Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Jun:Chapter 2:2.14.1-2.14.14.
doi: 10.1002/0471250953.bi0214s34.

Using MACS to identify peaks from ChIP-Seq data

Jianxing Feng  1 , Tao Liu  2 , Yong Zhang  1
Affiliations
Free PMC article

Using MACS to identify peaks from ChIP-Seq data

Jianxing Feng et al. Curr Protoc Bioinformatics. 2011 Jun.
Free PMC article

Abstract

Model-based Analysis of ChIP-Seq (MACS) is a command-line tool designed by X. Shirley Liu and colleagues to analyze data generated by ChIP-Seq experiments in eukaryotes, especially mammals. MACS can be used to identify transcription factor binding sites and histone modification-enriched regions if the ChIP-Seq data, with or without control samples, are given. This unit describes two basic protocols that provide detailed information on how to use MACS to identify either the binding sites of a transcription factor or the enriched regions of a histone modification with broad peaks. Furthermore, the basic ideas for the MACS algorithm and its appropriate usage are discussed.

PubMed Disclaimer

Figures

Figure 2.14.1
Figure 2.14.1
Shifting size model for FoxA1 ChIP-Seq data.
Figure 2.14.2
Figure 2.14.2
Visualization of wiggle and BED files for FoxA1 ChIP-Seq data in Affymetrix IGB. Genome region: chr1: 215,756,000 – 215,757,000.
Figure 2.14.3
Figure 2.14.3
Visualization of wiggle and BED files for H3K27me3 ChIP-Seq data in Affymetrix IGB. Genome region: chr1: 93,627,000 – 93,637,000.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129:823–837. - PubMed
    1. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006;38:1289–1297. - PubMed
    1. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007;316:1497–1502. - PubMed
    1. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. - PMC - PubMed
    1. Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M. FoxA1 translates epigenetic signatures into enhancer driven lineage-specific transcription. Cell. 2008;132:958–970. - PMC - PubMed

Publication types

Substances

LinkOut - more resources