YAP1 as a Novel Negative Biomarker of Immune Checkpoint Inhibitors for EGFR-Mutant Non-Small-Cell Lung Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37388902", "kind": "science-record", "revision": 2, "content_hash": "sha256:839c0bc9e8c00383a0c839079f95c529e4acd4b45d4b05322d2be56b55fc81b8", "created_at": "2026-11-01T19:02:09Z", "updated_at": "2026-11-01T21:31:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "YAP1 as a Novel Negative Biomarker of Immune Checkpoint Inhibitors for EGFR-Mutant Non-Small-Cell Lung Cancer.", "doi": "10.1155/2023/4689004", "pmid": "37388902", "authors": ["Ling-Chen Li", "Xie-Wan Chen", "Ling Fang", "Chun-Li Jian", "Yong-Xin Yu", "Xing-Yun Liao", "Jian-Guo Sun"], "journal": "Canadian respiratory journal", "year": 2023, "abstract": "Background: Immune checkpoint inhibitors (ICIs) have become a standard care in non-small-cell lung cancer (NSCLC). However, its application to epidermal growth factor receptor (EGFR)-mutant NSCLC patients is confronted with drug resistance. This study aimed to clarify the potential role of Yes1-associated transcriptional regulator (YAP1) in ICIs treatment for EGFR-mutant NSCLC population.\nMethods: All the clinical data of NSCLC were downloaded from Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) for GSE11969 and GSE72094. Based on YAP1 expression, all the NSCLC patients including the EGFR-mutant and EGFR-wildtype (WT) patients were divided into two groups, YAP1_High and YAP1_Low. Using cBioPortal, genetic alterations were analyzed for identification of immunogenicity in EGFR-mutant NSCLC. MR analysis was used to analyze the hub gene of EGFR. The infiltration of immune cells and the expression of the identified tumor-associated antigens were identified with TIMER. By graph learning-based dimensionality reduction analysis, the immune landscape was visualized. Moreover, survival analysis was performed to verify the predictive value of YAP1 in ICIs treatment for EGFR-mutant NSCLC population using Ren's research data (NCT03513666).\nResults: YAP1 was a poor prognostic factor of EGFR-mutant NSCLC population rather than lung adenocarcinoma (LUAD) patients. MR analysis revealed that the EGFR gene regulated YAP1 expression. YAP1 was identified as a hub gene closely associated with immunosuppressive microenvironment and poor prognosis in EGFR-mutant NSCLC population in TCGA LUAD. Tumors with YAP1_High showed an immune-\"cold\" and immunosuppressive phenotype, whereas those with YAP1_Low demonstrated an immune-\"hot\" and immunoactive phenotype. More importantly, it was verified that YAP1_High subpopulation had a significantly shorter progression-free survival (PFS) and overall survival (OS) after ICIs treatment in EGFR-mutant NSCLC patients in the clinical trial.\nConclusions: YAP1 mediates immunosuppressive microenvironment and poor prognosis in EGFR-mutant NSCLC population. YAP1 is a novel negative biomarker of ICIs treatment in EGFR-mutant NSCLC population. Clinical Trials. This trial is registered with NCT03513666.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier analysis of OS and PFS) was performed using Survminer [18] (R package). We calculated the hazard ratio (HR) and log-rank P value of the 95% confidence interval.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37388902", "locator": "sections[6] \"2.4. Survival Analysis\" paragraph 2", "quote": "Kaplan–Meier analysis of OS and PFS) was performed using Survminer [18] (R package). We calculated the hazard ratio (HR) and log-rank P value of the 95% confidence interval."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37388902", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "YAP1 was associated with poorer outcomes and an immunosuppressive tumor microenvironment in EGFR-mutant NSCLC, and high YAP1 expression was associated with shorter survival after immune checkpoint inhibitor treatment.