Development of a technique for the reconstruction and validation of gene network models based on gene expression profiles

Authors

DOI:

https://doi.org/10.15587/1729-4061.2018.123634

Keywords:

gene network, topological parameters, Harrington desirability index, gene expression, threshold coefficient

Abstract

We have developed a technique for the reconstruction and validation of models of gene networks based on the gene expression profiles derived in the course of DNA microchip experiments or by the method of RNA molecules sequencing. A structural block diagram is presented of a stepwise process for determining optimal parameters of the algorithm for reconstruction of a gene network that meet the optimum network topology. We proposed a comprehensive estimation criterion of a gene network topology based on the Harrington desirability function that contains network topological parameters as constituent components. The maximum value of this criterion corresponds to the optimal topology of a gene network. A technique for the validation of models of gene networks is based on a ROC analysis whose implementation implies a comparative analysis of the character of relations between relevant genes in the network on the basis of the totality of genes and gene networks based on the obtained biclusters. Qualitative reconstruction of a gene network makes it possible to explore the nature of interaction between genes that determine the process of functioning of a biological organism at different stages of development of complex genetic diseases for the purpose of early diagnosis and correction of a given process.

It was established that the gene network reconstructed based on the correlation output algorithm is more efficient in comparison with the gene network based on the algorithm ARACNE. The weighted average of relative validation criterion for the derived models based on the correlation output algorithm is significantly greater than the corresponding value when applying the algorithm of ARACNE. This fact indicates a higher degree of compliance with the character of relations between respective genes in the network based on the totality of genes and in the networks based on gene expression profiles in the obtained biclusters. Qualitative reconstruction of a gene network makes it possible to explore the character of development of a biological organism at the gene level, which creates preconditions for early diagnosis and adjustment of the development of different types of genetic diseases.

Author Biographies

Sergii Babichev, Jan Evangelista Purkyně University Pasteurova 1, Ústí nad Labem, Czech Republi, 40096 Kherson National Technical University Beryslavske highway, 24, Kherson, Ukraine, 73008

Associate professor

Department of Informatics

PhD, Associate Professor

Department of Informatics and Computer Science

Maksym Korobchynskyi, Military-Diplomatic Academy named after Eugene Bereznyak Melnykova str., 81, Kyiv, Ukraine, 04050

Doctor of Technical Sciences, Professor, Senior Researcher

Department No. 5

Oleksandr Lahodynskyi, Military-Diplomatic Academy named after Eugene Bereznyak Melnykova str., 81, Kyiv, Ukraine, 04050

Doctor of Pedagogical Sciences, Associate Professor, Head of Department

Department No. 6

Oleksandr Korchomnyi, Military-Diplomatic Academy named after Eugene Bereznyak Melnykova str., 81, Kyiv, Ukraine, 04050

PhD, Associate professor

Department No. 5

Volodymyr Basanets, Military-Diplomatic Academy named after Eugene Bereznyak Melnykova str., 81, Kyiv, Ukraine, 04050

PhD, Associte Professor

Department No. 6

Volodymyr Borynskyi, Military-Diplomatic Academy named after Eugene Bereznyak Melnykova str., 81, Kyiv, Ukraine, 04050

PhD, Associte Professor

Department No. 6

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Published

2018-02-15

How to Cite

Babichev, S., Korobchynskyi, M., Lahodynskyi, O., Korchomnyi, O., Basanets, V., & Borynskyi, V. (2018). Development of a technique for the reconstruction and validation of gene network models based on gene expression profiles. Eastern-European Journal of Enterprise Technologies, 1(4 (91), 19–32. https://doi.org/10.15587/1729-4061.2018.123634

Issue

Vol. 1 No. 4 (91) (2018): Mathematics and Cybernetics - applied aspects

Section

Mathematics and Cybernetics - applied aspects

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Copyright (c) 2018 Sergii Babichev, Maksym Korobchynskyi, Oleksandr Lahodynskyi, Oleksandr Korchomnyi, Volodymyr Basanets, Volodymyr Borynskyi

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