Figure 2.

Initial proposed logic circuitry controlling honokiol and IR effects on Notch signaling in SW480 cells. (A) Logic regulations were carefully considered for each interaction in the network. The graphical representation of the logical circuit is equivalent to the logic rules listed to right. Black edges with arrows indicate activating regulations and red edges with blunt ends indicate inhibiting regulations. The * after a node on the left-hand side of an expression indicates the value the node will assume at the next time step. (B) Asynchronous simulation of the logic network in (A) was performed under the four experimental conditions. The y-axis represents the probability a node is ON. Probabilities between 0.0 and 1.0 after the first 5–10 time steps indicate a node is oscillating in the steady state. (C) The predicted steady state values for the network are represented in discrete from. The red Xs indicate differences between predicted values and the experimental values in Figure 1B. The raw penalty of this network is 14. After scaling by the maximum raw penalty of 32, a scaled penalty of 0.44 was generated. Much of the difference between the simulated and experimental values can be attributed to predicted oscillations.