MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples

Weifang Liu, Yuchen Yang, Armen Abnousi, Qian Zhang, Naoki Kubo, Joshua S.Martin Beem, Yun Li, Ming Hu

研究成果: ジャーナルへの寄稿学術誌査読

抄録

Chromatin spatial organization (interactome) plays a critical role in genome function. Deep understanding of chromatin interactome can shed insights into transcriptional regulation mechanisms and human disease pathology. One essential task in the analysis of chromatin interactomic data is to identify long-range chromatin interactions. Existing approaches, such as HiCCUPS, FitHiC/FitHiC2, and FastHiC, are all designed for analyzing individual cell types or samples. None of them accounts for unbalanced sequencing depths and heterogeneity among multiple cell types or samples in a unified statistical framework. To fill in the gap, we have developed a novel statistical framework MUNIn (multiple-sample unifying long-range chromatin-interaction detector) for identifying long-range chromatin interactions from multiple samples. MUNIn adopts a hierarchical hidden Markov random field (H-HMRF) model, in which the status (peak or background) of each interacting chromatin loci pair depends not only on the status of loci pairs in its neighborhood region but also on the status of the same loci pair in other samples. To benchmark the performance of MUNIn, we performed comprehensive simulation studies and real data analysis and showed that MUNIn can achieve much lower false-positive rates for detecting sample-specific interactions (33.1%–36.2%), and much enhanced statistical power for detecting shared peaks (up to 74.3%), compared to uni-sample analysis. Our data demonstrated that MUNIn is a useful tool for the integrative analysis of interactomic data from multiple samples.

本文言語英語
論文番号100036
ジャーナルHuman Genetics and Genomics Advances
2
3
DOI
出版ステータス出版済み - 7月 8 2021
外部発表はい

!!!All Science Journal Classification (ASJC) codes

  • 分子医療
  • 遺伝学(臨床)

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