Using bioinformatics analysis to screen abnormal methylated differentially expressed hub genes of Kawasaki disease and construct diagnostic model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36458298", "kind": "science-record", "revision": 3, "content_hash": "sha256:f9a455c7dd65ed27639f7441301585a7d4a2ba43e47d3cbeda507dcb0f754bc4", "created_at": "2026-11-01T19:00:56Z", "updated_at": "2026-11-01T22:08:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Using bioinformatics analysis to screen abnormal methylated differentially expressed hub genes of Kawasaki disease and construct diagnostic model.", "doi": "10.1016/j.heliyon.2022.e11905", "pmid": "36458298", "authors": ["Hongxiao Sun", "Changying Liu", "Xu Zhang", "Panpan Liu", "Zhanhui Du", "Gang Luo", "Silin Pan"], "journal": "Heliyon", "year": 2022, "abstract": "Objective: By using bioinformatics analysis, abnormal methylated differentially expressed genes (MDEGs) in Kawasaki disease (KD) were identified and a random forest diagnostic model for KD was established.\nMethods: The expression (GSE18606, GSE68004, GSE73461) and methylation (GSE109430) profiles was retrieved and download from Gene Expression Omnibus (GEO). We conducted enrichment analyses by using R software. In addition, we constructed a protein interaction network, and obtained 6 hub genes. We used expression profiles GSE100154 from GEO to verify the hub genes. Finally, we constructed a diagnostic model based on random forest.\nResults: We got a total of 55 MDEGs (43 hyper-methylated, low-expressing genes and 12 hypo-methylated, high-expressed genes). Six hub genes (CD2, IL2RB, IL7R, CD177, IL1RN, and MYL9) were identified by Cytoscape software. The area under curve (AUC) of the six hub genes was from 0.745 to 0.898, and the combined AUC was 0.967. The random forest diagnostic model showed that AUC was 0.901.\nConclusion: The identification of 6 new hub genes improves our understanding of the molecular mechanism of KD, and the established model can be employed for accurate diagnosis and provide evidence for clinical diagnosis.", "claims": [{"id": "claim-method", "statement": "With 332 samples in all four gene expression datasets, we established a random forest model based on 6 hub genes by randomForset package [19].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36458298", "locator": "sections[8] \"Establishment of diagnostic model\" paragraph 2", "quote": "With 332 samples in all four gene expression datasets, we established a random forest model based on 6 hub genes by randomForset package [19]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data associated with this study has been deposited at GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36458298", "locator": "sections[22] \"Data availability statement\" paragraph 2", "quote": "Data associated with this study has been deposited at GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The random forest diagnostic model showed that AUC was 0.901.", "kind": "quantitative", "target": {"value": 0.901, "unit": "auc", "tolerance": null, "source": "The random forest diagnostic model showed that AUC was 0.901."}, "evidence": [{"asset": "source:pmid:36458298", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The random forest diagnostic model showed that AUC was 0.901."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The random forest diagnostic model showed that AUC was 0.901.", "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:36458298"], "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:GSE100154"], "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:GSE100154"], "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:36458298", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2022.e11905", "sha256": "sha256:3e54082fc146be5fa82b56592d9cb17fccc4af5d7f0bc46827368a927b9349d6", "bytes": 31965, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2022.e11905", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9706175", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100154", "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=GSE100154", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100154", "version": null, "note": "Data associated with this study has been deposited at GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data associated with this study has been deposited at GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2672284", "GSM2672285", "GSM2672286", "GSM2672287", "GSM2672288", "GSM2672289", "GSM2672290", "GSM2672291", "GSM2672292", "GSM2672293", "GSM2672294", "GSM2672295", "GSM2672296", "GSM2672297", "GSM2672298", "GSM2672299", "GSM2672300", "GSM2672301", "GSM2672302", "GSM2672303", "GSM2672304", "GSM2672305", "GSM2672306", "GSM2672307", "GSM2672308", "GSM2672309", "GSM2672310", "GSM2672311", "GSM2672312", "GSM2672313", "GSM2672314", "GSM2672315", "GSM2672316", "GSM2672317", "GSM2672318", "GSM2672319", "GSM2672320", "GSM2672321", "GSM2672322", "GSM2672323", "GSM2672324", "GSM2672325", "GSM2672326", "GSM2672327"], "sample_count": 44, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Kawasaki Datasets)", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE109430", "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=GSE109430", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE109430", "version": null, "note": "Data associated with this study has been deposited at GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data associated with this study has been deposited at GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2942822", "GSM2942823", "GSM2942824", "GSM2942825", "GSM2942826", "GSM2942827", "GSM2942828", "GSM2942829", "GSM2942830", "GSM2942831", "GSM2942832", "GSM2942833", "GSM2942834", "GSM2942835", "GSM2942836", "GSM2942837", "GSM2942838", "GSM2942839", "GSM2942840", "GSM2942841", "GSM2942842", "GSM2942843", "GSM2942844", "GSM2942845", "GSM2942846", "GSM2942847", "GSM2942848", "GSM2942849", "GSM2942850", "GSM2942851", "GSM2942852", "GSM2942853", "GSM2942854", "GSM2942855", "GSM2942856", "GSM2942857"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "13534", "taxon": "Homo sapiens", "title": "DNA methylation Profiling in Kawasaki disease (KD): DNA methylation profile in healthy control subjects, acute-phase KD subjects and convalescent-phase KD subjects", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE18606", "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=GSE18606", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18606", "version": null, "note": "Data associated with this study has been deposited at GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data associated with this study has been deposited at GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM462548", "GSM462549", "GSM462550", "GSM462551", "GSM462552", "GSM462553", "GSM462554", "GSM462555", "GSM462556", "GSM462557", "GSM462558", "GSM462559", "GSM462560", "GSM462561", "GSM462562", "GSM462563", "GSM462564", "GSM462565", "GSM462566", "GSM462567", "GSM462568", "GSM462569", "GSM462570", "GSM462571", "GSM462572", "GSM462573", "GSM462574", "GSM462575", "GSM462576", "GSM462577", "GSM462578", "GSM462579", "GSM462580", "GSM462581", "GSM462582", "GSM462583", "GSM462584", "GSM462585", "GSM462586", "GSM462587", "GSM462588", "GSM462589", "GSM462590", "GSM462591", "GSM462592", "GSM462593", "GSM462594", "GSM462595"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Transcript abundance patterns in Kawasaki disease patients IVIG-resistance", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE68004", "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=GSE68004", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68004", "version": null, "note": "Data associated with this study has been deposited at GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data associated with this study has been deposited at GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1660729", "GSM1660730", "GSM1660731", "GSM1660732", "GSM1660733", "GSM1660734", "GSM1660735", "GSM1660736", "GSM1660737", "GSM1660738", "GSM1660739", "GSM1660740", "GSM1660741", "GSM1660742", "GSM1660743", "GSM1660744", "GSM1660745", "GSM1660746", "GSM1660747", "GSM1660748", "GSM1660749", "GSM1660750", "GSM1660751", "GSM1660752", "GSM1660753", "GSM1660754", "GSM1660755", "GSM1660756", "GSM1660757", "GSM1660758", "GSM1660759", "GSM1660760", "GSM1660761", "GSM1660762", "GSM1660763", "GSM1660764", "GSM1660765", "GSM1660766", "GSM1660767", "GSM1660768", "GSM1660769", "GSM1660770", "GSM1660771