Dysregulation of the Immune Microenvironment Contributes to Malignant Progression and Has Prognostic Value in Bladder Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33392066", "kind": "science-record", "revision": 7, "content_hash": "sha256:30fd1e89a17c693713904e1834274b4b912731fb12701178405fb8bb827fc185", "created_at": "2026-11-01T15:41:21Z", "updated_at": "2026-11-01T22:02:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dysregulation of the Immune Microenvironment Contributes to Malignant Progression and Has Prognostic Value in Bladder Cancer.", "doi": "10.3389/fonc.2020.542492", "pmid": "33392066", "authors": ["Zongtai Zheng", "Shiyu Mao", "Wentao Zhang", "Ji Liu", "Cheng Li", "Ruiliang Wang", "Xudong Yao"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "OBJECTIVE: The malignant progression from non-muscle-invasive bladder cancer (NMIBC) to muscle-invasive bladder cancer (MIBC) is common and has detrimental effect on patients. We aimed to elucidate the underlying mechanisms of the malignant progression from an immunological perspective and establish a reliable signature for prognostic prediction and immunotherapeutic strategies.\nMETHODS: The Cell Type Identification by Estimating Relative Subsets of RNA Transcripts algorithm was applied to the GSE32894 data set to identify the different tumor-infiltrating immune cells involved in NMIBC and MIBC. Using weighted gene correlation network analysis, survival analysis and least absolute shrinkage and selection operator Cox analysis, we established an immune prognostic signature (IPS) based on 14 overall survival-associated immune genes in The Cancer Genome Atlas (TCGA). Functional enrichment analyses and nomogram were performed to explore the potential effects and prognostic performance of the IPS. Furthermore, the RNA-sequence data from our center were used to validate the expression levels of the selected immune genes in BLCA samples.\nRESULTS: Diverse proportions of macrophage subtypes were observed between NMIBC and MIBC. Patients with high risk scores had a worse prognosis than patients with low risk scores in training (TCGA) and validation data sets (GSE32894, GSE13507, and GSE48277). The IPS was a useful prognostic factor for patients treated with immunotherapy in the IMvigor210 trial. Hallmarks of multiple oncogenic pathways were significantly enriched in the high risk group. A novel nomogram model was established for prognostic predictions. The dysregulated expression of the selected immune genes between NMIBC and MIBC was also validated in BLCA samples.\nCONCLUSION: Dysregulation of the immune microenvironment promoted the malignant progression from NMIBC to MIBC. The IPS can stratify patients into different risk groups with distinct prognoses and immunotherapeutic susceptibility, thus facilitating personalized immunotherapy.", "claims": [{"id": "claim-method", "statement": "The differences in the immune cells proportions and the expression levels of 14 immune genes between NMIBC and MIBC were compared using Wilcoxon test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33392066", "locator": "sections[9] \"Statistical Analysis\" paragraph 2", "quote": "The differences in the immune cells proportions and the expression levels of 14 immune genes between NMIBC and MIBC were compared using Wilcoxon