Table 1.
Data used in this study.
Fig 1.
Construction of WGCNA co-expression network.
(A) Data before removing batch effects. (B) Data after removing batch effects. (C) Soft threshold β = 8 and scale-free topological fit index (R2). (D) Network analysis of gene expression in IS identifies distinct modules of co-expression data. (E) Relationships among modules. Heatmap plot of the adjacencies in the eigengene network. Each row and column in the heatmap corresponds to one module eigengene (labeled by color). In the heatmap, the red color represents high adjacency, while the blue color represents low adjacency. Squares of red color along the diagonal represent the meta-modules. (F) Heatmap plot of topological overlap in the gene network. In the heatmap, each row and column corresponds to a gene, the light color denotes low topological overlap, and the progressively darker red color denotes higher topological overlap. Dark squares along the diagonal correspond to modules. The gene dendrogram and module assignment are shown along the left and top. (G) Relationships between consensus module eigengenes and ubiquitination. Each row in the table corresponds to a consensus module, and each column corresponds to a sample or trait. Numbers in the table report the correlations between the corresponding module eigengenes and traits, with the p-values presented below the correlations in parentheses. The table is color coded based on correlation according to the color legend. (H) Correlation between module membership (MM) and gene significance (GS) for ubiquitination of all genes in the blue module. ‘Cor’ represents absolute correlation coefficient between GS and MM.
Fig 2.
(A) A volcano plot depicting the distribution of DEGs between the IS and control samples. Yellow, green, and gray dots represent gene expression levels corresponding to the upregulated, downregulated, and insignificant expression, respectively. (B) A heatmap depicting the top 5 DEGs with upregulated expression and top 5 DEGs with downregulated expression. (C) Venn plot shows the interaction between the DEGs and module genes. (D) The variations in the expression levels of the top 10-gene between IS and control groups were determined using the Wilcoxon tests. The asterisks represented the p-values (****p<0.0001, ***p<0.001, **p<0.01, *p<0.05).
Fig 3.
Significantly enriched pathways.
(A) GSEA ridge plot. (B) The heatmap illustrates the GSVA analysis results.
Fig 4.
ROC curves of (A) AIM2. (B) ZNF404. (C) NANP. (D) DHFR2. (E) TRAPPC10. (F) BCLAF3. (G) CHAC2. (H) SERPINB8. (I) ZNF57. (J) KHDC4. (K) ZNF322. (L) CDKN1A.
Fig 5.
Difference in immune infiltrations between the IS and control samples.
(A) The estimated proportions of infiltrating immune cells in the IS and control groups. (B) The heatmap presenting changes in immune infiltration levels between the IS and control groups. (C) Correlations between DHFR2 and eosinophils. (D) Correlation between DNAAF2 and eosinophils. (E) Correlation among the immune cells. The asterisks represent the p-values (****p<0.0001, ***p<0.001, **p<0.01, *p<0.05).
Fig 6.
Correlation between the hub genes and 50 hallmark signaling pathways.
(A) Comparison of the 50 HALLMARK signaling pathways between the IS group and controls. (B) Correlation between the hub genes and the 50 hallmark signaling pathways. The asterisks represent the p-values (****p<0.0001, ***p<0.001, **p<0.01, *p<0.05).
Fig 7.
The RBP–mRNA regulatory network; the blue and pink colors represent the RBPs and mRNAs, respectively.
Fig 8.
Construction of lncRNA-miRNA-mRNA network; the green, pink, and blue rectangles represent the lncRNA, mRNA, and miRNA, respectively.
Fig 9.
Interaction analysis of the hub genes.
(A) Characterized gene co-expression network. (B) GO analysis of the co-expressed genes.