Bioinformatic identification of important roles of COL1A1 and TNFRSF12A in cartilage injury and osteoporosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39847474", "kind": "science-record", "revision": 3, "content_hash": "sha256:fbea6d2745de074953922b2427ef7c1006c9f769a6c697c6f7f86c5382ec7df8", "created_at": "2026-11-01T20:30:08Z", "updated_at": "2026-11-01T22:13:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic identification of important roles of COL1A1 and TNFRSF12A in cartilage injury and osteoporosis.", "doi": "10.1080/15502783.2025.2454641", "pmid": "39847474", "authors": ["Muzi Liu", "Shiguo Gong", "Xin Sheng", "Zihong Zhang", "Xichun Wang"], "journal": "Journal of the International Society of Sports Nutrition", "year": 2025, "abstract": "OBJECTIVE: The aim of this study was to identify the key regulatory mechanisms of cartilage injury and osteoporosis through bioinformatics methods, and to provide a new theoretical basis and molecular targets for the diagnosis and treatment of the disease.\nMETHODS: Microarray data for cartilage injury (GSE129147) and osteoporosis (GSE230665) were first downloaded from the GEO database. Differential expression analysis was applied to identify genes that were significantly up-or down-regulated in the cartilage injury and osteoporosis samples. These genes were subjected to GO enrichment analysis and KEGG pathway analysis. In addition, we employed SVA and RRA methods to merge the two sets of data, eliminating batch effects and enhancing the statistical power of the analysis. Through WGCNA, we identified gene modules that were closely associated with disease phenotypes and then screened for key genes that intersected with differentially expressed genes. The diagnostic value of these genes as potential biomarkers was evaluated by ROC analysis. Moreover, we performed an immune infiltration analysis to explore the correlation between these core genes and immune cell infiltration.\nRESULTS: We performed GO enrichment analysis and KEGG pathway analysis of genes significantly up-or down-regulated in cartilage injury and osteoporosis samples. Important biological processes, cellular components and molecular functions, and key metabolic or signaling pathways associated with osteoporosis and cartilage injury were identified. Through WGCNA, we identified gene modules that were closely associated with the disease phenotype, from which we then screened for key genes that intersected with differentially expressed genes. Ultimately, we focused on two identified core genes, COL1A1 and TNFRSF12A, and assessed the diagnostic value of these genes as potential biomarkers by ROC analysis. Meanwhile, GSVA provided an in-depth view of the role of these genes in disease-specific biological pathways. Immune infiltration analysis further revealed the possible key role of COL1A1 and TNFRSF12A in regulating immune cell infiltration in osteoporosis and cartilage injury.\nCONCLUSION: COL1A1 and TNFRSF12A as key regulatory molecules in osteoporosis and cartilage injury.", "claims": [{"id": "claim-method", "statement": "RO curves were plotted using the R language “pROC” package to assess the accuracy of gene expression (mRNA)-based determination of the sample’s disease status [26].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39847474", "locator": "sections[7] \"Receiver operating characteristic (ROC) curve analysis\" paragraph 2", "quote": "RO curves were plotted using the R language “pROC” package to assess the accuracy of gene expression (mRNA)-based determination of the sample’s disease status [26]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "COL1A1 and TNFRSF12A showed high diagnostic value for the disease, with AUC values of 0.830 and 0.871, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39847474", "locator": "sections[13] \"Diagnostic value and functional enrichment of core genes COL1A1 and TNFRSF12A\" paragraph 2", "quote": "The diagnostic value of these genes as potential biomarkers was further assessed by the ROC analysis, which showed that the AUC values of COL1A1 and TNFRSF12A were 0.830 and 0.871, respectively, suggesting that both genes have high diagnostic value for the disease (Figure 5(b))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "COL1A1 and TNFRSF12A showed high diagnostic value for the disease, with AUC values of 0.830 and 0.871, respectively.", "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:39847474"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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