Topological Characteristics Of Target Genes Regulated By Abiotic-stress-responsible MiRNAs In A Rice PPI Network

In gene regulatory network,a large number of microRNAs(miRNAs)have been shown to response to abiotic stress conditions,such as drought,high salt and high temperature and so on.In the protein interaction network,the topological exploration of target genes regulated by stress-responsible miRNAs in a network fashion may be beneficial in discovering the particular molecular mechanisms associated with plant stress response.In this study,we select rice(Oryza sativa)as the research object,which has both economic value and edible value.Firstly,using the interolog method to predict the rice interactome network and then use the complex network theory to analyze the topological properties of target genes regulated by stress-responsible-miRNAs(stress-miR-targets)in the rice interactome network.The main research contents and results of this paper:(1)Construction of high quality rice protein interaction network.Using the interolog method,we computationally predicted the rice interactome network and we used two indexes of subcellular co-localization and co-expression,as the quality control for the predicted PPI data.At last,we get 2975 rice protein with 22933 non-redundant protein interaction.Prediction of the target genes regulated by rice ASRmiRs,the network nodes can be divided into two types: target genes of stress-miR-targets and targets gene of non-stress-miR-targets.(2)Based on complex network theory,the method of network topology characteristic measurements analysis is proposed.In the rice protein interaction network,we calculated degree,clustering coefficient,betweenness,topological coefficient,1N index,SDT,and ADT.The average values of seven network measurements were compared between stress-miR-targets and non-stress-miR-targets,the results showed that stress-miR-targets exhibit unique topological properties,and had significant difference between stress-miR-targets and non-stress-miR-targets.(3)Based on complex network theory,the methods of k-core decomposition algorithm and protein interaction probability analysis are proposed.The interaction probability between two types of genes were calculated,and the network is decomposed by k-core,extracting core node information,results showed that the stress-miR-targets had more tendency to interact with non-stress-miR-targets,and stress-miR-targets tended to locate at the peripheral position in the network,and not locate at the hubs node position.In conclusion,we find that the topological properties of two different types of target genes has obvious differences,reveals the regulation mechanisms of stress-miR-targets in rice abiotic stress response.The results also can provide valuable clues to clarify the molecular mechanisms of crop response to abiotic stress.