An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Date
2011
Authors
Mercier, E.
Droit, A.
Li, L.
Robertson, G.
Zhang, Xuekui
Gottardo, R.
Journal Title
Journal ISSN
Volume Title
Publisher
PLoS ONE
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.
Description
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Citation
Mercier, 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.0016432