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Global Translational Medicine Bioinformatics analysis of dilated cardiomyopathy

logFC ≥1 and adjusted P < 0.05 to determine the DEGs. 2.7. Statistical analysis
Using ggplot2 package in R (version 3.6.3), the volcano The R software pROC package and ggplot2 package were
plot and heat map of DEGs were plotted and the common used to analyze the data and plot the receiver operating
DEGs were obtained by Venn Diagram. characteristics (ROC) curve. Sensitivity and specificity
2.3. Enrichment analysis were determined by the area under the curve (AUC). The
higher is the AUC, the higher, and more consistent are the
The clusterProfiler package (version 3.6.3) in R was applied to sensitivity and specificity .
[19]
analyze and visualize the results of GO, Kyoto Encyclopedia
of Genes and Genomes (KEGG), and GSEA. Elements of 3. Results
the enrichment analysis include BPs, cell components, and
molecular functions (MFs) of the DEGs. If adjusted P < 0.05, 3.1. Identification of DEGs
the findings were considered to be significant. The reactome Using the GEO2R tool, 697 DEGs were screened from
[15]
pathway was analyzed by David database . GSE29819 and 62 DEGs were obtained from GSE57338.
Volcano plots (Figure 1A and B) and heat maps
2.4. PPI network construction and hub gene (Figure 2A and B) were plotted using R software. Venn
identification diagram of DCM tissues and NF tissues indicates that 28
The online database of STRING was used for analyzing the genes were in common, including 17 upregulated genes
reaction pathways and PPI network of the common DEGs . and 11 downregulated genes (Figure 2C).
[16]
The results were loaded into Cytoscape (version 3.7.2) for
visualization. The top 5 hub genes were determined by 3.2. Enrichment analysis
maximal clique centrality (MCC) algorithm and Degree BP analysis showed that the DEGs mainly participate
through CytoHubba plugin of Cytoscape software. in neutrophil degranulation and activation, neutrophil-
mediated immune response, extracellular structural
2.5. Validation of hub gene expression
organization, cell-matrix adhesion processes, positive
The ggplot2 package of R software was applied to visualize regulation of external stimuli, positive regulation of
gene expression in different datasets. inflammatory response, regulation of blood pressure,
cardiac cell and tissue development, and regulation
2.6. mRNA-miRNA-lncRNA network construction of Wnt signaling pathway and serine/threonine
Gene-miRNA interaction analysis of DEGs was kinase signaling pathway (Table 1 and Figure 3C).
performed by Network analyst using the comprehensive, Cellular component analysis revealed that the DEGs
experimentally validated miRNA-gene interaction data are associated with collagen-containing extracellular
in miRTarBase . Then, the miRNA-lncRNA network matrix, vacuolar lumen, azurophil granule, and primary
[17]
(Clip Date with medium stringency) was predicted by lysosome (Table 2 and Figure 3A). MF analysis showed
ENCORI . Finally, all predicted outcome was plotted into that the DEGs mainly take part in glycosaminoglycan
[18]
a network using Cytoscape software. binding, extracellular matrix structural constituent,

A B

Figure 1. (A) Volcano plot showing the DEGs from GSE29819. (B) Volcano plot showing the DEGs from GSE57338. Red points show the genes with
an up-regulated expression, the black ones show the genes with a non-significant expression, and the blue ones show the genes with a down-regulated
expression.

Volume 1 Issue 1 (2022) 3 https://doi.org/10.36922/gtm.v1i1.104