iPath

iPath calculates personalized pathway scores and tests their association with survival outcomes.

Key Features:

• Individual-level pathway scoring: Computes pathway scores one sample at a time using pre-defined pathways or gene sets.
• Prognostic biomarker identification: Identifies prognostic biomarker pathways from individual-level expression patterns.
• Survival outcome association testing: Tests the association between personalized pathway scores and survival outcomes.
• Pan-cancer analysis capability: Supports analysis across multiple cancer types from The Cancer Genome Atlas.
• Clinical outcome prediction: Predicts overall survival, tumor subtypes, and tumor stage classifications.

Scientific Applications:

• Cancer prognosis: Identifies highly predictive biomarkers for overall survival across 14 cancer types.
• Tumor subtype classification: Distinguishes tumor subtypes using pathway-based expression patterns.
• Tumor stage classification: Classifies tumor stages based on individual-level pathway scores.
• Biomarker robustness comparison: Evaluates pathway-based biomarkers against single-gene biomarkers for predictive effectiveness.

Methodology:

iPath uses a computational method to calculate personalized pathway scores from individual-level gene expression data for pre-defined pathways or gene sets, then tests association with survival outcomes.