Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32696617", "kind": "science-record", "revision": 7, "content_hash": "sha256:950794f1ea45edd255122c1c561da53860b3ac11199066f8d619cc590aad2dfa", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:01:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme.", "doi": "10.1111/jcmm.15615", "pmid": "32696617", "authors": ["Lan Jiang", "Min Zhong", "Tianbing Chen", "Xiaolong Zhu", "Hui Yang", "Kun Lv"], "journal": "Journal of cellular and molecular medicine", "year": 2020, "abstract": "Glioblastoma multiforme (GBM) is a very serious mortality of central nervous system cancer. The microarray data from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 (389 GBM tumour and 67 normal tissues) and the RNA-seq data from TCGA-GBM dataset (169 GBM and five normal samples) were chosen to find differentially expressed genes (DEGs). RRA (Robust rank aggregation) method was used to integrate seven datasets and calculate 133 DEGs (82 up-regulated and 51 down-regulated genes). Subsequently, through the PPI (protein-protein interaction) network and MCODE/ cytoHubba methods, we finally filtered out ten hub genes, including FOXM1, CDK4, TOP2A, RRM2, MYBL2, MCM2, CDC20, CCNB2, MYC and EZH2, from the whole network. Functional enrichment analyses of DEGs were conducted to show that these hub genes were enriched in various cancer-related functions and pathways significantly. We also selected CCNB2, CDC20 and MYBL2 as core biomarkers, and further validated them in CGGA, HPA and CCLE database, suggesting that these three core hub genes may be involved in the origin of GBM. All these potential biomarkers for GBM might be helpful for illustrating the important role of molecular mechanisms of tumorigenesis in the diagnosis, prognosis and targeted therapy of GBM cancer.", "claims": [{"id": "claim-data-access", "statement": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32696617", "locator": "sections[20] \"DATA AVAILABILITY STATEMENT\" paragraphs 1-3", "quote": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32696617"], "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:GSE13276"], "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": {"fold_change": "22 and edgeR method 23 (fold change > 2 and adjusted P‐valu"}, "inputs": ["data:geo:GSE13276"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32696617", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/jcmm.15615", "sha256": "sha256:0ae5cec3ec613e304f480b51e22a5cd93fcd873c70a5111aba76f49b10d278ad", "bytes": 40245, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/jcmm.15615", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7520335", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13276", "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=GSE13276", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13276", "version": null, "note": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM335185", "GSM335186", "GSM335187", "GSM335188", "GSM335189", "GSM335190", "GSM335191", "GSM335192", "GSM335193", "GSM335194", "GSM335195", "GSM335196", "GSM335197", "GSM335198", "GSM335199"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Candidate genes for the recurrence of glioblastoma multiforme identified by microarray ", "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:GSE2223", "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=GSE2223", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2223", "version": null, "note": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM40660", "GSM40661", "GSM40662", "GSM40663", "GSM40664", "GSM40665", "GSM40666", "GSM40667", "GSM40668", "GSM40669", "GSM40670", "GSM40671", "GSM40672", "GSM40673", "GSM40674", "GSM40675", "GSM40676", "GSM40677", "GSM40678", "GSM40679", "GSM40680", "GSM40681", "GSM40682", "GSM40683", "GSM40684", "GSM40685", "GSM40686", "GSM40687", "GSM40688", "GSM40689", "GSM40690", "GSM40691", "GSM40692", "GSM40693", "GSM40694", "GSM40695", "GSM40696", "GSM40697", "GSM40698", "GSM40699", "GSM40700", "GSM40701", "GSM40702", "GSM40703", "GSM40704", "GSM40705", "GSM40706", "GSM40707", "GSM40708", "GSM40709", "GSM40710", "GSM40711", "GSM40712", "GSM40713"], "sample_count": 