CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Research output: Contribution to journal › Article
Colleges, School and Institutes
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
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.
|Number of pages||17|
|Publication status||Published - 15 Jun 2016|
- Gene regulation, Nuclear organisation, Promoter-enhancer interactions, Capture Hi-C, Convolution background model, P value weighting