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pmid:37528851
Identification of a miRNA-mRNA regulatory network for post-stroke depression: a machine-learning approach.
Huaide Qiu · Likui Shen · Ying Shen · Yiming Mao
Frontiers in neurology · 2023 doi:10.3389/fneur.2023.1096911
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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Differentially expressed miRNAs (DE-miRNAs) were identified in blood samples collected from stroke patients vs. control using the Linear Models for Microarray Data (LIMMA) package, while the weighted correlation network analysis (WGCNA) revealed co-expressed gene modules correlated with the subject group. The intersection between DE-miRNAs and miRNAs identified by WGCNA was defined as stroke-related miRNAs, whose target mRNAs were stroke-related genes with the prediction based on three databases (miRDB, miRTarBase, and TargetScan). Using the GSE76826 dataset, the differentially expressed genes (DEGs) were identified. Overlapped DEGs between stroke-related genes and DEGs in late-onset MDD were retrieved, and these were potential mRNA biomarkers in PSD. With the overlapped DEGs, three machine-learning methods were employed to identify gene signatures for PSD, which were established with the intersection of gene sets identified by each algorithm. Based on the gene signatures, the upstream miRNAs were predicted, and a miRNA-mRNA network was constructed.\nResults: Using the GSE117064 dataset, we retrieved a total of 667 DE-miRNAs, which included 420 upregulated and 247 downregulated ones. Meanwhile, WGCNA identified two modules (blue and brown) that were significantly correlated with the subject group. A total of 117 stroke-related miRNAs were identified with the intersection of DE-miRNAs and WGCNA-related ones. Based on the miRNA-mRNA databases, we identified a list of 2,387 stroke-related genes, among which 99 DEGs in MDD were also embedded. Based on the 99 overlapped DEGs, we identified three gene signatures (SPATA2, ZNF208, and YTHDC1) using three machine-learning classifiers. Predictions of the three mRNAs highlight four miRNAs as follows: miR-6883-5p, miR-6873-3p, miR-4776-3p, and miR-6738-3p. Subsequently, a miRNA-mRNA network was developed.\nConclusion: The study highlighted gene signatures for PSD with three genes (SPATA2, ZNF208, and YTHDC1) and four upstream miRNAs (miR-6883-5p, miR-6873-3p, miR-4776-3p, and miR-6738-3p). These biomarkers could further our understanding of the pathogenesis of PSD.", "claims": [{"id": "claim-method", "statement": "The linear models for microarray data (LIMMA) package (23) in R software was applied to extract differentially expressed miRNAs (DE-miRNAs) between stroke and control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37528851", "locator": "sections[4] \"2.2. Differential analysis, WGCNA, and identification of stroke-related genes\" paragraph 2", "quote": "The linear models for microarray data (LIMMA) package (23) in R software was applied to extract differentially expressed miRNAs (DE-miRNAs) between stroke and control samples."