Integrated analysis of differentially expressed genes and miRNA expression profiles in dilated cardiomyopathy

Fig. 1. This is the flowchart for the study. DCM, dilated cardiomyopathy; DEGs, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes; PPI, protein-protein interaction; RRA, Robust Rank Aggregation.

Fig. 2. Volcano plots were utilized to perform differential expression analysis of DEGs from GSE1145, GSE29819, and GSE141910 datasets. The volcano plot of GSE1145 (A) showed that compared to the control group, there were 413 upregulated and 553 downregulated genes with expression changes of at least 2-fold. Similarly, the volcano plot of GSE29819 (B) revealed 439 upregulated and 466 downregulated genes. Finally, the volcano plot of GSE141910 (C) displayed 543 upregulated and 411 downregulated genes. The colored dots corresponding to upregulation, downregulation, and no significant change in mRNA are indicated by red, blue, and grey dots respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3. DEG heatmaps for GSE1145, GSE29819, and GSE141910. (A) GSE1145, (B) GSE29819, (C) GSE141910, (D) RobustRankAggreg (RRA) of three mRNA datasets. A–C: Green, DCM; Red, normal heart tissues. A–D: Red color was used to depict the upregulated genes, while blue color was used to depict the downregulated genes. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4. Statistical analysis of functional enrichment of DEGs. Bar charts were used to present top 20 results of GO enrichment analysis (A) and KEGG enrichment analysis (B), with P-values. The merged representation of panels C and D from the Metascape analysis shows the clustering of differentially expressed genes according to GO and KEGG pathways, where the color coding in panel C indicates the categorization of each gene within these classifications, and in panel D, the color intensity reflects the p-value significance of each gene. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5. An integrated PPI network has been constructed using DEGs and hub genes. (A) displayed all interactions between the integrated DEGs, with red and blue nodes representing upregulated and downregulated genes, respectively. (B) displayed the top 10 hub genes. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6. The miRNA dataset GSE209991 was analyzed to generate volcano plots and heat maps of DEMs. (A) The volcano plots displayed 41 miRNAs that were upregulated (represented by red dots), 129 miRNAs that were downregulated (represented by blue dots), and miRNAs that did not show significant changes (represented by grey dots). (B) The DE-miRNAs were presented in a heatmap. (C) A regulatory miRNA-mRNA network was generated, where upregulated miRNAs were represented by blue and downregulated miRNAs were represented by red. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7. ROC of De-miRNAs. AUC, area under the curve; ROC, receiver operating characteristic curves.