Development and Validation of Robust Ferroptosis-Related Genes in Myocardial Ischemia-Reperfusion Injury.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37623357", "kind": "science-record", "revision": 5, "content_hash": "sha256:dc883563c714a225c92f6d2e0a7e79eb0cf0da859738cf7acc63440a74e30e0c", "created_at": "2026-11-01T19:02:25Z", "updated_at": "2026-11-01T22:52:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and Validation of Robust Ferroptosis-Related Genes in Myocardial Ischemia-Reperfusion Injury.", "doi": "10.3390/jcdd10080344", "pmid": "37623357", "authors": ["Xiuxian Wei", "Yi Li", "Pengcheng Luo", "Yue Dai", "Tao Jiang", "Mulin Xu", "Yi Hao", "Cuntai Zhang", "Yu Liu"], "journal": "Journal of cardiovascular development and disease", "year": 2023, "abstract": "(1) Background: Despite the evidence that ferroptosis is involved in myocardial ischemia-reperfusion (MIR), the critical regulator of ferroptosis in MIR remains unclear. (2) Methods: We included three GEO datasets and a set of ferroptosis-related genes with 259 genes. Following the identification of the differentially expressed ferroptosis-related genes (DEFRGs) and hub genes, we performed the functional annotation, protein-protein interaction network, and immune infiltration analysis. The GSE168610 dataset, a cell model, and an animal model were then used to verify key genes. (3) Results: We identified 17 DEFRGs and 9 hub genes in the MIR samples compared to the control. Heme oxygenase 1 (Hmox1), activating transcription factor 3 (Atf3), epidermal growth factor receptor (Egfr), and X-box binding protein 1 (Xbp1) were significantly upregulated in response to ischemic and hypoxic stimuli. In contrast, glutathione peroxidase 4 (Gpx4) and vascular endothelial growth factor A (Vegfa) were consistently decreased in either the oxygen and glucose deprivation/reoxygenation cell or the MIR mouse model. (4) Conclusions: This study emphasized the relevance of ferroptosis in MIR. It has been successfully demonstrated that nine ferroptosis-related genes (Hmox1, Atf3, Egfr, Gpx4, Cd44, Vegfa, asparagine synthetase (Asns), Xbp1, and bromodomain containing 4 (Brd4)) are involved in the process. Additional studies are needed to explore potential therapeutic targets for MIR.", "claims": [{"id": "claim-method", "statement": "The identification of DEGs was performed using the Limma package in R software (version 4.2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37623357", "locator": "sections[5] \"2.3. Identification of DEGs and DEFRGs\" paragraph 2", "quote": "The identification of DEGs was performed using the Limma package in R software (version 4.2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the accession number (s) can be found in the article/Supplementary Material. All data generated or analyzed during this study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37623357", "locator": "sections[40] \"notes\" paragraph 1", "quote": "The datasets presented in this study can be found in online repositories. The names of the accession number (s) can be found in the article/Supplementary Material. All data generated or analyzed during this study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 17 differentially expressed ferroptosis-related genes and nine hub genes associated with myocardial ischemia-reperfusion.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37623357", "locator": "sections[24] \"3.1. The Overall Study Protocol and Identification of DEGs and DEFRGs\" paragraph 2", "quote": "Ultimately, 17 co-expressed DEFRGs were obtained, which contained 10 upregulated genes and 7 down-regulated genes (Supplementary Table S4)."}, {"asset": "source:pmid:37623357", "locator": "sections[26] \"3.3. PPI Network and Identification of Hub Genes\" paragraph 2", "quote": "A total of seven upregulated genes (epidermal growth factor receptor (Egfr), Hmox1, Atf3, X-box binding protein 1 (Xbp1), asparagine synthetase (Asns), Cd44, and bromodomain containing 4 (Brd4)) and two down-regulated genes (vascular endothelial growth factor A (Vegfa) and Gpx4) were chosen as the hub genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 17 differentially expressed ferroptosis-related genes and nine hub genes associated with myocardial ischemia-reperfusion.", "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:37623357"], "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:GSE168610"], "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:GSE168610"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37623357", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/jcdd10080344", "sha256": "sha256:d644aa5f11798714be6fd10b03115492cbb50afa37b08073d562d60203d0c80b", "bytes": 42991, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/jcdd10080344", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10455596", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE168610", "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=GSE168610", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE168610", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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(4) Conclusions: This study emphasized the", "se deprivation/reoxygenation cell or the MIR mouse model. (4) Conclusions: This study emphasize", "s (NIH Publication No. 85–23, revised 1996). Mice were numbered using an online number generator (h"], "order_basis": "paper_text_order:1159", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["2. Materials and Methods 2.2. Analysis of RNA-seq Data The RNA-seq data were obtained from the", "nd Methods 2.2. 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After standardization of the microarray data, there were 2920 DEGs in GSE4105 (1477"], "order_basis": "paper_text_order:3686", "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 identification of DEGs was performed using the Limma package in R software (version 4.2)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}