Author:
Cairns Jonathan,Freire-Pritchett Paula,Wingett Steven W.,Várnai Csilla,Dimond Andrew,Plagnol Vincent,Zerbino Daniel,Schoenfelder Stefan,Javierre Biola-Maria,Osborne Cameron,Fraser Peter,Spivakov Mikhail
Abstract
ABSTRACTCapture Hi-C (CHi-C) is a state-of-the art 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, in which many spatially dispersed regions are captured, such as in Promoter CHi-C. 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.
Publisher
Cold Spring Harbor Laboratory
Cited by
4 articles.
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