Identification of Prognostic Signature and Gliclazide as Candidate Drugs in Lung Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34249701", "kind": "science-record", "revision": 7, "content_hash": "sha256:c9ccd4d6e1d866f2d53fcaf7210f4dd7d1a0765ea82397e7207a4b61526233ea", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T22:04:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Prognostic Signature and Gliclazide as Candidate Drugs in Lung Adenocarcinoma.", "doi": "10.3389/fonc.2021.665276", "pmid": "34249701", "authors": ["Yang Cheng", "Kezuo Hou", "Yizhe Wang", "Yang Chen", "Xueying Zheng", "Jianfei Qi", "Bowen Yang", "Shiying Tang", "Xu Han", "Dongyao Shi", "Ximing Wang", "Yunpeng Liu", "Xuejun Hu", "Xiaofang Che"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "BACKGROUND: Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer, with high incidence and mortality. To improve the curative effect and prolong the survival of patients, it is necessary to find new biomarkers to accurately predict the prognosis of patients and explore new strategy to treat high-risk LUAD.\nMETHODS: A comprehensive genome-wide profiling analysis was conducted using a retrospective pool of LUAD patient data from the previous datasets of Gene Expression Omnibus (GEO) including GSE18842, GSE19188, GSE40791 and GSE50081 and The Cancer Genome Atlas (TCGA). Differential gene analysis and Cox proportional hazard model were used to identify differentially expressed genes with survival significance as candidate prognostic genes. The Kaplan-Meier with log-rank test was used to assess survival difference. A risk score model was developed and validated using TCGA-LUAD and GSE50081. Additionally, The Connectivity Map (CMAP) was used to predict drugs for the treatment of LUAD. The anti-cancer effect and mechanism of its candidate drugs were studied in LUAD cell lines.\nRESULTS: We identified a 5-gene signature (KIF20A, KLF4, KRT6A, LIFR and RGS13). Risk Score (RS) based on 5-gene signature was significantly associated with overall survival (OS). Nomogram combining RS with clinical pathology parameters could potently predict the prognosis of patients with LUAD. Moreover, gliclazide was identified as a candidate drug for the treatment of high-RS LUAD. Finally, gliclazide was shown to induce cell cycle arrest and apoptosis in LUAD cells possibly by targeting CCNB1, CCNB2, CDK1 and AURKA.\nCONCLUSION: This study identified a 5-gene signature that can predict the prognosis of patients with LUAD, and Gliclazide as a potential therapeutic drug for LUAD. It provides a new direction for the prognosis and treatment of patients with LUAD.", "claims": [{"id": "claim-method", "statement": "Univariate and multivariate Cox proportional hazard regression analysis was also performed to access the relationship between RS and OS.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34249701", "locator": "sections[14] \"Statistical Analysis\" paragraph 2", "quote": "Univariate and multivariate Cox proportional hazard regression analysis was also performed to access the relationship between RS and OS."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34249701", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."