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

Cairns, J; Freire-Pritchett, P; Wingett, SW; Várnai, C; Dimond, A; Plagnol, V; Zerbino, D; ... Spivakov, M; + view all (2016) CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol , 17 (1) p. 127. 10.1186/s13059-016-0992-2. Green open access

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Abstract

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.

Type: Article
Title: CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/s13059-016-0992-2
Publisher version: http://dx.doi.org/10.1186/s13059-016-0992-2
Language: English
Additional information: © The Author(s). 2016. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Keywords: Capture Hi-C, Convolution background model, Gene regulation, Nuclear organisation, P value weighting, Promoter-enhancer interactions
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: http://discovery.ucl.ac.uk/id/eprint/1511786
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