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pmid:35853971
Identification and validation of a novel 16-gene prognostic signature for patients with breast cancer.
Zhenhua Zhong · Wenqiang Jiang · Jing Zhang · Zhanwen Li · Fengfeng Fan
Scientific reports · 2022 doi:10.1038/s41598-022-16575-8
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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This study was to identify a novel gene signature that can accurately evaluate BRCA patient survival. The gene expression and clinical data of BRCA patients were collected from The Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of BRCA International Consortium (METABRIC) databases. Genes associated with prognosis were determined by Kaplan-Meier survival analysis and multivariate Cox regression analysis. A prognostic 16-gene score was established with linear combination of 16 genes. The prognostic value of the signature was validated in the METABRIC and GSE202203 datasets. Gene expression analysis was performed to investigate the diagnostic values of 16 genes. The 16-gene score was associated with shortened overall survival in BRCA patients independently of clinicopathological characteristics. The signalling pathways of cell cycle, oocyte meiosis, RNA degradation, progesterone mediated oocyte maturation and DNA replication were the top five most enriched pathways in the high 16-gene score group. The 16-gene nomogram incorporating the survival-related clinical factors showed improved prediction accuracies for 1-year, 3-year and 5-year survival (area under curve [AUC] = 0.91, 0.79 and 0.77 respectively). MORN3, IGJ, DERL1 exhibited high accuracy in differentiating BRCA tissues from normal breast tissues (AUC > 0.80 for all cases). 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"GSM6103711", "GSM6103712", "GSM6103713", "GSM6103714", "GSM6103715", "GSM6103716", "GSM6103717", "GSM6103718", "GSM6103719", "GSM6103720", "GSM6103721", "GSM6103722", "GSM6103723", "GSM6103724", "GSM6103725", "GSM6103726", "GSM6103727", "GSM6103728", "GSM6103729", "GSM6103730", "GSM6103731", "GSM6103732", "GSM6103733", "GSM6103734", "GSM6103735", "GSM6103736", "GSM6103737", "GSM6103738", "GSM6103739", "GSM6103740", "GSM6103741", "GSM6103742", "GSM6103743", "GSM6103744", "GSM6103745", "GSM6103746", "GSM6103747", "GSM6103748", "GSM6103749", "GSM6103750", "GSM6103751", "GSM6103752", "GSM6103753", "GSM6103754", "GSM6103755", "GSM6103756", "GSM6103757", "GSM6103758", "GSM6103759", "GSM6103760", "GSM6103761", "GSM6103762", "GSM6103763", "GSM6103764", "GSM6103765", "GSM6103766", "GSM6103767", "GSM6103768", "GSM6103769", "GSM6103770", "GSM6103771", "GSM6103772", "GSM6103773", "GSM6103774", "GSM6103775", "GSM6103776", "GSM6103777", "GSM6103778", "GSM6103779", "GSM6103780", "GSM6103781", "GSM6103782", "GSM6103783", "GSM6103784", "GSM6103785", "GSM6103786", "GSM6103787", "GSM6103788", "GSM6103789", "GSM6103790", "GSM6103791", "GSM6103792", "GSM6103793", "GSM6103794", "GSM6103795", "GSM6103796", "GSM6103797", "GSM6103798", "GSM6103799", "GSM6103800", "GSM6103801", "GSM6103802", "GSM6103803", "GSM6103804", "GSM6103805", "GSM6103806", "GSM6103807", "GSM6103808", "GSM6103809", "GSM6103810", "GSM6103811", "GSM6103812", "GSM6103813", "GSM6103814", "GSM6103815", "GSM6103816", "GSM6103817", "GSM6103818", "GSM6103819", "GSM6103820", "GSM6103822", "GSM6103824", "GSM6103825", "GSM6103828", "GSM6103830", "GSM6103832", "GSM6103834", "GSM6103836", "GSM6103838", "GSM6103840", "GSM6103842", "GSM6103844", "GSM6103845", "GSM6103846", "GSM6103847", "GSM6103848", "GSM6103849", "GSM6103850", "GSM6103851", "GSM6103852", "GSM6103853", "GSM6103854", "GSM6103855", "GSM6103856", "GSM6103857", "GSM6103858", "GSM6103859", "GSM6103860", "GSM6103861", "GSM6103862", "GSM6103863", "GSM6103864", "GSM6103865", "GSM6103866", "GSM6103867", "GSM6103868", "GSM6103869", "GSM6103870", "GSM6103871", "GSM6103872", "GSM6103873", "GSM6103874", "GSM6103875", "GSM6103876", "GSM6103877", "GSM6103878", "GSM6103879", "