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BMC Syst Biol. 2018 Jul 31;12(1):80. doi: 10.1186/s12918-018-0598-2.

A systematic survey of centrality measures for protein-protein interaction networks.

Author information

1
Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, P.O. Box 13164, Tehran, Iran.
2
Department of Systems Biology and Bioinformatics, University of Rostock, P.O. Box 18051, Rostock, Germany.
3
Faculty of New Sciences and Technologies, University of Tehran, P.O. Box 143995-71, Tehran, Iran.
4
Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
5
Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, P.O. Box 14115-134, Tehran, Iran. mirzaie@modares.ac.ir.
6
Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, P.O. Box 13164, Tehran, Iran. mjafari@pasteur.ac.ir.

Abstract

BACKGROUND:

Numerous centrality measures have been introduced to identify "central" nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measure may best suit the analysis of a given network. The choice of a suitable measure is furthermore complicated by the impact of the network topology on ranking influential nodes by centrality measures. To approach this problem systematically, we examined the centrality profile of nodes of yeast protein-protein interaction networks (PPINs) in order to detect which centrality measure is succeeding in predicting influential proteins. We studied how different topological network features are reflected in a large set of commonly used centrality measures.

RESULTS:

We used yeast PPINs to compare 27 common of centrality measures. The measures characterize and assort influential nodes of the networks. We applied principal component analysis (PCA) and hierarchical clustering and found that the most informative measures depend on the network's topology. Interestingly, some measures had a high level of contribution in comparison to others in all PPINs, namely Latora closeness, Decay, Lin, Freeman closeness, Diffusion, Residual closeness and Average distance centralities.

CONCLUSIONS:

The choice of a suitable set of centrality measures is crucial for inferring important functional properties of a network. We concluded that undertaking data reduction using unsupervised machine learning methods helps to choose appropriate variables (centrality measures). Hence, we proposed identifying the contribution proportions of the centrality measures with PCA as a prerequisite step of network analysis before inferring functional consequences, e.g., essentiality of a node.

KEYWORDS:

Centrality analysis; Clustering; Network science; Principal components analysis (PCA); Protein-protein interaction network (PPIN)

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