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.
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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 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: | https://discovery.ucl.ac.uk/id/eprint/1511786 |
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