Identification and validation of immune-related hub genes based on machine learning in prostate cancer and AOX1 is an oxidative stress-related biomarker.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37583929", "kind": "science-record", "revision": 5, "content_hash": "sha256:c7b7c8a843c01b74b0d7c0c18d056bbb425a5af77c8583e88248625b63dcdbac", "created_at": "2026-11-01T19:02:22Z", "updated_at": "2026-11-01T22:52:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of immune-related hub genes based on machine learning in prostate cancer and AOX1 is an oxidative stress-related biomarker.", "doi": "10.3389/fonc.2023.1179212", "pmid": "37583929", "authors": ["Xiaocong Mo", "Kaisheng Yuan", "Di Hu", "Cheng Huang", "Juyu Luo", "Hang Liu", "Yin Li"], "journal": "Frontiers in oncology", "year": 2023, "abstract": "To investigate potential diagnostic and prognostic biomarkers associated with prostate cancer (PCa), we obtained gene expression data from six datasets in the Gene Expression Omnibus (GEO) database. The datasets included 127 PCa cases and 52 normal controls. We filtered for differentially expressed genes (DEGs) and identified candidate PCa biomarkers using a least absolute shrinkage and selector operation (LASSO) regression model and support vector machine recursive feature elimination (SVM-RFE) analyses. A difference analysis was conducted on these genes in the test group. The discriminating ability of the train group was determined using the area under the receiver operating characteristic curve (AUC) value, with hub genes defined as those having an AUC greater than 85%. The expression levels and diagnostic utility of the biomarkers in PCa were further confirmed in the GSE69223 and GSE71016 datasets. Finally, the invasion of cells per sample was assessed using the CIBERSORT algorithm and the ESTIMATE technique. The possible prostate cancer (PCa) diagnostic biomarkers AOX1, APOC1, ARMCX1, FLRT3, GSTM2, and HPN were identified and validated using the GSE69223 and GSE71016 datasets. Among these biomarkers, AOX1 was found to be associated with oxidative stress and could potentially serve as a prognostic biomarker. Experimental validations showed that AOX1 expression was low in PCa cell lines. Overexpression of AOX1 significantly reduced the proliferation and migration of PCa cells, suggesting that the anti-tumor effect of AOX1 may be attributed to its impact on oxidative stress. Our study employed a comprehensive approach to identify PCa biomarkers and investigate the role of cell infiltration in PCa.", "claims": [{"id": "claim-method", "statement": "The R package ‘limma’ from http://www.bioconductor.org/ was used to detect differentially expressed genes (DEGs) between 127 PCa patients and 52 normal controls in the training group (13).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37583929", "locator": "sections[4] \"Identification of DEGs in PCa\" paragraph 2", "quote": "The R package ‘limma’ from http://www.bioconductor.org/ was used to detect differentially expressed genes (DEGs) between 127 PCa patients and 52 normal controls in the training group (13)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are available in the GEO database, [unique persistent identifier andhyperlink to datasets in http://www.ncbi.nlm.nih.gov/geo]. The datasets generated during and analyzed during the current studyare available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37583929", "locator": "sections[28] \"Data availability statement\" paragraph 2", "quote": "The datasets supporting the conclusions of this article are available in the GEO database, [unique persistent identifier andhyperlink to datasets in http://www.ncbi.nlm.nih.gov/geo]. The datasets generated during and analyzed during the current studyare available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The possible prostate cancer (PCa) diagnostic biomarkers AOX1, APOC1, ARMCX1, FLRT3, GSTM2, and HPN were identified and validated using the GSE69223 and GSE71016 datasets.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Then, a robust discrimination was proved in the GSE69223 and GSE71016 datasets, and the AUC of AOX1 was 0.726 (95% CI 0.641-0.810), APOC1 was 0.701 (95% CI 0.607-0.792), ARMCX1 was 0.722 (95% CI 0.625-0.808), FLRT3 was 0.719 (95% CI 0.625-0.804), GSTM2 was 0.696 (95% CI 0.600-0.785) and HPN was 0.789 (95%CI 0.707-0.863) ( Figures 4A–F )."