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pmid:34949204
Identification and development of a novel 5-gene diagnostic model based on immune infiltration analysis of osteoarthritis.
YaGuang Han · Jun Wu · ZhenYu Gong · YiQin Zhou · HaoBo Li · Bo Wang · QiRong Qian
Journal of translational medicine · 2021 doi:10.1186/s12967-021-03183-9
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Complete file
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Therefore, it is of great significance to explore OA biomarkers for the prevention, diagnosis, and treatment of OA.\nMETHODS AND MATERIALS: The GSE129147, GSE57218, GSE51588, GSE117999, and GSE98918 datasets with normal and OA samples were downloaded from the Gene Expression Omnibus (GEO) database. The GSE117999 and GSE98918 datasets were integrated, and immune infiltration was evaluated. The differentially expressed genes (DEGs) were analyzed using the limma package in R, and weighted gene co-expression network analysis (WGCNA) was used to explore the co-expression genes and co-expression modules. The co-expression module genes were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and hub genes were identified by the degree, MNC, closeness, and MCC algorithms. The hub genes were used to construct a diagnostic model based on support vector machines.\nRESULTS: The Immune Score in the OA samples was significantly higher than in the normal samples, and a total of 2313 DEGs were identified. Through WGCNA, we found that the yellow module was significantly positively correlated with the OA samples and Immune Score and negatively correlated with the normal samples. The 142 DEGs of the yellow module were related to biological processes such as regulation of inflammatory response, positive regulation of inflammatory response, blood vessel morphogenesis, endothelial cell migration, and humoral immune response. The intersections of the genes obtained by the 4 algorithms resulted in 5 final hub genes, and the diagnostic model constructed with these 5 genes showed good performance in the training and validation cohorts.\nCONCLUSIONS: The 5-gene diagnostic model can be used to diagnose OA and guide clinical decision-making.", "claims": [{"id": "claim-method", "statement": "An SVM classification model was constructed, and the sensitivity, specificity, and area under the receiver operating characteristic (ROC) curve (AUC) of the model were analyzed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34949204", "locator": "sections[9] \"Diagnostic model construction and validation\" paragraph 2", "quote": "An SVM classification model was constructed, and the sensitivity, specificity, and area under the receiver operating characteristic (ROC) curve (AUC) of the model were analyzed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34949204", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The 5-gene diagnostic model can be used to diagnose OA and guide clinical decision-making.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34949204", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The 5-gene diagnostic model can be used to diagnose OA and guide clinical decision-making."}, {"asset": "source:pmid:34949204", "locator": "sections[17] \"Construction and validation of the diagnostic model\" paragraph 3", "quote": "These results indicated that the diagnostic prediction model constructed in this study could effectively distinguish OA samples from normal samples, and the 5 genes could be used as reliable biomarkers for OA diagnosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The 5-gene diagnostic model can be used to diagnose OA and guide clinical decision-making.", "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:34949204"], "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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