{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24809982", "kind": "science-record", "revision": 7, "content_hash": "sha256:ccefd6f5ec859e123ab401980ac74b8fb1197d12d1cf913dc1b3a7fdc40eee40", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T21:58:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A long non-coding RNA signature to improve prognosis prediction of colorectal cancer.", "doi": "10.18632/oncotarget.1895", "pmid": "24809982", "authors": ["Ye Hu", "Hao-Yan Chen", "Chen-Yang Yu", "Jie Xu", "Ji-Lin Wang", "Jin Qian", "Xi Zhang", "Jing-Yuan Fang"], "journal": "Oncotarget", "year": 2014, "abstract": "Increasing evidence suggests long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers, however, few related lncRNA signatures have been established for prediction of cancer prognosis. We aimed to develop a lncRNA signature to improve prognosis prediction of colorectal cancer (CRC). Using a lncRNA-mining approach, we performed lncRNA expression profiling in large CRC cohorts from Gene Expression Ominus (GEO), including GSE39582 test series(N=436), internal validation series (N=117); and two independent validation series GSE14333 (N=197) and GSE17536(N=145). We established a set of six lncRNAs that were significantly correlated with the disease free survival (DFS) in the test series. Based on this six-lncRNA signature, the test series patients could be classified into high-risk and low-risk subgroups with significantly different DFS (HR=2.670; P<0.0001). The prognostic value of this six-lncRNA signature was confirmed in the internal validation series and another two independent CRC sets. Gene set enrichment analysis (GSEA) analysis suggested that risk score positively correlated with several cancer metastasis related pathways. Functional experiments demonstrated three dysregulated lncRNAs, AK123657, BX648207 and BX649059 were required for efficient invasion and proliferation suppression in CRC cell lines. Our results might provide an efficient classification tool for clinical prognosis evaluation of CRC.", "claims": [{"id": "claim-method", "statement": "The association between the lncRNA expression and patient's disease free survival (DFS) and disease specific survival (DSS) was assessed by univariable Cox regression analysis along with a permutation test using Biometric Research Branch-Array (BRB-Array) Tools [39].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24809982", "locator": "sections[15] \"Statistical analysis\" paragraph 2", "quote": "The association between the lncRNA expression and patient's disease free survival (DFS) and disease specific survival (DSS) was assessed by univariable Cox regression analysis along with a permutation test using Biometric Research Branch-Array (BRB-Array) Tools [39]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24809982", "locator": "sections[24] \"Data sharing statement\" paragraph 2", "quote": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used univariable and multivariable Cox proportional hazards regression, Kaplan–Meier analysis with log-rank tests, and GSEA; source microarray data and clinical data were obtained from the public GEO database, with prognostic lncRNAs selected in the GSE39582 test series and validated in internal and independent cohorts. The headline result was identification of a six-lncRNA signature that classified CRC patients into groups with significantly different disease-free survival.", "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:24809982"], "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:GSE14333"], "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:GSE14333"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24809982", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.1895", "sha256": "sha256:13a3500f3a27691cf0dc262464607ef57a73fe2c5796a83c963ef75b9b67e92f", "bytes": 