Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data
Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data
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DOI：
10.1093/bioinformatics/btz450
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发表时间：
2019-11-15
期刊：
影响因子：
5.8
通讯作者：
Spivakov, Mikhail
中科院分区：
文献类型：
--
作者：
Cairns, Jonathan;Orchard, William R.;Spivakov, Mikhail
摘要：捕获Hi-C是一种检测染色体相互作用的强大方法，至少在一端，涉及感兴趣的DNA区域，如基因启动子。我们提出了Chicdiff，一个R包，用于捕获Hi-C数据中的差分相互作用的鲁棒检测。Chicdiff通过定制的标准化和多个测试程序增强了计数数据的最先进的差分测试方法，这些测试程序可以解释Capture Hi-C的特定统计特性。我们验证了Chicdiff在人类单核细胞和CD4(+) T细胞中发表的启动子捕获Hi-C数据，鉴定了大量细胞类型特异性相互作用，并确认了启动子相互作用与基因表达之间的总体正相关。
The Summary: Capture Hi-C is a powerful approach for detecting chromosomal interactions involving, at least on one end, DNA regions of interest, such as gene promoters. We present Chicdiff, an R package for robust detection of differential interactions in Capture Hi-C data. Chicdiff enhances a state-of-the-art differential testing approach for count data with bespoke normalization and multiple testing procedures that account for specific statistical properties of Capture Hi-C. We validate Chicdiff on published Promoter Capture Hi-C data in human Monocytes and CD4(+) T cells, identifying multitudes of cell type-specific interactions, and confirming the overall positive association between promoter interactions and gene expression.