Noise levels for WT expression, in time.

Noise is a standard deviation using relative residuals, calculated by , where stoch and det are the stochastic and deterministic solutions at each position (energid), respectively; for experimental data, replace stoch with background-removed intensity and det with the trend found by 2D SSA (see Methods). This measure is calculated for the activated region, 15–45%EL (proximal promoter dependent). aAverage of the noise levels (standard deviation in brackets) for the 19 simulations shown in Figure 3F. mRNA was noisier than protein in every simulation (and p<0.01, for t-test on differences, for each time). The simulation in Figure 3AB has average noise levels (11% for mRNA, 5.4% for protein). bn = 3 embryos. mRNA was noisier than protein in each embryo (and p<0.05 for t-test). The embryo in Figure 3CD has noise of 22% for mRNA and 4.8% for protein. (Limiting analysis to the strongest mRNA expressing region, 30–45%EL, average mRNA noise decreases (to 25%) and becomes less variable (8.0% std. dev.), while protein noise remains stable (mean, 5.7%; std. dev., 1.3%), increasing the significance for their difference.)