Using the Protein-protein Interaction Network to Identifying the Biomarkers in Evolution of the Oocyte

Background Oocyte maturity includes nuclear and cytoplasmic maturity, both of which are important for embryo fertilization. The development of oocyte is not limited to the period of follicular growth, and starts from the embryonic period and continues throughout life. In this study, for the purpose of evaluating the effect of the FSH hormone on the expression of genes, GEO access codes for this data set, GSE38345, were used. Materials and methodsThe data are microarray and contain the gene expression information for cow's oocyte cells, that their maturation is influenced by the FSH hormone under laboratory conditions. Data analysis was performed by using the GEO2R software link. After identifying the genes and examining the different genes expressed, two gene groups included Increased and decreased expression genes are formed. The interaction of each of the gene groups was examined by using a string database, based on the co-expression information. The meaningful sub networks were explored using the clusterone software. Gene ontology was performed using the comparative GO database. The miRNA-mRNA interaction network was also studied based on the miRWalk database. Finally, meaningful networks and subnets obtained by cytoscape software were drawn. Results In a comparison between oocyte gene expression data in the pre-maturation and the post- maturation stage after treatment with FSH, 5958 increased genes and 4275 decreased genes expression were found. By examining the protein interaction network in the set of increased and decreased expression genes, based on string information, 262 increased and 147 decreased genes (high confidence (0.7) data) were found. In network of Increased expression genes in oocyte maturation, the RPS3, NUSAP1, TBL3 and ATP5H genes which are effective in the biological pathways of positive regulation of rRNA processing, cell division, mitochondrial ATP synthesis coupled proton, also in functional pathways, oxidative phosphorylation and progesterone-mediated were effective, also in decreased expression genes, WDR46 and MRPL22 genes are the most important that were effective in the biological pathways of SRP-dependent cotranslational proteins in targeting to membrane, RNA secondary structure, unwinding and functional pathways of ribosomal and RNA polymerase. The most important microarray gene in the protein network of increased and decreased expression genes bta-miR-10b-5p and miR-29b-2-5p gene were reported. Conclusion: In examining the genes expressed in the pathway of oocyte maturation, three groups of nuclear, mitochondria, microarray genes were determined. Increasing and decreasing gene expression helps maintain balance, which can be considered as a marker.