Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40804350", "kind": "science-record", "revision": 4, "content_hash": "sha256:74f2cd0a0d22f3e5d6eb3532e7e3c588c28fc10d55d6bd619dfe9cf1fa92a688", "created_at": "2026-11-01T20:30:54Z", "updated_at": "2026-11-01T22:57:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis.", "doi": "10.1038/s41598-025-11667-7", "pmid": "40804350", "authors": ["Chengze Qiu", "Zhiyong Zhang", "Haocheng Wang", "Na Liu", "Ruixin Li", "Zhiheng Wei", "Benjie Wang", "Nan Zhang"], "journal": "Scientific reports", "year": 2025, "abstract": "The purpose of this study was to search for genes related to ros induced oxidative stress in osteoarthritis(OA) cartilage through bioinformatics analysis, and to verify the expression of related genes in articular cartilage of OA patients. OA expression data and ROS-related genes were downloaded from GEO (GSE51588, GSE117999) and Molecular Signatures Databases. The limma package in R language was used to screen differently expressed genes (DEGs) from the GEO databases. WGCNA analysis and Venn diagrams were employed to screen genes that were differentially expressed between OA and control samples and had strong correlations with ROS as candidate genes. DEGs were screened by GO and KEGG enrichment analysis, as well as protein-protein interaction (PPI) analysis. Besides, the software Cytoscape and database STRING were utilized to screen hub genes networks. The hub genes were confirmed by analysis of the receiver operating characteristic (ROC) curve on the GSE51588 and GSE117999 databases. An artificial neural network model was constructed for the hub genes, and immune analysis was conducted using the ssGSEA algorithm. The expression of genes in OA and normal chondrocytes was verified through HE staining, immunohistochemistry, ROS detection, qRT-PCR and Western blotting test. This study identified five genes, including ALB, CDH1, HSPA8, HIST1H2BE and XDH, as hub genes. ROC curves, gene expression analysis, and artificial neural network diagrams indicated that ALB, HIST1H2BE and XDH had good diagnostic characteristics. GSEA showed that the XDH gene was significantly enriched in ROS pathways. Meanwhile, the expression of XDH were also confirmed to be significant differences between injured cartilage and normal cartilage in OA patients in vivo. Our study may provide new hub genes related to ROS-mediated oxidative stress in OA and validate the correlation between XDH gene and its transcripts with ROS pathways in OA. This offers potential clinical applications for understanding the pathology, diagnosis, and treatment of OA.", "claims": [{"id": "claim-method", "statement": "Use the\"limma” (Linear Models for Microarray Data;3.54.0;https://bioconductor.org/packages/release/bioc/html/limma.html)package to screen differentially expressed genes (DEGs), and select DEGs with adjusted P-value < 0.05 and |log2 fold change (FC)| > 1 as the criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40804350", "locator": "sections[4] \"Differential gene expression analysis\" paragraph 2", "quote": "Use the\"limma” (Linear Models for Microarray Data;3.54.0;https://bioconductor.org/packages/release/bioc/html/limma.html)package to screen differentially expressed genes (DEGs), and select DEGs with adjusted P-value < 0.05 and |log2 fold change (FC)| > 1 as the criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40804350", "locator": "sections[30] \"notes\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study identified five genes, including ALB, CDH1, HSPA8, HIST1H2BE and XDH, as hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40804350", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study identified five genes, including ALB, CDH1, HSPA8, HIST1H2BE and XDH, as hub genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study identified five genes, including ALB, CDH1, HSPA8, HIST1H2BE and XDH, as hub 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:40804350"], "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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