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pmid:35785353
Integrated Analysis of Immune-Related circRNA-miRNA-mRNA Regulatory Network in Ischemic Stroke.
Si Cao · Youjie Zeng · Minghua Chen · Wen Ouyang
Frontiers in neurology · 2022 doi:10.3389/fneur.2022.889855
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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However, studies focusing on circRNAs acting as microRNAs (miRNAs) sponges in regulating mRNA expression are currently scarce.\nMethods: In this study, expression profiles of circRNAs (GSE195442), miRNAs (GSE117064), and mRNAs (GSE58294) from the Gene Expression Omnibus (GEO) database were analyzed. Differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs (DEmRNAs) were identified by R software. The target miRNAs and target genes were predicted by several bioinformatics methods. Then, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEmRNAs. Subsequently, the protein-protein interaction (PPI) network and the competing endogenous RNA (ceRNA) regulatory network were visualized by Cytoscape software. Finally, we further constructed an immune-related circRNA-miRNA-mRNA regulatory sub-network in IS.\nResults: A total of 35 DEcircRNAs, 141 DEmiRNAs, and 356 DEmRNAs were identified. By comprehensive analysis of bioinformatics methods, we constructed a circRNA-miRNA-mRNA regulatory network, including 15 DEcircRNAs, eight DEmiRNAs, and 39 DEmRNAs. FGF9 was identified as an immune-related hub gene. Immune cell analysis indicated a significantly higher level of neutrophils in IS, and the expression of FGF9 was significantly negatively correlated with the level of neutrophils. Eventually, miR-767-5p was predicted as the upstream molecules of FGF9, and circ_0127785 and circ_0075008 were predicted as the upstream circRNAs of miR-767-5p.\nConclusion: Our study provides novel insights into the molecular mechanisms governing the progression of IS from the perspective of immune-related ceRNA networks.", "claims": [{"id": "claim-method", "statement": "DEcircRNAs, DEmiRNAs, and DEmRNAs were screened by the “limma” package in R software (22).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35785353", "locator": "sections[4] \"Differentially Expression Analysis\" paragraph 2", "quote": "DEcircRNAs, DEmiRNAs, and DEmRNAs were screened by the “limma” package in R software (22)."}], "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:35785353", "locator": "sections[20] \"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": "A total of 35 DEcircRNAs, 141 DEmiRNAs, and 356 DEmRNAs were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35785353", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 35 DEcircRNAs, 141 DEmiRNAs, and 356 DEmRNAs were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 35 DEcircRNAs, 141 DEmiRNAs, and 356 DEmRNAs were identified.", "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:35785353"], "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:GSE117064"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE117064"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35785353", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fneur.2022.889855", "sha256": 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"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", "GSM3269546", "GSM3269547", "GSM3269548", "GSM3269549", "GSM3269550", "GSM3269551", "GSM3269552", "GSM3269553", "GSM3269554", "GSM3269555", "GSM3269556", "GSM3269557", "GSM3269558", "GSM3269559", "GSM3269560", "GSM3269561", "GSM3269562", "GSM3269563", "GSM3269564", "GSM3269565", "GSM3269566", "GSM3269567", "GSM3269568", "GSM3269569", "GSM3269570", "GSM3269571", "GSM3269572", "GSM3269573", "GSM3269574", "GSM3269575", "GSM3269576", "GSM3269577", "GSM3269578", "GSM3269579", "GSM3269580", "GSM3269581", "GSM3269582", "GSM3269583", "GSM3269584", "GSM3269585", "GSM3269586", "GSM3269587", "GSM3269588", "GSM3269589", "GSM3269590", "GSM3269591", "GSM3269592", "GSM3269593", "GSM3269594", "GSM3269595", "GSM3269596", "GSM3269597", "GSM3269598", "GSM3269599", "GSM3269600", "GSM3269601", "GSM3269602", "GSM3269603", "GSM3269604", "GSM3269605", "GSM3269606", "GSM3269607", "GSM3269608", "GSM3269609", "GSM3269610", "GSM3269611", "GSM3269612", "GSM3269613", "GSM3269614", "GSM3269615", 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