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Related Experiment Video

Updated: Nov 10, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

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4DNvestigator: time series genomic data analysis toolbox.

Stephen Lindsly¹, Can Chen², Sijia Liu^3,4

¹Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

Nucleus (Austin, Tex.)

|April 2, 2021

Summary

This summary is machine-generated.

The 4DNvestigator toolbox integrates time-series genome structure and gene expression data. It offers new methods for analyzing dynamic changes in the 4D Nucleome, aiding biological interpretation.

Keywords:

4DN centrality entropy networks time series

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Area of Science:

Genomics
Systems Biology
Computational Biology

Background:

Understanding genome organization over time (4D Nucleome) is crucial but challenging due to data complexity.
Efficient tools are needed to integrate and analyze time-series genome structure (Hi-C) and gene expression (RNA-seq) data.

Purpose of the Study:

To develop a user-friendly, network-based toolbox called '4DNvestigator' for analyzing 4D Nucleome data.
To provide methods for quantifying temporal changes in genome structure and network properties.

Main Methods:

Development of the '4DNvestigator' toolbox.
Integration of time-series Hi-C and RNA-seq data.
Implementation of network entropy and tensor entropy calculations.
Statistical analysis of dynamic changes in Hi-C data across genomic scales.

Main Results:

The '4DNvestigator' toolbox enables efficient analysis of time-series genome-wide data.
Novel methods for quantifying network and tensor entropy are provided.
Statistical significance of temporal changes in Hi-C data can be assessed.

Conclusions:

'4DNvestigator' facilitates the interpretation of dynamic genome organization and gene expression.
The toolbox and methods advance the analysis of the 4D Nucleome.
This work supports a deeper understanding of genome regulation over time.