CYLD as a key regulator of myocardial infarction-to-heart failure transition revealed by multi-omics integration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40626177", "kind": "science-record", "revision": 3, "content_hash": "sha256:3902a0ec7492b48938c1cbfe53a422ad3785209fa91980a0acd24bdcd40f6a38", "created_at": "2026-11-01T20:30:43Z", "updated_at": "2026-11-01T22:14:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CYLD as a key regulator of myocardial infarction-to-heart failure transition revealed by multi-omics integration.", "doi": "10.3389/fgene.2025.1592985", "pmid": "40626177", "authors": ["Jingya Xu", "Zhonghua Dong", "Zhaodong Li", "Xuan Wang"], "journal": "Frontiers in genetics", "year": 2025, "abstract": "Introduction: Heart failure (HF) is the most common complication following myocardial infarction (MI) and frequently occurs during the postinfarction recovery phase. Despite the well-established association between HF and MI, the underlying molecular mechanisms driving their transition remain poorly understood.\nMethods: The aim of this study was to identify key regulatory genes involved in this transition via advanced computational tools. We conducted a comprehensive analysis of differentially expressed genes (DEGs) via Limma software, leveraging five independent datasets retrieved from the Gene Expression Omnibus (GEO) database: GSE59867, GSE62646, GSE168281, GSE267644, and GSE269269. Our multistep analytical pipeline included weighted gene coexpression network analysis (WGCNA) to map interacting genes, machine learning algorithms for robust classification, functional annotation via Kyoto Encyclopedia of Genes and Genomes (KEGG) to explore biological pathways, CIBERSORT correlation analysis linking hub genes with immune cell states, transcriptional regulation profiling of key hubs, and single-cell sequencing to assess the functional relevance of these hubs.\nResults: Our findings revealed that 413 DEGs were significantly different between MI and HF. WGCNA identified 98 genes associated with both conditions. Machine learning filtering further prioritized 10 hub genes: GPER1, E2F5, DZIP3, CYLD, ADAMTS2, ZNF366, ST14, SNORD28, LHFPL2, and HIVEP2. These hubs were significantly associated with immune-related processes, suggesting their potential role in the pathogenesis of HF after MI. Single-cell transcriptomic analysis demonstrated that CYLD exhibited the strongest correlation with the transition from MI to HF; using random forest modelling, we validated its predictive value in this context.\nDiscussion: In conclusion, our study identified CYLD as a critical regulator of the transition from MI to HF. Our findings underscore the potential of hub genes as targets for novel therapeutic interventions aimed at mitigating MI-to-HF progression and improving patient outcomes.", "claims": [{"id": "claim-method", "statement": "The diagnostic potential of CYLD was validated through receiver operating characteristic (ROC) analysis (AUC = 0.817, 95% CI 0.647–0.940) in an independent validation cohort (Supplementary Figure S7).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40626177", "locator": "sections[18] \"3.6 Functional and diagnostic validation of the CYLD\" paragraph 4", "quote": "The diagnostic potential of CYLD was validated through receiver operating characteristic (ROC) analysis (AUC = 0.817, 95% CI 0.647–0.940) in an independent validation cohort (Supplementary Figure S7)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40626177", "locator": "sections[22] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The diagnostic potential of CYLD was validated through receiver operating characteristic (ROC) analysis (AUC = 0.817, 95% CI 0.647–0.940) in an independent validation cohort (Supplementary Figure S7).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The diagnostic potential of CYLD was validated through receiver operating characteristic (ROC) analysis (AUC = 0.817, 95% CI 0.647–0.940) in an independent validation cohort (Supplementary Figure S7)."