| Objective To find the co-expression relationship between competing endogenous long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) in the osteogenic differentiation, and to construct the lncRNA-miRNA-mRNA network. Methods GSE89330, GSE72429, and GSE74837 were selected from NCBI gene expression comprehensive database (GEO Database). GEO2R web tool was used to filter the DEGs, DElncRNAs, and DEmiRNAs. Gene Ontology analysis (GO analysis) and Kyoto Encyclopedia of Genes, and Genomes (KEGG) pathway enrichment analysis were used to analyze the gene function enrichment via Visualization and Integrated Discovery (DAVID). miRWalk web tool and DIANA web tool lncBASE2.0 were used to predict the upstream potential miRNA targets and lncRNA targets of DEmiRNAs. Cytoscape was used to build the lncRNA-miRNA-mRNA network. After that, Retrieval of Interacting Genes (STRING) and Molecular Complex Detection (MCODE) were used to visualize the protein-protein interaction network (PPI network) of DEGs. At last, DEGs were subjected to screen the hub genes via GO analysis and KEGG analysis. Results A total of 186 DEGs were obtained in this study, including 81 down-regulated genes and 105 up-regulated genes. There were 89 DEmiRNA, including 25 down-regulated miRNA and 64 up-regulated miRNA. There were 441 DElncRNAs, including 205 down-regulated lncRNAs and 236 up-regulated lncRNAs. Finally, 84 DEGS, 7 DEmiRNA, and 11 DElncRNAs were selected to construct the lncRNA-miRNA-mRNA interaction network. GO analysis of 186 DEGs showed that their functions were mainly concentrated in inflammatory response and angiogenesis, and their molecular functions were mainly in the activation of growth factors. Through PPI network analysis, two network cluster modules were selected and 10 key genes (IL6, CXCL12, CXCL8, CCL2, HGF, LEP, VCAM1, CXCL1, SAA1, and FOS) were obtained. Conclusion The link between competing endogenous lncRNA and down-stream miRNA-mRNA is predicted via lncRNA-miRNA-mRNA interaction network. |