Pathway Analysis
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 |