RT Journal Article
SR Electronic
T1 CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 028068
DO 10.1101/028068
A1 Jonathan Cairns
A1 Paula Freire-Pritchett
A1 Steven W. Wingett
A1 Andrew Dimond
A1 Vincent Plagnol
A1 Daniel Zerbino
A1 Stefan Schoenfelder
A1 Biola-Maria Javierre
A1 Cameron Osborne
A1 Peter Fraser
A1 Mikhail Spivakov
YR 2015
UL http://biorxiv.org/content/early/2015/10/01/028068.abstract
AB Capture 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 with other Hi-C-like techniques. We present a noise model and algorithms for background correction and multiple testing that are specifically adapted to CHi-C data. 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 it are enriched for regulatory features and disease-associated SNPs.