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Stochasticity in gene expression impacts the dynamics and functions of gene regulatory circuits. Intrinsic noises, including those that are caused by low copy number of molecules and transcriptional bursting, are usually studied by stochastic simulations. However, the role of extrinsic factors, such as cell-to-cell variability and heterogeneity in the microenvironment, is still elusive. To evaluate the effects of both the intrinsic and extrinsic noises, we develop a method, named sRACIPE, by integrating stochastic analysis with random circuit perturbation (RACIPE) method. RACIPE uniquely generates and analyzes an ensemble of models with random kinetic parameters. Previously, we have shown that the gene expression from random models form robust and functionally related clusters. In sRACIPE we further develop two stochastic simulation schemes, aiming to reduce the computational cost without sacrificing the convergence of statistics. One scheme uses constant noise to capture the basins of attraction, and the other one uses simulated annealing to detect the stability of states. By testing the methods on several synthetic gene regulatory circuits and an epithelial–mesenchymal transition network in squamous cell carcinoma, we demonstrate that sRACIPE can interpret the experimental observations from single-cell gene expression data. We observe that parametric variation (the spread of parameters around a median value) increases the spread of the gene expression clusters, whereas high noise merges the states. Our approach quantifies the robustness of a gene circuit in the presence of noise and sheds light on a new mechanism of noise-induced hybrid states. We have implemented sRACIPE as an R package.

Role of noise and parametric variation in the dynamics of gene regulatory circuits