Bioinformatics analysis of differentially expressed genes in diabetic foot ulcer based on GEO gene dataset
10.3969/j.issn.1673-9701.2025.16.012
- VernacularTitle:基于GEO基因数据集的糖尿病足溃疡差异表达基因生物信息学分析
- Author:
Hongjie LI
1
Author Information
1. 义乌市中心医院内分泌科,浙江义乌 322000
- Publication Type:Journal Article
- Keywords:
Diabetic foot ulcer;
Differentially expressed gene;
Bioinformatics
- From:
China Modern Doctor
2025;63(16):47-51,61
- CountryChina
- Language:Chinese
-
Abstract:
Objective Explore the important genes related to occurrence and development of diabetic foot ulcer(DFU)through bioinformatics analysis.Methods Gene transcriptional profiling analysis was performed on the GSE143735 dataset of Gene Expression Omnibus(GEO).Patients in the dataset were divided into DFU group and non-DFU group based on whether they had DFU.The mRNA expression data of two groups of patients were analyzed for differentially expressed genes using GEO2R,and the volcano map was drawn.Gene ontology(GO)analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis were conducted through the DAVID database.The differentially expressed genes screened were placed into the String database for analysis.The protein-protein interaction network map was drawn using Cytoscape and the core genes were screened.Results A total of 706 differentially expressed genes were screened out,among which 470 were up-regulated genes and 236 were down-regulated genes.The results of GO analysis showed that the differentially expressed genes were mainly concentrated in cellular components such as nucleosomes,extracellular matrix containing collagen,and exosomes;molecular functions such as DNA binding,protein heterodimer activation,chromatin structure composition,nucleosome DNA binding,extracellular matrix structure composition,and serine inhibitor enzyme activation;biological processes such as nucleosome assembly,chromatin organization,keratinization,and telomere organization.The KEGG pathway analysis of differentially expressed genes mainly involved systemic lupus erythematosus,alcohol abuse,formation of extracellular traps of neutrophils,viral carcinogenesis,etc.Ten core genes,namely H2BC14,H3C14,H2BC17,H4C6,H2BC9,H3C1,H2BC3,H3C12,H3C13,and H2AC18,were obtained through protein interaction network screening.The expression levels of the above core genes in DFU group were significantly lower than those in non-DFU group.Conclusion The low expression of H2BC14,H3C14,H2BC17,H4C6,H2BC9,H3C1,H2BC3,H3C12,H3C13 and H2AC18 genes can be used as predictors of DFU in diabetic patients.The risk of DFU in patients can be predicted by detecting the expression levels of these genes.
