Identification of Key Biomarkers and Immune Infiltration in Sciatic Nerve of Diabetic Neuropathy BKS-db/db Mice by Bioinformatics Analysis

FIGURE 1. Standardization of GSE27382. (A,B) The green bar represents the data before normalization, and the red bar represents the data after normalization. (C) Volcano plots of DEGs in GSE27382. Red plots represent the upregulated genes with logFC > 2 and adjusted p-value < 0.05. Green plots represent the downregulated genes with logFC < −2 and adjusted p-value < 0.05. Black plots represent the remaining genes with no significant difference. (D) Heat maps of DEGs display of the most significant top 50 upregulated and downregulated genes.

FIGURE 2. GSEA identified GO and KEGG pathways enriched in the DN group and normal controls. (A) GO analysis of the top five significantly enriched gene set in DN group. (B) KEGG analysis of the top five significantly enriched pathways in DN group.

FIGURE 3. Protein–protein interaction network construction and analysis of differentially expressed genes. (A) Red nodes represent upregulated genes, and blue nodes represent downregulated genes. (B–D) Three significant modules with MCODE score > 5 and top 20 maximal clique centrality (MCC) protein nodes. Three modules extracted from the PPI network. Red nodes indicate upregulated DEGs and green nodes indicate downregulated DEGs. (E) Top 20 candidate genes with maximal clique centrality.

FIGURE 4. Gene transcription factor and hub genes identified. (A) Gene transcription factor (TF) regulatory network. Green hexagons stand for the transcription factor and red nodes stands for DEGs. (B) Hub genes identified by Venn diagram. The blue circle represents the 13 significant genes generated by module analysis, the red circle represents the top 20 candidate genes obtained by the MCC algorithm, and the green circle represents the 28 target genes predicted by TFs. (C) GO analysis of the hub gene constructed using BiNGO. The color depth of the node refers to the corrected p-value of the ontology. The size of the node refers to the number of genes involved in the ontology. p < 0.01 is statistically significant.

FIGURE 5. Landscape of immune infiltration between DN samples and normal samples. (A) The bar plot represents the relative percentage of 22 immune cells in each sample. (B) Cluster heat map based on 22 immune cell proportions of normal samples and DN samples. Red indicates a high percentage of immune cells and blue indicates a low percentage of immune cells. (C,D) Correlation matrix of the proportion of immune cells in the normal and DN groups. Red indicates positive correlation and blue indicates negative correlation. (E) The difference in immune infiltration between the normal and DN samples (blue for the normal group and red for the DN group, p value < 0.05 was considered statistically significant. (F) Principal component analysis of normal and DN samples. (G) Correlation index analysis of hub genes expression and immune infiltration level. Red indicates positive correlation and blue indicates negative correlation.

FIGURE 6. The mRNA levels for hub genes in glycotoxicity model and control group. (A–E) The transcript levels of Birc5, Bub1, Cdk1, Ccnb1 and Ccnb2 were significantly higher in the glycotoxicity model group compared to the control group. All experiments were repeated three times (n = 3). Mean ± SD., *p < 0.05, **p < 0.01.