MINI-REVIEW: Bioinformatics analysis of protein interaction networks: Statistics, Topologies, and Meeting the Standards of Experimental Biologists

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V. P. Bulgakov^1,2* and G. Sh. Tsitsiashvili³

¹Institute of Biology and Soil Sciences, Far East Branch of the Russian Academy of Sciences, pr. Stoletiya Vladivostoku 159, 690022 Vladivostok, Russia; fax: +7 (423) 231-0193; E-mail: bulgakov@ibss.dvo.ru

²Far Eastern Federal University, ul. Sukhanova 8, 690950 Vladivostok, Russia

³Institute of Applied Mathematics, Far East Branch of the Russian Academy of Sciences, ul. Radio 7, 690041 Vladivostok, Russia; fax: +7 (423) 231-1856; E-mail: guram@iam.dvo.ru

^* To whom correspondence should be addressed.

Received February 26, 2013; Revision received May 22, 2013

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In recent years, bioinformatics analyses of protein networks have allowed researchers to obtain exceptional theoretical predictions and subsequent experimental confirmations. The current view is that protein networks are scale-free networks and have a topology analogous to that of transport networks, the Internet, and social networks. However, an alternative hypothesis exists in which protein networks and scale-free networks possess significantly different properties. In this work, we show that existing information is insufficient to describe protein networks as scale-free networks.

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KEY WORDS: bioinformatics, protein–protein interaction networks, scale-free networks, probabilistic and statistical models, yeast interactome, Arabidopsis interactome

DOI: 10.1134/S0006297913100039

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