Figure 2

The central interactome. (A) Shortest path distance distributions. We first remark that distances between C.Prot entities (red) are closer than distances between proteins of the human interactome (black), i.e. short distances below 4, which is the mean and median distance, are over-represented. Remarkably, C.Prot is also closer than on average to the non C.Prot proteins (orange). The abundant C.Prot proteins are even closer to each other and to the non C.Prot proteins (cyan and blue). It shows that C.Prot (and its most abundant components) are embedded "uniformly" in the human proteome. (B) Power law distribution of the whole human interactome versus the central interactome. The central interactome is more connected (exponent -1.1), i.e. frequency of high node degrees decreases slower, than the whole (exponent -1.8). (C) Central interactome with mapped significant biological processes (Table 2). Processes not significantly enriched in C.Prot are in black and multiple GO annotations are depicted by a circle (color chosen randomly) as opposed to a square for single GO. Shared GO term ancestors at a node were removed to eliminate trivial multiple annotations and stay at the most specific levels. We note that, except for a few, processes are not strongly localized in this network. It does not represent juxtaposed pathways but rather an exchange platform. We also observe that most proteins have multiple GO BP annotations (circular node shape), which de facto establish additional exchanges between fundamental cellular processes. Finally, we recognized some important complexes: (a) exosome, (b) ubiquitinol-cytochrome c reducatase, (c) NADH dehydrogenase, (d) oligosaccharyl transferase, (e) proteasome, (f) COPI, (g) ribonucleoprotein/splicosome, (h) proton-transporting ATP synthase, (i) ribosome, (j) signal recognition particle, (k) cytochrome c oxidase subunits, (l) pyruvate/2-oxoglutarate dehydrogenase complex, (m) prefoldin, (n) condensin, (o) Signal peptidase complex, (p) COPII, (q) septin complex. Network visualized with Cytoscape [56].