A study of structural properties of gene network graphs for mathematical modeling of integrated mosaic gene networks.
Gene network modeling is one of the widely used approaches in systems biology. It allows for the study of complex genetic systems function, including so-called mosaic gene networks, which consist of functionally interacting subnetworks. We conducted a study of a mosaic gene networks modeling method based on integration of models of gene subnetworks by linear control functionals. An automatic modeling of 10,000 synthetic mosaic gene regulatory networks was carried out using computer experiments on gene knockdowns/knockouts. Structural analysis of graphs of generated mosaic gene regulatory networks has revealed that the most important factor for building accurate integrated mathematical models, among those analyzed in the study, is data on expression of genes corresponding to the vertices with high properties of centrality.
* The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
Olga V
OV
Petrovskaya
* The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
Evgeny D
ED
Petrovskiy
* The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.|† Otto von Guericke University Magdeburg, Medical Faculty, Department Translational Inflammation Research, Pfälzer Platz Building 28, Magdeburg, 39106, Germany.
Inna N
IN
Lavrik
* The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
Vladimir A
VA
Ivanisenko
D003198:Computer Simulation; D055785:Gene Knockdown Techniques; D055786:Gene Knockout Techniques; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D008962:Models, Theoretical; D049490:Systems Biology / Q000379:methods
Mosaic gene networks; gene networks modeling; graphs structural properties; integrated gene networks; ordinary differential equations