**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) [] and eXpanda (version 1.0.6) []. (**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.

## PubMed Commons