45721, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.1895", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4039159", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14333", "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=GSE14333", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14333", "version": null, "note": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM358341", "GSM358342", "GSM358343", "GSM358344", "GSM358345", "GSM358346", "GSM358347", "GSM358348", "GSM358349", "GSM358350", "GSM358351", "GSM358352", "GSM358353", "GSM358354", "GSM358355", "GSM358356", "GSM358357", "GSM358358", "GSM358359", "GSM358360", "GSM358361", "GSM358362", "GSM358363", "GSM358364", "GSM358365", "GSM358366", "GSM358367", "GSM358368", "GSM358369", "GSM358370", "GSM358371", "GSM358372", "GSM358373", "GSM358374", "GSM358375", "GSM358376", "GSM358377", "GSM358378", "GSM358379", "GSM358380", "GSM358381", "GSM358382", "GSM358383", "GSM358384", "GSM358385", "GSM358386", "GSM358387", "GSM358388", "GSM358389", "GSM358390", "GSM358391", "GSM358392", "GSM358393", "GSM358394", "GSM358395", "GSM358396", "GSM358397", "GSM358398", "GSM358399", "GSM358400", "GSM358401", "GSM358402", "GSM358403", "GSM358404", "GSM358405", "GSM358406", "GSM358407", "GSM358408", "GSM358409", "GSM358410", "GSM358411", "GSM358412", "GSM358413", "GSM358414", "GSM358415", "GSM358416", "GSM358417", "GSM358418", "GSM358419", "GSM358420", "GSM358421", "GSM358422", "GSM358423", "GSM358424", "GSM358425", "GSM358426", "GSM358427", "GSM358428", "GSM358429", "GSM358430", "GSM358431", "GSM358432", "GSM358433", "GSM358434", "GSM358435", "GSM358436", "GSM358437", "GSM358438", "GSM358439", "GSM358440", "GSM358441", "GSM358442", "GSM358443", "GSM358444", "GSM358445", "GSM358446", "GSM358447", "GSM358448", "GSM358449", "GSM358450", "GSM358451", "GSM358452", "GSM358453", "GSM358454", "GSM358455", "GSM358456", "GSM358457", "GSM358458", "GSM358459", "GSM358460", "GSM358461", "GSM358462", "GSM358463", "GSM358464", "GSM358465", "GSM358466", "GSM358467", "GSM358468", "GSM358469", "GSM358470", "GSM358471", "GSM358472", "GSM358473", "GSM358474", "GSM358475", "GSM358476", "GSM358477", "GSM358478", "GSM358479", "GSM358480", "GSM358481", "GSM358482", "GSM358483", "GSM358484", "GSM358485", "GSM358486", "GSM358487", "GSM358488", "GSM358489", "GSM358490", "GSM358491", "GSM358492", "GSM358493", "GSM358494", "GSM358495", "GSM358496", "GSM358497", "GSM358498", "GSM358499", "GSM358500", "GSM358501", "GSM358502", "GSM358503", "GSM358504", "GSM358505", "GSM358506", "GSM358507", "GSM358508", "GSM358509", "GSM358510", "GSM358511", "GSM358512", "GSM358513", "GSM358514", "GSM358515", "GSM358516", "GSM358517", "GSM358518", "GSM358519", "GSM358520", "GSM358521", "GSM358522", "GSM358523", "GSM358524", "GSM358525", "GSM358526", "GSM358527", "GSM358528", "GSM358529", "GSM358530", "GSM358531", "GSM358532", "GSM358533", "GSM358534", "GSM358535", "GSM358536", "GSM358537", "GSM358538", "GSM358539", "GSM358540", "GSM358541", "GSM358542", "GSM358543", "GSM358544", "GSM358545", "GSM358546", "GSM358547", "GSM358548", "GSM358549", "GSM358550", "GSM358551", "GSM358552", "GSM358553", "GSM358554", "GSM358555", "GSM358556", "GSM358557", "GSM358558", "GSM358559", "GSM358560", "GSM358561", "GSM358562", "GSM358563", "GSM358564", "GSM358565", "GSM358566", "GSM358567", "GSM358568", "GSM358569", "GSM358570", "GSM358571", "GSM358572", "GSM358573", "GSM358574", "GSM358575", "GSM358576", "GSM358577", "GSM358578", "GSM358579", "GSM358580", "GSM358581", "GSM358582", "GSM358583", "GSM358584", "GSM358585", "GSM358586", "GSM358587", "GSM358588", "GSM358589", "GSM358590", "GSM358591", "GSM358592", "GSM358593", "GSM358594", "GSM358595", "GSM358596", "GSM358597", "GSM358598", "GSM358599", "GSM358600", "GSM358601", "GSM358602", "GSM358603", "GSM358604", "GSM358605", "GSM358606", "GSM358607", "GSM358608", "GSM358609", "GSM358610", "GSM358611", "GSM358612", "GSM358613", "GSM358614", "GSM358615", "GSM358616", "GSM358617", "GSM358618", "GSM358619", "GSM358620", "GSM358621", "GSM358622", "GSM358623", "GSM358624", "GSM358625", "GSM358626", "GSM358627", "GSM358628", "GSM358629", "GSM358630"], "sample_count": 290, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from 290 primary colorectal