Fig. 1
From: Constructing network topologies for multiple signal-encoding functions
Defining objective functions for three distinct signal-encoding processes. a The temporal step functions (jump from Ii0 = 0.1 to Ii ∈[0.5, 1], i = 1,2,3) represent three external signals that mimic glucose limitation, osmotic stress or oxide stress in the yeast Msn2 stress responses, respectively. b The signals are received by the receptor nodes R1, R2, and R3, respectively, one signal at a time and are respectively encoded into different dynamics of the circuit’s output node O through the unknown signaling network. c The target output dynamics of the output node upon stimuli, i.e., F1 for oscillation (with Period > 0.1, Amplitude > 0.1), F2 for transient activation (with |Oend – Oini| < 0.1, Opeak – Oini > 0.2, |Oend – Oini| < 0.5(Opeak – Oini)), and F3 for sustained activation (Oend – Oini > 0.2), respectively. (d-f) Illustrations of implicit interactions between M1 and O1 when active enzyme R*1 simultaneously activates (d), or deactivates (e) the substrate enzymes M1 and O1, or when it activates M1 and deactivates O1 (f). The dashed links in the circuits represent the implicit interactions of mutual activations (d,e) and deactivations (f), respectively. (g,h) demonstrates an example where the same circuit exhibits completely distinct dynamical behaviors of oscillations (g) and steady state (h) when the substrate competition is considered (g) or not (h). Refer to additional file 1 for the rate equations and parameter values used in (d-h)