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pmid:35053403
Oncocytoma-Related Gene Signature to Differentiate Chromophobe Renal Cancer and Oncocytoma Using Machine Learning.
Khaled Bin Satter · Paul Minh Huy Tran · Lynn Kim Hoang Tran · Zach Ramsey · Katheine Pinkerton · Shan Bai · Natasha M Savage · Sravan Kavuri · Martha K Terris · Jin-Xiong She · Sharad Purohit
Cells · 2022 doi:10.3390/cells11020287
Paper
complete
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 datasets GSE11151, GSE19982, GSE2109, GSE8271 and GSE11024 were combined into a discovery dataset. The transcriptomic differences were identified with unsupervised learning in the discovery dataset (97.8% accuracy) with density based UMAP (DBU). The top 30 genes were identified by univariate gene expression analysis and ROC analysis, to create a gene signature called COGS. COGS, combined with DBU, was able to differentiate chRCC from RO in the discovery dataset with an accuracy of 97.8%. The classification accuracy of COGS was validated in an independent meta-dataset consisting of TCGA-KICH and GSE12090, where COGS could differentiate chRCC from RO with 100% accuracy. The differentially expressed genes were involved in carbohydrate metabolism, transcriptomic regulation by TP53, beta-catenin-dependent Wnt signaling, and cytokine (IL-4 and IL-13) signaling highly active in cancer cells. 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"GSM117677", "GSM117678", "GSM117679", "GSM117680", "GSM117681", "GSM117682", "GSM117683", "GSM117684", "GSM117685", "GSM117686", "GSM117687", "GSM117688", "GSM117689", "GSM117690", "GSM117691", "GSM117692", "GSM117693", "GSM117694", "GSM117695", "GSM117696", "GSM117697", "GSM117698", "GSM117699", "GSM117700", "GSM117701", "GSM117702", "GSM117703", "GSM117704", "GSM117705", "GSM117706", "GSM117707", "GSM117708", "GSM117709", "GSM117710", "GSM117711", "GSM117712", "GSM117713", "GSM117714", "GSM117715", "GSM117716", "GSM117717", "GSM117718", "GSM117719", "GSM117720", "GSM117721", "GSM117722", "GSM117723", "GSM117724", "GSM117725", "GSM117726", "GSM117727", "GSM117728", "GSM117729", "GSM117730", "GSM117731", "GSM117732", "GSM117734", "GSM117735", "GSM117736", "GSM117737", "GSM117738", "GSM117739", "GSM117740", "GSM117741", "GSM117742", "GSM117743", "GSM117744", "GSM117745", "GSM117746", "GSM117747", "GSM117748", "GSM117749", "GSM117750", "GSM117751", "GSM117752", "GSM117753", "GSM117754", "GSM117755", "GSM117756", "GSM117757", "GSM117758", "GSM117759", "GSM117760", "GSM117761", "GSM117762", "GSM117763", "GSM117765", "GSM117766", "GSM117767", "GSM117768", "GSM117769", "GSM117770", "GSM117771", "GSM117772", "GSM117774", "GSM117775", "GSM117776", "GSM117777", "GSM137895", "GSM137896", "GSM137897", "GSM137898", "GSM137899", "GSM137900", "GSM137901", "GSM137902", "GSM137903", "GSM137904", "GSM137905", "GSM137906", "GSM137907", "GSM137908", "GSM137909", "GSM137910", "GSM137911", "GSM137912", "GSM137913", "GSM137914", "GSM137915", "GSM137916", "GSM137917", "GSM137918", "GSM137919", "GSM137920", "GSM137921", "GSM137922", "GSM137923", "GSM137924", "GSM137925", "GSM137926", "GSM137927", "GSM137928", "GSM137929", "GSM137930", "GSM137931", "GSM137932", "GSM137933