54, "group_sizes": null, "group_sizes_basis": null, "platform": "1833", "taxon": "Homo sapiens", "title": "Gene expression profiling in human glial brain tumors", "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:GSE4058", "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=GSE4058", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE4058", "version": null, "note": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM93114", "GSM93115", "GSM93116", "GSM93117", "GSM93118", "GSM93119", "GSM93120", "GSM93121", "GSM93122", "GSM93123", "GSM93124", "GSM93125", "GSM93126", "GSM93127", "GSM93128", "GSM93129", "GSM93130", "GSM93131", "GSM93132", "GSM93133", "GSM93134", "GSM93135", "GSM93136", "GSM93137", "GSM93138", "GSM93139", "GSM93140", "GSM93141", "GSM93142", "GSM93143", "GSM93144", "GSM93145", "GSM93146", "GSM93147", "GSM93148", "GSM93149", "GSM93150", "GSM93151"], "sample_count": 38, "group_sizes": null, "group_sizes_basis": null, "platform": "2935;2778;3010;182;2648", "taxon": "Homo sapiens", "title": "Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme", "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:GSE4290", "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=GSE4290", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE4290", "version": null, "note": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM97793", "GSM97794", "GSM97795", "GSM97796", "GSM97797", "GSM97798", "GSM97799", "GSM97800", "GSM97801", "GSM97802", "GSM97803", "GSM97804", "GSM97805", "GSM97806", "GSM97807", "GSM97808", "GSM97809", "GSM97810", "GSM97811", "GSM97812", "GSM97813", "GSM97814", "GSM97815", "GSM97816", "GSM97817", "GSM97818", "GSM97819", "GSM97820", "GSM97821", "GSM97822", "GSM97823", "GSM97824", "GSM97825", "GSM97826", "GSM97827", "GSM97828", "GSM97829", "GSM97830", "GSM97831", "GSM97832", "GSM97833", "GSM97834", "GSM97835", "GSM97836", "GSM97837", "GSM97838", "GSM97839", "GSM97840", "GSM97841", "GSM97842", "GSM97843", "GSM97844", "GSM97845", "GSM97846", "GSM97847", "GSM97848", "GSM97849", "GSM97850", "GSM97851", "GSM97852", "GSM97853", "GSM97854", "GSM97855", "GSM97856", "GSM97857", "GSM97858", "GSM97859", "GSM97860", "GSM97861", "GSM97862", "GSM97863", "GSM97864", "GSM97865", "GSM97866", "GSM97867", "GSM97868", "GSM97869", "GSM97870", "GSM97871", "GSM97872", "GSM97873", "GSM97874", "GSM97875", "GSM97876", "GSM97877", "GSM97878", "GSM97879", "GSM97880", "GSM97881", "GSM97882", "GSM97883", "GSM97884", "GSM97885", "GSM97886", "GSM97887", "GSM97888", "GSM97889", "GSM97890", "GSM97891", "GSM97892", "GSM97893", "GSM97894", "GSM97895", "GSM97896", "GSM97897", "GSM97898", "GSM97899", "GSM97900", "GSM97901", "GSM97902", "GSM97903", "GSM97904", "GSM97905", "GSM97906", "GSM97907", "GSM97908", "GSM97909", "GSM97910", "GSM97911", "GSM97912", "GSM97913", "GSM97914", "GSM97915", "GSM97916", "GSM97917", "GSM97918", "GSM97919", "GSM97920", "GSM97921", "GSM97922", "GSM97923", "GSM97924", "GSM97925", "GSM97926", "GSM97927", "GSM97928", "GSM97929", "GSM97930", "GSM97931", "GSM97932", "GSM97933", "GSM97934", "GSM97935", "GSM97936", "GSM97937", "GSM97938", "GSM97939", "GSM97940", "GSM97941", "GSM97942", "GSM97943", "GSM97944", "GSM97945", "GSM97946", "GSM97947", "GSM97948", "GSM97949", "GSM97950", "GSM97951", "GSM97952", "GSM97953", "GSM97954", "GSM97955", "GSM97956", "GSM97957", "GSM97958", "GSM97959", "GSM97960", "GSM97961", "GSM97962", "GSM97963", "GSM97964", "GSM97965", "GSM97966", "GSM97967", "GSM97968", "GSM97969", "GSM97970", "GSM97971", "GSM97972"], "sample_count": 180, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data of glioma samples from Henry Ford Hospital", "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:GSE68848", "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=GSE68848", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68848", "version": null, "note": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1683515", "GSM1683516", "GSM1683517", "GSM1683518", "GSM1683519", "GSM1683520", "GSM1683521", "GSM1683522", "GSM1683523", "GSM1683524", "GSM1683525", "GSM1683526", "GSM1683527", "GSM1683528", "GSM1683529", "GSM1683530", "GSM1683531", "GSM1683532", "GSM1683533", "GSM1683534", "GSM1683535", "GSM1683536", "GSM1683537", "GSM1683538", "GSM1683539", "GSM1683540", "GSM1683541", "GSM1683542", "GSM1683543", "GSM1683544", "GSM1683545", "GSM1683546", "GSM1683547", "GSM1683548", "GSM1683549", "GSM1683550", "GSM1683551", "GSM1683552", "GSM1683553", "GSM1683554", "GSM1683555", "GSM1683556", "GSM1683557", "GSM1683558", "GSM1683559", "GSM1683560", "GSM1683561", "GSM1683562", "GSM1683563", "GSM1683564", "GSM1683565", "GSM1683566", "GSM1683567", "GSM1683568", "GSM1683569", "GSM1683570", "GSM1683571", "GSM1683572", "GSM1683573", "GSM1683574", "GSM1683575", "GSM1683576", "GSM1683577", "GSM1683578", "GSM1683579", "GSM1683580", "GSM1683581", "GSM1683582", "GSM1683583", "GSM1683584", "GSM1683585", "GSM1683586", "GSM1683587", "GSM1683588", "GSM1683589", "GSM1683590", "GSM1683591", "GSM1683592", "GSM1683593", "GSM1683594", "GSM1683595", "GSM1683596", "GSM1683597", "GSM1683598", "GSM1683599", "GSM1683600", "GSM1683601", "GSM1683602", "GSM1683603", "GSM1683604", "GSM1683605", "GSM1683606", "GSM1683607", "GSM1683608", "GSM1683609", "GSM1683610", "GSM1683611", "GSM1683612", "GSM1683613", "GSM1683614", "GSM1683615", "GSM1683616", "GSM1683617", "GSM1683618", "GSM1683619", "GSM1683620", "GSM1683621", "GSM1683622", "GSM1683623", "GSM1683624", "GSM1683625", "GSM1683626", "GSM1683627", "GSM1683628", "GSM1683629", "GSM1683630", "GSM1683631", "GSM1683632", "GSM1683633", "GSM1683634", "GSM1683635", "GSM1683636", "GSM1683637", "GSM1683638", "GSM1683639", "GSM1683640", "GSM1683641", "GSM1683642", "GSM1683643", "GSM1683644", "GSM1683645", "GSM1683646", "GSM1683647", "GSM1683648", "GSM1683649", "GSM1683650", "GSM1683651", "GSM1683652", "GSM1683653", "GSM1683654", "GSM1683655", "GSM1683656", "GSM1683657", "GSM1683658", "GSM1683659", "GSM1683660", "GSM1683661", "GSM1683662", "GSM1683663", "GSM1683664", "GSM1683665", "GSM1683666", "GSM1683667", "GSM1683668", "GSM1683669", "GSM1683670", "GSM1683671", "GSM1683672", "GSM1683673", "GSM1683674", "GSM1683675", "GSM1683676", "GSM1683677", "GSM1683678", "GSM1683679", "GSM1683680", "GSM1683681", "GSM1683682", "GSM1683683", "GSM1683684", "GSM1683685", "GSM1683686", "GSM1683687", "GSM1683688", "GSM1683689", "GSM1683690", "GSM1683691", "GSM1683692", "GSM1683693", "GSM1683694", "GSM1683695", "GSM1683696", "GSM1683697", "GSM1683698", "GSM1683699", "GSM1683700", "GSM1683701", "GSM1683702", "GSM1683703", "GSM1683704", "GSM1683705", "GSM1683706", "GSM1683707", "GSM1683708", "GSM1683709", "GSM1683710", "GSM1683711", "GSM1683712", "GSM1683713", "GSM1683714", "GSM1683715", "GSM1683716", "GSM1683717", "GSM1683718", "GSM1683719", "GSM1683720", "GSM1683721", "GSM1683722", "GSM1683723", "GSM1683724", "GSM1683725", "GSM1683726", "GSM1683727", "GSM1683728", "GSM1683729", "GSM1683730", "GSM1683731", "GSM1683732", "GSM1683733", "GSM1683734", "GSM1683735", "GSM1683736", "GSM1683737", "GSM1683738", "GSM1683739", "GSM1683740", "GSM1683741