Characterisation of key biomarkers in diabetic ulcers via systems bioinformatics

Figures

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  FIGURE 1. Bioinformatic analysis of the differentially expressed genes (DEGs) between healthy volunteers and diabetic ulcer patients. In (A) Box plot after data standardisation, different colours represent different data sets. (B) Principal component analysis (PCA) results before batch removal for multiple data sets. Different colours represent different data sets. (C) PCA results after batch removal, showing the intersection of these two data sets. Different colours represent different data sets. (D) Volcano plots of DEGs were constructed to adjust to fold‐change and P value. The red points represent the over‐expressed mRNAs and the blue points indicate the down‐expressed mRNAs. (E) Heatmap of the top 100 DEGs. Different colours represent the different expression trends

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  FIGURE 2. Weighted gene co‐expression analysis. (A) Gene cluster dendrogram clustered by weighted gene co‐expression network in different colours. (B) 10 co‐expression modules. (C) The heatmap of module‐trait relationships between healthy volunteers and diabetic ulcers. Number in and outside the bracket represents P‐value and Pearson coefficient, respectively. (D) Correlation analysis between module membership and gene significance in the turquoise modules

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  FIGURE 3. Functional enrichment of ulcer‐related genes. (A) Gene Ontology analysis of differentially expressed genes involving the biological processes, cellular components, and molecular functions. (B) Kyoto Encyclopedia of Genes and Genomes showing the signalling pathway associated with diabetic ulcers

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  FIGURE 4. PPI network construction and hub gene identification. (A) Venn Diagram of the hub genes identified using three graph‐theoretic algorithms including Degree, MCC, and MNC. (B) Protein–protein interaction network of the hub genes. (C) Sankey diagram for the correlation analysis of transcription factors and hub gene in ulcer. Each rectangle represents a gene, and the connection degree of each gene is displayed based on the size of the rectangle

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  FIGURE 5. The expression distribution of immune checkpoints related mRNAs in case and control groups, where the horizontal axis represents different mRNA and the vertical axis represents the mRNA expression distribution. Different colours represent different groups, and the upper left corner represents the significance P‐value test method. ***P < .001

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  FIGURE 6. Violin plot of the difference of proportion in 22 immune cells between diabetic ulcers and normal tissue by single‐sample gene set enrichment analysis analysis

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  FIGURE 7. Difference analysis of immune function status and performance status score between ulcer patients and normal subjects in the Gene Expression Omnibus data set

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  FIGURE 8. Experimental validation of the hub genes. mRNA expression levels of the hub differentially expressed genes detected by quantitative real‐time polymerase chain reaction. **P < .01, ***P < .001