", "GSM137934", "GSM137935", "GSM137936", "GSM137937", "GSM137938", "GSM137939", "GSM137940", "GSM137941", "GSM137942", "GSM137943", "GSM137944", "GSM137945", "GSM137946", "GSM137947", "GSM137948", "GSM137949", "GSM137950", "GSM137951", "GSM137952", "GSM137953", "GSM137954", "GSM137955", "GSM137956", "GSM137957", "GSM137958", "GSM137959", "GSM137960", "GSM137961", "GSM137962", "GSM137963", "GSM137964", "GSM137965", "GSM137966", "GSM137967", "GSM137968", "GSM137969", "GSM137970", "GSM137971", "GSM137972", "GSM137973", "GSM137974", "GSM137975", "GSM137976", "GSM137977", "GSM137978", "GSM137979", "GSM137980", "GSM137981", "GSM137982", "GSM137983", "GSM137984", "GSM137985", "GSM137986", "GSM137987", "GSM137988", "GSM137989", "GSM137990", "GSM137991", "GSM137992", "GSM137993", "GSM137994", "GSM137995", "GSM137996", "GSM137997", "GSM137998", "GSM137999", "GSM138000", "GSM138001", "GSM138002", "GSM138003", "GSM138004", "GSM138005", "GSM138006", "GSM138007", "GSM138008", "GSM138009", "GSM138010", "GSM138011", "GSM138012", "GSM138013", "GSM138014", "GSM138015", "GSM138016", "GSM138017", "GSM138018", "GSM138019", "GSM138020", "GSM138021", "GSM138022", "GSM138023", "GSM138024", "GSM138025", "GSM138026", "GSM138027", "GSM138028", "GSM138029", "GSM138030", "GSM138031", "GSM138032", "GSM138033", "GSM138034", "GSM138035", "GSM138036", "GSM138037", "GSM138038", "GSM138039", "GSM138040", "GSM138041", "GSM138042", "GSM138043", "GSM138044", "GSM138045", "GSM138046", "GSM138047", "GSM138048", "GSM138049", "GSM138050", "GSM138051", "GSM138052", "GSM138053", "GSM138054", "GSM152564", "GSM152565", "GSM152566", "GSM152567", "GSM152568", "GSM152569", "GSM152570", "GSM152571", "GSM152572", "GSM152573", "GSM152574", "GSM152575", "GSM152576", "GSM152577", "GSM152578", "GSM152579", "GSM152580", "GSM152581", "GSM152582", "GSM152583", "GSM152584", "GSM152585", "GSM152586", "GSM152587", "GSM152588", "GSM152589", "GSM152590", "GSM152591", "GSM152592", "GSM152593", "GSM152594", "GSM152595", "GSM152596", "GSM152597", "GSM152598", "GSM152599", "GSM152600", "GSM152601", "GSM152602", "GSM152603", "GSM152604", "GSM152605", "GSM152606", "GSM152607", "GSM152608", "GSM152609", "GSM152610", "GSM152611", "GSM152612", "GSM152613", "GSM152614", "GSM152615", "GSM152616", "GSM152617", "GSM152618", "GSM152619", "GSM152620", "GSM152621", "GSM152622", "GSM152623", "GSM152624", "GSM152625", "GSM152626", "GSM152627", "GSM152628", "GSM152629", "GSM152630", "GSM152631", "GSM152632", "GSM152633", "GSM152634", "GSM152635", "GSM152636", "GSM152637", "GSM152638", "GSM152639", "GSM152640", "GSM152641", "GSM152642", "GSM152643", "GSM152644", "GSM152645", "GSM152646", "GSM152647", "GSM152648", "GSM152649", "GSM152650", "GSM152651", "GSM152652", "GSM152653", "GSM152654", "GSM152655", "GSM152656", "GSM152657", "GSM152658", "GSM152659", "GSM152660", "GSM152661", "GSM152662", "GSM152663", "GSM152664", "GSM152665", "GSM152666", "GSM152667", "GSM152668", "GSM152669", "GSM152670", "GSM152671", "GSM152672", "GSM152673", "GSM152674", "GSM152675", "GSM152676", "GSM152677", "GSM152678", "GSM152679", "GSM152680", "GSM152681", "GSM152682", "GSM152683", "GSM152684", "GSM152685", "GSM152686", "GSM152687", "GSM152688", "GSM152689