Fig. 3.

Genes expressed in the analyzed pathway and their TFs: (a) STAT1 homodimer simulation and EMSA; (b) nuclear IRF1 simulation and western blot; (c–f) IRF1, STAT1, LMP2 and TAP1 gene expression, respectively, from RT-PCR and simulation results; in all plots simulation results are represented by the thick solid line, experimental data by circles; data for each plot was normalized to the area below it as described in Section 2. Time scale in all plots is in hours. Thin solid lines represent simulation with perturbed parameters, to show robustness of the model to the parameter changes (see Section 5.3 in the article and the Supplementary Material).