Fig. 7
From: WASABI: a dynamic iterative framework for gene regulatory network inference
GRN mechanistic and stochastic model. Our GRN model is composed of coupled piecewise deterministic Markov processes. In this example 2 genes are coupled. A gene i is represented by its promoter state (dashed box) which can switch randomly from ON to OFF, and OFF to ON, respectively at kon,i and koff,i mean rate. When promoter state is ON, mRNA molecules are continuously produced at a s0,i rate. mRNA molecules are constantly degraded at a d0,i rate. Proteins are constantly translated from mRNA at a s1,i rate and degraded at a d1,i rate. The interaction between a regulator gene j and a target gene i is defined by the dependence of kon,i and koff,i with respect to the protein level Pj of gene j and the interaction parameter θi,j. Likewise, a stimulus (yellow flash) can regulate a gene i by modulating its kon,i and koff,i switching rates with interaction parameter θi,0