CausalPath places differentially phosphorylated proteins into context of GPVI signaling. (A) Overview of CausalPath analysis of quantitative phosphoproteomics data. Additional details regarding CausalPath notation and functionality are found in supplemental Figure 7. (B) Merged summary of CausalPath models from conditions 1 and 2. Nodes (conventionally labeled with gene names) represent significantly modified phosphoproteins. Edges represent causal phosphorylation (green arrow) or dephosphorylation (red arrow) processes. Protein phosphorylation sites are shown with smaller “p” circles, where a green border indicates an activating site and red border indicates inactivating site. The background color of phosphorylation sites indicates their differential measurement from data, red indicating an increase and blue indicating a decrease. Nodes highlighted with light green background represent well established nodes in platelet signaling, further examined later. Nodes highlighted with light orange background represent new targets of interest in GPVI signaling, as detailed. In general, more kinases than phosphatases place directly into CausalPath models because kinase-substrate relations are more completely detailed in literature, and phosphorylation site-specific mechanisms of phosphatase regulation are less prevalent. Nonetheless, many phosphatase-associated mechanisms are apparent in CausalPath models (ie, SHP-2/PTPN11 dephosphorylation of PAG1; PKA phosphorylation of spinophilin/PPP1R9B⁸⁵ ); several phosphatase-associated proteins are also modified in an unspecified manner (ie, MYPT1/PPP1R12A; supplemental Figures 12 and 13).