HKC: An Algorithm to Predict Protein Complexes in Protein-Protein Interaction Networks

Figure 6

Examples of clusters predicted by HKC in MIPS data set. The nodes encircled by the red-dotted line are known complex in the complexcat benchmark, the nodes contained within the blue circle are clusters predicted by HKC, and the yellow node in each cluster denotes the seed of the cluster. (a) A cluster of size 11 perfectly matches with the TRAPP complex. (b) A cluster of size 14 shares 14 proteins with the SAGA complex (size 16), and their overlap ratio is 0.93. The two proteins YCL010c and YGL066w that are not contained in the predicted cluster are isolated nodes with only one edge connecting with the cluster. (c) An example of a well-matched cluster, involving 7 proteins, among which 6 is in common with the complex of cytoplasmic translation initiation factor 3 (eIF3). (d) A novel cluster detected by HKC, which does not match with any known protein complexes in the complexcat benchmark, and the proteins in the black circle form the docking complex that facilitates the import of peroxisomal matrix proteins according to GO annotation.