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

V. P. Bulgakov1,2* 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
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.
KEY WORDS: bioinformatics, protein–protein interaction networks, scale-free networks, probabilistic and statistical models, yeast interactome, Arabidopsis interactome

DOI: 10.1134/S0006297913100039