Different from the analysis on differentially expressed individual genes, another type of analysis focuses on differential expression or perturbation of pre-defined gene sets and is called gene set analysis. Gene set analysis demonstrated several major advantages over individual gene differential expression analysis. Gene sets are groups of genes that are functionally related according to current knowledge. Therefore, gene set analysis is considered a knowledge based analysis approach. Commonly used gene sets include those derived from KEGG pathways, Gene Ontology terms, gene groups that share some other functional annotations, such as common transcriptional regulators etc. Representative gene set analysis methods include Gene Set Enrichment Analysis (GSEA), which estimates significance of gene sets based on permutation of sample labels, and Generally Applicable Gene-set Enrichment (GAGE), which tests the significance of gene sets based on permutation of gene labels or a parametric distribution.