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pmid:29088792
Association of sirtuins with clinicopathological parameters and overall survival in gastric cancer.
Xiaobing Shen · Pengfei Li · Yuchao Xu · Xiaowei Chen · Haixiang Sun · Ying Zhao · Mengqi Liu · Wenwen Zhang
Oncotarget · 2017 doi:10.18632/oncotarget.20799
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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The results suggested that SIRT4, SIRT6, and SIRT7 were associated with Lauren classification and SIRT3-5 were associated with pStage in gastric cancer. Then an online database derived from 1,065 gastric cancer cases, Kaplan-Meier plotter, was used to explore the associations of the mRNA levels of sirtuins with overall survival in gastric cancer. Survival curves generated from Kaplan-Meier plotter suggested that high expression of SIRT1 mRNA was favorable for overall survival in gastric cancer (SIRT1: HR = 0.64, 95% CI = 0.54-0.76, P = 2.2E-07), high expressions of SIRT2-4 and SIRT6-7 were poor for overall survival (SIRT2: HR = 2.31, 95% CI = 1.87-2.87, P = 3.6E-15; SIRT3: HR = 1.99, 95% CI = 1.62-2.45, P = 2.6E-11; SIRT4: HR = 1.41, 95% CI = 1.19-1.68, P = 6.6E-05; SIRT6: HR = 2.02, 95% CI = 1.66-2.47, P = 1.7E-12; SIRT7: HR = 1.96, 95% CI = 1.63-2.35, P = 2.7E-13), whereas no significant association existed between SIRT5 mRNA expression and overall survival. Further analyses stratified by gender, stages, Lauren classification, differentiation, treatment, and HER2 status were also performed. In summary, high SIRT1 mRNA level was associated with better overall survival, SIRT2-4 and 6-7 were associated with poor overall survival, whereas SIRT5 did not show significant association with overall survival in gastric cancer.", "claims": [{"id": "claim-method", "statement": "The Chi-square test or Fisher’s exact test were performed to explore the correlations between sirtuins expression and clinicopathological parameters.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29088792", "locator": "sections[6] \"MATERIALS AND METHODS\" paragraph 2", "quote": "The Chi-square test or Fisher’s exact test were performed to explore the correlations between sirtuins expression and clinicopathological parameters."}], "state": "complete"}, {"id": "claim-data-access", "statement": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. 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GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM387788", "GSM387789", "GSM387790", "GSM387791", "GSM387792", "GSM387793", "GSM387794", "GSM387795", "GSM387796", "GSM387797", "GSM387798", "GSM387799", "GSM387800", "GSM387801", "GSM387802", "GSM387803", "GSM387804", "GSM387805", "GSM387806", "GSM387807", "GSM387808", "GSM387809", "GSM387810", "GSM387811", "GSM387812", "GSM387813", "GSM387814", "GSM387815", "GSM387816", "GSM387817", "GSM387818", "GSM387819", "GSM387820", "GSM387821", "GSM387822", "GSM387823", "GSM387824", "GSM387825", "GSM387826", "GSM387827", "GSM387828", "GSM387829", "GSM387830", "GSM387831", "GSM387832", "GSM387833", "GSM387834", "GSM387835", "GSM387836", "GSM387837", "GSM387838", "GSM387839", "GSM387840", "GSM387841", "GSM387842", "GSM387843", "GSM387844", "GSM387845", "GSM387846", "GSM387847", "GSM387848", "GSM387849", "GSM387850", "GSM387851", "GSM387852", "GSM387853", "GSM387854", "GSM387855", "GSM387856", "GSM387857", "GSM387858", "GSM387859", "GSM387860", "GSM387861", "GSM387862", "GSM387863", "GSM387864", "GSM387865", "GSM387866", "GSM387867", "GSM387868", "GSM387869", "GSM387870", "GSM387871", "GSM387872", "GSM387873", "GSM387874", "GSM387875", "GSM387876", "GSM387877", "GSM387878", "GSM387879", "GSM387880", "GSM387881", "GSM387882", "GSM387883", "GSM387884", "GSM387885", "GSM387886", "GSM387887", "GSM387888", "GSM387889", "GSM387890", "GSM387891", "GSM387892", "GSM387893", "GSM387894", "GSM387895", "GSM387896", "GSM387897", "GSM387898", "GSM387899", "GSM387900", "GSM387901", "GSM387902", "GSM387903", "GSM387904", "GSM387905", "GSM387906", "GSM387907", "GSM387908", "GSM387909", "GSM387910", "GSM387911", "GSM387912", "GSM387913", "GSM387914", "GSM387915", "GSM387916", "GSM387917", "GSM387918", "GSM387919", "GSM387920", "GSM387921", "GSM387922", "GSM387923", "GSM387924", "GSM387925", "GSM387926", "GSM387927", "GSM387928", "GSM387929", "GSM387930", "GSM387931", "GSM387932", "GSM387933", "GSM387934", "GSM387935", "GSM387936", "GSM387937", "GSM387938", "GSM387939", "GSM387940", "GSM387941", "GSM387942", "GSM387943", "GSM387944", "GSM387945", "GSM387946", "GSM387947", "GSM387948", "GSM387949", "GSM387950", "GSM387951", "GSM387952", "GSM387953", "GSM387954", "GSM387955", "GSM387956", "GSM387957", "GSM387958", "GSM387959", "GSM387960", "GSM387961", "GSM387962", "GSM387963", "GSM387964", "GSM387965", "GSM387966", "GSM387967", "GSM387968", "GSM387969", "GSM387970", "GSM387971", "GSM387972", "GSM387973", "GSM387974", "GSM387975", "GSM387976", "GSM387977", "GSM387978", "GSM387979", "GSM387980", "GSM387981", "GSM387982", "GSM387983", "GSM387984", "GSM387985", "GSM387986", "GSM387987"], "sample_count": 200, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gastric Cancer Project '08 (Singapore Patient Cohort)", "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:GSE22377", "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=GSE22377", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22377", "version": null, "note": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM556676", "GSM556677", "GSM556678", "GSM556679", "GSM556680", "GSM556681", "GSM556682", "GSM556683", "GSM556684", "GSM556685", "GSM556686", "GSM556687", "GSM556688", "GSM556689", "GSM556690", "GSM556691", "GSM556692", "GSM556693", "GSM556694", "GSM556695", "GSM556696", "GSM556697", "GSM556698", "GSM556699", "GSM556700", "GSM556701", "GSM556702", "GSM556703", "GSM556704", "GSM556705", "GSM556706", "GSM556707", "GSM556708", "GSM556709", "GSM556710", "GSM556711", "GSM556712", "GSM556713", "GSM556714", "GSM556715", "GSM556716", "GSM556717", "GSM556718"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA expression data from human adenocarcinomas of the stomach", "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:GSE29272", "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=GSE29272", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29272", "version": null, "note": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM723464", "GSM723465", "GSM723466", "GSM723467", "GSM723468", "GSM723469", "GSM723470", "GSM723471", "GSM723472", "GSM723473", "GSM723474", "GSM723475", "GSM723476", "GSM723477", "GSM723478", "GSM723479", "GSM723480", "GSM723481", "GSM723482", "GSM723483", "GSM723484", "GSM723485", "GSM723486", "GSM723487", "GSM723488", "GSM723489", "GSM723490", "GSM723491", "GSM723492", "GSM723493", "GSM723494", "GSM723495", "GSM723496", "GSM723497", "GSM723498", "GSM723499", "GSM723500", "GSM723501", "GSM723502", "GSM723503", "GSM723504", "GSM723505", "GSM723506", "GSM723507", "GSM723508", "GSM723509", "GSM723510", "GSM723511", "GSM723512", "GSM723513", "GSM723514", "GSM723515", "GSM723516", "GSM723517", "GSM723518", "GSM723519", "GSM723520", "GSM723521", "GSM723522", "GSM723523", "GSM723524", "GSM723525", "GSM723526", "GSM723527", "GSM723528", "GSM723529", "GSM723530", "GSM723531", "GSM723532", "GSM723533", "GSM723534", "GSM723535", "GSM723536", "GSM723537", "GSM723538", "GSM723539", "GSM723540", "GSM723541", "GSM723542", "GSM723543", "GSM723544", "GSM723545", "GSM723546", "GSM723547", "GSM723548", "GSM723549", "GSM723550", "GSM723551", "GSM723552", "GSM723553", "GSM723554", "GSM723555", "GSM723556", "GSM723557", "GSM723558", "GSM723559", "GSM723560", "GSM723561", "GSM723562", "GSM723563", "GSM723564", "GSM723565", "GSM723566", "GSM723567", "GSM723568", "GSM723569", "GSM723570", "GSM723571", "GSM723572", "GSM723573", "GSM723574", "GSM723575", "GSM723576", "GSM723577", "GSM723578", "GSM723579", "GSM723580", "GSM723581", "GSM723582", "GSM723583", "GSM723584", "GSM723585", "GSM723586", "GSM723587", "GSM723588", "GSM723589", "GSM723590", "GSM723591", "GSM723592", "GSM723593", "GSM723594", "GSM723595", "GSM723596", "GSM723597", "GSM723598", "GSM723599", "GSM723600", "GSM723601", "GSM723602", "GSM723603", "GSM723604", "GSM723605", "GSM723606", "GSM723607", "GSM723608", "GSM723609", "GSM723610", "GSM723611", "GSM723612", "GSM723613", "GSM723614", "GSM723615", "GSM723616", "GSM723617", "GSM723618", "GSM723619", "GSM723620", "GSM723621", "GSM723622", "GSM723623", "GSM723624", "GSM723625", "GSM723626", "GSM723627", "GSM723628", "GSM723629", "GSM723630", "GSM723631", "GSM723632", "GSM723633", "GSM723634", "GSM723635", "GSM723636", "GSM723637", "GSM723638", "GSM723639", "GSM723640", "GSM723641", "GSM723642", "GSM723643", "GSM723644", "GSM723645", "GSM723646", "GSM723647", "GSM723648", "GSM723649", "GSM723650", "GSM723651", "GSM723652", "GSM723653", "GSM723654", "GSM723655", "GSM723656", "GSM723657", "GSM723658", "GSM723659", "GSM723660", "GSM723661", "GSM723662", "GSM723663", "GSM723664", "GSM723665", "GSM723666", "GSM723667", "GSM723668", "GSM723669", "GSM723670", "GSM723671", "GSM723672", "GSM723673", "GSM723674", "GSM723675", "GSM723676", "GSM723677", "GSM723678", "GSM723679", "GSM723680", "GSM723681", "GSM723682", "GSM723683", "GSM723684", "GSM723685", "GSM723686", "GSM723687", "GSM723688", "GSM723689", "GSM723690", "GSM723691", "GSM723692", "GSM723693", "GSM723694", "GSM723695", "GSM723696", "GSM723697", "GSM723698", "GSM723699", "GSM723700", "GSM723701", "GSM723702", "GSM723703", "GSM723704", "GSM723705", "GSM723706", "GSM723707", "GSM723708", "GSM723709", "GSM723710", "GSM723711", "GSM723712", "GSM723713", "GSM723714", "GSM723715", "GSM723716", "GSM723717", "GSM723718", "GSM723719", "GSM723720", "GSM723721", "GSM723722", "GSM723723", "GSM723724", "GSM723725", "GSM723726", "GSM723727", "GSM723728", "GSM723729", "GSM723730", "GSM723731"], "sample_count": 268, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Affymetrix gene expression array data for cardia and non-cardia gastric cancer 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:GSE51105", "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=GSE51105", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51105", "version": null, "note": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1238811", "GSM1238812", "GSM1238813", "GSM1238814", "GSM1238815", "GSM1238816", "GSM1238817", "GSM1238818", "GSM1238819", "GSM1238820", "GSM1238821", "GSM1238822", "GSM1238823", "GSM1238824", "GSM1238825", "GSM1238826", "GSM1238827", "GSM1238828", "GSM1238829", "GSM1238830", "GSM1238831", "GSM1238832", "GSM1238833", "GSM1238834", "GSM1238835", "GSM1238836", "GSM1238837", "GSM1238838", "GSM1238839", "GSM1238840", "GSM1238841", "GSM1238842", "GSM1238843", "GSM1238844", "GSM1238845", "GSM1238846", "GSM1238847", "GSM1238848", "GSM1238849", "GSM1238850", "GSM1238851", "GSM1238852", "GSM1238853", "GSM1238854", "GSM1238855", "GSM1238856", "GSM1238857", "GSM1238858", "GSM1238859", "GSM1238860", "GSM1238861", "GSM1238862", "GSM1238863", "GSM1238864", "GSM1238865", "GSM1238866", "GSM1238867", "GSM1238868", "GSM1238869", "GSM1238870", "GSM1238871", "GSM1238872", "GSM1238873", "GSM1238874", "GSM1238875", "GSM1238876", "GSM1238877", "GSM1238878", "GSM1238879", "GSM1238880", "GSM1238881", "GSM1238882", "GSM1238883", "GSM1238884", "GSM1238885", "GSM1238886", "GSM1238887", "GSM1238888", "GSM1238889", "GSM1238890", "GSM1238891", "GSM1238892", "GSM1238893", "GSM1238894", "GSM1238895", "GSM1238896", "GSM1238897", "GSM1238898", "GSM1238899", "GSM1238900", "GSM1238901", "GSM1238902", "GSM1238903", "GSM1238904"], "sample_count": 94, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A signature predicting poor prognosis in gastric and ovarian cancer represents a coordinated macrophage and stromal-response.", "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:GSE62254", "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=GSE62254", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62254", "version": null, "note": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1523727", "GSM1523728", "GSM1523729", "GSM1523744", "GSM1523745", "GSM1523746", "GSM1523747", "GSM1523748", "GSM1523765", "GSM1523768", "GSM1523769", "GSM1523770", "GSM1523771", "GSM1523772", "GSM1523773", "GSM1523774", "GSM1523775", "GSM1523776", "GSM1523777", "GSM1523778", "GSM1523779", "GSM1523780", "GSM1523781", "GSM1523782", "GSM1523783", "GSM1523784", "GSM1523785", "GSM1523786", "GSM1523787", "GSM1523788", "GSM1523789", "GSM1523790", "GSM1523791", "GSM1523792", "GSM1523793", "GSM1523794", "GSM1523795", "GSM1523796", "GSM1523797", "GSM1523798", "GSM1523799", "GSM1523800", "GSM1523801", "GSM1523802", "GSM1523803", "GSM1523804", "GSM1523805", "GSM1523806", "GSM1523807", "GSM1523808", "GSM1523809", "GSM1523810", 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"GSM1524033", "GSM1524034", "GSM1524035", "GSM1524036", "GSM1524037", "GSM1524038", "GSM1524039", "GSM1524040", "GSM1524041", "GSM1524042", "GSM1524043", "GSM1524044", "GSM1524045", "GSM1524046", "GSM1524047", "GSM1524048", "GSM1524049", "GSM1524050", "GSM1524051", "GSM1524052", "GSM1524053", "GSM1524054", "GSM1524055", "GSM1524056", "GSM1524057", "GSM1524058", "GSM1524059", "GSM1524060", "GSM1524061", "GSM1524062", "GSM1524068", "GSM1524069", "GSM1524070", "GSM1524071", "GSM1524072"], "sample_count": 300, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study [gastric tumors]", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": 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"133", "138", "139", "137", "143*", "133"], ["1", "27", "11", "17", "12", "11", "13", "7", "17"], ["pStage", "", "", "", "", "", "", "", ""], ["1", "30", "14", "14", "17", "11*", "15", "22*", "8*"], ["2", "97", "42", "46", "50", "56", "55", "49", "57"], ["3", "96", "53", "49", "47", "52", "49", "42", "47"], ["4", "77", "41", "41", "36", "77", "31", "37", "38"]], "row_count": 28, "column_count": 9, "numeric_cells": 175, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:29088792:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c3ebeaecb6d0d5154076fe76ed07407033658d1225775533ef92319066f8549d", "bytes": 999, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#T2", "version": null, "note": "Sirtuins and clinicopathological parameters in patients with GC (GSE15459)", "structure": {"pmcid": "PMC5650347", "section_index": 3, "section_title": "Correlations of sirtuins with clinicopathological parameters in GC", "row_count": 16, "column_count": 9}, "table": {"label": "Table 2", "caption": "Sirtuins and clinicopathological parameters in patients with GC (GSE15459)", "rows": [["Parameter", "Cases", "SIRT1+", "SIRT2+", "SIRT3+", "SIRT4+", "SIRT5+", "SIRT6+", "SIRT7+"], ["Gender", "", "", "", "", "", "", "", ""], ["Male", "125", "63", "67", "65", "66", "59", "66", "63"], ["Female", "67", "33", "29", "31", "30", "37", "30", "33"], ["Age", "", "", "", "", "", "", "", ""], ["< 