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37388902", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "YAP1 mediates immunosuppressive microenvironment and poor prognosis in EGFR-mutant NSCLC population. YAP1 is a novel negative biomarker of ICIs treatment in EGFR-mutant NSCLC population."}, {"asset": "source:pmid:37388902", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "More importantly, it was verified that YAP1_High subpopulation had a significantly shorter progression-free survival (PFS) and overall survival (OS) after ICIs treatment in EGFR-mutant NSCLC patients in the clinical trial."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "YAP1 was associated with poorer outcomes and an immunosuppressive tumor microenvironment in EGFR-mutant NSCLC, and high YAP1 expression was associated with shorter survival after immune checkpoint inhibitor treatment.", "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:37388902"], "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:GSE11969"], "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": {"hazard_ratio": "survival analysis with hazard ratio and log-rank P value ca", "p_value": "zard ratio and log-rank P value calculation"}, "inputs": ["data:geo:GSE11969"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37388902", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2023/4689004", "sha256": "sha256:d00f5b29fe19da7c95598a7440821d48b1787621e25e5edaf8cbf1b6189cbd5a", "bytes": 39135, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2023/4689004", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10307059", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11969", "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=GSE11969", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11969", "version": null, "note": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM302996", "GSM302997", "GSM302998", "GSM302999", "GSM303000", "GSM303001", "GSM303002", "GSM303003", "GSM303004", "GSM303005", "GSM303006", "GSM303007", "GSM303008", "GSM303009", "GSM303010", "GSM303011", "GSM303012", "GSM303013", "GSM303014", "GSM303015", "GSM303016", "GSM303017", "GSM303018", "GSM303019", "GSM303020", "GSM303021", "GSM303022", "GSM303023", "GSM303024", "GSM303025", "GSM303026", "GSM303027", "GSM303028", "GSM303029", "GSM303030", "GSM303031", "GSM303032", "GSM303033", "GSM303034", "GSM303035", "GSM303036", "GSM303037", "GSM303038", "GSM303039", "GSM303040", "GSM303041", "GSM303042", "GSM303043", "GSM303044", "GSM303045", "GSM303046", "GSM303047", "GSM303048", "GSM303049", "GSM303050", "GSM303051", "GSM303052", "GSM303053", "GSM303054", "GSM303055", "GSM303056", "GSM303057", "GSM303058", "GSM303059", "GSM303060", "GSM303061", "GSM303062", "GSM303063", "GSM303064", "GSM303065", "GSM303066", "GSM303067", "GSM303068", "GSM303069", "GSM303070", "GSM303071", "GSM303072", "GSM303073", "GSM303074", "GSM303075", "GSM303076", "GSM303077", "GSM303078", "GSM303079", "GSM303080", "GSM303081", "GSM303082", "GSM303083", "GSM303084", "GSM303085", "GSM303086", "GSM303087", "GSM303088", "GSM303089", "GSM303090", "GSM303091", "GSM303092", "GSM303093", "GSM303094", "GSM303095", "GSM303096", "GSM303097", "GSM303098", "GSM303099", "GSM303100", "GSM303101", "GSM303102", "GSM303103", "GSM303104", "GSM303105", "GSM303106", "GSM303107", "GSM303108", "GSM303109", "GSM303110", "GSM303111", "GSM303112", "GSM303113", "GSM303114", "GSM303115", "GSM303116", "GSM303117", "GSM303118", "GSM303119", "GSM303120", "GSM303121", "GSM303122", "GSM303123", "GSM303124", "GSM303125", "GSM303126", "GSM303127", "GSM303128", "GSM303129", "GSM303130", "GSM303131", "GSM303132", "GSM303133", "GSM303134", "GSM303135", "GSM303136", "GSM303137", "GSM303138", "GSM303139", "GSM303140", "GSM303141", "GSM303142", "GSM303143", "GSM303144", "GSM303145", "GSM303146", "GSM303147", "GSM303148", "GSM303149", "GSM303150", "GSM303151", "GSM303152", "GSM303153", "GSM303154", "GSM303155", "GSM303156", "GSM303157", "GSM303158"], "sample_count": 