test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33392066", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33392066"], "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:GSE13507"], "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:group_comparison_wilcoxon", "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:GSE13507"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33392066", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2020.542492", "sha256": "sha256:e1083a508f380b40cc1d503582185014456a23555a3653a6e3745bf8d8f8b66d", "bytes": 32175, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2020.542492", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7773013", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13507", "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=GSE13507", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13507", "version": null, "note": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM340537", "GSM340538", "GSM340539", "GSM340540", "GSM340541", "GSM340542", "GSM340543", "GSM340544", "GSM340545", "GSM340546", "GSM340547", "GSM340548", "GSM340549", "GSM340550", "GSM340551", "GSM340552", "GSM340553", "GSM340554", "GSM340555", "GSM340556", "GSM340557", "GSM340558", "GSM340559", "GSM340560", "GSM340561", "GSM340562", "GSM340563", "GSM340564", "GSM340565", "GSM340566", "GSM340567", "GSM340568", "GSM340569", "GSM340570", "GSM340571", "GSM340572", "GSM340573", "GSM340574", "GSM340575", "GSM340576", "GSM340577", "GSM340578", "GSM340579", "GSM340580", "GSM340581", "GSM340582", "GSM340583", "GSM340584", "GSM340585", "GSM340586", "GSM340587", "GSM340588", "GSM340589", "GSM340590", "GSM340591", "GSM340592", "GSM340593", "GSM340594", "GSM340595", "GSM340596", "GSM340597", "GSM340598", "GSM340599", "GSM340600", "GSM340601", "GSM340602", "GSM340603", "GSM340604", "GSM340605", "GSM340606", "GSM340607", "GSM340608", "GSM340609", "GSM340610", "GSM340611", "GSM340612", "GSM340613", "GSM340614", "GSM340615", "GSM340616", "GSM340617", "GSM340618", "GSM340619", "GSM340620", "GSM340621", "GSM340622", "GSM340623", "GSM340624", "GSM340625", "GSM340626", "GSM340627", "GSM340628", "GSM340629", "GSM340630", "GSM340631", "GSM340632", "GSM340633", "GSM340634", "GSM340635", "GSM340636", "GSM340637", "GSM340638", "GSM340639", "GSM340640", "GSM340641", "GSM340642", "GSM340643", "GSM340644", "GSM340645", "GSM340646", "GSM340647", "GSM340648", "GSM340649", "GSM340650", "GSM340651", "GSM340652", "GSM340653", "GSM340654", "GSM340655", "GSM340656", "GSM340657", "GSM340658", "GSM340659", "GSM340660", "GSM340661", "GSM340662", "GSM340663", "GSM340664", "GSM340665", "GSM340666", "GSM340667", "GSM340668", "GSM340669", "GSM340670", "GSM340671", "GSM340672", "GSM340673", "GSM340674", "GSM340675", "GSM340676", "GSM340677", "GSM340678", "GSM340679", "GSM340680", "GSM340681", "GSM340682", "GSM340683", "GSM340684", "GSM340685", "GSM340686", "GSM340687", "GSM340688", "GSM340689", "GSM340690", "GSM340691", "GSM340692", "GSM340693", "GSM340694", "GSM340695", "GSM340696", "GSM340697", "GSM340698", "GSM340699", "GSM340700", "GSM340701", "GSM340702", "GSM340703", "GSM340704", "GSM340705", "GSM340706", "GSM340707", "GSM340708", "GSM340709", "GSM340710", "GSM340711", "GSM340712", "GSM340713", "GSM340714", "GSM340715", "GSM340716", "GSM340717", "GSM340718", "GSM340719", "GSM340720", "GSM340721", "GSM340722", "GSM340723", "GSM340724", "GSM340725", "GSM340726", "GSM340727", "GSM340728", "GSM340729", "GSM340730", "GSM340731", "GSM340732", "GSM340733", "GSM340734", "GSM340735", "GSM340736", "GSM340737", "GSM340738", "GSM340739", "GSM340740", "GSM340741", "GSM340742", "GSM340743", "GSM340744", "GSM340745", "GSM340746", "GSM340747", "GSM340748", "GSM340749", "GSM340750", "GSM340751", "GSM340752", "GSM340753", "GSM340754", "GSM340755", "GSM340756", "GSM340757", "GSM340758", "GSM340759", "GSM340760", "GSM340761", "GSM340762", "GSM340763", "GSM340764", "GSM340765", "GSM340766", "GSM340767", "GSM340768", "GSM340769", "GSM340770", "GSM340771", "GSM340772", "GSM340773", "GSM340774", "GSM340775", "GSM340776", "GSM340777", "GSM340778", "GSM340779", "GSM340780", "GSM340781", "GSM340782", "GSM340783", "GSM340784", "GSM340785", "GSM340786", "GSM340787", "GSM340788", "GSM340789", "GSM340790", "GSM340791", "GSM340792"], "sample_count": 256, "group_sizes": null, "group_sizes_basis": null, "platform": "6102", "taxon": "Homo sapiens", "title": "Predective Value of Prognosis-Related Gene Expression Study in Primary Bladder Cancer", "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:GSE31684", "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=GSE31684", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31684", "version": null, "note": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM786491", "GSM786492", "GSM786493", "GSM786494", "GSM786495", "GSM786496", "GSM786497", "GSM786498", "GSM786499", "GSM786500", "GSM786501", "GSM786502", "GSM786503", "GSM786504", "GSM786505", "GSM786506", "GSM786507", "GSM786508", "GSM786509", "GSM786510", "GSM786511", "GSM786512", "GSM786513", "GSM786514", "GSM786515", "GSM786516", "GSM786517", "GSM786518", "GSM786519", "GSM786520", "GSM786521", "GSM786522", "GSM786523", "GSM786524", "GSM786525", "GSM786526", "GSM786527", "GSM786528", "GSM786529", "GSM786530", "GSM786531", "GSM786532", "GSM786533", "GSM786534", "GSM786535", "GSM786536", "GSM786537", "GSM786538", "GSM786539", "GSM786540", "GSM786541", "GSM786542", "GSM786543", "GSM786544", "GSM786545", "GSM786546", "GSM786547", "GSM786548", "GSM786549", "GSM786550", "GSM786551", "GSM786552", "GSM786553", "GSM786554", "GSM786555", "GSM786556", "GSM786557", "GSM786558", "GSM786559", "GSM786560", "GSM786561", "GSM786562", "GSM786563", "GSM786564", "GSM786565", "GSM786566", "GSM786567", "GSM786568", "GSM786569", "GSM786570", "GSM786571", "GSM786572", "GSM786573", "GSM786574", "GSM786575", "GSM786576", "GSM786577", "GSM786578", "GSM786579", "GSM786580", "GSM786581", "GSM786582", "GSM786583"], "sample_count": 93, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer  ", "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:GSE32894", "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=GSE32894", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32894", "version": null, "note": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM814052", "GSM814053", "GSM814054", "GSM814055", "GSM814056", "GSM814057", "GSM814058", "GSM814059", "GSM814060", "GSM814061", "GSM814062", "GSM814063", "GSM814064", "GSM814065", "GSM814066", "GSM814067", "GSM814068", "GSM814069", "GSM814070", "GSM814071", "GSM814072", "GSM814073", "GSM814074", "GSM814075", "GSM814076", "GSM814077", "GSM814078", "GSM814079", "GSM814080", "GSM814081", "GSM814082", "GSM814083", "GSM814084", "GSM814085", "GSM814086", "GSM814087", "GSM814088", "GSM814089", "GSM814090", "GSM814091", "GSM814092", "GSM814093", "GSM814094", "GSM814095