GSM6103880", "GSM6103881", "GSM6103882", "GSM6103883", "GSM6103884", "GSM6103885", "GSM6103886", "GSM6103887", "GSM6103888", "GSM6103889", "GSM6103890", "GSM6103891", "GSM6103892", "GSM6103893", "GSM6103894", "GSM6103895", "GSM6103896", "GSM6103897", "GSM6103898", "GSM6103899", "GSM6103900", "GSM6103901", "GSM6103902", "GSM6103903", "GSM6103904", "GSM6103905", "GSM6103906", "GSM6103907", "GSM6103908", "GSM6103909", "GSM6103910", "GSM6103911", "GSM6103912", "GSM6103913", "GSM6103914", "GSM6103915", "GSM6103916", "GSM6103917", "GSM6103918", "GSM6103919", "GSM6103920", "GSM6103921", "GSM6103922", "GSM6103923", "GSM6103924", "GSM6103925", "GSM6103926", "GSM6103927", "GSM6103928", "GSM6103929", "GSM6103930", "GSM6103931", "GSM6103932", "GSM6103933", "GSM6103934", "GSM6103935", "GSM6103936", "GSM6103937", "GSM6103938", "GSM6103939", "GSM6103940", "GSM6103941", "GSM6103942", "GSM6103943", "GSM6103944", "GSM6103945", "GSM6103946", "GSM6103947", "GSM6103948", "GSM6103949", "GSM6103950", "GSM6103951", "GSM6103952", "GSM6103953", "GSM6103954", "GSM6103955", "GSM6103956", "GSM6103957", "GSM6103958", "GSM6103959", "GSM6103960", "GSM6103961", "GSM6103962", "GSM6103963", "GSM6103964", "GSM6103965", "GSM6103966", "GSM6103967", "GSM6103968", "GSM6103969", "GSM6103970", "GSM6103971", "GSM6103972", "GSM6103973", "GSM6103974", "GSM6103975", "GSM6103976", "GSM6103977", "GSM6103978", "GSM6103979", "GSM6103980", "GSM6103981", "GSM6103982", "GSM6103983", "GSM6103984", "GSM6103985", "GSM6103986", "GSM6103987", "GSM6103988", "GSM6103989", "GSM6103990", "GSM6103991", "GSM6103992", "GSM6103993", "GSM6103994", "GSM6103995", "GSM6103996", "GSM6103997", "GSM6103998", "GSM6103999", "GSM6104000", "GSM6104001", "GSM6104002", "GSM6104003", "GSM6104004", "GSM6104005", "GSM6104006", "GSM6104007", "GSM6104008", "GSM6104009", "GSM6104010", "GSM6104011", "GSM6104012", "GSM6104013", "GSM6104014", "GSM6104015", "GSM6104016", "GSM6104017", "GSM6104018", "GSM6104019", "GSM6104020", "GSM6104021", "GSM6104022", "GSM6104023", "GSM6104024", "GSM6104025", "GSM6104026", "GSM6104027", "GSM6104028", "GSM6104029", "GSM6104030", "GSM6104031", "GSM6104032", "GSM6104033", "GSM6104034", "GSM6104035", "GSM6104036", "GSM6104037", "GSM6104038", "GSM6104039", "GSM6104040", "GSM6104041", "GSM6104042", "GSM6104043", "GSM6104044", "GSM6104045", "GSM6104046", "GSM6104047", "GSM6104048", "GSM6104049", "GSM6104050", "GSM6104051", "GSM6104052", "GSM6104053", "GSM6104054", "GSM6104055", "GSM6104056", "GSM6104057", "GSM6104058", "GSM6104059", "GSM6104060", "GSM6104061", "GSM6104062", "GSM6104063", "GSM6104064", "GSM6104065", "GSM6104066", "GSM6104067", "GSM6104068", "GSM6104069", "GSM6104070", "GSM6104071", "GSM6104072", "GSM6104073", "GSM6104074", "GSM6104075", "GSM6104076", "GSM6104077", "GSM6104078", "GSM6104079", "GSM6104080", "GSM6104081", "GSM6104082", "GSM6104083", "GSM6104084", "GSM6104085", "GSM6104086", "GSM6104087", "GSM6104088", "GSM6104089", "GSM6104090", "GSM6104091", "GSM6104092", "GSM6104093", "GSM6104094", "GSM6104095", "GSM6104096", "GSM6104097", "GSM6104098", "GSM6104099", "GSM6104100", "GSM6104101", "GSM6104102", "GSM6104103", "GSM6104104", "GSM6104105", "GSM6104106", "GSM6104107", "GSM6104108", "GSM6104109", "GSM6104110", "GSM6104111", "GSM6104112", "GSM6104113", "GSM6104114", "GSM6104115", "GSM6104116", "GSM6104117", "GSM6104118", "GSM6104119", "GSM6104120", "GSM6104121", "GSM6104122", "GSM6104123", "GSM6104124", "GSM6104125", "GSM6104126", "GSM6104127", "GSM6104128", "GSM6104129", "GSM6104130", "GSM6104131", "GSM6104132", "GSM6104133", "GSM6104134", "GSM6104135", "GSM6104136", "GSM6104137", "GSM6104138", "GSM6104139", "GSM6104140", "GSM6104141", "GSM6104142", "GSM6104143", "GSM6104144", "GSM6104145", "GSM6104146", "GSM6104147", "GSM6104148", "GSM6104149", "GSM6104150", "GSM6104151", "GSM6104152", "GSM6104153", "GSM6104154", "GSM6104155", "GSM6104156", "GSM6104157", "GSM6104158", "GSM6104159", "GSM6104160", "GSM6104161", "GSM6104162", "GSM6104163", "GSM6104164", "GSM6104165", "GSM6104