cancers", "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:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM437093", "GSM437094", "GSM437095", "GSM437096", "GSM437097", "GSM437098", "GSM437099", "GSM437100", "GSM437101", "GSM437102", "GSM437103", "GSM437104", "GSM437105", "GSM437106", "GSM437107", "GSM437108", "GSM437109", "GSM437110", "GSM437111", "GSM437112", "GSM437113", "GSM437114", "GSM437115", "GSM437116", "GSM437117", "GSM437118", "GSM437119", "GSM437120", "GSM437121", "GSM437122", "GSM437123", "GSM437124", "GSM437125", "GSM437126", "GSM437127", "GSM437128", "GSM437129", "GSM437130", "GSM437131", "GSM437132", "GSM437133", "GSM437134", "GSM437135", "GSM437136", "GSM437137", "GSM437138", "GSM437139", "GSM437140", "GSM437141", "GSM437142", "GSM437143", "GSM437144", "GSM437145", "GSM437146", "GSM437147", "GSM437148", "GSM437149", "GSM437150", "GSM437151", "GSM437152", "GSM437153", "GSM437154", "GSM437155", "GSM437156", "GSM437157", "GSM437158", "GSM437159", "GSM437160", "GSM437161", "GSM437162", "GSM437163", "GSM437164", "GSM437165", "GSM437166", "GSM437167", "GSM437168", "GSM437169", "GSM437170", "GSM437171", "GSM437172", "GSM437173", "GSM437174", "GSM437175", "GSM437176", "GSM437177", "GSM437178", "GSM437179", "GSM437180", "GSM437181", "GSM437182", "GSM437183", "GSM437184", "GSM437185", "GSM437186", "GSM437187", "GSM437188", "GSM437189", "GSM437190", "GSM437191", "GSM437192", "GSM437193", "GSM437194", "GSM437195", "GSM437196", "GSM437197", "GSM437198", "GSM437199", "GSM437200", "GSM437201", "GSM437202", "GSM437203", "GSM437204", "GSM437205", "GSM437206", "GSM437207", "GSM437208", "GSM437209", "GSM437210", "GSM437211", "GSM437212", "GSM437213", "GSM437214", "GSM437215", "GSM437216", "GSM437217", "GSM437218", "GSM437219", "GSM437220", "GSM437221", "GSM437222", "GSM437223", "GSM437224", "GSM437225", "GSM437226", "GSM437227", "GSM437228", "GSM437229", "GSM437230", "GSM437231", "GSM437232", "GSM437233", "GSM437234", "GSM437235", "GSM437236", "GSM437237", "GSM437238", "GSM437239", "GSM437240", "GSM437241", "GSM437242", "GSM437243", "GSM437244", "GSM437245", "GSM437246", "GSM437247", "GSM437248", "GSM437249", "GSM437250", "GSM437251", "GSM437252", "GSM437253", "GSM437254", "GSM437255", "GSM437256", "GSM437257", "GSM437258", "GSM437259", "GSM437260", "GSM437261", "GSM437262", "GSM437263", "GSM437264", "GSM437265", "GSM437266", "GSM437267", "GSM437268", "GSM437269"], "sample_count": 177, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt 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:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1681353", "GSM1681354", "GSM1681355", "GSM1681356", "GSM1681357", "GSM1681358", "GSM1681359", "GSM1681360", "GSM1681361", "GSM1681362", "GSM1681363", "GSM1681364", "GSM1681365", "GSM1681366", "GSM1681367", "GSM1681368", "GSM1681369", "GSM1681370", "GSM1681371", "GSM971957", "GSM971958", "GSM971959", "GSM971960", "GSM971961", "GSM971962", "GSM971963", "GSM971964", "GSM971965", "GSM971966", "GSM971967", "GSM971968", "GSM971969", "GSM971970", "GSM971971", "GSM971972", "GSM971973", "GSM971974", "GSM971975", "GSM971976", "GSM971977", "GSM971978", "GSM971979", "GSM971980", "GSM971981", "GSM971982", "GSM971983", "GSM971984", "GSM971985", "GSM971986", "GSM971987", "GSM971988", "GSM971989", "GSM971990", "GSM971991", "GSM971992", "GSM971993", "GSM971994", "GSM971995", "GSM971996", "GSM971997", "GSM971998", "GSM971999", "GSM972000", "GSM972001", "GSM972002", "GSM972003", "GSM972004", "GSM972005", "GSM972006", "GSM972007", "GSM972008", "GSM972009", "GSM972010", "GSM972011", "GSM972012", "GSM972013", "GSM972014", "GSM972015", "GSM972016", "GSM972017", "GSM972018", "GSM972019", "GSM972020", "GSM972021", "GSM972022", "GSM972023", "GSM972024", "GSM972025", "GSM972026", "GSM972027", "GSM972028", "GSM972029", "GSM972030", "GSM972031", "GSM972032", "GSM972033", "GSM972034", "GSM972035", "GSM972036", "GSM972037", "GSM972038", "GSM972039", "GSM972040", "GSM972041", "GSM972042", "GSM972043", "GSM972044", "GSM972045", "GSM972046", "GSM972047", "GSM972048", "GSM972049", "GSM972050", "GSM972051", "GSM972052", "GSM972053", "GSM972054", "GSM972055", "GSM972056", "GSM972057", "GSM972058", "GSM972059", "GSM972060", "GSM972061", "GSM972062", "GSM972063", "GSM972064", "GSM972065", "GSM972066", "GSM972067", "GSM972068", "GSM972069", "GSM972070", "GSM972071", "GSM972072", "GSM972073", "GSM972074", "GSM972075", "GSM972076", "GSM972077", "GSM972078", "GSM972079", "GSM972080", "GSM972081", "GSM972082", "GSM972083", "GSM972084", "GSM972085", "GSM972086", "GSM972087", "GSM972088", "GSM972089", "GSM972090", "GSM972091", "GSM972092", "GSM972093", "GSM972094", "GSM972095", "GSM972096", "GSM972097", "GSM972098", "GSM972099", "GSM972100", "GSM972101", "GSM972102", "GSM972103", "GSM972104", "GSM972105", "GSM972106", "GSM972107", "GSM972108", "GSM972109", "GSM972110", "GSM972111", "GSM972112", "GSM972113", "GSM972114", "GSM972115", "GSM972116", "GSM972117", "GSM972118", "GSM972119", "GSM972120", "GSM972121", "GSM972122", "GSM972123", "GSM972124", "GSM972125", "GSM972126", "GSM972127", "GSM972128", "GSM972129", "GSM972130", "GSM972131", "GSM972132", "GSM972133", "GSM972134", "GSM972135", "GSM972136", "GSM972137", "GSM972138", "GSM972139", "GSM972140", "GSM972141", "GSM972142", "GSM972143", "GSM972144", "GSM972145", "GSM972146", "GSM972147", "GSM972148", "GSM972149", "GSM972150", "GSM972151", "GSM972152", "GSM972153", "GSM972154", "GSM972155", "GSM972156", "GSM972157", "GSM972158", "GSM972159", "GSM972160", "GSM972161", "GSM972162", "GSM972163", "GSM972164", "GSM972165", "GSM972166", "GSM972167", "GSM972168", "GSM972169", "GSM972170", "GSM972171", "GSM972172", "GSM972173", "GSM972174", "GSM972175", "GSM972176", "GSM972177", "GSM972178", "GSM972179", "GSM972180", "GSM972181", "GSM972182", "GSM972183", "GSM972184", "GSM972185", "GSM972186", "GSM972187", "GSM972188", "GSM972189", "GSM972190", "GSM972191", "GSM972192", "GSM972193", "GSM972194", "GSM972195", "GSM972196", "GSM972197", "GSM972198", "GSM972199", "GSM972200", "GSM972201", "GSM972202", "GSM972203", "GSM972204", "GSM972205", "GSM972206", "GSM972207", "GSM972208", "GSM972209", "GSM972210", "GSM972211", "GSM972212", "GSM972213", "GSM972214", "GSM972215", "GSM972216", "GSM972217", "GSM972218", "GSM972219", "GSM972220", "GSM972221", "GSM972222", "GSM972223", "GSM972224", "GSM972225", "GSM972226", "GSM972227", "GSM972228", "GSM972229", "GSM972230", "GSM972231", "GSM972232", "GSM972233", "GSM972234", "GSM972235", "GSM972236", "GSM972237", "GSM972238", "GSM972239", "GSM972240", "GSM972241", "GSM972242", "GSM972243", "GSM972244", "GSM972245", "GSM972246", "GSM972247", "GSM972248", "GSM972249", "GSM972250", "GSM972251", "GSM972252", "GSM972253", "GSM972254", "GSM972255", "GSM972256", "GSM972257", "GSM972258", "GSM972259", "GSM972260", "GSM972261", "GSM972262", "GSM972263", "GSM972264", "GSM972265", "GSM972266", "GSM972267", "GSM972268", "GSM972269", "GSM972270", "GSM972271", "GSM972272", "GSM972273", "GSM972274", "GSM972275", "GSM972276", "GSM972277", "GSM972278", "GSM972279", "GSM972280", "GSM972281", "GSM972282", "GSM972283", "GSM972284", "GSM972285", "GSM972286", "GSM972287", "GSM972288", "GSM972289", "GSM972290", "GSM972291", "GSM972292", "GSM972293", "GSM972294", "GSM972295", "GSM972296", "GSM972297", "GSM972298", "GSM972299", "GSM972300", "GSM972301", "GSM972302", "GSM972303", "GSM972304", "GSM972305", "GSM972306", "GSM972307", "GSM972308", "GSM972309", "GSM972310", "GSM972311", "GSM972312", "GSM972313", "GSM972314", "GSM972315", "GSM972316", "GSM972317", "GSM972318", "GSM972319", "GSM972320", "GSM972321", "GSM972322", "GSM972323", "GSM972324", "GSM972325", "GSM972326", "GSM972327", "GSM972328", "GSM972329", "GSM972330", "GSM972331", "GSM972332", "GSM972333", "GSM972334", "GSM972335", "GSM972336", "GSM972337", "GSM972338", "GSM972339", "GSM972340", "GSM972341", "GSM972342", "GSM972343", "GSM972344", "GSM972345", "GSM972346", "GSM972347", "GSM972348", "GSM972349", "GSM972350", "GSM972351", "GSM972352", "GSM972353", "GSM972354", "GSM972355", "GSM972356", "GSM972357", "GSM972358", "GSM972359", "GSM972360", "GSM972361", "GSM972362", "GSM972363", "GSM972364", "GSM972365", "GSM972366", "GSM972367", "GSM972368", "GSM972369", "GSM972370", "GSM972371", "GSM972372", "GSM972373", "GSM972374", "GSM972375", "GSM972376", "GSM972377", "GSM972378", "GSM972379", "GSM972380", "GSM972381", "GSM972382", "GSM972383", "GSM972384", "GSM972385", "GSM972386", "GSM972387", "GSM972388", "GSM972389", "GSM972390", "GSM972391", "GSM972392", "GSM972393", "GSM972394", "GSM972395", "GSM972396", "GSM972397", "GSM972398", "GSM972399", "GSM972400", "GSM972401", "GSM972402", "GSM972403", "GSM972404", "GSM972405", "GSM972406", "GSM972407", "GSM972408", "GSM972409", "GSM972410", "GSM972411", "GSM972412", "GSM972413", "GSM972414", "GSM972415", "GSM972416", "GSM972417", "GSM972418", "GSM972419", "GSM972420", "GSM972421", "GSM972422", "GSM972423", "GSM972424", "GSM972425", "GSM972426