", "GSM814096", "GSM814097", "GSM814098", "GSM814099", "GSM814100", "GSM814101", "GSM814102", "GSM814103", "GSM814104", "GSM814105", "GSM814106", "GSM814107", "GSM814108", "GSM814109", "GSM814110", "GSM814111", "GSM814112", "GSM814113", "GSM814114", "GSM814115", "GSM814116", "GSM814117", "GSM814118", "GSM814119", "GSM814120", "GSM814121", "GSM814122", "GSM814123", "GSM814124", "GSM814125", "GSM814126", "GSM814127", "GSM814128", "GSM814129", "GSM814130", "GSM814131", "GSM814132", "GSM814133", "GSM814134", "GSM814135", "GSM814136", "GSM814137", "GSM814138", "GSM814139", "GSM814140", "GSM814141", "GSM814142", "GSM814143", "GSM814144", "GSM814145", "GSM814146", "GSM814147", "GSM814148", "GSM814149", "GSM814150", "GSM814151", "GSM814152", "GSM814153", "GSM814154", "GSM814155", "GSM814156", "GSM814157", "GSM814158", "GSM814159", "GSM814160", "GSM814161", "GSM814162", "GSM814163", "GSM814164", "GSM814165", "GSM814166", "GSM814167", "GSM814168", "GSM814169", "GSM814170", "GSM814171", "GSM814172", "GSM814173", "GSM814174", "GSM814175", "GSM814176", "GSM814177", "GSM814178", "GSM814179", "GSM814180", "GSM814181", "GSM814182", "GSM814183", "GSM814184", "GSM814185", "GSM814186", "GSM814187", "GSM814188", "GSM814189", "GSM814190", "GSM814191", "GSM814192", "GSM814193", "GSM814194", "GSM814195", "GSM814196", "GSM814197", "GSM814198", "GSM814199", "GSM814200", "GSM814201", "GSM814202", "GSM814203", "GSM814204", "GSM814205", "GSM814206", "GSM814207", "GSM814208", "GSM814209", "GSM814210", "GSM814211", "GSM814212", "GSM814213", "GSM814214", "GSM814215", "GSM814216", "GSM814217", "GSM814218", "GSM814219", "GSM814220", "GSM814221", "GSM814222", "GSM814223", "GSM814224", "GSM814225", "GSM814226", "GSM814227", "GSM814228", "GSM814229", "GSM814230", "GSM814231", "GSM814232", "GSM814233", "GSM814234", "GSM814235", "GSM814236", "GSM814237", "GSM814238", "GSM814239", "GSM814240", "GSM814241", "GSM814242", "GSM814243", "GSM814244", "GSM814245", "GSM814246", "GSM814247", "GSM814248", "GSM814249", "GSM814250", "GSM814251", "GSM814252", "GSM814253", "GSM814254", "GSM814255", "GSM814256", "GSM814257", "GSM814258", "GSM814259", "GSM814260", "GSM814261", "GSM814262", "GSM814263", "GSM814264", "GSM814265", "GSM814266", "GSM814267", "GSM814268", "GSM814269", "GSM814270", "GSM814271", "GSM814272", "GSM814273", "GSM814274", "GSM814275", "GSM814276", "GSM814277", "GSM814278", "GSM814279", "GSM814280", "GSM814281", "GSM814282", "GSM814283", "GSM814284", "GSM814285", "GSM814286", "GSM814287", "GSM814288", "GSM814289", "GSM814290", "GSM814291", "GSM814292", "GSM814293", "GSM814294", "GSM814295", "GSM814296", "GSM814297", "GSM814298", "GSM814299", "GSM814300", "GSM814301", "GSM814302", "GSM814303", "GSM814304", "GSM814305", "GSM814306", "GSM814307", "GSM814308", "GSM814309", "GSM814310", "GSM814311", "GSM814312", "GSM814313", "GSM814314", "GSM814315", "GSM814316", "GSM814317", "GSM814318", "GSM814319", "GSM814320", "GSM814321", "GSM814322", "GSM814323", "GSM814324", "GSM814325", "GSM814326", "GSM814327", "GSM814328", "GSM814329", "GSM814330", "GSM814331", "GSM814332", "GSM814333", "GSM814334", "GSM814335", "GSM814336", "GSM814337", "GSM814338", "GSM814339", "GSM814340", "GSM814341", "GSM814342", "GSM814343", "GSM814344", "GSM814345", "GSM814346", "GSM814347", "GSM814348", "GSM814349", "GSM814350", "GSM814351", "GSM814352", "GSM814353", "GSM814354", "GSM814355", "GSM814356", "GSM814357", "GSM814358", "GSM814359"], "sample_count": 308, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "A Molecular Taxonomy of Urothelial Carcinoma", "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:GSE48277", "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=GSE48277", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48277", "version": null, "note": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1164253", "GSM1164254", "GSM1164255", "GSM1164256", "GSM1164257", "GSM1164258", "GSM1164259", "GSM1164260", "GSM1164261", "GSM1164262", "GSM1164263", "GSM1164264", "GSM1164265", "GSM1164266", "GSM1164267", "GSM1164268", "GSM1164269", "GSM1164270", "GSM1164271", "GSM1164272", "GSM1164273", "GSM1164274", "GSM1164275", "GSM1164276", "GSM1164277", "GSM1164278", "GSM1164279", "GSM1164280", "GSM1164281", "GSM1164282", "GSM1167333", "GSM1167334", "GSM1167335", "GSM1167336", "GSM1167337", "GSM1167338", "GSM1167339", "GSM1167340", "GSM1167341", "GSM1167342", "GSM1167343", "GSM1167344", "GSM1167345", "GSM1167346", "GSM1167347", "GSM1167348", "GSM1167349", "GSM1167350", "GSM1167351", "GSM1167352", "GSM1167353", "GSM1167354", "GSM1167355", "GSM1167356", "GSM1167357", "GSM1167358", "GSM1167359", "GSM1167360", "GSM1167361", "GSM1167362", "GSM1167363", "GSM1167364", "GSM1167365", "GSM1167366", "GSM1167367", "GSM1167368", "GSM1167369", "GSM1167370", "GSM1167371", "GSM1167372", "GSM1167373", "GSM1167374", "GSM1167375", "GSM1167376", "GSM1167377", "GSM1167378", "GSM1167379", "GSM1167380", "GSM1167381", "GSM1167382", "GSM1167383", "GSM1167384", "GSM1167385", "GSM1167386", "GSM1167387", "GSM1167388", "GSM1167389", "GSM1167390", "GSM1167391", "GSM1167392", "GSM1167393", "GSM1167394", "GSM1167395", "GSM1167396", "GSM1167397", "GSM1167398", "GSM1167399", "GSM1167400", "GSM1167401", "GSM1167402", "GSM1167403", "GSM1167404", "GSM1167405", "GSM1167406", "GSM1167407", "GSM1167408", "GSM1167409", "GSM1167410", "GSM1167411", "GSM1167412", "GSM1167413", "GSM1167414", "GSM1167415", "GSM1167416", "GSM1167417", "GSM1167418", "GSM1167419", "GSM1167420", "GSM1167421", "GSM1167422", "GSM1167423", "GSM1167424", "GSM1167425", "GSM1167426", "GSM1167427", "GSM1167428", "GSM1167429", "GSM1167430", "GSM1167431", "GSM1167432", "GSM1167433", "GSM1167434", "GSM1167435", "GSM1167436", "GSM1167437", "GSM1167438", "GSM1167439", "GSM1167440", "GSM1167441", "GSM1167442", "GSM1167443", "GSM1167444", "GSM1167445", "GSM1167446", "GSM1167447", "GSM1167448", "GSM1167449", "GSM1167450", "GSM1167451", "GSM1167452", "GSM1167453", "GSM1167454", "GSM1167455", "GSM1167456", "GSM1167457", "GSM1167458", "GSM1167459", "GSM1167460", "GSM1167461", "GSM1167462", "GSM1167463", "GSM1167464", "GSM1167465", "GSM1167466", "GSM1167467", "GSM1167468", "GSM1167469", "GSM1167470", "GSM1167471", "GSM1167472", "GSM1167473", "GSM1167474", "GSM1169026", "GSM1169027", "GSM1169028", "GSM1169029", "GSM1169030", "GSM1169031", "GSM1169032", "GSM1169033", "GSM1169034", "GSM1169035", "GSM1169036", "GSM1169037", "GSM1169038", "GSM1169039", "GSM1169040", "GSM1169041", "GSM1169042", "GSM1169043", "GSM1173901", "GSM1173902", "GSM1173903", "GSM1173904", "GSM1173905", "GSM1173906", "GSM1173907", "GSM1173908", "GSM1173909", "GSM1173910", "GSM1173911", "GSM1173912", "GSM1173913", "GSM1173914", "GSM1173915", "GSM1173916", "GSM1173917", "GSM1173918", "GSM1173919", "GSM1173920", "GSM1173921", "GSM1173922", "GSM1173923", "GSM1173924