Deregulated Gene Expression Profiles and Regulatory Networks in Adult and Pediatric RUNX1/RUNX1T1-Positive AML Patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36980682", "kind": "science-record", "revision": 3, "content_hash": "sha256:d9957c81256c554c8a565e955e787211fdc0cd491733a8d33c7a12bf26ce895d", "created_at": "2026-11-01T19:01:38Z", "updated_at": "2026-11-01T22:09:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Deregulated Gene Expression Profiles and Regulatory Networks in Adult and Pediatric RUNX1/RUNX1T1-Positive AML Patients.", "doi": "10.3390/cancers15061795", "pmid": "36980682", "authors": ["Peggy Kanellou", "Ilias Georgakopoulos-Soares", "Apostolos Zaravinos"], "journal": "Cancers", "year": 2023, "abstract": "Acute myeloid leukemia (AML) is a heterogeneous and complex disease concerning molecular aberrations and prognosis. RUNX1/RUNX1T1 is a fusion oncogene that results from the chromosomal translocation t(8;21) and plays a crucial role in AML. However, its impact on the transcriptomic profile of different age groups of AML patients is not completely understood. Here, we investigated the deregulated gene expression (DEG) profiles in adult and pediatric RUNX1/RUNX1T1-positive AML patients, and compared their functions and regulatory networks. We retrospectively analyzed gene expression data from two independent Gene Expression Omnibus (GEO) datasets (GSE37642 and GSE75461) and computed their differentially expressed genes and upstream regulators, using limma, GEO2Enrichr, and X2K. For validation purposes, we used the TCGA-LAML (adult) and TARGET-AML (pediatric) patient cohorts. We also analyzed the protein-protein interaction (PPI) networks, as well as those composed of transcription factors (TF), intermediate proteins, and kinases foreseen to regulate the top deregulated genes in each group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were further performed for the DEGs in each dataset. We found that the top upregulated genes in (both adult and pediatric) RUNX1/RUNX1T1-positive AML patients are enriched in extracellular matrix organization, the cell projection membrane, filopodium membrane, and supramolecular fiber. Our data corroborate that RUNX1/RUNX1T1 reprograms a large transcriptional network to establish and maintain leukemia via intricate PPI interactions and kinase-driven phosphorylation events.", "claims": [{"id": "claim-method", "statement": "We assessed statistical differences in gene expression between RUNX1/RUNX1T1-positive and RUNX1/RUNX1T1-negative AML samples through the Mann–Whitney U test, with an adj. p < 0.05 as a threshold for statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36980682", "locator": "sections[5] \"2.3. Statistical Analysis\" paragraph 2", "quote": "We assessed statistical differences in gene expression between RUNX1/RUNX1T1-positive and RUNX1/RUNX1T1-negative AML samples through the Mann–Whitney U test, with an adj. p < 0.05 as a threshold for statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article [and its Supplementary Information Files].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36980682", "locator": "sections[15] \"Data Availability Statement\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article [and its Supplementary Information Files]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:36980682"], "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:GSE37642"], "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:GSE37642"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36980682", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cancers15061795", "sha256": "sha256:a80a784d5ef9d1a714682ee473987e456d00e8ec7a1a3caacc347abd05c36c0b", "bytes": 