Expression levels and clinical significance of ferroptosis-related genes in patients with myocardial infarction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38253721", "kind": "science-record", "revision": 3, "content_hash": "sha256:8f0195bf170b9d81fe934a31dbde303acc394c16c90224c89434c9f992d90b2d", "created_at": "2026-11-01T19:20:09Z", "updated_at": "2026-11-01T22:11:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Expression levels and clinical significance of ferroptosis-related genes in patients with myocardial infarction.", "doi": "10.1038/s41598-023-49336-2", "pmid": "38253721", "authors": ["Lei Huang", "Xiaoyang Wang", "Bin Hu", "Shuling Rong"], "journal": "Scientific reports", "year": 2024, "abstract": "Myocardial infarction (MI) is the most serious type of cardiovascular disease and the leading cause of cardiac death.Ferroptosis is one of the newly discovered programmed cell death modes in MI, but its mechanism of action in MI has not been clarified.In this study, we analyzed the expression changes of ferroptosis-related genes in MI and explored the potential mechanisms of ferroptosis-related functions in myocardial infarction. Public data sets GSE19339, GSE97320 and GSE141512 were retrieved from the Gene Expression Omnibus (GEO) Datasets public database. After data preprocessing, differentially expressed genes were screened, and differentially expressed ferroptosis-related genes associated with myocardial infarction were obtained. The biological function and signaling pathway enrichment analysis were performed to establish the PPI interaction network specific to heart tissue, and the differential diagnosis significance of differentially expressed ferroptosis-related genes associated with myocardial infarction was analyzed by ROC curve and decision tree model.A total of 317 genes showed significant changes in expression levels in patients with myocardial infarction, including 205 down-regulated genes and 112 up-regulated genes.Gene Ontology (GO) enrichment analysis and functional classification of Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways showed that these genes were mainly involved in signaling pathways or biological functions related to inflammation and apoptosis.Five differentially expressed ferroptosis-related genes (SLC2A3, EPAS1, HMOX1, ATM, FANCD2) were obtained, all of which played key biological functions in cardiac tissue function. SLC2A3, EPAS1, HMOX1, ATM and FANCD2 genes all had good diagnostic value for myocardial infarction (P < 0.05). The increase of SLC2A3, EPAS1 and HMOX1 are risk factors for myocardial infarction, while ATM and FANCD2 are protective factors.Decision tree analysis showed that SLC2A3, HMOX1, ATM, FANCD2 gene had higher net yield in diagnosing myocardial infarction. In summary, the mechanism of ferroptosis is involved in the occurrence and progression of myocardial infarction. In this study, five differentially expressed ferroptosis-related genes associated with myocardial infarction were retrieved, which may be good biomarkers of ferroptosis after MI.These findings also suggest that the differential expression of ferroptosis-related genes associated with myocardial infarction has significant diagnostic significance for myocardial infarction.", "claims": [{"id": "claim-method", "statement": "SPSS 26.0 statistical software was used, with myocardial infarction as the result variable, and ROC curve analysis was used to screen the influencing factors of ferroptosis-related genes on the diagnosis of myocardial infarction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38253721", "locator": "sections[14] \"Statistical analysis\" paragraph 2", "quote": "SPSS 26.0 statistical software was used, with myocardial infarction as the result variable, and ROC curve analysis was used to screen the influencing factors of ferroptosis-related genes on the diagnosis of myocardial infarction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38253721", "locator": "sections[27] \"notes\" paragraph 1", "quote": "The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Five differentially expressed ferroptosis-related genes—SLC2A3, EPAS1, HMOX1, ATM, and FANCD2—showed significant diagnostic value for myocardial infarction.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "SLC2A3, EPAS1, HMOX1, ATM and FANCD2 genes all had good diagnostic value for myocardial infarction (P < 0.05)."}, "evidence": [{"asset": "source:pmid:38253721", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Five differentially expressed ferroptosis-related genes (SLC2A3, EPAS1, HMOX1, ATM, FANCD2) were obtained, all of which played key biological functions in cardiac tissue function."