The Integrative Analysis of Competitive Endogenous RNA Regulatory Networks in Coronary Artery Disease

Abstract

Background: Coronary artery disease (CAD) is the leading cause of cardiovascular death. The competitive endogenous RNAs (ceRNAs) hypothesis is a new theory that explains the relationship between lncRNAs and miRNAs. The mechanism of ceRNAs in the pathological process of CAD has not been fully elucidated. The objective of this study was to explore the ceRNA mechanism in CAD using the integrative bioinformatics analysis and provide new research ideas for the occurrence and development of CAD.Methods: The GSE113079 dataset was downloaded, and differentially expressed lncRNAs (DElncRNAs) and genes (DEGs) were identified using the limma package in the R language. Weighted gene correlation network analysis (WGCNA) was performed on DElncRNAs and DEGs to explore lncRNAs and genes associated with CAD. Functional enrichment analysis was performed on hub genes in the significant module identified via WGCNA. Four online databases, including TargetScan, miRDB, miRTarBase, and Starbase, combined with an online tool, miRWalk, were used to construct ceRNA regulatory networks.Results: DEGs were clustered into ten co-expression modules with different colors using WGCNA. The brown module was identified as the key module with the highest correlation coefficient. 188 hub genes were identified in the brown module for functional enrichment analysis. DElncRNAs were clustered into sixteen modules, including seven modules related to CAD with the correlation coefficient more than 0.5. Three ceRNA networks were identified, including OIP5-AS1-miR-204-5p/miR-211-5p-SMOC1, OIP5-AS1-miR-92b-3p-DKK3, and OIP5-AS1-miR-25-3p-TMEM184B.Conclusion: Three ceRNA regulatory networks identified in this study may play crucial roles in the occurrence and development of CAD, which provide novel insights into the ceRNA mechanism in CAD.

Identification of Biomarkers Associated With CD8+ T Cells in Coronary Artery Disease and Their Pan-Cancer Analysis

“…Another 17 transcription factors are not studied for their association with CAD. In addition, there is growing evidence that competitive endogenous RNAs (ceRNAs) play a key role in CAD and cancer ( 69 ). However, there is still a lack of ceRNA networks that can predict the diagnosis and treatment of CAD.…”

Construction of an acute myeloid leukemia prognostic model based on m6A-related efferocytosis-related genes

“…The "limma" package, a package for analyzing gene expression data generated by microarray or RNA-seq technology (19), was used to obtain the DEGs in the GSE9476 dataset. The screening criteria was: p value < 0.05 and |log 2 FoldChange| > 0.5 (20,21). The "VennDiagram" package (22) was applied to visualize the differentially expressed ERGs (DE-ERGs).…”

TMEM184B promotes proliferation, migration and invasion, and inhibits apoptosis in hypopharyngeal squamous cell carcinoma

“…revealed that TMEM184B is one of the five hub genes involved in the progression of ANCA-GN through immune-related signalling pathways. Similarly, Ji et al26 found that TMEM184B might crucially influence the occurrence and development of coronary artery disease by participating in the OIP5-AS1-miR-25-3p-TMEM184B ceRNA regulatory network. The roles of TMEM184B in the biological processes of cancer are also gaining attention.…”