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. 2021 Oct 12;10:e69324. doi: 10.7554/eLife.69324

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© 2021, Ham et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 5. — These heatmaps estimate the level of overshoot in the pathway-reporter approach for the nascent-protein and mature-protein reporters; blue regions show an overshoot of less than $≃ 0.05$ .

Here, the intrinsic contribution is calculated using stochastic simulations of the model $𝐌_{4}$ . For the mature-protein and nascent-protein reporters, we consider three different values of the parameter μ, specifically $μ = 2$ , $μ = 10$ , and $μ = 20$ . In all cases, the parameter $δ_{p}$ and the on-rate λ are varied between 0.01 and 0.5, and 0.5 and 5, respectively. The parameters of the model $𝐌_{4}$ are scaled so that $δ_{M} = 1$ . The maturation rate is fixed at 20, with the parameters $K_{N}$ and $K_{P}$ chosen to produce a mean protein level of 1000, a mean nascent mRNA level of 5 and a mean mature mRNA level of 50. Each individual pixel is generated from a sample of size 3000, although there is still some instability in the convergence for the nascent-protein reporter, particularly as the overshoot estimation starts to increase, and particularly as μ is larger. To produce more accurate values, the case of $μ = 2$ was averaged over two full experiments while $μ = 20$ was averaged over three. This was also done for the mature-protein reporter, however for these images there was almost no visible difference between the various runs of the experiment and their averages. Each of the three μ values takes approximately 7–10 hr of computation, depending on lead in time before sampling within a simulation. Figure 5—figure supplement 1 gives a heatmap for the overshoot in the pathway-reporter approach for nascent-mature pathway reporters.

Figure 5—figure supplement 1. — These heatmaps estimate the level of overshoot in the pathway-reporter approach for the nascent-protein and mature-protein reporters; blue regions show an overshoot of less than $≃ 0.05$ .

Here, the intrinsic contribution is calculated using stochastic simulations of the model $𝐌_{4}$ . For the mature-protein and nascent-protein reporters, we consider three different values of the parameter μ, specifically $μ = 2$ , $μ = 10$ , and $μ = 20$ . In all cases, the parameter $δ_{p}$ and the on-rate λ are varied between 0.01 and 0.5, and 0.5 and 5, respectively. The parameters of the model $𝐌_{4}$ are scaled so that $δ_{M} = 1$ . The maturation rate is fixed at 20, with the parameters $K_{N}$ and $K_{P}$ chosen to produce a mean protein level of 1000, a mean nascent mRNA level of 5 and a mean mature mRNA level of 50. Each individual pixel is generated from a sample of size 3000, although there is still some instability in the convergence for the nascent-protein reporter, particularly as the overshoot estimation starts to increase, and particularly as μ is larger. To produce more accurate values, the case of $μ = 2$ was averaged over two full experiments while $μ = 20$ was averaged over three. This was also done for the mature-protein reporter, however for these images there was almost no visible difference between the various runs of the experiment and their averages. Each of the three μ values takes approximately 7–10 hr of computation, depending on lead in time before sampling within a simulation. Figure 5—figure supplement 1 gives a heatmap for the overshoot in the pathway-reporter approach for nascent-mature pathway reporters.