DEsubs

DEsubs performs network-based extraction and analysis of disease-perturbed subpathways from RNA-seq experimental data to support systems-level interpretation of pathway networks.

Key Features:

• Network Construction and Processing: Constructs and processes pathway networks and supports multiple operation modes for tailored analysis.
• Subpathway Extraction: Applies algorithms to extract subpathways perturbed under disease conditions from pathway networks.
• Visualization: Generates visual representations of pathway networks and their extracted subpathways to aid interpretation.
• Enrichment Analysis: Performs enrichment analysis of identified subpathways with respect to biological and pharmacological features.

Scientific Applications:

• Systems Biology Analysis: Enables network-based systems biology studies for both modelers and experimentalists.
• Drug Target and Biomarker Discovery: Supports identification of systems-level drug targets and biomarkers from disease-perturbed subpathways.
• Disease Mechanism Investigation: Facilitates investigation of molecular mechanisms underlying diseases to inform targeted therapeutic strategies.

Methodology:

Performs network-based analysis of pathway networks using RNA-seq experimental data and is implemented as an R package following Bioconductor guidelines.