}], "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 authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37528851", "locator": "sections[13] \"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 authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study highlighted gene signatures for PSD with three genes (SPATA2, ZNF208, and YTHDC1) and four upstream miRNAs (miR-6883-5p, miR-6873-3p, miR-4776-3p, and miR-6738-3p).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37528851", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The study highlighted gene signatures for PSD with three genes (SPATA2, ZNF208, and YTHDC1) and four upstream miRNAs (miR-6883-5p, miR-6873-3p, miR-4776-3p, and miR-6738-3p)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study highlighted gene signatures for PSD with three genes (SPATA2, ZNF208, and YTHDC1) and four upstream miRNAs (miR-6883-5p, miR-6873-3p, miR-4776-3p, and miR-6738-3p).", "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:37528851"], "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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"GSM3268694", "GSM3268695", "GSM3268696", "GSM3268697", "GSM3268698", "GSM3268699", "GSM3268700", "GSM3268701", "GSM3268702", "GSM3268703", "GSM3268704", "GSM3268705", "GSM3268706", "GSM3268707", "GSM3268708", "GSM3268709", "GSM3268710", "GSM3268711", "GSM3268712", "GSM3268713", "GSM3268714", "GSM3268715", "GSM3268716", "GSM3268717", "GSM3268718", "GSM3268719", "GSM3268720", "GSM3268721", "GSM3268722", "GSM3268723", "GSM3268724", "GSM3268725", "GSM3268726", "GSM3268727", "GSM3268728", "GSM3268729", "GSM3268730", "GSM3268731", "GSM3268732", "GSM3268733", "GSM3268734", "GSM3268735", "GSM3268736", "GSM3268737", "GSM3268738", "GSM3268739", "GSM3268740", "GSM3268741", "GSM3268742", "GSM3268743", "GSM3268744", "GSM3268745", "GSM3268746", "GSM3268747", "GSM3268748", "GSM3268749", "GSM3268750", "GSM3268751", "GSM3268752", "GSM3268753", "GSM3268754", "GSM3268755", "GSM3268756", "GSM3268757", "GSM3268758", "GSM3268759", "GSM3268760", "GSM3268761", "GSM3268762", "GSM3268763", "GSM3268764", "GSM3268765", "GSM3268766", "GSM3268767", "GSM3268768", "GSM3268769", "GSM3268770", "GSM3268771", "GSM3268772", "GSM3268773", "GSM3268774", "GSM3268775", "GSM3268776", "GSM3268777", "GSM3268778", "GSM3268779", "GSM3268780", "GSM3268781", "GSM3268782", "GSM3268783", "GSM3268784", "GSM3268785", "GSM3268786", "GSM3268787", "GSM3268788", "GSM3268789", "GSM3268790", "GSM3268791", "GSM3268792", "GSM3268793", "GSM3268794", "GSM3268795", "GSM3268796", "GSM3268797", "GSM3268798", "GSM3268799", "GSM3268800", "GSM3268801", "GSM3268802", "GSM3268803", "GSM3268804", "GSM3268805", "GSM3268806", "GSM3268807", "GSM3268808", "GSM3268809", "GSM3268810", "GSM3268811", "GSM3268812", "GSM3268813", "GSM3268814", "GSM3268815", "GSM3268816", "GSM3268817", "GSM3268818", "GSM3268819", "GSM3268820", "GSM3268821", "GSM3268822", "GSM3268823", "GSM3268824", "GSM3268825", "GSM3268826", "GSM3268827", "GSM3268828", "GSM3268829", "GSM3268830", "GSM3268831", "GSM3268832", "GSM3268833", "GSM3268834", "GSM3268835", "GSM3268836", "GSM3268837", "GSM3268838", "GSM3268839", "GSM3268840", "GSM3268841", "GSM3268842", "GSM3268843", "GSM3268844", "GSM3268845", "GSM3268846", "GSM3268847", "GSM3268848", "GSM3268849", "GSM3268850", "GSM3268851", "GSM3268852", "GSM3268853", "GSM3268