Yeast mitochondrial cytochrome bc1 complex: PPI network, composite network, SWC-weighted network, and likelihood network. The PPI subgraph includes many extraneous edges and external neighboring proteins. In the composite network, the extra edges from the other data sources induce a full clique among the complex proteins, although the number of extraneous edges increases dramatically as well. In the SWC-weighted network, the complex's subgraph is still relatively dense, with fewer extraneous edges remaining, allowing the complex to be easily found by both IPCA and RNSC (although missing one protein). In the likelihood network, diverse data sources connect many proteins within the cluster with high SWC scores. CYT1-RIP1-QCR2 are fully connected with each other via all three data sources with moderate to high co-complexness, making them a central triplet within the cluster, while CYT1-COR1-QCR2 and CYT1-QCR7-QCR2 are connected with two or more data sources with moderate to high co-complexness, deeply embedded in the cluster as well. The other proteins appear less central in the cluster, especially COB, a fringe member which is only connected via functional associations to four proteins.
Yong et al. BMC Systems Biology 2012 6(Suppl 2):S13 doi:10.1186/1752-0509-6-S2-S13