Fraction of practically identifiable (see Methods for definition) transcriptional interactions (differences between bound and unbound transcriptional parameters) vs. the number of cells sampled per time point (N_cells) for the three input perturbations. At low values of N_cells, corresponding to a large impact of stochastic gene expression, the single-step perturbation actually allows the greatest number of transcriptional regulatory interactions to be determined with 95% confidence. As the number of sampled cells is increased, however, the double-pulse perturbation becomes more effective for determining the regulatory interactions. This result differs from the previous (Figs. 4,5) in that it demonstrates a trade-off between the richness of the perturbation and sensitivity to the effects of stochastic gene expression.