Figure 5

Reconstructed network using PMI. Graphical representation of the network structure captured by calculating PMI based on protein presence in cliques. Subgraphs representing important biological processes are inside boxes and magnified: APC complex (A); sumoylation pathway (B); Golgi and vesicles (C); proteasome (D); splicing (E); Skp1 and signalosome (F); ERAD (G); peroxisome (H). The colors are the same as in Figure 1. The layout of the graph to group together functionally linked dense subgraphs was achieved using the edge-weighted spring embedded (Kamada-Kawai) algorithm, which has previously been shown to be very effective for such depictions [113].