", "GSM972427", "GSM972428", "GSM972429", "GSM972430", "GSM972431", "GSM972432", "GSM972433", "GSM972434", "GSM972435", "GSM972436", "GSM972437", "GSM972438", "GSM972439", "GSM972440", "GSM972441", "GSM972442", "GSM972443", "GSM972444", "GSM972445", "GSM972446", "GSM972447", "GSM972448", "GSM972449", "GSM972450", "GSM972451", "GSM972452", "GSM972453", "GSM972454", "GSM972455", "GSM972456", "GSM972457", "GSM972458", "GSM972459", "GSM972460", "GSM972461", "GSM972462", "GSM972463", "GSM972464", "GSM972465", "GSM972466", "GSM972467", "GSM972468", "GSM972469", "GSM972470", "GSM972471", "GSM972472", "GSM972473", "GSM972474", "GSM972475", "GSM972476", "GSM972477", "GSM972478", "GSM972479", "GSM972480", "GSM972481", "GSM972482", "GSM972483", "GSM972484", "GSM972485", "GSM972486", "GSM972487", "GSM972488", "GSM972489", "GSM972490", "GSM972491", "GSM972492", "GSM972493", "GSM972494", "GSM972495", "GSM972496", "GSM972497", "GSM972498", "GSM972499", "GSM972500", "GSM972501", "GSM972502", "GSM972503", "GSM972504", "GSM972505", "GSM972506", "GSM972507", "GSM972508", "GSM972509", "GSM972510", "GSM972511", "GSM972512", "GSM972513", "GSM972514", "GSM972515", "GSM972516", "GSM972517", "GSM972518", "GSM972519", "GSM972520", "GSM972521", "GSM972522"], "sample_count": 585, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]", "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:GSE40966", "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=GSE40966", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40966", "version": null, "note": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1005664", "GSM1005665", "GSM1005666", "GSM1005667", "GSM1005668", "GSM1005669", "GSM1005670", "GSM1005671", "GSM1005672", "GSM1005673", "GSM1005674", "GSM1005675", "GSM1005676", "GSM1005677", "GSM1005678", "GSM1005679", "GSM1005680", "GSM1005681", "GSM1005682", "GSM1005683", "GSM1005684", "GSM1005685", "GSM1005686", "GSM1005687", "GSM1005688", "GSM1005689", "GSM1005690", "GSM1005691", "GSM1005692", "GSM1005693", "GSM1005694", "GSM1005695", "GSM1005696", "GSM1005697", "GSM1005698", "GSM1005699", "GSM1005700", "GSM1005701", "GSM1005702", "GSM1005703", "GSM1005704", "GSM1005705", "GSM1005706", "GSM1005707", "GSM1005708", "GSM1005709", "GSM1005710", "GSM1005711", "GSM1005712", "GSM1005713", "GSM1005714", "GSM1005715", "GSM1005716", "GSM1005717", "GSM1005718", "GSM1005719", "GSM1005720", "GSM1005721", "GSM1005722", "GSM1005723", "GSM1005724", "GSM1005725", "GSM1005726", "GSM1005727", "GSM1005728", "GSM1005729", "GSM1005730", "GSM1005731", "GSM1005732", "GSM1005733", "GSM1005734", "GSM1005735", "GSM1005736", "GSM1005737", "GSM1005738", "GSM1005739", "GSM1005740", "GSM1005741", "GSM1005742", "GSM1005743", "GSM1005744", "GSM1005745", "GSM1005746", "GSM1005747", "GSM1005748", "GSM1005749", "GSM1005750", "GSM1005751", "GSM1005752", "GSM1005753", "GSM1005754", "GSM1005755", "GSM1005756", "GSM1005757", "GSM1005758", "GSM1005759", "GSM1005760", "GSM1005761", "GSM1005762", "GSM1005763", "GSM1005764", "GSM1005765", "GSM1005766", "GSM1005767", "GSM1005768", "GSM1005769", "GSM1005770", "GSM1005771", "GSM1005772", "GSM1005773", "GSM1005774", "GSM1005775", "GSM1005776", "GSM1005777", "GSM1005778", "GSM1005779", "GSM1005780", "GSM1005781", "GSM1005782", "GSM1005783", "GSM1005784", "GSM1005785", "GSM1005786", "GSM1005787", "GSM1005788", "GSM1005789", "GSM1005790", "GSM1005791", "GSM1005792", "GSM1005793", "GSM1005794", "GSM1005795", "GSM1005796", "GSM1005797", "GSM1005798", "GSM1005799", "GSM1005800", "GSM1005801", "GSM1005802", "GSM1005803", "GSM1005804", "GSM1005805", "GSM1005806", "GSM1005807", "GSM1005808", "GSM1005809", "GSM1005810", "GSM1005811", "GSM1005812", "GSM1005813", "GSM1005814", "GSM1005815", "GSM1005816", "GSM1005817", "GSM1005818", "GSM1005819", "GSM1005820", "GSM1005821", "GSM1005822", "GSM1005823", "GSM1005824", "GSM1005825", "GSM1005826", "GSM1005827", "GSM1005828", "GSM1005829", "GSM1005830", "GSM1005831", "GSM1005832", "GSM1005833", "GSM1005834", "GSM1005835", "GSM1005836", "GSM1005837", "GSM1005838", "GSM1005839", "GSM1005840", "GSM1005841", "GSM1005842", "GSM1005843", "GSM1005844", "GSM1005845", "GSM1005846", "GSM1005847", "GSM1005848", "GSM1005849", "GSM1005850", "GSM1005851", "GSM1005852", "GSM1005853", "GSM1005854", "GSM1