854", "GSM3268855", "GSM3268856", "GSM3268857", "GSM3268858", "GSM3268859", "GSM3268860", "GSM3268861", "GSM3268862", "GSM3268863", "GSM3268864", "GSM3268865", "GSM3268866", "GSM3268867", "GSM3268868", "GSM3268869", "GSM3268870", "GSM3268871", "GSM3268872", "GSM3268873", "GSM3268874", "GSM3268875", "GSM3268876", "GSM3268877", "GSM3268878", "GSM3268879", "GSM3268880", "GSM3268881", "GSM3268882", "GSM3268883", "GSM3268884", "GSM3268885", "GSM3268886", "GSM3268887", "GSM3268888", "GSM3268889", "GSM3268890", "GSM3268891", "GSM3268892", "GSM3268893", "GSM3268894", "GSM3268895", "GSM3268896", "GSM3268897", "GSM3268898", "GSM3268899", "GSM3268900", "GSM3268901", "GSM3268902", "GSM3268903", "GSM3268904", "GSM3268905", "GSM3268906", "GSM3268907", "GSM3268908", "GSM3268909", "GSM3268910", "GSM3268911", "GSM3268912", "GSM3268913", "GSM3268914", "GSM3268915", "GSM3268916", "GSM3268917", "GSM3268918", "GSM3268919", "GSM3268920", "GSM3268921", "GSM3268922", "GSM3268923", "GSM3268924", "GSM3268925", "GSM3268926", "GSM3268927", "GSM3268928", "GSM3268929", "GSM3268930", "GSM3268931", "GSM3268932", "GSM3268933", "GSM3268934", "GSM3268935", "GSM3268936", "GSM3268937", "GSM3268938", "GSM3268939", "GSM3268940", "GSM3268941", "GSM3268942", "GSM3268943", "GSM3268944", "GSM3268945", "GSM3268946", "GSM3268947", "GSM3268948", "GSM3268949", "GSM3268950", "GSM3268951", "GSM3268952", "GSM3268953", "GSM3268954", "GSM3268955", "GSM3268956", "GSM3268957", "GSM3268958", "GSM3268959", "GSM3268960", "GSM3268961", "GSM3268962", "GSM3268963", "GSM3268964", "GSM3268965", "GSM3268966", "GSM3268967", "GSM3268968", "GSM3268969", "GSM3268970", "GSM3268971", "GSM3268972", "GSM3268973", "GSM3268974", "GSM3268975", "GSM3268976", "GSM3268977", "GSM3268978", "GSM3268979", "GSM3268980", "GSM3268981", "GSM3268982", "GSM3268983", "GSM3268984", "GSM3268985", "GSM3268986", "GSM3268987", "GSM3268988", "GSM3268989", "GSM3268990", "GSM3268991", "GSM3268992", "GSM3268993", "GSM3268994", "GSM3268995", "GSM3268996", "GSM3268997", "GSM3268998", "GSM3268999", "GSM3269000", "GSM3269001", "GSM3269002", "GSM3269003", "GSM3269004", "GSM3269005", "GSM3269006", "GSM3269007", "GSM3269008", "GSM3269009", "GSM3269010", "GSM3269011", "GSM3269012", "GSM3269013", "GSM3269014", "GSM3269015", "GSM3269016", "GSM3269017", "GSM3269018", "GSM3269019", "GSM3269020", "GSM3269021", "GSM3269022", "GSM3269023", "GSM3269024", "GSM3269025", "GSM3269026", "GSM3269027", "GSM3269028", "GSM3269029", "GSM3269030", "GSM3269031", "GSM3269032", "GSM3269033", "GSM3269034", "GSM3269035", "GSM3269036", "GSM3269037", "GSM3269038", "GSM3269039", "GSM3269040", "GSM3269041", "GSM3269042", "GSM3269043", "GSM3269044", "GSM3269045", "GSM3269046", "GSM3269047", "GSM3269048", "GSM3269049", "GSM3269050", "GSM3269051", "GSM3269052", "GSM3269053", "GSM3269054", "GSM3269055", "GSM3269056", "GSM3269057", "GSM3269058", "GSM3269059", "GSM3269060", "GSM3269061", "GSM3269062", "GSM3269063", "GSM3269064", "GSM3269065", "GSM3269066", "GSM3269067", "GSM3269068", "GSM3269069", "GSM3269070", "GSM3269071", "GSM3269072", "GSM3269073", "GSM3269074", "GSM3269075", "GSM3269076", "GSM3269077", "GSM3269078", "GSM3269079", "GSM3269080", "GSM3269081", "GSM3269082", "GSM3269083", "GSM3269084", "GSM3269085", "GSM