}, "evidence": [{"asset": "source:pmid:40626177", "locator": "sections[18] \"3.6 Functional and diagnostic validation of the CYLD\" paragraph 4", "quote": "The diagnostic potential of CYLD was validated through receiver operating characteristic (ROC) analysis (AUC = 0.817, 95% CI 0.647–0.940) in an independent validation cohort (Supplementary Figure S7)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The diagnostic potential of CYLD was validated through receiver operating characteristic (ROC) analysis (AUC = 0.817, 95% CI 0.647–0.940) in an independent validation cohort (Supplementary Figure S7).", "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:40626177"], "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:GSE168281"], "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:GSE168281"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40626177", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2025.1592985", "sha256": "sha256:cc8dfcb7115991011dc1758c899bb852ab0901ee68a7052ba9a4b8f5916671dd", "bytes": 34620, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2025.1592985", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12229883", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE168281", "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=GSE168281", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE168281", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5135512", "GSM5135513", "GSM5135514", "GSM5135515", "GSM5135516", "GSM5135517", "GSM5135518", "GSM5135519", "GSM5135520"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Uncovering potential lncRNAs and mRNAs in progression from acute myocardial infarction to myocardial fibrosis to heart failure", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE226794", "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=GSE226794", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE226794", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM7083828", "GSM7083829", "GSM7677371"], "sample_count": 3, "group_sizes": null, "group_sizes_basis": null, "platform": "24676;11154", "taxon": "Homo sapiens", "title": "3D-cultured blastoids model human embryogenesis from pre-implantation to early gastrulation stages", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE267644", "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=GSE267644", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE267644", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM8271495", "GSM8271496", "GSM8271497", "GSM8271498", "GSM8271499", "GSM8271500", "GSM8271501", "GSM8271502", "GSM8271503", "GSM8271504", "GSM8271505"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing [scRNA-seq HF]", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE269269", "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=GSE269269", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE269269", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM8311198", "GSM8311199", "GSM8311200", "GSM8311201", "GSM8311202", "GSM8311203", "GSM8311204", "GSM8311205", "GSM8311206", "GSM8311207"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells From Acute Myocardial Infarction", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE59867", "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=GSE59867", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59867", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1448335", "GSM1448336", "GSM1448337", "GSM1448338", "GSM1448339", "GSM1448340", "GSM1448341", "GSM1448342", "GSM1448343", "GSM1448344", "GSM1448345", "GSM1448346", "GSM1448347", "GSM1448348", "GSM1448349", "GSM1448350", "GSM1448351", "GSM1448352", "GSM1448353", "GSM1448354", "GSM1448355", "GSM1448356", "GSM1448357", "GSM1448358", "GSM1448359", "GSM1448360", "GSM1448361", "GSM1448362", "GSM1448363", "GSM1448364", "GSM1448365", "GSM1448366", "GSM1448367", "GSM1448368", "GSM1448369", "GSM1448370", "GSM1448371", "GSM1448372", "GSM1448373", "GSM1448374", "GSM1448375", "GSM1448376", "GSM1448377", "GSM1448378", "GSM1448379", "GSM1448380", "GSM1448381", "GSM1448382", "GSM1448383", "GSM1448384", "GSM1448385", "GSM1448386", "GSM1448387", "GSM1448388", "GSM1448389", "GSM1448390", "GSM1448391", "GSM1448392", "GSM1448393", "GSM1448394", "GSM1448395", "GSM1448396", "GSM1448397", "GSM1448398", "GSM1448399", "GSM1448400", "GSM1448401", "GSM1448402", "GSM1448403", "GSM1448404", "GSM1448405", "GSM1448406", "GSM1448407", "GSM1448408", "GSM1448409", "GSM1448410", "GSM1448411", "GSM1448412", "GSM1448413", "GSM1448414", "GSM1448415", "GSM1448416", "GSM1448417", "GSM1448418", "GSM1448419", "GSM1448420", "GSM1448421", "GSM1448422", "GSM1448423", "GSM1448424", "GSM1448425", "GSM1448426", "GSM1448427", "GSM1448428", "GSM1448429", "GSM1448430", "GSM1448431", "GSM1448432", "GSM1448433", "GSM1