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Interrogating the topological robustness of gene regulatory circuits by randomization

Fig 1

Schematics of the random circuit perturbation (RACIPE) method.

(A) The gene regulatory network for a specific cellular function is decomposed into two parts–a core gene circuit modeled by chemical rate equations and the other peripheral genes whose contribution to the network is regarded as random perturbations to the kinetic parameters of the core circuit; (B) RACIPE generates an ensemble of models, each of which is simulated by the same rate equations but with randomly sampled kinetic parameters. For each model, multiple runs of simulations are performed, starting from different initial conditions, to identify all possible stable steady states; (C) The in silico gene expression data derived from all of the models are subject to statistical analysis.

Fig 1

doi: https://doi.org/10.1371/journal.pcbi.1005456.g001