005855", "GSM1005856", "GSM1005857", "GSM1005858", "GSM1005859", "GSM1005860", "GSM1005861", "GSM1005862", "GSM1005863", "GSM1005864", "GSM1005865", "GSM1005866", "GSM1005867", "GSM1005868", "GSM1005869", "GSM1005870", "GSM1005871", "GSM1005872", "GSM1005873", "GSM1005874", "GSM1005875", "GSM1005876", "GSM1005877", "GSM1005878", "GSM1005879", "GSM1005880", "GSM1005881", "GSM1005882", "GSM1005883", "GSM1005884", "GSM1005885", "GSM1005886", "GSM1005887", "GSM1005888", "GSM1005889", "GSM1005890", "GSM1005891", "GSM1005892", "GSM1005893", "GSM1005894", "GSM1005895", "GSM1005896", "GSM1005897", "GSM1005898", "GSM1005899", "GSM1005900", "GSM1005901", "GSM1005902", "GSM1005903", "GSM1005904", "GSM1005905", "GSM1005906", "GSM1005907", "GSM1005908", "GSM1005909", "GSM1005910", "GSM1005911", "GSM1005912", "GSM1005913", "GSM1005914", "GSM1005915", "GSM1005916", "GSM1005917", "GSM1005918", "GSM1005919", "GSM1005920", "GSM1005921", "GSM1005922", "GSM1005923", "GSM1005924", "GSM1005925", "GSM1005926", "GSM1005927", "GSM1005928", "GSM1005929", "GSM1005930", "GSM1005931", "GSM1005932", "GSM1005933", "GSM1005934", "GSM1005935", "GSM1005936", "GSM1005937", "GSM1005938", "GSM1005939", "GSM1005940", "GSM1005941", "GSM1005942", "GSM1005943", "GSM1005944", "GSM1005945", "GSM1005946", "GSM1005947", "GSM1005948", "GSM1005949", "GSM1005950", "GSM1005951", "GSM1005952", "GSM1005953", "GSM1005954", "GSM1005955", "GSM1005956", "GSM1005957", "GSM1005958", "GSM1005959", "GSM1005960", "GSM1005961", "GSM1005962", "GSM1005963", "GSM1005964", "GSM1005965", "GSM1005966", "GSM1005967", "GSM1005968", "GSM1005969", "GSM1005970", "GSM1005971", "GSM1005972", "GSM1005973", "GSM1005974", "GSM1005975", "GSM1005976", "GSM1005977", "GSM1005978", "GSM1005979", "GSM1005980", "GSM1005981", "GSM1005982", "GSM1005983", "GSM1005984", "GSM1005985", "GSM1005986", "GSM1005987", "GSM1005988", "GSM1005989", "GSM1005990", "GSM1005991", "GSM1005992", "GSM1005993", "GSM1005994", "GSM1005995", "GSM1005996", "GSM1005997", "GSM1005998", "GSM1005999", "GSM1006000", "GSM1006001", "GSM1006002", "GSM1006003", "GSM1006004", "GSM1006005", "GSM1006006", "GSM1006007", "GSM1006008", "GSM1006009", "GSM1006010", "GSM1006011", "GSM1006012", "GSM1006013", "GSM1006014", "GSM1006015", "GSM1006016", "GSM1006017", "GSM1006018", "GSM1006019", "GSM1006020", "GSM1006021", "GSM1006022", "GSM1006023", "GSM1006024", "GSM1006025", "GSM1006026", "GSM1006027", "GSM1006028", "GSM1006029", "GSM1006030", "GSM1006031", "GSM1006032", "GSM1006033", "GSM1006034", "GSM1006035", "GSM1006036", "GSM1006037", "GSM1006038", "GSM1006039", "GSM1006040", "GSM1006041", "GSM1006042", "GSM1006043", "GSM1006044", "GSM1006045", "GSM1006046", "GSM1006047", "GSM1006048", "GSM1006049", "GSM1006050", "GSM1006051", "GSM1006052", "GSM1006053", "GSM1006054", "GSM1006055", "GSM1006056", "GSM1006057", "GSM1006058", "GSM1006059", "GSM1006060", "GSM1006061", "GSM1006062", "GSM1006063", "GSM1006064", "GSM1006065", "GSM1006066", "GSM1006067", "GSM1006068", "GSM1006069", "GSM1006070", "GSM1006071", "GSM1006072", "GSM1006073", "GSM1006074", "GSM1006075", "GSM1006076", "GSM1006077", "GSM1006078", "GSM1006079", "GSM1006080", "GSM1006081", "GSM1006082", "GSM1006083", "GSM1006084", "GSM1006085", "GSM1006086", "GSM1006087", "GSM1006088", "GSM1006089", "GSM1006090", "GSM1006091", "GSM1006092", "GSM1006093", "GSM1006094", "GSM1006095", "GSM1006096", "GSM1006097", "GSM1006098", "GSM1006099", "GSM1006100", "GSM1006101", "GSM1006102", "GSM1006103", "GSM1006104", "GSM1006105", "GSM1006106", "GSM1006107", "GSM1006108", "GSM1006109", "GSM1006110", "GSM1006111", "GSM1006112", "GSM1006113", "GSM1006114", "GSM1006115", "GSM1006116", "GSM1006117", "GSM1006118", "GSM1006119", "GSM1006120", "GSM1006121", "GSM1006122", "GSM1006123", "GSM1006124", "GSM1006125", "GSM1006126"], "sample_count": 463, "group_sizes": null, "group_sizes_basis": null, "platform": "16070", "taxon": "Homo sapiens", "title": "Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [CGH]", "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:24809982:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b2101c9adf9a3c35ad4ea4ee415eb44a2eead3a2402fd752624aac49f5037f76", "bytes": 579, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "LncRNAs significantly associated