Transcriptome Profile Reveals Differences between Remote and Ischemic Myocardium after Acute Myocardial Infarction in a Swine Model

Figures

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  Figure 1. Transcriptomic results. Representative TTC-stained heart slice obtained from an animal belonging to the study. Sampling was performed from the ischemic (yellow circle) and remote (blue circle) areas (A). Pie chart represents the 14,430 transcripts identified by microarrays and assigned with ID, where the green slice represents the proportional value of down-regulated genes, the red slice represents the up-regulated genes, and the grey slice represents no changed genes (B). DEGs are visualized in a volcano plot according to FDR p-value (-log10) and fold change (log2). Green dots represent down-regulated genes and red dots, up-regulated genes (C). DEGs: differentially expressed genes. FDR p-value < 0.05. Fold change: >2 or <−2.

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  Figure 2. Proteomic validation. Venn diagram shows the intersection between DEGs identified by transcriptomic (yellow circle) and genes identified by proteomic (blue circle) (A). The scatter plot shows the correlation analysis of the expression changes through both transcriptomics and proteomics for the Venn diagram intersection data, including linear regression analysis. Genes that were significantly regulated (FDR < 0.05) in both RNA and protein are highlighted in yellow, validated genes that were not significantly regulated (FDR > 0.05) in protein are highlighted in blue, and not validated by protein abundance are highlighted in red (B). DEGs: differentially expressed genes. R2: coefficient of determination. rp: Pearson correlation coefficient.

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  Figure 3. Enrichment analysis of validated genes. Bar charts show enrichment results using only validated DEGs by proteomics. Levels of enriched biological process (A), enriched cell component (B), and enriched molecular function (C) are expressed in percent of genes and divided by max level. DEGs: differentially expressed genes. Max Level: maximal annotated level of this term in the GO graph (tree).

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  Figure 4. DEGs up- and down-regulated. Number of DEGs validated by proteomics and divided in up- and down-regulated are shown in bar graph (A). Enrichment analysis of both datasets were performed using g:Profiler tool and Reactome data source. The green bar graph represents number of down-regulated genes in Reactome terms (B), and the red graph, the number of up-regulated genes in Reactome terms (C).

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  Figure 5. DEGs in the immune system process. Voronoi pathway visualization (Reacfoam) for the identified proteins in the Immune system (R-SSC-168256) term. The yellow color code denotes over-representation of that pathway in our input dataset. Light grey signifies pathways which are not significantly over-represented.

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  Figure 6. Protein–protein Interaction Enrichment Analysis. Protein–protein interaction analysis of validated DEGs by using the molecular complex detection (MCODE). Each network represents different clusters where the temporal dynamic clustering analysis MCODE algorithm was applied. Reactome enrichment analysis was applied to each MCODE network. Each node represents proteins, and the edge represents the specific interaction between proteins. DEGs: differentially expressed genes.