Version Compatibility

Reference examples tested with: ReactomePA 1.54+, reactome.db 1.95+, clusterProfiler 4.18+.

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

reactome.db is a LOCAL Bioconductor annotation package pinned to the Bioconductor release, so enrichPathway/gsePathway are reproducible offline given the package version - unlike KEGG and WikiPathways, which query a live database. The reactome.org web AnalysisService tracks the current quarterly Reactome release and can therefore disagree with a local ReactomePA run (see Failure Modes).

Reactome Pathway Enrichment

"Which curated Reactome pathways does my gene list over-represent?" -> Test each Reactome pathway for over-representation against a measured background, then deduplicate the hierarchy - because a Reactome result is one signal projected onto a tree of nested reactions, not a list of independent findings.

• R: enrichPathway(gene_entrez, organism='human', universe=measured_entrez, readable=TRUE)

Scope: ORA (enrichPathway) and GSEA (gsePathway) over Reactome reaction-rolled-to-pathway gene sets, the ENTREZ-only constraint, hierarchy deduplication, the human-curated-only species caveat, the local viewPathway reaction-network plot, and the ReactomeGSA comparative pointer. The hypergeometric test and background-universe theory -> go-enrichment. The GSEA running-sum engine and ranking metric -> gsea. The DE list / ranking statistic -> differential-expression/de-results. Dotplot/emapplot/cnetplot/gseaplot2 -> enrichment-visualization.