Gene Set Enrichment Analysis is a bioinformatics tool that determines whether a set of genes (e.g. a gene ontology (GO) group or a pathway) shows statistically significant, concordant differences between two experimental groups (1,2). Briefly, the goal of GSEA is to determine whether the genes belonging to a gene set are randomly distributed throughout the ranked (by expression) list of all the genes that should be taken into consideration (e.g. gene model), or are primarily found at the top or at the bottom of the list.

References

1. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545-15550. doi:10.1073/pnas.0506580102
2. Mootha VK, Lindgren CM, Eriksson KF, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34(3):267-273. doi:10.1038/ng1180