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name: bio-pathway-reactome description: Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Performs over-representation analysis and GSEA with visualization and pathway hierarchy exploration. tool_type: r primary_tool: ReactomePA measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

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Reactome Pathway Enrichment

Core Pattern - Over-Representation Analysis

library(ReactomePA)
library(org.Hs.eg.db)

pathway_result <- enrichPathway(
    gene = entrez_ids,         # Character vector of Entrez IDs
    organism = 'human',        # human, rat, mouse, celegans, yeast, zebrafish, fly
    pvalueCutoff = 0.05,
    pAdjustMethod = 'BH',
    readable = TRUE            # Convert to gene symbols
)

head(as.data.frame(pathway_result))

Prepare Gene List from DE Results

library(clusterProfiler)

de_results <- read.csv('de_results.csv')
sig_genes <- de_results[de_results$padj < 0.05 & abs(de_results$log2FoldChange) > 1, 'gene_symbol']

gene_ids <- bitr(sig_genes, fromType = 'SYMBOL', toType = 'ENTREZID', OrgDb = org.Hs.eg.db)
entrez_ids <- gene_ids$ENTREZID

GSEA on Reactome Pathways

# Create ranked gene list (named vector sorted by statistic)
gene_list <- de_results$log2FoldChange
names(gene_list) <- de_results$entrez_id
gene_list <- sort(gene_list, decreasing = TRUE)

gsea_result <- gsePathway(
    geneList = gene_list,
    organism = 'human',
    pvalueCutoff = 0.05,
    pAdjustMethod = 'BH',
    verbose = FALSE
)

head(as.data.frame(gsea_result))

With Background Universe

all_genes <- de_results$entrez_id  # All tested genes

pathway_result <- enrichPathway(
    gene = entrez_ids,
    universe = all_genes,      # Background gene set
    organism = 'human',
    pvalueCutoff = 0.05,
    readable = TRUE
)

Visualization

library(enrichplot)

# Dot plot
dotplot(pathway_result, showCategory = 15)

# Bar plot
barplot(pathway_result, showCategory = 15)

# Enrichment map (requires pairwise_termsim first)
pathway_result <- pairwise_termsim(pathway_result)
emapplot(pathway_result)

# Gene-concept network
cnetplot(pathway_result, categorySize = 'pvalue')

# GSEA plot
gseaplot2(gsea_result, geneSetID = 1:3)

View Pathway in Browser

# Open pathway in Reactome browser
viewPathway('R-HSA-109582', organism = 'human')  # Uses pathway ID

# Get pathway ID from results
top_pathway_id <- pathway_result@result$ID[1]
viewPathway(top_pathway_id, organism = 'human')

Export Results

results_df <- as.data.frame(pathway_result)
write.csv(results_df, 'reactome_enrichment.csv', row.names = FALSE)

# Key columns: ID, Description, GeneRatio, BgRatio, pvalue, p.adjust, geneID, Count

Different Organisms

# Mouse
pathway_mouse <- enrichPathway(gene = mouse_entrez, organism = 'mouse', readable = TRUE)

# Rat
pathway_rat <- enrichPathway(gene = rat_entrez, organism = 'rat', readable = TRUE)

# Zebrafish
pathway_zfish <- enrichPathway(gene = zfish_entrez, organism = 'zebrafish', readable = TRUE)

# Supported: human, rat, mouse, celegans, yeast, zebrafish, fly

Compare Clusters

# Compare pathways across multiple gene lists
gene_clusters <- list(
    upregulated = up_genes,
    downregulated = down_genes
)

compare_result <- compareCluster(
    geneClusters = gene_clusters,
    fun = 'enrichPathway',
    organism = 'human',
    pvalueCutoff = 0.05
)

dotplot(compare_result)

Key Parameters

Parameter	Default	Description
gene	required	Vector of Entrez IDs
organism	human	Species name
pvalueCutoff	0.05	P-value threshold
pAdjustMethod	BH	Adjustment method
universe	NULL	Background genes
minGSSize	10	Min genes per pathway
maxGSSize	500	Max genes per pathway
readable	FALSE	Convert to symbols

Supported Organisms

Organism	Name	OrgDb
Human	human	org.Hs.eg.db
Mouse	mouse	org.Mm.eg.db
Rat	rat	org.Rn.eg.db
Zebrafish	zebrafish	org.Dr.eg.db
Fly	fly	org.Dm.eg.db
C. elegans	celegans	org.Ce.eg.db
Yeast	yeast	org.Sc.sgd.db

Related Skills

• go-enrichment - Gene Ontology enrichment
• kegg-pathways - KEGG pathway enrichment
• wikipathways - WikiPathways enrichment
• gsea - Gene Set Enrichment Analysis
• enrichment-visualization - Visualization functions

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