Identification of autophagy-related genes in diabetic foot ulcer based on bioinformatic analysis.

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Differentially expressed genes (DEGs) between DFU and healthy samples were analysed from the Gene Expression Omnibus (GEO) datasets, GSE7014 and GSE29221. The roles of autophagy-related DEGs were investigated using protein-protein interaction (PPI) networks, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, Gene Ontology (GO) enrichment, and Gene Set Enrichment Analysis (GSEA). Immune cell infiltration's correlation with these DEGs was also assessed. From the Human Autophagy Database (HADB), 232 autophagy-related genes (ARGs) were identified, with an intersection of 17 key DEGs between GSE7014 and GSE29221. These genes are involved in pathways like autophagy-animal, NOD-like receptor signalling, and apoptosis. In the protein network, epidermal growth factor receptor (EGFR) and phosphatase and tensin homologue (PTEN) showed significant interactions with ARGs. Survival analysis indicated the prognostic importance of calpain 2 (CAPN2), integrin subunit beta 1 (ITGB1), and vesicle-associated membrane protein 3 (VAMP3). Lower immune scores were observed in the type 2 diabetes mellitus (DM2) group than in controls. Autophagy and ARGs significantly influence DFU pathophysiology.", "claims": [{"id": "claim-method", "statement": "We first obtained the matrix profile of ARGs in GSE7014 and GSE29221, screened the DEGs in GSE7014 disease group and normal group, GSE29221 disease versus normal cohort via limma package, 20 and plotted the DEG volcano plot with the ggplot2 package to demonstrate the DE of DEGs, which met the p value <0.05 and |log2 FC| > 0.5 criteria, and performed cluster Heatmap assessment in GSE7014 and GSE29221 with heatmaps, 21 to demonstrate the DEGs profile in disease versus normal cohort.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37909396", "locator": "sections[4] \"Analysis of differential expression (DE) of ARGs\" paragraph 2", "quote": "We first obtained the matrix profile of ARGs in GSE7014 and GSE29221, screened the DEGs in GSE7014 disease group and normal group, GSE29221 disease versus normal cohort via limma package, 20 and plotted the DEG volcano plot with the ggplot2 package to demonstrate the DE of DEGs, which met the p value <0.05 and |log2 FC| > 0.5 criteria, and performed cluster Heatmap assessment in GSE7014 and GSE29221 with heatmaps, 21 to demonstrate the DEGs profile in disease versus normal cohort."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37909396", "locator": "sections[24] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data that support the findings of this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The intersection of differentially expressed genes between GSE7014 and GSE29221 contained 17 key autophagy-related genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37909396", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "From the Human Autophagy Database (HADB), 232 autophagy‐related genes (ARGs) were identified, with an intersection of 17 key DEGs between GSE7014 and GSE29221."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The intersection of differentially expressed genes between GSE7014 and GSE29221 contained 17 key autophagy-related genes.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37909396"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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