Construction and analysis of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer

Abstract

Background There is a growing body of evidence suggesting that long non-coding RNAs(lncRNAs) can function as a microRNA(miRNA) sponge in various diseases including oral cancer. However, we are still not very clear about the pathophysiological function of lncRNAs. Methods We constructed a lncRNA-miRNA-mRNA network in oral cancer based on the competitive endogenous RNA(ceRNA) theory with the human expression profiles GSE74530 from the Gene Expression Omnibus (GEO) database and used topological analysis to determine the hub lncRNAs in the regulatory ceRNA network. Then, function enrichment analysis was performed by R package Cluster Profiler. Results A total of 238 potential co-dysregulated competing triples were obtained in the lncRNA-assoicated ceRNA network of oral cancer, which consisted of 10 lncRNA nodes, 41 miRNA nodes, and 122 mRNA nodes. Additionally, we found three lncRNAs( HCP5 , AGAP11 , HCG22 ) exhibiting superior potential as diagnostic and prognostic markers of oral cancer. Conclusions Our findings will provide novel insights for understanding the ceRNA regulation in oral cancer and identify three novel lncRNAs as potential molecular biomarkers.

Novel LncRNA OXCT1-AS1 indicates poor prognosis and contributes to tumorigenesis by regulating miR-195/CDC25A axis in glioblastoma

“…We conducted Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analyses for the mRNAs involved in the constructed lncRNA-related network using the R package “clusterprofiler”, with a set of cut-off criteria at P < 0.05 [ 24 ]. The online database Retrieval of Interacting Gene (STRING) was used to construct a protein-protein interaction (PPI) network [ 25 ].…”

Novel LncRNA OXCT1-AS1 Indicates Poor Prognosis and Contributes to Tumorigenesis by Regulating miR-195/CDC25A Axis in Glioblastoma

“…We conducted Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analyses for the mRNAs involved in the constructed lncRNA related network using the R package "clusterpro ler", with a set of cut-off criteria at P <0.05 [24]. The online database Retrieval of Interacting Gene (STRING) was used to construct Protein-protein interaction (PPI) network [25].…”