wyeth@cmmt.ubc.ca.
authors.forename: Wyeth W
authors.initials: WW
authors.lastname: Wasserman
mesh_terms: D000465:Algorithms; D000818:Animals; D001482:Base Composition; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D059372:Nucleotide Motifs; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors