Eph receptor B6 shapes a cold immune microenvironment, inhibiting anti-cancer immunity and immunotherapy response in bladder cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37637034", "kind": "science-record", "revision": 4, "content_hash": "sha256:ecf114f923f51816d3ecaa979b7cd309ff24ad12ef9285366d4e009017bb88d9", "created_at": "2026-11-01T19:02:25Z", "updated_at": "2026-11-01T22:52:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Eph receptor B6 shapes a cold immune microenvironment, inhibiting anti-cancer immunity and immunotherapy response in bladder cancer.", "doi": "10.3389/fonc.2023.1175183", "pmid": "37637034", "authors": ["Xiaolong Jia", "Dongxu Zhang", "Cheng Zhou", "Zejun Yan", "Zhaohui Jiang", "Liping Xie", "Junhui Jiang"], "journal": "Frontiers in oncology", "year": 2023, "abstract": "Background: The role of Eph receptors and related ephrin (EFN) ligands (as the largest family of transmembrane-bound RTKs) in immunomodulation in many types of cancer, especially bladder cancer (BLCA), is scarcely known.\nMethods: A pan-cancer dataset was retrieved from The Cancer Genome Atlas (TCGA) to explore the relation between Eph receptor/EFN ligand family genes and immunomodulators and tumor-infiltrated immune cells (TIICs). Local BLCA, GSE32894, and GSE31684 cohorts were applied to validate. The IMvigor210 cohort was employed to explore the relationship between EPHB6 and immunotherapy response. Moreover, association between EPHB6 and molecular subtype was investigated to explore potential therapeutic strategies. Immunohistochemical staining of CD8 and CD68 was performed to validate the correlation between EPHB6 and TIICs.\nResults: The pan-cancer analysis revealed variations in the immunological effects of Eph receptor/EFN ligand family genes across different types of cancer. EPHB6 expression negatively correlated with the expression of the majority of immunomodulators (including HLA and immune checkpoints), and CD8 T cells and macrophages in both the TCGA-BLCA and validation BLCA cohorts, shaping a cold immune microenvironment with inhibited immunity. In the IMvigor210 cohort, patients with high-EPHB6 highly correlated with a non-inflamed, low PD-L1 expression immune phenotype, and correspondingly, with less responders to immunotherapy. The high-EPHB6 group, enriched with the basal subtype, presented significantly fewer TP53 and more FGFR3 genomic alterations. Finally, a novel EPHB6-related Genes signature, with reliable and robust ability in prognosis prediction, was constructed.\nConclusions: This study comprehensively investigated the immunological effects of Eph receptor/EFN ligand family genes pan-cancer, and specially identified the immunosuppressive role of EPHB6 in BLCA. Furthermore, EPHB6 may predict the molecular subtype and prognosis of BLCA, and serve as a novel therapeutic target to improve the sensitivity of immunotherapy.", "claims": [{"id": "claim-method", "statement": "The univariate Cox regression analysis found 35 genes to be significantly associated with the prognosis of BLCA ( Supplementary Table 2 ). After calculation, the combinational algorithms of RF and Ridge exhibited the best performance ( Figure 9D ), identifying a total of 21 genes enrolled in the EPHB6-related Genes signature (EBGs; Supplementary Table 2 ).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37637034", "locator": "sections[21] \"Prognostic significance of EPHB6 in BLCA\" paragraph 2", "quote": "The univariate Cox regression analysis found 35 genes to be significantly associated with the prognosis of BLCA ( Supplementary Table 2 ). After calculation, the combinational algorithms of RF and Ridge exhibited the best performance ( Figure 9D ), identifying a total of 21 genes enrolled in the EPHB6-related Genes signature (EBGs; Supplementary Table 2 )."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37637034", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Moreover, the performance of EBGs signature was validated in other four independent BLCA cohorts, and consistently higher EBGs score indicated an inferior OS.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37637034", "locator": "sections[21] \"Prognostic significance of EPHB6 in BLCA\" paragraph 2", "quote": "Moreover, the performance of EBGs signature was validated in other four independent BLCA cohorts, and consistently higher EBGs score indicated an inferior OS."}, {"asset": "source:pmid:37637034", "locator": "sections[21] \"Prognostic significance of EPHB6 in BLCA\" paragraph 2", "quote": "All the AUC values of EBGs signature in predicting prognosis for patients with BLCA were approximately 0.65 ( Figure 9E )."