To account for the factor that even random networks can exhibit a baseline degree of rich-club effect, the null model is generated by randomizing the original network while preserving its degree distribution.
This should be compared to a null expectation of 50 ± 6 paralogous pairs at l = 2 found by randomizing the YPD network while keeping in- and out-degrees [ 4].
That is, we generate families of null models by randomizing the regulatory networks while maintaining the in- and out-degree for the nodes and with a bias for neighborhood correlations of a GO annotation (see Fig. 3(g)).
We calculated the significance of the observed number of triples, by randomizing the ataxia interaction network and preserving its degree distribution.
To analyze the interconnection tendency of proteins of the same/different age classes, we first generate 1000 random networks by randomizing the corresponding relationships between proteins and their ages in real network.
We also randomly generated a functional miRNA-target network by randomizing the FPI and the Seq miRNA-target networks and target did not show any significant enrichment.
We simulated the case of zero conservation by randomizing the orthologous pairs while preserving the network structure.
Bakshy et al. [22] have reported a large scale experiment performed on the Facebook social network by randomizing the exposition of users to the items published by their friends, in order to expose the role of the social links in the propagation of an information, and to show the existence of a genuine influence phenomenon between Facebook friends.
Thus, we assessed the network topologies for the PIN with the aim of uncovering intrinsic properties that distinguish our network from 1) a network constructed based on a hypergeometric model alone and 2) a network constructed by randomizing the PIN scores.
In this study, a set of 1000 random networks was formed by randomizing the connections of the group-average neonatal connectome, maintaining an identical level of overall sparsity, as well as preserving the degree sequence of the network (i.e., hubs remain hubs), but with the underlying network organization randomized.
