Model-based Analysis of ChIP-Seq (MACS)

被引：11424

作者：

Zhang, Yong ^{[2
]}

Liu, Tao ^{[2
]}

Meyer, Clifford A. ^{[2
]}

Eeckhoute, Jerome ^{[3
,4
,5
]}

Johnson, David S. ^{[6
]}

Bernstein, Bradley E. ^{[7
,8
,9
,10
,11
]}

Nussbaum, Chad ^{[10
,11
]}

Myers, Richard M. ^{[12
]}

Brown, Myles ^{[3
,4
,5
]}

Li, Wei ^{[1
]}

Liu, X. Shirley ^{[2
]}

机构：

[1] Baylor Coll Med, Dept Mol & Cellular Biol, Dan L Duncan Canc Ctr, Div Biostat, Houston, TX 77030 USA

[2] Harvard Univ, Dana Farber Canc Inst, Dept Biostat & Computat Biol, Sch Publ Hlth, Boston, MA 02115 USA

[3] Brigham & Womens Hosp, Dana Farber Canc Inst, Dept Med Oncol, Div Mol & Cellular Onocl, Boston, MA 02115 USA

[4] Brigham & Womens Hosp, Dept Med, Boston, MA 02115 USA

[5] Harvard Univ, Sch Med, Boston, MA 02115 USA

[6] Gene Secur Network Inc, Redwood City, CA 94063 USA

[7] Harvard Univ, Sch Med, Dept Pathol, Charlestown, MA 02129 USA

[8] Massachusetts Gen Hosp, Ctr Canc Res, Charlestown, MA 02129 USA

[9] Massachusetts Gen Hosp, Mol Pathol Unit, Charlestown, MA 02129 USA

[10] Broad Inst Harvard, Cambridge, MA 02142 USA

[11] MIT, Cambridge, MA 02142 USA

[12] Stanford Univ, Med Ctr, Dept Genet, Stanford, CA 94305 USA

来源：

GENOME BIOLOGY | 2008年 / 9卷 / 09期

关键词：

D O I：

10.1186/gb-2008-9-9-r137

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：9

共 13 条

[1] High-resolution profiling of histone methylations in the human genome
Barski, Artern
Cuddapah, Suresh
Cui, Kairong
Roh, Tae-Young
Schones, Dustin E.
Wang, Zhibin
Wei, Gang
Chepelev, Iouri
Zhao, Keji
[J]. CELL, 2007, 129 (04) : 823 - 837
[2] Genome-wide analysis of estrogen receptor binding sites
Carroll, Jason S.
Meyer, Clifford A.
Song, Jun
Li, Wei
Geistlinger, Timothy R.
Eeckhoute, Jerome
Brodsky, Alexander S.
Keeton, Erika Krasnickas
Fertuck, Kirsten C.
Hall, Giles F.
Wang, Qianben
Bekiranov, Stefan
Sementchenko, Victor
Fox, Edward A.
Silver, Pamela A.
Gingeras, Thomas R.
Liu, X. Shirley
Brown, Myles
[J]. NATURE GENETICS, 2006, 38 (11) : 1289 - 1297
[3] Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
Iyer, VR
Horak, CE
Scafe, CS
Botstein, D
Snyder, M
Brown, PO
[J]. NATURE, 2001, 409 (6819) : 533 - 538
[4] Genome-wide mapping of in vivo protein-DNA interactions
Johnson, David S.
Mortazavi, Ali
Myers, Richard M.
Wold, Barbara
[J]. SCIENCE, 2007, 316 (5830) : 1497 - 1502
[5] Model-based analysis of tiling-arrays for ChIP-chip
Johnson, W. Evan
Li, Wei
Meyer, Clifford A.
Gottardo, Raphael
Carroll, Jason S.
Brown, Myles
Liu, X. Shirley
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (33) : 12457 - 12462
[6] Genome-wide analysis of protein-DNA interactions
Kim, Tae Hoon
Ren, Bing
[J]. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2006, 7 : 81 - 102
[7] FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription
Lupien, Mathieu
Eeckhoute, Jerome
Meyer, Clifford A.
Wang, Qianben
Zhang, Yong
Li, Wei
Carroll, Jason S.
Liu, X. Shirley
Brown, Myles
[J]. CELL, 2008, 132 (06) : 958 - 970
[8] Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, Tarjei S.
Ku, Manching
Jaffe, David B.
Issac, Biju
Lieberman, Erez
Giannoukos, Georgia
Alvarez, Pablo
Brockman, William
Kim, Tae-Kyung
Koche, Richard P.
Lee, William
Mendenhall, Eric
O'Donovan, Aisling
Presser, Aviva
Russ, Carsten
Xie, Xiaohui
Meissner, Alexander
Wernig, Marius
Jaenisch, Rudolf
Nusbaum, Chad
Lander, Eric S.
Bernstein, Bradley E.
[J]. NATURE, 2007, 448 (7153) : 553 - U2
[9] Global variation in copy number in the human genome
Redon, Richard
Ishikawa, Shumpei
Fitch, Karen R.
Feuk, Lars
Perry, George H.
Andrews, T. Daniel
Fiegler, Heike
Shapero, Michael H.
Carson, Andrew R.
Chen, Wenwei
Cho, Eun Kyung
Dallaire, Stephanie
Freeman, Jennifer L.
Gonzalez, Juan R.
Gratacos, Monica
Huang, Jing
Kalaitzopoulos, Dimitrios
Komura, Daisuke
MacDonald, Jeffrey R.
Marshall, Christian R.
Mei, Rui
Montgomery, Lyndal
Nishimura, Kunihiro
Okamura, Kohji
Shen, Fan
Somerville, Martin J.
Tchinda, Joelle
Valsesia, Armand
Woodwark, Cara
Yang, Fengtang
Zhang, Junjun
Zerjal, Tatiana
Zhang, Jane
Armengol, Lluis
Conrad, Donald F.
Estivill, Xavier
Tyler-Smith, Chris
Carter, Nigel P.
Aburatani, Hiroyuki
Lee, Charles
Jones, Keith W.
Scherer, Stephen W.
Hurles, Matthew E.
[J]. NATURE, 2006, 444 (7118) : 444 - 454
[10] Genome-wide location and function of DNA binding proteins
Ren, B
Robert, F
Wyrick, JJ
Aparicio, O
Jennings, EG
Simon, I
Zeitlinger, J
Schreiber, J
Hannett, N
Kanin, E
Volkert, TL
Wilson, CJ
Bell, SP
Young, RA
[J]. SCIENCE, 2000, 290 (5500) : 2306 - +

← 1 2 →