Figure 2

Identification and clustering of functional kinetic motifs. (A) The solution map, in which each black dot represents the simulation result, as measured by deviations DD and DS, for one parameter set and the large black dot in the upper right corner represents many simulation results, because the values of their DD and DS were both set at 15 to indicate ill-behaved dynamics (see Methods). The resulting dynamics from both the deterministic (i.e. without perturbation) and stochastic (i.e. with perturbation) simulation for the simulated 4-gene transcriptional repression network fell into one of four groups. The vast majority (99.2%) failed to produce the specified dynamics, i.e. the specified steady-state concentration of the protein product of each of the four genes, in either the deterministic or the stochastic simulation, while a very low percentage succeeded in one, but not both, of the two types of simulation (0.1% for each). Those that succeeded in both also accounted for a very small percentage (0.6%) of the kinetic parameters simulated. A typical dynamics is shown for each of the four groups as insets; that on the left is deterministic and that on the right stochastic. (B) Clusters of kinetic motifs. The functional sets (2,355 sets or 0.6% of those sampled) were hierarchically clustered based on the integer sequence of their kinetic efficiency levels, which are colour-coded according to the spectrum shown to the far right, and each cluster could be represented by a motif logo (see Methods).