Published in
BioMed Central, Genome Biology, 1(17)
DOI: 10.1186/s13059-016-0992-2
Links
- ORCID
- ORCID
- ORCID
- ORCID
- Crossref | PDF
- Crossref | PDF
- BioMed Central | PDF
- [genomebiology.com] | PDF
- [dx.doi.org] | PDF
- [kclpure.kcl.ac.uk] | PDF
- [spiral.imperial.ac.uk] | PDF
- [discovery.ucl.ac.uk] | PDF
- [europepmc.org] | PDF
- [kclpure.kcl.ac.uk] | PDF
- [www.ncbi.nlm.nih.gov] | PDF
Tools
CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data
,
Csilla Vรกrnai,
Paula Freire-Pritchett,
Wingett Sw,
Csilla Várnai ,
Andrew Dimond,
Vincent Plagnol,
Daniel Zerbino,
Stefan Schoenfelder,
Javierre Bm,
Biola-Maria Javierre,
Cameron Osborne,
Peter Fraser ,
Mikhail Spivakov
Full text: Download
Abstract
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.