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. 2022 Aug 2:2022:6971238.
doi: 10.1155/2022/6971238. eCollection 2022.

Weighted Gene Coexpression Network Analysis Identifies Crucial Genes Involved in Coronary Atherosclerotic Heart Disease

Jinli Bao  1
Affiliations

Weighted Gene Coexpression Network Analysis Identifies Crucial Genes Involved in Coronary Atherosclerotic Heart Disease

Jinli Bao. Dis Markers. .

Abstract

Background: Coronary atherosclerotic heart disease (CHD) is a lethal disease with an unstated pathogenic mechanism. Therefore, it is urgent to develop innovative strategies to ameliorate the outcome of CHD patients and explore novel biomarkers connected to the pathogenicity of CHD.

Methods: The weighted gene coexpression network analysis (WGCNA) was carried out on a coronary atherosclerosis dataset GSE90074 to determine the crucial modules and hub genes for their prospective relationship to CHD. After the different modules associated with CHD have been identified, the Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched pathway analyses were conducted. The protein-protein interaction (PPI) network was thereafter performed for the critical module using STRING and Cytoscape.

Results: The yellow module was recognized as the most critical module associated with CHD. The enriched pathways in the yellow module included those related to inflammatory response, positive regulation of extracellular signal-regulated kinase1/2 (ERK1/2) cascade, lipid catabolic process, cellular response to oxidative stress, apoptotic pathway, and NF-kappa B pathway. Further CytoHubba analysis revealed the top five hub genes (MMP14, CD28, CaMK4, RGS1, and DDAH1) associated with CHD development.

Conclusions: The current study provides the prognosis, novel hub genes, and signaling pathways for treating coronary atherosclerosis. However, their potential biological roles require deeper investigation.

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Conflict of interest statement

The author declares no conflict of interest.

Figures

Figure 1
Figure 1
Creation of weighted gene coexpression network. (a) A sample cluster dendrogram. (b) The soft thresholding powers for the scale-free network.
Figure 2
Figure 2
Evaluation of the key modules. (a) Cluster diagram of the various gene modules. (b) The TOM heatmap plot.
Figure 3
Figure 3
The correlation analysis between the different modules. (a) Module-trait relationship. (b) Hierarchical clustering analysis for the modules.
Figure 4
Figure 4
The creation of module-trait relations. The association between the modules and the clinical traits. Each row relates to a specific module, and the column corresponds to the different clinical traits.
Figure 5
Figure 5
Connection between the different modules of interest and the clinical traits in the yellow module.
Figure 6
Figure 6
Functional enrichment analysis of the various genes in the yellow module. (a) GO, Gene Ontology. (b) KEGG, Kyoto Encyclopedia of Genes and Genomes.
Figure 7
Figure 7
Construction of PPI network related to the yellow module. The hub genes with the highest connectivity in the yellow module.
Figure 8
Figure 8
ROC curves for the hub genes. ROC: receiver operating characteristic; AUC: area under curve.
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