", "GSM1660772", "GSM1660773", "GSM1660774", "GSM1660775", "GSM1660776", "GSM1660777", "GSM1660778", "GSM1660779", "GSM1660780", "GSM1660781", "GSM1660782", "GSM1660783", "GSM1660784", "GSM1660785", "GSM1660786", "GSM1660787", "GSM1660788", "GSM1660789", "GSM1660790", "GSM1660791", "GSM1660792", "GSM1660793", "GSM1660794", "GSM1660807", "GSM1660808", "GSM1660809", "GSM1660810", "GSM1660811", "GSM1660812", "GSM1660813", "GSM1660814", "GSM1660815", "GSM1660816", "GSM1660817", "GSM1660818", "GSM1660819", "GSM1660820", "GSM1660821", "GSM1660822", "GSM1660823", "GSM1660824", "GSM1660825", "GSM1660826", "GSM1660827", "GSM1660828", "GSM1660829", "GSM1660830", "GSM1660831", "GSM1660832", "GSM1660833", "GSM1660834", "GSM1660835", "GSM1660836", "GSM1660837", "GSM1660838", "GSM1660839", "GSM1660840", "GSM1660841", "GSM1660842", "GSM1660843", "GSM1660844", "GSM1660845", "GSM1660846", "GSM1660847", "GSM1660848", "GSM1660849", "GSM1660850", "GSM1660851", "GSM1660852", "GSM1660853", "GSM1660854", "GSM1660855", "GSM1660856", "GSM1660857", "GSM1660858", "GSM1660859", "GSM1660860", "GSM1660861", "GSM1660862", "GSM1660863", "GSM1660864", "GSM1660865", "GSM1660866", "GSM1660867", "GSM1660868", "GSM1660869", "GSM1660870", "GSM1660877", "GSM1660878", "GSM1660879", "GSM1660880", "GSM1660881", "GSM1660882", "GSM1660883", "GSM1660884", "GSM1660885", "GSM1660886", "GSM1660887", "GSM1660888", "GSM1660889", "GSM1660890", "GSM1660891", "GSM1660892", "GSM1660893", "GSM1660894", "GSM1660895", "GSM1660896", "GSM1660897", "GSM1660898", "GSM1660899", "GSM1660900", "GSM1660901", "GSM1660902", "GSM1660903", "GSM1660904", "GSM1660905", "GSM1660906", "GSM1660907", "GSM1660908"], "sample_count": 162, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Whole blood Transcriptional Profiles as a Prognostic and Diagnostic Tool in Complete and Incomplete Kawasaki Disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE73461", "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=GSE73461", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73461", "version": null, "note": "Data associated with this study has been deposited at GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data associated with this study has been deposited at GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1894312", "GSM1894313", "GSM1894314", "GSM1894315", "GSM1894316", "GSM1894317", "GSM1894318", "GSM1894319", "GSM1894320", "GSM1894321", "GSM1894322", "GSM1894323", "GSM1894324", "GSM1894325", "GSM1894326", "GSM1894327", "GSM1894328", "GSM1894329", "GSM1894330", "GSM1894331", "GSM1894332", "GSM1894333", "GSM1894334", "GSM1894335", "GSM1894336", "GSM1894337", "GSM1894338", "GSM1894339", "GSM1894340", "GSM1894341", "GSM1894342", "GSM1894343", "GSM1894344", "GSM1894345", "GSM1894346", "GSM1894347", "GSM1894348", "GSM1894349", "GSM1894350", "GSM1894351", "GSM1894352", "GSM1894353", "GSM1894354", "GSM1894355", "GSM1894356", "GSM1894357", "GSM1894358", "GSM1894359", "GSM1894360", "GSM1894361", "GSM1894362", "GSM1894363", "GSM1894364", "GSM1894365", "GSM1894366", "GSM1894367", "GSM1894368", "GSM1894369", "GSM1894370", "GSM1894371", "GSM1894372", "GSM1894373", "GSM1894374", "GSM1894375", "GSM1894376", "GSM1894377", "GSM1894378", "GSM1894379", "GSM1894380", "GSM1894381", "GSM1894382", "GSM1894383", "GSM1894384", "GSM1894385", "GSM1894386", "GSM1894387", "GSM1894388", "GSM1894389", "GSM1894390", "GSM1894391", "GSM1894392", "GSM1894393", "GSM1894394", "GSM1894395", "GSM1894396", "GSM1894397", "GSM1894398", "GSM1894399", "GSM1894400", "GSM1894401", "GSM1894402", "GSM1894403", "GSM1894404", "GSM1894405", "GSM1894406", "GSM1894407", "GSM1894408", "GSM1894409", "GSM1894410", "GSM1894411", "GSM1894412", "GSM1894413", "GSM1894414", "GSM1894415", "GSM1894416", "GSM1894417", "GSM1894418", "GSM1894419", "GSM1894420", "GSM1894421", "GSM1894422", "GSM1894423", "GSM1894424", "GSM1894425", "GSM1894426", "GSM1894427", "GSM1894428", "GSM1894429", "GSM1894430", "GSM1894431", "GSM1894432", "GSM1894433", "GSM1894434", "GSM1894435", "GSM1894436", "GSM1894437", "GSM1894438", "GSM1894439", "GSM1894440", "GSM1894441", "GSM1894442", "GSM1894443", "GSM1894444", "GSM1894445", "GSM1894446", "GSM1894447", "GSM1894448", "GSM1894449", "GSM1894450", "GSM1894451", "GSM1894452", "GSM1894453