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. 2025 Oct 21;11:117. doi: 10.1038/s41540-025-00590-2

Fig. 6. mRNA stability contributes to gene expression clusters driven by JNK activation.

Fig. 6

A–C Predicted scaled mRNA expression from our ODE model of JNK signaling was aligned to experimentally measured gene expression clusters for sustained (A), transient (B), or pulsed (C) JNK activity. Colored lines represent predicted mRNA expression for variable mRNA half-lives, with black lines showing experimentally measured gene expression dynamics. Root mean square error (RMSE) was computed for each prediction and shown to the right of each plot. D–F A parameter scan across 200 mRNA decay rates (αm) from 0.02 h−1 to 1.4 h−1 was conducted across all genes, and the average root mean square error was computed. Data plots show the average RMSE of all genes ±SD, with the minimal point being the predicted decay rate for each cluster. G Box plots showing average mRNA half-lives from multiple studies for genes within each identified cluster. Individual colors represent the average mRNA half-life from each study. H Bar graphs show model predictions for the average half-life of all genes within each cluster ±SEM.