SubtypeDrug

SubtypeDrug prioritizes cancer subtype-specific drugs by integrating molecular, histological, and clinical data to identify dysregulated subpathways and candidate therapeutics.

Key Features:

• Integration of multi-omics and clinical data: Uses gene expression profiles including GEO accession GSE45827 alongside molecular, histological, and clinical data to inform subtype classification and drug prioritization.
• Subpathway analysis: Extracts subpathways from broader biological pathways to enable targeted examination of pathway segments.
• Dysregulated subpathway identification: Identifies subpathways that are dysregulated in cancer subtypes and by specific drugs.
• Sample-specific activity profiling: Infers activity profiles for subpathways on a per-sample basis to capture heterogeneity across cancer samples.
• Reverse association evaluation: Evaluates drug–disease associations at the subpathway level to identify potential therapeutic candidates.
• Subtype sample set enrichment analysis and visualization: Performs subtype-level sample set enrichment analysis to nominate candidate drugs and provides visualization of results.
• Implementation: Implemented in R as an analysis package.

Scientific Applications:

• Subtype-specific drug prioritization: Prioritizes candidate therapeutics that target dysregulated subpathways specific to defined cancer subtypes.
• Mechanistic interpretation of drug action: Reveals biological functions and subpathways regulated by drugs within distinct cancer subtypes to support personalized treatment strategies.

Methodology:

Integrates genetic perturbation data, drug action mechanisms, and biological pathway information with cancer subtype classifications; extracts subpathways; infers sample-specific subpathway activity profiles; identifies dysregulated subpathways; evaluates reverse drug–disease associations at the subpathway level; and performs subtype sample set enrichment analysis.