Identification and verification of ferroptosis-related genes in the synovial tissue of osteoarthritis using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36106017", "kind": "science-record", "revision": 4, "content_hash": "sha256:deb6c3453930a37c92f88279b0acc2a01e5c3c583ecdd025c8cd6aaed6bd8eee", "created_at": "2026-11-01T18:15:21Z", "updated_at": "2026-11-01T22:07:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and verification of ferroptosis-related genes in the synovial tissue of osteoarthritis using bioinformatics analysis.", "doi": "10.3389/fmolb.2022.992044", "pmid": "36106017", "authors": ["Lin Xia", "Ningji Gong"], "journal": "Frontiers in molecular biosciences", "year": 2022, "abstract": "Background: Osteoarthritis (OA) is a major factor causing pain and disability. Studies performed to date have suggested that synovitis is possibly a critical OA-related pathological change. Ferroptosis represents a novel type of lipid peroxidation-induced iron-dependent cell death. However, its effect on OA remains largely unclear. Objective: This work focused on identifying and validating the possible ferroptosis-related genes (FRGs) involved in synovitis of OA through bioinformatics analysis. Materials and Methods: The microarray dataset GSE55235 was downloaded in the database Gene Expression Omnibus (GEO). By the Venn diagram and GEO2R, differentially expressed genes (DEGs) and ferroptosis DEGs (FDEGs) were detected. 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 construct hub gene networks. Moreover, this study used the database NetworkAnalyst to predict the target miRNAs of the hub genes. Finally, the hub genes were confirmed by analysis of the receiver operating characteristic (ROC) curve on the GSE12021 and GSE1919 databases. Considering the relationship between ferroptosis and immunity, this study applied CIBERSORTx to analyze the immune infiltration in OA in addition. Results: This work discovered seven genes, including ATF3, IL6, CDKN1A, IL1B, EGR1, JUN, and CD44, as the hub FDEGs. The ROC analysis demonstrated that almost all hub genes had good diagnostic properties in GSE12021 and GSE 1919. Conclusion: This study discovered seven FDEGs to be the possible diagnostic biomarkers and therapeutic targets of synovitis during OA, which sheds more light on the pathogenesis of OA at the transcriptome level.", "claims": [{"id": "claim-method", "statement": "The DEGs were screened and identified based on the program GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r) in GSE55235.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36106017", "locator": "sections[4] \"2.2 Identification of differentially expressed genes\" paragraph 2", "quote": "The DEGs were screened and identified based on the program GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r) in GSE55235."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36106017", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GEO2R analysis of GSE55235 identified 1,443 differentially expressed genes, including 920 upregulated and 523 downregulated genes.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Genes of |log FC| > 1 and p < 0.05 were identified as DEGs. Totally 1,443 DEGs, containing 920 upregulated and 523 downregulated DEGs were detected."}, "evidence": [{"asset": "source:pmid:36106017", "locator": "sections[12] \"3.1 Identification of differentially expressed genes and ferroptosis differentially expressed genes\" paragraph 2", "quote": "Genes of |log FC| > 1 and p < 0.05 were identified as DEGs. Totally 1,443 DEGs, containing 920 upregulated and 523 downregulated DEGs were detected."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GEO2R analysis of GSE55235 identified 1,443 differentially expressed genes, including 920 upregulated and 523 downregulated 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:36106017"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE12021"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE12021"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36106017", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmolb.2022.992044", "sha256": 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further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM34379", "GSM34383", "GSM34385", "GSM34388", "GSM34391", "GSM34393", "GSM34394", "GSM34395", "GSM34396", "GSM34397", "GSM34398", "GSM34399", "GSM34400", "GSM34401", "GSM34402"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "91", "taxon": "Homo sapiens", "title": "Rheumatoid arthritis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE55235", "role": "raw", "format": "geo-series", "media_type": 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