166", "GSM6104167", "GSM6104168", "GSM6104169", "GSM6104170", "GSM6104171", "GSM6104172", "GSM6104173", "GSM6104174", "GSM6104175", "GSM6104176", "GSM6104177", "GSM6104178", "GSM6104179", "GSM6104180", "GSM6104181", "GSM6104182", "GSM6104183", "GSM6104184", "GSM6104185", "GSM6104186", "GSM6104187", "GSM6104188", "GSM6104189", "GSM6104190", "GSM6104191", "GSM6104192", "GSM6104193", "GSM6104194", "GSM6104195", "GSM6104196", "GSM6104197", "GSM6104198", "GSM6104199", "GSM6104200", "GSM6104201", "GSM6104202", "GSM6104203", "GSM6104204", "GSM6104205", "GSM6104206", "GSM6104207", "GSM6104208", "GSM6104209", "GSM6104210", "GSM6104211", "GSM6104212", "GSM6104213", "GSM6104214", "GSM6104215", "GSM6104216", "GSM6104217", "GSM6104218", "GSM6104219", "GSM6104220", "GSM6104221", "GSM6104222", "GSM6104223", "GSM6104224", "GSM6104225", "GSM6104226", "GSM6104227", "GSM6104228", "GSM6104229", "GSM6104230", "GSM6104231", "GSM6104232", "GSM6104233", "GSM6104234", "GSM6104235", "GSM6104236", "GSM6104237", "GSM6104238", "GSM6104239", "GSM6104240", "GSM6104241", "GSM6104242", "GSM6104243", "GSM6104244", "GSM6104245", "GSM6104246", "GSM6104247", "GSM6104248", "GSM6104249", "GSM6104250", "GSM6104251", "GSM6104252", "GSM6104253", "GSM6104254", "GSM6104255", "GSM6104256", "GSM6104257", "GSM6104258", "GSM6104259", "GSM6104260", "GSM6104261", "GSM6104262", "GSM6104263", "GSM6104264", "GSM6104265", "GSM6104266", "GSM6104267", "GSM6104268", "GSM6104269", "GSM6104270", "GSM6104271", "GSM6104272", "GSM6104273", "GSM6104274", "GSM6104275", "GSM6104276", "GSM6104277", "GSM6104278", "GSM6104279", "GSM6104280", "GSM6104281", "GSM6104282", "GSM6104283", "GSM6104284", "GSM6104285", "GSM6104286", "GSM6104287", "GSM6104288", "GSM6104289", "GSM6104290", "GSM6104291", "GSM6104292", "GSM6104293", "GSM6104294", "GSM6104295", "GSM6104296", "GSM6104297", "GSM6104298", "GSM6104299", "GSM6104300", "GSM6104301", "GSM6104302", "GSM6104303", "GSM6104304", "GSM6104305", "GSM6104306", "GSM6104307", "GSM6104308", "GSM6104309", "GSM6104310", "GSM6104311", "GSM6104312", "GSM6104313", "GSM6104314", "GSM6104315", "GSM6104316", "GSM6104317", "GSM6104318", "GSM6104319", "GSM6104320", "GSM6104321", "GSM6104322", "GSM6104323", "GSM6104324", "GSM6104325", "GSM6104326", "GSM6104327", "GSM6104328", "GSM6104329", "GSM6104330", "GSM6104331", "GSM6104332", "GSM6104333", "GSM6104334", "GSM6104335", "GSM6104336", "GSM6104337", "GSM6104338", "GSM6104339", "GSM6104340", "GSM6104341", "GSM6104342", "GSM6104343", "GSM6104344", "GSM6104345", "GSM6104346", "GSM6104347", "GSM6104348", "GSM6104349", "GSM6104350", "GSM6104351", "GSM6104352", "GSM6104353", "GSM6104354", "GSM6104355", "GSM6104356", "GSM6104357", "GSM6104358", "GSM6104359", "GSM6104360", "GSM6104361", "GSM6104362", "GSM6104363", "GSM6104364", "GSM6104365", "GSM6104366", "GSM6104367", "GSM6104368", "GSM6104369", "GSM6104370", "GSM6104371", "GSM6104372", "GSM6104373", "GSM6104374", "GSM6104375", "GSM6104376", "GSM6104377", "GSM6104378", "GSM6104379", "GSM6104380", "GSM6104381", "GSM6104382", "GSM6104383", "GSM6104384", "GSM6104385", "GSM6104386", "GSM6104387", "GSM6104388", "GSM6104389", "GSM6104390", "GSM6104391", "GSM6104392", "GSM6104393", "GSM6104394", "GSM6104395", "GSM6104396", "GSM6104397", "GSM6104398", "GSM6104399", "GSM6104400", "GSM6104401", "GSM6104402", "GSM6104403", "GSM6104404", "GSM6104405", "GSM6104406", "GSM6104407", "GSM6104408", "GSM6104409", "GSM6104410", "GSM6104411", "GSM6104412", "GSM6104413", "GSM6104414", "GSM6104415", "GSM6104416", "GSM6104417", "GSM6104418", "GSM6104419", "GSM6104420", "GSM6104421", "GSM6104422", "GSM6104423", "GSM6104424", "GSM6104425", "GSM6104426", "GSM6104427", "GSM6104428", "GSM6104429", "GSM6104430", "GSM6104431", "GSM6104432", "GSM6104433", "GSM6104434", "GSM6104435", "GSM6104436", "GSM6104437", "GSM6104438", "GSM6104439", "GSM6104440", "GSM6104441", "GSM6104442", "GSM6104443", "GSM6104444", "GSM6104445", "GSM6104446", "GSM6104447", "GSM6104448", "GSM6104449", "GSM6104450", "GSM6104451", "GSM6104452", "