Comparison of the dynamics-based network with known cellular signaling pathways. (A) Known epidermal growth factor receptor (EGFR) signal transduction pathways in the EGFR (NetPath) analysis obtained from the NetPath database. Phosphorylation reactions are indicated by directed arrows from protein kinases to their target substrate. Red protein nodes indicate that the phosphorylation dynamics of the peptide or peptides were included in the dynamics-based network with R > 0.99. (B) Density distribution for the shortest path lengths (SPLs) of all reachable two-phosphopeptide nodes in the dynamics-based network (bars). Each asterisk denotes a pair of proteins in the EGFR (NetPath) known signaling pathway data; the asterisk color denotes the SPL of the two proteins in the known signaling network, and the position of each asterisk denotes the SPL of the corresponding two phosphopeptides in the dynamics-based network. (C-G) Comparison of SPLs in the dynamics-based network with those in each of the five known signaling networks. (C) EGFR (NetPath), (D) All (NetPath), (E) All - EGFR (NetPath), (F) Kinases (Phospho.ELM), and (G) All (Phospho.ELM). In each panel, the SPLs of the two proteins in the known network were assigned to the bins indicated on the horizontal axis; for protein pairs in each bin, we calculated the SPLs of their corresponding peptide pairs in the dynamics-based network (only for the reachable peptide pairs in this network), and the resulting mean value is shown on the vertical axis. The bin labeled "All" also included unreachable pairs in the known network. (D) In the comparison with EGFR (NetPath), Pearson's correlation coefficient (R) was calculated without the "All" bin.