{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34422970", "kind": "science-record", "revision": 8, "content_hash": "sha256:86bbfc6b932970ecdb3eb4fae8853b2cf889649534991c0dc227f11e94e86337", "created_at": "2026-11-01T15:41:49Z", "updated_at": "2026-11-01T22:04:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic and immune implications of a novel ferroptosis-related ten-gene signature in lung adenocarcinoma.", "doi": "10.21037/atm-20-7936", "pmid": "34422970", "authors": ["Chao Ma", "Feng Li", "Huan Luo"], "journal": "Annals of translational medicine", "year": 2021, "abstract": "BACKGROUND: Lung cancer has been the focus of attention for many researchers in recent years due to its leading contribution to cancer-related death worldwide, with lung adenocarcinoma (LUAD) being the most common histological type. Ferroptosis, a novel iron-dependent form of regulated cell death, can be induced by sorafenib. Emerging evidence shows that triggering ferroptosis has potential as a cancer therapy. This work aimed to build a ferroptosis-related gene signature for predicting the outcome of LUAD.\nMETHODS: The TCGA-LUAD dataset was set as the training cohort, and the GSE72094 and GSE68465 datasets were set as the validation cohorts. Sixty-two ferroptosis-related genes were retrieved from the literature. A univariate Cox regression model was constructed for the training cohort to preliminarily screen for potential prognostic ferroptosis-related genes. A gene signature was generated from a LASSO Cox regression model and assessed with the training and validation cohorts through Kaplan-Meier, Cox, and ROC analyses. In addition, the correlation between the risk score and autophagy-related genes was determined by the Pearson test. Finally, GSEA and immune infiltrating analyses were performed to better study the functional annotation of the signature and the role of each kind of immune cell.\nRESULTS: A ten-gene signature was constructed from the training cohort and validated in three cohorts by Kaplan-Meier and Cox regression analyses, revealing its independent prognostic value in LUAD. Moreover, a ROC analysis conducted with all cohort data confirmed the predictive ability of the ten-gene signature for LUAD prognosis. A total of 62.85% (308/490) of autophagy-related genes were found to be significantly correlated with risk scores. GSEA detailed the exact pathways related to the gene signature, and immune-infiltrating analyses identified crucial roles for resting mast cells and resting dendritic cells in the prognosis of LUAD.\nCONCLUSIONS: We identified a novel ferroptosis-related ten-gene signature (PHKG2, PGD, PEBP1, NCOA4, GLS2, CISD1, ATP5G3, ALOX15, ALOX12B, and ACSL3) that can accurately predict LUAD prognosis and is closely linked to resting mast cells and resting dendritic cells.", "claims": [{"id": "claim-data-access", "statement": "The TCGA-LUAD dataset was chosen as the training cohort and downloaded from the GDC Xena Hub (https://gdc.xenahubs.net). Five hundred patients with LUAD in the TCGA-LUAD dataset who had both gene expression and survival data available were included in our research.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34422970", "locator": "sections[3] \"Cohorts and ferroptosis-related genes\" paragraph 2", "quote": "The TCGA-LUAD dataset was chosen as the training cohort and downloaded from the GDC Xena Hub (https://gdc.xenahubs.net). Five hundred patients with LUAD in the TCGA-LUAD dataset who had both gene expression and survival data available were included in our research."