For each pair of networks, the overlap between all possible pairs of modules was calculated along with the probability of observing such overlap by chance. For comparisons among CTX, CN and CB, probe set identities were used as unique identifiers; for comparisons with CTX_95, gene symbols were used. The significance of module overlap was assessed for each module in a given network with all modules in the comparison network using a one-sided hypergeometric test (as we were interested in testing for over-representation; see Supplementary Methods for an example). To account for multiple comparisons, a Bonferroni correction was applied on the basis of the number of modules in the comparison network. Modules from different networks with significant overlap (corrected hypergeometric P value < 0.05) were assigned the same color and number, with networks denoted by letters (for example, M9A for CTX, M9B for CTX_95, M9C for CN and M9D for CB). If a module showed significant overlap with more than one module from another network, color/number assignment was determined by the lowest P value.
