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Feb 16, 2011;6 (2): e16432.

An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.

Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphael Gottardo
Author Information
  1. Eloi Mercier: Computational Biology Unit, Institut de Recherche Clinique de Montreal, Montreal, Canada.
PMID: 21358819 DOI: 10.1371/journal.pone.0016432

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.

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Grants

  1. R01-HG005692/NHGRI NIH HHS
  2. Z01 ES101765/Intramural NIH HHS
  3. R01 HG005692-01/NHGRI NIH HHS
  4. R01 HG005692/NHGRI NIH HHS
  5. ES101765-05/NIEHS NIH HHS
  6. R01 HG005692-02/NHGRI NIH HHS

MeSH Term

Algorithms
Base Sequence
Binding Sites
CCCTC-Binding Factor
Chromatin
Chromatin Immunoprecipitation
Chromosome Mapping
HeLa Cells
Hepatocyte Nuclear Factor 3-alpha
Humans
Molecular Sequence Data
Protein Binding
Repressor Proteins
STAT1 Transcription Factor
Sequence Analysis, DNA
Sequence Homology
Systems Integration
Transcription Factors
Tumor Cells, Cultured

Chemicals

CCCTC-Binding Factor
CTCF protein, human
Chromatin
FOXA1 protein, human
Hepatocyte Nuclear Factor 3-alpha
Repressor Proteins
STAT1 Transcription Factor
Transcription Factors
Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Validation Study
Article has an altmetric score of 1

Word Cloud

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