Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
Figure 3
A schematic diagram (A) and a flowchart (B) show the process of network growth by the CG model.
(A) The CG model mimics sequential incorporation of new proteins to crystals grown in solution. In stage I, the initial set of proteins (red) form seeds of new crystals. In stage II, a new protein is added, which either forms a new seed crystal (n) or attaches to an existing crystal (e). In the latter case, the protein e attaches to one protein in the crystal (solid arrow) and then further interacts with nearby proteins (dotted arrow). In stages III and IV, the second- (orange) and third- (yellow) generation proteins repeat the process of stage II, with the result that the early generation tends to be located at the core of each crystal and the late generation at the periphery. (B) Similarly, the CG model starts with a small number of seed nodes (N0). In each cycle, modules are defined and a new node is added that makes a fixed number of connections (ΔE). A new node creates a new module at a probability Pnew and makes connections to any other node in accordance with the AP rule. Otherwise, one module (crystal) is randomly selected and the new node is connected exclusively to the nodes in the selected module. After ΔE connections are made, modules are redefined and the cycle is repeated.