domains / families / science / reactome-pathways

reactome-pathways

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Tests a gene list or ranked gene vector for over-representation or coordinated shifts in Reactome's curated, peer-reviewed, reaction-level pathways using ReactomePA's enrichPathway (ORA) and gsePathway (GSEA), reading the local reactome.db so a run is reproducible given the Bioconductor release. Covers why Reactome's atomic unit is the REACTION and pathways are nested containers so a parent and child enrich on the same genes and double-count one signal, why only human is curated and every other species is orthology-inferred, why enrichPathway has NO keyType argument and returns nothing unless genes are ENTREZ (bitr first), and why viewPathway draws a LOCAL reaction network from a pathway NAME. Use when reaction-level granularity, peer-reviewed curation, or an offline-reproducible database is wanted; for comparative multi-sample or multi-omics analysis use ReactomeGSA. The DE list comes from differential-expression; plots from enrichment-visualization.

When to use

• ORA (enrichPathway) over Reactome reaction-rolled-to-pathway gene sets
• GSEA (gsePathway) over Reactome reaction-rolled-to-pathway gene sets
• Hierarchy deduplication
• ENTREZ-only constraint handling
• Human-curated-only species caveat
• Local viewPathway reaction-network plot
• Reaction-level granularity analysis
• Offline-reproducible database analysis

When not to use

• Comparative multi-sample or multi-omics analysis
• Hypergeometric test and background-universe theory
• GSEA running-sum engine and ranking metric
• DE list / ranking statistic generation
• Dotplot/emapplot/cnetplot/gseaplot2 visualization

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