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Figure 3 | BMC Systems Biology

Figure 3

From: Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

Figure 3

Results from the Boolean and continuous simulations of the T-cell model using the manually determined parameter set. The vertical dashed lines in (A, B, F) mark (from left to right): the switching on of the inputs, the total activation of the transcription factors, the activation of the feedback loops and the total deactivation of the transcription factors. (A) Boolean simulation using synchronous updates. (B) Continuous simulation using HillCubes. (C) Upper figure: difference between the time course from (A) and the time course from (B). Lower figure: correlation between the discrete and the continuous expression pattern of the lower 29 species at each time point 0 <t < 100. The curve was smoothened using a moving-average filter with 5 time-units window length. (D) Ratio of activation and deactivation time, ρ, for τFyn = τZAP-70 = 1, 2, ..., 20. Other parameters are set to n = 3, k = 0.3, τ = 1, kfast = 0.1 and kslow = 0.8. For τFyn = τZAP-70 = 1 the cascade was not activated properly. (E) Ratio of activation and deactivation time, ρ, for 20 different kfast and kslow. log10 (kfast) and log10 (kslow) are uniform from [-2, 0]. Other parameters are set to n = 3, k = 0.3, τ = 1, τFyn = τZAP-70 = 10. In the white areas the cascade was not activated properly. (F) Comparison between time course y(t) with the manually determined parameters and time course y3(t) with the decreased threshold in the activation of LAT-phosp by ZAP-70 as described in the section about monotony properties. Plotted is the difference y'(t) - y(t).

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