A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs-Reference-Cited by-同舟云学术

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A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs

Published:2012-07-26 Issue:8 Volume:7 Page:1551-1568
ISSN:1754-2189
Container-title:Nature Protocols
language:en
Short-container-title:Nat Protoc

Author:

Thomas-Chollier Morgane,Darbo Elodie,Herrmann Carl,Defrance Matthieu,Thieffry Denis,van Helden Jacques

Publisher

Springer Science and Business Media LLC

Subject

General Biochemistry, Genetics and Molecular Biology

Link

https://www.nature.com/articles/nprot.2012.088.pdf

Reference46 articles.

1. Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).

2. Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007).

3. Pepke, S., Wold, B. & Mortazavi, A. Computation for ChIP-seq and RNA-seq studies. Nat. Methods 6, S22–S32 (2009).

4. Boeva, V. et al. De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res. 38, e126 (2010).

5. Machanick, P. & Bailey, T.L. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27, 1696 (2011).

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