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34422970"], "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:GSE68465"], "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:GSE68465"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34422970", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-20-7936", "sha256": "sha256:e7a68e5752a4517e78a6fce76ead1e5a37d230abd307fe575bf288c108d6382f", "bytes": 38851, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm-20-7936", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8339871", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE68465", "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=GSE68465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68465", "version": null, "note": "The TCGA-LUAD dataset was chosen as the training cohort and downloaded from the GDC Xena Hub (https://gdc.xenahubs.net). Five hundred patients with LUAD in the TCGA-LUAD dataset who had both gene expression and survival data available were included in our research.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The TCGA-LUAD dataset was chosen as the training cohort and downloaded from the GDC Xena Hub (https://gdc.xenahubs.net). Five hundred patients with LUAD in the TCGA-LUAD dataset who had both gene expression and survival data available were included in our research.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1672281", "GSM1672282", "GSM1672283", "GSM1672284", "GSM1672285", "GSM1672286", "GSM1672287", "GSM1672288", "GSM1672289", "GSM1672290", "GSM1672291", "GSM1672292", "GSM1672293", "GSM1672294", "GSM1672295", "GSM1672296", "GSM1672297", "GSM1672298", "GSM1672299", "GSM1672300", "GSM1672301", "GSM1672302", "GSM1672303", "GSM1672304", "GSM1672305", "GSM1672306", "GSM1672307", "GSM1672308", "GSM1672309", "GSM1672310", "GSM1672311", "GSM1672312", "GSM1672313", "GSM1672314", "GSM1672315", "GSM1672316", "GSM1672317", "GSM1672318", "GSM1672319", "GSM1672320", "GSM1672321", "GSM1672322", "GSM1672323", "GSM1672324", "GSM1672325", "GSM1672326", "GSM1672327", "GSM1672328", "GSM1672329", "GSM1672330", "GSM1672331", "GSM1672332", "GSM1672333", "GSM1672334", "GSM1672335", "GSM1672336", "GSM1672337", "GSM1672338", "GSM1672339", "GSM1672340", "GSM1672341", "GSM1672342", "GSM1672343", "GSM1672344", "GSM1672345", "GSM1672346", "GSM1672347", "GSM1672348", "GSM1672349", "GSM1672350", "GSM1672351", "GSM1672352", "GSM1672353", "GSM1672354", "GSM1672355", "GSM1672356", "GSM1672357", "GSM1672358", "GSM1672359", "GSM1672360", "GSM1672361", "GSM1672362", "GSM1672363", "GSM1672364", "GSM1672365", "GSM1672366", "GSM1672367", "GSM1672368", "GSM1672369", "GSM1672370", "GSM1672371", "GSM1672372", "GSM1672373", "GSM1672374", "GSM1672375", "GSM1672376", "GSM1672377", "GSM1672378", "GSM1672379", "GSM1672380", "GSM1672381", "GSM1672382", "GSM1672383", "GSM1672384", "GSM1672385", "GSM1672386", "GSM1672387", "GSM1672388", "GSM1672389", "GSM1672390", "GSM1672391", "GSM1672392", "GSM1672393", "GSM1672394", "GSM1672395", "GSM1672396", "GSM1672397", "GSM1672398", "GSM1672399", "GSM1672400", "GSM1672401", "GSM1672402", "GSM1672403", "GSM1672404", "GSM1672405", "GSM1672406", "GSM1672407", "GSM1672408", "GSM1672409", "GSM1672410", "GSM1672411", "GSM1672412", "GSM1672413", "GSM1672414", "GSM1672415", "GSM1672416", "GSM1672417", "GSM1672418", "GSM1672419", "GSM1672420", "GSM1672421", "GSM1672422", "GSM1672423", "GSM1672424", "GSM1672425", "GSM1672426", "GSM1672427", "GSM1672428", "GSM1672429", "GSM1672430", "GSM1672431", "GSM1672432", "GSM1672433", "GSM1672434", "GSM1672435", "GSM1672436", "GSM1672437", "GSM1672438", "GSM1672439", "GSM1672440", "GSM1672441", "GSM1672442", "GSM1672443", "GSM1672444", "GSM1672445", "GSM1672446", "GSM1672447", "GSM1672448", "GSM1672449", "GSM1672450", "GSM1672451", "GSM1672452", "GSM1672453", "GSM1672454", "GSM1672455", "GSM1672456", "GSM1672457", "GSM1672458", "GSM1672459", "GSM1672460", "GSM1672461", "GSM1672462", "GSM1672463", "GSM1672464", "GSM1672465", "GSM1672466", "GSM1672467", "GSM1672468", "GSM1672469", "GSM1672470", "GSM1672471", "GSM1672472", "GSM1672473", "GSM1672474", "GSM1672475", "GSM1672476", "GSM1672477", "GSM1672478", "GSM1672479", "GSM1672480", "GSM1672481", "GSM1672482", "GSM1672483", "GSM1672484", "GSM1672485", "GSM1672486", "GSM1672487", "GSM1672488", "GSM1672489", "GSM1672490", "GSM1672491", "GSM1672492", "GSM1672493", "GSM1672494", "GSM1672495", "GSM1672496", "GSM1672497", "GSM1672498", "GSM1672499", "GSM1672500", "GSM1672501", "GSM1672502", "GSM1672503", "GSM1672504