Figure 1

Characteristics of the phosphorylation dynamics-based network. (A) We generated the dynamics-based network by connecting pairs of peptides with similar (R > 0.99) time courses of phosphorylation activities. The network was visualized using Cytoscape (version 2.6.1) [45] and eXpanda (version 1.0.6) [46]. (B) Network density of the whole dynamics-based network and of the cytoplasmic and nucleic subnetworks. (C) Cumulative proportion, P ≥ (k), for the node degrees (k) based on analysis of the whole dynamics-based network simultaneously (i.e., not separately as in Figure D) (R > 0.99). For each group of cytoplasmic and nucleic nodes in the network, circles represent the proportions of proteins having more than k interacting partners. (D) Cumulative proportion for the node degrees with the cytoplasmic and nucleic subnetworks analyzed separately. (E, I, K) Patterns of the cellular fractions (cytoplasmic and nucleic): (E) binary, (I) triangular, and (K) square motifs that appeared in the dynamics-based network. The names of each motif pattern appear under the corresponding diagram: T, triangular; B, binary; S, square. (F-H, J, L) Appearance of each motif (proportion of total) in the dynamics-based network. (F-H) Triangular motifs appeared in the dynamics-based network of (F) R > 0.99, (G) R > 0.98, and (H) R > 0.97. (J) Binary and (L) square motifs appeared in the dynamics-based network with R > 0.99. Black bars represent percentages of the corresponding motif patterns in the real dynamics-based network; white bars represent the mean values of the percentages estimated using negative controls generated by random edge rewiring (RER, n = 1000). Error bars represent standard deviations. Significance levels: *, P < 0.05; **, P < 0.01; ***, P < 0.001.