A study of structural properties of gene network graphs for mathematical modeling of integrated mosaic gene networks

Abstract

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.

Database of Potential Promoter Sequences in the Capsicum annuum Genome

“…The created classes of promoter sequences can reflect the participation of genes in genetic regulatory networks. It can be assumed that the more similar the classes of matrices, as shown in Figure 3 , the closer to each other the genes are in the genetic regulatory network near which these promoters are located [ 37 ]. In this sense, Figure 3 is an image of the promoter-level genetic network that exists in the C. annuum cell.…”