Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
Figure 1
Interaction density (D) patterns depend upon the attachment rule.
The protein age groups G1, G2, and G3 emerge at times t = 1, 2, and 3, respectively. In all cases, the first age group, G1, makes intra-group connections at t = 1. (A) In the random attachment (RA) model, G2 makes connections to G1 and within G2 with an equal probability at t = 2, showing that D1,1 = D1,2. Similarly, G3 makes connections to G1, G2, and within G3 (D1,3 = D2,3 = D3,3). The interaction densities between protein age groups are shown in the right panel. (B) In the preferential attachment (PA) model, G2 attaches more frequently to G1 than within G2 because, on average, G1 is more connected (D1,2>D2,2). At t = 3, G3 is preferentially connected to older groups in the order of G1>G2>G3 (D1,3>D2,3>D3,3). (C) In anti-preferential attachment (AP), the interaction density shows the reverse pattern to PA. Because a new node prefers less-connected nodes or younger groups, the density pattern shows D1,2<D2,2 and D1,3<D2,3<D3,3. Therefore, the interaction density (D) decreases in AP but increases in PA from top to bottom in the right panel.