Figure 9.

Biological GRNs exhibit unique memory properties

(A) Violin plots of the set of GRNs from the Cell Collective database (https://cellcollective.org/) are compared (in terms of memories) with their configuration models. We show the median (violet dashed line), 5^th percentile (teal line), and 95^th percentile (pink line). The actual frequency of memory of the real GRN is represented as a red star. Only the “Aurora Kinase in Neuroblastoma” network from Cell Collective is plotted. The violin plots of memories for all the 35 GRNs are given in Supplemental information (Data S2, plots 1–35). We calculated the conditional entropy among the different types of memories of GRNs and configuration models, normalized these conditional entropies, applied Gaussian smoothing, and visualized the results obtained from (B) GRNs and (C) configuration models. Notably, GRNs are different from their randomized counterparts in terms of how much the appearance of one type of memory implies (predicts) the existence of any other type of memory (i.e., biological GRNs have more functional linkage among the different types of memory than is expected by chance).