CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

被引：265

作者：

Cairns, Jonathan ^{[1
]}

Freire-Pritchett, Paula ^{[1
]}

Wingett, Steven W. ^{[1
,2
]}

Varnai, Csilla ^{[1
]}

Dimond, Andrew ^{[1
]}

Plagnol, Vincent ^{[3
]}

Zerbino, Daniel ^{[4
]}

Schoenfelder, Stefan ^{[1
]}

Javierre, Biola-Maria ^{[1
]}

Osborne, Cameron ^{[5
]}

Fraser, Peter ^{[1
]}

Spivakov, Mikhail ^{[1
]}

机构：

[1] Babraham Inst, Nucl Dynam Programme, Cambridge, England

[2] Babraham Inst, Bioinformat Grp, Cambridge, England

[3] UCL Genet Inst, London, England

[4] European Bioinformat Inst, European Mol Biol Lab, Cambridge, England

[5] Kings Coll London, Dept Med & Mol Genet, London, England

来源：

GENOME BIOLOGY | 2016年 / 17卷

基金：

英国医学研究理事会; 英国生物技术与生命科学研究理事会;

关键词：

Gene regulation; Nuclear organisation; Promoter-enhancer interactions; Capture Hi-C; Convolution background model; P value weighting; FALSE DISCOVERY CONTROL; CAJAL BODIES; BIASES;

D O I：

10.1186/s13059-016-0992-2

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：

Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO (http://regulatorygenomicsgroup.org/chicago), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.

引用

页数：17

共 55 条

[51] A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data [J].

Xu, Zheng ;

Zhang, Guosheng ;

Jin, Fulai ;

Chen, Mengjie ;

Furey, Terrence S. ;

Sullivan, Patrick F. ;

Qin, Zhaohui ;

Hu, Ming ;

Li, Yun .

BIOINFORMATICS, 2016, 32 (05) :650-656

[52] Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture [J].

Yaffe, Eitan ;

Tanay, Amos .

NATURE GENETICS, 2011, 43 (11) :1059-U40

[53] A comparative encyclopedia of DNA elements in the mouse genome [J].

Yue, Feng ;

Cheng, Yong ;

Breschi, Alessandra ;

Vierstra, Jeff ;

Wu, Weisheng ;

Ryba, Tyrone ;

Sandstrom, Richard ;

Ma, Zhihai ;

Davis, Carrie ;

Pope, Benjamin D. ;

Shen, Yin ;

Pervouchine, Dmitri D. ;

Djebali, Sarah ;

Thurman, Robert E. ;

Kaul, Rajinder ;

Rynes, Eric ;

Kirilusha, Anthony ;

Marinov, Georgi K. ;

Williams, Brian A. ;

Trout, Diane ;

Amrhein, Henry ;

Fisher-Aylor, Katherine ;

Antoshechkin, Igor ;

DeSalvo, Gilberto ;

See, Lei-Hoon ;

Fastuca, Meagan ;

Drenkow, Jorg ;

Zaleski, Chris ;

Dobin, Alex ;

Prieto, Pablo ;

Lagarde, Julien ;

Bussotti, Giovanni ;

Tanzer, Andrea ;

Denas, Olgert ;

Li, Kanwei ;

Bender, M. A. ;

Zhang, Miaohua ;

Byron, Rachel ;

Groudine, Mark T. ;

McCleary, David ;

Pham, Long ;

Ye, Zhen ;

Kuan, Samantha ;

Edsall, Lee ;

Wu, Yi-Chieh ;

Rasmussen, Matthew D. ;

Bansal, Mukul S. ;

Kellis, Manolis ;

Keller, Cheryl A. ;

Morrissey, Christapher S. .

NATURE, 2014, 515 (7527) :355-+

[54] A powerful FDR control procedure for multiple hypotheses [J].

Zhao, Haibing ;

Fung, Wing Kam .

COMPUTATIONAL STATISTICS & DATA ANALYSIS, 2016, 98 :60-70

[55] Exploring long-range genome interactions using the WashU Epigenome Browser [J].

Zhou, Xin ;

Lowdon, Rebecca F. ;

Li, Daofeng ;

Lawson, Heather A. ;

Madden, Pamela A. F. ;

Costello, Joseph F. ;

Wang, Ting .

NATURE METHODS, 2013, 10 (05) :375-376

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