Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes (gene sets) shows statistically significant, concordant differences between two biological conditions.
GSEA has two modes:
- Classic mode (recommended): User will input normalized gene expression values as GMT files. GSEA ranks genes based on differences between conditions. Genes on the top part of the ranked list are over expressed in condition1 and genes on the bottom part of the ranked list are under expressed in condition2. GSEA will identify gene sets that are enriched (overrepresented) among the highest and lowest ranked genes as postively and negatively enriched gene sets respectively.
- Pre-ranked mode: User will input a list of genes, already ranked by something like fold change or pvalue in RNK file format. Genes on the top part of the ranked list are over expressed in condition1 and genes on the bottom part of the ranked list are under expressed in condition2. GSEA will identify gene sets that are enriched (overrepresented) among the highest and lowest ranked genes as postively and negatively enriched gene sets respectively.
GSEA can be downloaded here.