bio-pathway-reactome

You run Reactome pathway enrichment by applying the ReactomePA enrichPathway function to your gene list. This identifies enriched peer-reviewed biological pathways from your differential expression results by processing input Entrez IDs.

Yes, you can use the gsePathway function to run GSEA on a ranked gene list. This detects coordinated expression changes across Reactome pathways, allowing you to identify pathways enriched based on continuous metric ranking rather than binary gene selection.

Yes, you need Entrez IDs as input for Reactome pathway enrichment. The ReactomePA package requires these identifiers to map genes to Reactome pathways, alongside proper organism annotations provided through OrgDb.

Yes, ReactomePA supports cross-species analyses for human, mouse, rat, and other organisms. You must configure the proper organism annotations via OrgDb to ensure the Reactome pathways map correctly to your specific model organism's Entrez IDs.

enrichPathway performs over-representation analysis on a discrete gene list to find enriched Reactome pathways, while gsePathway runs GSEA on a ranked gene list to detect coordinated changes. Choose enrichPathway for binary gene sets and gsePathway for continuous differential expression metrics.