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An effective method for computing the noise in biochemical networks

机译:一种计算生化网络噪声的有效方法

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摘要

We present a simple yet effective method, which is based on power series expansion, for computing exact binomial moments that can be in turn used to compute steady-state probability distributions as well as the noise in linear or nonlinear biochemical reaction networks. When the method is applied to representative reaction networks such as the ON-OFF models of gene expression, gene models of promoter progression, gene auto-regulatory models, and common signaling motifs, the exact formulae for computing the intensities of noise in the species of interest or steady-state distributions are analytically given. Interestingly, we find that positive (negative) feedback does not enlarge (reduce) noise as claimed in previous works but has a counter-intuitive effect and that the multi-OFF (or ON) mechanism always attenuates the noise in contrast to the common ON-OFF mechanism and can modulate the noise to the lowest level independently of the mRNA mean. Except for its power in deriving analytical expressions for distributions and noise, our method is programmable and has apparent advantages in reducing computational cost.
机译:我们提出了一种基于幂级数展开的简单而有效的方法,用于计算精确的二项式矩,进而可用于计算稳态概率分布以及线性或非线性生化反应网络中的噪声。当该方法应用于代表性的反应网络时,例如基因表达的开-关模型,启动子进程的基因模型,基因自动调节模型和常见的信号基序,可以精确地计算出该物种中噪声强度的公式。给出了兴趣或稳态分布。有趣的是,我们发现正反馈(负反馈)并没有像以前的作品中那样扩大(减少)噪声,但是具有反直觉的效果,并且与通常的ON相比,multi-OFF(或ON)机制始终会衰减噪声。 -OFF机制,可独立于mRNA平均值将噪声调节至最低水平。除了在推导分布和噪声的解析表达式方面的能力外,我们的方法是可编程的,在降低计算成本方面具有明显的优势。

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