}], "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:34249701"], "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:GSE18842"], "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:GSE18842"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34249701", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2021.665276", "sha256": "sha256:cf730d25f1da46a49469f01005be72b482535508126e4d75a881c92a6d6e3096", "bytes": 39590, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2021.665276", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8264429", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE18842", "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=GSE18842", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18842", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM466947", "GSM466948", "GSM466949", "GSM466950", "GSM466951", "GSM466952", "GSM466953", "GSM466954", "GSM466955", "GSM466956", "GSM466957", "GSM466958", "GSM466959", "GSM466960", "GSM466961", "GSM466962", "GSM466963", "GSM466964", "GSM466965", "GSM466966", "GSM466967", "GSM466968", "GSM466969", "GSM466970", "GSM466971", "GSM466972", "GSM466973", "GSM466974", "GSM466975", "GSM466976", "GSM466977", "GSM466978", "GSM466979", "GSM466980", "GSM466981", "GSM466982", "GSM466983", "GSM466984", "GSM466985", "GSM466986", "GSM466987", "GSM466988", "GSM466989", "GSM466990", "GSM466991", "GSM466992", "GSM466993", "GSM466994", "GSM466995", "GSM466996", "GSM466997", "GSM466998", "GSM466999", "GSM467000", "GSM467001", "GSM467002", "GSM467003", "GSM467004", "GSM467005", "GSM467006", "GSM467007", "GSM467008", "GSM467009", "GSM467010", "GSM467011", "GSM467012", "GSM467013", "GSM467014", "GSM467015", "GSM467016", "GSM467017", "GSM467018", "GSM467019", "GSM467020", "GSM467021", "GSM467022", "GSM467023", "GSM467024", "GSM467025", "GSM467026", "GSM467027", "GSM467028", "GSM467029", "GSM467030", "GSM467031", "GSM467032", "GSM467033", "GSM467034", "GSM467035", "GSM467036", "GSM467037"], "sample_count": 91, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression analysis of human lung cancer and control samples", "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:GSE19188", "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=GSE19188", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19188", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM475656", "GSM475657", "GSM475658", "GSM475659", "GSM475660", "GSM475661", "GSM475662", "GSM475663", "GSM475664", "GSM475665", "GSM475666", "GSM475667", "GSM475668", "GSM475669", "GSM475670", "GSM475671", "GSM475672", "GSM475673", "GSM475674", "GSM475675", "GSM475676", "GSM475677", "GSM475678", "GSM475679", "GSM475680", "GSM475681", "GSM475682", "GSM475683", "GSM475684", "GSM475685", "GSM475686", "GSM475687", "GSM475688", "GSM475689", "GSM475690", "GSM475691", "GSM475692", "GSM475693", "GSM475694", "GSM475695", "GSM475696", "GSM475697", "GSM475698", "GSM475699", "GSM475700", "GSM475701", "GSM475702", "GSM475703", "GSM475704", "GSM475705", "GSM475706", "GSM475707", "GSM475708", "GSM475709", "GSM475710", "GSM475711", "GSM475712", "GSM475713", "GSM475714", "GSM475715", "GSM475716", "GSM475717", "GSM475718", "GSM475719", "GSM475720", "GSM475721", "GSM475722", "GSM475723", "GSM475724", "GSM475725", "GSM475726", "GSM475727", "GSM475728", "GSM475729", "GSM475730", "GSM475731", "GSM475732", "GSM475733", "GSM475734", "GSM475735", "GSM475736", "GSM475737", "GSM475738", "GSM475739", "GSM475740", "GSM475741", "GSM475742", "GSM475743", "GSM475744", "GSM475745", "GSM475746", "GSM475747", "GSM475748", "GSM475749", "GSM475750", "GSM475751", "GSM475752", "GSM475753", "GSM475754", "GSM475755", "GSM475756", "GSM475757", "GSM475758", "GSM475759", "GSM475760", "GSM475761", "GSM475762", "GSM475763", "GSM475764", "GSM475765", "GSM475766", "GSM475767", "GSM475768", "GSM475769", "GSM475770", "GSM475771", "GSM475772", "GSM475773", "GSM475774", "GSM475775", "GSM475776", "GSM475777", "GSM475778", "GSM475779", "GSM475780", "GSM475781", "GSM475782", "GSM475783", "GSM475784", "GSM475785", "GSM475786", "GSM475787", "GSM475788", "GSM475789", "GSM475790", "GSM475791", "GSM475792", "GSM475793", "GSM475794", "GSM475795", "GSM475796", "GSM475797", "GSM475798", "GSM475799", "GSM475800", "GSM475801", "GSM475802", "GSM475803", "GSM475804", "GSM475805", "GSM475806", "GSM475807", "GSM475808", "GSM475809", "GSM475810", "GSM475811"], "sample_count": 156, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data for early stage NSCLC", "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:GSE40791", "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=GSE40791", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40791", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1001510", "GSM1001511", "GSM1001512", "GSM1001513", "GSM1001514", "GSM1001515", "GSM1001516", "GSM1001517", "GSM1001518", "GSM1001519", "GSM1001520", "GSM1001521", "GSM1001522", "GSM1001523", "GSM1001524", "GSM1001525", "GSM1001526", "GSM1001527", "GSM1001528", "GSM1001529", "GSM1001530", "GSM1001531", "GSM1001532", "GSM1001533", "GSM1001534", "GSM1001535", "GSM1001536", "GSM1001537", "GSM1001538", "GSM1001539", "GSM1001540", "GSM1001541", "GSM1001542", "GSM1001543", "GSM1001544", "GSM1001545", "GSM1001546", "GSM1001547", "GSM1001548", "GSM1001549", "GSM1001550", "GSM1001551", "GSM1001552", "GSM1001553", "GSM1001554", "GSM1001555", "GSM1001556", "GSM1001557", "GSM1001558", "GSM1001559", "GSM1001560", "GSM1001561", "GSM1001562", "GSM1001563", "GSM1001564", "GSM1001565", "GSM1001566", "GSM1001567", "GSM1001568", "GSM1001569", "GSM1001570", "GSM1001571", "GSM1001572", "GSM1001573", "GSM1001574", "GSM1001575", "GSM1001576", "GSM1001577", "GSM1001578", "GSM1001579", "GSM1001580", "GSM1001581", "GSM1001582", "GSM1001583", "GSM1001584", "GSM1001585", "GSM1001586", "GSM1001587", "GSM1001588", "GSM1001589", "GSM1001590", "GSM1001591", "GSM1001592", "GSM1001593", "GSM1001594", "GSM1001595", "GSM1001596", "GSM1001597", "GSM1001598", "GSM1001599", "GSM1001600", "GSM1001601", "GSM1001602", "GSM1001603", "GSM1001604", "GSM1001605", "GSM1001606", "GSM1001607", "GSM1001608", "GSM1001609", "GSM1001610", "GSM1001611", "GSM1001612", "GSM1001613", "GSM1001614", "GSM1001615", "GSM1001616", "GSM1001617", "GSM1001618", "GSM1001619", "GSM1001620", "GSM1001621", "GSM1001622", "GSM1001623", "GSM1001624", "GSM1001625", "GSM1001626", "GSM1001627", "GSM1001628", "GSM1001629", "GSM1001630", "GSM1001631", "GSM1001632", "GSM1001633", "GSM1001634", "GSM1001635", "GSM1001636", "GSM1001637", "GSM1001638", "GSM1001639", "GSM1001640", "GSM1001641", "GSM1001642", "GSM1001643", "GSM1001644", "GSM1001645", "GSM1001646", "GSM1001647", "GSM1001648", "GSM1001649", "GSM1001650", "GSM1001651", "GSM1001652", "GSM1001653", "GSM1001654", "GSM1001655", "GSM1001656", "GSM1001657", "GSM1001658", "GSM1001659", "GSM1001660", "GSM1001661", "GSM1001662", "GSM1001663", "GSM1001664", "GSM1001665", "GSM1001666", "GSM1001667", "GSM1001668", "GSM1001669", "GSM1001670", "GSM1001671", "GSM1001672", "GSM1001673", "GSM1001674", "GSM1001675", "GSM1001676", "GSM1001677", "GSM1001678", "GSM1001679", "GSM1001680", "GSM1001681", "GSM1001682", "GSM1001683", "GSM1001684", "GSM1001685", "GSM1001686", "GSM1001687", "GSM1001688", "GSM1001689", "GSM1001690", "GSM1001691", "GSM1001692", "GSM1001693", "GSM1001694", "GSM1001695", "GSM1001696", "GSM1001697", "GSM1001698", "GSM1001699", "GSM1001700", "GSM1001701", "GSM1001702", "GSM1001703"], "sample_count": 194, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Usp44 binds centrin to regulate centrosome positioning and suppress