Oct 1, 2015

CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

BioRxiv : the Preprint Server for Biology
Jonathan CairnsPeter Fraser


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.

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Mentioned in this Paper

Operator gene
Drug Interactions
Formaldehyde dehydrogenase (glutathione)
Single Nucleotide Polymorphism
ING2 protein, human
Chicago acid

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