psSubpathway

psSubpathway identifies phenotype-specific subpathways from cancer gene expression data to extract local pathway regions that explain subtype- and stage-associated pathway activity.

Key Features:

• R implementation: Implemented as an R-based software package for analysis of transcriptomic data.
• Flexible identification: Detects subpathways across multiple phenotype categories, including cancer subtypes and developmental stages.
• Network-based approach: Operates within a network-based systems biology framework by extracting subpathways from pathway networks.
• Subtype and stage specificity: Infers subtype-specific subpathways and identifies dynamic changes in subpathways associated with cancer developmental stages.
• Activity inference and visualization: Infers subpathway activities from gene expression data and provides visualization of activity levels across samples.
• Biomarker identification: Identifies abnormal subpathways within multi-phenotype datasets to support discovery of phenotype-specific biomarkers.

Scientific Applications:

• Cancer subtype characterization: Dissects local pathway regions to distinguish molecular signatures of cancer subtypes.
• Progression and stage analysis: Detects dynamic subpathway changes associated with developmental stages of cancer.
• Biomarker discovery: Supports identification of subpathway-level biomarkers for phenotype-specific diagnostics and prognostics.
• Pathway-centric interpretation of transcriptomes: Provides pathway-focused interpretation of gene expression datasets to link molecular changes to pathway activity.

Methodology:

psSubpathway extracts subpathways from pathway networks, infers subpathway activities using gene expression data, identifies subtype-specific and dynamically changing subpathways, and visualizes subpathway activity across samples.