A ferroptosis-related signature predicts the clinical diagnosis and prognosis, and associates with the immune microenvironment of lung cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38743344", "kind": "science-record", "revision": 5, "content_hash": "sha256:2a42bc751f39a4ad6afb50844e4544a6f4de7f78e32ce81177dd1942cf99c8b9", "created_at": "2026-11-01T19:20:42Z", "updated_at": "2026-11-01T22:54:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A ferroptosis-related signature predicts the clinical diagnosis and prognosis, and associates with the immune microenvironment of lung cancer.", "doi": "10.1007/s12672-024-01032-x", "pmid": "38743344", "authors": ["Hua Zhou", "Xiaoting Zhou", "Runying Zhu", "Zhongquan Zhao", "Kang Yang", "Zhenghai Shen", "Hongwen Sun"], "journal": "Discover oncology", "year": 2024, "abstract": "Targeting ferroptosis-related pathway is a potential strategy for treatment of lung cancer (LC). Consequently, exploration of ferroptosis-related markers is important for treating LC. We collected LC clinical data and mRNA expression profiles from TCGA and GEO database. Ferroptosis-related genes (FRGs) were obtained through FerrDB database. Expression analysis was performed to obtain differentially expressed FRGs. Diagnostic and prognostic models were constructed based on FRGs by LASSO regression, univariate, and multivariate Cox regression analysis, respectively. External verification cohorts GSE72094 and GSE157011 were used for validation. The interrelationship between prognostic risk scores based on FRGs and the tumor immune microenvironment was analyzed. Immunocytochemistry, Western blotting, and RT-qPCR detected the FRGs level. Eighteen FRGs were used for diagnostic models, 8 FRGs were used for prognostic models. The diagnostic model distinguished well between LC and normal samples in training and validation cohorts of TCGA. The prognostic models for TCGA, GSE72094, and GSE157011 cohorts significantly confirmed lower overall survival (OS) in high-risk group, which demonstrated excellent predictive properties of the survival model. Multivariate Cox regression analysis further confirmed risk score was an independent risk factor related with OS. Immunoassays revealed that in high-risk group, a significantly higher proportion of Macrophages_M0, Neutrophils, resting Natural killer cells and activated Mast cells and the level of B7H3, CD112, CD155, B7H5, and ICOSL were increased. In conclusion, diagnostic and prognostic models provided superior diagnostic and predictive power for LC and revealed a potential link between ferroptosis and TIME.", "claims": [{"id": "claim-method", "statement": "The genes were screened by the least absolute shrinkage and selection operator (LASSO) regression and intersected with univariate Cox regression models, and multivariate Cox regression analysis was carried on intersected genes to build prognostic risk scores of FRGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38743344", "locator": "sections[5] \"Establishment and verification of FRGs prognostic model\" paragraph 2", "quote": "The genes were screened by the least absolute shrinkage and selection operator (LASSO) regression and intersected with univariate Cox regression models, and multivariate Cox regression analysis was carried on intersected genes to build prognostic risk scores of FRGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38743344", "locator": "sections[29] \"notes\" paragraph 1", "quote": "The datasets supporting the conclusions of this article are included within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The ferroptosis-related prognostic risk score was associated with significantly shorter overall survival in the high-risk group (P = 2.3e-10, HR = 1.89, 95% CI 1.55–2.3).