tumorigenesis", "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:GSE50081", "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=GSE50081", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50081", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1213669", "GSM1213670", "GSM1213671", "GSM1213672", "GSM1213673", "GSM1213674", "GSM1213675", "GSM1213676", "GSM1213677", "GSM1213678", "GSM1213679", "GSM1213680", "GSM1213681", "GSM1213682", "GSM1213683", "GSM1213684", "GSM1213685", "GSM1213686", "GSM1213687", "GSM1213688", "GSM1213689", "GSM1213690", "GSM1213691", "GSM1213692", "GSM1213693", "GSM1213694", "GSM1213695", "GSM1213696", "GSM1213697", "GSM1213698", "GSM1213699", "GSM1213700", "GSM1213701", "GSM1213702", "GSM1213703", "GSM1213704", "GSM1213705", "GSM1213706", "GSM1213707", "GSM1213708", "GSM1213709", "GSM1213710", "GSM1213711", "GSM1213712", "GSM1213713", "GSM1213714", "GSM1213715", "GSM1213716", "GSM1213717", "GSM1213718", "GSM1213719", "GSM1213720", "GSM1213721", "GSM1213722", "GSM1213723", "GSM1213724", "GSM1213725", "GSM1213726", "GSM1213727", "GSM1213728", "GSM1213729", "GSM1213730", "GSM1213731", "GSM1213732", "GSM1213733", "GSM1213734", "GSM1213735", "GSM1213736", "GSM1213737", "GSM1213738", "GSM1213739", "GSM1213740", "GSM1213741", "GSM1213742", "GSM1213743", "GSM1213744", "GSM1213745", "GSM1213746", "GSM1213747", "GSM1213748", "GSM1213749", "GSM1213750", "GSM1213751", "GSM1213752", "GSM1213753", "GSM1213754", "GSM1213755", "GSM1213756", "GSM1213757", "GSM1213758", "GSM1213759", "GSM1213760", "GSM1213761", "GSM1213762", "GSM1213763", "GSM1213764", "GSM1213765", "GSM1213766", "GSM1213767", "GSM1213768", "GSM1213769", "GSM1213770", "GSM1213771", "GSM1213772", "GSM1213773", "GSM1213774", "GSM1213775", "GSM1213776", "GSM1213777", "GSM1213778", "GSM1213779", "GSM1213780", "GSM1213781", "GSM1213782", "GSM1213783", "GSM1213784", "GSM1213785", "GSM1213786", "GSM1213787", "GSM1213788", "GSM1213789", "GSM1213790", "GSM1213791", "GSM1213792", "GSM1213793", "GSM1213794", "GSM1213795", "GSM1213796", "GSM1213797", "GSM1213798", "GSM1213799", "GSM1213800", "GSM1213801", "GSM1213802", "GSM1213803", "GSM1213804", "GSM1213805", "GSM1213806", "GSM1213807", "GSM1213808", "GSM1213809", "GSM1213810", "GSM1213811", "GSM1213812", "GSM1213813", "GSM1213814", "GSM1213815", "GSM1213816", "GSM1213817", "GSM1213818", "GSM1213819", "GSM1213820", "GSM1213821", "GSM1213822", "GSM1213823", "GSM1213824", "GSM1213825", "GSM1213826", "GSM1213827", "GSM1213828", "GSM1213829", "GSM1213830", "GSM1213831", "GSM1213832", "GSM1213833", "GSM1213834", "GSM1213835", "GSM1213836", "GSM1213837", "GSM1213838", "GSM1213839", "GSM1213840", "GSM1213841", "GSM1213842", "GSM1213843", "GSM1213844", "GSM1213845", "GSM1213846", "GSM1213847", "GSM1213848", "GSM1213849"], "sample_count": 181, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Validation of a histology-independent prognostic gene signature for early stage, non-small cell lung cancer including stage IA patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34249701:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6563a4c16072a26ac0c2c6383a45d90910696a5717c3d33ee46a8693f7646c9b", "bytes": 626, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T1", "version": null, "note": "Characteristics of the public microarray datasets used in this study.", "structure": {"pmcid": "PMC8264429", "section_index": 16, "section_title": "Construction and Assessment of a Five-Gene Prognostic Signature", "row_count": 6, "column_count": 5}, "table": {"label": "Table 1", "caption": "Characteristics of the public microarray datasets used in this study.", "rows": [["Study", "Species/array platform", "Samples", "Type", "Function"], ["TCGA-LUAD", "Human