Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Department of Mathematics, University of Michigan, Ann Arbor, MI, USA.
Nucleus. 2021 Dec;12(1):58-64. doi: 10.1080/19491034.2021.1910437.
Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the '4DNvestigator', a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.
有关基因组组织和随时间变化的输出的数据，或称为 4D 核组学（4DN），需要综合分析才能得出有意义的结论。因此，需要开发有效的工具来整合这些数据，特别是针对时间维度。我们提出了“4DNvestigator”，这是一个用户友好的基于网络的工具包，用于分析全基因组基因组结构（Hi-C）和基因表达（RNA-seq）时间序列数据。此外，我们还提供了方法来量化网络熵、张量熵，以及在不同基因组尺度下时间序列 Hi-C 数据中具有统计学意义的变化。
