Figure 2

Representing arbitrarily complex gene regulatory mechanisms with a graph-based framework. (A) Cartoon schematic for a simple transcriptional regulatory mechanism involving equilibrium (binding and dissociation) and non-equilibrium energy consuming (phosphorylation) steps. Each step is a particular molecular arrangement that can be thought of as a ‘microstate’ which has a certain probability of being occupied based on the interactions, rates and concentrations of the molecules. (B) Graph depiction of the cartoon gene regulatory mechanism. Each node represents a microstate, the edges the interactions/reactions, and the edge labels are the rates.