", "GSM1173925", "GSM1173926", "GSM1173927", "GSM1173928", "GSM1173929", "GSM1173930", "GSM1173931", "GSM1173932", "GSM1173933", "GSM1173934", "GSM1173935", "GSM1173936", "GSM1173937", "GSM1173938", "GSM1173939", "GSM1173940", "GSM1173941", "GSM1173942", "GSM1173943", "GSM1173944", "GSM1173945", "GSM1173946", "GSM1173947", "GSM1173948", "GSM1173949", "GSM1173950", "GSM1173951", "GSM1173952", "GSM1173953", "GSM1173954", "GSM1173955", "GSM1173956", "GSM1173957", "GSM1173968", "GSM1173969", "GSM1173970", "GSM1173971", "GSM1173972", "GSM1173973", "GSM1173974", "GSM1173975", "GSM1173976", "GSM1173977", "GSM1173978", "GSM1173979", "GSM1173980", "GSM1173981", "GSM1173982", "GSM1173983", "GSM1173986", "GSM1173987", "GSM1173988", "GSM1173989", "GSM1173990", "GSM1173991", "GSM1173992", "GSM1173993", "GSM1173994", "GSM1173995", "GSM1173996", "GSM1173997", "GSM1173998", "GSM1173999", "GSM1174000", "GSM1174001", "GSM1174002", "GSM1174003", "GSM1174004", "GSM1174005", "GSM1174006", "GSM1174007", "GSM1174008", "GSM1174009", "GSM1174010", "GSM1174011", "GSM1174012", "GSM1174013", "GSM1174014", "GSM1174015", "GSM1174016", "GSM1174017", "GSM1174018", "GSM1174019", "GSM1174020", "GSM1174021", "GSM1174022", "GSM1174023", "GSM1174024", "GSM1174025", "GSM1174026", "GSM1174027", "GSM1174028", "GSM1261392", "GSM1261393", "GSM1261394", "GSM1261395", "GSM1261396", "GSM1261397", "GSM1261398", "GSM1261399", "GSM1261400", "GSM1261401", "GSM1261402", "GSM1261403", "GSM1261404", "GSM1261405", "GSM1261406", "GSM1261407", "GSM1261408", "GSM1261409", "GSM1261410", "GSM1261411", "GSM1261412", "GSM1261413", "GSM1261414", "GSM1263201", "GSM1263202", "GSM1263203", "GSM1263204", "GSM1263205", "GSM1263206", "GSM1263207", "GSM1263208", "GSM1263209", "GSM1263210", "GSM1263211", "GSM1263212", "GSM1263213", "GSM1263214", "GSM1263215", "GSM1263216", "GSM1263217", "GSM1263218", "GSM1263219", "GSM1263220"], "sample_count": 349, "group_sizes": null, "group_sizes_basis": null, "platform": "10558;6947;14951", "taxon": "Homo sapiens", "title": "Identification of distinct basal and luminal subsets of human bladder cancers with different sensitivities to frontline chemotherapy", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33392066:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8609ffa2bcd97b9febd159d8309fb31f3b2627947999fb446619ac6dd01d0f9d", "bytes": 1414, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "Information of data sets used in this study.", "structure": {"pmcid": "PMC7773013", "section_index": 4, "section_title": "Data Collection", "row_count": 27, "column_count": 7}, "table": {"label": "Table 1", "caption": "Information of data sets used in this study.", "rows": [["Characteristic, n (%)", "", "GSE32894 (n = 308)", "GSE13507 (n = 165)", "GSE31684 (n = 93)", "GSE48277 (n = 159)", "TCGA (n = 403)"], ["Subtype", "NMIBC", "213", "103", "10", "10", "3"], ["", "MIBC", "93", "62", "83", "149", "400"], ["", "Unknown", "2", "–", "–", "–", "–"], ["Age (years)", "≥65", "88", "69", "65", "31", "254"], ["", "<65", "220", "96", "28", "42", "149"], ["", "Unknown", "–", "–", "–", "86", "–"], ["Gender", "Male", "80", "135", "68", "59", "299"], ["", "Female", "228", "30", "25", "14", "104"], ["", "Unknown", "–", "–", "–", "–", "–"], ["Stage", "I", "–", "103", "–", "6", "2"], ["", "II", "–", "1", "–", "35", "128"], ["", "III", "–", "0", "–", "81", "138"], ["", "IV", "–", "1", "–", "33", "132"], ["", "Unknown", "–", "60", "–", "4", "3"], ["Grade", "Low", "–", "105", "6", "–", "21"], ["", "High", "–", "60", "87", "–", "378"], ["", "Grade