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pmid:33052139
Weighted gene coexpression network analysis identifies the key role associated with acute coronary syndrome.
Yong Wang · Liu Miao · Lin Tao · Jian-Hong Chen · Chuan-Meng Zhu · Ye Li · Bin Qi · Fei Liao · Rong-Shan Li
Aging · 2020 doi:10.18632/aging.103859
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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We downloaded the dataset (GSE56045) from the Gene Expression Omnibus (GEO) database and analyzed weighted gene coexpression networks (WGCNA). Gene Ontology annotation, Disease Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using R software. The protein-protein interaction (PPI) network was constructed using Cytoscape, and the Molecular Complex Detection app was employed to identify significant modules and hub genes. The hub genes were then validated in other microarrays and patients by RT-PCR. Two modules were identified and associated with coronary artery disease (CAD) and included 219 genes. After function and PPI analyses, 24 genes were identified to be potentially associated with CAD. Linear correlation was performed to calculate the relationship between the gene expression levels and coronary artery calcification score and found that CCR7 (R = -0.081, P = 0.0065), CD2 (R = -0.075, P = 0.0012), CXCR5 (R = -0.065, P = 0.029) and IL7R (R = -0.06, P = 0.043) should be validated in other dataset. By comparing the gene expression levels in different groups in GSE23561, GSE34822, GSE59867, GSE60993 and GSE129935, only two genes (CCR7 and CXCR5) showed significance. The nomogram showed that CXCR5 showed the risk of ACS. Further analysis in chest patients found CXCR5 played a key role resulting in ACS. Our WGCNA analysis identified CXCR5 as a risk factor for ACS, and the potential pathogenesis may be associated with immune inflammation.", "claims": [{"id": "claim-method", "statement": "First, we analyzed the relationship between the expression level of these 24 genes and the coronary artery calcification score by linear correlation in GSE56045.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33052139", "locator": "sections[7] \"Dataset validation\" paragraph 2", "quote": "First, we analyzed the relationship between the expression level of these 24 genes and the coronary artery calcification score by linear correlation in GSE56045."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded GSE56045 [21] microarray data from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/). These datasets were based on the platform of the GPL10558 Illumina HumanHT-12 V4.0 expression BeadChip. 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"GSM1352268", "GSM1352269", "GSM1352270", "GSM1352271", "GSM1352272", "GSM1352273", "GSM1352274", "GSM1352275", "GSM1352276", "GSM1352277", "GSM1352278", "GSM1352279", "GSM1352280", "GSM1352281", "GSM1352282", "GSM1352283", "GSM1352284", "GSM1352285", "GSM1352286", "GSM1352287", "GSM1352288", "GSM1352289", "GSM1352290", "GSM1352291", "GSM1352292", "GSM1352293", "GSM1352294", "GSM1352295", "GSM1352296", "GSM1352297", "GSM1352298", "GSM1352299", "GSM1352300", "GSM1352301", "GSM1352302", "GSM1352303", "GSM1352304", "GSM1352305", "GSM1352306", "GSM1352307", "GSM1352308", "GSM1352309", "GSM1352310", "GSM1352311", "GSM1352312", "GSM1352313", "GSM1352314", "GSM1352315", "GSM1352316", "GSM1352317", "GSM1352318", "GSM1352319", "GSM1352320", "GSM1352321", "GSM1352322", "GSM1352323", "GSM1352324", "GSM1352325", "GSM1352326", "GSM1352327", "GSM1352328", "GSM1352329", "GSM1352330", "GSM1352331", "GSM1352332", "GSM1352333", "GSM1352334", "GSM1352335", "GSM1352336", "GSM1352337", "GSM1352338", "GSM1352339", "GSM1352340", "GSM1352341", "GSM1352342", "GSM1352343", "GSM1352344", "GSM1352345", "GSM1352346", "GSM1352347", "GSM1352348", "GSM1352349", "GSM1352350", "GSM1352351", "GSM1352352", "GSM1352353", "GSM1352354", "GSM1352355", "GSM1352356", "GSM1352357", "GSM1352358", "GSM1352359", "GSM1352360", "GSM1352361", "GSM1352362", "GSM1352363", "GSM1352364", "GSM1352365", "GSM1352366", "GSM1352367", "GSM1352368", "GSM1352369", "GSM1352370", "GSM1352371", "GSM1352372", "GSM1352373", "GSM1352374", "GSM1352375", "GSM1352376", "GSM1352377", "GSM1352378", "GSM1352379", "GSM1352380", "GSM1352381", "GSM1352382", "GSM1352383", "GSM1352384", "GSM1352385", "GSM1352386", "GSM1352387", "GSM1352388", "GSM1352389", "GSM1352390", "GSM1352391", "GSM1352392", "GSM1352393", "GSM1352394", "GSM1352395", "GSM1352396", "GSM1352397", "GSM1352398", "GSM1352399", "GSM1352400", "GSM1352401", "GSM1352402", "GSM1352403", "GSM1352404", "GSM1352405", "GSM1352406", "GSM1352407", "GSM1352408", "GSM1352409", "GSM1352410", "GSM1352411", "GSM1352412", "GSM1352413", "GSM1352414", "GSM1352415", "GSM1352416", "GSM1352417", "GSM1352418", "GSM1352419", "GSM1352420", "GSM1352421", "GSM1352422", "GSM1352423", "GSM1352424", "GSM1352425", "GSM1352426", "GSM1352427", "GSM1352428", "GSM1352429", "GSM1352430", "GSM1352431", "GSM1352432", "GSM1352433", "GSM1352434", "GSM1352435", "GSM1352436", "GSM1352437", "GSM1352438", "GSM1352439", "GSM1352440", "GSM1352441", "GSM1352442", "GSM1352443", "GSM1352444", "GSM1352445", "GSM1352446", "GSM1352447", "GSM1352448", "GSM1352449", "GSM1352450", "GSM1352451", "GSM1352452", "GSM1352453", "GSM1352454", "GSM1352455", "GSM1352456", "GSM1352457", "GSM1352458", "GSM1352459", "GSM1352460", "GSM1352461", "GSM1352462", "GSM1352463", "GSM1352464", "GSM1352465", "GSM1352466", "GSM1352467", "GSM1352468", "GSM1352469", "GSM1352470", "GSM1352471", "GSM1352472", "GSM1352473", "GSM1352474", "GSM1352475", "GSM1352476", "GSM1352477", "GSM1352478", "GSM1352479", "GSM1352480", "GSM1352481", "GSM1352482", "GSM1352483", "GSM1352484", "GSM1352485", "GSM1352486", "GSM1352487", "GSM1352488", "GSM1352489", "GSM1352490", "GSM1352491", "GSM1352492", "GSM1352493", "GSM1352494", "GSM1352495", "GSM1352496", "GSM1352497", "GSM1352498", "GSM1352499", "GSM1352500", "GSM1352501", "GSM1352502", "GSM1352503", "GSM1352504", "GSM1352505", "GSM1352506", "GSM1352507", "GSM1352508", "GSM1352509", "GSM1352510", "GSM1352511", "GSM1352512", "GSM1352513", "GSM1352514", "GSM1352515", "GSM1352516", "GSM1352517", "GSM1352518", "GSM1352519", "GSM1352520", "GSM1352521", "GSM1352522", "GSM1352523", "GSM1352524", "GSM1352525", "GSM1352526", "GSM1352527", "GSM1352528", "GSM1352529", "GSM1352530", "GSM1352531", "GSM1352532", "GSM1352533", "GSM1352534", "GSM1352535", "GSM1352536", "GSM1352537", "GSM1352538", "GSM1352539", "GSM1352540", "GSM1352541", "GSM1352542", "GSM1352543", "GSM1352544", "GSM1352545", "GSM1352546", "GSM1352547", "GSM1352548", "GSM1352549", "GSM1352550", "GSM1352551", "GSM1352552", "GSM1352553", "GSM1352554", "GSM1352555