Comparison of different module detection methods for simulation II. Figures a) through d) correspond to modules of increasing dependency. The clustering trees correspond to average linkage hierarchical clustering with the pairwise topological overlap measure. The first color band underneath each clustering tree color-codes true simulated module membership. The plot under the color band shows the performance of the MAST procedure (blue line) as a function of different MAST parameters. The y-axis reports the Rand index versus the percentage of genes that were assigned to a module (x-axis). The red curve in the plot corresponds to the Rand index of the hierarchical clustering procedure that defines modules as branches. Note that when there is a strong dependence between the modules (Figure d), the MAST procedure outperforms hierarchical clustering.