4DNvestigator: time series genomic data analysis toolbox.

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.