", "GSM152690", "GSM152691", "GSM152692", "GSM152693", "GSM152694", "GSM152695", "GSM152696", "GSM152697", "GSM152698", "GSM152699", "GSM152700", "GSM152701", "GSM152702", "GSM152703", "GSM152704", "GSM152705", "GSM152706", "GSM152707", "GSM152708", "GSM152709", "GSM152710", "GSM152711", "GSM152712", "GSM152713", "GSM152714", "GSM152715", "GSM152716", "GSM152717", "GSM152718", "GSM152719", "GSM152720", "GSM152721", "GSM152722", "GSM152723", "GSM152724", "GSM152725", "GSM152726", "GSM152727", "GSM152728", "GSM152729", "GSM152730", "GSM152731", "GSM152732", "GSM152733", "GSM152734", "GSM152735", "GSM152736", "GSM152737", "GSM152738", "GSM152739", "GSM152740", "GSM152741", "GSM152742", "GSM152743", "GSM152744", "GSM152745", "GSM152746", "GSM152747", "GSM152748", "GSM152749", "GSM152750", "GSM152751", "GSM152752", "GSM152753", "GSM152754", "GSM152755", "GSM152756", "GSM152757", "GSM152758", "GSM152759", "GSM152760", "GSM152761", "GSM152762", "GSM152763", "GSM152764", "GSM152765", "GSM152766", "GSM152767", "GSM152768", "GSM152769", "GSM152770", "GSM152771", "GSM152772", "GSM152773", "GSM152774", "GSM152775", "GSM152776", "GSM152777", "GSM152778", "GSM152779", "GSM152780", "GSM152781", "GSM152782", "GSM152783", "GSM152784", "GSM152785", "GSM152786", "GSM152787", "GSM152788", "GSM152789", "GSM152790", "GSM152791", "GSM152792", "GSM152793", "GSM152794", "GSM152795", "GSM152796", "GSM152797", "GSM152798", "GSM152799", "GSM152800", "GSM152801", "GSM152802", "GSM152803", "GSM179778", "GSM179779", "GSM179780", "GSM179781", "GSM179782", "GSM179783", "GSM179784", "GSM179785", "GSM179786", "GSM179787", "GSM179788", "GSM179789", "GSM179790", "GSM179791", "GSM179792", "GSM179793", "GSM179794", "GSM179795", "GSM179796", "GSM179797", "GSM179798", "GSM179799", "GSM179800", "GSM179801", "GSM179802", "GSM179803", "GSM179804", "GSM179805", "GSM179806", "GSM179807", "GSM179808", "GSM179809", "GSM179810", "GSM179811", "GSM179812", "GSM179813", "GSM179814", "GSM179815", "GSM179816", "GSM179817", "GSM179818", "GSM179819", "GSM179820", "GSM179821", "GSM179822", "GSM179823", "GSM179824", "GSM179825", "GSM179826", "GSM179827", "GSM179828", "GSM179829", "GSM179830", "GSM179831", "GSM179832", "GSM179833", "GSM179834", "GSM179835", "GSM179836", "GSM179837", "GSM179838", "GSM179839", "GSM179840", "GSM179841", "GSM179842", "GSM179843", "GSM179844", "GSM179845", "GSM179846", "GSM179847", "GSM179848", "GSM179849", "GSM179850", "GSM179851", "GSM179852", "GSM179853", "GSM179854", "GSM179855", "GSM179856", "GSM179857", "GSM179858", "GSM179859", "GSM179860", "GSM179861", "GSM179862", "GSM179863", "GSM179864", "GSM179865", "GSM179866", "GSM179867", "GSM179868", "GSM179869", "GSM179870", "GSM179871", "GSM179872", "GSM179873", "GSM179874", "GSM179875", "GSM179876", "GSM179877", "GSM179878", "GSM179879", "GSM179880", "GSM179881", "GSM179882", "GSM179883", "GSM179884", "GSM179885", "GSM179886", "GSM179887", "GSM179888", "GSM179889", "GSM179890", "GSM179891", "GSM179892", "GSM179893", "GSM179894", "GSM179895", "GSM179896", "GSM179897", "GSM179898", "GSM179899", "GSM179900", "GSM179901", "GSM179902", "GSM179903", "GSM179904", "GSM179905", "GSM179906", "GSM179907", "GSM179908", "GSM179909", "GSM179910