with the disease free survival in the test series patients (N=436)", "structure": {"pmcid": "PMC4039159", "section_index": 4, "section_title": "Identification of prognostic lncRNAs from the test series", "row_count": 7, "column_count": 4}, "table": {"label": "Table 1", "caption": "LncRNAs significantly associated with the disease free survival in the test series patients (N=436)", "rows": [["Gene symbol", "Permutation P valuea,b", "Hazard ratioa", "Coefficient"], ["AK024680", "5.47E-04", "1.329", "0.07826"], ["AK123657", "1.70E-05", "0.713", "−0.143"], ["CR622106", "1.23E-05", "0.669", "−0.19355"], ["BX649059", "5.71E-05", "0.724", "−0.00172"], ["BX648207", "1.46E-04", "0.739", "−0.20855"], ["AK026784", "1.99E-04", "1.379", "0.24326"]], "row_count": 7, "column_count": 4, "numeric_cells": 24, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:24809982:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:19c2d4e889bc79b6af350bcb0f918e09adc684c7686f633b6601281cecd88225", "bytes": 3268, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T2", "version": null, "note": "Univariable and multivariable Cox regression analysis in each data set", "structure": {"pmcid": "PMC4039159", "section_index": 5, "section_title": "The six-lncRNA signature and patients' survival in the test series", "row_count": 46, "column_count": 7}, "table": {"label": "Table 2", "caption": "Univariable and multivariable Cox regression analysis in each data set", "rows": [["Variables", "Univariable modela", "Multivariable modela"], ["", "HR", "95% CI of HR", "P value", "HR", "95% CI of HR", "P value"], ["GSE39582 test series(N=436)", "", "", "", "", ""], ["Six-lncRNA risk score", "2.717", "2.005 to 3.682", "<0.0001", "2.353", "1.723 to 3.214", "<0.0001"], ["Age", "1", "0.988 to 1.012", "0.9588", "1.005", "0.992 to 1.018", "0.4308"], ["AJCC stage", "", "", "", "", "", ""], ["1", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["2", "5.749", "0.793 to 41.661", "0.0835", "4.051", "0.557to 29.452", "0.1669"], ["3", "9.263", "1.284 to 66.828", "0.0273", "6.07", "0.837 to 44.028", "0.0745"], ["4", "31.434", "4.281 to 230.822", "0.0007", "20.837", "2.813 to 154.324", "0.003"], ["Gender", "1.337", "0.955 to 1.871", "0.0911", "1.585", "1.126 to 2.232", "0.0082"], ["GSE39582 valiation series(N=117)", "", "", "", "", ""], ["Six-lncRNA risk score", "2.271", "1.424 to 3.622", "0.0006", "2.095", "1.190 to 3.688", "0.0103"], ["Age", "1.000", "0.973 to 1.028", "0.9815", "1.02", "0.987 to 1.054", "0.2458"], ["AJCC stage", "", "", "", "", "", ""], ["1", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["2", "2674096", "0.000 to", "0.9906", "1994681", "0.000 to", "0.9916"], ["3", "9681475", "0.000 to", "0.9898", "6897474", "0.000 to", "0.9909"], ["4", "1.57E+08", "0.000 to", "0.9880", "1.52E+00", "0.000 to", "0.9891"], ["Gender", "1.060", "0.543 to 2.073", "0.8639", "1.456", "0.711 to 2.983", "0.3044"], ["Entire GSE39582 set(N=553)", "", "", "", "", ""], ["Six-lncRNA risk score", "2.565", "1.992 to 3.302", "<0.0001", "2.221", "1.703 to 2.896", "<0.0001"], ["Age", "1.000", "0.989 to 1.011", "0.9544", "1.007", "0.995 to 1.019", "0.2574"], ["AJCC stage", "", "", "", "", "", ""], ["1", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["2", "7.717", "1.069 to 55.692", "0.0427", "5.203", "0.718 to 37.701", "0.1026"], ["3", "14.808", "2.061 to 106.413", "0.0074", "9.431", "1.305 to 68.148", "0.0262"], ["4", "52.841", "7.232 to 386.063", "<0.0001", "33.045", "4.621to 250.808", "0.0005"], ["Gender", "1.271", "0.941 to 1.717", "0.1177", "1.534", "1.130 to 2.083", "0.0061"], ["GSE14333 set(N=197)", "", "", "", "", ""], ["Six-lncRNA risk score", "3.229", "1.814 to 5.749", "<0.0001", "2.589", "1.411 to 4.752", "0.0021"], ["Age", "0.978", "0.957 to 1", "0.9544", "0.991", "0.968 to 1.015", "0.4679"], ["Duke stageb", "", "", "", "", "", ""], ["A", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["B", "2.927", "0.665 to 12.889", "0.1555", "2.533", "0.574 to 11.184", "0.2200"], ["C", "6.897", "1.639 to 29.025", "0.0084", "5.204", "1.223 to 22.147", "0.0256"], ["Gender", "1.118", "0.612 to 2.042", "0.7171", "0.997", "0.533 to 1.868", "0.9935"], ["GSE17536 set(N=145)", "", "", "", "", ""], ["Six-lncRNA risk score", "3.25", "1.658 to 6.368", "0.0006", "2.892", "1.407 