Figure 4

Significant gene sets detected in the leukemia data set (GSEA-Category, Globaltest, PCOT2, sigPathway). (a) The GSEA-Category, Globaltest and PCOT2 approaches detected 72 (GSEA-Category), 77 (Globaltest) and 67 (PCOT2) gene sets as undergoing significant changes in expression activity, after correction for multiple testing, with 57 gene sets detected as significantly altered by all three approaches. The two methods which incorporate correlation structure into their assessment procedure (Globaltest and PCOT2) exhibited strong agreement in the gene sets they found to be altered (63 significant gene sets in common). (b) Of the 57 changed gene sets identified in common by GSEA-Category, Globaltest and PCOT2, 7 were also found by sigPathway.