65", "84", "42", "38", "47", "40", "41", "45", "42"], ["≥ 65", "108", "54", "58", "49", "56", "55", "51", "54"], ["Lauren classification", "", "", "", "", "", "", "", ""], ["Intestinal", "99", "43", "49", "43", "50", "49", "54", "60*"], ["Diffuse", "75", "42", "39", "45", "41", "38", "33", "28"], ["Mixed", "18", "11", "8", "8", "5", "9", "9", "8"], ["pStage", "", "", "", "", "", "", "", ""], ["1", "31", "17", 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16, "column_count": 9}, "table": {"label": "Table 3", "caption": "Sirtuins and clinicopathological parameters in patients with GC (integrated analysis of GSE62254 and GSE15459)", "rows": [["Parameters", "Cases", "SIRT1+", "SIRT2+", "SIRT3+", "SIRT4+", "SIRT5+", "SIRT6+", "SIRT7+"], ["Gender", "", "", "", "", "", "", "", ""], ["Male", "324", "161", "163", "167", "159", "157", "159", "164"], ["Female", "168", "85", "83", "79", "87", "89", "87", "82"], ["Age", "", "", "", "", "", "", "", ""], ["< 65", "245", "120", "120", "125", "127", "120", "115", "123"], ["≥ 65", "247", "126", "126", "121", "119", "126", "131", "115"], ["Lauren classification", "", "", "", "", "", "", "", ""], ["Intestinal", "249", "118", "124", "128", "119*", "131", "137*", "145*"], ["Diffuse", "217", "113", "111", "107", "119", "102", "95", "92"], ["Mixed", "26", "15", "11", "11", "8", "13", "14", "9"], ["pStage", "", "", "", "", "", "", "", ""], ["1", "61", "31", "38", "39*", "28*", "34*", "37", "25"], ["2", "126", 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[["Sirtuins", "Cases", "HR", "95% CI", "P-value"], ["SIRT1", "876", "0.64", "0.54–0.76", "2.2E-07"], ["SIRT2", "876", "2.31", "1.87–2.87", "3.6E-15"], ["SIRT3", "876", "1.99", "1.62–2.45", "2.6E-11"], ["SIRT4", "876", "1.41", "1.19–1.68", "6.6E-05"], ["SIRT5", "631", "1.14", "0.92–1.42", "2.3E-01"], ["SIRT6", "876", "2.02", "1.66–2.47", "1.7E-12"], ["SIRT7", "876", "1.96", "1.63–2.35", "2.7E-13"]], "row_count": 8, "column_count": 5, "numeric_cells": 29, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:29088792:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43adcc77f99a545bcb3b68f2724d51541c4e9e322ea0ad6c3b4d939ab2087746", "bytes": 996, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#T5", "version": null, "note": "Correlations of sirtuins with OS in GC stratified by gender", "structure": {"pmcid": "PMC5650347", "section_index": 4, "section_title": "Correlations of sirtuins with OS in GC in overall", "row_count": 15, "column_count": 6}, "table": {"label": "Table 5", "caption": "Correlations of sirtuins with OS in GC stratified by gender", "rows": [["Sirtuins", "Gender", "Cases", "HR", "95% CI", "P-value"], ["SIRT1", "Male", "545", "0.45", "0.31–0.66", "1.7E-05"], ["", "Female", "236", "0.63", "0.51–0.77", "1.3E-05"], ["SIRT2", "Male", "545", "2.08", "1.38–3.14", "3.5E-04"], ["", "Female", "236", "2.62", "2.02–3.40", "6.2E-14"], ["SIRT3", "Male", "545", "2.12", "1.41–3.18", "2.1E-04"], ["", "Female", "236", "2.07", "1.60–2.67", "1.8E-08"], ["SIRT4", "Male", "545", "1.88", "1.33–2.68", "3.3E-04"], ["", "Female", "236", "1.46", "1.16–1.84", "1.4E-03"], ["SIRT5", "Male", "349", "0.76", "0.48–1.20", "2.3E-01"], ["", "Female", "187", "0.80", "0.57–1.12", "2.0E-01"], ["SIRT6", "Male", "545", "2.24", "1.41–3.55", "4.4E-04"], ["", "Female", "236", "2.26", "1.75–2.92", "1.6E-10"], ["SIRT7", "Male", "545", "1.96", "1.38–2.79", "1.2E-04"], ["", "Female", "236", "2.12", "1.68–2.67", "6.6E-11"]], "row_count": 15, "column_count": 6, "numeric_cells": 57, "header_rows": 