A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

被引：47

作者：

Lun, Desmond S. ^{[1
,2
]}

Sherrid, Ashley ^{[3
,4
]}

Weiner, Brian ^{[5
]}

Sherman, David R. ^{[3
,6
]}

Galagan, James E. ^{[5
,7
,8
]}

机构：

[1] Univ S Australia, Sch Math & Stat, Phen & Bioinformat Res Ctr, Mawson Lakes, SA 5095, Australia

[2] Univ S Australia, Australian Ctr Plant Funct Genom, Mawson Lakes, SA 5095, Australia

[3] Seattle Biomed Res Inst, Seattle, WA 98109 USA

[4] Univ Washington, Mol & Cellular Biol Grad Program, Seattle, WA 98195 USA

[5] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[6] Univ Washington, Dept Global Hlth, Seattle, WA 98195 USA

[7] Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

[8] Boston Univ, Dept Microbiol, Boston, MA 02215 USA

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 12期

关键词：

MODEL-BASED ANALYSIS; MYCOBACTERIUM-TUBERCULOSIS; HYPOXIC RESPONSE; DNA; PROTEIN; SYSTEM; ARRAYS; GABP;

D O I：

10.1186/gb-2009-10-12-r142

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 CSDeconv, a computational method that determines locations of transcription factor binding from ChIP-seq data. CSDeconv differs from prior methods in that it uses a blind deconvolution approach that allows closely-spaced binding sites to be called accurately. We apply CSDeconv to novel ChIP-seq data for DosR binding in Mycobacterium tuberculosis and to existing data for GABP in humans and show that it can discriminate binding sites separated by as few as 40 bp.

引用

页数：12

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