", "GSM1672505", "GSM1672506", "GSM1672507", "GSM1672508", "GSM1672509", "GSM1672510", "GSM1672511", "GSM1672512", "GSM1672513", "GSM1672514", "GSM1672515", "GSM1672516", "GSM1672517", "GSM1672518", "GSM1672519", "GSM1672520", "GSM1672521", "GSM1672522", "GSM1672523", "GSM1672524", "GSM1672525", "GSM1672526", "GSM1672527", "GSM1672528", "GSM1672529", "GSM1672530", "GSM1672531", "GSM1672532", "GSM1672533", "GSM1672534", "GSM1672535", "GSM1672536", "GSM1672537", "GSM1672538", "GSM1672539", "GSM1672540", "GSM1672541", "GSM1672542", "GSM1672543", "GSM1672544", "GSM1672545", "GSM1672546", "GSM1672547", "GSM1672548", "GSM1672549", "GSM1672550", "GSM1672551", "GSM1672552", "GSM1672553", "GSM1672554", "GSM1672555", "GSM1672556", "GSM1672557", "GSM1672558", "GSM1672559", "GSM1672560", "GSM1672561", "GSM1672562", "GSM1672563", "GSM1672564", "GSM1672565", "GSM1672566", "GSM1672567", "GSM1672568", "GSM1672569", "GSM1672570", "GSM1672571", "GSM1672572", "GSM1672573", "GSM1672574", "GSM1672575", "GSM1672576", "GSM1672577", "GSM1672578", "GSM1672579", "GSM1672580", "GSM1672581", "GSM1672582", "GSM1672583", "GSM1672584", "GSM1672585", "GSM1672586", "GSM1672587", "GSM1672588", "GSM1672589", "GSM1672590", "GSM1672591", "GSM1672592", "GSM1672593", "GSM1672594", "GSM1672595", "GSM1672596", "GSM1672597", "GSM1672598", "GSM1672599", "GSM1672600", "GSM1672601", "GSM1672602", "GSM1672603", "GSM1672604", "GSM1672605", "GSM1672606", "GSM1672607", "GSM1672608", "GSM1672609", "GSM1672610", "GSM1672611", "GSM1672612", "GSM1672613", "GSM1672614", "GSM1672615", "GSM1672616", "GSM1672617", "GSM1672618", "GSM1672619", "GSM1672620", "GSM1672621", "GSM1672622", "GSM1672623", "GSM1672624", "GSM1672625", "GSM1672626", "GSM1672627", "GSM1672628", "GSM1672629", "GSM1672630", "GSM1672631", "GSM1672632", "GSM1672633", "GSM1672634", "GSM1672635", "GSM1672636", "GSM1672637", "GSM1672638", "GSM1672639", "GSM1672640", "GSM1672641", "GSM1672642", "GSM1672643", "GSM1672644", "GSM1672645", "GSM1672646", "GSM1672647", "GSM1672648", "GSM1672649", "GSM1672650", "GSM1672651", "GSM1672652", "GSM1672653", "GSM1672654", "GSM1672655", "GSM1672656", "GSM1672657", "GSM1672658", "GSM1672659", "GSM1672660", "GSM1672661", "GSM1672662", "GSM1672663", "GSM1672664", "GSM1672665", "GSM1672666", "GSM1672667", "GSM1672668", "GSM1672669", "GSM1672670", "GSM1672671", "GSM1672672", "GSM1672673", "GSM1672674", "GSM1672675", "GSM1672676", "GSM1672677", "GSM1672678", "GSM1672679", "GSM1672680", "GSM1672681", "GSM1672682", "GSM1672683", "GSM1672684", "GSM1672685", "GSM1672686", "GSM1672687", "GSM1672688", "GSM1672689", "GSM1672690", "GSM1672691", "GSM1672692", "GSM1672693", "GSM1672694", "GSM1672695", "GSM1672696", "GSM1672697", "GSM1672698", "GSM1672699", "GSM1672700", "GSM1672701", "GSM1672702", "GSM1672703", "GSM1672704", "GSM1672705", "GSM1672706", "GSM1672707", "GSM1672708", "GSM1672709", "GSM1672710", "GSM1672711", "GSM1672712", "GSM1672713", "GSM1672714", "GSM1672715", "GSM1672716", "GSM1672717", "GSM1672718", "GSM1672719", "GSM1672720", "GSM1672721", "GSM1672722", "GSM1672723", "GSM1672724", "GSM1672725", "GSM1672726", "GSM1672727", "GSM1672728", "GSM1672729", "GSM1672730", "GSM1672731", "GSM1672732", "GSM1672733", "GSM1672734", "GSM1672735", "GSM1672736", "GSM1672737", "GSM1672738", "GSM1672739", "GSM1672740", "GSM1672741", "GSM1672742"], "sample_count": 462, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "caArray_jacob-00182: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo: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 TCGA-LUAD dataset was chosen as the training cohort and downloaded from the GDC Xena Hub (https://gdc.xenahubs.net). Five hundred patients with LUAD in the TCGA-LUAD dataset who had both gene expression and survival data available were included in our research.