GSM6104453", "GSM6104454", "GSM6104455", "GSM6104456", "GSM6104457", "GSM6104458", "GSM6104459", "GSM6104460", "GSM6104461", "GSM6104462", "GSM6104463", "GSM6104464", "GSM6104465", "GSM6104466", "GSM6104467", "GSM6104468", "GSM6104469", "GSM6104470", "GSM6104471", "GSM6104472", "GSM6104473", "GSM6104474", "GSM6104475", "GSM6104476", "GSM6104477", "GSM6104478", "GSM6104479", "GSM6104480", "GSM6104481", "GSM6104482", "GSM6104483", "GSM6104484", "GSM6104485", "GSM6104486", "GSM6104487", "GSM6104488", "GSM6104489", "GSM6104490", "GSM6104491", "GSM6104492", "GSM6104493", "GSM6104494", "GSM6104495", "GSM6104496", "GSM6104497", "GSM6104498", "GSM6104499", "GSM6104500", "GSM6104501", "GSM6104502", "GSM6104503", "GSM6104504", "GSM6104505", "GSM6104506", "GSM6104507", "GSM6104508", "GSM6104509", "GSM6104510", "GSM6104511", "GSM6104512", "GSM6104513", "GSM6104514", "GSM6104515", "GSM6104516", "GSM6104517", "GSM6104518", "GSM6104519", "GSM6104520", "GSM6104521", "GSM6104522", "GSM6104523", "GSM6104524", "GSM6104525", "GSM6104526", "GSM6104527", "GSM6104528", "GSM6104529", "GSM6104530", "GSM6104531", "GSM6104532", "GSM6104533", "GSM6104534", "GSM6104535", "GSM6104536", "GSM6104537", "GSM6104538", "GSM6104539", "GSM6104540", "GSM6104541", "GSM6104542", "GSM6104543", "GSM6104544", "GSM6104545", "GSM6104546", "GSM6104547", "GSM6104548", "GSM6104549", "GSM6104550", "GSM6104551", "GSM6104552", "GSM6104553", "GSM6104554", "GSM6104555", "GSM6104556", "GSM6104557", "GSM6104558", "GSM6104559", "GSM6104560", "GSM6104561", "GSM6104562", "GSM6104563", "GSM6104564", "GSM6104565", "GSM6104566", "GSM6104567", "GSM6104568", "GSM6104569", "GSM6104570", "GSM6104571", "GSM6104572", "GSM6104573", "GSM6104574", "GSM6104575", "GSM6104576", "GSM6104577", "GSM6104578", "GSM6104579", "GSM6104580", "GSM6104581", "GSM6104582", "GSM6104583", "GSM6104584", "GSM6104585", "GSM6104586", "GSM6104587", "GSM6104588", "GSM6104589", "GSM6104590", "GSM6104591", "GSM6104592", "GSM6104593", "GSM6104594", "GSM6104595", "GSM6104596", "GSM6104597", "GSM6104598", "GSM6104599", "GSM6104600", "GSM6104601", "GSM6104602", "GSM6104603", "GSM6104604", "GSM6104605", "GSM6104606", "GSM6104607", "GSM6104608", "GSM6104609", "GSM6104610", "GSM6104611", "GSM6104612", "GSM6104613", "GSM6104614", "GSM6104615", "GSM6104616", "GSM6104617", "GSM6104618", "GSM6104619", "GSM6104620", "GSM6104621", "GSM6104622", "GSM6104623", "GSM6104624", "GSM6104625", "GSM6104626", "GSM6104627", "GSM6104628", "GSM6104629", "GSM6104630", "GSM6104631", "GSM6104632", "GSM6104633", "GSM6104634", "GSM6104635", "GSM6104636", "GSM6104637", "GSM6104638", "GSM6104639", "GSM6104640", "GSM6104641", "GSM6104642", "GSM6104643", "GSM6104644", "GSM6104645", "GSM6104646", "GSM6104647", "GSM6104648", "GSM6104649", "GSM6104650", "GSM6104651", "GSM6104652", "GSM6104653", "GSM6104654", "GSM6104655", "GSM6104656", "GSM6104657", "GSM6104658", "GSM6104659", "GSM6104660", "GSM6104661", "GSM6104662", "GSM6104663", "GSM6104664", "GSM6104665", "GSM6104666", "GSM6104667", "GSM6104668", "GSM6104669", "GSM6104670", "GSM6104671", "GSM6104672", "GSM6104673", "GSM6104674", "GSM6104675", "GSM6104676", "GSM6104677", "GSM6104678", "GSM6104679", "GSM6104680", "GSM6104681", "GSM6104682", "GSM6104683", "GSM6104684", "GSM6104685", "GSM6104686", "GSM6104687", "GSM6104688", "GSM6104689", "GSM6104690", "GSM6104691", "GSM6104692", "GSM6104693", "GSM6104694", "GSM6104695", "GSM6104696", "GSM6104697", "GSM6104698", "GSM6104699", "GSM6104700", "GSM6104701", "GSM6104702", "GSM6104703", "GSM6104704", "GSM6104705", "GSM6104706", "GSM6104707", "GSM6104708", "GSM6104709", "GSM6104710", "GSM6104711", "GSM6104712", "GSM6104713", "GSM6104714", "GSM6104715", "GSM6104716", "GSM6104717", "GSM6104718", "GSM6104719", "GSM6104720", "GSM6104721", "GSM6104722", "GSM6104723", "GSM6104724", "GSM6104725", "GSM6104726", "GSM6104727", "GSM6104728", "GSM6104729", "GSM6104730", "GSM6104731", "GSM6104732", "GSM6104733", "GSM6104734", "GSM6104735", "GSM6104736", "GSM6104737", "GSM6104738", "GSM6104739", "GSM6104740", "GSM6104741", "GSM6104742", "GSM6104743", "GSM6104744", "GSM6104745", "GSM6104746", "GSM6104747", "GSM6104748", "GSM6104749", "GSM6104750", "GSM6104751", "GSM6104752", "GSM6104753", "GSM6104754", "GSM6104755", "GSM6104756", "GSM6104757", "GSM6104758", "GSM6104759", "GSM6104760", "GSM6104761", "GSM6104762", "GSM6104763", "GSM6104764", "GSM6104765", "GSM6104766", "GSM6104767", "GSM6104768", "GSM6104769", "GSM6104770", "GSM6104771", "GSM6104772", "GSM6104773", "GSM6104774", "GSM6104775", "GSM6104776", "GSM6104777", "GSM6104778", "GSM6104779", "GSM6104780", "GSM6104781", "GSM6104782", "GSM6104783", "GSM6104784", "GSM6104785", "GSM6104786", "GSM6104787", "GSM6104788", "GSM6104789", "GSM6104790", "GSM6104791", "GSM6104792", "GSM6104793", "GSM6104794", "GSM6104795", "GSM6104796", "GSM6104797", "GSM6104798", "GSM6104799", "GSM6104800", "GSM6104801", "GSM6104802", "GSM6104803", "GSM6104804", "GSM6104805", "GSM6104806", "GSM6104807", "GSM6104808", "GSM6104809", "GSM6104810", "GSM6104811", "GSM6104812", "GSM6104813", "GSM6104814", "GSM6104815", "GSM6104816", "GSM6104817", "GSM6104818", "GSM6104819", "GSM6104820", "GSM6104821", "GSM6104822", "GSM6104823", "GSM6104824", "GSM6104825", "GSM6104826", "GSM6104827", "GSM6104828", "GSM6104829", "GSM6104830", "GSM6104831", "GSM6104832", "GSM6104833", "GSM6104834", "GSM6104835", "GSM6104836", "GSM6104837", "GSM6104838", "GSM6104839", "GSM6104840", "GSM6104841", "GSM6104842", "GSM6104843", "GSM6104844", "GSM6104845", "GSM6104846", "GSM6104847", "GSM6104848", "GSM6104849", "GSM6104850", "GSM6104851", "GSM6104852", "GSM6104853", "GSM6104854", "GSM6104855", "GSM6104856", "GSM6104857", "GSM6104858", "GSM6104859", "GSM6104860", "GSM6104861", "GSM6104862", "GSM6104863", "GSM6104864", "GSM6104865", "GSM6104866", "GSM6104867", "GSM6104868", "GSM6104869", "GSM6104870", "GSM6104871", "GSM6104872", "GSM6104873", "GSM6104874", "GSM6104875", "GSM6104876", "GSM6104877", "GSM6104878", "GSM6104879", "GSM6104880", "GSM6104881", "GSM6104882", "GSM6104883", "GSM6104884", "GSM6104885", "GSM6104886", "GSM6104887", "GSM6104888", "GSM6104889", "GSM6104890", "GSM6104891", "GSM6104892", "GSM6104893", "GSM6104894", "GSM6104895", "GSM6104896", "GSM6104897", "GSM6104898", "GSM6104899", "GSM6104900", "GSM6104901", "GSM6104902", "GSM6104903", "GSM6104904", "GSM6104905", "GSM6104906", "GSM6104907", "GSM6104908", "GSM6104909", "GSM6104910", "GSM6104911", "GSM6104912", "GSM6104913", "GSM6104914", "GSM6104915", "GSM6104916", "GSM6104917", "GSM6104918", "GSM6104919", "GSM6104920", "GSM6104921", "GSM6104922", "GSM6104923", "GSM6104924", "GSM6104925", "GSM6104926", "GSM6104927", "GSM6104928", "GSM6104929", "GSM6104930", "GSM6104931", "GSM6104932", "GSM6104933", "GSM6104934", "GSM6104935", "GSM6104936", "GSM6104937", "GSM6104938", "GSM6104939", "GSM6104940", "GSM6104941", "GSM6104942", "GSM6104943", "GSM6104944", "GSM6104945", "GSM6104946", "GSM6104947", "GSM6104948", "GSM6104949", "GSM6104950", "GSM6104951", "GSM6104952", "GSM6104953", "GSM6104954", "GSM6104955", "GSM6104956", "GSM6104957", "GSM6104958", "GSM6104959", "GSM6104960", "GSM6104961", "GSM6104962", "GSM6104963", "GSM6104964", "GSM6104965", "GSM6104966", "GSM6104967", "GSM6104968", "GSM6104969", "GSM6104970", "GSM6104971", "GSM6104972", "GSM6104973", "GSM6104974", "GSM6104975", "GSM6104976", "GSM6104977", "GSM6104978", "GSM6104979", "GSM6104980", "GSM6104981", "GSM6104982", "GSM6104983", "GSM6104984", "GSM6104985", "GSM6104986", "GSM6104987", "GSM6104988", "GSM6104989", "GSM6104990", "GSM6104991", "GSM6104992", "GSM6104993", "GSM6104994", "GSM6104995", "GSM6104996", "GSM6104997", "GSM6104998", "GSM6104999", "GSM6105000", "GSM6105001", "GSM6105002", "GSM6105003", "GSM6105004", "GSM6105005", "GSM6105006", "GSM6105007", "GSM6105008", "GSM6105009", "GSM6105010", "GSM6105011", "GSM6105012", "GSM6105013", "GSM6105014", "GSM6105015", "GSM6105016", "GSM6105017", "GSM6105018", "GSM6105019", "GSM6105020", "GSM6105021", "GSM6105022", "GSM6105023", "GSM6105024", "GSM6105025", "GSM6105026", "GSM6105027", "GSM6105028", "GSM6105029", "GSM6105030", "GSM6105031", "GSM6105032", "GSM6105033", "GSM6105034", "GSM6105035", "GSM6105036", "GSM6105037", "GSM6105038", "GSM6105039", "GSM6105040", "GSM6105041", "GSM6105042", "GSM6105043", "GSM6105044", "GSM6105045", "GSM6105046", "GSM6105047", "GSM6105048", "GSM6105049", "GSM6105050", "GSM6105051", "GSM6105052", "GSM6105053", "GSM6105054", "GSM6105055", "GSM6105056", "GSM6105057", "GSM6105058", "GSM6105059", "GSM6105060", "GSM6105061", "GSM6105062", "GSM6105063", "GSM6105064", "GSM6105065", "GSM6105066", "GSM6105067", "GSM6105068", "GSM6105069", "GSM6105070", "GSM6105071", "GSM6105072", "GSM6105073", "GSM6105074", "GSM6105075", "GSM6105076", "GSM6105077", "GSM6105078", "GSM6105079", "GSM6105080", "GSM6105081", "GSM6105082", "GSM6105083", "GSM6105084", "GSM6105085", "GSM6105086", "GSM6105087", "GSM6105088", "GSM6105089", "GSM6105090", "GSM6105091", "GSM6105092", "GSM6105093", "GSM6105094", "GSM6105095", "GSM6105096", "GSM6105097", "GSM6105098", "GSM6105099", "GSM6105100", "GSM6105101", "GSM6105102", "GSM6105103", "GSM6105104", "GSM6105105", "GSM6105106", "GSM6105107", "GSM6105108", "GSM6105109", "GSM6105110", "GSM6105111", "GSM6105112", "GSM6105113", "GSM6105114", "GSM6105115", "GSM6105116", "GSM6105117", "GSM6105118", "GSM6105119", "GSM6105120", "GSM6105121", "GSM6105122", "GSM6105123", "GSM6105124", "GSM6105125", "GSM6105126", "GSM6105127", "GSM6105128", "GSM6105129", "GSM6105130", "GSM6105131", "GSM6105132", "GSM6105133", "GSM6105134", "GSM6105135", "GSM6105136", "GSM6105137", "GSM6105138", "GSM6105139", "GSM6105140", "GSM6105141", "GSM6105142", "GSM6105143", "GSM6105144", "GSM6105145", "GSM6105146", "GSM6105147", "GSM6105148", "GSM6105149", "GSM6105150", "GSM6105151", "GSM6105152", "GSM6105153", "GSM6105154", "GSM6105155", "GSM6105156", "GSM6105157", "GSM6105158", "GSM6105159", "GSM6105160", "GSM6105161", "GSM6105162", "GSM6105163", "GSM6105164", "GSM6105165", "GSM6105166", "GSM6105167", "GSM6105168", "GSM6105169", "GSM6105170", "GSM6105171", "GSM6105172", "GSM6105173", "GSM6105174", "GSM6105175", "GSM6105176", "GSM6105177", "GSM6105178", "GSM6105179", "GSM6105180", "GSM6105181", "GSM6105182", "GSM6105183", "GSM6105184", "GSM6105185", "GSM6105186", "GSM6105187", "GSM6105188", "GSM6105189", "GSM6105190", "GSM6105191", "GSM6105192", "GSM6105193", "GSM6105194", "GSM6105195", "GSM6105196", "GSM6105197", "GSM6105198", "GSM6105199", "GSM6105200", "GSM6105201", "GSM6105202", "GSM6105203", "GSM6105204", "GSM6105205", "GSM6105206", "GSM6105207", "GSM6105208", "GSM6105209", "GSM6105210", "GSM6105211", "GSM6105212", "GSM6105213", "GSM6105214", "GSM6105215", "GSM6105216", "GSM6105217", "GSM6105218", "GSM6105219", "GSM6105220", "GSM6105221", "GSM6105222", "GSM6105223", "GSM6105224", "GSM6105225", "GSM6105226", "GSM6105227", "GSM6105228", "GSM6105229", "GSM6105230", "GSM6105231", "GSM6105232", "GSM6105233", "GSM6105234", "GSM6105235", "GSM6105236", "GSM6105237", "GSM6105238", "GSM6105239", "GSM6105240", "GSM6105241", "GSM6105242", "GSM6105243", "GSM6105244", "GSM6105245", "GSM6105246", "GSM6105247", "GSM6105248", "GSM6105249", "GSM6105250", "GSM6105251", "GSM6105252", "GSM6105253", "GSM6105254", "GSM6105255", "GSM6105256", "GSM6105257", "GSM6105258", "GSM6105259", "GSM6105260", "GSM6105261", "GSM6105262", "GSM6105263", "GSM6105264", "GSM6105265", "GSM6105266", "GSM6105267", "GSM6105268", "GSM6105269", "GSM6105270", "GSM6105271", "GSM6105272", "GSM6105273", "GSM6105274", "GSM6105275", "GSM6105276", "GSM6105277", "GSM6105278", "GSM6105279", "GSM6105280", "GSM6105281", "GSM6105282", "GSM6105283", "GSM6105284", "GSM6105285", "GSM6105286", "GSM6105287", "GSM6105288", "GSM6105289", "GSM6105290", "GSM6105291", "GSM6105292", "GSM6105293", "GSM6105294", "GSM6105295", "GSM6105296", "GSM6105297", "GSM6105298", "GSM6105299", "GSM6105300", "GSM6105301", "GSM6105302", "GSM6105303", "GSM6105304", "GSM6105305", "GSM6105306", "GSM6105307", "GSM6105308", "GSM6105309", "GSM6105310", "GSM6105311", "GSM6105312