DEsubs

DEsubs extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments.

Key Features:

• Network-based subpathway extraction: Extracts disease-perturbed subpathways within a pathway network from RNA-seq data.
• Customizable framework: Provides an extensive and customizable framework covering a broad range of operation modes at all stages of subpathway analysis.
• Pathway network construction and processing: Supports multiple operation modes for pathway network construction and processing.
• Subpathway extraction: Implements multiple operation modes for subpathway extraction.
• Visualization: Includes visualization capabilities for subpathway analysis results.
• Enrichment analysis: Performs enrichment analysis with regard to various biological and pharmacological features.

Scientific Applications:

• Systems-level biomarker identification: Identifies more robust systems-level biomarkers for complex diseases.
• Disease-perturbed subpathway analysis: Enables case-specific analysis of disease-perturbed subpathways from RNA-seq expression experiments.

Methodology:

DEsubs uses a network-based systems biology approach to extract disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments, with customizable operation modes at all stages of subpathway analysis including pathway network construction and processing, subpathway extraction, visualization, and enrichment analysis.