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Fig. 5 | BMC Systems Biology

Fig. 5

From: Use of transcriptomic data for extending a model of the AppA/PpsR system in Rhodobacter sphaeroides

Fig. 5

The pucB gene expression pattern when PpsRred binds the puc promoter and acts as a repressor of that (Case (ii)). Here, we compare the pucB gene expression pattern obtained from our modelling and micro-array data analysis. The black filled circles show the experimental data obtained from our micro-array data analysis which we compare with model results for varying parameters one by one. a Effect of changes in blue light irradiation (I) on the shape of the curve obtained from the simulation. b Effect of changes in parameter α on the shape of the curve obtained from the simulation. Similarly (c) and (d) present changes in the pucB gene expression pattern if we change the parameter values of β and γ, respectively. Note that the model result for the parameter combination which would fit the data very well is shown by red coloured solid lines in all panels. That particular parameter combination is considered as the default parameter values in all simulations. The default parameters are: I = 0.001, α = 6, β = 500, γ = 2.1, δ = 1, and Keq = ∞. Like in Fig. 4, we have assumed that 30% O2 200–380 μM and 0% O2 = 0 μM as well as the total concentration of PpsR is assumed to be 100 nM. We have increased and/or decreased each parameter value by at least two orders of magnitudes from their default values. The model results in this case are unable to explain the experimental gene expression pattern. Here, we do not feel the need of calculating normalised SSE as from the visual inspection we do not see any hope for a good data fitting

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