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Fig. 6 | BMC Systems Biology

Fig. 6

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

Fig. 6

Case (iii) when PpsRred binds the puc promoter and acts as an activator of that. Similar to the Fig. 5 here we show how our model results vary if the value of a particular parameter is increased and/or decreased from their default values and those are compared with the experimental data. The black filled circles show the micro-array data. Model results for varying parameter values are shown in different panels as: I in a, α in b, β in c and γ in d. We see that like case (ii) the model results in this case also unable to explain the experimental gene expression pattern. Here, similar to Fig. 5 we do not calculate normalised SSE for each curve as from visual inspection we do not see any hope for good data fitting. The default parameters are: I= 0.001, α = 6, β = 500, γ = 2.1, δ = 1, and Keq = ∞. Here, 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

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