", "GSM1683742", "GSM1683743", "GSM1683744", "GSM1683745", "GSM1683746", "GSM1683747", "GSM1683748", "GSM1683749", "GSM1683750", "GSM1683751", "GSM1683752", "GSM1683753", "GSM1683754", "GSM1683755", "GSM1683756", "GSM1683757", "GSM1683758", "GSM1683759", "GSM1683760", "GSM1683761", "GSM1683762", "GSM1683763", "GSM1683764", "GSM1683765", "GSM1683766", "GSM1683767", "GSM1683768", "GSM1683769", "GSM1683770", "GSM1683771", "GSM1683772", "GSM1683773", "GSM1683774", "GSM1683775", "GSM1683776", "GSM1683777", "GSM1683778", "GSM1683779", "GSM1683780", "GSM1683781", "GSM1683782", "GSM1683783", "GSM1683784", "GSM1683785", "GSM1683786", "GSM1683787", "GSM1683788", "GSM1683789", "GSM1683790", "GSM1683791", "GSM1683792", "GSM1683793", "GSM1683794", "GSM1683795", "GSM1683796", "GSM1683797", "GSM1683798", "GSM1683799", "GSM1683800", "GSM1683801", "GSM1683802", "GSM1683803", "GSM1683804", "GSM1683805", "GSM1683806", "GSM1683807", "GSM1683808", "GSM1683809", "GSM1683810", "GSM1683811", "GSM1683812", "GSM1683813", "GSM1683814", "GSM1683815", "GSM1683816", "GSM1683817", "GSM1683818", "GSM1683819", "GSM1683820", "GSM1683821", "GSM1683822", "GSM1683823", "GSM1683824", "GSM1683825", "GSM1683826", "GSM1683827", "GSM1683828", "GSM1683829", "GSM1683830", "GSM1683831", "GSM1683832", "GSM1683833", "GSM1683834", "GSM1683835", "GSM1683836", "GSM1683837", "GSM1683838", "GSM1683839", "GSM1683840", "GSM1683841", "GSM1683842", "GSM1683843", "GSM1683844", "GSM1683845", "GSM1683846", "GSM1683847", "GSM1683848", "GSM1683849", "GSM1683850", "GSM1683851", "GSM1683852", "GSM1683853", "GSM1683854", "GSM1683855", "GSM1683856", "GSM1683857", "GSM1683858", "GSM1683859", "GSM1683860", "GSM1683861", "GSM1683862", "GSM1683863", "GSM1683864", "GSM1683865", "GSM1683866", "GSM1683867", "GSM1683868", "GSM1683869", "GSM1683870", "GSM1683871", "GSM1683872", "GSM1683873", "GSM1683874", "GSM1683875", "GSM1683876", "GSM1683877", "GSM1683878", "GSM1683879", "GSM1683880", "GSM1683881", "GSM1683882", "GSM1683883", "GSM1683884", "GSM1683885", "GSM1683886", "GSM1683887", "GSM1683888", "GSM1683889", "GSM1683890", "GSM1683891", "GSM1683892", "GSM1683893", "GSM1683894", "GSM1683895", "GSM1683896", "GSM1683897", "GSM1683898", "GSM1683899", "GSM1683900", "GSM1683901", "GSM1683902", "GSM1683903", "GSM1683904", "GSM1683905", "GSM1683906", "GSM1683907", "GSM1683908", "GSM1683909", "GSM1683910", "GSM1683911", "GSM1683912", "GSM1683913", "GSM1683914", "GSM1683915", "GSM1683916", "GSM1683917", "GSM1683918", "GSM1683919", "GSM1683920", "GSM1683921", "GSM1683922", "GSM1683923", "GSM1683924", "GSM1683925", "GSM1683926", "GSM1683927", "GSM1683928", "GSM1683929", "GSM1683930", "GSM1683931", "GSM1683932", "GSM1683933", "GSM1683934", "GSM1683935", "GSM1683936", "GSM1683937", "GSM1683938", "GSM1683939", "GSM1683940", "GSM1683941", "GSM1683942", "GSM1683943", "GSM1683944", "GSM1683945", "GSM1683946", "GSM1683947", "GSM1683948", "GSM1683949", "GSM1683950", "GSM1683951", "GSM1683952", "GSM1683953", "GSM1683954", "GSM1683955", "GSM1683956", "GSM1683957", "GSM1683958", "GSM1683959", "GSM1683960", "GSM1683961", "GSM1683962", "GSM1683963", "GSM1683964", "GSM1683965", "GSM1683966", "GSM1683967", "GSM1683968", "GSM1683969", "GSM1683970", "GSM1683971", "GSM1683972", "GSM1683973", "GSM1683974", "GSM1683975", "GSM1683976", "GSM1683977", "GSM1683978", "GSM1683979", "GSM1683980", "GSM1683981", "GSM1683982", "GSM1683983", "GSM1683984", "GSM1683985", "GSM1683986", "GSM1683987", "GSM1683988", "GSM1683989", "GSM1683990", "GSM1683991", "GSM1683992", "GSM1683993", "GSM1683994", "GSM1683995", "GSM1683996", "GSM1683997", "GSM1683998", "GSM1683999", "GSM1684000", "GSM1684001", "GSM1684002", "GSM1684003", "GSM1684004", "GSM1684005", "GSM1684006", "GSM1684007", "GSM1684008", "GSM1684009", "GSM1684010", "GSM1684011", "GSM1684012", "GSM1684013", "GSM1684014", "GSM1684015", "GSM1684016", "GSM1684017", "GSM1684018", "GSM1684019", "GSM1684020", "GSM1684021", "GSM1684022", "GSM1684023", "GSM1684024", "GSM1684025", "GSM1684026", "GSM1684027", "GSM1684028", "GSM1684029", "GSM1684030", "GSM1684031", "GSM1684032", "GSM1684033", "GSM1684034", "GSM1684035", "GSM1684036", "GSM1684037", "GSM1684038", "GSM1684039", "GSM1684040", "GSM1684041", "GSM1684042", "GSM1684043", "GSM1684044", "GSM1684045", "GSM1684046", "GSM1684047", "GSM1684048", "GSM1684049", "GSM1684050", "GSM1684051", "GSM1684052", "GSM1684053", "GSM1684054", "GSM1684055", "GSM1684056", "GSM1684057", "GSM1684058", "GSM1684059", "GSM1684060", "GSM1684061", "GSM1684062", "GSM1684063", "GSM1684064", "GSM1684065", "GSM1684066", "GSM1684067", "GSM1684068", "GSM1684069", "GSM1684070", "GSM1684071", "GSM1684072", "GSM1684073", "GSM1684074", "GSM1684075", "GSM1684076", "GSM1684077", "GSM1684078", "GSM1684079", "GSM1684080", "GSM1684081", "GSM1684082", "GSM1684083", "GSM1684084", "GSM1684085", "GSM1684086", "GSM1684087", "GSM1684088", "GSM1684089", "GSM1684090", "GSM1684091", "GSM1684092", "GSM1684093", "GSM1684094"], "sample_count": 580, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "caArray_fine-00037: Rembrandt_GeneExpression", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE70231", "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=GSE70231", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70231", "version": null, "note": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1721044", "GSM1721045", "GSM1721046", "GSM1721047", "GSM1721048", "GSM1721049", "GSM1721050", "GSM1721051", "GSM1721052", "GSM1721053", "GSM1721054", "GSM1721055", "GSM1721056", "GSM1721057", "GSM1721058", "GSM1721059", "GSM1721060", "GSM1721061", "GSM1721062", "GSM1721063", "GSM1721064", "GSM1721065", "GSM1721066", "GSM1721067", "GSM1721068", "GSM1721069", "GSM1721070", "GSM1721071", "GSM1721072", "GSM1721073", "GSM1721074", "GSM1721075", "GSM1721076", "GSM1721077", "GSM1721078", "GSM1721079", "GSM1721080", "GSM1721081", "GSM1721082", "GSM1721083", "GSM1721084", "GSM1721085", "GSM1721086", "GSM1721087", "GSM1721088", "GSM1721089", "GSM1721090", "GSM1721091", "GSM1721092", "GSM1721093", "GSM1721094"], "sample_count": 51, "group_sizes": null, "group_sizes_basis": null, "platform": "80", "taxon": "Homo sapiens", "title": "caArray_hanas-00078: Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis", "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:32696617:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1ec83c0979beaf68169a34a7232c9c113ae76b4c9dacd0be3d38c88120aea4ce", "bytes": 457, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#jcmm15615-tbl-0001", "version": null, "note": "The selected samples for this current study", "structure": {"pmcid": "PMC7520335", "section_index": 7, "section_title": "The overall collection of datasets and identification of DEGs", "row_count": 8, "column_count": 4}, "table": {"label": "Table 1", "caption": "The selected samples for this current study", "rows": [["GEO accessions", "GBM number", "Normal number", "Reference"], ["GSE2223", "29", "4", "15"], ["GSE4058", "29", "3", "16"], ["GSE4290", "77", "23", "17"], ["GSE13276", "5", "3", "18"], ["GSE68848", "228", "28", "19"], ["GSE70231", "21", "6", "20"], ["TCGA‐GBM", "169", "5", "25"]], "row_count": 8, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[7]/table-wrap[1]#jcmm15615-tbl-0001"}}], "gaps": ["asset:data:geo:GSE13276 not downloaded", "asset:data:geo:GSE13276 licence not read", "asset:data:geo:GSE2223 not downloaded", "asset:data:geo:GSE2223 licence not read", "asset:data:geo:GSE4058 not downloaded", "asset:data:geo:GSE4058 licence not