tools-only Reactome Pathway Enrichment - Usage Guide
Overview
ReactomePA provides pathway enrichment analysis using the Reactome database, a curated peer-reviewed knowledgebase of biological pathways with deep hierarchy and reaction-level detail.
Prerequisites
if (!require('BiocManager', quietly = TRUE))
install.packages('BiocManager')
BiocManager::install(c('ReactomePA', 'org.Hs.eg.db', 'enrichplot'))
Quick Start
Tell your AI agent what you want to do:
- "Run Reactome pathway enrichment on my significant genes"
- "Find peer-reviewed curated pathways enriched in my gene list"
- "Use Reactome instead of KEGG for pathway analysis"
Example Prompts
Basic Enrichment
"Run Reactome pathway enrichment on my differentially expressed genes from deseq2_results.csv"
"Perform Reactome enrichment on my significant genes and show the top 20 pathways"
Visualization
"Create a dotplot of my Reactome enrichment results"
"Open the most enriched Reactome pathway in the browser"
Comparison with KEGG
"Run both Reactome and KEGG enrichment on my genes and compare results"
GSEA with Reactome
"Run Reactome GSEA on my ranked gene list"
What the Agent Will Do
- Load DE results and extract significant genes
- Convert gene IDs to Entrez format (required for ReactomePA)
- Run enrichPathway() with readable = TRUE for gene symbols
- Generate visualizations and export results
- Optionally view pathways in Reactome browser
Reactome vs KEGG
| Feature | Reactome | KEGG |
|---|---|---|
| Curation | Peer-reviewed | Expert curated |
| Access | Open source | Requires license for commercial |
| Hierarchy | Deep pathway hierarchy | Flat pathway list |
| Detail | Reaction-level detail | Pathway-level |
| Updates | Quarterly | Ongoing |
| Organisms | 7 species | 4000+ species |
Understanding Results
| Column | Description |
|---|---|
| ID | Reactome pathway ID (R-HSA-XXXXX) |
| Description | Pathway name |
| GeneRatio | Genes in list / genes in pathway |
| BgRatio | Pathway genes / total genes |
| pvalue | Raw p-value |
| p.adjust | Adjusted p-value (BH) |
| qvalue | Q-value |
| geneID | Genes in pathway |
| Count | Number of genes |
Tips
- Reactome requires Entrez gene IDs - convert from symbols first with bitr()
- Use readable = TRUE in enrichPathway() to get gene symbols in output
- viewPathway() opens interactive pathway visualization in browser
- Reactome has fewer species than KEGG but more detailed pathway annotation
- Combine Reactome with KEGG/WikiPathways for comprehensive pathway coverage
- See enrichment-visualization skill for dotplot() and other plots