dcHiC detects differential compartments across multiple Hi-C datasets.
dcHiC detects differential compartments across multiple Hi-C datasets.
复制标题
DCHIC检测多个HI-C数据集的差异隔室。
DOI：
10.1038/s41467-022-34626-6
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发表时间：
2022-11-11
影响因子：
16.6
通讯作者：
Ay, Ferhat
中科院分区：
文献类型：
--
作者：
Chakraborty, Abhijit;Wang, Jeffrey G.;Ay, Ferhat
哺乳动物基因组的区室组织及其变化在不同的生物过程中发挥着重要作用。在这里，我们介绍 dcHiC，它利用多元距离测量来识别多个接触图之间划分的显着变化。通过对来自体外小鼠神经分化 (n = 3)、小鼠造血 (n = 10)、人类 LCL (n = 20) 和出生后小鼠大脑发育 (n = 3 阶段) 的四组批量和单细胞接触图评估 dcHiC，我们展示了其在检测生物学相关变化（包括正交验证的变化）方面的有效性和灵敏度。 dcHiC 报告了与细胞身份相关的动态调节基因的区域，以及染色质状态、亚区室、复制时间和核纤层蛋白关联的相关变化。凭借其高效的实施，dcHiC 可实现高分辨率区室分析以及独立浏览器可视化、差异交互识别和时间序列聚类。 dcHiC 是 Hi-C 分析工具箱的重要补充，适用于不断增长的批量和单细胞接触图。网址：https://github.com/ay-lab/dcHiC。哺乳动物基因组的组织在许多生物过程中发挥着作用。在这里，作者报告了 dcHiC，这是一种使用多变量距离测量来识别多个全基因组染色质接触图之间的区划变化的工具，并将其应用于不同的人类和小鼠数据集。
The compartmental organization of mammalian genomes and its changes play important roles in distinct biological processes. Here, we introduce dcHiC, which utilizes a multivariate distance measure to identify significant changes in compartmentalization among multiple contact maps. Evaluating dcHiC on four collections of bulk and single-cell contact maps from in vitro mouse neural differentiation (n = 3), mouse hematopoiesis (n = 10), human LCLs (n = 20) and post-natal mouse brain development (n = 3 stages), we show its effectiveness and sensitivity in detecting biologically relevant changes, including those orthogonally validated. dcHiC reported regions with dynamically regulated genes associated with cell identity, along with correlated changes in chromatin states, subcompartments, replication timing and lamin association. With its efficient implementation, dcHiC enables high-resolution compartment analysis as well as standalone browser visualization, differential interaction identification and time-series clustering. dcHiC is an essential addition to the Hi-C analysis toolbox for the ever-growing number of bulk and single-cell contact maps. Available at: https://github.com/ay-lab/dcHiC. The organisation of mammalian genomes plays a role in many biological processes. Here the authors report dcHiC, a tool which uses a multivariate distance measure to identify changes in compartmentalisation among multiple genome-wide chromatin contact maps, and apply this to different human and mouse datasets.
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DOI：
10.1093/dnares/dsr016
发表时间：
2011-08
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Scheubert L;Schmidt R;Repsilber D;Lustrek M;Fuellen G
通讯作者：
Fuellen G
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Dixon JR;Jung I;Selvaraj S;Shen Y;Antosiewicz-Bourget JE;Lee AY;Ye Z;Kim A;Rajagopal N;Xie W;Diao Y;Liang J;Zhao H;Lobanenkov VV;Ecker JR;Thomson JA;Ren B
通讯作者：
Ren B
影响因子：
4.6
作者：
Chen, Weisheng V.;Maniatis, Tom
通讯作者：
Maniatis, Tom
影响因子：
15.1
作者：
Athanasiu, Lavinia;Giddaluru, Sudheer;Le Hellard, Stephanie
通讯作者：
Le Hellard, Stephanie