In this paper, we chose to evaluate the six gene-set analysis methods empirically using three analyses with the NCI-60 microarray data, each of the three corresponding to a phenotype defined based on mutated vs. wild-type of known cancer genes: CDKN2A, PTEN, and p53. Our goal was to compare gene-set analysis methods based on biological criteria. This evidence concerns the gene CDKN2A and cancer.