MAnorm2 for quantitatively comparing groups of ChIP-seq samples.

Genome Research
Shiqi TuZhen Shao

Abstract

Eukaryotic gene transcription is regulated by a large cohort of chromatin-associated proteins, and inferring their differential binding sites between cellular contexts requires a rigorous comparison of the corresponding ChIP-seq data. We present MAnorm2, a new computational tool for quantitatively comparing groups of ChIP-seq samples. MAnorm2 uses a hierarchical strategy for normalization of ChIP-seq data and assesses within-group variability of ChIP-seq signals based on an empirical Bayes framework. In this framework, MAnorm2 allows for abundant differential ChIP-seq signals between groups of samples as well as very different global within-group variability between groups. Using a number of real ChIP-seq data sets, we observed that MAnorm2 clearly outperformed existing tools for differential ChIP-seq analysis, especially when the groups of samples being compared had distinct global within-group variability.

References

Dec 19, 2003·Nucleic Acids Research·Donna KarolchikW James Kent
Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Aug 1, 2007·Nature Methods·Elaine R Mardis
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Mar 29, 2011·Nature·Jason ErnstBradley E Bernstein
Mar 20, 2012·Genome Biology·Zhen ShaoDavid J Waxman
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Oct 19, 2013·Science·Maya KasowskiMichael Snyder
Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth
Aug 12, 2014·Science·David Lara-AstiasoIdo Amit
Sep 17, 2014·Nature Reviews. Genetics·Clifford A Meyer, X Shirley Liu
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Feb 5, 2015·Nature Reviews. Molecular Cell Biology·Sven HeinzChristopher K Glass
Feb 20, 2015·Nature·UNKNOWN Roadmap Epigenomics ConsortiumManolis Kellis
Aug 25, 2015·Cell·Sebastian M WaszakEmmanouil T Dermitzakis
Jan 15, 2016·Briefings in Bioinformatics·Sebastian SteinhauserCarl Herrmann
Mar 17, 2016·Briefings in Bioinformatics·Ryuichiro Nakato, Katsuhiko Shirahige
Oct 7, 2017·Cell Stem Cell·Menno Ter HuurneHendrik G Stunnenberg
Jun 19, 2019·Cancer Research·Zhoufeng WangWeimin Li
Jun 30, 2019·Scientific Reports·Haley M AmemiyaAlan P Boyle

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