Integrated Bioinformatics-Based Identification of Potential Diagnostic Biomarkers Associated with Diabetic Foot Ulcer Development

Abstract

The present study was designed to detect possible biomarkers associated with diabetic foot ulcer (DFU) incidence in an effort to develop novel treatments for this condition. The GSE7014 and GSE29221 gene expression datasets were downloaded from the Gene Expression Omnibus (GEO) database, after which differentially expressed genes (DEGs) were identified between DFU and healthy samples. These DEGs were then arranged into a protein-protein interaction (PPI) network, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) term enrichment analyses were performed to explore the functional roles of these genes. In total, 1192 DEGs were identified in the GSE7014 dataset (900 upregulated, 292 downregulated), while 1177 were identified in the GSE29221 dataset (257 upregulated, 919 downregulated). GO analyses revealed these DEGs to be significantly enriched in biological processes including sarcomere organization, muscle filament sliding, and the regulation of cardiac conduction, molecular functions including structural constituent of muscle, protein binding, and calcium ion binding, and cellular components including Z disc, myosin filament, and M band. These DEGs were also enriched in the adrenergic signaling in cardiomyoctes, dilated cardiomyopathy, and tight junction KEGG pathways. Together, the findings of these bioinformatics analyses thus identified key hub genes associated with DFU development.

The Construction and Analysis of Infiltrating Immune Cell and ceRNA Networks in Diabetic Foot Ulcer

“…constructed the ceRNA network of DFU consisting of 8 circRNAs, 11 miRNAs, and 91 mRNAs, and GO analysis showed that hub genes including BCL2, CDND1, and SMAD4 are potential diagnostic biomarkers in DFU ( 7 ). At the same time, Qian et al ( 32 ). identified 1,192 DEGs in the GSE7014 dataset (900 upregulated and 292 downregulated) and 1,176 DEGs in the GSE29221 dataset (257 upregulated and 919 downregulated).…”

“…Liao et al constructed the ceRNA network of DFU consisting of 8 circRNAs, 11 miRNAs, and 91 mRNAs, and GO analysis showed that hub genes including BCL2, CDND1, and SMAD4 are potential diagnostic biomarkers in DFU (7). At the same time, Qian et al (32). Angiogenesis extends blood vessels through vascular branching.…”

Polygonatum sibiricum polysaccharides (PSP) improve the palmitic acid (PA)-induced inhibition of survival, inflammation, and glucose uptake in skeletal muscle cells

“…Using GEO2R to analyze the GSE29221 dataset in this study, we found that IRAK3 mRNA expression was downregulated in diabetic patients. In previous studies, the GSE29221 dataset was used to analyze the key genes involved in diabetes and diabetes complications [ 21 , 33 , 34 ]. Our purpose was to analyze the genes involved in PSP and miR-340-3p regulated glucose uptake by skeletal muscle cells in diabetes, thus being different from the purpose of previous studies.…”

Bioinformatics analysis identifies ferroptosis‑related genes in the regulatory mechanism of myocardial infarction

“…A heatmap cluster and volcano plot of the DEGs were created using the ‘ggplot2’ packages via R software. Furthermore, by intersecting with ferroptosis-related genes, the ferroptosis-related DEGs were obtained and the heat map of ferroptosis-related DEGs was created using the ‘pheatmap’ package ( 26 ).…”