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pmid:33999966
Comparison of machine-learning methodologies for accurate diagnosis of sepsis using microarray gene expression data.
Dominik Schaack · Markus A Weigand · Florian Uhle
PloS one · 2021 doi:10.1371/journal.pone.0251800
Paper
complete
Experiment
partial
Data
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Analysis
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Execution
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Complete file
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Publicly available data series were extracted from NCBI Gene Expression Omnibus and EMBL-EBI ArrayExpress to create a comprehensive meta-analysis microarray expression set (meta-expression set). Measurements had to be obtained via microarray-technique from whole blood samples of adult or pediatric patients with sepsis diagnosed based on international consensus definition immediately after admission to the intensive care unit. We aggregate trauma patients, systemic inflammatory response syndrome (SIRS) patients, and healthy controls in a non-septic entity. Differential expression (DE) analysis is compared with machine-learning-based solutions like decision tree (DT), random forest (RF), support vector machine (SVM), and deep-learning neural networks (DNNs). We evaluated classifier training and discrimination performance in 100 independent iterations. To test diagnostic resilience, we gradually degraded expression data in multiple levels. 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"GSM901752", "GSM901753", "GSM901754", "GSM901755", "GSM901756", "GSM901757", "GSM901758", "GSM901759", "GSM901760", "GSM901761", "GSM901762", "GSM901763", "GSM901764", "GSM901765", "GSM901766", "GSM901767", "GSM901768", "GSM901769", "GSM901770", "GSM901771", "GSM901772", "GSM901773", "GSM901774", "GSM901775", "GSM901776", "GSM901777", "GSM901778", "GSM901779", "GSM901780", "GSM901781", "GSM901782", "GSM901783", "GSM901784", "GSM901785", "GSM901786", "GSM901787", "GSM901788", "GSM901789", "GSM901790", "GSM901791", "GSM901792", "GSM901793", "GSM901794", "GSM901795", "GSM901796", "GSM901797", "GSM901798", "GSM901799", "GSM901800", "GSM901801", "GSM901802", "GSM901803", "GSM901804", "GSM901805", "GSM901806", "GSM901807", "GSM901808", "GSM901809", "GSM901810", "GSM901811", "GSM901812", "GSM901813", "GSM901814", "GSM901815", "GSM901816", "GSM901817", "GSM901818", "GSM901819", "GSM901820", "GSM901821", "GSM901822", "GSM901823", "GSM901824", "GSM901825", "GSM901826", "GSM901827", "GSM901828", "GSM901829", "GSM901830", "GSM901831", "GSM901832", "GSM901833", "GSM901834", "GSM901835", "GSM901836", "GSM901837", "GSM901838", "GSM901839", "GSM901840", "GSM901841", "GSM901842", "GSM901843", "GSM901844", "GSM901845", "GSM901846", "GSM901847", "GSM901848", "GSM901849", "GSM901850", "GSM901851", "GSM901852", "GSM901853", "GSM901854", "GSM901855", "GSM901856", "GSM901857", "GSM901858", "GSM901859", "GSM901860", "GSM901861", "GSM901862", "GSM901863", "GSM901864", "GSM901865", "GSM901866", "GSM901867", "GSM901868", "GSM901869", "GSM901870", "GSM901871", "GSM901872", "GSM901873", "GSM901874", "GSM901875", "GSM901876", "GSM901877", "GSM901878", "GSM901879", "GSM901880", "GSM901881", "GSM901882", "GSM901883", "GSM901884", "GSM901885", "GSM901886", "GSM901887", "GSM901888", "GSM901889", "GSM901890", "GSM901891", "GSM901892", "GSM901893", "GSM901894", "GSM901895", "GSM901896", "GSM901897", "GSM901898", "GSM901899", "GSM901900", "GSM901901", "GSM901902", "GSM901903", "GSM901904", "GSM901905", "GSM901906", "GSM901907", "GSM901908