65058, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cancers15061795", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10046396", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE37642", "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=GSE37642", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37642", "version": null, "note": "All data generated or analyzed during this study are included in this published article [and its Supplementary Information Files].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article [and its Supplementary Information Files].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM923596", "GSM923597", "GSM923598", "GSM923599", "GSM923600", "GSM923601", "GSM923602", "GSM923603", "GSM923604", "GSM923605", "GSM923606", "GSM923607", "GSM923608", "GSM923609", "GSM923610", "GSM923611", "GSM923612", "GSM923613", "GSM923614", "GSM923615", "GSM923616", "GSM923617", "GSM923618", "GSM923619", "GSM923620", "GSM923621", "GSM923622", "GSM923623", "GSM923624", "GSM923625", "GSM923626", "GSM923627", "GSM923628", "GSM923629", "GSM923630", "GSM923631", "GSM923632", "GSM923633", "GSM923634", "GSM923635", "GSM923636", "GSM923637", "GSM923638", "GSM923639", "GSM923640", "GSM923641", "GSM923642", "GSM923643", "GSM923644", "GSM923645", "GSM923646", "GSM923647", "GSM923648", "GSM923649", "GSM923650", "GSM923651", "GSM923652", "GSM923653", "GSM923654", "GSM923655", "GSM923656", "GSM923657", "GSM923658", "GSM923659", "GSM923660", "GSM923661", "GSM923662", "GSM923663", "GSM923664", "GSM923665", "GSM923666", "GSM923667", "GSM923668", "GSM923669", "GSM923670", "GSM923671", "GSM923672", "GSM923673", "GSM923674", "GSM923675", "GSM923676", "GSM923677", "GSM923678", "GSM923679", "GSM923680", "GSM923681", "GSM923682", "GSM923683", "GSM923684", "GSM923685", "GSM923686", "GSM923687", "GSM923688", "GSM923689", "GSM923690", "GSM923691", "GSM923692", "GSM923693", "GSM923694", "GSM923695", "GSM923696", "GSM923697", "GSM923698", "GSM923699", "GSM923700", "GSM923701", "GSM923702", "GSM923703", "GSM923704", "GSM923705", "GSM923706", "GSM923707", "GSM923708", "GSM923709", "GSM923710", "GSM923711", "GSM923712", "GSM923713", "GSM923714", "GSM923715", "GSM923716", "GSM923717", "GSM923718", "GSM923719", "GSM923720", "GSM923721", "GSM923722", "GSM923723", "GSM923724", "GSM923725", "GSM923726", "GSM923727", "GSM923728", "GSM923729", "GSM923730", "GSM923731", "GSM923732", "GSM923733", "GSM923734", "GSM923735", "GSM923736", "GSM923737", "GSM923738", "GSM923739", "GSM923740", "GSM923741", "GSM923742", "GSM923743", "GSM923744", "GSM923745", "GSM923746", "GSM923747", "GSM923748", "GSM923749", "GSM923750", "GSM923751", "GSM923752", "GSM923753", "GSM923754", "GSM923755", "GSM923756", "GSM923757", "GSM923758", "GSM923759", "GSM923760", "GSM923761", "GSM923762", "GSM923763", "GSM923764", "GSM923765", "GSM923766", "GSM923767", "GSM923768", "GSM923769", "GSM923770", "GSM923771", "GSM923772", "GSM923773", "GSM923774", "GSM923775", "GSM923776", "GSM923777", "GSM923778", "GSM923779", "GSM923780", "GSM923781", "GSM923782", "GSM923783", "GSM923784", "GSM923785", "GSM923786", "GSM923787", "GSM923788", "GSM923789", "GSM923790", "GSM923791", "GSM923792", "GSM923793", "GSM923794", "GSM923795", "GSM923796", "GSM923797", "GSM923798", "GSM923799", "GSM923800", "GSM923801", "GSM923802", "GSM923803", "GSM923804", "GSM923805", "GSM923806", "GSM923807", "GSM923808", "GSM923809", "GSM923810", "GSM923811", "GSM923812", "GSM923813", "GSM923814", "GSM923815", "GSM923816", "GSM923817", "GSM923818", "GSM923819