C3D: a tool to predict 3D genomic interactions between cis-regulatory elements

被引：11

作者：

Mehdi, Tahmid ^{[1
,2
]}

Bailey, Swneke D. ^{[1
]}

Guilhamon, Paul ^{[1
]}

Lupien, Mathieu ^{[1
,3
,4
]}

机构：

[1] Univ Hlth Network, Princess Margaret Canc Ctr, Toronto, ON M5G 1L7, Canada

[2] Univ Waterloo, Dept Stat & Actuarial Sci, Waterloo, ON M5G 1L7, Canada

[3] Univ Toronto, Dept Med Biophys, Toronto, ON N2L 3G1, Canada

[4] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada

来源：

BIOINFORMATICS | 2019年 / 35卷 / 05期

关键词：

D O I：

10.1093/bioinformatics/bty717

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation The 3D genome architecture influences the regulation of genes by facilitating chromatin interactions between distal cis-regulatory elements and gene promoters. We implement Cross Cell-type Correlation based on DNA accessibility (C3D), a customizable computational tool that predicts chromatin interactions using an unsupervised algorithm that utilizes correlations in chromatin measurements, such as DNaseI hypersensitivity signals. Results C3D accurately predicts 32.7%, 18.3% and 24.1% of interactions, validated by ChIA-PET assays, between promoters and distal regions that overlie DNaseI hypersensitive sites in K562, MCF-7 and GM12878 cells, respectively.

引用

页码：877 / 879

页数：3

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