", "GSM901909", "GSM901910", "GSM901911", "GSM901912", "GSM901913", "GSM901914", "GSM901915", "GSM901916", "GSM901917", "GSM901918", "GSM901919", "GSM901920", "GSM901921", "GSM901922", "GSM901923", "GSM901924", "GSM901925", "GSM901926", "GSM901927", "GSM901928", "GSM901929", "GSM901930", "GSM901931", "GSM901932", "GSM901933", "GSM901934", "GSM901935", "GSM901936", "GSM901937", "GSM901938", "GSM901939", "GSM901940", "GSM901941", "GSM901942", "GSM901943", "GSM901944", "GSM901945", "GSM901946", "GSM901947", "GSM901948", "GSM901949", "GSM901950", "GSM901951", "GSM901952", "GSM901953", "GSM901954", "GSM901955", "GSM901956", "GSM901957", "GSM901958", "GSM901959", "GSM901960", "GSM901961", "GSM901962", "GSM901963", "GSM901964", "GSM901965", "GSM901966", "GSM901967", "GSM901968", "GSM901969", "GSM901970", "GSM901971", "GSM901972", "GSM901973", "GSM901974", "GSM901975", "GSM901976", "GSM901977", "GSM901978", "GSM901979", "GSM901980", "GSM901981", "GSM901982", "GSM901983", "GSM901984", "GSM901985", "GSM901986", "GSM901987", "GSM901988", "GSM901989", "GSM901990", "GSM901991", "GSM901992", "GSM901993", "GSM901994", "GSM901995", "GSM901996", "GSM901997", "GSM901998", "GSM901999", "GSM902000", "GSM902001", "GSM902002", "GSM902003", "GSM902004", "GSM902005", "GSM902006", "GSM902007", "GSM902008", "GSM902009", "GSM902010", "GSM902011", "GSM902012", "GSM902013", "GSM902014", "GSM902015", "GSM902016", "GSM902017", "GSM902018", "GSM902019", "GSM902020", "GSM902021", "GSM902022", "GSM902023", "GSM902024", "GSM902025", "GSM902026", "GSM902027", "GSM902028", "GSM902029", "GSM902030", "GSM902031", "GSM902032", "GSM902033", "GSM902034", "GSM902035", "GSM902036", "GSM902037", "GSM902038", "GSM902039", "GSM902040", "GSM902041", "GSM902042", "GSM902043", "GSM902044", "GSM902045", "GSM902046", "GSM902047", "GSM902048", "GSM902049", "GSM902050", "GSM902051", "GSM902052", "GSM902053", "GSM902054", "GSM902055", "GSM902056", "GSM902057", "GSM902058", "GSM902059", "GSM902060", "GSM902061", "GSM902062", "GSM902063", "GSM902064", "GSM902065", "GSM902066", "GSM902067", "GSM902068", "GSM902069", "GSM902070", "GSM902071", "GSM902072", "GSM902073", "GSM902074", "GSM902075", "GSM902076", "GSM902077", "GSM902078", "GSM902079", "GSM902080", "GSM902081", "GSM902082", "GSM902083", "GSM902084", "GSM902085", "GSM902086", "GSM902087", "GSM902088", "GSM902089", "GSM902090", "GSM902091", "GSM902092", "GSM902093", "GSM902094", "GSM902095", "GSM902096", "GSM902097", "GSM902098", "GSM902099", "GSM902100", "GSM902101", "GSM902102", "GSM902103", "GSM902104", "GSM902105", "GSM902106", "GSM902107", "GSM902108", "GSM902109", "GSM902110", "GSM902111", "GSM902112", "GSM902113", "GSM902114", "GSM902115", "GSM902116", "GSM902117", "GSM902118", "GSM902119", "GSM902120", "GSM902121", "GSM902122", "GSM902123", "GSM902124", "GSM902125", "GSM902126", "GSM902127", "GSM902128", "GSM902129", "GSM902130", "GSM902131", "GSM902132", "GSM902133", "GSM902134", "GSM902135", "GSM902136", "GSM902137", "GSM902138", "GSM902139", "GSM902140", "GSM902141", "GSM902142", "GSM902143", "GSM902144", "GSM902145", "GSM902146", "GSM902147", "GSM902148", "GSM902149", "GSM902150", "GSM902151", "GSM902152", "GSM902153", "GSM902154", "GSM902155", "GSM902156", "GSM902157", "GSM902158", "GSM902159", "GSM902160", "GSM902161", "GSM902162", "GSM902163", "GSM902164", "GSM902165", "GSM902166", "GSM902167", "GSM902168", "GSM902169"], "sample_count": 857, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A genomic storm in critically injured humans", "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:GSE37069", "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=GSE37069", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37069", "version": null, "note": "This study thus included all available microarray-based blood samples of trauma-related GEO data series GSE36809 [29]. After careful examination of the associated metadata, we could identify 185 individuals in total with severe blunt trauma besides the 35 healthy controls in the data series.