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The results demonstrated that, compared with the low-risk group, OS was statistically dwindled in the high-risk group (Fig. 4A; P = 2.3e-10, HR = 1.89, 95% CI 1.55–2.3)."}, "evidence": [{"asset": "source:pmid:38743344", "locator": "sections[16] \"Evaluating prognostic risk scores associated with ferroptosis\" paragraph 2", "quote": "The results demonstrated that, compared with the low-risk group, OS was statistically dwindled in the high-risk group (Fig. 4A; P = 2.3e-10, HR = 1.89, 95% CI 1.55–2.3)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The ferroptosis-related prognostic risk score was associated with significantly shorter overall survival in the high-risk group (P = 2.3e-10, HR = 1.89, 95% CI 1.55–2.3).", "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:38743344"], "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:GSE157011"], "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:GSE157011"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38743344", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-024-01032-x", "sha256": "sha256:ba32e194a7a6b28dd7803a7cb467629f2e2e0871b3c3e058247a6de090f7bbd2", "bytes": 42980, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-024-01032-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11093956", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE157011", "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=GSE157011", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE157011", "version": null, "note": "The datasets supporting the conclusions of this article are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusions of this article are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4750372", "GSM4750373", "GSM4750374", "GSM4750375", "GSM4750376", "GSM4750377", "GSM4750378", "GSM4750379", "GSM4750380", "GSM4750381", "GSM4750382", "GSM4750383", "GSM4750384", "GSM4750385", "GSM4750386", "GSM4750387", "GSM4750388", "GSM4750389", "GSM4750390", "GSM4750391", "GSM4750392", "GSM4750393", "GSM4750394", "GSM4750395", "GSM4750396", "GSM4750397", "GSM4750398", "GSM4750399", "GSM4750400", "GSM4750401", "GSM4750402", "GSM4750403", "GSM4750404", "GSM4750405", "GSM4750406", "GSM4750407", "GSM4750408", "GSM4750409", "GSM4750410", "GSM4750411", "GSM4750412", "GSM4750413", "GSM4750414", "GSM4750415", "GSM4750416", "GSM4750417", "GSM4750418", "GSM4750419", "GSM4750420", "GSM4750421", "GSM4750422", "GSM4750423", "GSM4750424", "GSM4750425", "GSM4750426", "GSM4750427", "GSM4750428", "GSM4750429", "GSM4750430", "GSM4750431", "GSM4750432", "GSM4750433", "GSM4750434", "GSM4750435", "GSM4750436", "GSM4750437", "GSM4750438", "GSM4750439", "GSM4750440", "GSM4750441", "GSM4750442", "GSM4750443", "GSM4750444", "GSM4750445", "GSM4750446", "GSM4750447", "GSM4750448", "GSM4750449", "GSM4750450", "GSM4750451", "GSM4750452", "GSM4750453", "GSM4750454", "GSM4750455", "GSM4750456", "GSM4750457", "GSM4750458", "GSM4750459", "GSM4750460", "GSM4750461", "GSM4750462", "GSM4750463", "GSM4750464", "GSM4750465", "GSM4750466", "GSM4750467", "GSM4750468", "GSM4750469", "GSM4750470", "GSM4750471", "GSM4750472", "GSM4750473", "GSM4750474", "GSM4750475", "GSM4750476", "GSM4750477", "GSM4750478", "GSM4750479", "GSM4750480", "GSM4750481", "GSM4750482", "GSM4750483", "GSM4750484", "GSM4750485", "GSM4750486", "GSM4750487", "GSM4750488", "GSM4750489", "GSM4750490", "GSM4750491", "GSM4750492", "GSM4750493", "GSM4750494", "GSM4750495", "GSM4750496", "GSM4750497", "GSM4750498", "GSM4750499", "GSM4750500", "GSM4750501", "GSM4750502", "GSM4750503", "GSM4750504", "GSM4750505", "GSM4750506", "GSM4750507", "GSM4750508", "GSM4750509", "GSM4750510", "GSM4750511", "GSM4750512", "GSM4750513", "GSM4750514", "GSM4750515", "GSM4750516", "GSM4750517", "GSM4750518", "GSM4750519", "GSM4750520", "GSM4750521", "GSM4750522", "GSM4750523", "GSM4750524", "GSM4750525", "GSM4750526", "GSM4750527", "GSM4750528", "GSM4750529", "GSM4750530", "GSM4750531", "GSM4750532", "GSM4750533", "GSM4750534", "GSM4750535", "GSM4750536", "GSM4750537", "GSM4750538", "GSM4750539", "GSM4750540", "GSM4750541", "GSM4750542", "GSM4750543", "GSM4750544", "GSM4750545", "GSM4750546", "GSM4750547", "GSM4750548", "GSM4750549", "GSM4750550", "GSM4750551", "GSM4750552", "GSM4750553", "GSM4750554", "GSM4750555", "GSM4750556", "GSM4750557", "GSM4750558", "GSM4750559", "GSM4750560", "GSM4750561", "GSM4750562", "GSM4750563", "GSM4750564", "GSM4750565", "GSM4750566", "GSM4750567", "GSM4750568", "GSM4750569", "GSM4750570", "GSM4750571", "GSM4750572", "GSM4750573", "GSM4750574", "GSM4750575", "GSM4750576", "GSM4750577", "GSM4750578", "GSM4750579", "GSM4750580", "GSM4750581", "GSM4750582", "GSM4750583", "GSM4750584", "GSM4750585", "GSM4750586", "GSM4750587", "GSM4750588", "GSM4750589", "GSM4750590", "GSM4750591", "GSM4750592", "GSM4750593", "GSM4750594", "GSM4750595", "GSM4750596", "GSM4750597", "GSM4750598", "GSM4750599", "GSM4750600", "GSM4750601", "GSM4750602", "GSM4750603", "GSM4750604", "GSM4750605", "GSM4750606", "GSM4750607", "GSM4750608", "GSM4750609", "GSM4750610", "GSM4750611", "GSM4750612", "GSM4750613", "GSM4750614", "GSM4750615", "GSM4750616", "GSM4750617", "GSM4750618", "GSM4750619", "GSM4750620", "GSM4750621", "GSM4750622", "GSM4750623", "GSM4750624", "GSM4750625", "GSM4750626", "GSM4750627", "GSM4750628", "GSM4750629", "GSM4750630", "GSM4750631", "GSM4750632", "GSM4750633", "GSM4750634", "GSM4750635", "GSM4750636", "GSM4750637", "GSM4750638", "GSM4750639", "GSM4750640", "GSM4750641", "GSM4750642", "GSM4750643", "GSM4750644", "GSM4750645", "GSM4750646", "GSM4750647", "GSM4750648", "GSM4750649", "GSM4750650", "GSM4750651", "GSM4750652", "GSM4750653", "GSM4750654", "GSM4750655", "GSM4750656", "GSM4750657", "GSM4750658", "GSM4750659", "GSM4750660", "GSM4750661", "GSM4750662", "GSM4750663", "GSM4750664", "GSM4750665", "GSM4750666", "GSM4750667", "GSM4750668", "GSM4750669", "GSM4750670", "GSM4750671", "GSM4750672", "GSM4750673", "GSM4750674", "GSM4750675", "GSM4750676", "GSM4750677", "GSM4750678", "GSM4750679", "GSM4750680", "GSM4750681", "GSM4750682", "GSM4750683", "GSM4750684", "GSM4750685", "GSM4750686", "GSM4750687", "GSM4750688", "GSM4750689", "GSM4750690", "GSM4750691", "GSM4750692", "GSM4750693", "GSM4750694", "GSM4750695", "GSM4750696", "GSM4750697", "GSM4750698", "GSM4750699", "GSM4750700", "GSM4750701", "GSM4750702", "GSM4750703", "GSM4750704", "GSM4750705", "GSM4750706", "GSM4750707", "GSM4750708", "GSM4750709", "GSM4750710", "GSM4750711", "GSM4750712", "GSM4750713", "GSM4750714", "GSM4750715", "GSM4750716", "GSM4750717", "GSM4750718", "GSM4750719", "GSM4750720", "GSM4750721", "GSM4750722", "GSM4750723", "GSM4750724", "GSM4750725", "GSM4750726", "GSM4750727", "GSM4750728", "GSM4750729", "GSM4750730", "GSM4750731", "GSM4750732", "GSM4750733", "GSM4750734", "GSM4750735", "GSM4750736", "GSM4750737", "GSM4750738", "GSM4750739", "GSM4750740", "GSM4750741", "GSM4750742", "GSM4750743", "GSM4750744", "GSM4750745", "GSM4750746", "GSM4750747", "GSM4750748", "GSM4750749", "GSM4750750", "GSM4750751", "GSM4750752", "GSM4750753", "GSM4750754", "GSM4750755", "GSM4750756", "GSM4750757", "GSM4750758", "GSM4750759", "GSM4750760", "GSM4750761", "GSM4750762", "GSM4750763", "GSM4750764", "GSM4750765", "GSM4750766", "GSM4750767", "GSM4750768", "GSM4750769", "GSM4750770", "GSM4750771", "GSM4750772", "GSM4750773", "GSM4750774", "GSM4750775", "GSM4750776", "GSM4750777", "GSM4750778", "GSM4750779", "GSM4750780", "GSM4750781", "GSM4750782", "GSM4750783", "GSM4750784", "GSM4750785", "GSM4750786", "GSM4750787", "GSM4750788", "GSM4750789", "GSM4750790", "GSM4750791", "GSM4750792", "GSM4750793", "GSM4750794", "GSM4750795", "GSM4750796", "GSM4750797", "GSM4750798", "GSM4750799", "GSM4750800", "GSM4750801", "GSM4750802", "GSM4750803", "GSM4750804", "GSM4750805", "GSM4750806", "GSM4750807", "GSM4750808", "GSM4