Prediction of key coding genes and miRNAs associated with rheumatoid arthritis using bioinformatics

Acta Universitatis Medicinalis Anhui 2020 02 v.55 228-234     font:big middle small

Found programs:

Authors:Ding Xiao; Hao Ying; Wang Weishan

Keywords:rheumatoid arthritis;bioinformatics;protein-protein interaction network;key gene;microRNA

DOI:10.19405/j.cnki.issn1000-1492.2020.02.014

〔Abstract〕 Objective To screen synovitis-related core differential genes and interacting microRNAs(miRNAs) in rheumatoid arthritis(RA) using bioinformatics. Methods The gene chip GSE55235 was downloaded from the GEO database, and the differentially expressed genes were screened by R software 3.5.0, and functional enrichment analysis was performed by David online database. The protein interaction network was established by using String 10.5,Cytoscape v3.6.1 and MCODE to screen out the core genes during RA development. miRNAs that interact with core genes were predicted by CyTargetLinker. Results 605 differentially expressed genes were screened, of which 314 were up-regulated and 291 were down-regulated.Their functions were mainly concentrated in the process of immune reaction and biosynthesis and binding of macromolecules. The protein interaction network contained a total of 552 nodes and 5 163 interaction edges. The first four cluster modules were listed and 10 core genes were screened: protein tyrosine phosphatase receptor type C(PTPRC), vascular endothelial growth factor(VEGF), fibronectin 1(FN1), integrin Subunit Alpha M(ITGAM), epidermal growth factor(EGFR), CD86, matrix metalloproteinase-9(MMP-9), integrin subunit Beta 2(ITGB2), TYRO protein tyrosine kinase binding protein(TYROBP) and MYC. It was predicted that 36 miRNAs could interact with three core genes by CyTargetLinker. Conclusion The selected core genes and interacting miRNAs may be potential targets for RA treatment.