Figure 2
Difference in assortativity among eukaryote PINs. ( A ) <Knn(k)>, the mean of the degrees among the neighbors of k-degree nodes, in the PINs of yeast (black square), worm (magenta plus), fly (blue triangle), human (green cross), and malaria parasite (red diamond). For yeast and human PINs, <Knn(k)> for MIPS and Rual et al. datasets, respectively, are shown, and the results for the other yeast and human datasets are provided in Additional file 2: Figure S2. Dashed lines in black, magenta, blue, green, and red represent k-0.47, k-0.29, k-0.35, k-0.26, and k-0.02, respectively. ( B ) Duplication of a node changes the value of ν in <Knn(k)> ~ k-ν. A diagram below each network indicates the distribution of <Knn(k)> and the value of ν. ( C ) The distribution of <Knn(k)> in the networks generated by the DDD model with the asymmetric divergence (DDD+A; left) and the symmetric divergence (DDD+S; right). Blue diamonds, green crosses, and red diamonds indicate the results with σ = -0.05 (-0.05), -0.03 (-0.03), and 0 (0), respectively, for DDD+A (DDD+S). These results were obtained by taking the mean among 100 networks generated by simulations. Black squares indicate <Knn(k)> in the yeast PIN for MIPS. Dashed lines in black, blue, green, and red represent k-0.47 (k-0.47), k-0.51 (k-0.48), k-0.37 (k-0.38), and k-0.18 (k-0.26), respectively, for DDD+A (DDD+S).