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pmid:34526059
Comprehensive analysis of EMT-related genes and lncRNAs in the prognosis, immunity, and drug treatment of colorectal cancer.
Yang Yang · Mingyang Feng · LiangLiang Bai · Weiting Liao · Kexun Zhou · Mengxi Zhang · Qiuji Wu · Feng Wen · Wanting Lei · Pengfei Zhang · Nan Zhang · Jiaxing Huang · Qiu Li
Journal of translational medicine · 2021 doi:10.1186/s12967-021-03065-0
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Experiment
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Complete file
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However, there are still many unknowns about the specific mechanism of EMT in tumor. At present, a comprehensive analysis of EMT-related genes in colorectal cancer (CRC) is still lacking.\nMETHODS: All the data were downloaded from public databases including TCGA database (488 tumor samples and 52 normal samples) as the training set and the GEO database (GSE40967 including 566 tumor samples and 19 normal samples, GSE12945 including 62 tumor samples, GSE17536 including 177 tumor samples, GSE17537 including 55 tumor samples) as the validation sets. One hundred and sixty-six EMT-related genes (EMT-RDGs) were selected from the Molecular Signatures Database. Bioinformatics methods were used to analyze the correlation between EMT-RDGs and CRC prognosis, metastasis, drug efficacy, and immunity.\nRESULTS: We finally obtained nine prognostic-related EMT-RDGs (FGF8, NOG, PHLDB2, SIX2, SNAI1, TBX5, TIAM1, TWIST1, TCF15) through differential expression analysis, Unicox and Lasso regression analysis, and then constructed a risk prognosis model. There were significant differences in clinical characteristics, 22 immune cells, and immune functions between the high-risk and low-risk groups and the different states of the nine prognostic-related EMT-RDGs. The methylation level and mutation status of nine prognostic-related EMT-RDGs all affect their regulation of EMT. The Cox proportional hazards regression model was also constructed by the methylation sites of nine prognostic-related EMT-RDGs. In addition, the expression of FGF8, PHLDB2, SIX2, and SNAIL was higher and the expression level of NOG and TWIST1 was lower in the non-metastasis CRC group. Nine prognostic-related EMT-RDGs also affected the drug treatment response of CRC.\nCONCLUSIONS: Targeting these nine prognostic-related EMT-RDGs can regulate CRC metastasis and immune, which is beneficial for the prognosis of CRC patients, improve drug sensitivity in CRC patients.", "claims": [{"id": "claim-method", "statement": "All data analysis and visualization are performed in R.4.2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34526059", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "All data analysis and visualization are performed in R.4.2."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34526059", "locator": "sections[35] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34526059"], "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. 