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Are RNA networks scale-free? (English) Zbl 1437.62174
Author’s abstract: 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 A.-L. Barabási and R. Albert [Science 286, No. 5439, 509–512 (1999; Zbl 1226.05223)], 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.
MSC:
62G32 Statistics of extreme values; tail inference
62G07 Density estimation
05C82 Small world graphs, complex networks (graph-theoretic aspects)
68R05 Combinatorics in computer science
92D20 Protein sequences, DNA sequences
62P10 Applications of statistics to biology and medical sciences; meta analysis
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