Weighted gene co‑expression network analysis in identification of key genes and networks for ischemic‑reperfusion remodeling myocardium

Figure 1.. Different soft-thresholding powers (b) were analyzed for (A) the topology scale-free fitting and (B) mean connectivity as a function of the power evaluated from ischemia reperfusion myocardium data.

Figure 2.. Heatmap of the gene coexpression network. The heatmap descriped adjacencies among genes in the analysis. A single gene correspond to each row and column of the heatmap. Low adjacencies are indicated by yellow colour and higher adjacencies are indicated by progressively red colour. The genes in the analysis were clustered in modules labeled by a color code (blue, yellow, brown, green and turquoise), which are shown by squares under gene dendrogram along the diagonal.

Figure 3.. Hierarchical clustering analysis of all differentially expressed genes (DEGs) in each module. Blue color represents downregulation of genes. Red indicates upregulation of genes. Different gene expression patterns following IR were shown as different color modules. (A) The blue module enriched the DEGs between 7d-IR and other groups. (B) The brown module enriched DEGs between IR and sham group. (C) The green module enriched DEGs between 2d-IR and other groups. (D) The red module enriched DEGs between days 2 and 7. (E) The turquoise module enriched the dynamic expression of DEGs. (F) The yellow module enriched DEGs between sham-7 day and other groups. IR, ischemia reperfusion.

Figure 4.. Gene Ontology enrichment analysis of all differentially expressed genes (DEGs) in each module. DEGs in each module were subjected into biological process enrichment. Top 10 significantly enriched biological process were shown here (P<0.05) for (A) blue, (B) yellow, (C) brown, (D) green, (E) turquoise, and (F) red modules.

Figure 5.. Pathway enrichment of all DEGs in each module. DEGs in each module were performed KEGG enrichment. Significantly enriched KEGGs (P<0.05) are shown here for (A) blue, (B) yellow, (C) brown, (D) green and (E) turquoise modules. DEGs, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 6.. Protein-protein interaction network of the differentially expressed genes in each module. The nodes indicate proteins. The edges indicate interactions between proteins. Highlighted yellow nodes represent molecular complexes identified by molecular complex detection algorithm of cytoscape software. Core protein-protein interaction networks were shown here for (A) blue, (B) yellow, (C) brown, (D) green, (E) turquoise, and (F) red modules.