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The TCGA-LUAD dataset was chosen as the training cohort and downloaded from the GDC Xena Hub (https://gdc.xenahubs.net). Five hundred patients with LUAD in the TCGA-LUAD dataset who had both gene expression and survival data available were included in our research.", "access_statement_kind": "repository_route_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}}, {"id": "asset:table:pmid:34422970:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a8f449ef2de4d59b5d29ccdcf8c3ba1fb5845e9d1e6247113cc0f6a59bf20ac3", "bytes": 4027, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t1", "version": null, "note": "Clinical characteristics of patients involved in the study", "structure": {"pmcid": "PMC8339871", "section_index": 10, "section_title": "Cohorts’ characteristics", "row_count": 98, "column_count": 4}, "table": {"label": "Table 1", "caption": "Clinical characteristics of patients involved in the study", "rows": [["Characteristics", "Training cohort (TCGA-LUAD, 500 cases)", "Validation cohort (GSE72094, 442 cases)", "Validation cohort (GSE68465, 443 cases)"], ["Age", "", "", ""], ["<65", "219 (43.8%)", "115 (26.02%)", "214 (48.31%)"], ["≥65", "271 (54.2%)", "306 (69.23%)", "229 (51.69%)"], ["Unknown", "10 (2%)", "21 (4.75%)", "0"], ["Gender", "", "", ""], ["Female", "270 (54%)", "240 (54.3%)", "220 (49.66%)"], ["Male", "230 (46%)", "202 (45.7%)", "223 (50.34%)"], ["T classification", "", "", ""], ["T1", "167 (33.4%)", "NA", "150 (33.86%)"], ["T2", "267 (53.4%)", "NA", "251 (56.66%)"], ["T3", "45 (9%)", "NA", "28 (6.32%)"], ["T4", "18 (3.6%)", "NA", "12 (2.71%)"], ["Unknown", "3 (0.6%)", "NA", "2 (0.45%)"], ["N classification", "", "", ""], ["N0", "324 (64.8%)", "NA", "299 (67.49%)"], ["N1", "94 (18.8%)", "NA", "88 (19.86%)"], ["N2", "69 (13.8%)", "NA", "53 (11.96%)"], ["N3", "2 (0.4%)", "NA", "0"], ["Unknown", "11 (2.2%)", "NA", "3 (0.68%)"], ["M classification", "", "", ""], ["M0", "332 (66.4%)", "NA", "NA"], ["M1", "24 (4.8%)", "NA", "NA"], ["Unknown", "144 (28.8%)", "NA", "NA"], ["Tumor stage", "", "", ""], ["Stage I", "268 (53.6%)", "265 (59.95%)", "NA"], ["Stage II", "119 (23.8%)", "69 (15.61%)", "NA"], ["Stage III", "80 (16%)", "63 (14.25%)", "NA"], ["Stage IV", "25 (5%)", "17 (3.85%)", "NA"], ["Unknown", "8 (1.6%)", "28 (6.33%)", "NA"], ["Race", "", "", ""], ["White", "386 (77.2%)", "399 (90.27%)", "295 (66.59%)"], ["Black or African American", "52 (10.4%)", "13 (2.94%)", "12 (2.71%)"], ["American Indian or Alaska Native", "1 (0.2%)", "0", "1 (0.23%)"], ["Asian", "7 (1.4%)", "3 (0.68%)", "6 (1.35%)"], ["Unknown", "54 (10.8%)", "27 (6.11%)", "129 (29.12%)"], ["Ethnicity", "", "", ""], ["Hispanic or Latino", "7 (1.4%)", "10 (2.26%)", "NA"], ["Not Hispanic or Latino", "381 (76.2%)", "402 (90.95%)", "NA"], ["Unknown", "112 (22.4%)", "30 (6.79%)", "NA"], ["Tobacco smoking history", "", "", ""], ["Ever", "415 (83%)", "335 (75.79%)", "300 (67.72%)"], ["Never", "71 (14.2%)", "33 (7.47%)", "49 (11.06%)"], ["Unknown", "14 (2.8%)", "74 (16.74%)", "94 (21.22%)"], ["Number pack-years smoked", "", "", ""], ["<30", "115 (23%)", "NA", "NA"], ["≥30", "227 (45.4%)", "NA", "NA"], ["Unknown", "158 (31.6%)", "NA", "NA"], ["Radiation therapy", "", "", ""], ["Yes", "58 (11.6%)", "NA", "65 (14.67%)"], ["No", "361 (72.2%)", "NA", "364 (82.17%)"], ["Unknown", "81 (16.2%)", "NA", "14 (3.16%)"], ["Chemotherapy", "", "", ""], ["Yes", "NA", "NA", "89 (20.09%)"], ["No", "NA", "NA", "341 (76.98%)"], ["Unknown", "NA", "NA", "13 (2.93%)"], ["Additional pharmaceutical therapy", "", ""], ["Yes", "61 (12.2%)", "NA", "NA"], ["No", "68 (13.6%)", "NA", "NA"], ["Unknown", "371 (74.2%)", "NA", "NA"], ["Additional radiation therapy", "", "", ""], ["Yes", "61 (12.2%)", "NA", "NA"], ["No", "71 (14.2%)", "NA", "NA"], ["Unknown", "368 (73.6%)", "NA", "NA"], ["EGFR mutation", "", "", ""], ["Yes", "80 (16%)", "47 (10.63%)", "NA"], ["No", "191 (38.2%)", "395 (89.37%)", "NA"], ["Unknown", "229 (45.8%)", "0", "NA"], ["KRAS mutation", "", "", ""], ["Yes", "23 (4.6%)", "154 (34.84%)", "NA"], ["No", "39 (7.8%)", "288 (65.16%)", "NA"], ["Unknown", "438 (87.6%)", "0", "NA"], ["STK11 mutation", "", "", ""], ["Yes", "NA", "68 (15.38%)", "NA"], ["No", "NA", "374 (84.62%)", "NA"], ["TP53 