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

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