", "GSM1352556", "GSM1352557", "GSM1352558", "GSM1352559", "GSM1352560", "GSM1352561", "GSM1352562", "GSM1352563", "GSM1352564", "GSM1352565", "GSM1352566", "GSM1352567", "GSM1352568", "GSM1352569", "GSM1352570", "GSM1352571", "GSM1352572", "GSM1352573", "GSM1352574", "GSM1352575", "GSM1352576", "GSM1352577", "GSM1352578", "GSM1352579", "GSM1352580", "GSM1352581", "GSM1352582", "GSM1352583", "GSM1352584", "GSM1352585", "GSM1352586", "GSM1352587", "GSM1352588", "GSM1352589", "GSM1352590", "GSM1352591", "GSM1352592", "GSM1352593", "GSM1352594", "GSM1352595", "GSM1352596", "GSM1352597", "GSM1352598", "GSM1352599", "GSM1352600", "GSM1352601", "GSM1352602", "GSM1352603", "GSM1352604", "GSM1352605", "GSM1352606", "GSM1352607", "GSM1352608", "GSM1352609", "GSM1352610", "GSM1352611", "GSM1352612", "GSM1352613", "GSM1352614", "GSM1352615", "GSM1352616", "GSM1352617", "GSM1352618", "GSM1352619", "GSM1352620", "GSM1352621", "GSM1352622", "GSM1352623", "GSM1352624", "GSM1352625", "GSM1352626", "GSM1352627", "GSM1352628", "GSM1352629", "GSM1352630", "GSM1352631", "GSM1352632", "GSM1352633", "GSM1352634", "GSM1352635", "GSM1352636", "GSM1352637", "GSM1352638", "GSM1352639", "GSM1352640", "GSM1352641", "GSM1352642", "GSM1352643", "GSM1352644", "GSM1352645", "GSM1352646", "GSM1352647", "GSM1352648", "GSM1352649", "GSM1352650", "GSM1352651", "GSM1352652", "GSM1352653", "GSM1352654", "GSM1352655", "GSM1352656", "GSM1352657", "GSM1352658", "GSM1352659", "GSM1352660", "GSM1352661", "GSM1352662", "GSM1352663", "GSM1352664", "GSM1352665", "GSM1352666", "GSM1352667", "GSM1352668", "GSM1352669", "GSM1352670", "GSM1352671", "GSM1352672", "GSM1352673", "GSM1352674", "GSM1352675", "GSM1352676", "GSM1352677", "GSM1352678", "GSM1352679", "GSM1352680", "GSM1352681", "GSM1352682", "GSM1352683", "GSM1352684", "GSM1352685", "GSM1352686", "GSM1352687", "GSM1352688", "GSM1352689", "GSM1352690", "GSM1352691", "GSM1352692", "GSM1352693", "GSM1352694", "GSM1352695", "GSM1352696", "GSM1352697", "GSM1352698", "GSM1352699", "GSM1352700", "GSM1352701", "GSM1352702", "GSM1352703", "GSM1352704", "GSM1352705", "GSM1352706", "GSM1352707", "GSM1352708", "GSM1352709", "GSM1352710", "GSM1352711", "GSM1352712", "GSM1352713", "GSM1352714", "GSM1352715", "GSM1352716", "GSM1352717", "GSM1352718", "GSM1352719", "GSM1352720", "GSM1352721", "GSM1352722", "GSM1352723", "GSM1352724", "GSM1352725", "GSM1352726", "GSM1352727", "GSM1352728", "GSM1352729", "GSM1352730", "GSM1352731", "GSM1352732", "GSM1352733", "GSM1352734", "GSM1352735", "GSM1352736", "GSM1352737", "GSM1352738", "GSM1352739", "GSM1352740", "GSM1352741", "GSM1352742", "GSM1352743", "GSM1352744", "GSM1352745", "GSM1352746", "GSM1352747", "GSM1352748", "GSM1352749", "GSM1352750", "GSM1352751", "GSM1352752", "GSM1352753", "GSM1352754", "GSM1352755", "GSM1352756", "GSM1352757", "GSM1352758", "GSM1352759", "GSM1352760", "GSM1352761", "GSM1352762", "GSM1352763", "GSM1352764", "GSM1352765", "GSM1352766", "GSM1352767", "GSM1352768", "GSM1352769", "GSM1352770", "GSM1352771", "GSM1352772", "GSM1352773", "GSM1352774", "GSM1352775", "GSM1352776", "GSM1352777", "GSM1352778", "GSM1352779", "GSM1352780", "GSM1352781", "GSM1352782", "GSM1352783", "GSM1352784", "GSM1352785", "GSM1352786", "GSM1352787", "GSM1352788", "GSM1352789", "GSM1352790", "GSM1352791", "GSM1352792", "GSM1352793", "GSM1352794", "GSM1352795", "