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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >Quantitative modeling of the saccharomyces cerevisiae FLR1 regulatory network using an s-system formalism
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Quantitative modeling of the saccharomyces cerevisiae FLR1 regulatory network using an s-system formalism

机译：使用S系统形式主义对啤酒酵母FLR1调控网络进行定量建模

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In this study we address the problem of finding a quantitative mathematical model for the genetic network regulating the stress response of the yeast Saccharomyces cerevisiae to the agricultural fungicide mancozeb. An S-system formalism was used to model the interactions of a five-gene network encoding four transcription factors (Yap1, Yrr1, Rpn4 and Pdr3) regulating the transcriptional activation of the FLR1 gene. Parameter estimation was accomplished by decoupling the resulting system of nonlinear ordinary differential equations into a larger nonlinear algebraic system, and using the LevenbergMarquardt algorithm to fit the models predictions to experimental data. The introduction of constraints in the model, related to the putative topology of the network, was explored. The results show that forcing the network connectivity to adhere to this topology did not lead to better results than the ones obtained using an unrestricted network topology. Overall, the modeling approach obtained partial success when trained on the nonmutant datasets, although further work is required if one wishes to obtain more accurate prediction of the time courses.
机译：在这项研究中，我们解决了寻找定量数学模型的问题，该数学模型调节了酿酒酵母对农用杀菌剂mancozeb的应激反应的遗传网络。 S系统形式主义被用来模拟编码四个调节FLR1基因转录激活的转录因子（Yap1，Yrr1，Rpn4和Pdr3）的五基因网络的相互作用。通过将所得的非线性常微分方程组解耦为一个较大的非线性代数系统，并使用LevenbergMarquardt算法将模型预测与实验数据拟合，可以完成参数估计。探索了模型中与网络的假定拓扑有关的约束的引入。结果表明，与使用无限制网络拓扑获得的结果相比，强制网络连接遵循此拓扑不会产生更好的结果。总的来说，当在非突变数据集上进行训练时，建模方法获得了部分成功，尽管如果希望获得对时间过程的更准确预测，还需要进一步的工作。

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