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "This study thus included all available microarray-based blood samples of trauma-related GEO data series GSE36809 [29]. After careful examination of the associated metadata, we could identify 185 individuals in total with severe blunt trauma besides the 35 healthy controls in the data series.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM909644", "GSM909645", "GSM909646", "GSM909647", "GSM909648", "GSM909649", "GSM909650", "GSM909651", "GSM909652", "GSM909653", "GSM909654", "GSM909655", "GSM909656", "GSM909657", "GSM909658", "GSM909659", "GSM909660", "GSM909661", "GSM909662", "GSM909663", "GSM909664", "GSM909665", "GSM909666", "GSM909667", "GSM909668", "GSM909669", "GSM909670", "GSM909671", "GSM909672", "GSM909673", "GSM909674", "GSM909675", "GSM909676", "GSM909677", "GSM909678", "GSM909679", "GSM909680", "GSM909681", "GSM909682", "GSM909683", "GSM909684", "GSM909685", "GSM909686", "GSM909687", "GSM909688", "GSM909689", "GSM909690", "GSM909691", "GSM909692", "GSM909693", "GSM909694", "GSM909695", "GSM909696", "GSM909697", "GSM909698", "GSM909699", "GSM909700", "GSM909701", "GSM909702", "GSM909703", "GSM909704", "GSM909705", "GSM909706", "GSM909707", "GSM909708", "GSM909709", "GSM909710", "GSM909711", "GSM909712", "GSM909713", "GSM909714", "GSM909715", "GSM909716", "GSM909717", "GSM909718", "GSM909719", "GSM909720", "GSM909721", "GSM909722", "GSM909723", "GSM909724", "GSM909725", "GSM909726", "GSM909727", "GSM909728", "GSM909729", "GSM909730", "GSM909731", "GSM909732", "GSM909733", "GSM909734", "GSM909735", "GSM909736", "GSM909737", "GSM909738", "GSM909739", "GSM909740", "GSM909741", "GSM909742", "GSM909743", "GSM909744", "GSM909745", "GSM909746", "GSM909747", "GSM909748", "GSM909749", "GSM909750", "GSM909751", "GSM909752", "GSM909753", "GSM909754", "GSM909755", "GSM909756", "GSM909757", "GSM909758", "GSM909759", "GSM909760", "GSM909761", "GSM909762", "GSM909763", "GSM909764", "GSM909765", "GSM909766", "GSM909767", "GSM909768", "GSM909769", "GSM909770", "GSM909771", "GSM909772", "GSM909773", "GSM909774", "GSM909775", "GSM909776", "GSM909777", "GSM909778", "GSM909779", "GSM909780", "GSM909781", "GSM909782", "GSM909783", "GSM909784", "GSM909785", "GSM909786", "GSM909787", "GSM909788", "GSM909789", "GSM909790", "GSM909791", "GSM909792", "GSM909793", "GSM909794", "GSM909795", "GSM909796", "GSM909797", "GSM909798", "GSM909799", "GSM909800", "GSM909801", "GSM909802", "GSM909803", "GSM909804", "GSM909805", "GSM909806", "GSM909807", "GSM909808", "GSM909809", "GSM909810", "GSM909811", "GSM909812", "GSM909813", "GSM909814", "GSM909815", "GSM909816", "GSM909817", "GSM909818", "GSM909819", "GSM909820", "GSM909821", "GSM909822", "GSM909823", "GSM909824", "GSM909825", "GSM909826", "GSM909827", "GSM909828", "GSM909829", "GSM909830", "GSM909831", "GSM909832", "GSM909833", "GSM909834", "GSM909835", "GSM909836", "GSM909837", "GSM909838", "GSM909839", "GSM909840", "GSM909841", "GSM909842", "GSM909843", "GSM909844", "GSM909845", "GSM909846", "GSM909847", "GSM909848", "GSM909849", "GSM909850", "GSM909851", "GSM909852", "GSM909853", "GSM909854", 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