GSM1352796", "GSM1352797", "GSM1352798", "GSM1352799", "GSM1352800", "GSM1352801", "GSM1352802", "GSM1352803", "GSM1352804", "GSM1352805", "GSM1352806", "GSM1352807", "GSM1352808", "GSM1352809", "GSM1352810", "GSM1352811", "GSM1352812", "GSM1352813", "GSM1352814", "GSM1352815", "GSM1352816", "GSM1352817", "GSM1352818", "GSM1352819", "GSM1352820", "GSM1352821", "GSM1352822", "GSM1352823", "GSM1352824", "GSM1352825", "GSM1352826", "GSM1352827", "GSM1352828", "GSM1352829", "GSM1352830", "GSM1352831", "GSM1352832", "GSM1352833", "GSM1352834", "GSM1352835", "GSM1352836", "GSM1352837", "GSM1352838", "GSM1352839", "GSM1352840", "GSM1352841", "GSM1352842", "GSM1352843", "GSM1352844", "GSM1352845", "GSM1352846", "GSM1352847", "GSM1352848", "GSM1352849", "GSM1352850", "GSM1352851", "GSM1352852", "GSM1352853", "GSM1352854", "GSM1352855", "GSM1352856", "GSM1352857", "GSM1352858", "GSM1352859", "GSM1352860", "GSM1352861", "GSM1352862", "GSM1352863", "GSM1352864", "GSM1352865", "GSM1352866", "GSM1352867", "GSM1352868", "GSM1352869", "GSM1352870", "GSM1352871", "GSM1352872", "GSM1352873", "GSM1352874", "GSM1352875", "GSM1352876", "GSM1352877", "GSM1352878", "GSM1352879", "GSM1352880", "GSM1352881", "GSM1352882", "GSM1352883", "GSM1352884", "GSM1352885", "GSM1352886", "GSM1352887", "GSM1352888", "GSM1352889", "GSM1352890", "GSM1352891", "GSM1352892", "GSM1352893", "GSM1352894", "GSM1352895", "GSM1352896", "GSM1352897", "GSM1352898", "GSM1352899", "GSM1352900", "GSM1352901", "GSM1352902", "GSM1352903", "GSM1352904", "GSM1352905", "GSM1352906", "GSM1352907", "GSM1352908", "GSM1352909", "GSM1352910", "GSM1352911", "GSM1352912", "GSM1352913", "GSM1352914", "GSM1352915", "GSM1352916", "GSM1352917", "GSM1352918", "GSM1352919", "GSM1352920", "GSM1352921", "GSM1352922", "GSM1352923", "GSM1352924", "GSM1352925", "GSM1352926", "GSM1352927", "GSM1352928", "GSM1352929", "GSM1352930", "GSM1352931", "GSM1352932", "GSM1352933", "GSM1352934", "GSM1352935", "GSM1352936", "GSM1352937", "GSM1352938", "GSM1352939", "GSM1352940", "GSM1352941", "GSM1352942", "GSM1352943", "GSM1352944", "GSM1352945", "GSM1352946", "GSM1352947", "GSM1352948", "GSM1352949", "GSM1352950", "GSM1352951", "GSM1352952", "GSM1352953", "GSM1352954", "GSM1352955", "GSM1352956", "GSM1352957", "GSM1352958", "GSM1352959", "GSM1352960", "GSM1352961", "GSM1352962", "GSM1352963", "GSM1352964", "GSM1352965", "GSM1352966", "GSM1352967", "GSM1352968", "GSM1352969", "GSM1352970", "GSM1352971", "GSM1352972", "GSM1352973", "GSM1352974", "GSM1352975", "GSM1352976", "GSM1352977", "GSM1352978", "GSM1352979", "GSM1352980", "GSM1352981", "GSM1352982", "GSM1352983", "GSM1352984", "GSM1352985", "GSM1352986", "GSM1352987", "GSM1352988", "GSM1352989", "GSM1352990", "GSM1352991", "GSM1352992", "GSM1352993", "GSM1352994", "GSM1352995", "GSM1352996", "GSM1352997", "GSM1352998", "GSM1352999", "GSM1353000", "GSM1353001", "GSM1353002", "GSM1353003", "GSM1353004", "GSM1353005", "GSM1353006", "GSM1353007", "GSM1353008", "GSM1353009", "GSM1353010", "GSM1353011", "GSM1353012", "GSM1353013", "GSM1353014", "GSM1353015", "GSM1353016", "GSM1353017", "GSM1353018", "GSM1353019", "GSM1353020", "GSM1353021", "GSM1353022", "GSM1353023", "GSM1353024", "GSM1353025", "GSM1353026", "GSM1353027", "GSM1353028", "GSM1353029", "GSM1353030", "GSM1353031", "GSM1353032", "GSM1353033", "GSM1353034", "GSM1353035", "GSM1353