750809", "GSM4750810", "GSM4750811", "GSM4750812", "GSM4750813", "GSM4750814", "GSM4750815", "GSM4750816", "GSM4750817", "GSM4750818", "GSM4750819", "GSM4750820", "GSM4750821", "GSM4750822", "GSM4750823", "GSM4750824", "GSM4750825", "GSM4750826", "GSM4750827", "GSM4750828", "GSM4750829", "GSM4750830", "GSM4750831", "GSM4750832", "GSM4750833", "GSM4750834", "GSM4750835", "GSM4750836", "GSM4750837", "GSM4750838", "GSM4750839", "GSM4750840", "GSM4750841", "GSM4750842", "GSM4750843", "GSM4750844", "GSM4750845", "GSM4750846", "GSM4750847", "GSM4750848", "GSM4750849", "GSM4750850", "GSM4750851", "GSM4750852", "GSM4750853", "GSM4750854", "GSM4750855"], "sample_count": 484, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Multi-institutional prospective validation of prognostic mRNA signatures in early stage squamous lung cancer (Alliance)", "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:GSE72094", "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=GSE72094", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72094", "version": null, "note": "The datasets supporting the conclusions of this article are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusions of this article are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1854797", "GSM1854798", "GSM1854799", "GSM1854800", "GSM1854801", "GSM1854802", "GSM1854803", "GSM1854804", "GSM1854805", "GSM1854806", "GSM1854807", "GSM1854808", "GSM1854809", "GSM1854810", "GSM1854811", "GSM1854812", "GSM1854813", "GSM1854814", "GSM1854815", "GSM1854816", "GSM1854817", "GSM1854818", "GSM1854819", "GSM1854820", "GSM1854821", "GSM1854822", "GSM1854823", "GSM1854824", "GSM1854825", "GSM1854826", "GSM1854827", "GSM1854828", "GSM1854829", "GSM1854830", "GSM1854831", "GSM1854832", "GSM1854833", "GSM1854834", "GSM1854835", "GSM1854836", "GSM1854837", "GSM1854838", "GSM1854839", "GSM1854840", "GSM1854841", "GSM1854842", "GSM1854843", "GSM1854844", "GSM1854845", "GSM1854846", "GSM1854847", "GSM1854848", "GSM1854849", "GSM1854850", "GSM1854851", "GSM1854852", "GSM1854853", "GSM1854854", "GSM1854855", "GSM1854856", "GSM1854857", "GSM1854858", "GSM1854859", "GSM1854860", "GSM1854861", "GSM1854862", "GSM1854863", "GSM1854864", "GSM1854865", "GSM1854866", "GSM1854867", "GSM1854868", "GSM1854869", "GSM1854870", "GSM1854871", "GSM1854872", "GSM1854873", "GSM1854874", "GSM1854875", "GSM1854876", "GSM1854877", "GSM1854878", "GSM1854879", "GSM1854880", "GSM1854881", "GSM1854882", "GSM1854883", "GSM1854884", "GSM1854885", "GSM1854886", "GSM1854887", "GSM1854888", "GSM1854889", "GSM1854890", "GSM1854891", "GSM1854892", "GSM1854893", "GSM1854894", "GSM1854895", "GSM1854896", "GSM1854897", "GSM1854898", "GSM1854899", "GSM1854900", "GSM1854901", "GSM1854902", "GSM1854903", "GSM1854904", "GSM1854905", "GSM1854906", "GSM1854907", "GSM1854908", "GSM1854909", "GSM1854910", "GSM1854911", "GSM1854912", "GSM1854913", "GSM1854914", "GSM1854915", "GSM1854916", "GSM1854917", "GSM1854918", "GSM1854919", "GSM1854920", "GSM1854921", "GSM1854922", "GSM1854923", "GSM1854924", "GSM1854925", "GSM1854926", "GSM1854927", "GSM1854928", "GSM1854929", "GSM1854930", "GSM1854931", "GSM1854932", "GSM1854933", "GSM1854934", "GSM1854935", "GSM1854936", "GSM1854937", "GSM1854938", "GSM1854939", "GSM1854940", "GSM1854941", "GSM1854942", "GSM1854943", "GSM1854944", "GSM1854945", "GSM1854946", "GSM1854947", "GSM1854948", "GSM1854949", "GSM1854950", "GSM1854951", "GSM1854952", "GSM1854953", "GSM1854954", "GSM1854955", "GSM1854956", "GSM1854957", "GSM1854958", "GSM1854959", "GSM1854960", "GSM1854961", "GSM1854962", "GSM1854963", "GSM1854964", "GSM1854965", "GSM1854966", "GSM1854967", "GSM1854968", "GSM1854969", "GSM1854970", "GSM1854971", "GSM1854972", "GSM1854973", "GSM1854974", "GSM1854975", "GSM1854976", "GSM1854977", "GSM1854978", "GSM1854979", "GSM1854980", "GSM1854981", "GSM1854982", "GSM1854983", "GSM1854984