DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments

Area of Science:

• Systems biology
• Bioinformatics
• Computational biology

Background:

• Identifying disease-specific molecular pathways is crucial for understanding complex diseases.
• RNA-sequencing (RNA-seq) experiments generate large datasets that require sophisticated analysis tools.
• Existing methods may lack the flexibility to pinpoint specific, perturbed subpathways within larger biological networks.

Purpose of the Study:

• To introduce DEsubs, a novel R package designed for network-based systems biology analysis.
• To enable the extraction and analysis of disease-perturbed subpathways from RNA-seq data.
• To provide a flexible framework for identifying robust systems-level drug targets and biomarkers.

Main Methods:

• DEsubs utilizes a network-based approach to analyze pathway data.
• The package offers customizable operation modes for pathway network construction, processing, and subpathway extraction.
• Includes visualization and enrichment analysis capabilities for biological and pharmacological features.

Main Results:

• DEsubs facilitates the identification of disease-perturbed subpathways.
• The package provides a case-specific approach to systems biology analysis.
• Enables the discovery of potential drug targets and biomarkers for complex diseases.

Conclusions:

• DEsubs is a comprehensive R package for systems biology research.
• It empowers researchers to conduct detailed subpathway analysis on RNA-seq data.
• The tool aids in identifying robust therapeutic targets and biomarkers for complex diseases.