Screening of differentially expressed miRNAs related to muscle strain and their target gene

Muscle strain is one of the most common muscle injuries seen in the office of a practicing physician. To get a better understanding of this injury, we identified the differentially expressed miRNAs in muscle stem cells collected from injured muscle tissues of mouse. In this study, we downloaded the gene expression microarray (GSE26780) from Gene Expression Omnibus database. The dataset contained a total of 12 samples (murine muscle stem cells), including normal controls and samples collected from tissues at different time points after the injury. Differentially expreesed miRNAs were identified by LIMMA package and target genes of mmu-miR-143 were found by TargetScan. Then, a protein-protein interaction (PPI) network was constructed for the products of these target genes by using KUPS. Finally, Cytoscape and its plugins were used to identify and analyze the modules in this network. According to the results, 121, 136 and 148 differentially expressed miRNAs were identified in injured samples at each time point, and among them, 60 miRNAs were overlapping between all three groups. The expression values of mmu-miR-143 were most significantly altered over time at 36–72 h after the injury. Therefore, 510 target genes of mmu-miR-143 were found and a PPI network for the products of these target genes was constructed. Moreover, two modules were identified in the PPI network. Together with the previous studies, we suppose that proteins in module B, most of which are collagens or integrins, most likely participate in healing of strain injuries through cell adhesion processes.