", "GSM1854985", "GSM1854986", "GSM1854987", "GSM1854988", "GSM1854989", "GSM1854990", "GSM1854991", "GSM1854992", "GSM1854993", "GSM1854994", "GSM1854995", "GSM1854996", "GSM1854997", "GSM1854998", "GSM1854999", "GSM1855000", "GSM1855001", "GSM1855002", "GSM1855003", "GSM1855004", "GSM1855005", "GSM1855006", "GSM1855007", "GSM1855008", "GSM1855009", "GSM1855010", "GSM1855011", "GSM1855012", "GSM1855013", "GSM1855014", "GSM1855015", "GSM1855016", "GSM1855017", "GSM1855018", "GSM1855019", "GSM1855020", "GSM1855021", "GSM1855022", "GSM1855023", "GSM1855024", "GSM1855025", "GSM1855026", "GSM1855027", "GSM1855028", "GSM1855029", "GSM1855030", "GSM1855031", "GSM1855032", "GSM1855033", "GSM1855034", "GSM1855035", "GSM1855036", "GSM1855037", "GSM1855038", "GSM1855039", "GSM1855040", "GSM1855041", "GSM1855042", "GSM1855043", "GSM1855044", "GSM1855045", "GSM1855046", "GSM1855047", "GSM1855048", "GSM1855049", "GSM1855050", "GSM1855051", "GSM1855052", "GSM1855053", "GSM1855054", "GSM1855055", "GSM1855056", "GSM1855057", "GSM1855058", "GSM1855059", "GSM1855060", "GSM1855061", "GSM1855062", "GSM1855063", "GSM1855064", "GSM1855065", "GSM1855066", "GSM1855067", "GSM1855068", "GSM1855069", "GSM1855070", "GSM1855071", "GSM1855072", "GSM1855073", "GSM1855074", "GSM1855075", "GSM1855076", "GSM1855077", "GSM1855078", "GSM1855079", "GSM1855080", "GSM1855081", "GSM1855082", "GSM1855083", "GSM1855084", "GSM1855085", "GSM1855086", "GSM1855087", "GSM1855088", "GSM1855089", "GSM1855090", "GSM1855091", "GSM1855092", "GSM1855093", "GSM1855094", "GSM1855095", "GSM1855096", "GSM1855097", "GSM1855098", "GSM1855099", "GSM1855100", "GSM1855101", "GSM1855102", "GSM1855103", "GSM1855104", "GSM1855105", "GSM1855106", "GSM1855107", "GSM1855108", "GSM1855109", "GSM1855110", "GSM1855111", "GSM1855112", "GSM1855113", "GSM1855114", "GSM1855115", "GSM1855116", "GSM1855117", "GSM1855118", "GSM1855119", "GSM1855120", "GSM1855121", "GSM1855122", "GSM1855123", "GSM1855124", "GSM1855125", "GSM1855126", "GSM1855127", "GSM1855128", "GSM1855129", "GSM1855130", "GSM1855131", "GSM1855132", "GSM1855133", "GSM1855134", "GSM1855135", "GSM1855136", "GSM1855137", "GSM1855138", "GSM1855139", "GSM1855140", "GSM1855141", "GSM1855142", "GSM1855143", "GSM1855144", "GSM1855145", "GSM1855146", "GSM1855147", "GSM1855148", "GSM1855149", "GSM1855150", "GSM1855151", "GSM1855152", "GSM1855153", "GSM1855154", "GSM1855155", "GSM1855156", "GSM1855157", "GSM1855158", "GSM1855159", "GSM1855160", "GSM1855161", "GSM1855162", "GSM1855163", "GSM1855164", "GSM1855165", "GSM1855166", "GSM1855167", "GSM1855168", "GSM1855169", "GSM1855170", "GSM1855171", "GSM1855172", "GSM1855173", "GSM1855174", "GSM1855175", "GSM1855176", "GSM1855177", "GSM1855178", "GSM1855179", "GSM1855180", "GSM1855181", "GSM1855182", "GSM1855183", "GSM1855184", "GSM1855185", "GSM1855186", "GSM1855187", "GSM1855188", "GSM1855189", "GSM1855190", "GSM1855191", "GSM1855192", "GSM1855193", "GSM1855194", "GSM1855195", "GSM1855196", "GSM1855197", "GSM1855198", "GSM1855199", "GSM1855200", "GSM1855201", "GSM1855202", "GSM1855203", "GSM1855204", "GSM1855205", "GSM1855206", "GSM1855207", "GSM1855208", "GSM1855209", "GSM1855210", "GSM1855211", "GSM1855212", "GSM1855213", "GSM1855214", "GSM1855215", "GSM1855216", "GSM1855217", "GSM1855218", "GSM1855219", "GSM1855220", "GSM1855221", "GSM1855222", "GSM1855223", "GSM1855224", "GSM1855225", "GSM1855226", "GSM1855227", "GSM1855228", "GSM1855229", "GSM1855230", "GSM1855231", "GSM1855232", "GSM1855233", "GSM1855234", "GSM1855235", "GSM1855236", "GSM1855237", "GSM1855238"], "sample_count": 442, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "KRAS mutation-associated gene expression, p53 and STK11 mutations, proliferation and immune surveillance in lung adenocarcinoma", "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:GSE157011 not downloaded", "asset:data:geo:GSE157011 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:GSE72094 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The genes were screened by the least absolute shrinkage and selection operator (LASSO) regression and intersected with univariate Cox regression models, and multivariate Cox regression analysis was carried on intersected genes to build prognostic risk scores of FRGs."