title: An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.
abstract: ChIP-Seq has become the standard method for genome-wide profiling DNA association of transcription factors. To simplify analyzing and interpreting ChIP-Seq data, which typically involves using multiple applications, we describe an integrated, open source, R-based analysis pipeline. The pipeline addresses data input, peak detection, sequence and motif analysis, visualization, and data export, and can readily be extended via other R and Bioconductor packages. Using a standard multicore computer, it can be used with datasets consisting of tens of thousands of enriched regions. We demonstrate its effectiveness on published human ChIP-Seq datasets for FOXA1, ER, CTCF and STAT1, where it detected co-occurring motifs that were consistent with the literature but not detected by other methods. Our pipeline provides the first complete set of Bioconductor tools for sequence and motif analysis of ChIP-Seq and ChIP-chip data.
authors.affiliation: Computational Biology Unit, Institut de Recherche Clinique de Montreal, Montreal, Canada.
authors.forename: Eloi
authors.initials: E
authors.lastname: Mercier
authors.forename: Arnaud
authors.initials: A
authors.lastname: Droit
authors.forename: Leping
authors.initials: L
authors.lastname: Li
authors.forename: Gordon
authors.initials: G
authors.lastname: Robertson
authors.forename: Xuekui
authors.initials: X
authors.lastname: Zhang
authors.forename: Raphael
authors.initials: R
authors.lastname: Gottardo
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods*; D006367:HeLa Cells; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data; D011485:Protein Binding; D012097:Repressor Proteins / Q000378:metabolism; D050794:STAT1 Transcription Factor / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods; D017385:Sequence Homology; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism*; D014407:Tumor Cells, Cultured
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D002843:Chromatin; C496499:FOXA1 protein, human; D051541:Hepatocyte Nuclear Factor 3-alpha; D012097:Repressor Proteins; D050794:STAT1 Transcription Factor; D014157:Transcription Factors