3269086", "GSM3269087", "GSM3269088", "GSM3269089", "GSM3269090", "GSM3269091", "GSM3269092", "GSM3269093", "GSM3269094", "GSM3269095", "GSM3269096", "GSM3269097", "GSM3269098", "GSM3269099", "GSM3269100", "GSM3269101", "GSM3269102", "GSM3269103", "GSM3269104", "GSM3269105", "GSM3269106", "GSM3269107", "GSM3269108", "GSM3269109", "GSM3269110", "GSM3269111", "GSM3269112", "GSM3269113", "GSM3269114", "GSM3269115", "GSM3269116", "GSM3269117", "GSM3269118", "GSM3269119", "GSM3269120", "GSM3269121", "GSM3269122", "GSM3269123", "GSM3269124", "GSM3269125", "GSM3269126", "GSM3269127", "GSM3269128", "GSM3269129", "GSM3269130", "GSM3269131", "GSM3269132", "GSM3269133", "GSM3269134", "GSM3269135", "GSM3269136", "GSM3269137", "GSM3269138", "GSM3269139", "GSM3269140", "GSM3269141", "GSM3269142", "GSM3269143", "GSM3269144", "GSM3269145", "GSM3269146", "GSM3269147", "GSM3269148", "GSM3269149", "GSM3269150", "GSM3269151", "GSM3269152", "GSM3269153", "GSM3269154", "GSM3269155", "GSM3269156", "GSM3269157", "GSM3269158", "GSM3269159", "GSM3269160", "GSM3269161", "GSM3269162", "GSM3269163", "GSM3269164", "GSM3269165", "GSM3269166", "GSM3269167", "GSM3269168", "GSM3269169", "GSM3269170", "GSM3269171", "GSM3269172", "GSM3269173", "GSM3269174", "GSM3269175", "GSM3269176", "GSM3269177", "GSM3269178", "GSM3269179", "GSM3269180", "GSM3269181", "GSM3269182", "GSM3269183", "GSM3269184", "GSM3269185", "GSM3269186", "GSM3269187", "GSM3269188", "GSM3269189", "GSM3269190", "GSM3269191", "GSM3269192", "GSM3269193", "GSM3269194", "GSM3269195", "GSM3269196", "GSM3269197", "GSM3269198", "GSM3269199", "GSM3269200", "GSM3269201", "GSM3269202", "GSM3269203", "GSM3269204", "GSM3269205", "GSM3269206", "GSM3269207", "GSM3269208", "GSM3269209", "GSM3269210", "GSM3269211", "GSM3269212", "GSM3269213", "GSM3269214", "GSM3269215", "GSM3269216", "GSM3269217", "GSM3269218", "GSM3269219", "GSM3269220", "GSM3269221", "GSM3269222", "GSM3269223", "GSM3269224", "GSM3269225", "GSM3269226", "GSM3269227", "GSM3269228", "GSM3269229", "GSM3269230", "GSM3269231", "GSM3269232", "GSM3269233", "GSM3269234", "GSM3269235", "GSM3269236", "GSM3269237", "GSM3269238", "GSM3269239", "GSM3269240", "GSM3269241", "GSM3269242", "GSM3269243", "GSM3269244", "GSM3269245", "GSM3269246", "GSM3269247", "GSM3269248", "GSM3269249", "GSM3269250", "GSM3269251", "GSM3269252", "GSM3269253", "GSM3269254", "GSM3269255", "GSM3269256", "GSM3269257", "GSM3269258", "GSM3269259", "GSM3269260", "GSM3269261", "GSM3269262", "GSM3269263", "GSM3269264", "GSM3269265", "GSM3269266", "GSM3269267", "GSM3269268", "GSM3269269", "GSM3269270", "GSM3269271", "GSM3269272", "GSM3269273", "GSM3269274", "GSM3269275", "GSM3269276", "GSM3269277", "GSM3269278", "GSM3269279", "GSM3269280", "GSM3269281", "GSM3269282", "GSM3269283", "GSM3269284", "GSM3269285", "GSM3269286", "GSM3269287", "GSM3269288", "GSM3269289", "GSM3269290", "GSM3269291", "GSM3269292", "GSM3269293", "GSM3269294", "GSM3269295", "GSM3269296", "GSM3269297", "GSM3269298", "GSM3269299", "GSM3269300", "GSM3269301", "GSM3269302", "GSM3269303", "GSM3269304", "GSM3269305", "GSM3269306", "GSM3269307", "GSM3269308", "GSM3269309", "GSM3269310", "GSM3269311", "GSM3269312", "GSM3269313", "GSM3269314", "GSM3269315", "GSM3269316", "GSM3269317", "