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The nucleotide composition and Kimura's 2-parameter (K2P) genetic distance [40] between networks were calculated in MEGA 4.0 [4.0.
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Node degree, average path length, betweenness centrality of both the nodes and the links, clustering coefficient of the network, and the intersection between the TPPIN network and the link weight-randomized networks, were calculated.
Topological parameters of the networks were calculated with the Cytoscape plugin Network Analyzer [90].
Median-joining networks were calculated with Network 4.2 (Fluxus-Engineering).
The networks were calculated using all transcripts and all samples.
CRVs of each protein in the three networks were calculated.
Pearson correlations between the gene expression values of RIF-predicted RF and DE genes in each one of the three IPA networks were calculated.
Median-Joining networks were calculated for the eight Alpine endemics with Network v.4.6.0.0 (Fluxus Technology Ltd).
Additionally the amount of network stability between these networks was calculated.
Though energy conversion between two networks is calculated in the above references, an IPGN is still seen as a single network in terms of control and operation, and such treatment cannot reflect the interaction between two networks which are operated by different companies.
In this framework, in a given pair of PPI networks, the alignment score between two PPI networks is calculated based on matches, mismatches, and duplications.
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