Dataset Information

Null Model and Community Structure in Multiplex Networks.

ABSTRACT: The multiple relationships among objects in complex systems can be described well by multiplex networks, which contain rich information of the connections between objects. The null model of networks, which can be used to quantify the specific nature of a network, is a powerful tool for analysing the structural characteristics of complex systems. However, the null model for multiplex networks remains largely unexplored. In this paper, we propose a null model for multiplex networks based on the node redundancy degree, which is a natural measure for describing the multiple relationships in multiplex networks. Based on this model, we define the modularity of multiplex networks to study the community structures in multiplex networks and demonstrate our theory in practice through community detection in four real-world networks. The results show that our model can reveal the community structures in multiplex networks and indicate that our null model is a useful approach for providing new insights into the specific nature of multiplex networks, which are difficult to quantify.

SUBMITTER: Zhai X

PROVIDER: S-EPMC5818485 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Publications

Null Model and Community Structure in Multiplex Networks.

Zhai Xuemeng X Zhou Wanlei W Fei Gaolei G Liu Weiyi W Xu Zhoujun Z Jiao Chengbo C Lu Cai C Hu Guangmin G

Scientific reports 20180219 1

The multiple relationships among objects in complex systems can be described well by multiplex networks, which contain rich information of the connections between objects. The null model of networks, which can be used to quantify the specific nature of a network, is a powerful tool for analysing the structural characteristics of complex systems. However, the null model for multiplex networks remains largely unexplored. In this paper, we propose a null model for multiplex networks based on the no ...[more]

PMID: 29459696

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Project description:Much attention has recently been given to the statistical significance of topological features observed in biological networks. Here, we consider residue interaction graphs (RIGs) as network representations of protein structures with residues as nodes and inter-residue interactions as edges. Degree-preserving randomized models have been widely used for this purpose in biomolecular networks. However, such a single summary statistic of a network may not be detailed enough to capture the complex topological characteristics of protein structures and their network counterparts. Here, we investigate a variety of topological properties of RIGs to find a well fitting network null model for them. The RIGs are derived from a structurally diverse protein data set at various distance cut-offs and for different groups of interacting atoms. We compare the network structure of RIGs to several random graph models. We show that 3-dimensional geometric random graphs, that model spatial relationships between objects, provide the best fit to RIGs. We investigate the relationship between the strength of the fit and various protein structural features. We show that the fit depends on protein size, structural class, and thermostability, but not on quaternary structure. We apply our model to the identification of significantly over-represented structural building blocks, i.e., network motifs, in protein structure networks. As expected, choosing geometric graphs as a null model results in the most specific identification of motifs. Our geometric random graph model may facilitate further graph-based studies of protein conformation space and have important implications for protein structure comparison and prediction. The choice of a well-fitting null model is crucial for finding structural motifs that play an important role in protein folding, stability and function. To our knowledge, this is the first study that addresses the challenge of finding an optimized null model for RIGs, by comparing various RIG definitions against a series of network models.

Dataset Information

Null Model and Community Structure in Multiplex Networks.

Publications

Null Model and Community Structure in Multiplex Networks.

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