", "GSM179911", "GSM179912", "GSM179913", "GSM179914", "GSM179915", "GSM179916", "GSM179917", "GSM179918", "GSM179919", "GSM179920", "GSM179921", "GSM179922", "GSM179923", "GSM179924", "GSM179925", "GSM179926", "GSM179927", "GSM179928", "GSM179929", "GSM179930", "GSM179931", "GSM179932", "GSM179933", "GSM179934", "GSM179935", "GSM179936", "GSM179937", "GSM179938", "GSM179939", "GSM179940", "GSM179941", "GSM179942", "GSM179943", "GSM179944", "GSM179945", "GSM179946", "GSM179947", "GSM179948", "GSM179949", "GSM179950", "GSM179951", "GSM179952", "GSM179953", "GSM179954", "GSM179955", "GSM179956", "GSM179957", "GSM203622", "GSM203623", "GSM203624", "GSM203625", "GSM203626", "GSM203627", "GSM203628", "GSM203629", "GSM203630", "GSM203631", "GSM203632", "GSM203633", "GSM203634", "GSM203635", "GSM203636", "GSM203637", "GSM203638", "GSM203639", "GSM203640", "GSM203641", "GSM203642", "GSM203643", "GSM203644", "GSM203645", "GSM203646", "GSM203647", "GSM203648", "GSM203649", "GSM203650", "GSM203651", "GSM203652", "GSM203653", "GSM203654", "GSM203655", "GSM203656", "GSM203657", "GSM203658", "GSM203659", "GSM203660", "GSM203661", "GSM203662", "GSM203663", "GSM203664", "GSM203665", "GSM203666", "GSM203667", "GSM203668", "GSM203669", "GSM203670", "GSM203671", "GSM203672", "GSM203673", "GSM203674", "GSM203675", "GSM203676", "GSM203677", "GSM203678", "GSM203679", "GSM203680", "GSM203681", "GSM203682", "GSM203683", "GSM203684", "GSM203685", "GSM203686", "GSM203687", "GSM203688", "GSM203689", "GSM203690", "GSM203691", "GSM203692", "GSM203693", "GSM203694", "GSM203695", "GSM203696", "GSM203697", "GSM203698", "GSM203699", "GSM203700", "GSM203701", "GSM203702", "GSM203703", "GSM203704", "GSM203705", "GSM203706", "GSM203707", "GSM203708", "GSM203709", "GSM203710", "GSM203711", "GSM203712", "GSM203713", "GSM203714", "GSM203715", "GSM203716", "GSM203717", "GSM203718", "GSM203719", "GSM203720", "GSM203721", "GSM203722", "GSM203723", "GSM203724", "GSM203725", "GSM203726", "GSM203727", "GSM203728", "GSM203729", "GSM203730", "GSM203731", "GSM203732", "GSM203733", "GSM203734", "GSM203735", "GSM203736", "GSM203737", "GSM203738", "GSM203739", "GSM203740", "GSM203741", "GSM203742", "GSM203743", "GSM203744", "GSM203745", "GSM203746", "GSM203747", "GSM203748", "GSM203749", "GSM203750", "GSM203751", "GSM203752", "GSM203753", "GSM203754", "GSM203755", "GSM203756", "GSM203757", "GSM203758", "GSM203759", "GSM203760", "GSM203761", "GSM203762", "GSM203763", "GSM203764", "GSM203765", "GSM203766", "GSM203767", "GSM203768", "GSM203769", "GSM203770", "GSM203771", "GSM203772", "GSM203773", "GSM203774", "GSM203775", "GSM203776", "GSM203777", "GSM203778", "GSM203779", "GSM203780", "GSM203781", "GSM203782", "GSM203783", "GSM203784", "GSM203785", "GSM203786", "GSM203787", "GSM203788", "GSM203789", "GSM203790", 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Histopathology and other clinical information are also available with the datasets.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data for this study are publicly available and can be downloaded from the gene expression omnibus (GEO) or ArrayExpress website using the accession number. 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