pathfindR

pathfindR performs active-subnetwork-oriented pathway enrichment analysis by integrating protein-protein interaction (PPI) networks to identify biologically relevant pathways from gene lists in class-comparison omics experiments.

Key Features:

• Integration of PPI Information: Integrates protein-protein interaction (PPI) network data with user-provided gene lists to inform pathway analysis.
• Active Subnetwork Identification: Identifies active subnetworks in a PPI network based on genes derived from class-comparison omics experiments.
• Pathway Enrichment Analysis: Performs pathway enrichment analysis specifically on the identified active subnetworks.
• Clustering and Visualization: Clusters enriched pathways and provides visualization functions to summarize and present pathway results.
• Pathway Scoring: Implements a scoring function that estimates the overall activity level of each pathway per sample.

Scientific Applications:

• Disease pathway identification: Identifies literature-supported disease-related pathways and ranks known disease-associated pathways in gene expression datasets.
• Comparative omics analysis: Applied to class-comparison omics experiments to uncover condition-specific pathways that may be missed by conventional methods.
• Mechanistic insight and target prioritization: Aids in uncovering novel insights into disease mechanisms and prioritizing potential therapeutic targets by highlighting active pathways.

Methodology:

Integrates PPI networks, identifies active subnetworks from gene lists derived from two-group omics comparisons, performs pathway enrichment on those subnetworks, clusters enriched pathways, provides visualization of results, and computes per-sample pathway activity scores.