036", "GSM1353037", "GSM1353038", "GSM1353039", "GSM1353040", "GSM1353041", "GSM1353042", "GSM1353043", "GSM1353044", "GSM1353045", "GSM1353046", "GSM1353047", "GSM1353048", "GSM1353049", "GSM1353050", "GSM1353051", "GSM1353052", "GSM1353053", "GSM1353054", "GSM1353055", "GSM1353056", "GSM1353057", "GSM1353058", "GSM1353059", "GSM1353060", "GSM1353061", "GSM1353062", "GSM1353063", "GSM1353064", "GSM1353065", "GSM1353066", "GSM1353067", "GSM1353068", "GSM1353069", "GSM1353070", "GSM1353071", "GSM1353072", "GSM1353073", "GSM1353074", "GSM1353075", "GSM1353076", "GSM1353077", "GSM1353078", "GSM1353079", "GSM1353080", "GSM1353081", "GSM1353082", "GSM1353083", "GSM1353084", "GSM1353085", "GSM1353086", "GSM1353087", "GSM1353088", "GSM1353089", "GSM1353090", "GSM1353091", "GSM1353092", "GSM1353093", "GSM1353094", "GSM1353095", "GSM1353096", "GSM1353097", "GSM1353098", "GSM1353099", "GSM1353100", "GSM1353101", "GSM1353102", "GSM1353103", "GSM1353104", "GSM1353105", "GSM1353106", "GSM1353107", "GSM1353108", "GSM1353109", "GSM1353110", "GSM1353111", "GSM1353112", "GSM1353113", "GSM1353114", "GSM1353115", "GSM1353116", "GSM1353117", "GSM1353118", "GSM1353119", "GSM1353120", "GSM1353121", "GSM1353122", "GSM1353123", "GSM1353124", "GSM1353125", "GSM1353126", "GSM1353127", "GSM1353128", "GSM1353129", "GSM1353130", "GSM1353131", "GSM1353132", "GSM1353133", "GSM1353134", "GSM1353135", "GSM1353136", "GSM1353137", "GSM1353138", "GSM1353139", "GSM1353140", "GSM1353141", "GSM1353142", "GSM1353143", "GSM1353144", "GSM1353145", "GSM1353146", "GSM1353147", "GSM1353148", "GSM1353149", "GSM1353150", "GSM1353151", "GSM1353152", "GSM1353153", "GSM1353154", "GSM1353155", "GSM1353156", "GSM1353157", "GSM1353158", "GSM1353159", "GSM1353160", "GSM1353161", "GSM1353162", "GSM1353163", "GSM1353164", "GSM1353165", "GSM1353166", "GSM1353167", "GSM1353168", "GSM1353169", "GSM1353170", "GSM1353171", "GSM1353172", "GSM1353173", "GSM1353174", "GSM1353175", "GSM1353176", "GSM1353177", "GSM1353178", "GSM1353179", "GSM1353180", "GSM1353181", "GSM1353182", "GSM1353183", "GSM1353184", "GSM1353185", "GSM1353186", "GSM1353187", "GSM1353188", "GSM1353189", "GSM1353190", "GSM1353191", "GSM1353192", "GSM1353193", "GSM1353194", "GSM1353195", "GSM1353196", "GSM1353197", "GSM1353198", "GSM1353199", "GSM1353200", "GSM1353201", "GSM1353202", "GSM1353203"], "sample_count": 1202, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Transcriptomics and methylomics of human monocytes [transcriptome]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE59867", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59867", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59867", "version": null, "note": "We downloaded GSE56045 [21] microarray data from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/). These datasets were based on the platform of the GPL10558 Illumina HumanHT-12 V4.0 expression BeadChip. GSE56045 contains 1,202 peripheral blood samples, as well as clinical information, such as age, whole-blood cell count, and the coronary artery calcification plaque score.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded GSE56045 [21] microarray data from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/). These datasets were based on the platform of the GPL10558 Illumina HumanHT-12 V4.0 expression BeadChip. GSE56045 contains 1,202 peripheral blood samples, as well as clinical information, such as age, whole-blood cell count, and the coronary artery calcification plaque score.