GSM3269318", "GSM3269319", "GSM3269320", "GSM3269321", "GSM3269322", "GSM3269323", "GSM3269324", "GSM3269325", "GSM3269326", "GSM3269327", "GSM3269328", "GSM3269329", "GSM3269330", "GSM3269331", "GSM3269332", "GSM3269333", "GSM3269334", "GSM3269335", "GSM3269336", "GSM3269337", "GSM3269338", "GSM3269339", "GSM3269340", "GSM3269341", "GSM3269342", "GSM3269343", "GSM3269344", "GSM3269345", "GSM3269346", "GSM3269347", "GSM3269348", "GSM3269349", "GSM3269350", "GSM3269351", "GSM3269352", "GSM3269353", "GSM3269354", "GSM3269355", "GSM3269356", "GSM3269357", "GSM3269358", "GSM3269359", "GSM3269360", "GSM3269361", "GSM3269362", "GSM3269363", "GSM3269364", "GSM3269365", "GSM3269366", "GSM3269367", "GSM3269368", "GSM3269369", "GSM3269370", "GSM3269371", "GSM3269372", "GSM3269373", "GSM3269374", "GSM3269375", "GSM3269376", "GSM3269377", "GSM3269378", "GSM3269379", "GSM3269380", "GSM3269381", "GSM3269382", "GSM3269383", "GSM3269384", "GSM3269385", "GSM3269386", "GSM3269387", "GSM3269388", "GSM3269389", "GSM3269390", "GSM3269391", "GSM3269392", "GSM3269393", "GSM3269394", "GSM3269395", "GSM3269396", "GSM3269397", "GSM3269398", "GSM3269399", "GSM3269400", "GSM3269401", "GSM3269402", "GSM3269403", "GSM3269404", "GSM3269405", "GSM3269406", "GSM3269407", "GSM3269408", "GSM3269409", "GSM3269410", "GSM3269411", "GSM3269412", "GSM3269413", "GSM3269414", "GSM3269415", "GSM3269416", "GSM3269417", "GSM3269418", "GSM3269419", "GSM3269420", "GSM3269421", "GSM3269422", "GSM3269423", "GSM3269424", "GSM3269425", "GSM3269426", "GSM3269427", "GSM3269428", "GSM3269429", "GSM3269430", "GSM3269431", "GSM3269432", "GSM3269433", "GSM3269434", "GSM3269435", "GSM3269436", "GSM3269437", "GSM3269438", "GSM3269439", "GSM3269440", "GSM3269441", "GSM3269442", "GSM3269443", "GSM3269444", "GSM3269445", "GSM3269446", "GSM3269447", "GSM3269448", "GSM3269449", "GSM3269450", "GSM3269451", "GSM3269452", "GSM3269453", "GSM3269454", "GSM3269455", "GSM3269456", "GSM3269457", "GSM3269458", "GSM3269459", "GSM3269460", "GSM3269461", "GSM3269462", "GSM3269463", "GSM3269464", "GSM3269465", "GSM3269466", "GSM3269467", "GSM3269468", "GSM3269469", "GSM3269470", "GSM3269471", "GSM3269472", "GSM3269473", "GSM3269474", "GSM3269475", "GSM3269476", "GSM3269477", "GSM3269478", "GSM3269479", "GSM3269480", "GSM3269481", "GSM3269482", "GSM3269483", "GSM3269484", "GSM3269485", "GSM3269486", "GSM3269487", "GSM3269488", "GSM3269489", "GSM3269490", "GSM3269491", "GSM3269492", "GSM3269493", "GSM3269494", "GSM3269495", "GSM3269496", "GSM3269497", "GSM3269498", "GSM3269499", "GSM3269500", "GSM3269501", "GSM3269502", "GSM3269503", "GSM3269504", "GSM3269505", "GSM3269506", "GSM3269507", "GSM3269508", "GSM3269509", "GSM3269510", "GSM3269511", "GSM3269512", "GSM3269513", "GSM3269514", "GSM3269515", "GSM3269516", "GSM3269517", "GSM3269518", "GSM3269519", "GSM3269520", "GSM3269521", "GSM3269522", "GSM3269523", "GSM3269524", "GSM3269525", "GSM3269526", "GSM3269527", "GSM3269528", "GSM3269529", "GSM3269530", "GSM3269531", "GSM3269532", "GSM3269533", "GSM3269534", "GSM3269535", "GSM3269536", "GSM3269537", "GSM3269538", "GSM3269539", "GSM3269540", "GSM3269541", "GSM3269542", "GSM3269543", "GSM3269544", "GSM3269545", 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