The current state of methods for gene regulatory networks reconstruction

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Лях І. № 2 (63) 97-111 Image Image

The paper presents the analysis of current methods of gene regulatory networks (GRN) reconstruction on the basis of gene expressions data with the allocation of their advantages, disadvantages and ways of further improvement. The gene regulatory network is represented as both an oriented and non-oriented graph, where the weight of the arc determines the strength of the corresponding connection. Within the framework of this review, the following methods of gene regulatory networks reconstruction are considered: based on the analysis of correlations; based on the analysis of mutual information between genes and/or transcription factors; based on Bayesian networks; based on differential equations and based on regression analysis. The analysis of the relevant methods has allowed one to conclude that the current state of development of this subject area is determined by the hybridization of existing models, methods and algorithms. Currently, there is no effective information technology for gene regulatory network reconstruction, which takes into account the optimization of the network topology by estimating the distribution of topological parameters in synthetic and reconstructed networks, comparative analysis of different methods for gene regulatory networks reconstruction to form the optimal network topology. The use of ensembles of methods to reconstruct the gene regulatory networks helps to increase the adequacy of the reconstructed gene regulatory network relative to biological gene networks, which, in turn, contributes to a better understanding of the nature of the genes and/or transcription factors interaction in the network.

Keywords: gene regulatory network, an algorithm of gene regulatory network reconstruction, transcription factor, activating connection, inhibitory connection, oriented graph, undirected graph.

doi: 10.32403/1998-6912-2021-2-63-97-111


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