Use of Machine Learning for the Identification and Validation of Immunogenic Cell Death Biomarkers and Immunophenotypes in Coronary Artery Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38229693", "kind": "science-record", "revision": 3, "content_hash": "sha256:ff5f099f4cbcf1e420c0600c92723ec2c7132eb21dfd3b560ce24599f009d49f", "created_at": "2026-11-01T19:20:08Z", "updated_at": "2026-11-01T22:11:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Use of Machine Learning for the Identification and Validation of Immunogenic Cell Death Biomarkers and Immunophenotypes in Coronary Artery Disease.", "doi": "10.2147/JIR.S439315", "pmid": "38229693", "authors": ["Yan-Jiao Zhang", "Chao Huang", "Xiu-Guang Zu", "Jin-Ming Liu", "Yong-Jun Li"], "journal": "Journal of inflammation research", "year": 2024, "abstract": "Objective: Immunogenic cell death (ICD) is part of the immune system's response to coronary artery disease (CAD). In this study, we bioinformatically evaluated the diagnostic and therapeutic utility of immunogenic cell death-related genes (IRGs) and their relationship with immune infiltration features in CAD.\nMethods: We acquired the CAD-related datasets GSE12288, GSE71226, and GSE120521 from the Gene Expression Omnibus (GEO) database and the IRGs from the GeneCards database. After identifying the immune cell death-related differentially expressed genes (IRDEGs), we developed a risk model and detected immune subtypes in CAD. IRDEGs were identified using least absolute shrinkage and selection operator (LASSO) analysis. Using a nomogram, we confirmed that both the LASSO model and ICD signature genes had good diagnostic performance.\nResults: There was a high degree of coincidence and immune representativeness between two CAD groups based on characteristic genes and hub genes. Hub genes were associated with the interaction of neuroactive ligands with receptors and cell adhesion receptors. The two groups differed in terms of adipogenesis, allograft rejection, and apoptosis, as well as the ICD signature and hub gene expression levels. The two CAD-ICD subtypes differed in terms of immune infiltration.\nConclusion: Quantitative real-time PCR (qRT-PCR) correlated CAD with the expression of OAS3, ITGAV, and PIBF1. The ICD signature genes are candidate biomarkers and reference standards for immune grouping in CAD and can be beneficial in precise immune-targeted therapy.", "claims": [{"id": "claim-method", "statement": "We used the algorithm in the R package UMAP32 to evaluate the genetic characteristics of patients with CAD and categorize them into different subtypes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38229693", "locator": "sections[6] \"Identification of ICD Subtypes\" paragraph 2", "quote": "We used the algorithm in the R package UMAP32 to evaluate the genetic characteristics of patients with CAD and categorize them into different subtypes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Files, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38229693", "locator": "sections[27] \"Data Sharing Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Files, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After identifying the immune cell death-related differentially expressed genes (IRDEGs), we developed a risk model and detected immune subtypes in CAD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38229693", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "After identifying the immune cell death-related differentially expressed genes (IRDEGs), we developed a risk model and detected immune subtypes in CAD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "After identifying the immune cell death-related differentially expressed genes (IRDEGs), we developed a risk model and detected immune subtypes in CAD.", "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:38229693"], "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:GSE120521"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE120521"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38229693", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S439315", "sha256": "sha256:ad8dd5499020dfef1b347311019c70c957022d6e536389c72cee7fb882cbe120", "bytes": 61242, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JIR.S439315", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10790656", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE120521", "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=GSE120521", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE120521", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Files, 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 Files, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3402504", "GSM3402505", "GSM3402506", "GSM3402507", "GSM3402508", "GSM3402509", "GSM3402510", "GSM3402511"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "RNA-seq of stable and unstable section of human atherosclerotic plaques", "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:GSE12288", "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=GSE12288", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12288", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Files, 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 