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1448335", "GSM1448336", "GSM1448337", "GSM1448338", "GSM1448339", "GSM1448340", "GSM1448341", "GSM1448342", "GSM1448343", "GSM1448344", "GSM1448345", "GSM1448346", "GSM1448347", "GSM1448348", "GSM1448349", "GSM1448350", "GSM1448351", "GSM1448352", "GSM1448353", "GSM1448354", "GSM1448355", "GSM1448356", "GSM1448357", "GSM1448358", "GSM1448359", "GSM1448360", "GSM1448361", "GSM1448362", "GSM1448363", "GSM1448364", "GSM1448365", "GSM1448366", "GSM1448367", "GSM1448368", "GSM1448369", "GSM1448370", "GSM1448371", "GSM1448372", "GSM1448373", "GSM1448374", "GSM1448375", "GSM1448376", "GSM1448377", "GSM1448378", "GSM1448379", "GSM1448380", "GSM1448381", "GSM1448382", "GSM1448383", "GSM1448384", "GSM1448385", "GSM1448386", "GSM1448387", 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"GSM1448601", "GSM1448602", "GSM1448603", "GSM1448604", "GSM1448605", "GSM1448606", "GSM1448607", "GSM1448608", "GSM1448609", "GSM1448610", "GSM1448611", "GSM1448612", "GSM1448613", "GSM1448614", "GSM1448615", "GSM1448616", "GSM1448617", "GSM1448618", "GSM1448619", "GSM1448620", "GSM1448621", "GSM1448622", "GSM1448623", "GSM1448624", "GSM1448625", "GSM1448626", "GSM1448627", "GSM1448628", "GSM1448629", "GSM1448630", "GSM1448631", "GSM1448632", "GSM1448633", "GSM1448634", "GSM1448635", "GSM1448636", "GSM1448637", "GSM1448638", "GSM1448639", "GSM1448640", "GSM1448641", "GSM1448642", "GSM1448643", "GSM1448644", "GSM1448645", "GSM1448646", "GSM1448647", "GSM1448648", "GSM1448649", "GSM1448650", "GSM1448651", "GSM1448652", "GSM1448653", "GSM1448654", "GSM1448655", "GSM1448656", "GSM1448657", "GSM1448658", "GSM1448659", "GSM1448660", "GSM1448661", "GSM1448662", "GSM1448663", "GSM1448664", "GSM1448665", "GSM1448666", "GSM1448667", "GSM1448668", "GSM1448669", "GSM1448670", "GSM1448671", "GSM1448672", "GSM1448673", "GSM1448674", "GSM1448675", "GSM1448676", "GSM1448677", "GSM1448678", "GSM1448679", "GSM1448680", "GSM1448681", "GSM1448682", "GSM1448683", "GSM1448684", "GSM1448685", "GSM1448686", "GSM1448687", "GSM1448688", "GSM1448689", "GSM1448690", "GSM1448691", "GSM1448692", "GSM1448693", "GSM1448694", "GSM1448695", "GSM1448696", "GSM1448697", "GSM1448698", "GSM1448699", "GSM1448700", "GSM1448701", "GSM1448702", "GSM1448703", "GSM1448704", "GSM1448705", "GSM1448706", "GSM1448707", "GSM1448708", "GSM1448709", "GSM1448710", "GSM1448711", "GSM1448712", "GSM1448713", "GSM1448714", "GSM1448715", "GSM1448716", "GSM1448717", "GSM1448718", "GSM1448719", "GSM1448720", "GSM1448721", "GSM1448722", "GSM1448723", "GSM1448724", "GSM1620759", "GSM1620760", "GSM1620761", "GSM1620762", "GSM1620763", "GSM1620764", "GSM1620765", "GSM1620766", "GSM1620767", "GSM1620768", "GSM1620769", "GSM1620770", "GSM1620771", "GSM1620772", "GSM1620773", "GSM1620774", "GSM1620775", "GSM1620776", "GSM1620777", "GSM1620778", "GSM1620779", "GSM1620780", "GSM1620781", "GSM1620782", "GSM1620783", "GSM1620784", "GSM1620785", "GSM1620786", "GSM1620787", "GSM1620788", "GSM1620789", "GSM1620790", "GSM1620791", "GSM1620792", "GSM1620793", "GSM1620794", "GSM1620795", "GSM1620796", "GSM1620797", "GSM1620798", "GSM1620799", "GSM1620800", "GSM1620801", "GSM1620802", "GSM1620803", "GSM1620804"], "sample_count": 436, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profiling reveals potential prognostic biomarkers associated with the progression of heart failure", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE60993", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60993", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE60993", "version": null, "note": "We downloaded GSE56045 [21] microarray data from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/). These datasets were based on the platform of the GPL10558 Illumina HumanHT-12 V4.0 expression BeadChip. GSE56045 contains 1,202 peripheral blood samples, as well as clinical information, such as age, whole-blood cell count, and the coronary artery calcification plaque score.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded GSE56045 [21] microarray data from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/). These datasets were based on the platform of the GPL10558 Illumina HumanHT-12 V4.0 expression BeadChip. GSE56045 contains 1,202 peripheral blood samples, as well as clinical information, such as age, whole-blood cell count, and the coronary artery calcification plaque score.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1495313", "GSM1495314", "GSM1495315", "GSM1495316", "GSM1495317", "GSM1495318", "GSM1495319", "GSM1495320", "GSM1495321", "GSM1495322", "GSM1495323", "GSM1495324", "GSM1495325", "GSM1495326", "GSM1495327", "GSM1495328", "GSM1495329", "GSM1495330", "GSM1495331", "GSM1495332", "GSM1495333", "GSM1495334", "GSM1495335", "GSM1495336", "GSM1495337", "GSM1495338", "GSM1495339", "GSM1495340", "GSM1495341", "GSM1495342", "GSM1495343", "GSM1495344", "GSM1495345"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Assessment and Diagnostic Relevance of Novel Serum Biomarkers for Early Decision of ST-elevation Myocardial Infarction", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33052139:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4f03c09541ec5a80ce8eaa425a7d4030251d52dad532aef2fbc8d2a0c171d329", "bytes": 2600, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#t1", "version": null, "note": "Comparison of demographic, lifestyle characteristics and serum lipid levels among different groups.", "structure": {"pmcid": "PMC7732301", "section_index": 8, "section_title": "Subject validation", "row_count": 27, "column_count": 6}, "table": {"label": "Table 1", "caption": "Comparison of demographic, lifestyle characteristics and serum lipid levels among different groups.", "rows": [["Parameter", "Control", "CAD", "UA", "NSTEMI", "STEMI"], ["Number", "312", "320", "304", "290", "302"], ["Male/female", "94/220", "89/231", "92/210", "84/202", "98/202"], ["Age (years)1", "55.32±8.31", "54.16±9.05", "55.59±8.54", "56.43±9.83", "55.94±9.17"], ["Height (cm)", "166.24±6.82", "168.59±7.29", "167.55±7.28", "166.52±6.94", "167.23±9.13"], ["Weight (kg)", "52.46±6.84", "54.74±10.82", "57.63±9.11a", "57.92±8.77a", "57.52±9.23a"], ["Body mass index (kg/m2)", "29.29±5.13", "30.44±6.47a", "30.67±7.12a", "30.79±6.74a", "30.77±6.09a"], ["Waist circumference (cm)", "74.49±6.74", "73.55±9.48", "76.03±8.15", "76.24±7.17", "76.15±6.27"], ["Smoking status [n (%)]", "81(26.0)", "114(35.6) a", "142(46.7) a", "138(47.6) a", "144(47.6) a"], ["Alcohol consumption [n (%)]", "75(24.0)", "84(26.2)", "70(23.0)", "81(27.9) a", "71(23.5)"], ["SBP (mmHg)", "124.14±17.14", "129.21±21.11a", "147.15±23.96c", "139.47±22.14b", "103.45±17.16c"], ["DBP (mmHg)", "80.52±11.16", "81.33±11.25", "88.54±14.23a", "84.43±11.21", "68.54±12.15c"], ["PP (mmHg)", "49.64±14.13", "51.42±13.59", "51.66±15.24", "50.84±15.22", "50.22±14.21"], ["Glucose (mmol/L)", "5.91±1.83", "6.13±2.22", "7.79±2.43b", "8.46±2.79c", "8.69±2.78c"], ["TC (mmol/L)", "4.93±1.21", "5.21±1.17a", "5.63±1.12a", "5.99±1.18a", "5.83±1.43a"], ["TG (mmol/L)2", "1.49(0.51)", "1.53(1.22)", "1.52(1.21)", "1.44(1.32)", "1.51(1.26)"], ["HDL-C (mmol/L)", "1.52±0.44", "1.32±0.26a", "1.35±0.34a", "1.44±0.28a", "1.48±0.32"], ["LDL-C (mmol/L)", "2.86±0.81", "3.23±0.74a", "3.98±0.79a", "3.79±0.88a", "3.92±0.84a"], ["ApoA1 (g/L)", "1.24±0.24", "1.17±0.22", "1.18±0.26", "1.18±0.26", "1.14±0.28"], ["ApoB (g/L)", "0.84±0.19", "0.82±0.32", "0.81±0.31", "0.94±0.31", "0.88±0.28"], ["ApoA1/ApoB", "1.67±0.50", "1.66±0.57", "1.64±0.58", "1.65±0.61", "1.67±0.54"], ["Heart rate (beats/minutes)", "72.41±10.19", "72.33±10.32", "76.28±10.61a", "76.43±9.31a", "79.76±10.14a"], ["Creatinine, (μmol/L)", "72.34±12.22", "71.36±11.34", "74.53±11.62", "76.55±10.23", "76.58±12.74"], ["Uric acid, (μmol/L)", "283.83±76.19", "286.89±74.32", "279.88±81.31", "285.91±81.31", "283.86±75.28"], ["Troponin T, (μg/L)", "0.01±0.02", "0.02±0.02", "0.02±0.01", "2.74±3.93c", "2.86±6.28c"], ["CK, (U/L)", "88.84±45.28", "87.84±48.31", "91.88±50.33", "1111.92±683.31c", "1124.88±783.28c"], ["CKMB, (U/L)", "12.44±3.63", "13.11±2.78", "13.22±3.32", "129.88±61.45c", "132.76±59.17c"]], "row_count": 27, "column_count": 6, "numeric_cells": 132, "header_rows": 0, "locator": "section[8]/table-wrap[1]#t1"}}], "gaps": ["asset:data:geo:GSE129935 not downloaded", "asset:data:geo:GSE129935 licence not read", "asset:data:geo:GSE23561 not downloaded", "asset:data:geo:GSE23561 licence not read", "asset:data:geo:GSE34822 not downloaded", "asset:data:geo:GSE34822 licence not read", "asset:data:geo:GSE56045 not downloaded", "asset:data:geo:GSE56045 licence not read", "asset:data:geo:GSE59867 not downloaded", "asset:data:geo:GSE59867 licence not read", "asset:data:geo:GSE60993 not downloaded", "asset:data:geo:GSE60993 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}, {"id": "method-5", "family": null, "specific": null, "label": "Linear correlation", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "First, we analyzed the relationship between the expression level of these 24 genes and the coronary artery calcification score by linear correlation in GSE56045."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE56045", "GSE23561", "GSE34822", "GSE59867", "GSE60993", "GSE129935"], "resolved_accessions": ["GSE56045", "GSE23561", "GSE34822", "GSE59867", "GSE60993", "GSE129935"], "statements": ["We downloaded GSE56045 [21] microarray data from GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/). These datasets were based on the platform of the GPL10558 Illumina HumanHT-12 V4.0 expression BeadChip. GSE56045 contains 1,202 peripheral blood samples, as well as clinical information, such as age, whole-blood cell count, and the coronary artery calcification plaque score."], "basis": "The paper names GSE56045, GSE23561, GSE34822, GSE59867, GSE60993, GSE129935 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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