Model-based analysis of ChIP-Seq (MACS).

Genome Biology
Yong ZhangX Shirley Liu

Abstract

We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.

References

May 26, 2006·Annual Review of Genomics and Human Genetics·Tae Hoon Kim, Bing Ren
Aug 10, 2006·Proceedings of the National Academy of Sciences of the United States of America·W Evan JohnsonX Shirley Liu
Oct 3, 2006·Nature Genetics·Jason S CarrollMyles Brown
Nov 24, 2006·Nature·Richard RedonMatthew E Hurles
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Jul 3, 2007·Nature·Tarjei S MikkelsenBradley E Bernstein
Aug 31, 2007·Genome Biology·Jun S SongX Shirley Liu

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Citations

Jan 14, 2012·Cellular and Molecular Life Sciences : CMLS·Nuria C Bramswig, Klaus H Kaestner
Sep 6, 2013·Acta Neuropathologica·Katja KobowIngmar Blümcke
Nov 30, 2012·Chromosoma·Elisa FioritoAntoni Hurtado
May 17, 2012·Journal of Mammary Gland Biology and Neoplasia·Siv GilfillanAntoni Hurtado
Oct 1, 2013·Cell Death and Differentiation·B WangE C Ren
Jun 7, 2013·Journal of Human Genetics·Hiroshi Kimura
Aug 30, 2011·Nature·Mitchell GuttmanEric S Lander
Jun 23, 2012·Nature·Matthew F BarberKatrin F Chua
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 21, 2012·Nature·Peng LiWarren J Leonard
May 24, 2013·Nature·Emily C DykhuizenGerald R Crabtree
Jun 4, 2013·Nature·Rahul RoychoudhuriNicholas P Restifo
Jun 25, 2013·Nature·Albert E AlmadaPhillip A Sharp
Jun 19, 2013·Nature Biotechnology·Vibhor KumarShyam Prabhakar
Aug 23, 2011·Nature Cell Biology·Constance RichterJuergen A Knoblich
Jul 16, 2013·Nature Cell Biology·Erna MagnúsdóttirM Azim Surani
May 9, 2013·Nature Communications·Enid Yi Ni LamShankar Balasubramanian
Jun 14, 2013·Nature Communications·Haiyun GanFuchou Tang
Sep 18, 2013·Nature Communications·Michael N C FletcherKerstin B Meyer
Dec 20, 2011·Nature Genetics·Vijay K TiwariChristian Beisel

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Methods Mentioned

BETA
immunoprecipitation
ChIP-Seq
ChIP
ChIP-chip
ChIPSeq
PCR

Software Mentioned

Linux
QuEST
MAT
Solexa
MA2C
MACS
ChIPSeq Peak Finder
MATscore
FindPeaks

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