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"GSM2180445", "GSM2180446", "GSM2180447", "GSM2180448", "GSM2180449", "GSM2180450", "GSM2180451", "GSM2180452", "GSM2180453", "GSM2180454", "GSM2180455", "GSM2180456", "GSM2180457", "GSM2180458", "GSM2180459", "GSM2180460", "GSM2180461", "GSM2180462", "GSM2180463", "GSM2180464", "GSM2180465", "GSM2180466", "GSM2180467", "GSM2180468", "GSM2180469", "GSM2180470", "GSM2180471", "GSM2180472", "GSM2180473", "GSM2180474", "GSM2180475", "GSM2180476", "GSM2180477", "GSM2180478", "GSM2180479", "GSM2180480", "GSM2180481", "GSM2180482", "GSM2180483", "GSM2180484", "GSM2180485", "GSM2180486", "GSM2180487", "GSM2180488", "GSM2180489", "GSM2180490", "GSM2180491", "GSM2180492", "GSM2180493", "GSM2180494", "GSM2180495", "GSM2180496", "GSM2180497", "GSM2180498", "GSM2180499", "GSM2180500", "GSM2180501", "GSM2180502", "GSM2180503", "GSM2180504", "GSM2180505", "GSM2180506", "GSM2180507", "GSM2180508", "GSM2180509", "GSM2180510", "GSM2180511", "GSM2180512", "GSM2180513", "GSM2180514", "GSM2180515", "GSM2180516", "GSM2180517", "GSM2180518", "GSM2180519", "GSM2180520", "GSM2180521", "GSM2180522", "GSM2180523", "GSM2180524", "GSM2180525", "GSM2180526", "GSM2180527", "GSM2180528", "GSM2180529", "GSM2180530", "GSM2180531", "GSM2180532", "GSM2180533", "GSM2180534", "GSM2180535", "GSM2180536", "GSM2180537", "GSM2180538", "GSM2180539", "GSM2180540", "GSM2180541", "GSM2180542", "GSM2180543", "GSM2180544", "GSM2180545", "GSM2180546", "GSM2180547", "GSM2180548", "GSM2180549", "GSM2180550", "GSM2180551", "GSM2180552", "GSM2180553", "GSM2180554", "GSM2180555", "GSM2180556", "GSM2180557", "GSM2180558", "GSM2180559", "GSM2180560", "GSM2180561", "GSM2180562", "GSM2180563", "GSM2180564", "GSM2180565", "GSM2180566", "GSM2180567", "GSM2180568", "GSM2180569", "GSM2180570", "GSM2180571", "GSM2180572", "GSM2180573", "GSM2180574", "GSM2180575", "GSM2180576", "GSM2180577", "GSM2180578", "GSM2180579", "GSM2180580", "GSM2180581", "GSM2180582", "GSM2180583", "GSM2180584", "GSM2180585", "GSM2180586", "GSM2180587", "GSM2180588", "GSM2180589", "GSM2180590", "GSM2180591", "GSM2180592", "GSM2180593", "GSM2180594", "GSM2180595", "GSM2180596", "GSM2180597", "GSM2180598", "GSM2180599", "GSM2180600", "GSM2180601", "GSM2180602", "GSM2180603", "GSM2180604", "GSM2180605", "GSM2180606", "GSM2180607", "GSM2180608", "GSM2180609", "GSM2180610", "GSM2180611", "GSM2180612", "GSM2180613", "GSM2180614", "GSM2180615", "GSM2180616", "GSM2180617", "GSM2180618", "GSM2180619", "GSM2180620", "GSM2180621", "GSM2180622", "GSM2180623", "GSM2180624", "GSM2180625", "GSM2180626", "GSM2180627", "GSM2180628", "GSM2180629", "GSM2180630", "GSM2180631", "GSM2180632", "GSM2180633", "GSM2180634", "GSM2180635", "GSM2180636", "GSM2180637", "GSM2180638", "GSM2180639", "GSM2180640", "GSM2180641", "GSM2180642", "GSM2180643", "GSM2180644", "GSM2180645", "GSM2180646", "GSM2180647", "GSM2180648", "GSM2180649", "GSM2180650", "GSM2180651", "GSM2180652", "GSM2180653", "GSM2180654", "GSM2180655", "GSM2180656", "GSM2180657", "GSM2180658", "GSM2180659", "GSM2180660", "GSM2180661", "GSM2180662", "GSM2180663", "GSM2180664", "GSM2180665", "GSM2180666", "GSM2180667", "GSM2180668", "GSM2180669", "GSM2180670", "GSM2180671", "GSM2180672", "GSM2180673", "GSM2180674", "GSM2180675", "GSM2180676", "GSM2180677", "GSM2180678", "GSM2180679", "GSM2180680", "GSM2180681", "GSM2