}, {"asset": "source:pmid:38253721", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "SLC2A3, EPAS1, HMOX1, ATM and FANCD2 genes all had good diagnostic value for myocardial infarction (P < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Five differentially expressed ferroptosis-related genes—SLC2A3, EPAS1, HMOX1, ATM, and FANCD2—showed significant diagnostic value for myocardial infarction.", "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:38253721"], "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:GSE141512"], "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:GSE141512"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38253721", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-023-49336-2", "sha256": "sha256:25cafc05c15c4c7760c0a352cec9eead4b304b9da41dc0954b6bceec03ac22c5", "bytes": 22965, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-023-49336-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10803342", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE141512", "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=GSE141512", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE141512", "version": null, "note": "The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4205353", "GSM4205354", "GSM4205355", "GSM4205356", "GSM4205357", "GSM4205358", "GSM4205359", "GSM4205360", "GSM4205361", "GSM4205362", "GSM4205363", "GSM4205364"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "17586", "taxon": "Homo sapiens", "title": "Expression data for patients with myocardial infarction (MI) vs healthy patients", "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:GSE19339", "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=GSE19339", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19339", "version": null, "note": "The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM480382", "GSM480383", "GSM480384", "GSM480385", "GSM480386", "GSM480387", "GSM480388", "GSM480389"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Differential gene expression in thrombus-derived white blood cells of patients with acute coronary syndrome", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE97320", "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=GSE97320", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97320", "version": null, "note": "The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2561549", "GSM2561550", "GSM2561551", "GSM2561552", "GSM2561553", "GSM2561554"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Differential gene expression profiles in peripheral blood in Northeast Chinese Han people with acute myocardial infarction", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE141512 not downloaded", "asset:data:geo:GSE141512 licence not read", "asset:data:geo:GSE19339 not downloaded", "asset:data:geo:GSE19339 licence not read", "asset:data:geo:GSE97320 not downloaded", "asset:data:geo:GSE97320 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "decision_tree", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "decision tree"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-4", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}, {"id": "method-5", "family": null, "specific": null, "label": "Receiver operating characteristic curve analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "SPSS 26.0 statistical software was used, with myocardial infarction as the result variable, and ROC curve analysis was used to screen the influencing factors of ferroptosis-related genes on the diagnosis of myocardial infarction."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: decision_tree."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE19339", "GSE97320", "GSE141512"], "resolved_accessions": ["GSE19339", "GSE97320", "GSE141512"], "statements": ["The gene expression profiles of GSE19339,GSE97320 and GSE141512 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19339,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97320 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141512)."], "basis": "The paper names GSE19339, GSE97320, GSE141512 in Gene Expression Omnibus (GEO) Datasets public database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "assets": ["source:pmid:38253721", "data:geo:GSE141512"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE141512"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:05:50Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 6706, "completion_tokens": 1661, "cached_tokens": 264}}, "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:38253721", "type": "paper", "label": "pmid:38253721"}, {"id": "source:pmid:38253721", "type": "manuscript", "label": "PMID 38253721 full text"}, {"id": "data:geo:GSE141512", "type": "dataset", "label": "GEO GSE141512"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38253721", "type": "paper", "label": "pmid:38253721"}, {"id": "source:pmid:38253721", "type": "manuscript", "label": "PMID 38253721 full text"}, {"id": "data:geo:GSE141512", "type": "dataset", "label": "GEO GSE141512"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38253721", "type": "extraction", "used": ["source:pmid:38253721"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE141512", "type": "accession_resolution", "used": ["data:geo:GSE141512"], "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:38253721", "parent_hash": "sha256:7af583f7ce1852378470dae313077d9f0388d4541f36dec989d9e354599995ed", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE141512 licence not read", "asset:data:geo:GSE141512 not downloaded", "asset:data:geo:GSE19339 licence not read", "asset:data:geo:GSE19339 not downloaded", "asset:data:geo:GSE97320 licence not read", "asset:data:geo:GSE97320 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ogical functions related to inflammation and apoptosis.Five differentially expressed ferroptosis-re"], "order_basis": "paper_text_order:1574", "id": "assay:1"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["decision tree"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}