Files, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM308566", "GSM308567", "GSM308568", "GSM308569", "GSM308570", "GSM308571", "GSM308572", "GSM308573", "GSM308574", "GSM308575", "GSM308576", "GSM308577", "GSM308578", "GSM308579", "GSM308580", "GSM308581", "GSM308582", "GSM308583", "GSM308584", "GSM308585", "GSM308586", "GSM308587", "GSM308588", "GSM308589", "GSM308590", "GSM308591", "GSM308592", "GSM308593", "GSM308594", "GSM308595", "GSM308596", "GSM308597", "GSM308598", "GSM308599", "GSM308600", "GSM308601", "GSM308602", "GSM308603", "GSM308604", "GSM308605", "GSM308606", "GSM308607", "GSM308608", "GSM308609", "GSM308610", "GSM308611", "GSM308612", "GSM308613", "GSM308614", "GSM308615", "GSM308616", "GSM308617", "GSM308618", "GSM308619", "GSM308620", "GSM308621", "GSM308622", "GSM308623", "GSM308624", "GSM308625", "GSM308626", "GSM308627", "GSM308628", "GSM308629", "GSM308630", "GSM308631", "GSM308632", "GSM308633", "GSM308634", "GSM308635", "GSM308636", "GSM308637", "GSM308638", "GSM308639", "GSM308640", "GSM308641", "GSM308642", "GSM308643", "GSM308644", "GSM308645", "GSM308646", "GSM308647", "GSM308648", "GSM308649", "GSM308650", "GSM308651", "GSM308652", "GSM308653", "GSM308654", "GSM308655", "GSM308656", "GSM308657", "GSM308658", "GSM308659", "GSM308660", "GSM308661", "GSM308662", "GSM308663", "GSM308664", "GSM308665", "GSM308666", "GSM308667", "GSM308668", "GSM308669", "GSM308670", "GSM308671", "GSM308672", "GSM308673", "GSM308674", "GSM308675", "GSM308676", "GSM308677", "GSM308678", "GSM308679", "GSM308680", "GSM308681", "GSM308682", "GSM308683", "GSM308684", "GSM308685", "GSM308686", "GSM308687", "GSM308688", "GSM308689", "GSM308690", "GSM308691", "GSM308692", "GSM308693", "GSM308694", "GSM308695", "GSM308696", "GSM308697", "GSM308698", "GSM308699", "GSM308700", "GSM308701", "GSM308702", "GSM308703", "GSM308704", "GSM308705", "GSM308706", "GSM308707", "GSM308708", "GSM308709", "GSM308710", "GSM308711", "GSM308712", "GSM308713", "GSM308714", "GSM308715", "GSM308716", "GSM308717", "GSM308718", "GSM308719", "GSM308720", "GSM308721", "GSM308722", "GSM308723", "GSM308724", "GSM308725", "GSM308726", "GSM308727", "GSM308728", "GSM308729", "GSM308730", "GSM308731", "GSM308732", "GSM308733", "GSM308734", "GSM308735", "GSM308736", "GSM308737", "GSM308738", "GSM308739", "GSM308740", "GSM308741", "GSM308742", "GSM308743", "GSM308744", "GSM308745", "GSM308746", "GSM308747", "GSM308748", "GSM308749", "GSM308750", "GSM308751", "GSM308752", "GSM308753", "GSM308754", "GSM308755", "GSM308756", "GSM308757", "GSM308758", "GSM308759", "GSM308760", "GSM308761", "GSM308762", "GSM308763", "GSM308764", "GSM308765", "GSM308766", "GSM308767", "GSM308768", "GSM308769", "GSM308770", "GSM308771", "GSM308772", "GSM308773", "GSM308774", "GSM308775", "GSM308776", "GSM308777", "GSM308778", "GSM308779", "GSM308780", "GSM308781", "GSM308782", "GSM308783", "GSM308784", "GSM308785", "GSM308786", "GSM308787"], "sample_count": 222, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Gene expression patterns in peripheral blood correlate with the extent of coronary artery disease", "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:GSE71226", "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=GSE71226", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71226", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Files, 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 Files, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1830987", "GSM1830988", "GSM1830989", "GSM1830990", "GSM1830991", "GSM1830992"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from coronary heart disease in Chinese Han people", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE120521 not downloaded", "asset:data:geo:GSE120521 licence not read", "asset:data:geo:GSE12288 not downloaded", "asset:data:geo:GSE12288 licence not read", "asset:data:geo:GSE71226 not downloaded", "asset:data:geo:GSE71226 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-2", "family": null, "specific": null, "label": "Uniform Manifold Approximation and Projection (UMAP)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used the algorithm in the R package UMAP32 to evaluate the genetic characteristics of patients with CAD and categorize them into different subtypes."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE12288", "GSE71226", "GSE120521"], "resolved_accessions": ["GSE12288", "GSE71226", "GSE120521"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Files, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE12288, GSE71226, GSE120521 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": [], "assets": ["source:pmid:38229693", "data:geo:GSE120521"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE120521"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:05:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15422, "completion_tokens": 1576, "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:38229693", "type": "paper", "label": "pmid:38229693"}, {"id": "source:pmid:38229693", "type": "manuscript", "label": "PMID 38229693 full text"}, {"id": "data:geo:GSE120521", "type": "dataset", "label": "GEO GSE120521"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38229693", "type": "paper", "label": "pmid:38229693"}, {"id": "source:pmid:38229693", "type": "manuscript", "label": "PMID 38229693 full text"}, {"id": "data:geo:GSE120521", "type": "dataset", "label": "GEO GSE120521"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38229693", "type": "extraction", "used": ["source:pmid:38229693"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE120521", "type": "accession_resolution", "used": ["data:geo:GSE120521"], "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:38229693", "parent_hash": "sha256:97098d6da0e6ede51ea761eb1b0990ee5953333f0dc667bd6811cc7efe1a3616", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE120521 licence not read", "asset:data:geo:GSE120521 not downloaded", "asset:data:geo:GSE12288 licence not read", "asset:data:geo:GSE12288 not downloaded", "asset:data:geo:GSE71226 licence not read", "asset:data:geo:GSE71226 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "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": 0.93, "evidence": ["ms of adipogenesis, allograft rejection, and apoptosis, as well as the ICD signature and hub gene e", ", hallmark allograft rejection, and hallmark apoptosis were significantly activated in cluster 1 (P"], "order_basis": "paper_text_order:1280", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["mmune infiltration. Conclusion: Quantitative real-time PCR (qRT-PCR) correlated CAD with the expression"], "order_basis": "paper_text_order:1444", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}