Summary of the Effect of Perturbation Reported by Experimental and Simulated Methods.

The up arrow (↑) indicates that the perturbation caused a rise in the level of the phosphorylated protein; the straight line (−) indicates no change; and the down arrow (↓) indicates that a decrease occurred. Values in the Experiment column were estimated by comparing lanes 4 and 2 in Figure 9. We estimated the Simulation column by determining whether the top quartile of the distribution for the final time point was above, below, or at zero. In some cases it is difficult to judge for certain whether the total quantity of the phosphorylated protein changed or remained the same—both for the experimental and computational cases. In these situations, we indicated the uncertainty by listing the possible changes that the protein could have feasibly undergone.