mutation", "", "", ""], ["Yes", "NA", "111 (25.11%)", "NA"], ["No", "NA", "331 (74.89%)", "NA"], ["EML4-ALK mutation", "", "", ""], ["Yes", "34 (6.8%)", "NA", "NA"], ["No", "207 (41.4%)", "NA", "NA"], ["Unknown", "259 (51.8%)", "NA", "NA"], ["Tumor intermediate dimension", "", ""], ["<1", "287 (57.4%)", "NA", "NA"], ["≥1", "88 (17.6%)", "NA", "NA"], ["Unknown", "125 (25%)", "NA", "NA"], ["Location in lung parenchyma", "", "", ""], ["Central lung", "62 (12.4%)", "NA", "NA"], ["Peripheral lung", "118 (23.6%)", "NA", "NA"], ["Unknown", "320 (64%)", "NA", "NA"], ["Person neoplasm cancer status", "", ""], ["With tumor", "134 (26.8%)", "NA", "NA"], ["Tumor free", "243 (48.6%)", "NA", "NA"], ["Unknown", "123 (24.6%)", "NA", "NA"], ["Vital status", "", "", ""], ["Alive", "318 (63.6%)", "298 (67.42%)", "207 (46.73%)"], ["Dead", "182 (36.4%)", "122 (27.6%)", "236 (53.27%)"], ["Unknown", "0", "22 (4.98%)", "NA"]], "row_count": 98, "column_count": 4, "numeric_cells": 143, "header_rows": 1, "locator": "section[10]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:34422970:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:af60f9de62ac4bb361a71c47a9ed9536397621443f7d9a8296ad931a5388110f", "bytes": 1757, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#t2", "version": null, "note": "14 ferroptosis-related potential prognostic genes generated from the training cohort", "structure": {"pmcid": "PMC8339871", "section_index": 11, "section_title": "Identification of a prognostic ferroptosis-related gene signature from the training cohort", "row_count": 16, "column_count": 6}, "table": {"label": "Table 2", "caption": "14 ferroptosis-related potential prognostic genes generated from the training cohort", "rows": [["Gene symbol", "Description", "HR", "95% confidence interval", "P value"], ["Lower", "Upper"], ["PEBP1", "Phosphatidylethanolamine-Binding Protein 1", "0.603658936", "0.464865289", "0.78389185", "0.000152746"], ["ACSL3", "Acyl-CoA Synthetase Long-Chain Family Member 3", "1.435108616", "1.157210163", "1.779743045", "0.001003251"], ["GLS2", "Glutaminase 2", "0.356469987", "0.176890046", "0.71836067", "0.003911814"], ["GCLC", "Glutamate-Cysteine Ligase Catalytic Subunit", "1.135847381", "1.034367787", "1.24728292", "0.007639188"], ["SLC7A11", "Solute Carrier Family 7 Member 11", "1.137868621", "1.023951703", "1.264459052", "0.016406631"], ["PHKG2", "Phosphorylase Kinase Catalytic Subunit Gamma 2", "0.69374619", "0.511654438", "0.940642238", "0.018577862"], ["PGD", "Phosphogluconate Dehydrogenase", "1.177966423", "1.02132216", "1.358635842", "0.02446422"], ["CISD1", "CDGSH Iron Sulfur Domain 1", "1.403301444", "1.041497232", "1.890792296", "0.025931782"], ["ALOX12B", "Arachidonate 12-Lipoxygenase, 12R Type", "1.528527805", "1.03748207", "2.251988076", "0.031866869"], ["DPP4", "Dipeptidyl Peptidase 4", "0.911077238", "0.836744384", "0.992013511", "0.031983077"], ["ALOX15", "Arachidonate 15-Lipoxygenase", "0.857033797", "0.740142144", "0.992386306", "0.039196308"], ["ATP5G3", "ATP Synthase Membrane Subunit C Locus 3", "1.311553769", "1.01163069", "1.700396506", "0.040633369"], ["ABCC1", "ATP Binding Cassette Subfamily C Member 1", "1.23437377", "1.007318781", "1.512608156", "0.042328557"], ["NCOA4", "Nuclear Receptor Coactivator 4", "0.776056577", "0.603024235", "0.998738982", "0.048865024"]], "row_count": 16, "column_count": 6, "numeric_cells": 72, "header_rows": 2, "locator": "section[11]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:34422970:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e371ce4db74b4bb3c542daa5d9d067e9016cd44760ffb44ffd99c1d8d8179dd1", "bytes": 902, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#t3", "version": null, "note": "10 ferroptosis-related prognostic genes obtained from LASSO Cox regression model", "structure": {"pmcid": "PMC8339871", "section_index": 11, "section_title": "Identification of a prognostic ferroptosis-related gene signature from the training cohort", "row_count": 11, "column_count": 3}, "table": {"label": "Table 3", "caption": "10 