1, "locator": "section[4]/table-wrap[2]#T5"}}, {"id": "asset:table:pmid:29088792:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:74b74be1b8b5c2c19472adf01353ff242db61d4091f5aea7b6217696d42693f2", "bytes": 1581, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[3]#T6", "version": null, "note": "Correlations of sirtuins with OS in GC stratified by stages", "structure": {"pmcid": "PMC5650347", "section_index": 4, "section_title": "Correlations of sirtuins with OS in GC in overall", "row_count": 29, "column_count": 6}, "table": {"label": "Table 6", "caption": "Correlations of sirtuins with OS in GC stratified by stages", "rows": [["Sirtuins", "Stage", "Cases", "HR", "95% CI", "P-value"], ["SIRT1", "1", "67", "0.38", "0.14–1.06", "5.6E-02"], ["", "2", "140", "1.55", "0.78–3.06", "2.1E-01"], ["", "3", "305", "0.59", "0.43–0.81", "9.4E-04"], ["", "4", "148", "0.81", "0.55–1.19", "2.8E-01"], ["SIRT2", "1", "67", "4.71", "1.33–16.74", "8.5E-03"], ["", "2", "140", "2.55", "1.37–4.76", "2.3E-03"], ["", "3", "305", "2.60", "1.79–3.77", "2.1E-07"], ["", "4", "148", "1.65", "1.11–2.46", "1.3E-02"], ["SIRT3", "1", "67", "11.02", "1.44–84.40", "3.9E-03"], ["", "2", "140", "3.36", "1.69–6.70", "2.5E-04"], ["", "3", "305", "2.21", "1.52–3.21", "1.8E-05"], ["", "4", "148", "0.76", "0.50–1.14", "1.8E-01"], ["SIRT4", "1", "67", "1.88", "0.70–5.08", "2.1E-01"], ["", "2", "140", "2.25", "1.22–4.18", "8.1E-03"], ["", "3", "305", "1.43", "1.08–1.90", "1.3E-02"], ["", "4", "148", "1.32", "0.89–1.97", "1.6E-01"], ["SIRT5", "1", "62", "3.00", "0.66–13.58", "1.3E-01"], ["", "2", "135", "1.91", "0.91–4.03", "8.1E-02"], ["", "3", "197", 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"version": null, "note": "Correlations of sirtuins with OS in GC stratified by lauren classification", "structure": {"pmcid": "PMC5650347", "section_index": 4, "section_title": "Correlations of sirtuins with OS in GC in overall", "row_count": 22, "column_count": 6}, "table": {"label": "Table 7", "caption": "Correlations of sirtuins with OS in GC stratified by lauren classification", "rows": [["Sirtuins", "Lauren classification", "Cases", "HR", "95% CI", "P-value"], ["SIRT1", "Intestinal", "320", "0.51", "0.37–0.70", "2.1E-05"], ["", "Diffuse", "141", "1.26", "0.88–1.81", "2.1E-01"], ["", "Mixed", "32", "0.43", "0.15–1.22", "1.0E-01"], ["SIRT2", "Intestinal", "320", "3.39", "2.32–4.95", "2.4E-11"], ["", "Diffuse", "141", "1.71", "1.17–2.51", "5.4E-03"], ["", "Mixed", "32", "2.02", "0.57–7.23", "2.7E-01"], ["SIRT3", "Intestinal", "320", "2.74", "1.89–3.96", "2.4E-08"], ["", "Diffuse", "141", "1.44", "1.01–2.04", "4.3E-02"], ["", "Mixed", "32", "4.07", "1.14–14.47", "1.9E-02"], ["SIRT4", 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[["Sirtuins", "HER2 status", "Cases", "HR", "95% CI", "P-value"], ["SIRT1", "Negative", "532", "0.64", "0.51–0.81", "1.4E-04"], ["", "Positive", "344", "0.58", "0.42–0.80", "7.3E-04"], ["SIRT2", "Negative", "532", "2.20", "1.71–2.83", "3.9E-10"], ["", "Positive", "344", "1.58", "1.14–2.18", "5.5E-03"], ["SIRT3", "Negative", "532", "1.68", "1.31–2.15", "3.2E-05"], ["", "Positive", "344", "1.52", "1.11–2.06", "7.7E-03"], ["SIRT4", "Negative", "532", "1.60", "1.27–2.00", "4.7E-05"], ["", "Positive", "344", "1.28", "0.98–1.67", "7.0E-02"], ["SIRT5", "Negative", "429", "0.83", "0.62–1.12", "2.2E-01"], ["", "Positive", "202", "0.63", "0.43–0.94", "2.2E-02"], ["SIRT6", "Negative", "532", "1.81", "1.43–2.29", "5.2E-07"], ["", "Positive", "344", "1.76", "1.28–2.41", "3.8E-04"], ["SIRT7", "Negative", "532", "1.91", "1.53–2.40", "1.0E-08"], ["", "Positive", "344", "1.60", "1.23–2.07", "3.8E-04"]], "row_count": 15, "column_count": 6, "numeric_cells": 57, "header_rows": 1, "locator": "section[4]/table-wrap[7]#T10"}}], "gaps": ["asset:data:geo:GSE14210 not