Illumina HiSeq 2000", "332 Cancer", "LUAD", "Training set"], ["GSE50081", "(GPL570)", "128 Cancer", "LUAD", "Validation set"], ["GSE18842", "(GPL570)", "45 Normal and 46 Cancer", "NSCLC", "For DEGs"], ["GSE19188", "(GPL570)", "65 Normal and 91 Cancer", "NSCLC", "For DEGs"], ["GSE40791", "(GPL570)", "100 Normal and 94 Cancer", "NSCLC", "For DEGs"]], "row_count": 6, "column_count": 5, "numeric_cells": 14, "header_rows": 1, "locator": "section[16]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34249701:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b4cb09c8de08d81942b9938e16b6515606b0bad99af2332af426b05ff12a9197", "bytes": 657, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T2", "version": null, "note": "Multivariate Cox regression analysis of the 5-gene signature.", "structure": {"pmcid": "PMC8264429", "section_index": 16, "section_title": "Construction and Assessment of a Five-Gene Prognostic Signature", "row_count": 6, "column_count": 6}, "table": {"label": "Table 2", "caption": "Multivariate Cox regression analysis of the 5-gene signature.", "rows": [["ID", "Coef", "HR", "HR.95L", "HR.95H", "P-value"], ["KIF20A", "0.301291283", "1.351602983", "1.103810884", "1.65502139", "0.003547525"], ["LIFR", "−0.182264632", "0.833380772", "0.672709557", "1.032427002", "0.095329705"], ["RGS13", "−1.100168875", "0.332814875", "0.117059758", "0.946232446", "0.039052759"], ["KLF4", "0.240230298", "1.27154195", "1.070939257", "1.509720483", "0.006100447"], ["KRT6A", "0.085854478", "1.089647749", "1.012552387", "1.172613123", "0.0218395"]], "row_count": 6, "column_count": 6, "numeric_cells": 29, "header_rows": 1, "locator": "section[16]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:34249701:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7b5518d8517552ec672cc4ea98632b3703bf996c16d97b10359c4f5ce2f8f3dc", "bytes": 630, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#T3", "version": null, "note": "Eight candidate drugs of connectivity map analysis.", "structure": {"pmcid": "PMC8264429", "section_index": 19, "section_title": "Screening of Potential Drugs for LUAD by CMAP Analysis", "row_count": 10, "column_count": 4}, "table": {"label": "Table 3", "caption": "Eight candidate drugs of connectivity map analysis.", "rows": [["CMAP name", "Mean", "P", "Percent non-null"], ["medrysone", "−0.68", "0.00064", "100"], ["0175029-0000", "−0.649", "0.00073", "100"], ["ginkgolide A", "−0.73", "0.00105", "100"], ["repaglinide", "−0.722", "0.00275", "100"], ["trioxysalen", "−0.663", "0.00336", "100"], ["gliclazide", "−0.66", "0.00432", "100"], ["0173570-0000", "−0.734", "0.00465", "100"], ["eucatropine", "−0.621", "0.00528", "100"], ["0297417-0002B", "−0.658", "0.00863", "100"]], "row_count": 10, "column_count": 4, "numeric_cells": 30, "header_rows": 1, "locator": "section[19]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:34249701:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3aab4eefc56eef7f51da2e536f28fb06aa54a310527a86c87f1881ad2a09ab52", "bytes": 323, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#T4", "version": null, "note": "Binding energy for targets with their drugs.", "structure": {"pmcid": "PMC8264429", "section_index": 21, "section_title": "Identification of the Candidate Targets of Gliclazide by Molecular Docking Analysis", "row_count": 6, "column_count": 2}, "table": {"label": "Table 4", "caption": "Binding energy for targets with their drugs.", "rows": [["Protein", "Docking score (kcal/mol)"], ["", "Gliclazide"], ["CCNB1", "−8.9"], ["CCNB2", "−8.6"], ["CDK1", "−8.3"], ["AURKA", "−6.9"]], "row_count": 6, "column_count": 2, "numeric_cells": 