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pmid:37621964
Identifying potential circulating miRNA biomarkers for the diagnosis and prediction of ovarian cancer using machine-learning approach: application of Boruta.
Farzaneh Hamidi · Neda Gilani · Reza Arabi Belaghi · Hanif Yaghoobi · Esmaeil Babaei · Parvin Sarbakhsh · Jamileh Malakouti
Frontiers in digital health · 2023 doi:10.3389/fdgth.2023.1187578
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Experiment
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Data
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Complete file
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Because of the lack of typical symptoms and effective biomarkers for noninvasive screening, most patients develop advanced-stage ovarian cancer by the time of diagnosis. MicroRNAs (miRNAs) are a type of non-coding RNA molecule that has been linked to human cancers. Specifying diagnostic biomarkers to determine non-cancer and cancer samples is difficult.\nMethods: By using Boruta, a novel random forest-based feature selection in the machine-learning techniques, we aimed to identify biomarkers associated with ovarian cancer using cancerous and non-cancer samples from the Gene Expression Omnibus (GEO) database: GSE106817. In this study, we used two independent GEO data sets as external validation, including GSE113486 and GSE113740. We utilized five state-of-the-art machine-learning algorithms for classification: logistic regression, random forest, decision trees, artificial neural networks, and XGBoost.\nResults: Four models discovered in GSE113486 had an AUC of 100%, three in GSE113740 with AUC of over 94%, and four in GSE113486 with AUC of over 94%. We identified 10 miRNAs to distinguish ovarian cancer cases from normal controls: hsa-miR-1290, hsa-miR-1233-5p, hsa-miR-1914-5p, hsa-miR-1469, hsa-miR-4675, hsa-miR-1228-5p, hsa-miR-3184-5p, hsa-miR-6784-5p, hsa-miR-6800-5p, and hsa-miR-5100. Our findings suggest that miRNAs could be used as possible biomarkers for ovarian cancer screening, for possible intervention.", "claims": [{"id": "claim-method", "statement": "By using Boruta, a novel random forest-based feature selection in the machine-learning techniques, we aimed to identify biomarkers associated with ovarian cancer using cancerous and non-cancer samples from the Gene Expression Omnibus (GEO) database: GSE106817.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37621964", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "By using Boruta, a novel random forest-based feature selection in the machine-learning techniques, we aimed to identify biomarkers associated with ovarian cancer using cancerous and non-cancer samples from the Gene Expression Omnibus (GEO) database: GSE106817."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37621964", "locator": "sections[28] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 10 miRNAs to distinguish ovarian cancer cases from normal controls: hsa-miR-1290, hsa-miR-1233-5p, hsa-miR-1914-5p, hsa-miR-1469, hsa-miR-4675, hsa-miR-1228-5p, hsa-miR-3184-5p, hsa-miR-6784-5p, hsa-miR-6800-5p, and hsa-miR-5100.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37621964", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 10 miRNAs to distinguish ovarian cancer cases from normal controls: hsa-miR-1290, hsa-miR-1233-5p, hsa-miR-1914-5p, hsa-miR-1469, hsa-miR-4675, hsa-miR-1228-5p, hsa-miR-3184-5p, hsa-miR-6784-5p, hsa-miR-6800-5p, and hsa-miR-5100."