期刊
GENOME BIOLOGY
卷 17, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s13059-016-0992-2
关键词
Gene regulation; Nuclear organisation; Promoter-enhancer interactions; Capture Hi-C; Convolution background model; P value weighting
资金
- Biotechnology and Biological Sciences Research Council
- Medical Research Council of the UK
- European Molecular Biology Laboratory
- Biotechnology and Biological Sciences Research Council [BBS/E/B/000C0404, BBS/E/B/000C0405] Funding Source: researchfish
- Medical Research Council [MR/L007150/1] Funding Source: researchfish
- BBSRC [BBS/E/B/000C0405, BBS/E/B/000C0404] Funding Source: UKRI
- MRC [MR/L007150/1] Funding Source: UKRI
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.
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