", "GSM923820", "GSM923821", "GSM923822", "GSM923823", "GSM923824", "GSM923825", "GSM923826", "GSM923827", "GSM923828", "GSM923829", "GSM923830", "GSM923831", "GSM923832", "GSM923833", "GSM923834", "GSM923835", "GSM923836", "GSM923837", "GSM923838", "GSM923839", "GSM923840", "GSM923841", "GSM923842", "GSM923843", "GSM923844", "GSM923845", "GSM923846", "GSM923847", "GSM923848", "GSM923849", "GSM923850", "GSM923851", "GSM923852", "GSM923853", "GSM923854", "GSM923855", "GSM923856", "GSM923857", "GSM923858", "GSM923859", "GSM923860", "GSM923861", "GSM923862", "GSM923863", "GSM923864", "GSM923865", "GSM923866", "GSM923867", "GSM923868", "GSM923869", "GSM923870", "GSM923871", "GSM923872", "GSM923873", "GSM923874", "GSM923875", "GSM923876", "GSM923877", "GSM923878", "GSM923879", "GSM923880", "GSM923881", "GSM923882", "GSM923883", "GSM923884", "GSM923885", "GSM923886", "GSM923887", "GSM923888", "GSM923889", "GSM923890", "GSM923891", "GSM923892", "GSM923893", "GSM923894", "GSM923895", "GSM923896", "GSM923897", "GSM923898", "GSM923899", "GSM923900", "GSM923901", "GSM923902", "GSM923903", "GSM923904", "GSM923905", "GSM923906", "GSM923907", "GSM923908", "GSM923909", "GSM923910", "GSM923911", "GSM923912", "GSM923913", "GSM923914", "GSM923915", "GSM923916", "GSM923917", "GSM923918", "GSM923919", "GSM923920", "GSM923921", "GSM923922", "GSM923923", "GSM923924", "GSM923925", "GSM923926", "GSM923927", "GSM923928", "GSM923929", "GSM923930", "GSM923931", "GSM923932", "GSM923933", "GSM923934", "GSM923935", "GSM923936", "GSM923937", "GSM923938", "GSM923939", "GSM923940", "GSM923941", "GSM923942", "GSM923943", "GSM923944", "GSM923945", "GSM923946", "GSM923947", "GSM923948", "GSM923949", "GSM923950", "GSM923951", "GSM923952", "GSM923953", "GSM923954", "GSM923955", "GSM923956", "GSM923957", "GSM923958", "GSM923959", "GSM923960", "GSM923961", "GSM923962", "GSM923963", "GSM923964", "GSM923965", "GSM923966", "GSM923967", "GSM923968", "GSM923969", "GSM923970", "GSM923971", "GSM923972", "GSM923973", "GSM923974", "GSM923975", "GSM923976", "GSM923977", "GSM923978", "GSM923979", "GSM923980", "GSM923981", "GSM923982", "GSM923983", "GSM923984", "GSM923985", "GSM923986", "GSM923987", "GSM923988", "GSM923989", "GSM923990", "GSM923991", "GSM923992", "GSM923993", "GSM923994", "GSM923995", "GSM923996", "GSM923997", "GSM923998", "GSM923999", "GSM924000", "GSM924001", "GSM924002", "GSM924003", "GSM924004", "GSM924005", "GSM924006", "GSM924007", "GSM924008", "GSM924009", "GSM924010", "GSM924011", "GSM924012", "GSM924013", "GSM924014", "GSM924015", "GSM924016", "GSM924017", "GSM924018", "GSM924019", "GSM924020", "GSM924021", "GSM924022", "GSM924023", "GSM924024", "GSM924025", "GSM924026", "GSM924027", "GSM924028", "GSM924029", "GSM924030", "GSM924031", "GSM924032", "GSM924033", "GSM924034", "GSM924035", "GSM924036", "GSM924037", "GSM924038", "GSM924039", "GSM924040", "GSM924041", "GSM924042", "GSM924043", "GSM924044", "GSM924045", "GSM924046", "GSM924047", "GSM924048", "GSM924049", "GSM924050", "GSM924051", "GSM924052", "GSM924053", "GSM924054", "GSM924055", "GSM924056", "GSM924057", "GSM924058", "GSM924059", "GSM924060", "GSM924061", "GSM924062", "GSM924063", "GSM924064", "GSM924065", "GSM924066", "GSM924067", "GSM924068", "GSM924069", "GSM924070", "GSM924071", "GSM924072", "GSM924073", "GSM924074", "GSM924075", "GSM924076", "GSM924077", "GSM924078", "GSM924079", "GSM924080", "GSM924081", "GSM924082", "GSM924083", "GSM924084", "GSM924085", "GSM924086", "GSM924087", "GSM924088", "GSM924089", "GSM924090", "GSM924091", "GSM924092", "GSM924093", "GSM924094", "GSM924095", "GSM924096", "GSM924097", "GSM924098", "GSM924