Experimental validation and bioinformatics analysis of hub genes in myocardial infarction

Figures & data

Figure 1. The flowchart of the whole study.

Figure 2. The screening results of DEMis. (A) Volcano plot of differentially expressed miRNAs (|log2FC| > 0.5, adjusted P < 0.05). (B) The differential expression heatmap of miRNAs.

Figure 3. GO and transcription factor enrichment analysis of DEMis. (A) The transcription factor enrichment analysis of DEMis. (B) The cellular component terms related to DEMis in GO enrichment analysis. (C) The biological process terms related to DEMis in GO enrichment analysis. (D) The molecular function terms related to DEMis in GO enrichment analysis.

Table 1. The differentially expressed miRNAs.

miRNA	Log2FC	P.Value	adj P Value	miRNA	Log2FC	P.Value	adj P Value
hsa-let-7d-3p	−1.329952296	0.002813309	0.019559195	hsa-miR-342-3p	0.783525428	0.001325391	0.015265551
hsa-miR-139-3p	−1.011280172	0.002448441	0.018331914	hsa-miR-362-3p	−1.507771538	0.000290584	0.006794929
hsa-miR-140-5p	−0.536912582	0.004245845	0.02530177	hsa-miR-454-3p	−0.562055187	0.011601639	0.049096793
hsa-miR-142-3p	−1.079085274	0.000262228	0.006794929	hsa-miR-548a-5p	−1.045410073	0.000114372	0.006679341
hsa-miR-142-5p	−0.813378145	0.000934816	0.012997	hsa-miR-548c-5p	−0.862953656	0.005312552	0.031025306
hsa-miR-146b-5p	−0.55668717	0.007125103	0.03650053	hsa-miR-590-5p	−1.19770241	0.000313307	0.006794929
hsa-miR-15a-3p	−0.837549733	0.000604576	0.010901652	hsa-miR-624-5p	−0.894550888	0.003023462	0.020531415
hsa-miR-15b-3p	−0.564301756	0.011449673	0.049096793	hsa-miR-628-5p	−0.584201713	0.008913947	0.042670039
hsa-miR-17-3p	−1.040488246	0.000208604	0.006794929	hsa-miR-7-1-3p	−0.825556659	0.002801531	0.019559195
hsa-miR-186-3p	−0.887284607	0.000979226	0.012997	hsa-miR-9-3p	−1.184708206	0.002053319	0.0166547
hsa-miR-199a-5p	−0.636618962	0.001391683	0.015265551	hsa-miR-30a-3p	0.895789115	0.001324768	0.015265551
hsa-miR-199b-3p	−0.551858404	0.006154074	0.034557495	hsa-miR-30d-3p	−0.731947928	0.001999163	0.0166547
hsa-miR-20a-3p	−0.659248665	0.001952144	0.0166547	hsa-miR-326	−0.574824158	0.003331187	0.02121675
hsa-miR-21-3p	−0.682735824	0.001479101	0.01542491	hsa-miR-335-3p	−1.178726846	0.00125125	0.015265551
hsa-miR-24-1-5p	−1.06975106	0.000325784	0.006794929

Figure 4. The screening results of DEMs. (A) Volcano plot of differentially expressed mRNAs (|log2FC| > 0.5, adjusted P < 0.05). (B) The differential expression heatmap of mRNAs. (C and D) Venn diagram was drawn to show the overlapping genes between up-/down-regulated miRNA targets and up-/down- regulated mRNAs.

Figure 5. Construction of miRNA-mRNA network. (A) The network of all the DEMis and DEMs. (B) The top 10 genes with shortest paths in the betweenness algorithm analysis. (C) The top 10 genes with shortest paths in the closeness algorithm analysis. (D) The top 10 genes with shortest paths in the degree algorithm analysis. (E) The overlapping genes of betweenness, closeness, and degree analysis results.

Table 2. The overlapping miRNAs of Degree, Closeness, and Betweenness algorithm analysis.

miRNA	Log2FC	adj. P value	Degree	Closeness	Betweenness
hsa-miR-139-3p	−1.011280172	0.018331914	45	138.9166667	8803.295663
hsa-miR-17-3p	−1.040488246	0.006794929	50	142.75	11002.59881
hsa-miR-326	−0.574824158	0.02121675	63	155.6666667	17123.01624
hsa-miR-24-1-5p	−1.06975106	0.006794929	39	134.3333333	7612.011707
hsa-miR-15a-3p	−0.837549733	0.010901652	54	146	12862.13071

Figure 6. The final ceRNA network and its sub-network. (A) The final ceRNA network consisted of 5 miRNAs and their targets. (B) The key module of final network.

Figure 7. GO and pathway analysis of DEMS in the miRNA-mRNA network. (A) The top 10 pathways related to DEMs were shown in the bubble chart. (B) The biological process terms related to DEMs in GO enrichment analysis. (C) The cellular component terms related DEMs in GO enrichment analysis. (D) The molecular function terms related DEMs in GO enrichment analysis.

Figure 8. Immune analysis of GSE24519: (A) The proportion of immune cells. (B) The difference analysis of immune cell enrichment scores between MI and normal tissues. (C) The correlation analysis between hub genes and specific immune cells.

Figure 9. Validation of DEMis and DEMs expression. (A) The qRT-PCR results of key miRNAs. (B) The qRT-PCR results of key mRNAs.

Data availability statement

The microarray data that support the findings of this study are available in the Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geoprofiles. The data of experiments in this study are included in the Figshare database (https://doi.org/10.6084/m9.figshare.20280393.v1).