ferroptosis-related prognostic genes obtained from LASSO Cox regression model", "rows": [["Gene symbol", "Description", "Risk coefficient"], ["PHKG2", "Phosphorylase Kinase Catalytic Subunit Gamma 2", "−0.376487238"], ["PGD", "Phosphogluconate Dehydrogenase", "0.027750809"], ["PEBP1", "Phosphatidylethanolamine Binding Protein 1", "−0.369553219"], ["NCOA4", "Nuclear Receptor Coactivator 4", "−0.498545244"], ["GLS2", "Glutaminase 2", "−0.399525822"], ["CISD1", "CDGSH Iron Sulfur Domain 1", "0.313326653"], ["ATP5G3", "ATP Synthase Membrane Subunit C Locus 3", "0.019018653"], ["ALOX15", "Arachidonate 15-Lipoxygenase", "−0.049973524"], ["ALOX12B", "Arachidonate 12-Lipoxygenase, 12R Type", "0.323899465"], ["ACSL3", "Acyl-CoA Synthetase Long Chain Family Member 3", "0.246495026"]], "row_count": 11, "column_count": 3, "numeric_cells": 21, "header_rows": 1, "locator": "section[11]/table-wrap[2]#t3"}}, {"id": "asset:table:pmid:34422970:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f958976cfdaae725dac9f3b89b533f2f1ab7b0b3a4a3044246dc661fcd3105ff", "bytes": 7789, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#t4", "version": null, "note": "Univariate analysis and multivariate analysis of the correlation of gene signature risk score with outcomes among lung adenocarcinoma patients in three cohorts", "structure": {"pmcid": "PMC8339871", "section_index": 12, "section_title": "Prognostic ability of the ten-gene signature", "row_count": 67, "column_count": 10}, "table": {"label": "Table 4", "caption": "Univariate analysis and multivariate analysis of the correlation of gene signature risk score with outcomes among lung adenocarcinoma patients in three cohorts", "rows": [["Variable", "Univariate Cox analysis", "", "Multivariate Cox analysis"], ["coef", "HR (95% CI)", "z", "P value", "coef", "HR (95% CI)", "z", "P value"], ["TCGA-LUAD (overall survival)^", "", "", "", "", "", "", "", "", ""], ["Gender (male vs. female)", "0.048", "1.05 (0.784–1.4)", "0.322", "7.47E-01", "", "", "", "", ""], ["Age", "0.00816", "1.01 (0.993–1.02)", "1.05", "2.94E-01", "", "", "", "", ""], ["Tumor stage II (vs. stage I)", "0.905", "2.47 (1.72–3.56)", "4.87", "1.09E-06*", "", "1.32", "3.75 (1.44–9.8)", "2.7", "6.93E-03"], ["Tumor stage III (vs. stage I)", "1.25", "3.49 (2.38–5.12)", "6.4", "1.51E-10*", "", "0.455", "1.58 (0.445–5.59)", "0.705", "4.81E-01"], ["Tumor stage IV (vs. stage I)", "1.34", "3.82 (2.2–6.62)", "4.76", "1.92E-06*", "", "−0.107", "0.899 (0.255–3.17)", "−0.166", "8.68E-01"], ["Tobacco smoking history (ever vs. never)", "−0.127", "0.88 (0.583–1.33)", "−0.605", "5.45E-01", "", "", "", "", ""], ["Number pack years smoked", "0.00327", "1 (0.996–1.01)", "0.938", "3.48E-01", "", "", "", "", ""], ["Race (White vs. non-White)", "0.36", "1.43 (0.875–2.34)", "1.43", "1.53E-01", "", "", "", "", ""], ["Ethnicity (Hispanic or Latino vs. Non-Hispanic or Latino)", "0.387", "1.47 (0.466–4.65)", "0.658", "5.10E-01", "", "", "", "", ""], ["Tumor intermediate dimension", "0.441", "1.55 (0.922–2.62)", "1.65", "9.80E-02", "", "", "", "", ""], ["Radiation therapy (yes vs. no)", "0.763", "2.14 (1.44–3.19)", "3.76", "1.73E-04*", "", "0.446", "1.56 (0.415–5.88)", "0.66", "5.09E-01"], ["Additional pharmaceutical therapy (yes vs. no)", "−0.502", "0.605 (0.382–0.959)", "−2.14", "3.26E-02*", "", "−1.03", "0.356 (0.158–0.8)", "−2.5", "1.25E-02*"], ["Additional radiation therapy (yes vs. no)", "−0.0153", "0.985 (0.625–1.55)", "−0.0661", "9.47E-01", "", "", "", "", ""], ["Location in lung parenchyma (central lung vs. peripheral lung)", "0.0908", "1.09 (0.684–1.75)", "0.378", "7.06E-01", "", "", "", "", ""], ["KRAS mutation (yes vs. no)", "0.492", "1.63 (0.672–3.98)", "1.08", "2.78E-01", "", "", "", "", ""], ["EGFR mutation (yes vs. no)", "0.268", "1.31 (0.828–2.06)", "1.15", "2.50E-01", "", "", "", "", ""], ["EML4-ALK mutation (yes vs. no)", "0.592", "1.81 (1.01–3.24)", "1.98", "4.73E-02*", "", "1.18", "3.25 (1.22–8.63)", "2.36", "1.84E-02*"], ["Risk score", "1.22", "3.39 (2.49–4.62)", "7.76", "8.78E-15*", "", "1.99", "7.32 (2.88–18.6)", "4.18", "2.94E-05*"], ["TCGA-LUAD (progression-free survival)#", "", "", "", "", "", "", "", "", ""], ["Gender (male vs. female)", "0.07", "1.07 (0.815–1.41)", "0.499", "6.17E-01", "", "", "", "", ""], ["Age", "−0.000998", "0.999 (0.985–1.01)", "−0.141", "8.88E-01", "", "", "", "", ""], ["Tumor stage II (vs. stage I)", "0.798", "2.22 (1.61–3.07)", "4.85", "1.22E-06*", "", "1.2", "3.33 (1.92–5.78)", "4.28", "1.88E-05*"], ["Tumor stage III (vs. stage I)", "0.709", "2.03 (1.38–2.99)", "3.61", "3.10E-04*", "", "0.95", "2.59 (1.31–5.11)", "2.73", "6.25E-03*"], ["Tumor stage IV (vs. stage I)", "0.849", "2.34 (1.32–4.13)", "2.93", "3.40E-03*", "", "0.828", "2.29 (0.979–5.35)", "1.91", "5.60E-02"], ["Tobacco smoking history (ever vs. never)", "−0.0557", "0.946 (0.637–1.4)", "−0.276", "7.82E-01", "", "", "", "", ""], ["Number pack years smoked", "−0.000552", "0.999 (0.993–1.01)", "−0.165", "8.69E-01", "", "", "", "", ""], ["Race (White vs. non-White)", "0.0557", "1.06 (0.703–1.59)", "0.268", "7.89E-01", "", "", "", "", ""], ["Ethnicity (Hispanic or Latino vs. non-Hispanic or Latino)", "0.291", "1.34 (0.495–3.62)", "0.574", "5.66E-01", "", "", "", "", ""], ["Tumor intermediate dimension", "0.328", "1.39 (0.84–2.29)", "1.28", "2.01E-01", "", "", "", "", ""], ["Radiation therapy (yes vs. no)", "0.707", "2.03 (1.42–2.89)", "3.92", "9.01E-05*", "", "0.432", "1.54 (0.829–2.86)", "1.37", "1.72E-01"], ["Additional pharmaceutical therapy (yes vs. no)", "0.27", "1.31 (0.914–1.88)", "1.47", "1.41E-01", "", "", "", "", ""], ["Additional radiation therapy (yes vs. no)", "0.16", "1.17 (0.825–1.67)", "0.89", "3.73E-01", "", "", "", "", ""], ["Location in lung parenchyma (central lung vs. peripheral lung)", "−0.0709", "0.932 (0.584–1.49)", "−0.298", "7.66E-01", "", "", "", "", ""], ["KRAS mutation (yes vs. no)", "−0.275", "0.759 (0.316–1.82)", "−0.616", "5.38E-01", "", "", "", "", ""], ["EGFR mutation (yes vs. no)", "0.483", "1.62 (1.06–2.49)", "2.21", "2.71E-02*", "", "0.277", "1.32 (0.812–2.14)", "1.12", "2.64E-01"], ["EML4-ALK mutation (yes vs. no)", "0.509", "1.66 (0.965–2.87)", "1.83", "6.72E-02", "", "", "", "", ""], ["Risk score", "0.853", "2.35 (1.74–3.16)", "5.63", "1.80E-08*", "", "0.727", "2.07 (1.22–3.52)", "2.68", "7.35E-03*"], ["GSE72094 (overall survival)&", "", "", "", "", "", "", "", "", ""], ["Gender (male vs. female)", "0.44", "1.55 (1.07–2.25)", "2.33", "1.98E-02*", "", "0.464", "1.59 (1.09–2.33)", "2.39", "1.67E-02*"], ["Age", "0.00696", "1.01 (0.988–1.03)", "0.702", "4.83E-01", "", "", "", "", ""], ["Race (White vs. non-White)", "−0.0694", "0.933 (0.38–2.29)", "−0.151", "8.80E-01", "", "", "", "", ""], ["Ethnicity (Hispanic or Latino vs. non-Hispanic or Latino)", "−0.642", "0.526 (0.0733–3.78)", "−0.638", "5.24E-01", "", "", "", "", ""], ["Tobacco smoking history (ever vs. never)", "0.314", "1.37 (0.597–3.14)", "0.741", "4.59E-01", "", "", "", "", ""], ["Tumor stage II (vs. stage I)", "0.758", "2.13 (1.32–3.44)", "3.11", "1.85E-03*", "", "0.708", "2.03 (1.25–3.28)", "2.88", "3.92E-03*"], ["Tumor stage III (vs. stage I)", "1.13", "3.09 (1.93–4.97)", "4.67", "3.00E-06*", "", "1.17", "3.22 (1.99–5.22)", "4.76", "1.91E-06*"], ["Tumor stage IV (vs. stage I)", "1.21", "3.35 (1.59–7.06)", "3.18", "1.48E-03*", "", "1.14", "3.13 (1.48–6.62)", "2.99", "2.80E-03*"], ["KRAS mutation (yes vs. no)", "0.376", "1.46 (1–2.12)", "1.97", "4.92E-02*", "", "0.157", "1.17 (0.796–1.72)", "0.799", "4.24E-01"], ["EGFR mutation (yes vs. no)", "−1.34", "0.262 (0.0965–0.71)", "−2.63", "8.49E-03*", "", "−0.926", "0.396 (0.143–1.1)", "−1.78", "7.52E-02"], ["STK11 mutation (yes vs. no)", "−0.0393", "0.961 (0.58–1.59)", "−0.153", "8.79E-01", "", "", "", "", ""], ["TP53 mutation (yes vs. no)", "0.211", "1.23 (0.82–1.86)", "1.01", "3.13E-01", "", "", "", "", ""], ["Risk score", "0.613", "1.85 (1.47–2.31)", "5.33", "1.00E-07*", "", "0.508", "1.66 (1.31–2.11)", "4.14", "3.54E-05*"], ["GSE68465 (overall survival)$", "", "", "", "", "", "", "", "", ""], ["Gender (male vs. female)", "0.33", "1.39 (1.07–1.8)", "2.5", "1.25E-02*", "", "0.324", "1.38 (1.05–1.83)", "2.27", "2.32E-02*"], ["Age", "0.0266", "1.03 (1.01–1.04)", "3.97", "7.16E-05*", "", "0.0357", "1.04 (1.02–1.05)", "4.93", "8.10E-07*"], ["Race (White vs. non-White)", "0.32", "1.38 (0.702–2.71)", "0.931", "3.52E-01", "", "", "", "", ""], ["Chemotherapy (yes vs. no)", "0.488", "1.63 (1.22–2.18)", "3.29", "9.99E-04*", "", "0.243", "1.28 (0.861–1.89)", "1.21", "2.25E-01"], ["Radiation therapy (yes vs. no)", "0.698", "2.01 (1.47–2.75)", "4.37", "1.26E-05*", "", "0.26", "1.3 (0.838–2)", "1.17", "2.43E-01"], ["T classification (T2 vs. T1)", "0.381", "1.46 (1.09–1.97)", "2.52", "1.18E-02*", "", "0.126", "1.13 (0.829–1.55)", "0.786", "4.32E-01"], ["T classification (T3 vs. T1)", "1.2", "3.31 (2.06–5.34)", "4.92", "8.78E-07*", "", "0.76", "2.14 (1.29–3.55)", "2.94", "3.27E-03*"], ["T classification (T4 vs. T1)", "1.45", "4.26 (2.17–8.34)", "4.22", "2.41E-05*", "", "1.06", "2.89 (1.36–6.13)", "2.77", "5.59E-03*"], ["N classification (N1 vs. N0)", "0.821", "2.27 (1.67–3.09)", "5.23", "1.74E-07*", "", "0.775", "2.17 (1.57–3)", "4.69", "2.74E-06*"], ["N classification (N2 vs. N0)", "1.36", "3.9 (2.77–5.48)", "7.82", "5.47E-15", "", "1.24", "3.45 (2.33–5.09)", "6.22", "5.08E-10*"], ["Tobacco smoking history (ever vs. never)", "0.22", "1.25 (0.79–1.96)", "0.946", "3.44E-01", "", "", "", "", ""], ["Risk score", "0.331", "1.39 (1.18–1.64)", "3.94", "8.17E-05*", "", "0.356", "1.43 (1.19–1.71)", "3.84", "1.22E-04*"]], "row_count": 67, "column_count": 10, "numeric_cells": 370, "header_rows": 2, "locator": "section[12]/table-wrap[1]#t4"}}], "gaps": ["asset:data:geo:GSE68465 not downloaded", "asset:data:geo:GSE68465 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": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-3", "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 analysis"}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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", "GSE68465"], "resolved_accessions": ["GSE72094", "GSE68465"], "statements": ["The TCGA-LUAD dataset was chosen as the training cohort and downloaded from the GDC Xena Hub (https://gdc.xenahubs.net). Five hundred patients with LUAD in the TCGA-LUAD dataset who had both gene expression and survival data available were included in our research."], "basis": "The paper names GSE72094, GSE68465 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:34422970", "data:geo:GSE68465", "asset:table:pmid:34422970:1", "asset:table:pmid:34422970:2", "asset:table:pmid:34422970:3", "asset:table:pmid:34422970:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE68465"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:46:13Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 3, "usage": {"prompt_tokens": 26836, "completion_tokens": 2616, "cached_tokens": 792}}, "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:34422970", "type": "paper", "label": "pmid:34422970"}, {"id": "source:pmid:34422970", "type": "manuscript", "label": "PMID 34422970 full text"}, {"id": "data:geo:GSE68465", "type": "dataset", "label": "GEO GSE68465"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34422970", "type": "paper", "label": "pmid:34422970"}, {"id": "source:pmid:34422970", "type": "manuscript", "label": "PMID 34422970 full text"}, {"id": "data:geo:GSE68465", "type": "dataset", "label": "GEO GSE68465"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34422970", "type": "extraction", "used": ["source:pmid:34422970"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE68465", "type": "accession_resolution", "used": ["data:geo:GSE68465"], "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:34422970", "parent_hash": "sha256:4e059392ef9dc8043caa45f12c48a7a3059ff9797ce93d5df4ad04dd35b2095d", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE68465 licence not read", "asset:data:geo:GSE68465 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": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:44:07+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}