I", "48", "–", "–", "–", "–"], ["", "Grade II", "103", "–", "–", "–", "–"], ["", "Grade III", "154", "–", "–", "–", "–"], ["", "Unknown", "3", "–", "–", "–", "4"], ["N stage", "N0", "49", "1", "–", "110", "234"], ["", "N1-3", "22", "104", "–", "47", "128"], ["", "Unknown", "237", "60", "–", "2", "41"], ["M stage", "M0", "–", "1", "59", "157", "196"], ["", "M1", "–", "104", "34", "2", "11"], ["", "Unknown", "–", "60", "–", "–", "196"]], "row_count": 27, "column_count": 7, "numeric_cells": 88, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE31684 not downloaded", "asset:data:geo:GSE31684 licence not read", "asset:data:geo:GSE32894 not downloaded", "asset:data:geo:GSE32894 licence not read", "asset:data:geo:GSE48277 not downloaded", "asset:data:geo:GSE48277 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The differences in the immune cells proportions and the expression levels of 14 immune genes between NMIBC and MIBC were compared using Wilcoxon test."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-5", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "Principal components analysis"}}, {"id": "method-6", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE32894", "GSE13507", "GSE48277", "GSE31684"], "resolved_accessions": ["GSE32894", "GSE13507", "GSE48277", "GSE31684"], "statements": ["Publicly available datasets were analyzed in this study, these can be found in The Cancer Genome Atlas (http://cancergenome.nih.gov/); the NCBI Gene Expression Omnibus (GSE32894, GSE13507, GSE48277, and GSE31684)."], "basis": "The paper names GSE32894, GSE13507, GSE48277, GSE31684 in NCBI 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:33392066", "data:geo:GSE13507", "asset:table:pmid:33392066:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13507"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:56Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 23238, "completion_tokens": 2249, "cached_tokens": 785}}, "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:33392066", "type": "paper", "label": "pmid:33392066"}, {"id": "source:pmid:33392066", "type": "manuscript", "label": "PMID 33392066 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33392066", "type": "paper", "label": "pmid:33392066"}, {"id": "source:pmid:33392066", "type": "manuscript", "label": "PMID 33392066 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33392066", "type": "extraction", "used": ["source:pmid:33392066"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13507", "type": "accession_resolution", "used": ["data:geo:GSE13507"], "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:33392066", "parent_hash": "sha256:ecebe1d8d9ff062605c6b832b6ad1057b57bb3e4d4b39ebee1909c31314cb327", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE31684 licence not read", "asset:data:geo:GSE31684 not downloaded", "asset:data:geo:GSE32894 licence not read", "asset:data:geo:GSE32894 not downloaded", "asset:data:geo:GSE48277 licence not read", "asset:data:geo:GSE48277 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The differences in the immune cells proportions and the expression levels of 14 immune genes between NMIBC and MIBC were compared using Wilcoxon test."], "order_basis": "analysis_only", "id": "assay:1"}]}