NR4A2 may be a potential diagnostic biomarker for myocardial infarction: A comprehensive bioinformatics analysis and experimental validation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36618351", "kind": "science-record", "revision": 4, "content_hash": "sha256:480b2110c305259c47a181bebc6a8d6d957059d6ee34d13a8146d3ba53852160", "created_at": "2026-11-01T19:01:10Z", "updated_at": "2026-11-01T22:51:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "NR4A2 may be a potential diagnostic biomarker for myocardial infarction: A comprehensive bioinformatics analysis and experimental validation.", "doi": "10.3389/fimmu.2022.1061800", "pmid": "36618351", "authors": ["Dongsheng Wei", "Jiajie Qi", "Yuxuan Wang", "Luzhen Li", "Guanlin Yang", "Xinyong He", "Zhe Zhang"], "journal": "Frontiers in immunology", "year": 2022, "abstract": "Background: Myocardial infarction is a well-established severe consequence of coronary artery disease. However, the lack of effective early biomarkers accounts for the lag time before clinical diagnosis of myocardial infarction. The present study aimed to predict critical genes for the diagnosis of MI by immune infiltration analysis and establish a nomogram.\nMethods: Gene microarray data were downloaded from Gene Expression Omnibus (GEO). Differential expression analysis, single-cell sequencing, and disease ontology (DO) enrichment analysis were performed to determine the distribution of Differentially Expressed Genes (DEGs) in cell subpopulations and their correlation with MI. Next, the level of infiltration of 16 immune cells and immune functions and their hub genes were analyzed using a Single-sample Gene Set Enrichment Analysis (ssGSEA). In addition, the accuracy of critical markers for the diagnosis of MI was subsequently assessed using receiver operating characteristic curves (ROC). One datasets were used to test the accuracy of the model. Finally, the genes with the most diagnostic value for MI were screened and experimentally validated.\nResults: 335 DEGs were identified in GSE66360, including 280 upregulated and 55 downregulated genes. Single-cell sequencing results demonstrated that DEGs were mainly distributed in endothelial cells. DO enrichment analysis suggested that DEGs were highly correlated with MI. In the MI population, macrophages, neutrophils, CCR, and Parainflammation were significantly upregulated compared to the average population. NR4A2 was identified as the gene with the most significant diagnostic value in the immune scoring and diagnostic model. 191 possible drugs for the treatment of myocardial infarction were identified by drug prediction analysis. Finally, our results were validated by Real-time Quantitativepolymerase chain reaction and Western Blot of animal samples.\nConclusion: Our comprehensive in silico analysis revealed that NR4A2 has huge prospects for application in diagnosing patients with MI.", "claims": [{"id": "claim-method", "statement": "Finally, the eligible DEGs were screening and electing by the linear models for microarray (LIMMA) data package; P-value < 0.05, and |log2 FC| > 1 (16).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36618351", "locator": "sections[4] \"Characteristics of differentially expressed genes from dataset GSE66360\" paragraph 2", "quote": "Finally, the eligible DEGs were screening and electing by the linear models for microarray (LIMMA) data package; P-value < 0.05, and |log2 FC| > 1 (16)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36618351", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential expression analysis using Limma on the GEO dataset GSE66360 identified 335 DEGs, including 280 upregulated and 55 downregulated genes.", "kind": "quantitative", "target": {"value": 4.1, "unit": "correlation coefficient", "tolerance": null, "source": "Dataset GSE66360 was selected and underwent differential expression analysis using the “Limma” package in R 4.1.3 software. Three hundred thirty-five DEGs were identified, including 280 up- and 55 downregulated genes (log2FC > 1 and P-value <0.05)."