", "GSM6105313", "GSM6105314", "GSM6105315", "GSM6105316", "GSM6105317", "GSM6105318", "GSM6105319", "GSM6105320", "GSM6105321", "GSM6105322", "GSM6105323", "GSM6105324", "GSM6105325", "GSM6105326", "GSM6105327", "GSM6105328", "GSM6105329", "GSM6105330", "GSM6105331", "GSM6105332", "GSM6105333", "GSM6105334", "GSM6105335", "GSM6105336", "GSM6105337", "GSM6105338", "GSM6105339", "GSM6105340", "GSM6105341", "GSM6105342", "GSM6105343", "GSM6105344", "GSM6105345", "GSM6105346", "GSM6105347", "GSM6105348", "GSM6105349", "GSM6105350", "GSM6105351", "GSM6105352", "GSM6105353", "GSM6105354", "GSM6105355", "GSM6105356", "GSM6105357", "GSM6105358", "GSM6105359", "GSM6105360", "GSM6105361", "GSM6105362", "GSM6105363", "GSM6105364", "GSM6105365", "GSM6105366", "GSM6105367", "GSM6105368", "GSM6105369", "GSM6105370", "GSM6105371", "GSM6105372", "GSM6105373", "GSM6105374", "GSM6105375", "GSM6105376", "GSM6105377", "GSM6105378", "GSM6105379", "GSM6105380", "GSM6105381", "GSM6105382", "GSM6105383", "GSM6105384", "GSM6105385", "GSM6105386", "GSM6105387", "GSM6105388", "GSM6105389", "GSM6105390", "GSM6105391", "GSM6105392", "GSM6105393", "GSM6105394", "GSM6105395", "GSM6105396", "GSM6105397", "GSM6105398", "GSM6105399", "GSM6105400", "GSM6105401", "GSM6105402", "GSM6105403", "GSM6105404", "GSM6105405", "GSM6105406", "GSM6105407", "GSM6105408", "GSM6105409", "GSM6105410", "GSM6105411", "GSM6105412", "GSM6105413", "GSM6105414", "GSM6105415", "GSM6105416", "GSM6105417", "GSM6105418", "GSM6105419", "GSM6105420", "GSM6105421", "GSM6105422", "GSM6105423", "GSM6105424", "GSM6105425", "GSM6105426", "GSM6105427", "GSM6105428", "GSM6105429", "GSM6105430", "GSM6105431", "GSM6105432", "GSM6105433", "GSM6105434", "GSM6105435", "GSM6105436", "GSM6105437", "GSM6105438", "GSM6105439", "GSM6105440", "GSM6105441", "GSM6105442", "GSM6105443", "GSM6105444", "GSM6105445", "GSM6105446", "GSM6105447", "GSM6105448", "GSM6105449", "GSM6105450", "GSM6105451", "GSM6105452", "GSM6105453", "GSM6105454", "GSM6105455", "GSM6105456", "GSM6105457", "GSM6105458", "GSM6105459", "GSM6105460", "GSM6105461", "GSM6105462", "GSM6105463", "GSM6105464", "GSM6105465", "GSM6105466", "GSM6105467", "GSM6105468", "GSM6105469", "GSM6105470", "GSM6105471", "GSM6105472", "GSM6105473", "GSM6105474", "GSM6105475", "GSM6105476", "GSM6105477", "GSM6105478", "GSM6105479", "GSM6105480", "GSM6105481", "GSM6105482", "GSM6105483", "GSM6105484", "GSM6105485", "GSM6105486", "GSM6105487", "GSM6105488", "GSM6105489", "GSM6105490", "GSM6105491", "GSM6105492", "GSM6105493", "GSM6105494", "GSM6105495", "GSM6105496", "GSM6105497", "GSM6105498", "GSM6105499", "GSM6105500", "GSM6105501", "GSM6105502", "GSM6105503", "GSM6105504", "GSM6105505", "GSM6105506", "GSM6105507", "GSM6105508", "GSM6105509", "GSM6105510", "GSM6105511", "GSM6105512", "GSM6105513", "GSM6105514", "GSM6105515", "GSM6105516", "GSM6105517", "GSM6105518", "GSM6105519", "GSM6105520", "GSM6105521", "GSM6105522", "GSM6105523", "GSM6105524", "GSM6105525", "GSM6105526", "GSM6105527", "GSM6105528", "GSM6105529", "GSM6105530", "GSM6105531", "GSM6105532", "GSM6105533", "GSM6105534", "GSM6105535", "GSM6105536", "GSM6105537", "GSM6105538", "GSM6105539", "GSM6105540", "GSM6105541", "GSM6105542", "GSM6105543", "GSM6105544", "GSM6105545", "GSM6105546", "GSM6105547", "GSM6105548", "GSM6105549", "GSM6105550", "GSM6105551", "GSM6105552", "GSM6105553", "GSM6105554", "GSM6105555", "GSM6105556", "GSM6105557", "GSM6105558", "GSM6105559", "GSM6105560", "GSM6105561", "GSM6105562", "GSM6105563", "GSM6105564", "GSM6105565", "GSM6105566", "GSM6105567", "GSM6105568", "GSM6105569", "GSM6105570", "GSM6105571", "GSM6105572", "GSM6105573", "GSM6105574", "GSM6105575", "GSM6105576", "GSM6105577", "GSM6105578", "GSM6105579", "GSM6105580", "GSM6105581", "GSM6105582", "GSM6105583", "GSM6105584", "GSM6105585", "GSM6105586", "GSM6105587", "GSM6105588", "GSM6105589", "GSM6105590", "GSM6105591", "GSM6105592", "GSM6105593", "GSM6105594", "GSM6105595", "GSM6105596", "GSM6105597", "GSM6105598", "GSM6105599", "GSM6105600", "GSM6105601", "GSM6105602", "GSM6105603", "GSM6105604", "GSM6105605", "GSM6105606", "GSM6105607", "GSM6105608", "GSM6105609", "GSM6105610", "GSM6105611", "GSM6105612", "GSM6105613", "GSM6105614", "GSM6105615", "GSM6105616", "GSM6105617", "GSM6105618", "GSM6105619", "GSM6105620", "GSM6105621", "GSM6105622", "GSM6105623", "GSM6105624", "GSM6105625", "GSM6105626", "GSM6105627", "GSM6105628", "GSM6105629", "GSM6105630", "GSM6105631", "GSM6105632", "GSM6105633", "GSM6105634", "GSM6105635", "GSM6105636", "GSM6105637", "GSM6105638", "GSM6105639", "GSM6105640", "GSM6105641", "GSM6105642", "GSM6105643", "GSM6105644", "GSM6105645", "GSM6105646", "GSM6105647", "GSM6105648", "GSM6105649", "GSM6105650", "GSM6105651", "GSM6105652", "GSM6105653", "GSM6105654", "GSM6105655", "GSM6105656", "GSM6105657", "GSM6105658", "GSM6105659", "GSM6105660", "GSM6105661", "GSM6105662", "GSM6105663", "GSM6105664", "GSM6105665", "GSM6105666", "GSM6105667", "GSM6105668", "GSM6105669", "GSM6105670", "GSM6105671", "GSM6105672", "GSM6105673", "GSM6105674", "GSM6105675", "GSM6105676", "GSM6105677", "GSM6105678", "GSM6105679", "GSM6105680", "GSM6105681", "GSM6105682", "GSM6105683", "GSM6105684", "GSM6105685", "GSM6105686", "GSM6105687", "GSM6105688", "GSM6105689", "GSM6105690", "GSM6105691", "GSM6105692", "GSM6105693", "GSM6105694", "GSM6105695", "GSM6105696", "GSM6105697", "GSM6105698", "GSM6105699", "GSM6105700", "GSM6105701", "GSM6105702", "GSM6105703", "GSM6105704", "GSM6105705", "GSM6105706", "GSM6105707", "GSM6105708", "GSM6105709", "GSM6105710", 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"gaps": ["asset:data:geo:GSE202203 not downloaded", "asset:data:geo:GSE202203 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": "Genes associated with prognosis were determined by Kaplan–Meier survival analysis and multivariate Cox regression analysis."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "student t test"}}, {"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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 0.05, "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": ["GSE202203"], "resolved_accessions": ["GSE202203"], "statements": ["The datasets generated and/or analysed during the current study are available in the figshare repository (figshare ID: 15048003, https://figshare.com/s/df0ee21997f1aa0da4bd)."], "basis": "The paper names GSE202203 in GEO database 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:35853971", "data:geo:GSE202203"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE202203"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:56:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10727, "completion_tokens": 2889, "cached_tokens": 128}}, "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:35853971", "type": "paper", "label": "pmid:35853971"}, {"id": "source:pmid:35853971", "type": "manuscript", "label": "PMID 35853971 full text"}, {"id": "data:geo:GSE202203", "type": "dataset", "label": "GEO GSE202203"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35853971", "type": "paper", "label": "pmid:35853971"}, {"id": "source:pmid:35853971", "type": "manuscript", "label": "PMID 35853971 full text"}, {"id": "data:geo:GSE202203", "type": "dataset", "label": "GEO GSE202203"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35853971", "type": "extraction", "used": ["source:pmid:35853971"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE202203", "type": "accession_resolution", "used": ["data:geo:GSE202203"], "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:35853971", "parent_hash": "sha256:691d3a695e2ae6b9440f5fc67afe345631825e79cf95ee06046178862be2f967", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE202203 licence not read", "asset:data:geo:GSE202203 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Genes associated with prognosis were determined by Kaplan–Meier survival analysis and multivariate Cox regression analysis."], "order_basis": "analysis_only", "id": "assay:1"}]}