Pathway Enrichment

Pathway Enrichment Analysis (PEA) is a widely used method to interpret large-scale omics datasets by identifying biological pathways that are overrepresented among a list of differentially expressed genes, proteins, or other features. This page gathers presentations, tools, and readings to help you apply PEA thoughtfully and avoid common pitfalls.

BCB-SR Pathway Enrichment Analysis Presentation

Web Tool Summary Table

Tool	ORA	GSEA	Topology	GO	KEGG	Reactome	MSigDB	Other Databases
g:Profiler	✅	🔶		✅	✅	✅	✅	TRANSFAC, miRTarBase, WikiPathways
Enrichr	✅			✅	✅	✅	✅	ChEA, DrugMatrix, TF/miRNA
DAVID	✅			✅	✅	✅		Panther, BioCarta
WebGestalt	✅	✅	✅	✅	✅	✅	✅	WikiPathways, user-defined sets
Reactome	✅	✅				✅
PantherDB	✅	✅		✅				Panther Pathways
Metascape	✅			✅	✅	✅	✅	CORUM, WikiPathways
ShinyGO	✅			✅	✅		🔸	Limited subset of MSigDB
PathDIP	✅		✅	✅	✅	✅		PID, BioCarta, PPI-aware pathways
GSEA-MSigDB		✅		✅	✅	✅	✅	Hallmark, C1–C7 collections
ExpressAnalyst	✅	✅		✅	✅	✅	✅	BioCarta, WikiPathways
Cytoscape EnrichMap		✅		Any	Any	Any	Any	Visualization