4, "header_rows": 2, "locator": "section[21]/table-wrap[1]#T4"}}], "gaps": ["asset:data:geo:GSE18842 not downloaded", "asset:data:geo:GSE18842 licence not read", "asset:data:geo:GSE19188 not downloaded", "asset:data:geo:GSE19188 licence not read", "asset:data:geo:GSE40791 not downloaded", "asset:data:geo:GSE40791 licence not read", "asset:data:geo:GSE50081 not downloaded", "asset:data:geo:GSE50081 licence not read"]}, "analysis": {"state": "partial", "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": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "log-rank"}}, {"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": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-4", "family": null, "specific": null, "label": "Univariate and multivariate Cox proportional hazard regression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Univariate and multivariate Cox proportional hazard regression analysis was also performed to access the relationship between RS and OS."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["GSE18842", "GSE19188", "GSE40791", "GSE50081"], "resolved_accessions": ["GSE18842", "GSE19188", "GSE40791", "GSE50081"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE18842, GSE19188, GSE40791, GSE50081 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": ["survival_km"], "assets": ["source:pmid:34249701", "data:geo:GSE18842", "asset:table:pmid:34249701:1", "asset:table:pmid:34249701:2", "asset:table:pmid:34249701:3", "asset:table:pmid:34249701:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE18842"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:07Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 29376, "completion_tokens": 1766, "cached_tokens": 784}}, "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:34249701", "type": "paper", "label": "pmid:34249701"}, {"id": "source:pmid:34249701", "type": "manuscript", "label": "PMID 34249701 full text"}, {"id": "data:geo:GSE18842", "type": "dataset", "label": "GEO GSE18842"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34249701", "type": "paper", "label": "pmid:34249701"}, {"id": "source:pmid:34249701", "type": "manuscript", "label": "PMID 34249701 full text"}, {"id": "data:geo:GSE18842", "type": "dataset", "label": "GEO GSE18842"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34249701", "type": "extraction", "used": ["source:pmid:34249701"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE18842", "type": "accession_resolution", "used": ["data:geo:GSE18842"], "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:34249701", "parent_hash": "sha256:649023cac97c951efe4bd3bdd12c01bdfd3e86dda0c21e62d33e1b3d6400e85b", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE18842 licence not read", "asset:data:geo:GSE18842 not downloaded", "asset:data:geo:GSE19188 licence not read", "asset:data:geo:GSE19188 not downloaded", "asset:data:geo:GSE40791 licence not read", "asset:data:geo:GSE40791 not downloaded", "asset:data:geo:GSE50081 licence not read", "asset:data:geo:GSE50081 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["de was shown to induce cell cycle arrest and apoptosis in LUAD cells possibly by targeting CCNB1, C"], "order_basis": "paper_text_order:1614", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["my of Sciences (Shanghai, China). Cells were cultured in RPMI1640 medium supplemented with 10% fetal", "t each experiment. Two human LUAD cell lines A549 and H1299 were purchased from Shanghai Insti"], "order_basis": "paper_text_order:2221", "id": "assay:2"}, {"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": "consumes_earlier_output", "id": "assay:3"}]}