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Phase transitions and assortativity in models of gene regulatory networks evolved under different selection processes
Journal of The Royal Society Interface ( IF 3.9 ) Pub Date : 2021-04-14 , DOI: 10.1098/rsif.2020.0790
Brandon Alexander 1, 2, 3 , Alexandra Pushkar 4 , Michelle Girvan 2, 3, 5, 6
Affiliation  

We study a simplified model of gene regulatory network evolution in which links (regulatory interactions) are added via various selection rules that are based on the structural and dynamical features of the network nodes (genes). Similar to well-studied models of ‘explosive’ percolation, in our approach, links are selectively added so as to delay the transition to large-scale damage propagation, i.e. to make the network robust to small perturbations of gene states. We find that when selection depends only on structure, evolved networks are resistant to widespread damage propagation, even without knowledge of individual gene propensities for becoming ‘damaged’. We also observe that networks evolved to avoid damage propagation tend towards disassortativity (i.e. directed links preferentially connect high degree ‘source’ genes to low degree ‘target’ genes and vice versa). We compare our simulations to reconstructed gene regulatory networks for several different species, with genes and links added over evolutionary time, and we find a similar bias towards disassortativity in the reconstructed networks.



中文翻译:

在不同选择过程下进化的基因调控网络模型中的相变和分类

我们研究了基因调控网络进化的简化模型,其中通过基于网络节点(基因)的结构和动态特征的各种选择规则添加链接(调控相互作用)。与经过充分研究的“爆炸性”渗透模型类似,在我们的方法中,选择性地添加链接以延迟向大规模损伤传播的过渡,即使网络对基因状态的小扰动具有鲁棒性。We find that when selection depends only on structure, evolved networks are resistant to widespread damage propagation, even without knowledge of individual gene propensities for becoming 'damaged'. 我们还观察到,为避免损害传播而进化的网络倾向于不协调性(即 定向链接优先将高度“源”基因连接到低度“目标”基因,反之亦然)。我们将我们的模拟与几种不同物种的重建基因调控网络进行了比较,随着进化时间的推移增加了基因和链接,我们发现在重建的网络中存在类似的不协调性偏见。

更新日期:2021-04-14
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