渠化降低了生物网络调节的非线性。

IF 3.5 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY NPJ Systems Biology and Applications Pub Date : 2024-06-13 DOI:10.1038/s41540-024-00392-y
Claus Kadelka, David Murrugarra
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引用次数: 0

摘要

基因调控网络等生物网络具有理想的特性。与随机网络相比,它们更具鲁棒性和可控性。这就促使人们寻找生物网络在进化过程中融入的结构和动态特征。最近对已发表的、由专家编辑的布尔生物网络模型进行的荟萃分析发现了几个这样的特征,这些特征通常被称为设计原则。其中包括:生物网络富含某些重复出现的网络图案;动态更新规则比预期的更冗余、更偏向、更渠化;与同类随机网络相比,生物网络的动态可通过线性和低阶近似得到更好的近似。由于这些特征大多相互关联,因此最重要的是厘清因果关系,即了解哪些特征是进化主动选择的,从而真正构成进化设计原则。在这里,我们将已发表的布尔生物网络模型与不同的空模型集合进行了比较,结果表明,生物网络中大量的管道化现象几乎可以完全解释最近推测的高近似性。此外,对随机 N-K 考夫曼模型的分析表明,近似性与网络的动态鲁棒性密切相关。
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Canalization reduces the nonlinearity of regulation in biological networks.

Biological networks, such as gene regulatory networks, possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated into biological networks. A recent meta-analysis of published, expert-curated Boolean biological network models has revealed several such features, often referred to as design principles. Among others, the biological networks are enriched for certain recurring network motifs, the dynamic update rules are more redundant, more biased, and more canalizing than expected, and the dynamics of biological networks are better approximable by linear and lower-order approximations than those of comparable random networks. Since most of these features are interrelated, it is paramount to disentangle cause and effect, that is, to understand which features evolution actively selects for, and thus truly constitute evolutionary design principles. Here, we compare published Boolean biological network models with different ensembles of null models and show that the abundance of canalization in biological networks can almost completely explain their recently postulated high approximability. Moreover, an analysis of random N-K Kauffman models reveals a strong dependence of approximability on the dynamical robustness of a network.

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来源期刊
NPJ Systems Biology and Applications
NPJ Systems Biology and Applications Mathematics-Applied Mathematics
CiteScore
5.80
自引率
0.00%
发文量
46
审稿时长
8 weeks
期刊介绍: npj Systems Biology and Applications is an online Open Access journal dedicated to publishing the premier research that takes a systems-oriented approach. The journal aims to provide a forum for the presentation of articles that help define this nascent field, as well as those that apply the advances to wider fields. We encourage studies that integrate, or aid the integration of, data, analyses and insight from molecules to organisms and broader systems. Important areas of interest include not only fundamental biological systems and drug discovery, but also applications to health, medical practice and implementation, big data, biotechnology, food science, human behaviour, broader biological systems and industrial applications of systems biology. We encourage all approaches, including network biology, application of control theory to biological systems, computational modelling and analysis, comprehensive and/or high-content measurements, theoretical, analytical and computational studies of system-level properties of biological systems and computational/software/data platforms enabling such studies.
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