099", "GSM924100", "GSM924101", "GSM924102", "GSM924103", "GSM924104", "GSM924105", "GSM924106", "GSM924107", "GSM924108", "GSM924109", "GSM924110", "GSM924111", "GSM924112", "GSM924113", "GSM924114", "GSM924115", "GSM924116", "GSM924117", "GSM924118", "GSM924119", "GSM924120", "GSM924121", "GSM924122", "GSM924123", "GSM924124", "GSM924125", "GSM924126", "GSM924127", "GSM924128", "GSM924129", "GSM924130", "GSM924131", "GSM924132", "GSM924133", "GSM924134", "GSM924135", "GSM924136", "GSM924137", "GSM924138", "GSM924139", "GSM924140", "GSM924141", "GSM924142", "GSM924143", "GSM924144", "GSM924145", "GSM924146", "GSM924147", "GSM924148", "GSM924149", "GSM924150", "GSM924151", "GSM924152", "GSM924153", "GSM924154", "GSM924155", "GSM924156", "GSM924157", "GSM924158", "GSM924159", "GSM924160", "GSM924161", "GSM924162", "GSM924163", "GSM924164", "GSM924165", "GSM924166", "GSM924167", "GSM924168", "GSM924169", "GSM924170", "GSM924171", "GSM924172", "GSM924173", "GSM924174", "GSM924175", "GSM924176", "GSM924177", "GSM924178", "GSM924179", "GSM924180", "GSM924181", "GSM924182", "GSM924183", "GSM924184", "GSM924185", "GSM924186", "GSM924187", "GSM924188", "GSM924189", "GSM924190", "GSM924191", "GSM924192", "GSM924193", "GSM924194", "GSM924195", "GSM924196", "GSM924197", "GSM924198", "GSM924199", "GSM924200", "GSM924201", "GSM924202", "GSM924203", "GSM924204", "GSM924205", "GSM924206", "GSM924207", "GSM924208", "GSM924209", "GSM924210", "GSM924211", "GSM924212", "GSM924213", "GSM924214", "GSM924215", "GSM924216", "GSM924217", "GSM924218", "GSM924219", "GSM924220", "GSM924221", "GSM924222", "GSM924223", "GSM924224", "GSM924225", "GSM924226", "GSM924227", "GSM924228", "GSM924229", "GSM924230", "GSM924231", "GSM924232", "GSM924233", "GSM924234", "GSM924235", "GSM924236", "GSM924237", "GSM924238", "GSM924239", "GSM924240", "GSM924241", "GSM924242", "GSM924243", "GSM924244", "GSM924245", "GSM924246", "GSM924247", "GSM924248", "GSM924249", "GSM924250", "GSM924251", "GSM924252", "GSM924253", "GSM924254", "GSM924255", "GSM924256", "GSM924257", "GSM924258", "GSM924259", "GSM924260", "GSM924261", "GSM924262", "GSM924263", "GSM924264", "GSM924265", "GSM924266", "GSM924267", "GSM924268", "GSM924269", "GSM924270", "GSM924271", "GSM924272", "GSM924273", "GSM924274", "GSM924275", "GSM924276", "GSM924277", "GSM924278", "GSM924279", "GSM924280", "GSM924281", "GSM924282", "GSM924283", "GSM924284", "GSM924285", "GSM924286", "GSM924287", "GSM924288", "GSM924289", "GSM924290", "GSM924291", "GSM924292", "GSM924293", "GSM924294", "GSM924295", "GSM924296", "GSM924297", "GSM924298", "GSM924299", "GSM924300", "GSM924301", "GSM924302", "GSM924303", "GSM924304", "GSM924305", "GSM924306", "GSM924307", "GSM924308", "GSM924309", "GSM924310", "GSM924311", "GSM924312", "GSM924313", "GSM924314", "GSM924315", "GSM924316", "GSM924317", "GSM924318", "GSM924319", "GSM924320", "GSM924321", "GSM924322", "GSM924323", "GSM924324", "GSM924325", "GSM924326", "GSM924327", "GSM924328", "GSM924329", "GSM924330", "GSM924331", "GSM924332", "GSM924333", "GSM924334", "GSM924335", "GSM924336", "GSM924337", "GSM924338", "GSM924339", "GSM924340", "GSM924341", "GSM924342", "GSM924343", "GSM924344", "GSM924345", "GSM924346", "GSM924347", "GSM924348", "GSM924349", "GSM924350", "GSM924351", "GSM924352", "GSM924353", "GSM924354", "GSM924355", "GSM924356", "GSM924357", "GSM924358", "GSM924359", "GSM924360", "GSM924361", "GSM924362", "GSM924363", "GSM924364", "GSM924365", "GSM924366", "GSM924367", "GSM924368", "GSM924369", "GSM924370", "GSM924371", "GSM924372", "GSM924373", "GSM924374", "GSM924375", "GSM924376", "GSM924377", "GSM924378", "GSM924379", "GSM924380", "GSM924381", "GSM924382", "GSM924383", "GSM924384", "GSM924385", "GSM924386", "GSM924387", "GSM924388", "GSM924389", "GSM924390", "GSM924391", "GSM924392", "GSM924393", "GSM924394", "GSM924395", "GSM924396", "GSM924397", "GSM924398", "GSM924399", "GSM924400", "GSM924401", "GSM924402", "GSM924403", "GSM924404", "GSM924405", "GSM924406", "GSM924407", "GSM924408", "GSM924409", "GSM924410", "GSM924411", "GSM924412", "GSM924413", "GSM924414", "GSM924415", "GSM924416", "GSM924417", "GSM924418", "GSM924419", "GSM924420", "GSM924421", "GSM924422", "GSM924423", "GSM924424", "GSM924425", "GSM924426", "GSM924427", "GSM924428", "GSM924429", "GSM924430", "GSM924431", "GSM924432", "GSM924433", "GSM924434", "GSM924435", "GSM924436", "GSM924437", "GSM924438", "GSM924439", "GSM924440", "GSM924441", "GSM924442", "GSM924443", "GSM924444", "GSM924445", "GSM924446", "GSM924447", "GSM924448", "GSM924449", "GSM924450", "GSM924451", "GSM924452", "GSM924453", "GSM924454", "GSM924455", "GSM924456", "GSM924457", "GSM924458", "GSM924459", "GSM924460", "GSM924461", "GSM924462", "GSM924463", "GSM924464", "GSM924465", "GSM924466", "GSM924467", "GSM924468", "GSM924469", "GSM924470", "GSM924471", "GSM924472", "GSM924473", "GSM924474", "GSM924475", "GSM924476", "GSM924477", "GSM924478", "GSM924479", "GSM924480", "GSM924481", "GSM924482", "GSM924483", "GSM924484", "GSM924485", "GSM924486", "GSM924487", "GSM924488", "GSM924489", "GSM924490", "GSM924491", "GSM924492", "GSM924493", "GSM924494", "GSM924495", "GSM924496", "GSM924497", "GSM924498", "GSM924499", "GSM924500", "GSM924501", "GSM924502", "GSM924503", "GSM924504", "GSM924505", "GSM924506", "GSM924507", "GSM924508", "GSM924509", "GSM924510", "GSM924511", "GSM924512", "GSM924513", "GSM924514", "GSM924515", "GSM924516", "GSM924517", "GSM924518", "GSM924519", "GSM924520", "GSM924521", "GSM924522", "GSM924523", "GSM924524", "GSM924525", "GSM924526", "GSM924527", "GSM924528", "GSM924529", "GSM924530", "GSM924531", "GSM924532", "GSM924533", "GSM924534", "GSM924535", "GSM924536", "GSM924537", "GSM924538", "GSM924539", "GSM924540", "GSM924541", "GSM924542", "GSM924543", "GSM924544", "GSM924545", "GSM924546", "GSM924547", "GSM924548", "GSM924549", "GSM924550", "GSM924551", "GSM924552", "GSM924553", "GSM924554", "GSM924555", "GSM924556", "GSM924557", "GSM924558", "GSM924559", "GSM924560", "GSM924561", "GSM924562", "GSM924563", "GSM924564", "GSM924565", "GSM924566", "GSM924567", "GSM924568", "GSM924569", "GSM924570", "GSM924571", "GSM924572", "GSM924573", "GSM924574", "GSM924575", "GSM924576", "GSM924577", "GSM924578", "GSM924579"], "sample_count": 984, "group_sizes": null, "group_sizes_basis": null, "platform": "570;96;97", "taxon": "Homo sapiens", "title": "Prognostic gene signature for AML", "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:GSE75461", "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=GSE75461", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75461", "version": null, "note": "All data generated or analyzed during this study are included in this published article [and its Supplementary Information Files].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article [and its Supplementary Information Files].