Fig. 6

Module preservation. a Table showing gene overlap between each pair of methylation and expression modules. Each row of the table corresponds to one methylation module (labeled by color as well as text), and each column corresponds to one expression module. Numbers in the table indicate gene counts in the intersection of the corresponding modules. Coloring of the table encodes − log(p), with p being the Fisher’s exact test p value for the overlap of the two modules. The stronger the red color, the more significant the overlap is between a methylation module for 3′UTR and an expression module. b Plot showing statistical analysis results for module preservation test to check preservation of 3′UTR methylation modules against expression modules based on the density and connectivity patterns of genes in each module. The left panel shows the medianRank of the observed preservation statics and the right panel shows the distribution of Z_summary statistics obtained from a permutation analysis for each methylation module. A module with a lower median rank tends to exhibit stronger observed preservation statistics than a module with a higher median rank. The Z_summary statistic of a given module summarizes the evidence that the network connections of the module are more significantly preserved than those of random set of genes of equal size. The significance thresholds for Z_summary are Z_summary < 2 implies no evidence that the module is preserved, 2 < Z_summary < 10 implies weak to moderate evidence, and Z_summary > 10 implies strong evidence for module preservation between co-expression module and 3′UTR methylation module