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Genome Biol. 2016 Jun 15;17(1):127. doi: 10.1186/s13059-016-0992-2.

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

Author information

1
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
2
Bioinformatics Group, Babraham Institute, Cambridge, UK.
3
UCL Genetics Institute, London, UK.
4
European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
5
Department of Medical and Molecular Genetics, King's College, London, UK.
6
Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK. mikhail.spivakov@babraham.ac.uk.

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.

KEYWORDS:

Capture Hi-C; Convolution background model; Gene regulation; Nuclear organisation; P value weighting; Promoter-enhancer interactions

PMID:
27306882
PMCID:
PMC4908757
DOI:
10.1186/s13059-016-0992-2
[Indexed for MEDLINE]
Free PMC Article

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