An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq

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dc.contributor.authorMercier, E.
dc.contributor.authorDroit, A.
dc.contributor.authorLi, L.
dc.contributor.authorRobertson, G.
dc.contributor.authorZhang, Xuekui
dc.contributor.authorGottardo, R.
dc.date.accessioned2021-08-18T18:25:50Z
dc.date.available2021-08-18T18:25:50Z
dc.date.copyright2011en_US
dc.date.issued2011
dc.description.abstractChIP-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.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipRaphael Gottardo was supported by National Institutes of Health (NIH) grant no. R01-HG005692; Leping Li was supported in part by Intramural Research Program of the NIH, National Institute of Environmental Health Sciences (ES101765-05); Arnaud Droit was supported by The Network of Applied Genetic Medicine (RMGA); and Gordon Robertson was supported by the MORGEN (Dissecting Gene Expression Networks in Mammalian Organogenesis) project, which was funded by Genome Canada, Genome British Columbia, the Heart and Stroke Foundation of BC/Yukon, the British Columbia Knowledge Development Fund, the Juvenile Diabetes Research Foundation, the Vancouver Foundation, the BC Cancer Foundation, and the Michael Smith Foundation for Health Research.en_US
dc.identifier.citationMercier, E., Droit, A., Li, L., Robertson, G., Zhang, X., Gottardo, R. (2011). An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq. PLoS ONE, 6(2). https://doi.org/10.1371/journal.pone.0016432en_US
dc.identifier.urihttps://doi.org/10.1371/journal.pone.0016432
dc.identifier.urihttp://hdl.handle.net/1828/13275
dc.language.isoenen_US
dc.publisherPLoS ONEen_US
dc.subject.departmentDepartment of Mathematics and Statistics
dc.titleAn Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seqen_US
dc.typeArticleen_US

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