downloaded", "asset:data:geo:GSE14210 licence not read", "asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE22377 not downloaded", "asset:data:geo:GSE22377 licence not read", "asset:data:geo:GSE29272 not downloaded", "asset:data:geo:GSE29272 licence not read", "asset:data:geo:GSE51105 not downloaded", "asset:data:geo:GSE51105 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE62254 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Chi-square test or Fisher’s exact test were 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"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": ["chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: chi_square."}, "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": ["GSE62254", "GSE15459", "GSE14210", "GSE22377", "GSE29272", "GSE51105"], "resolved_accessions": ["GSE62254", "GSE15459", "GSE14210", "GSE22377", "GSE29272", "GSE51105"], "statements": ["To investigate the associations of sirtuins mRNA levels with clinicopathological parameters, we downloaded gastric cancer mRNA profile data and corresponding clinical data from publicly available GEO database. GSE62254 and GSE15459 with large number of gastric cancer patient samples and complete clinical information were selected, which had been also included in the Kaplan-Meier plotter database."], "basis": "The paper names GSE62254, GSE15459, GSE14210, GSE22377, GSE29272, GSE51105 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["chi_square_test"], "assets": ["source:pmid:29088792", "data:geo:GSE14210", "asset:table:pmid:29088792:1", "asset:table:pmid:29088792:2", "asset:table:pmid:29088792:3", "asset:table:pmid:29088792:4", "asset:table:pmid:29088792:5", "asset:table:pmid:29088792:6", "asset:table:pmid:29088792:7", "asset:table:pmid:29088792:8", "asset:table:pmid:29088792:9", "asset:table:pmid:29088792:10"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14210"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:35Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 79269, "completion_tokens": 6267, "cached_tokens": 2080}}, "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:29088792", "type": "paper", "label": "pmid:29088792"}, {"id": "source:pmid:29088792", "type": "manuscript", "label": "PMID 29088792 full text"}, {"id": "data:geo:GSE14210", "type": "dataset", "label": "GEO GSE14210"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29088792", "type": "paper", "label": "pmid:29088792"}, {"id": "source:pmid:29088792", "type": "manuscript", "label": "PMID 29088792 full text"}, {"id": "data:geo:GSE14210", "type": "dataset", "label": "GEO GSE14210"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29088792", "type": "extraction", "used": ["source:pmid:29088792"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14210", "type": "accession_resolution", "used": ["data:geo:GSE14210"], "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:29088792", "parent_hash": "sha256:99dd737794921cb0bbbf3f622ecf4f0f5538d19725e18a8d4d1bee427ec215e8", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE14210 licence not read", "asset:data:geo:GSE14210 not downloaded", "asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE22377 licence not read", "asset:data:geo:GSE22377 not downloaded", "asset:data:geo:GSE29272 licence not read", "asset:data:geo:GSE29272 not downloaded", "asset:data:geo:GSE51105 licence not read", "asset:data:geo:GSE51105 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE62254 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Chi-square test or Fisher’s exact test were performed to explore the correlations between sirtuins expression and clinicopathological parameters."], "order_basis": "analysis_only", "id": "assay:1"}]}