Are RNA networks scale-free?
Are RNA networks scale-free?
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DOI：
10.1007/s00285-019-01463-z
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发表时间：
2020-01-16
影响因子：
1.9
通讯作者：
Clote, P.
中科院分区：
文献类型：
--
作者：
Clote, P.
一个网络是无标度的，如果它的连通性密度函数与幂律分布成正比。有人认为，无标度网络可以解释在某些物理和生物现象中观察到的鲁棒性，因为存在一些高度连接的枢纽节点和大量的小度节点可以提供平均任何两个节点之间的交替路径-这种鲁棒性已经在代谢网络，基因相互作用网络和蛋白质折叠的研究中提出。巴拉巴西和阿尔伯特提出了一个理论解释，解释了为什么许多网络看起来是无标度的。他们认为，扩展网络（其中新节点优先连接到高度连接的节点）往往是无标度的。在本文中，我们提供了第一个有效的算法来计算的连接密度函数的合奏的所有均聚物的二级结构的用户指定的长度一个高度非平凡的结果，因为这样的网络的指数大小排除了它们的枚举。由于现有的幂律拟合软件，如powerlaw，不能用于确定幂律适合我们的指数大RNA连接数据，我们还实现了有效的代码来计算幂律比例因子和相关的Kolmogorov-Smirnov p值的最大似然估计。假设检验强烈表明，均聚物RNA二级结构网络不是无标度的，而且，这似乎是真实的（非均聚物）RNA网络的情况。
A network is scale-free if its connectivity density function is proportional to a power-law distribution. It has been suggested that scale-free networks may provide an explanation for the robustness observed in certain physical and biological phenomena, since the presence of a few highly connected hub nodes and a large number of small-degree nodes may provide alternate paths between any two nodes on average-such robustness has been suggested in studies of metabolic networks, gene interaction networks and protein folding. A theoretical justification for why many networks appear to be scale-free has been provided by Barabasi and Albert, who argue that expanding networks, in which new nodes are preferentially attached to highly connected nodes, tend to be scale-free. In this paper, we provide the first efficient algorithm to compute the connectivity density function for the ensemble of all homopolymer secondary structures of a user-specified length-a highly nontrivial result, since the exponential size of such networks precludes their enumeration. Since existent power-law fitting software, such as powerlaw, cannot be used to determine a power-law fit for our exponentially large RNA connectivity data, we also implement efficient code to compute the maximum likelihood estimate for the power-law scaling factor and associated Kolmogorov-Smirnov p value. Hypothesis tests strongly indicate that homopolymer RNA secondary structure networks are not scale-free; moreover, this appears to be the case for real (non-homopolymer) RNA networks.