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We identified 10 miRNAs to distinguish ovarian cancer cases from normal controls: hsa-miR-1290, hsa-miR-1233-5p, hsa-miR-1914-5p, hsa-miR-1469, hsa-miR-4675, hsa-miR-1228-5p, hsa-miR-3184-5p, hsa-miR-6784-5p, hsa-miR-6800-5p, and hsa-miR-5100.", "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:37621964"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE106817"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:machine_learning_random_forest", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE106817"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:machine_learning_random_forest"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37621964", "role": "manuscript", "format": "xml", "media_type": "application/xml", 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"GSM2851955", "GSM2851956", "GSM2851957", "GSM2851958", "GSM2851959", "GSM2851960", "GSM2851961", "GSM2851962", "GSM2851963", "GSM2851964", "GSM2851965", "GSM2851966", "GSM2851967", "GSM2851968", "GSM2851969", "GSM2851970", "GSM2851971", "GSM2851972", "GSM2851973", "GSM2851974", "GSM2851975", "GSM2851976", "GSM2851977", "GSM2851978", "GSM2851979", "GSM2851980", "GSM2851981", "GSM2851982", "GSM2851983", "GSM2851984", "GSM2851985", "GSM2851986", "GSM2851987", "GSM2851988", "GSM2851989", "GSM2851990", "GSM2851991", "GSM2851992", "GSM2851993", "GSM2851994", "GSM2851995", "GSM2851996", "GSM2851997", "GSM2851998", "GSM2851999", "GSM2852000", "GSM2852001", "GSM2852002", "GSM2852003", "GSM2852004", "GSM2852005", "GSM2852006", "GSM2852007", "GSM2852008", "GSM2852009", "GSM2852010", "GSM2852011", "GSM2852012", "GSM2852013", "GSM2852014", "GSM2852015", "GSM2852016", "GSM2852017", "GSM2852018", "GSM2852019", "GSM2852020", "GSM2852021", "GSM2852022", "GSM2852023", "GSM2852024", "GSM2852025", 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"GSM2852239", "GSM2852240", "GSM2852241", "GSM2852242", "GSM2852243", "GSM2852244", "GSM2852245", "GSM2852246", "GSM2852247", "GSM2852248", "GSM2852249", "GSM2852250", "GSM2852251", "GSM2852252", "GSM2852253", "GSM2852254", "GSM2852255", "GSM2852256", "GSM2852257", "GSM2852258", "GSM2852259", "GSM2852260", "GSM2852261", "GSM2852262", "GSM2852263", "GSM2852264", "GSM2852265", "GSM2852266", "GSM2852267", "GSM2852268", "GSM2852269", "GSM2852270", "GSM2852271", "GSM2852272", "GSM2852273", "GSM2852274", "GSM2852275", "GSM2852276", "GSM2852277", "GSM2852278", "GSM2852279", "GSM2852280", "GSM2852281", "GSM2852282", "GSM2852283", "GSM2852284", "GSM2852285", "GSM2852286", "GSM2852287", "GSM2852288", "GSM2852289", "GSM2852290", "GSM2852291", "GSM2852292", "GSM2852293", "GSM2852294", "GSM2852295", "GSM2852296", "GSM2852297", "GSM2852298", "GSM2852299", "GSM2852300", "GSM2852301", "GSM2852302", "GSM2852303", "GSM2852304", "GSM2852305", "GSM2852306", "GSM2852307", "GSM2852308", "GSM2852309", "GSM2852310", "GSM2852311", "GSM2852312", "GSM2852313", "GSM2852314", "GSM2852315", "GSM2852316", "GSM2852317", "GSM2852318", "GSM2852319", "GSM2852320", "GSM2852321", "GSM2852322", "GSM2852323", "GSM2852324", "GSM2852325", "GSM2852326", "GSM2852327", "GSM2852328", "GSM2852329", "GSM2852330", "GSM2852331", "GSM2852332", "GSM2852333", "GSM2852334", "GSM2852335", "GSM2852336", "GSM2852337", "GSM2852338", "GSM2852339", "GSM2852340", "GSM2852341", "GSM2852342", "GSM2852343", "GSM2852344", "GSM2852345", "GSM2852346", "GSM2852347", "GSM2852348", "GSM2852349", "GSM2852350", "GSM2852351