Fig. 3: Parameter inference, identifiability, and reproducibility.

A Number of genes for which parameters were identifiable, partially identifiable, or non-identifiable (left panel). Distribution of 95% confidence interval range for identifiable parameters. Also see the Supplementary Data file. Source data are provided as a Source Data file. B Distribution of the parameter values for the different replicates. The distributions are similar for the different replicates and the bulk of the distributions span a 30 to 100-fold difference between the genes depending on the parameter. C Reproducibility of each parameter. The color of the point corresponds to the fit quality metric for the worst replicate, the line corresponds to 95% confidence interval, with the color corresponding to the fit quality of that replicate. Parameters k₁’ and k₂ that were identifiable for both replicates are also quite reproducible, while k₂’ and k_{cyto_deg} are very reproducible and well-defined. The dashed red line indicates the 2-fold reproducibility window. D Reproducibility of composite parameter k₁’/k₂. Even though k₁’ and k₂ are well not defined for some genes, their ratio may be highly reproducible and well-defined. The dashed red line indicates the twofold reproducibility window. E Comparison of model-inferred half-life with half-life values determined with the actinomycin-D method. The dashed lines link replicates of the model-inferred half-life. The green line indicates a 1:1 relationship and the dashed red line a 2-fold range. We notice a high correlation between the two half-life estimates (Spearman rank correlation of 0.8) but that the model seems to capture a larger range in half-lives than the actinomycin-D method.