448434", "GSM1448435", "GSM1448436", "GSM1448437", "GSM1448438", "GSM1448439", "GSM1448440", "GSM1448441", "GSM1448442", "GSM1448443", "GSM1448444", "GSM1448445", "GSM1448446", "GSM1448447", "GSM1448448", "GSM1448449", "GSM1448450", "GSM1448451", "GSM1448452", "GSM1448453", "GSM1448454", "GSM1448455", "GSM1448456", "GSM1448457", "GSM1448458", "GSM1448459", "GSM1448460", "GSM1448461", "GSM1448462", "GSM1448463", "GSM1448464", "GSM1448465", "GSM1448466", "GSM1448467", "GSM1448468", "GSM1448469", "GSM1448470", "GSM1448471", "GSM1448472", "GSM1448473", "GSM1448474", "GSM1448475", "GSM1448476", "GSM1448477", "GSM1448478", "GSM1448479", "GSM1448480", "GSM1448481", "GSM1448482", "GSM1448483", "GSM1448484", "GSM1448485", "GSM1448486", "GSM1448487", "GSM1448488", "GSM1448489", "GSM1448490", "GSM1448491", "GSM1448492", "GSM1448493", "GSM1448494", "GSM1448495", "GSM1448496", "GSM1448497", "GSM1448498", "GSM1448499", "GSM1448500", "GSM1448501", "GSM1448502", "GSM1448503", "GSM1448504", "GSM1448505", "GSM1448506", "GSM1448507", "GSM1448508", "GSM1448509", "GSM1448510", "GSM1448511", "GSM1448512", "GSM1448513", "GSM1448514", "GSM1448515", "GSM1448516", "GSM1448517", "GSM1448518", "GSM1448519", "GSM1448520", "GSM1448521", "GSM1448522", "GSM1448523", "GSM1448524", "GSM1448525", "GSM1448526", "GSM1448527", "GSM1448528", "GSM1448529", "GSM1448530", "GSM1448531", "GSM1448532", "GSM1448533", "GSM1448534", "GSM1448535", "GSM1448536", "GSM1448537", "GSM1448538", "GSM1448539", "GSM1448540", "GSM1448541", "GSM1448542", "GSM1448543", "GSM1448544", "GSM1448545", "GSM1448546", "GSM1448547", "GSM1448548", "GSM1448549", "GSM1448550", "GSM1448551", "GSM1448552", "GSM1448553", "GSM1448554", "GSM1448555", "GSM1448556", "GSM1448557", "GSM1448558", "GSM1448559", "GSM1448560", "GSM1448561", "GSM1448562", "GSM1448563", "GSM1448564", "GSM1448565", "GSM1448566", "GSM1448567", "GSM1448568", "GSM1448569", "GSM1448570", "GSM1448571", "GSM1448572", "GSM1448573", "GSM1448574", "GSM1448575", "GSM1448576", "GSM1448577", "GSM1448578", "GSM1448579", "GSM1448580", "GSM1448581", "GSM1448582", "GSM1448583", "GSM1448584", "GSM1448585", "GSM1448586", "GSM1448587", "GSM1448588", "GSM1448589", "GSM1448590", "GSM1448591", "GSM1448592", "GSM1448593", "GSM1448594", "GSM1448595", "GSM1448596", "GSM1448597", "GSM1448598", "GSM1448599", "GSM1448600", "GSM1448601", "GSM1448602", "GSM1448603", "GSM1448604", "GSM1448605", "GSM1448606", "GSM1448607", "GSM1448608", "GSM1448609", "GSM1448610", "GSM1448611", "GSM1448612", "GSM1448613", "GSM1448614", "GSM1448615", "GSM1448616", "GSM1448617", "GSM1448618", "GSM1448619", "GSM1448620", "GSM1448621", "GSM1448622", "GSM1448623", "GSM1448624", "GSM1448625", "GSM1448626", "GSM1448627", "GSM1448628", "GSM1448629", "GSM1448630", "GSM1448631", "GSM1448632", "GSM1448633", "GSM1448634", "GSM1448635", "GSM1448636", "GSM1448637", "GSM1448638", "GSM1448639", "GSM1448640", "GSM1448641", "GSM1448642", "GSM1448643", "GSM1448644", "GSM1448645", "GSM1448646", "GSM1448647", "GSM1448648", "GSM1448649", "GSM1448650", "GSM1448651", "GSM1448652", "GSM1448653", "GSM1448654", "GSM1448655", "GSM1448656", "GSM1448657", "GSM1448658", "GSM1448659", "GSM1448660", "GSM1448661", "GSM1448662", "GSM1448663", "GSM1448664", "GSM1448665", "GSM1448666", "GSM1448667", "GSM1448668", "GSM1448669", "GSM1448670", "GSM1448671", "GSM1448672", "GSM1448673", "GSM1448674", "GSM1448675", "GSM1448676", "GSM1448677", "GSM1448678", "GSM1448679", "GSM1448680", "GSM1448681", "GSM1448682", "GSM1448683", "GSM1448684", "GSM1448685", "GSM1448686", "GSM1448687", "GSM1448688", "GSM1448689", "GSM1448690", "GSM1448691", "GSM1448692", "GSM1448693", "GSM1448694", "GSM1448695", "GSM1448696", "GSM1448697", "GSM1448698", "GSM1448699", "GSM1448700", "GSM1448701", "GSM1448702", "GSM1448703", "GSM1448704", "GSM1448705", "GSM1448706", "GSM1448707", "GSM1448708", "GSM1448709", "GSM1448710", "GSM1448711", "GSM1448712", "GSM1448713", "GSM1448714", "GSM1448715", "GSM1448716", "GSM1448717", "GSM1448718", "GSM1448719", "GSM1448720", "GSM1448721", "GSM1448722", "GSM1448723", "GSM1448724", "GSM1620759", "GSM1620760", "GSM1620761", "GSM1620762", "GSM1620763", "GSM1620764", "GSM1620765", "GSM1620766", "GSM1620767", "GSM1620768", "GSM1620769", "GSM1620770", "GSM1620771", "GSM1620772", "GSM1620773", "GSM1620774", "GSM1620775", "GSM1620776", "GSM1620777", "GSM1620778", "GSM1620779", "GSM1620780", "GSM1620781", "GSM1620782", "GSM1620783", "GSM1620784", "GSM1620785", "GSM1620786", "GSM1620787", "GSM1620788", "GSM1620789", "GSM1620790", "GSM1620791", "GSM1620792", "GSM1620793", "GSM1620794", "GSM1620795", "GSM1620796", "GSM1620797", "GSM1620798", "GSM1620799", "GSM1620800", "GSM1620801", "GSM1620802", "GSM1620803", "GSM1620804"], "sample_count": 436, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profiling reveals potential prognostic biomarkers associated with the progression of heart failure", "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: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": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "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}}], "gaps": ["asset:data:geo:GSE168281 not downloaded", "asset:data:geo:GSE168281 licence not read", "asset:data:geo:GSE226794 not downloaded", "asset:data:geo:GSE226794 licence not read", "asset:data:geo:GSE267644 not downloaded", "asset:data:geo:GSE267644 licence not read", "asset:data:geo:GSE269269 not downloaded", "asset:data:geo:GSE269269 licence not read", "asset:data:geo:GSE59867 not downloaded", "asset:data:geo:GSE59867 licence not read", "asset:data:geo:GSE62646 not downloaded", "asset:data:geo:GSE62646 licence not read"]}, "analysis": {"state": "partial", "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": 0.7, "band": "medium", "quote": "Limma"}}, {"id": "method-2", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-3", "family": null, "specific": null, "label": "receiver operating characteristic (ROC) analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The diagnostic potential of CYLD was validated through receiver operating characteristic (ROC) analysis (AUC = 0.817, 95% CI 0.647–0.940) in an independent validation cohort (Supplementary Figure S7)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 95.0, "unit": "per cent", "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-auc", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 0.817, "unit": "auc", "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."}], "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": ["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": ["GSE59867", "GSE62646", "GSE168281", "GSE267644", "GSE269269", "GSE226794"], "resolved_accessions": ["GSE59867", "GSE62646", "GSE168281", "GSE267644", "GSE269269", "GSE226794"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE59867, GSE62646, GSE168281, GSE267644, GSE269269, GSE226794 in Gene Expression Omnibus (GEO) database 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:40626177", "data:geo:GSE168281"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE168281"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:56:14Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9669, "completion_tokens": 2479, "cached_tokens": 256}}, "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:40626177", "type": "paper", "label": "pmid:40626177"}, {"id": "source:pmid:40626177", "type": "manuscript", "label": "PMID 40626177 full text"}, {"id": "data:geo:GSE168281", "type": "dataset", "label": "GEO GSE168281"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40626177", "type": "paper", "label": "pmid:40626177"}, {"id": "source:pmid:40626177", "type": "manuscript", "label": "PMID 40626177 full text"}, {"id": "data:geo:GSE168281", "type": "dataset", "label": "GEO GSE168281"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40626177", "type": "extraction", "used": ["source:pmid:40626177"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE168281", "type": "accession_resolution", "used": ["data:geo:GSE168281"], "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:40626177", "parent_hash": "sha256:e41f2e2da286487ef9d346a66f0b4e9fac66f167143d16520946c9da11a6c979", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE168281 licence not read", "asset:data:geo:GSE168281 not downloaded", "asset:data:geo:GSE226794 licence not read", "asset:data:geo:GSE226794 not downloaded", "asset:data:geo:GSE267644 licence not read", "asset:data:geo:GSE267644 not downloaded", "asset:data:geo:GSE269269 licence not read", "asset:data:geo:GSE269269 not downloaded", "asset:data:geo:GSE59867 licence not read", "asset:data:geo:GSE59867 not downloaded", "asset:data:geo:GSE62646 licence not read", "asset:data:geo:GSE62646 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": 0.7, "evidence": ["Limma"], "order_basis": "analysis_only", "id": "assay:1"}]}