Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules

Frontiers in Genetics
Mirko RonzioGiulio Pavesi

Abstract

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq) has opened new avenues of research in the genome-wide characterization of regulatory DNA-protein interactions at the genetic and epigenetic level. As a consequence, it has become the de facto standard for studies on the regulation of transcription, and literally thousands of data sets for transcription factors and cofactors in different conditions and species are now available to the scientific community. However, while pipelines and best practices have been established for the analysis of a single experiment, there is still no consensus on the best way to perform an integrated analysis of multiple datasets in the same condition, in order to identify the most relevant and widespread regulatory modules composed by different transcription factors and cofactors. We present here a computational pipeline for this task, that integrates peak summit colocalization, a novel statistical framework for the evaluation of its significance, and motif enrichment analysis. We show examples of its application to ENCODE data, that led to the identification of relevant regulatory modules composed of different factors, as well as the organization on DNA of the binding m...Continue Reading

References

May 17, 2000·Bioinformatics·G D Stormo
Nov 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Peter J SaboJohn A Stamatoyannopoulos
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Feb 28, 2009·Journal of Cellular Biochemistry·Melissa J Fullwood, Yijun Ruan
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Apr 14, 2011·Bioinformatics·Philip Machanick, Timothy L Bailey
May 17, 2011·Genome Biology·Sean ThomasJohn A Stamatoyannopoulos
May 24, 2011·Nucleic Acids Research·Zhizhuo ZhangEdwin Cheung
Apr 21, 2012·Briefings in Bioinformatics·Federico ZambelliGiulio Pavesi
May 23, 2012·Nucleic Acids Research·Timothy L Bailey, Philip Machanick
Sep 8, 2012·Nature·Mark B GersteinMichael Snyder
Sep 8, 2012·Genome Research·Stephen G LandtMichael Snyder
Nov 19, 2013·Cell·Dan XieMichael Snyder
Feb 20, 2015·Nature·UNKNOWN Roadmap Epigenomics ConsortiumManolis Kellis
Feb 26, 2016·Nature Methods·Jeff Vierstra, John A Stamatoyannopoulos
May 14, 2016·Briefings in Bioinformatics·Reuben ThomasKatherine S Pollard
Aug 16, 2016·PloS One·Martin HaubrockEdgar Wingender
Nov 1, 2017·Nucleic Acids Research·Edgar WingenderJürgen Dönitz
Nov 10, 2017·Nature Protocols·Jason Ernst, Manolis Kellis
Nov 11, 2017·Nucleic Acids Research·Carrie A DavisJ Michael Cherry
Oct 12, 2018·Bioinformatics·Chakravarthi KanduriGeir Kjetil Sandve
Dec 6, 2018·Nucleic Acids Research·Marius GheorgheAnthony Mathelier
May 1, 2019·EMBO Reports·Janet C HarwoodAdrian J Harwood
Oct 19, 2019·Briefings in Bioinformatics·Stefania SalvatoreGeir Kjetil Sandve

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Citations

Dec 29, 2020·PLoS Computational Biology·Mirko RonzioDiletta Dolfini

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Methods Mentioned

BETA
ChIP-Seq
footprinting
SELEX
RNA-Seq

Software Mentioned

bedtools
ChromHMM
Weeder
ENCODE Epigenomics
Atlas
HOMER
ReMap
ChIP
MEME
house

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