Gene set enrichment analysis (GSEA and ssGSEA)

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.