read", "asset:data:geo:GSE4290 not downloaded", "asset:data:geo:GSE4290 licence not read", "asset:data:geo:GSE68848 not downloaded", "asset:data:geo:GSE68848 licence not read", "asset:data:geo:GSE70231 not downloaded", "asset:data:geo:GSE70231 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "22 and edgeR method 23 (fold change > 2 and adjusted P‐valu"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "Deseq2"}}, {"id": "method-2", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "22 and edgeR method 23 (fold change > 2 and adjusted P‐valu"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "edgeR"}}, {"id": "method-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "22 and edgeR method 23 (fold change > 2 and adjusted P‐valu"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "Limma"}}, {"id": "method-4", "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": "PPI"}}], "targets": [], "gaps": []}, "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: deseq2."}, "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": ["GSE2223", "GSE4058", "GSE4290", "GSE13276", "GSE68848", "GSE70231"], "resolved_accessions": ["GSE2223", "GSE4058", "GSE4290", "GSE13276", "GSE68848", "GSE70231"], "statements": ["The microarray data of human tissue from GSE2223, GSE4058, GSE4290, GSE13276, GSE68848 and GSE70231 were downloaded from the Gene Expression Omnibus (GEO) database.\nTCGA‐GBM database."], "basis": "The paper names GSE2223, GSE4058, GSE4290, GSE13276, GSE68848, GSE70231 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:32696617", "data:geo:GSE13276", "asset:table:pmid:32696617:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13276"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:06:35Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 33678, "completion_tokens": 3434, "cached_tokens": 11392}}, "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:32696617", "type": "paper", "label": "pmid:32696617"}, {"id": "source:pmid:32696617", "type": "manuscript", "label": "PMID 32696617 full text"}, {"id": "data:geo:GSE13276", "type": "dataset", "label": "GEO GSE13276"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32696617", "type": "paper", "label": "pmid:32696617"}, {"id": "source:pmid:32696617", "type": "manuscript", "label": "PMID 32696617 full text"}, {"id": "data:geo:GSE13276", "type": "dataset", "label": "GEO GSE13276"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32696617", "type": "extraction", "used": ["source:pmid:32696617"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13276", "type": "accession_resolution", "used": ["data:geo:GSE13276"], "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:32696617", "parent_hash": "sha256:90584816c84ac10f62f1d069f7f96934e4db99890ddcb5d232f2d1735c324a68", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE13276 licence not read", "asset:data:geo:GSE13276 not downloaded", "asset:data:geo:GSE2223 licence not read", "asset:data:geo:GSE2223 not downloaded", "asset:data:geo:GSE4058 licence not read", "asset:data:geo:GSE4058 not downloaded", "asset:data:geo:GSE4290 licence not read", "asset:data:geo:GSE4290 not downloaded", "asset:data:geo:GSE68848 licence not read", "asset:data:geo:GSE68848 not downloaded", "asset:data:geo:GSE70231 licence not read", "asset:data:geo:GSE70231 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["tality of central nervous system cancer. The microarray data from GSE2223, GSE4058, GSE4290, GSE1327", "Data preparation and RRA method analyses The microarray data of human tissue from GSE2223, 15 GSE405"], "order_basis": "paper_text_order:156", "id": "assay:1"}, {"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": 0.8, "evidence": ["Deseq2"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}