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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

  1. Load DE results and extract significant genes
  2. Convert gene IDs to Entrez format (required for ReactomePA)
  3. Run enrichPathway() with readable = TRUE for gene symbols
  4. Generate visualizations and export results
  5. 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