", "GSM2852352", "GSM2852353", "GSM2852354", "GSM2852355", "GSM2852356", "GSM2852357", "GSM2852358", "GSM2852359", "GSM2852360", "GSM2852361", "GSM2852362", "GSM2852363", "GSM2852364", "GSM2852365", "GSM2852366", "GSM2852367", "GSM2852368", "GSM2852369", "GSM2852370", "GSM2852371", "GSM2852372", "GSM2852373", "GSM2852374", "GSM2852375", "GSM2852376", "GSM2852377", "GSM2852378", "GSM2852379", "GSM2852380", "GSM2852381", "GSM2852382", "GSM2852383", "GSM2852384", "GSM2852385", "GSM2852386", "GSM2852387", "GSM2852388", "GSM2852389", "GSM2852390", "GSM2852391", "GSM2852392", "GSM2852393", "GSM2852394", "GSM2852395", "GSM2852396", "GSM2852397", "GSM2852398", "GSM2852399", "GSM2852400", "GSM2852401", "GSM2852402", "GSM2852403", "GSM2852404", "GSM2852405", "GSM2852406", "GSM2852407", "GSM2852408", "GSM2852409", "GSM2852410", "GSM2852411", "GSM2852412", "GSM2852413", "GSM2852414", "GSM2852415", "GSM2852416", "GSM2852417", "GSM2852418", "GSM2852419", "GSM2852420", "GSM2852421", "GSM2852422", "GSM2852423", "GSM2852424", "GSM2852425", "GSM2852426", "GSM2852427", "GSM2852428", "GSM2852429", "GSM2852430", "GSM2852431", "GSM2852432", "GSM2852433", "GSM2852434", "GSM2852435", "GSM2852436", "GSM2852437", "GSM2852438", "GSM2852439", "GSM2852440", "GSM2852441", "GSM2852442", "GSM2852443", "GSM2852444", "GSM2852445", "GSM2852446", "GSM2852447", "GSM2852448", "GSM2852449", "GSM2852450", "GSM2852451", "GSM2852452", "GSM2852453", "GSM2852454", "GSM2852455", "GSM2852456", "GSM2852457", "GSM2852458", "GSM2852459", "GSM2852460", "GSM2852461", "GSM2852462", "GSM2852463", "GSM2852464", "GSM2852465", "GSM2852466", "GSM2852467", "GSM2852468", "GSM2852469", "GSM2852470", "GSM2852471", "GSM2852472", "GSM2852473", "GSM2852474", "GSM2852475", "GSM2852476", "GSM2852477", "GSM2852478", "GSM2852479", "GSM2852480", "GSM2852481", "GSM2852482", "GSM2852483", "GSM2852484", "GSM2852485", "GSM2852486", "GSM2852487", "GSM2852488", "GSM2852489", "GSM2852490", "GSM2852491", "GSM2852492", "GSM2852493", "GSM2852494", "GSM2852495", "GSM2852496", "GSM2852497", "GSM2852498", "GSM2852499", "GSM2852500", "GSM2852501", "GSM2852502", "GSM2852503", "GSM2852504", "GSM2852505", "GSM2852506", "GSM2852507", "GSM2852508", "GSM2852509", "GSM2852510", "GSM2852511", "GSM2852512", "GSM2852513", "GSM2852514", "GSM2852515", "GSM2852516", "GSM2852517", "GSM2852518", "GSM2852519", "GSM2852520", "GSM2852521", "GSM2852522", 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"GSM2852594", "GSM2852595", "GSM2852596", "GSM2852597", "GSM2852598", "GSM2852599", "GSM2852600", "GSM2852601", "GSM2852602", "GSM2852603", "GSM2852604", "GSM2852605", "GSM2852606", "GSM2852607", "GSM2852608", "GSM2852609", "GSM2852610", "GSM2852611", "GSM2852612", "GSM2852613", "GSM2852614", "GSM2852615", "GSM2852616", "GSM2852617", "GSM2852618", "GSM2852619", "GSM2852620", "GSM2852621", "GSM2852622", "GSM2852623", "GSM2852624", "GSM2852625", "GSM2852626", "GSM2852627", "GSM2852628", "GSM2852629", "GSM2852630", "GSM2852631", "GSM2852632", "GSM2852633", "GSM2852634", "GSM2852635", "GSM2852636", "GSM2852637", "GSM2852638", "GSM2852639", "GSM2852640", "GSM2852641", "GSM2852642", "GSM2852643", "GSM2852644", "GSM2852645", "GSM2852646", "GSM2852647", "GSM2852648", "GSM2852649", "GSM2852650", "GSM2852651", "GSM2852652", "GSM2852653", "GSM2852654", "GSM2852655", "GSM2852656", "GSM2852657", "GSM2852658", "GSM2852659", "GSM2852660", "GSM2852661", "GSM2852662", "GSM2852663", "GSM2852664", "GSM2852665", "GSM2852666", "GSM2852667", "GSM2852668", "GSM2852669", "GSM2852670", "GSM2852671", "GSM2852672", "GSM2852673", "GSM2852674", "GSM2852675", "GSM2852676", "GSM2852677", "GSM2852678", "GSM2852679", "GSM2852680", "GSM2852681", "GSM2852682", "GSM2852683", "GSM2852684", "GSM2852685", "GSM2852686", "GSM2852687", "GSM2852688", "GSM2852689", "GSM2852690", "GSM2852691", "GSM2852692", "GSM2852693", "GSM2852694", "GSM2852695", "GSM2852696", "GSM2852697", "GSM2852698", "GSM2852699", "GSM2852700", "GSM2852701", "GSM2852702", "GSM2852703", "GSM2852704", "GSM2852705", "GSM2852706", "GSM2852707", "GSM2852708", "GSM2852709", "GSM2852710", "GSM2852711", "GSM2852712", "GSM2852713", "GSM2852714", "GSM2852715", "GSM2852716", "GSM2852717", "GSM2852718", "GSM2852719", "GSM2852720", "GSM2852721", "GSM2852722", "GSM2852723", "GSM2852724", "GSM2852725", "GSM2852726", "GSM2852727", "GSM2852728", "GSM2852729", "GSM2852730", "GSM2852731", "GSM2852732", "GSM2852733", "GSM2852734", "GSM2852735", "GSM2852736", "GSM2852737", "GSM2852738", "GSM2852739", "GSM2852740", "GSM2852741", "GSM2852742", "GSM2852743", "GSM2852744", "GSM2852745", "GSM2852746", "GSM2852747", "GSM2852748", "GSM2852749", "GSM2852750", "GSM2852751", "GSM2852752", "GSM2852753", "GSM2852754", "GSM2852755", "GSM2852756", "GSM2852757", "GSM2852758", "GSM2852759", "GSM2852760", "GSM2852761", "GSM2852762", "GSM2852763", "GSM2852764", "GSM2852765", "GSM2852766", "GSM2852767", "GSM2852768", "GSM2852769", "GSM2852770", "GSM2852771", "GSM2852772", "GSM2852773", "GSM2852774", "GSM2852775", "GSM2852776", "GSM2852777", "GSM2852778", "GSM2852779", "GSM2852780", "GSM2852781", "GSM2852782", "GSM2852783", "GSM2852784", "GSM2852785", "GSM2852786", "GSM2852787", "GSM2852788", "GSM2852789", "GSM2852790", "GSM2852791", "GSM2852792", "GSM2852793", "GSM2852794", "GSM2852795", "GSM2852796", "GSM2852797", "GSM2852798", "GSM2852799", "GSM2852800", "GSM2852801", "GSM2852802", "GSM2852803", "GSM2852804", "GSM2852805", "GSM2852806", "GSM2852807", "GSM2852808", "GSM2852809", "GSM2852810", "GSM2852811", "GSM2852812", "GSM2852813", "GSM2852814", "GSM2852815", "GSM2852816", "GSM2852817", "GSM2852818", "GSM2852819", "GSM2852820", "GSM2852821", "GSM2852822", "GSM2852823", "GSM2852824", "GSM2852825", "GSM2852826", "GSM2852827", "GSM2852828", "GSM2852829", "GSM2852830", "GSM2852831", "GSM2852832", "GSM2852833", "GSM2852834", "GSM2852835", "GSM2852836", "GSM2852837", "GSM2852838", "GSM2852839", "GSM2852840", "GSM2852841", "GSM2852842", "GSM2852843", "GSM2852844", "GSM2852845", "GSM2852846", "GSM2852847", "GSM2852848", "GSM2852849", "GSM2852850", "GSM2852851", "GSM2852852", "GSM2852853", "GSM2852854", "GSM2852855", "GSM2852856", "GSM2852857", "GSM2852858", "GSM2852859", "GSM2852860", "GSM2852861", "GSM2852862", "GSM2852863", "GSM2852864", "GSM2852865", "GSM2852866", "GSM2852867", "GSM2852868", "GSM2852869", "GSM2852870", "GSM2852871", "GSM2852872", "GSM2852873", "GSM2852874", "GSM2852875", "GSM2852876", "GSM2852877", "GSM2852878", "GSM2852879", "GSM2852880", "GSM2852881", "GSM2852882", "GSM2852883", "GSM2852884", "GSM2852885", "GSM2852886", "GSM2852887", "GSM2852888", "GSM2852889", "GSM2852890", "GSM2852891", "GSM2852892", "GSM2852893", "GSM2852894", "GSM2852895", "GSM2852896", "GSM2852897", "GSM2852898", "GSM2852899", "GSM2852900", "GSM2852901", "GSM2852902", "GSM2852903", "GSM2852904", "GSM2852905", "GSM2852906", "GSM2852907", "GSM2852908", "GSM2852909", "GSM2852910", "GSM2852911", "GSM2852912", "GSM2852913", "GSM2852914", "GSM2852915", "GSM2852916", "GSM2852917", "GSM2852918", "GSM2852919", "GSM2852920", "GSM2852921", "GSM2852922", "GSM2852923", "GSM2852924", "GSM2852925", "GSM2852926", "GSM2852927", "GSM2852928", "GSM2852929", "GSM2852930", "GSM2852931", "GSM2852932", "GSM2852933", "GSM2852934", "GSM2852935", "GSM2852936", "GSM2852937", "GSM2852938", "GSM2852939", "GSM2852940", "GSM2852941", "GSM2852942", "GSM2852943", "GSM2852944", "GSM2852945", "GSM2852946", "GSM2852947", "GSM2852948", "GSM2852949", "GSM2852950", "GSM2852951", "GSM2852952", "GSM2852953", "GSM2852954", "GSM2852955", "GSM2852956", "GSM2852957", "GSM2852958", "GSM2852959", "GSM2852960", "GSM2852961", "GSM2852962", "GSM2852963", "GSM2852964", "GSM2852965", "GSM2852966", "GSM2852967", "GSM2852968", "GSM2852969", "GSM2852970", "GSM2852971", "GSM2852972", "GSM2852973", "GSM2852974", "GSM2852975", "GSM2852976", "GSM2852977", "GSM2852978", "GSM2852979", "GSM2852980", "GSM2852981", "GSM2852982", "GSM2852983", "GSM2852984", "GSM2852985", "GSM2852986", "GSM2852987", "GSM2852988", "GSM2852989", "GSM2852990", "GSM2852991", "GSM2852992", "GSM2852993", "GSM2852994", "GSM2852995", "GSM2852996", "GSM2852997", "GSM2852998", "GSM2852999", "GSM2853000", "GSM2853001", "GSM2853002", "GSM2853003", "GSM2853004", "GSM2853005", "GSM2853006", "GSM2853007", "GSM2853008", "GSM2853009", "GSM2853010", "GSM2853011", "GSM2853012", "GSM2853013", "GSM2853014", "GSM2853015", "GSM2853016", "GSM2853017", "GSM2853018", "GSM2853019", "GSM2853020", "GSM2853021", "GSM2853022", "GSM2853023", "GSM2853024", "GSM2853025", "GSM2853026", "GSM2853027", "GSM2853028", "GSM2853029", "GSM2853030", "GSM2853031", "GSM2853032", "GSM2853033", "GSM2853034", "GSM2853035", "GSM2853036", "GSM2853037", "GSM2853038", "GSM2853039", "GSM2853040", "GSM2853041", "GSM2853042", "GSM2853043", "GSM2853044", "GSM2853045", "GSM2853046", "GSM2853047", "GSM2853048", "GSM2853049", "GSM2853050", "GSM2853051", "GSM2853052", "GSM2853053", "GSM2853054", "GSM2853055", "GSM2853056", "GSM2853057", "GSM2853058", "GSM2853059", "GSM2853060", "GSM2853061", "GSM2853062", "GSM2853063", "GSM2853064", "GSM2853065", "GSM2853066", "GSM2853067", "GSM2853068", "GSM2853069", "GSM2853070", "GSM2853071", "GSM2853072", "GSM2853073", "GSM2853074", "GSM2853075", "GSM2853076", "GSM2853077", "GSM2853078", "GSM2853079", "GSM2853080", "GSM2853081", "GSM2853082", "GSM2853083", "GSM2853084", "GSM2853085", "GSM2853086", "GSM2853087", "GSM2853088", "GSM2853089", "GSM2853090", "GSM2853091", "GSM2853092", "GSM2853093", "GSM2853094", "GSM2853095", "GSM2853096", "GSM2853097", "GSM2853098", "GSM2853099", "GSM2853100", "GSM2853101", "GSM2853102", "GSM2853103", "GSM2853104", "GSM2853105", "GSM2853106", "GSM2853107", "GSM2853108", "GSM2853109", "GSM2853110", "GSM2853111", "GSM2853112", "GSM2853113", "GSM2853114", "GSM2853115", "GSM2853116", "GSM2853117", "GSM2853118", "GSM2853119", "GSM2853120", "GSM2853121", "GSM2853122", "GSM2853123", "GSM2853124", "GSM2853125", "GSM2853126", "GSM2853127", "GSM2853128", "GSM2853129", "GSM2853130", "GSM2853131", "GSM2853132", "GSM2853133", "GSM2853134", "GSM2853135", "GSM2853136", "GSM2853137", "GSM2853138", "GSM2853139", "GSM2853140", "GSM2853141", "GSM2853142", "GSM2853143", "GSM2853144", "GSM2853145", "GSM2853146", "GSM2853147", "GSM2853148", "GSM2853149", "GSM2853150", "GSM2853151", "GSM2853152", "GSM2853153", "GSM2853154", "GSM2853155", "GSM2853156", "GSM2853157", "GSM2853158", "GSM2853159", "GSM2853160", "GSM2853161", 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