Figure 7

Modules from the unstratified total network and stratified subnetworks show low compatibility. Using each of the three clustering algorithms, modules were extracted from the unstratified total network, coarse-stratified cell culture subnetwork, and moderate-stratified tissue-specific subnetworks. Modular Compatibility scores Cp were calculated between two sets of modules. Green dots are average Cp calculated between modules extracted from the total network and those from each of the stratified subnetworks, with the same parameter settings applied for clustering. Blue stars are average Cp between two sets of modules from the same network (the total network, or any subnetwork) with different parameter settings for clustering. Because the density-based clustering method allows overlaps among modules, i.e., proteins or interactions may belong to multiple modules, and thus counted multiple times, which leads to higher overlaps and Cp scores between modules. Therefore, the separation of corresponding average Cp scores is not as explicit as those of results based on the other two clustering methods.