进化调控网络的基因复制模型

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摘要翻译：
背景：基因复制是分子网络进化的重要环节。因此，许多作者认为基因复制是形成分子网络拓扑结构的驱动力。特别是，人们注意到，通过复制生长将作为一种隐含的优先附着方式，从而提供观察到的分子网络的广泛程度分布。结果：我们扩展了当前的基因复制和重连模型，包括方向和分子网络不是单向生长的结果。我们引入上游站点和下游形状来量化复制和重新布线期间的潜在链接。我们发现，这本身就产生了对原核生物基因组位点转录因子的观察尺度。该动力学模型可以生成无标度分布p(k)&prop；1/k^&gamma；在非增长情况下，指数&gamma；=1；在网络增长情况下，指数&gamma；>1。结论：我们发现基因的复制和上游区域的大量重组可以产生遗传调控网络的主要特征。然而，我们的稳态度分布与数据一致，从而表明选择性剪枝是复制基因的一个主要附加限制。我们的分析表明，如果基因上游区域之间也有实质性的重组，基因复制只能是观察到的广泛程度分布的主要原因。
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英文标题：
《On Gene Duplication Models for Evolving Regulatory Networks》
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作者：
Jakob Enemark and Kim Sneppen
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最新提交年份：
2007
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分类信息：

一级分类：Quantitative Biology        数量生物学
二级分类：Populations and Evolution        种群与进化
分类描述：Population dynamics, spatio-temporal and epidemiological models, dynamic speciation, co-evolution, biodiversity, foodwebs, aging; molecular evolution and phylogeny; directed evolution; origin of life
种群动力学；时空和流行病学模型；动态物种形成；协同进化；生物多样性；食物网；老龄化；分子进化和系统发育；定向进化；生命起源
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一级分类：Quantitative Biology        数量生物学
二级分类：Other Quantitative Biology        其他定量生物学
分类描述：Work in quantitative biology that does not fit into the other q-bio classifications
不适合其他q-bio分类的定量生物学工作
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英文摘要：
  Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted that growth via duplication would act as an implicit way of preferential attachment, and thereby provide the observed broad degree distributions of molecular networks.   Results: We extend current models of gene duplication and rewiring by including directions and the fact that molecular networks are not a result of unidirectional growth. We introduce upstream sites and downstream shapes to quantify potential links during duplication and rewiring. We find that this in itself generates the observed scaling of transcription factors for genome sites in procaryotes. The dynamical model can generate a scale-free degree distribution, p(k)∝ 1/k^γ, with exponent γ=1 in the non-growing case, and with γ>1 when the network is growing.   Conclusions: We find that duplication of genes followed by substantial recombination of upstream regions could generate main features of genetic regulatory networks. Our steady state degree distribution is however to broad to be consistent with data, thereby suggesting that selective pruning acts as a main additional constraint on duplicated genes. Our analysis shows that gene duplication can only be a main cause for the observed broad degree distributions, if there is also substantial recombinations between upstream regions of genes.
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PDF链接：
https://arxiv.org/pdf/0704.3808

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关键词：distribution Quantitative Biodiversity Combinations duplication networks 因子 位点 degree main