}, "evidence": [{"asset": "source:pmid:37583929", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The possible prostate cancer (PCa) diagnostic biomarkers AOX1, APOC1, ARMCX1, FLRT3, GSTM2, and HPN were identified and validated using the GSE69223 and GSE71016 datasets."}, {"asset": "source:pmid:37583929", "locator": "sections[22] \"Identification and validation of diagnostic feature biomarkers for PCa\" paragraph 2", "quote": "Then, a robust discrimination was proved in the GSE69223 and GSE71016 datasets, and the AUC of AOX1 was 0.726 (95% CI 0.641-0.810), APOC1 was 0.701 (95% CI 0.607-0.792), ARMCX1 was 0.722 (95% CI 0.625-0.808), FLRT3 was 0.719 (95% CI 0.625-0.804), GSTM2 was 0.696 (95% CI 0.600-0.785) and HPN was 0.789 (95%CI 0.707-0.863) ( Figures 4A–F )."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The possible prostate cancer (PCa) diagnostic biomarkers AOX1, APOC1, ARMCX1, FLRT3, GSTM2, and HPN were identified and validated using the GSE69223 and GSE71016 datasets.", "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:37583929"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37583929", "data:geo:GSE14206"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14206"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:50:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10283, "completion_tokens": 2402, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37583929", "type": "paper", "label": "pmid:37583929"}, {"id": "source:pmid:37583929", "type": "manuscript", "label": "PMID 37583929 full text"}, {"id": "data:geo:GSE14206", "type": "dataset", "label": "GEO GSE14206"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37583929", "type": "paper", "label": "pmid:37583929"}, {"id": "source:pmid:37583929", "type": "manuscript", "label": "PMID 37583929 full text"}, {"id": "data:geo:GSE14206", "type": "dataset", "label": "GEO GSE14206"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37583929", "type": "extraction", "used": ["source:pmid:37583929"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14206", "type": "accession_resolution", "used": ["data:geo:GSE14206"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37583929", "parent_hash": "sha256:6649f56cc4f82a344ddde674a5693ef84624fa119f27410f252bfc8b30626ff9", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE14206 licence not read", "asset:data:geo:GSE14206 not downloaded", "asset:data:geo:GSE46602 licence not read", "asset:data:geo:GSE46602 not downloaded", "asset:data:geo:GSE55945 licence not read", "asset:data:geo:GSE55945 not downloaded", "asset:data:geo:GSE69223 licence not read", "asset:data:geo:GSE69223 not downloaded", "asset:data:geo:GSE71016 licence not read", "asset:data:geo:GSE71016 not downloaded", "asset:data:geo:GSE8511 licence not read", "asset:data:geo:GSE8511 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["the ‘ggpubr’ package (24). Cell culture and transfection The PCa cell lines (LNCaP, PC3, and DU145) a", "d approximately 80-90% confluence, they were transfected following the provided instructions. Statist", "3). Figure 7D showed that the overexpression transfection was clearly successful in PCa cell lines. CC", "l prostate cell line. (D) The overexpression transfection was clearly successful in PCa cell lines. (E"], "order_basis": "paper_text_order:2274", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["the normal prostate cell line (RWPE-1) were cultured in RPMI-1640 medium. Oe-AOX1 and its negative c"], "order_basis": "paper_text_order:2378", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on was clearly successful in PCa cell lines. CCK-8 detection reveled that overexpression of AOX", "clearly successful in PCa cell lines. (E, F) CCK-8 reveled that overexpression of AOX1 could si"], "order_basis": "paper_text_order:3867", "id": "assay:3"}, {"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": 1.0, "evidence": ["The R package ‘limma’ from http://www.bioconductor.org/ was used to detect differentially expressed genes (DEGs) between 127 PCa patients and 52 normal controls in the training group (13)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}