}, "evidence": [{"asset": "source:pmid:36618351", "locator": "sections[16] \"Identification of DEGs\" paragraph 2", "quote": "Dataset GSE66360 was selected and underwent differential expression analysis using the “Limma” package in R 4.1.3 software. Three hundred thirty-five DEGs were identified, including 280 up- and 55 downregulated genes (log2FC > 1 and P-value <0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential expression analysis using Limma on the GEO dataset GSE66360 identified 335 DEGs, including 280 upregulated and 55 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:36618351"], "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:GSE180678"], "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:GSE180678"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36618351", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2022.1061800", "sha256": "sha256:c050bfb17405dbdfa2f0d6976a77a60b040060062639b74f62b6c649fb842645", "bytes": 36855, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2022.1061800", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9815548", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE180678", "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=GSE180678", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE180678", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5467651"], "sample_count": 1, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Hypoxia inducible factors individually facilitate inflammatory myeloid metabolism and inefficient cardiac repair", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE62646", "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=GSE62646", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62646", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1530765", "GSM1530766", "GSM1530767", "GSM1530768", "GSM1530769", "GSM1530770", "GSM1530771", "GSM1530772", "GSM1530773", "GSM1530774", "GSM1530775", "GSM1530776", "GSM1530777", "GSM1530778", "GSM1530779", "GSM1530780", "GSM1530781", "GSM1530782", "GSM1530783", "GSM1530784", "GSM1530785", "GSM1530786", "GSM1530787", "GSM1530788", "GSM1530789", "GSM1530790", "GSM1530791", "GSM1530792", "GSM1530793", "GSM1530794", "GSM1530795", "GSM1530796", "GSM1530797", "GSM1530798", "GSM1530799", "GSM1530800", "GSM1530801", "GSM1530802", "GSM1530803", "GSM1530804", "GSM1530805", "GSM1530806", "GSM1530807", "GSM1530808", "GSM1530809", "GSM1530810", "GSM1530811", "GSM1530812", "GSM1530813", "GSM1530814", "GSM1530815", "GSM1530816", "GSM1530817", "GSM1530818", "GSM1530819", "GSM1530820", "GSM1530821", "GSM1530822", "GSM1530823", "GSM1530824", "GSM1530825", "GSM1530826", "GSM1530827", "GSM1530828", "GSM1530829", "GSM1530830", "GSM1530831", "GSM1530832", "GSM1530833", "GSM1530834", "GSM1530835", "GSM1530836", "GSM1530837", "GSM1530838", "GSM1530839", "GSM1530840", "GSM1530841", "GSM1530842", "GSM1530843", "GSM1530844", "GSM1530845", "GSM1530846", "GSM1530847", "GSM1530848", "GSM1530849", "GSM1530850", "GSM1530851", "GSM1530852", "GSM1530853", "GSM1530854", "GSM1530855", "GSM1530856", "GSM1530857", "GSM1530858", "GSM1530859", "GSM1530860", "GSM1530861", "GSM1530862"], "sample_count": 98, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Altered gene expression pattern in peripheral blood mononuclear cells in patients with acute myocardial infarction", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE66360", "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=GSE66360", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66360", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1620819", "GSM1620820", "GSM1620821", "GSM1620822", "GSM1620823", "GSM1620824", "GSM1620825", "GSM1620826", "GSM1620827", "GSM1620828", "GSM1620829", "GSM1620830", "GSM1620831", "GSM1620832", "GSM1620833", "GSM1620834", "GSM1620835", "GSM1620836", "GSM1620837", "GSM1620838", "GSM1620839", "GSM1620840", "GSM1620841", "GSM1620842", "GSM1620843", "GSM1620844", "GSM1620845", "GSM1620846", "GSM1620847", "GSM1620848", "GSM1620849", "GSM1620850", "GSM1620851", "GSM1620852", "GSM1620853", "GSM1620854", "GSM1620855", "GSM1620856", "GSM1620857", "GSM1620858", "GSM1620859", "GSM1620860", "GSM1620861", "GSM1620862", "GSM1620863", "GSM1620864", "GSM1620865", "GSM1620866", "GSM1620867", "GSM1620868", "GSM1620869", "GSM1620870", "GSM1620871", "GSM1620872", "GSM1620873", "GSM1620874", "GSM1620875", "GSM1620876", "GSM1620877", "GSM1620878", "GSM1620879", "GSM1620880", "GSM1620881", "GSM1620882", "GSM1620883", "GSM1620884", "GSM1620885", "GSM1620886", "GSM1620887", "GSM1620888", "GSM1620889", "GSM1620890", "GSM1620891", "GSM1620892", "GSM1620893", "GSM1620894", "GSM1620895", "GSM1620896", "GSM1620897", "GSM1620898", "GSM1620899", "GSM1620900", "GSM1620901", "GSM1620902", "GSM1620903", "GSM1620904", "GSM1620905", "GSM1620906", "GSM1620907", "GSM1620908", "GSM1620909", "GSM1620910", "GSM1620911", "GSM1620912", "GSM1620913", "GSM1620914", "GSM1620915", "GSM1620916", "GSM1620917"], "sample_count": 99, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A Whole Blood Molecular Signature for the Identification of Acute Myocardial Infarction Without Relying Upon Myonecrosis (microarray)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE180678 not downloaded", "asset:data:geo:GSE180678 licence not read", "asset:data:geo:GSE62646 not downloaded", "asset:data:geo:GSE62646 licence not read", "asset:data:geo:GSE66360 not downloaded", "asset:data:geo:GSE66360 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Finally, the eligible DEGs were screening and electing by the linear models for microarray (LIMMA) data package; P-value < 0.05, and |log2 FC| > 1 (16)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 4.1, "unit": "correlation coefficient", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "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": []}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE66360", "GSE62646", "GSE180678"], "resolved_accessions": ["GSE66360", "GSE62646", "GSE180678"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/. The accession number(s) can be found in the article."], "basis": "The paper names GSE66360, GSE62646, GSE180678 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36618351", "data:geo:GSE180678"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE180678"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:22:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9966, "completion_tokens": 1625, "cached_tokens": 188}}, "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:36618351", "type": "paper", "label": "pmid:36618351"}, {"id": "source:pmid:36618351", "type": "manuscript", "label": "PMID 36618351 full text"}, {"id": "data:geo:GSE180678", "type": "dataset", "label": "GEO GSE180678"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36618351", "type": "paper", "label": "pmid:36618351"}, {"id": "source:pmid:36618351", "type": "manuscript", "label": "PMID 36618351 full text"}, {"id": "data:geo:GSE180678", "type": "dataset", "label": "GEO GSE180678"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36618351", "type": "extraction", "used": ["source:pmid:36618351"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE180678", "type": "accession_resolution", "used": ["data:geo:GSE180678"], "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:36618351", "parent_hash": "sha256:4842d327c738f5391c12f66949650f4e429ecb1d06fd291e1a6cce6a0287c846", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE180678 licence not read", "asset:data:geo:GSE180678 not downloaded", "asset:data:geo:GSE62646 licence not read", "asset:data:geo:GSE62646 not downloaded", "asset:data:geo:GSE66360 licence not read", "asset:data:geo:GSE66360 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ysis and establish a nomogram. Methods: Gene microarray data were downloaded from Gene Expression Om", "Materials and methods Microarray data extracted from gene expression omnibus", "in Figure 1 . Dataset GSE66360 based on the Affymetrix platform ( Table 1 ) was downloaded from the"], "order_basis": "paper_text_order:472", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["me Quantitativepolymerase chain reaction and Western Blot of animal samples. Conclusion: Our comprehen"], "order_basis": "paper_text_order:1995", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s. Experimental animal preparation Twenty SD rats were divided into an experimental group (n=17) an", "uccessful modeling. After the operation, the rats were fed for seven days. The rat’s abdominal aort", "s. Experimental animal preparation Twenty SD rats were divided into an experimental group (n=1", "group (n=3). After 7 days of adaptation, the rats underwent ligation of the anterior descendin"], "order_basis": "paper_text_order:4165", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["o two groups for quantitative real-time PCR (qPCR) and WB (MI=3, control=3). This study was ap", "tration analysis, immune-related gene model, QPCR, WB experimental results data analysis, and", "ided 6 rats into two groups for quantitative real-time PCR (qPCR) and WB (MI=3, control=3). This study"], "order_basis": "paper_text_order:4821", "id": "assay:4"}, {"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": ["Finally, the eligible DEGs were screening and electing by the linear models for microarray (LIMMA) data package; P-value < 0.05, and |log2 FC| > 1 (16)."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}