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. 2017 Sep 27;5(3):251–267.e3. doi: 10.1016/j.cels.2017.08.014

Figure 2.

Figure 2

PID Profiles for Three-Gene Networks

(A) Mean PID values for three-gene networks with different topologies. PID values are calculated using data simulated from three-gene networks with the topologies illustrated above each plot; the models used for simulation assumed mass action (green) or thermodynamic (orange) kinetics. For each three-gene network, 12 PID values were calculated from the simulated data — there are four PID contributions with each gene treated as the target gene in turn, consisting of a redundant, synergistic, and two unique contributions (Equation 5 in Box 1). Each line graph shows the mean PID values calculated from simulations using different initial conditions (error bars indicate 1 SD), with the horizontal axis labels indicating the PID contribution, e.g., the first four values show the PID values with gene X as the target, consisting of the redundancy (R), unique contributions from gene Y (Y) and gene Z (Z), and the synergistic contribution (S). The vertical dashed gray lines in the one-edge plot indicate the unique PID values that are used as the basis for our inference algorithm. Here, all regulatory interactions are assumed to be activating, the additional stimulating ligand targeted gene X, and the values indicated are the mean PID values calculated from five sets of simulations (with different randomly sampled initial conditions); results obtained with models that include both activating and inhibitory regulation are shown in Figure S1.

(B) Visualizations of the directed 50-node networks, produced by GeneNetWeaver (Schaffter et al., 2011); node degree distributions for the 50- and 100-node GeneNetWeaver networks used in this study are shown in Figure S2.

(C) Mean PID profiles for gene triplets in the 50-gene S. cerevisiae 1 network. Every triplet of nodes (genes) in the network was assigned to one of six possible classes (based on the known connectivity of genes, as indicated in network diagrams above each plot). Each line graph shows the mean PID values calculated across triplets with the same topology, with the horizontal axis labels indicating the PID contribution.