", "GSM1894454", "GSM1894455", "GSM1894456", "GSM1894457", "GSM1894458", "GSM1894459", "GSM1894460", "GSM1894461", "GSM1894462", "GSM1894463", "GSM1894464", "GSM1894465", "GSM1894466", "GSM1894467", "GSM1894468", "GSM1894469", "GSM1894470", "GSM1894471", "GSM1894472", "GSM1894473", "GSM1894474", "GSM1894475", "GSM1894476", "GSM1894477", "GSM1894478", "GSM1894479", "GSM1894480", "GSM1894481", "GSM1894482", "GSM1894483", "GSM1894484", "GSM1894485", "GSM1894486", "GSM1894487", "GSM1894488", "GSM1894489", "GSM1894490", "GSM1894491", "GSM1894492", "GSM1894493", "GSM1894494", "GSM1894495", "GSM1894496", "GSM1894497", "GSM1894498", "GSM1894499", "GSM1894500", "GSM1894501", "GSM1894502", "GSM1894503", "GSM1894504", "GSM1894505", "GSM1894506", "GSM1894507", "GSM1894508", "GSM1894509", "GSM1894510", "GSM1894511", "GSM1894512", "GSM1894513", "GSM1894514", "GSM1894515", "GSM1894516", "GSM1894517", "GSM1894518", "GSM1894519", "GSM1894520", "GSM1894521", "GSM1894522", "GSM1894523", "GSM1894524", "GSM1894525", "GSM1894526", "GSM1894527", "GSM1894528", "GSM1894529", "GSM1894530", "GSM1894531", "GSM1894532", "GSM1894533", "GSM1894534", "GSM1894535", "GSM1894536", "GSM1894537", "GSM1894538", "GSM1894539", "GSM1894540", "GSM1894541", "GSM1894542", "GSM1894543", "GSM1894544", "GSM1894545", "GSM1894546", "GSM1894547", "GSM1894548", "GSM1894549", "GSM1894550", "GSM1894551", "GSM1894552", "GSM1894553", "GSM1894554", "GSM1894555", "GSM1894556", "GSM1894557", "GSM1894558", "GSM1894559", "GSM1894560", "GSM1894561", "GSM1894562", "GSM1894563", "GSM1894564", "GSM1894565", "GSM1894566", "GSM1894567", "GSM1894568", "GSM1894569", "GSM1894570", "GSM1894571", "GSM1894572", "GSM1894573", "GSM1894574", "GSM1894575", "GSM1894576", "GSM1894577", "GSM1894578", "GSM1894579", "GSM1894580", "GSM1894581", "GSM1894582", "GSM1894583", "GSM1894584", "GSM1894585", "GSM1894586", "GSM1894587", "GSM1894588", "GSM1894589", "GSM1894590", "GSM1894591", "GSM1894592", "GSM1894593", "GSM1894594", "GSM1894595", "GSM1894596", "GSM1894597", "GSM1894598", "GSM1894599", "GSM1894600", "GSM1894601", "GSM1894602", "GSM1894603", "GSM1894604", "GSM1894605", "GSM1894606", "GSM1894607", "GSM1894608", "GSM1894609", "GSM1894610", "GSM1894611", "GSM1894612", "GSM1894613", "GSM1894614", "GSM1894615", "GSM1894616", "GSM1894617", "GSM1894618", "GSM1894619", "GSM1894620", "GSM1894621", "GSM1894622", "GSM1894623", "GSM1894624", "GSM1894625", "GSM1894626", "GSM1894627", "GSM1894628", "GSM1894629", "GSM1894630", "GSM1894631", "GSM1894632", "GSM1894633", "GSM1894634", "GSM1894635", "GSM1894636", "GSM1894637", "GSM1894638", "GSM1894639", "GSM1894640", "GSM1894641", "GSM1894642", "GSM1894643", "GSM1894644", "GSM1894645", "GSM1894646", "GSM1894647", "GSM1894648", "GSM1894649", "GSM1894650", "GSM1894651", "GSM1894652", "GSM1894653", "GSM1894654", "GSM1894655", "GSM1894656", "GSM1894657", "GSM1894658", "GSM1894659", "GSM1894660", "GSM1894661", "GSM1894662", "GSM1894663", "GSM1894664", "GSM1894665", "GSM1894666", "GSM1894667", "GSM1894668", "GSM1894669", "GSM1894670", "GSM1894671", "GSM1894672", "GSM1894673", "GSM1894674", "GSM1894675", "GSM1894676", "GSM1894677", "GSM1894678", "GSM1894679", "GSM1894680", "GSM1894681", "GSM1894682", "GSM1894683", "GSM1894684", "GSM1894685", "GSM1894686", "GSM1894687", "GSM1894688", "GSM1894689", "GSM1894690", "GSM1894691", "GSM1894692", "GSM1894693", "GSM1894694", "GSM1894695", "GSM1894696", "GSM1894697", "GSM1894698", "GSM1894699", "GSM1894700", "GSM1894701", "GSM1894702", "GSM1894703", "GSM1894704", "GSM1894705", "GSM1894706", "GSM1894707", "GSM1894708", "GSM1894709", "GSM1894710", "GSM1894711", "GSM1894712", "GSM1894713", "GSM1894714", "GSM1894715", "GSM1894716", "GSM1894717", "GSM1894718", "GSM1894719", "GSM1894720", "GSM1894721", "GSM1894722", "GSM1894723", "GSM1894724", "GSM1894725", "GSM1894726", "GSM1894727", "GSM1894728", "GSM1894729", "GSM1894730", "GSM1894731", "GSM1894732", "GSM1894733", "GSM1894734", "GSM1894735", "GSM1894736", "GSM1894737", "GSM1894738", "GSM1894739", "GSM1894740", "GSM1894741", "GSM1894742", "GSM1894743", "GSM1894744", "GSM1894745", "GSM1894746", "GSM1894747", "GSM1894748", "GSM1894749", "GSM1894750", "GSM1894751", "GSM1894752", "GSM1894753", "GSM1894754", "GSM1894755", "GSM1894756", "GSM1894757", "GSM1894758", "GSM1894759", "GSM1894760", "GSM1894761", "GSM1894762", "GSM1894763", "GSM1894764", "GSM1894765", "GSM1894766", "GSM1894767", "GSM1894768", "GSM1894769", "GSM1894770"], "sample_count": 459, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Diagnosis of Kawasaki Disease in children using host RNA expression [Discovery_Dataset]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE100154 not downloaded", "asset:data:geo:GSE100154 licence not read", "asset:data:geo:GSE109430 not downloaded", "asset:data:geo:GSE109430 licence not read", "asset:data:geo:GSE18606 not downloaded", "asset:data:geo:GSE18606 licence not read", "asset:data:geo:GSE68004 not downloaded", "asset:data:geo:GSE68004 licence not read", "asset:data:geo:GSE73461 not downloaded", "asset:data:geo:GSE73461 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "With 332 samples in all four gene expression datasets, we established a random forest model based on 6 hub genes by randomForset package [19]."}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "Limma"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 0.901, "unit": "auc", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_differs_from_extractor", "method.machine_learning_random_forest"]}, "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": ["machine_learning_random_forest"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_forest."}, "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": ["GSE18606", "GSE68004", "GSE73461", "GSE109430", "GSE100154"], "resolved_accessions": ["GSE18606", "GSE68004", "GSE73461", "GSE109430", "GSE100154"], "statements": ["Data associated with this study has been deposited at GEO database."], "basis": "The paper names GSE18606, GSE68004, GSE73461, GSE109430, GSE100154 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36458298", "data:geo:GSE100154"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "machine_learning_random_forest", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100154"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:17:50Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10442, "completion_tokens": 2033, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36458298", "type": "paper", "label": "pmid:36458298"}, {"id": "source:pmid:36458298", "type": "manuscript", "label": "PMID 36458298 full text"}, {"id": "data:geo:GSE100154", "type": "dataset", "label": "GEO GSE100154"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36458298", "type": "paper", "label": "pmid:36458298"}, {"id": "source:pmid:36458298", "type": "manuscript", "label": "PMID 36458298 full text"}, {"id": "data:geo:GSE100154", "type": "dataset", "label": "GEO GSE100154"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36458298", "type": "extraction", "used": ["source:pmid:36458298"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100154", "type": "accession_resolution", "used": ["data:geo:GSE100154"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:36458298", "parent_hash": "sha256:07fe8b2fd243072c57bbb1718039820f82d54a9861ee8f780daf4cd0fce5e113", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE100154 licence not read", "asset:data:geo:GSE100154 not downloaded", "asset:data:geo:GSE109430 licence not read", "asset:data:geo:GSE109430 not downloaded", "asset:data:geo:GSE18606 licence not read", "asset:data:geo:GSE18606 not downloaded", "asset:data:geo:GSE68004 licence not read", "asset:data:geo:GSE68004 not downloaded", "asset:data:geo:GSE73461 licence not read", "asset:data:geo:GSE73461 not downloaded", "execution.not_run", "method.machine_learning_random_forest", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:machine_learning_random_forest"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["regulated DEGs in three expression profiling microarray datasets. The methylation profiling microarr", "croarray datasets. The methylation profiling microarray dataset was analyzed to screen differentiall"], "order_basis": "paper_text_order:1712", "id": "assay:1"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["With 332 samples in all four gene expression datasets, we established a random forest model based on 6 hub genes by randomForset package [19]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}