180682", "GSM2180683", "GSM2180684", "GSM2180685", "GSM2180686", "GSM2180687", "GSM2180688", "GSM2180689", "GSM2180690", "GSM2180691", "GSM2180692", "GSM2180693", "GSM2180694", "GSM2180695", "GSM2180696", "GSM2180697", "GSM2180698", "GSM2180699", "GSM2180700", "GSM2180701", "GSM2180702", "GSM2180703", "GSM2180704", "GSM2180705", "GSM2180706", "GSM2180707", "GSM2180708", "GSM2180709", "GSM2180710", "GSM2180711", "GSM2180712", "GSM2180713", "GSM2180714", "GSM2180715", "GSM2180716", "GSM2180717", "GSM2180718", "GSM2180719", "GSM2180720", "GSM2180721", "GSM2180722", "GSM2180723", "GSM2180724", "GSM2180725", "GSM2180726", "GSM2180727", "GSM2180728", "GSM2180729", "GSM2180730", "GSM2180731", "GSM2180732", "GSM2180733", "GSM2180734", "GSM2180735", "GSM2180736", "GSM2180737", "GSM2180738", "GSM2180739", "GSM2180740", "GSM2180741", "GSM2180742", "GSM2180743", "GSM2180744", "GSM2180745", "GSM2180746", "GSM2180747", "GSM2180748", "GSM2180749", "GSM2180750", "GSM2180751", "GSM2180752", "GSM2180753", "GSM2180754", "GSM2180755", "GSM2180756", "GSM2180757", "GSM2180758", "GSM2180759", "GSM2180760", "GSM2180761", "GSM2180762", "GSM2180763", "GSM2180764", "GSM2180765", "GSM2180766", "GSM2180767", "GSM2180768", "GSM2180769", "GSM2180770", "GSM2180771", "GSM2180772", "GSM2180773", "GSM2180774", "GSM2180775", "GSM2180776", "GSM2180777", "GSM2180778", "GSM2180779", "GSM2180780", "GSM2180781", "GSM2180782", "GSM2180783", "GSM2180784", "GSM2180785", "GSM2180786", "GSM2180787", "GSM2180788", "GSM2180789", "GSM2180790", "GSM2180791", "GSM2180792", "GSM2180793", "GSM2180794", "GSM2180795", "GSM2180796", "GSM2180797", "GSM2180798", "GSM2180799", "GSM2180800", "GSM2180801", "GSM2180802", "GSM2180803", "GSM2180804", "GSM2180805", "GSM2180806", "GSM2180807", "GSM2180808", "GSM2180809", "GSM2180810", "GSM2180811", "GSM2180812", "GSM2180813", "GSM2180814", "GSM2180815", "GSM2180816", "GSM2180817", "GSM2180818", "GSM2180819", "GSM2180820", "GSM2180821", "GSM2180822", "GSM2180823", "GSM2180824", "GSM2180825", "GSM2180826", "GSM2180827", "GSM2180828", "GSM2180829", "GSM2180830", "GSM2180831", "GSM2180832", "GSM2180833", "GSM2180834", "GSM2180835", "GSM2180836", "GSM2180837", "GSM2180838", "GSM2180839", "GSM2180840", "GSM2180841", "GSM2180842", "GSM2180843", "GSM2180844", "GSM2180845", "GSM2180846", "GSM2180847", "GSM2180848", "GSM2180849", "GSM2180850", "GSM2180851", "GSM2180852", "GSM2180853", "GSM2180854", "GSM2180855", "GSM2180856", "GSM2180857", "GSM2180858", "GSM2180859", "GSM2180860", "GSM2180861", "GSM2180862", "GSM2180863", "GSM2180864", "GSM2180865", "GSM2180866", "GSM2180867", "GSM2180868", "GSM2180869", "GSM2180870", "GSM2180871", "GSM2180872", "GSM2180873", "GSM2180874", "GSM2180875", "GSM2180876", "GSM2180877", "GSM2180878", "GSM2180879", "GSM2180880", "GSM2180881", "GSM2180882", "GSM2180883", "GSM2180884", "GSM2180885", "GSM2180886", "GSM2180887", "GSM2180888", "GSM2180889", "GSM2180890", "GSM2180891", "GSM2180892", "GSM2180893", "GSM2180894", "GSM2180895", "GSM2180896", "GSM2180897", "GSM2180898", "GSM2180899", "GSM2180900", "GSM2180901", "GSM2180902", "GSM2180903", "GSM2180904", "GSM2180905", "GSM2180906", "GSM2180907", "GSM2180908", "GSM2180909", "GSM2180910", "GSM2180911", "GSM2180912", "GSM2180913", "GSM2180914", "GSM2180915", "GSM2180916", "GSM2180917", "GSM2180918", "GSM2180919", "GSM2180920", "GSM2180921", "GSM2180922", "GSM2180923", "GSM2180924", "GSM2180925", "GSM2180926", "GSM2180927", "GSM2180928", "GSM2180929", "GSM2180930", "GSM2180931", "GSM2180932", "GSM2180933", "GSM2180934", "GSM2180935", "GSM2180936", "GSM2180937", "GSM2180938", "GSM2180939", "GSM2180940", "GSM2180941", "GSM2180942", "GSM2180943", "GSM2180944", "GSM2180945", "GSM2180946", "GSM2180947", "GSM2180948", "GSM2180949", "GSM2180950", "GSM2180951", "GSM2180952", "GSM2180953", "GSM2180954", "GSM2180955", "GSM2180956", "GSM2180957", "GSM2180958", "GSM2180959", "GSM2180960", "GSM2180961", "GSM2180962", "GSM2180963", "GSM2180964", "GSM2180965", "GSM2180966", "GSM2180967", "GSM2180968", "GSM2180969", "GSM2180970", "GSM2180971", "GSM2180972", "GSM2180973", "GSM2180974", "GSM2180975", "GSM2180976", "GSM2180977", "GSM2180978", "GSM2180979", "GSM2180980", "GSM2180981", "GSM2180982", "GSM2180983", "GSM2180984", "GSM2180985", "GSM2180986", "GSM2180987", "GSM2180988", "GSM2180989", "GSM2180990", "GSM2180991", "GSM2180992", "GSM2180993", "GSM2180994", "GSM2180995", "GSM2180996", "GSM2180997", "GSM2180998", "GSM2180999", "GSM2181000", "GSM2181001", "GSM2181002", "GSM2181003", "GSM2181004", "GSM2181005", "GSM2181006", "GSM2181007", "GSM2181008", "GSM2181009", "GSM2181010", "GSM2181011", "GSM2181012", "GSM2181013", "GSM2181014", "GSM2181015", "GSM2181016", "GSM2181017", "GSM2181018", "GSM2181019", "GSM2181020", "GSM2181021", "GSM2181022", "GSM2181023", "GSM2181024", "GSM2181025", "GSM2181026", "GSM2181027", "GSM2181028", "GSM2181029", "GSM2181030", "GSM2181031", "GSM2181032", "GSM2181033", "GSM2181034", "GSM2181035", "GSM2181036", "GSM2181037", "GSM2181038", "GSM2181039", "GSM2181040", "GSM2181041", "GSM2181042", "GSM2181043", "GSM2181044", "GSM2181045", "GSM2181046", "GSM2181047", "GSM2181048", "GSM2181049", "GSM2181050", "GSM2181051", "GSM2181052", "GSM2181053", "GSM2181054", "GSM2181055", "GSM2181056", "GSM2181057", "GSM2181058", "GSM2181059", "GSM2181060", "GSM2181061", "GSM2181062", "GSM2181063", "GSM2181064", "GSM2181065", "GSM2181066", "GSM2181067", "GSM2181068", "GSM2181069", "GSM2181070", "GSM2181071", "GSM2181072", "GSM2181073", "GSM2181074", "GSM2181075", "GSM2181076", "GSM2181077", "GSM2181078", "GSM2181079", "GSM2181080", "GSM2181081", "GSM2181082", "GSM2181083", "GSM2181084", "GSM2181085", "GSM2181086", "GSM2181087", "GSM2181088", "GSM2181089", "GSM2181090", "GSM2181091", "GSM2181092", "GSM2181093", "GSM2181094", "GSM2181095", "GSM2181096", "GSM2181097", "GSM2181098", "GSM2181099", "GSM2181100", "GSM2181101", "GSM2181102", "GSM2181103", "GSM2181104", "GSM2181105", "GSM2181106", "GSM2181107", "GSM2181108", "GSM2181109", "GSM2181110", "GSM2181111", "GSM2181112", "GSM2181113", "GSM2181114", "GSM2181115", "GSM2181116", "GSM2181117", "GSM2181118", "GSM2181119", "GSM2181120", "GSM2181121", "GSM2181122", "GSM2181123", "GSM2181124", "GSM2181125", "GSM2181126", "GSM2181127", "GSM2181128", "GSM2181129", "GSM2181130", "GSM2181131", "GSM2181132", "GSM2181133", "GSM2181134", "GSM2181135", "GSM2181136", "GSM2181137", "GSM2181138", "GSM2181139", "GSM2181140", "GSM2181141", "GSM2181142", "GSM2181143", "GSM2181144", "GSM2181145", "GSM2181146", "GSM2181147", "GSM2181148", "GSM2181149", "GSM2181150", "GSM2181151", "GSM2181152", "GSM2181153", "GSM2181154", "GSM2181155", "GSM2181156", "GSM2181157", "GSM2181158", "GSM2181159", "GSM2181160", "GSM2181161", "GSM2181162", "GSM2181163", "GSM2181164", "GSM2181165", "GSM2181166", "GSM2181167", "GSM2181168", "GSM2181169", "GSM2181170", "GSM2181171", "GSM2181172", "GSM2181173", "GSM2181174", "GSM2181175", "GSM2181176", "GSM2181177", "GSM2181178", "GSM2181179", "GSM2181180", "GSM2181181", "GSM2181182", "GSM2181183", "GSM2181184", "GSM2181185", "GSM2181186", "GSM2181187", "GSM2181188", "GSM2181189", "GSM2181190", "GSM2181191", "GSM2181192", "GSM2181193", "GSM2181194", "GSM2181195", "GSM2181196", "GSM2181197", "GSM2181198", "GSM2181199", "GSM2181200", "GSM2181201", "GSM2181202", "GSM2181203", "GSM2181204", "GSM2181205", "GSM2181206", "GSM2181207", "GSM2181208", "GSM2181209", "GSM2181210", "GSM2181211", "GSM2181212", "GSM2181213", "GSM2181214", "GSM2181215", "GSM2181216", "GSM2181217", "GSM2181218", "GSM2181219", "GSM2181220", "GSM2181221", "GSM2181222", "GSM2181223", "GSM2181224", "GSM2181225", "GSM2181226", "GSM2181227", "GSM2181228", "GSM2181229", "GSM2181230", "GSM2181231", "GSM2181232", "GSM2181233", "GSM2181234", "GSM2181235", "GSM2181236", "GSM2181237", "GSM2181238", "GSM2181239", "GSM2181240", "GSM2181241", "GSM2181242", "GSM2181243", "GSM2181244", "GSM2181245", "GSM2181246", "GSM2181247", "GSM2181248", "GSM2181249", "GSM2181250", "GSM2181251", "GSM2181252", "GSM2181253", "GSM2181254", "GSM2181255", "GSM2181256", "GSM2181257", "GSM2181258", "GSM2181259", "GSM2181260", "GSM2181261", "GSM2181262", "GSM2181263", "GSM2181264", "GSM2181265", "GSM2181266", "GSM2181267", "GSM2181268", "GSM2181269", "GSM2181270", "GSM2181271", "GSM2181272", "GSM2181273", "GSM2181274", "GSM2181275", "GSM2181276", "GSM2181277", "GSM2181278", "GSM2181279", "GSM2181280", "GSM2181281", "GSM2181282", "GSM2181283", "GSM2181284", "GSM2181285", "GSM2181286", "GSM2181287", "GSM2181288", "GSM2181289", "GSM2181290", "GSM2181291", "GSM2181292", "GSM2181293", "GSM2181294", "GSM2181295", "GSM2181296", "GSM2181297", "GSM2181298", "GSM2181299", "GSM2181300", "GSM2181301", "GSM2181302", "GSM2181303", "GSM2181304", "GSM2181305", "GSM2181306", "GSM2181307", "GSM2181308", "GSM2181309", "GSM2181310", "GSM2181311", "GSM2181312", "GSM2181313", "GSM2181314", "GSM2181315", "GSM2181316", "GSM2181317", "GSM2181318", "GSM2181319", "GSM2181320", "GSM2181321", "GSM2181322", "GSM2181323", "GSM2181324", "GSM2181325", "GSM2181326", "GSM2181327", "GSM2181328", "GSM2181329", "GSM2181330", "GSM2181331", "GSM2181332", "GSM2181333", "GSM2181334", "GSM2181335", "GSM2181336", "GSM2181337", "GSM2181338", "GSM2181339", "GSM2181340", "GSM2181341", "GSM2181342", "GSM2181343", "GSM2181344", "GSM2181345", "GSM2181346", "GSM2181347", "GSM2181348", "GSM2181349", "GSM2181350", "GSM2181351", "GSM2181352", "GSM2181353", "GSM2181354", "GSM2181355", "GSM2181356", "GSM2181357", "GSM2181358", "GSM2181359", "GSM2181360", "GSM2181361", "GSM2181362", "GSM2181363", "GSM2181364", "GSM2181365", "GSM2181366", "GSM2181367", 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