Fig. 6: Holimap for post-translational and post-transcriptional networks.
From: Holimap: an accurate and efficient method for solving stochastic gene network dynamics
a, b Post-translational networks. a Network with autoregulation and protein sequestration50. b Network with autoregulation and protein phosphorylation51. c Three-parameter Holimap for post-translational networks. d, e Post-transcriptional networks. d Network with autoregulation and mRNA degradation control52. e Network with microRNA-mRNA interactions53. Here α is the binding rate of microRNA to its mRNA target and β is the unbinding rate. f Three-parameter Holimap for post-transcriptional networks. All high-order interactions between genes, proteins, and RNAs are replaced by effective first-order switching and degradation reactions. g Comparison of the protein distributions for the four networks at two time points computed using the SSA with 105 trajectories, SSA with 2000 trajectories, and SSA + Holimap (with 2000 trajectories). h Comparison of the CPU times and the accuracy (measured by HDs averaged over ten-time points) of the SSA and SSA + Holimap for the four networks. The distributions obtained from the SSA with 105 trajectories are used as a proxy of ground truth when computing the HDs. See Supplementary Note 1 for the technical details of this figure. Source data are provided as a Source Data file.
