A simulation study using microarray data and synthetic testing gene sets. (a-c) p-values on the differential expression of testing gene sets with increasing levels of enrichment of up-regulated genes, when GAGE (a, b), GSEA (a, b) and PAGE (c) were applied. (d) The series of beta distribution curves with 1 ≤ β ≤ 10 and fixed α = 1 used to sample the testing gene sets with increasing levels of up-regulation from a sorted whole gene list. For each β value, we generated testing gene sets of two different size n = 10 genes (small sets) and n = 50 genes (large sets), 100 gene sets each. We then applied GAGE, PAGE or GSEA to test the overall expression level up-regulation in these gene sets. Mean p-values plus with standard error were shown. See Methods and Results for details. Note that GAGE with both 1-on-1 and 1-on-grp options produces similar results, although only the former is shown here.