@article {Cairns028068, author = {Jonathan Cairns and Paula Freire-Pritchett and Steven W. Wingett and Andrew Dimond and Vincent Plagnol and Daniel Zerbino and Stefan Schoenfelder and Biola-Maria Javierre and Cameron Osborne and Peter Fraser and Mikhail Spivakov}, title = {CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data}, elocation-id = {028068}, year = {2015}, doi = {10.1101/028068}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2015/10/01/028068}, eprint = {https://www.biorxiv.org/content/early/2015/10/01/028068.full.pdf}, journal = {bioRxiv} }