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1912865", "GSM1912866", "GSM1912867", "GSM1912868", "GSM1912869", "GSM1912870", "GSM1912871", "GSM1912872", "GSM1912873", "GSM1912874", "GSM1912875", "GSM1912876", "GSM1912877", "GSM1912878", "GSM1955456", "GSM1955457", "GSM1955458", "GSM1955459", "GSM1955460", "GSM1955461", "GSM1955462", "GSM1955463", "GSM1955464", "GSM1955465", "GSM1955466", "GSM1955467", "GSM1955468", "GSM1955469", "GSM1955470", "GSM1955471", "GSM1955472", "GSM1955473", "GSM1955474", "GSM1955475", "GSM1955476", "GSM1955477", "GSM1955478", "GSM1955479", "GSM1955480", "GSM1955481", "GSM1955482", "GSM1955483", "GSM1955484", "GSM1955485", "GSM1955486", "GSM1955487", "GSM1955488", "GSM1955489", "GSM1955490", "GSM1955491", "GSM1955492", "GSM1955493", "GSM1955494", "GSM1955495", "GSM1955496", "GSM1955497", "GSM1955498", "GSM1955499", "GSM1955500", "GSM1955501", "GSM1955502", "GSM1955503", "GSM1955504", "GSM1955505", "GSM1955506", "GSM1955507", "GSM1955508", "GSM1955509", "GSM1955510", "GSM1955511", "GSM1955512", "GSM1955513", "GSM1955514", "GSM1955515", "GSM1955516", "GSM1955517", "GSM1955518", "GSM1955519", "GSM1955520", "GSM1955521", "GSM1955522", "GSM1955523", "GSM1955524", "GSM1955525", "GSM1955526"], "sample_count": 85, "group_sizes": null, "group_sizes_basis": null, "platform": "17586", "taxon": "Homo sapiens", "title": "Pediatric AML classification according to C/EBPδ expression", "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:GSE37642 not downloaded", "asset:data:geo:GSE37642 licence not read", "asset:data:geo:GSE75461 not downloaded", "asset:data:geo:GSE75461 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.7, "band": "medium", "quote": "limma"}}, {"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": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-4", "family": null, "specific": null, "label": "Mann–Whitney U test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We assessed statistical differences in gene expression between RUNX1/RUNX1T1-positive and RUNX1/RUNX1T1-negative AML samples through the Mann–Whitney U test, with an adj. p < 0.05 as a threshold for statistical significance."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE37642", "GSE75461"], "resolved_accessions": ["GSE37642", "GSE75461"], "statements": ["All data generated or analyzed during this study are included in this published article [and its Supplementary Information Files]."], "basis": "The paper names GSE37642, GSE75461 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36980682", "data:geo:GSE37642"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE37642"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:35:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 20967, "completion_tokens": 2099, "cached_tokens": 256}}, "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:36980682", "type": "paper", "label": "pmid:36980682"}, {"id": "source:pmid:36980682", "type": "manuscript", "label": "PMID 36980682 full text"}, {"id": "data:geo:GSE37642", "type": "dataset", "label": "GEO GSE37642"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36980682", "type": "paper", "label": "pmid:36980682"}, {"id": "source:pmid:36980682", "type": "manuscript", "label": "PMID 36980682 full text"}, {"id": "data:geo:GSE37642", "type": "dataset", "label": "GEO GSE37642"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36980682", "type": "extraction", "used": ["source:pmid:36980682"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE37642", "type": "accession_resolution", "used": ["data:geo:GSE37642"], "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:36980682", "parent_hash": "sha256:4c23408a0197a960fef26571678a0f59cf9e8840fe47d11c81d6653fe28d3dcb", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE37642 licence not read", "asset:data:geo:GSE37642 not downloaded", "asset:data:geo:GSE75461 licence not read", "asset:data:geo:GSE75461 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["limma"], "order_basis": "analysis_only", "id": "assay:1"}]}