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].