Mining Arabidopsis Thaliana Salt Stress Risk Factors Based On Systems Biology

At present,the factors such as global warming and population growth are becoming more and more serious.Soil salinization is also becoming more and more serious.It has become a recognized agricultural and ecological problem all over the world.Salt stress is the most important and most common abiotic stress in the world's agricultural production.It is one of the main abiotic factors that affect plant growth and crop yield.The northeast region is a typical saline alkali land distribution area in China,so it is of great practical significance to study salt stress in plants in Northeast China.The emergence of genomics has made the research of plant salt tolerance enter a new era.Plant studies have changed from single gene research to genome research.A large number of systematic studies on gene structure and function have appeared,and have identified a large number of salt resistant genes.In recent years,with the development of high-throughput sequencing and bioinformatics,people gradually realize that the molecular mechanism of plant salt stress is related to the interaction of multiple genes.Therefore,how to effectively and accurately identify the molecular markers related to salt stress in plants and their regulatory relationships from large amounts of large data is a major challenge.In this study,we chose Arabidopsis thaliana which is a common model organism as the research object,and used data mining approach of combining biology knowledge based on systems biology to identify risk factors related to salt stress in Arabidopsis(genes,GO terms,KEGG pathways,and network modules).First of all,five datasets of gene microarray downloaded from the GEO database were analyzed to identify the differentially expressed genes related to salt stress.We used AgriGO and WebGestalt online analysis tool to do biological functional annotation of differentially expressed gene identified in Arabidopsis thaliana under salt stress and identified GO terms and KEGG pathways based on the biological function database.Considering the influence of modest effect genes,we developed a pathway analysis strategy based on modest effect genes,and applied it to GSE46205 data.We identified three significantly enriched pathways based on modest effect genes.Finally,we found that five pathways may be related to salt stress.They are plant hormone signal transduction,MAPK signaling pathway-plant,Spliceosome,Ribosome,biogenesis in eukaryotes and Circadian rhythm-plant.The first three of these have reported as salt-related pathways in literature.The target relationship between these pathways and salt stress is further confirmed by future experimental and theoretical studies.In addition,we identify genes related to salt stress by combining protein-protein interaction(PPI)network and existing databases.First of all,we chose 41 genes which were related to salt stress from Arabidopsis salt stress response transcription factor database(STIFDB2)stress as seed genes and applied random walk with restart method to identify candidate salt-related genes in PPI network.If the gene is very similar to the seed gene in the PPI network,the gene is considered to be a candidate gene.Finally,we list the genes that rank in the top 10.In these genes,we found that two genes of AT3G03000 and AT3G62870 are differentially expressed genes in GSE46205,which also shows this method is effective.Secondly,we constructed differentially expressed genes interaction network from five datasets,and identify the six network modules by MCODE algorithm.Then we identified the pathways which were annotated by network modules and found there were two annotated pathways.They are Ribosome and Ribosome biogenesis in eukaryotes.It is again indicated Ribosome biogenesis in eukaryotes may be related to salt stess.We also use the MCC algorithm in CytoHubba to screen out 10 Hub nodes in the differentially expressed genes interaction network,and these 10 genes are also the target genes for subsequent research.In conclusion,our study used a systems biology approach to identify salt stress related genes,GO terms and biological pathways in Arabidopsis thaliana.These results can not only help us understand the molecular mechanism of salt stress and transgenic breeding in Arabidopsis thaliana,but also provide a reference for the study of other plant abiotic stress.