to 5.944", "0.0039"], ["Age", "0.984", "0.961 to 1.007", "0.1595", "0.996", "0.970 to 1.022", "0.7465"], ["AJCC stage", "", "", "", "", "", ""], ["1", "1.00(referent)", "", "", "1.00(referent)", "", ""], ["2", "5.382", "0.695 to 41.708", "0.1071", "4.66", "0.591 to 36.756", "0.1422"], ["3", "10.645", "1.428 to 79.327", "0.021", "8.445", "1.109 to 64.275", "0.0394"], ["4", "14.655", "1.637 to 131.184", "0.0164", "14.329", "1.572 to 130.581", "0.0184"], ["Gender", "1", "0.520 to 1.925", "1", "0.986", "0.482 to 2.019", "0.9703"]], "row_count": 46, "column_count": 7, "numeric_cells": 207, "header_rows": 2, "locator": "section[5]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE40966 not downloaded", "asset:data:geo:GSE40966 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The association between the lncRNA expression and patient's disease free survival (DFS) and disease specific survival (DSS) was assessed by univariable Cox regression analysis along with a permutation test using Biometric Research Branch-Array (BRB-Array) Tools [39]."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-3", "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": 0.8, "band": "high", "quote": "Kaplan Meier"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-5", "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 analysis"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "classification_metrics", "expected_value": 0.0001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE39582", "GSE14333", "GSE17536", "GSE40966"], "resolved_accessions": ["GSE39582", "GSE14333", "GSE17536", "GSE40966"], "statements": ["The gene expression data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE39582(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582), GSE17536 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536),GSE14333(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333), GSE40966(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40966)."], "basis": "The paper names GSE39582, GSE14333, GSE17536, GSE40966 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": ["cox_ph"], "assets": ["source:pmid:24809982", "data:geo:GSE14333", "asset:table:pmid:24809982:1", "asset:table:pmid:24809982:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14333"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:16Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 95963, "completion_tokens": 4938, "cached_tokens": 72522}}, "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:24809982", "type": "paper", "label": "pmid:24809982"}, {"id": "source:pmid:24809982", "type": "manuscript", "label": "PMID 24809982 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:24809982", "type": "paper", "label": "pmid:24809982"}, {"id": "source:pmid:24809982", "type": "manuscript", "label": "PMID 24809982 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-24809982", "type": "extraction", "used": ["source:pmid:24809982"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14333", "type": "accession_resolution", "used": ["data:geo:GSE14333"], "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:24809982", "parent_hash": "sha256:136b03618518539de5c053bce278902cd496773adc144e3a5aa9a1fffd526e3c", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE40966 licence not read", "asset:data:geo:GSE40966 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lysis in each data set MATERIALS AND METHODS Microarray data processing and lncRNA profile mining Th", "A customized R scripts was used to perform a microarray expression calculation according to the re-m"], "order_basis": "paper_text_order:3812", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["o a database for non-coding RNA of human and mouse derived from RNAdb [37]. A customized R scri"], "order_basis": "paper_text_order:4461", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The association between the lncRNA expression and patient's disease free survival (DFS) and disease specific survival (DSS) was assessed by univariable Cox regression analysis along with a permutation test using Biometric Research Branch-Array (BRB-Array) Tools [39]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T02:47:39+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}}}