163, "group_sizes": null, "group_sizes_basis": null, "platform": "7015", "taxon": "Homo sapiens", "title": "Expression Profile-Defined Classification of Lung Adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE13522", "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=GSE13522", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13522", "version": null, "note": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM340996", "GSM340997", "GSM340998", "GSM340999", "GSM341000", "GSM341001", "GSM341002", "GSM341003", "GSM341004", "GSM341005", "GSM341006", "GSM341007", "GSM341008", "GSM341009", "GSM341010", "GSM341011", "GSM341012", "GSM341013", "GSM341014", "GSM341015", "GSM341016", "GSM341017", "GSM341018", "GSM341019", "GSM341020", "GSM341021", "GSM341022", "GSM341023", "GSM341024", "GSM341025", "GSM341026", "GSM341027", "GSM341028"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Transcriptional response in skin of mouse 24 hours after intradermal infection with Trypanosoma cruzi", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31210", "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=GSE31210", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31210", "version": null, "note": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM773540", "GSM773541", "GSM773542", "GSM773543", "GSM773544", "GSM773545", "GSM773546", "GSM773547", "GSM773548", "GSM773549", "GSM773550", "GSM773551", "GSM773552", "GSM773553", "GSM773554", "GSM773555", "GSM773556", "GSM773557", "GSM773558", "GSM773559", "GSM773560", "GSM773561", "GSM773562", "GSM773563", "GSM773564", "GSM773565", "GSM773566", "GSM773567", "GSM773568", "GSM773569", "GSM773570", "GSM773571", "GSM773572", "GSM773573", "GSM773574", "GSM773575", "GSM773576", "GSM773577", "GSM773578", "GSM773579", "GSM773580", "GSM773581", "GSM773582", "GSM773583", "GSM773584", "GSM773585", "GSM773586", "GSM773587", "GSM773588", "GSM773589", "GSM773590", "GSM773591", "GSM773592", "GSM773593", "GSM773594", "GSM773595", "GSM773596", "GSM773597", "GSM773598", "GSM773599", "GSM773600", "GSM773601", "GSM773602", "GSM773603", "GSM773604", "GSM773605", "GSM773606", "GSM773607", "GSM773608", "GSM773609", "GSM773610", "GSM773611", "GSM773612", "GSM773613", "GSM773614", "GSM773615", "GSM773616", "GSM773617", "GSM773618", "GSM773619", "GSM773620", "GSM773621", "GSM773622", "GSM773623", "GSM773624", "GSM773625", "GSM773626", "GSM773627", "GSM773628", "GSM773629", "GSM773630", "GSM773631", "GSM773632", "GSM773633", "GSM773634", "GSM773635", "GSM773636", "GSM773637", "GSM773638", "GSM773639", "GSM773640", "GSM773641", "GSM773642", "GSM773643", "GSM773644", "GSM773645", "GSM773646", "GSM773647", "GSM773648", "GSM773649", "GSM773650", "GSM773651", "GSM773652", "GSM773653", "GSM773654", "GSM773655", "GSM773656", "GSM773657", "GSM773658", "GSM773659", "GSM773660", "GSM773661", "GSM773662", "GSM773663", "GSM773664", "GSM773665", "GSM773666", "GSM773667", "GSM773668", "GSM773669", "GSM773670", "GSM773671", "GSM773672", "GSM773673", "GSM773674", "GSM773675", "GSM773676", "GSM773677", "GSM773678", "GSM773679", "GSM773680", "GSM773681", "GSM773682", "GSM773683", "GSM773684", "GSM773685", "GSM773686", "GSM773687", "GSM773688", "GSM773689", "GSM773690", "GSM773691", "GSM773692", "GSM773693", "GSM773694", "GSM773695", "GSM773696", "GSM773697", "GSM773698", "GSM773699", "GSM773700", "GSM773701", "GSM773702", "GSM773703", "GSM773704", "GSM773705", "GSM773706", "GSM773707", "GSM773708", "GSM773709", "GSM773710", "GSM773711", "GSM773712", "GSM773713", "GSM773714", "GSM773715", "GSM773716", "GSM773717", "GSM773718", "GSM773719", "GSM773720", "GSM773721", "GSM773722", "GSM773723", "GSM773724", "GSM773725", "GSM773726", "GSM773727", "GSM773728", "GSM773729", "GSM773730", "GSM773731", "GSM773732", "GSM773733", "GSM773734", "GSM773735", "GSM773736", "GSM773737", "GSM773738", "GSM773739", "GSM773740", "GSM773741", "GSM773742", "GSM773743", "GSM773744", "GSM773745", "GSM773746", "GSM773747", "GSM773748", "GSM773749", "GSM773750", "GSM773751", "GSM773752", "GSM773753", "GSM773754", "GSM773755", "GSM773756", "GSM773757", "GSM773758", "GSM773759", "GSM773760", "GSM773761", "GSM773762", "GSM773763", "GSM773764", "GSM773765", "GSM773766", "GSM773767", "GSM773768", "GSM773769", "GSM773770", "GSM773771", "GSM773772", "GSM773773", "GSM773774", "GSM773775", "GSM773776", "GSM773777", "GSM773778", "GSM773779", "GSM773780", "GSM773781", "GSM773782", "GSM773783", "GSM773784", "GSM773785"], "sample_count": 246, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data for pathological stage I-II lung adenocarcinomas", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo: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 used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666).", "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:GSE11969 not downloaded", "asset:data:geo:GSE11969 licence not read", "asset:data:geo:GSE13522 not downloaded", "asset:data:geo:GSE13522 licence not read", "asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE31210 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": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "survival analysis with hazard ratio and log-rank P value ca", "p_value": "zard ratio and log-rank P value calculation"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan–Meier analysis of OS and PFS) was performed using Survminer [18] (R package). We calculated the hazard ratio (HR) and log-rank P value of the 95% confidence interval."}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE11969", "GSE72094", "GSE31210", "GSE13522"], "resolved_accessions": ["GSE11969", "GSE72094", "GSE31210", "GSE13522"], "statements": ["The datasets used in the present study are obtained from the corresponding author upon reasonable request. Our data were obtained from Gene Expression Omnibus (GEO), TCGA LUAD and a phase-II, multicenter, open-label trial from Ren's research (NCT03513666)."], "basis": "The paper names GSE11969, GSE72094, GSE31210, GSE13522 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:37388902", "data:geo:GSE11969"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE11969"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:45:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12489, "completion_tokens": 2908, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37388902", "type": "paper", "label": "pmid:37388902"}, {"id": "source:pmid:37388902", "type": "manuscript", "label": "PMID 37388902 full text"}, {"id": "data:geo:GSE11969", "type": "dataset", "label": "GEO GSE11969"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37388902", "type": "paper", "label": "pmid:37388902"}, {"id": "source:pmid:37388902", "type": "manuscript", "label": "PMID 37388902 full text"}, {"id": "data:geo:GSE11969", "type": "dataset", "label": "GEO GSE11969"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37388902", "type": "extraction", "used": ["source:pmid:37388902"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE11969", "type": "accession_resolution", "used": ["data:geo:GSE11969"], "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:37388902", "parent_hash": "sha256:14ca561a4363eda6190bbe3f78609c678cfc16c45b291fbb0124ea35eced42f6", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE11969 licence not read", "asset:data:geo:GSE11969 not downloaded", "asset:data:geo:GSE13522 licence not read", "asset:data:geo:GSE13522 not downloaded", "asset:data:geo:GSE31210 licence not read", "asset:data:geo:GSE31210 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": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan–Meier analysis of OS and PFS) was performed using Survminer [18] (R package). We calculated the hazard ratio (HR) and log-rank P value of the 95% confidence interval."], "order_basis": "analysis_only", "id": "assay:1"}]}