PGNet identifies three biomodules. A) The significance exists among top ranks but not the bottom ranks when comparing orders of two genome-wide gene expression statistics, one is the correlation with SEMA3A and the other is the differential expression between t-AML and control. The black line records the overlap among the top 150 ranks, while the orange line is the estimated overlap by chance. In addition, the expected overlap and 95% confidence intervals derived from a hypergeometric distribution are shown. B) 52 intersecting genes were commonly identified when the second statistic of the PGNet algorithm comparing t-AML to controls or -7/del7q t-AML to controls (subpanel 1). The expression values of these 52 genes (gray) are lines along with t-AML and control samples in subpanel 2, the red line sketches SEMA3A and the blue lines outline the other EZH2 targets in prostate cancer. C) Functional enrichment analysis identifies three sub-sets of genes from SEMA3A and the 52 genes, each sub-set significantly over-represented one MSigDB defined functional gene-sets (p < 0.001, count>5). Genes are marked as circles, and their functional terms are marked as squares. The expression pattern of EZH2 targets is highlighted as blue lines in Fig B2.