The current state of methods, models and algorithms for gene regulatory networks validation and simulation

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Liakh I. M., Durniak B. V., Бабічев С. А. № 2 (82) 92-103 Image Image

The paper presents an analysis of current methods of gene regulatory networks validation and simulation on the basis of genes expression data with the allocation of their advantages, shortcoming and ways for the further improvement of the existing techniques. The gene regulatory network is represented as a directed or non-directed graph, in which the weight of the arc determines the strength of the appropriate connection. The way to increase the efficiency of the reconstructed gene network is determined by analyzing synthetic and reconstructed timing systems both in topology and in the presence or absence of connection between the relevant elements of the network, and the nature of the corresponding connections. The conducted analysis has allowed one to allocate the unsolved part of the general problem, which is the absence of effective technology of gene regulatory networks validation, which takes into account the comparative analysis of the topologies of synthetic and reconstructed gene regulatory networks by the distribution of the relevant topological parameters, the values of which determine the structure of the networks on the one hand and, the absence of the information technology of gene regulatory network simulation that allows one to predict with a high degree of reliability the nature of the target genes and transcription factors interacting in order to better understand the patterns of the network elements interconnection, taking into account the type of disease, on the other hand. The structural block chart of the step-by-step procedure of gene expression data generation, selection of a subset of informative genes, reconstruction, validation and simulation of gene regulatory networks is proposed. The practical implementation of the proposed procedure involves the use of different methods taking into account the appropriate stage. It is shown that it is possible to increase the efficiency of the respective stage implementation by hybridization of models with joint application of various methods and algorithms for an increase of reliability of decision-making at the corresponding stage.

Keywords: gene regulatory network, validation, simulation, gene expression, re­gu­la­tory interaction of genes.

doi: 10.32403/0554-4866-2021-2-82-92-103

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