Development and validation of an immune-related gene signature for prognosis in Lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36728032", "kind": "science-record", "revision": 3, "content_hash": "sha256:59cc1984b837b38a7427c81d2475020375831069eb5e7cc9c0174b9587b7bbb7", "created_at": "2026-11-01T19:01:17Z", "updated_at": "2026-11-01T22:08:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and validation of an immune-related gene signature for prognosis in Lung adenocarcinoma.", "doi": "10.1049/syb2.12057", "pmid": "36728032", "authors": ["Zehuai Guo", "Xiangjun Qi", "Zeyun Li", "Jianying Yang", "Zhe Sun", "Peiqin Li", "Ming Chen", "Yang Cao"], "journal": "IET systems biology", "year": 2023, "abstract": "The most common type of lung cancer tissue is lung adenocarcinoma. The TCGA-LUAD cohort retrieved from the TCGA dataset was considered the internal training cohort, while GSE68465 and GSE13213 datasets from the GEO database were used as the external test cohort. The TCGA-LUAD cohort was classified into two immune subtypes using single-sample gene set enrichment analysis of the immune gene set and unsupervised clustering analysis. The ESTIMATE algorithm, the CIBERSORT algorithm, and HLA family expression levels again validated the reliability of this typing. We performed Venn analysis using immune-related genes from the immport dataset and differentially expressed genes from the subtypes to retrieve differentially expressed immune genes (DEIGs). In addition, DEIGs were used to construct a prognostic model with the least absolute shrinkage and selection operator regression analysis. A reliable risk model consisting of 11 DEIGs, including S100P, INHA, SEMA7A, INSL4, CD40LG, AGER, SERPIND1, CD1D, CX3CR1, SFTPD, and CD79A, was then built, and its reliability was further confirmed by ROC curve and calibration plot analysis. The high-risk score subgroup had a poor prognosis and a lower tumour immune dysfunction and exclusion score, indicating a greater likelihood of anti-PD-1/cytotoxic T lymphocyte antigen 4 benefit.", "claims": [{"id": "claim-method", "statement": "Premised on p < 0.01, univariate Cox regression analysis revealed 37 genes in the training cohort (Figure 4c). Following that, the LASSO Cox regression method was executed (Figure 4d,e).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36728032", "locator": "sections[14] \"Prognosis models of DEIGs\" paragraph 2", "quote": "Premised on p < 0.01, univariate Cox regression analysis revealed 37 genes in the training cohort (Figure 4c). Following that, the LASSO Cox regression method was executed (Figure 4d,e)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are openly available in NCBI Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, The Cancer Genome Atlas Program at https://portal.gdc.cancer.gov/repository, and ImmPort Portal database at https://www.immport.org/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36728032", "locator": "sections[26] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data that support the findings of this study are openly available in NCBI Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, The Cancer Genome Atlas Program at https://portal.gdc.cancer.gov/repository, and ImmPort Portal database at https://www.immport.org/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A reliable risk model consisting of 11 DEIGs, including S100P, INHA, SEMA7A, INSL4, CD40LG, AGER, SERPIND1, CD1D, CX3CR1, SFTPD, and CD79A, was then built, and its reliability was further confirmed by ROC curve and calibration plot analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36728032", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A reliable risk model consisting of 11 DEIGs, including S100P, INHA, SEMA7A, INSL4, CD40LG, AGER, SERPIND1, CD1D, CX3CR1, SFTPD, and CD79A, was then built, and its reliability was further confirmed by ROC curve and calibration plot analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A reliable risk model consisting of 11 DEIGs, including S100P, INHA, SEMA7A, INSL4, CD40LG, AGER, SERPIND1, CD1D, CX3CR1, SFTPD, and CD79A, was then built, and its reliability was further confirmed by ROC curve and calibration plot analysis.", "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:36728032"], "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. 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Following that, the LASSO Cox regression method was executed (Figure 4d,e)."}}, {"id": "method-2", "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"}}], "targets": [], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE68465", "GSE13213"], "resolved_accessions": ["GSE68465", "GSE13213"], "statements": ["The data that support the findings of this study are openly available in NCBI Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, The Cancer Genome Atlas Program at https://portal.gdc.cancer.gov/repository, and ImmPort Portal database at https://www.immport.org/."], "basis": "The paper names GSE68465, GSE13213 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:36728032", "data:geo:GSE13213"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13213"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:25:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12168, "completion_tokens": 1749, "cached_tokens": 128}}, "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:36728032", "type": "paper", "label": "pmid:36728032"}, {"id": "source:pmid:36728032", "type": "manuscript", "label": "PMID 36728032 full text"}, {"id": "data:geo:GSE13213", "type": "dataset", "label": "GEO GSE13213"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36728032", "type": "paper", "label": "pmid:36728032"}, {"id": "source:pmid:36728032", "type": "manuscript", "label": "PMID 36728032 full text"}, {"id": "data:geo:GSE13213", "type": "dataset", "label": "GEO GSE13213"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36728032", "type": "extraction", "used": ["source:pmid:36728032"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13213", "type": "accession_resolution", "used": ["data:geo:GSE13213"], "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:36728032", "parent_hash": "sha256:8c4765a1310354eb593b1fb8a032255902d561fa5a3757cc62c92306922f9c10", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE13213 licence not read", "asset:data:geo:GSE13213 not downloaded", "asset:data:geo:GSE68465 licence not read", "asset:data:geo:GSE68465 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Premised on p < 0.01, univariate Cox regression analysis revealed 37 genes in the training cohort (Figure 4c). Following that, the LASSO Cox regression method was executed (Figure 4d,e)."], "order_basis": "analysis_only", "id": "assay:1"}]}