Podkolodnyy N.L.   Podkolodnaya N.   Yakubova Z.D.   Podkolodnaya O.A.  

Computer analysis of biological networks

Reporter: Podkolodnyy N.L.

The paper presents the methods of analysis of the structure of biological networks of different nature, including gene networks, molecular interaction networks, networks of gene co-expressions, diseases network, etc. The problems of standardization representation networks, methods of analysis of local and global topological properties of networks, methods of detection of the network subsystems and methods of comparing of network structure have been considered. The original method of calculation of the integral structural characteristics of the network as a principal component based on the structural characteristics of the local units – graphlets have been proposed.
On this basis, we developed a method of comparing the network and a statistical criterion for testing the hypothesis under consideration the network of its structural model in the form of random graphs.
The use of these approaches has allowed us to reconstruct an expanded version of the gene network of the mammalian circadian oscillator, to analyze the structure of the gene network, and to identify the central component of the circadian oscillator, which includes basic regulatory circuits passing through the key element of the circadian clock---the protein Clock/Bmal1 [1]. This structural model, which includes both the central component and functional subsystems interacting with it, can be the basis for building an extended mathematical model of the dynamics of the gene network regulating the circadian oscillator.

The work was supported by the RSF (the project № 14-24-00123).

1. OA Podkolodnaya, NN Podkolodnaya, NL Podkolodny  The Mammalian Circadian Clock: Gene Regulatory Network and Computer Analysis // Russian Journal of Genetics: Applied Research, 2015, Volume 5, № 3.

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