# Gene set enrichment analysis (GSEA and ssGSEA)

Source: https://onco.cc/terms/gsea/  
OnCo record `gsea` (Term). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

Gene set enrichment analysis asks whether the genes that changed in an experiment cluster in a known pathway or signature, turning a list of genes into a biological story.

## Summary

Gene set enrichment analysis identifies classes of genes that are over-represented in a large gene list and may be associated with a phenotype (Wikipedia); Subramanian and colleagues' GSEA ranks all genes by association with a phenotype and tests whether a set concentrates at the top or bottom. Single-sample GSEA, introduced by Barbie and colleagues, scores one sample at a time, producing per-patient pathway activity scores that can be model features. The gene sets come from MSigDB (hallmark, KEGG, Reactome, GO collections). Enrichment describes; it does not prove mechanism.

## Fields

- Kind: Term
- Last checked: 2026-09-24
- Also known as: gene set enrichment analysis; gene set enrichment; GSEA; ssGSEA; single-sample GSEA; pathway enrichment; enrichment analysis; enrichment score
- Tags: cansim-terms

## Notes

- Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/gsea-ssgsea.

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis
- Subramanian et al., Gene set enrichment analysis (PNAS 2005): https://doi.org/10.1073/pnas.0506580102
- Barbie et al., ssGSEA introduced in Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 (Nature 2009): https://doi.org/10.1038/nature08460
- MSigDB: https://www.gsea-msigdb.org/gsea/msigdb/
- Wikipedia: https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis

## Connected records

- terms: [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [Gene co-expression structure](https://onco.cc/terms/gene-co-expression/), [Pathway activation state (phosphosignalling)](https://onco.cc/terms/pathway-activation-state/)

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