}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Log-rank"}}, {"id": "method-3", "family": "differential_expression", "specific": "deseq2", "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": 0.8, "band": "high", "quote": "Deseq2"}}, {"id": "method-4", "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": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-5", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-6", "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": 0.8, "band": "high", "quote": "ROC curve"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "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-hazard-ratio", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 1.89, "unit": "hazard ratio", "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": "classification_metrics", "expected_value": 2.0, "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": ["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": ["GSE72094", "GSE157011"], "resolved_accessions": ["GSE72094", "GSE157011"], "statements": ["The datasets supporting the conclusions of this article are included within the article."], "basis": "The paper names GSE72094, GSE157011 in 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:38743344", "data:geo:GSE157011"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE157011"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:18:32Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12378, "completion_tokens": 2944, "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:38743344", "type": "paper", "label": "pmid:38743344"}, {"id": "source:pmid:38743344", "type": "manuscript", "label": "PMID 38743344 full text"}, {"id": "data:geo:GSE157011", "type": "dataset", "label": "GEO GSE157011"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38743344", "type": "paper", "label": "pmid:38743344"}, {"id": "source:pmid:38743344", "type": "manuscript", "label": "PMID 38743344 full text"}, {"id": "data:geo:GSE157011", "type": "dataset", "label": "GEO GSE157011"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38743344", "type": "extraction", "used": ["source:pmid:38743344"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE157011", "type": "accession_resolution", "used": ["data:geo:GSE157011"], "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:38743344", "parent_hash": "sha256:b05750113d9580c6396804b927eb839e35e6a81e2492fa19d3685a4eb930f00d", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE157011 licence not read", "asset:data:geo:GSE157011 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE72094 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["vironment was analyzed. Immunocytochemistry, Western blotting, and RT-qPCR detected the FRGs level. Eighte"], "order_basis": "paper_text_order:888", "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": 0.99, "evidence": [". Immunocytochemistry, Western blotting, and RT-qPCR detected the FRGs level. Eighteen FRGs were", "mmunocytochemistry, Western blotting, and RT-qPCR detected the FRGs level. Eighteen FRGs were"], "order_basis": "paper_text_order:910", "id": "assay:2"}, {"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": ["The genes were screened by the least absolute shrinkage and selection operator (LASSO) regression and intersected with univariate Cox regression models, and multivariate Cox regression analysis was carried on intersected genes to build prognostic risk scores of FRGs."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}