Consensus cluster analysis of apoptosis-related genes in patients with osteoarthritis and their correlation with immune cell infiltration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37860011", "kind": "science-record", "revision": 3, "content_hash": "sha256:3dea1e1868daea3456a0f5387be8955937279cb6c95e1bafe33443e67694dc28", "created_at": "2026-11-01T19:02:43Z", "updated_at": "2026-11-01T22:10:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Consensus cluster analysis of apoptosis-related genes in patients with osteoarthritis and their correlation with immune cell infiltration.", "doi": "10.3389/fimmu.2023.1202758", "pmid": "37860011", "authors": ["Enming Yu", "Mingshu Zhang", "Gongping Xu", "Xiaoqi Liu", "Jinglong Yan"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "Background: Osteoarthritis (OA) progression involves multiple factors, including cartilage erosion as the basic pathological mechanism of degeneration, and is closely related to chondrocyte apoptosis. To analyze the correlation between apoptosis and OA development, we selected apoptosis genes from the differentially expressed genes (DEGs) between OA and normal samples from the Gene Expression Omnibus (GEO) database, used lasso regression analysis to identify characteristic genes, and performed consensus cluster analysis to further explore the pathogenesis of this disease.\nMethods: The Gene expression profile datasets of OA samples, GSE12021 and GSE55235, were downloaded from GEO. The datasets were combined and analyzed for DEGs. Apoptosis-related genes (ARGs) were collected from the GeneCards database and intersected with DEGs for apoptosis-related DEGs (ARDEGs). Least absolute shrinkage and selection operator (LASSO) regression analysis was performed to obtain characteristic genes, and a nomogram was constructed based on these genes. A consensus cluster analysis was performed to divide the patients into clusters. The immune characteristics, functional enrichment, and immune infiltration statuses of the clusters were compared. In addition, a protein-protein interaction network of mRNA drugs, mRNA-transcription factors (TFs), and mRNA-miRNAs was constructed.\nResults: A total of 95 DEGs were identified, of which 47 were upregulated and 48 were downregulated, and 31 hub genes were selected as ARDEGs. LASSO regression analysis revealed nine characteristic genes: growth differentiation factor 15 (GDF15), NAMPT, TLR7, CXCL2, KLF2, REV3L, KLF9, THBD, and MTHFD2. Clusters A and B were identified, and neutrophil activation and neutrophil activation involved in the immune response were highly enriched in Cluster B, whereas protein repair and purine salvage signal pathways were enriched in Cluster A. The number of activated natural killer cells in Cluster B was significantly higher than that in Cluster A. GDF15 and KLF9 interacted with 193 and 32 TFs, respectively, and CXCL2 and REV3L interacted with 48 and 82 miRNAs, respectively.\nConclusion: ARGs could predict the occurrence of OA and may be related to different degrees of OA progression.", "claims": [{"id": "claim-method", "statement": "Least absolute shrinkage and selection operator (LASSO) regression analysis was performed to obtain characteristic genes, and a nomogram was constructed based on these genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37860011", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Least absolute shrinkage and selection operator (LASSO) regression analysis was performed to obtain characteristic genes, and a nomogram was constructed based on these genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are publicly available. This data can be found here: https://www.jianguoyun.com/p/DbKXe40Q1ujHCxig64IFIAA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37860011", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are publicly available. This data can be found here: https://www.jianguoyun.com/p/DbKXe40Q1ujHCxig64IFIAA."}], "state": "complete"}, {"id": "claim-target-result", "statement": "LASSO regression analysis revealed nine characteristic genes: growth differentiation factor 15 (GDF15), NAMPT, TLR7, CXCL2, KLF2, REV3L, KLF9, THBD, and MTHFD2.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37860011", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "LASSO regression analysis revealed nine characteristic genes: growth differentiation factor 15 (GDF15), NAMPT, TLR7, CXCL2, KLF2, REV3L, KLF9, THBD, and MTHFD2."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "LASSO regression analysis revealed nine characteristic genes: growth differentiation factor 15 (GDF15), NAMPT, TLR7, CXCL2, KLF2, REV3L, KLF9, THBD, and MTHFD2.", "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:37860011"], "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": {"log2fc_threshold": "ombined data set, with |log2FC| > 1 and P< 0"}, "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:37860011", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2023.1202758", "sha256": "sha256:fa193da8d1bbdd5c2c1cdcc3b591780d21d992707d12cbd73c1446d75f21cf09", "bytes": 43962, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2023.1202758", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10582959", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12021", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12021", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12021", "version": null, "note": "The original contributions presented in the study are publicly available. 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To analyze the correlation between apoptosi", "poptosis. To analyze the correlation between apoptosis and OA development, we selected apoptosis ge", "en apoptosis and OA development, we selected apoptosis genes from the differentially expressed gene"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["limma"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}