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Moreover, the performance of EBGs signature was validated in other four independent BLCA cohorts, and consistently higher EBGs score indicated an inferior OS.", "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:37637034"], "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": "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:GSE13507"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37637034", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2023.1175183", "sha256": "sha256:e5cb793cb0a55e40abfefb5537c136d7c6fb66d6ccedbff3396ecebd992816ca", "bytes": 75062, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2023.1175183", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10450340", "source": "europe_pmc_fulltext", "coverage": "whole_body", "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": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "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:GSE188715", "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=GSE188715", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE188715", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5688738", "GSM5688739", "GSM5688740", "GSM5688741", "GSM5688742", "GSM5688743", "GSM5688744", "GSM5688745", "GSM5688746", "GSM5688747", "GSM5688748", "GSM5688749", "GSM5688750", "GSM5688751", "GSM5688752", "GSM5688753", "GSM5688754", "GSM5688755", "GSM5688756", "GSM5688757", "GSM5688758", "GSM5688759", "GSM5688760", "GSM5688761", "GSM5688762", "GSM5688763", "GSM5688764", "GSM5688765", "GSM5688766", "GSM5688767", "GSM5688768", "GSM5688770", "GSM5688772", "GSM5688774", "GSM5688775", "GSM5688777", "GSM5688779", "GSM5688781", "GSM5688783", "GSM5688785", "GSM5688786", "GSM5688787", "GSM5688788", "GSM5688789", "GSM5688790", "GSM5688791", "GSM5688792", "GSM5688793", "GSM5688794", "GSM5688795", "GSM5688796", "GSM5688797", "GSM5688798", "GSM5688799", "GSM5688800", "GSM5688801", "GSM5688802", "GSM5688803", "GSM5688804", "GSM5688805", "GSM5688806", "GSM5688807", "GSM5688808", "GSM5688809", "GSM5688810", "GSM5688811", "GSM5688812", "GSM5688813", "GSM5688814", "GSM5688815"], "sample_count": 70, "group_sizes": null, "group_sizes_basis": null, "platform": "28038", "taxon": "Homo sapiens", "title": "RNAseq of bladder cancer samples from Xiangya hospital", "resolution_checked_at": "2026-11-01T18:06:43Z", "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": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "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:GSE32548", "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=GSE32548", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32548", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM806803", "GSM806804", "GSM806805", "GSM806806", "GSM806807", "GSM806808", "GSM806809", "GSM806810", "GSM806811", "GSM806812", "GSM806813", "GSM806814", "GSM806815", "GSM806816", "GSM806817", "GSM806818", "GSM806819", "GSM806820", "GSM806821", "GSM806822", "GSM806823", "GSM806824", "GSM806825", "GSM806826", "GSM806827", "GSM806828", "GSM806829", "GSM806830", "GSM806831", "GSM806832", "GSM806833", "GSM806834", "GSM806835", "GSM806836", "GSM806837", "GSM806838", "GSM806839", "GSM806840", "GSM806841", "GSM806842", "GSM806843", "GSM806844", "GSM806845", "GSM806846", "GSM806847", "GSM806848", "GSM806849", "GSM806850", "GSM806851", "GSM806852", "GSM806853", "GSM806854", "GSM806855", "GSM806856", "GSM806857", "GSM806858", "GSM806859", "GSM806860", "GSM806861", "GSM806862", "GSM806863", "GSM806864", "GSM806865", "GSM806866", "GSM806867", "GSM806868", "GSM806869", "GSM806870", "GSM806871", "GSM806872", "GSM806873", "GSM806874", "GSM806875", "GSM806876", "GSM806877", "GSM806878", "GSM806879", "GSM806880", "GSM806881", "GSM806882", "GSM806883", "GSM806884", "GSM806885", "GSM806886", "GSM806887", "GSM806888", "GSM806889", "GSM806890", "GSM806891", "GSM806892", "GSM806893", "GSM806894", "GSM806895", "GSM806896", "GSM806897", "GSM806898", "GSM806899", "GSM806900", "GSM806901", "GSM806902", "GSM806903", "GSM806904", "GSM806905", "GSM806906", "GSM806907", "GSM806908", "GSM806909", "GSM806910", "GSM806911", "GSM806912", "GSM806913", "GSM806914", "GSM806915", "GSM806916", "GSM806917", "GSM806918", "GSM806919", "GSM806920", "GSM806921", "GSM806922", "GSM806923", "GSM806924", "GSM806925", "GSM806926", "GSM806927", "GSM806928", "GSM806929", "GSM806930", "GSM806931", "GSM806932", "GSM806933"], "sample_count": 131, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (gene expression)", "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": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "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}}], "gaps": ["asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE188715 not downloaded", "asset:data:geo:GSE188715 licence not read", "asset:data:geo:GSE31684 not downloaded", "asset:data:geo:GSE31684 licence not read", "asset:data:geo:GSE32548 not downloaded", "asset:data:geo:GSE32548 licence not read", "asset:data:geo:GSE32894 not downloaded", "asset:data:geo:GSE32894 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The univariate Cox regression analysis found 35 genes to be significantly associated with the prognosis of BLCA ( Supplementary Table 2 ). After calculation, the combinational algorithms of RF and Ridge exhibited the best performance ( Figure 9D ), identifying a total of 21 genes enrolled in the EPHB6-related Genes signature (EBGs; Supplementary Table 2 )."}}, {"id": "method-2", "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-3", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE32548", "GSE13507", "GSE188715", "GSE32894", "GSE31684"], "resolved_accessions": ["GSE32548", "GSE13507", "GSE188715", "GSE32894", "GSE31684"], "statements": ["The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation."], "basis": "The paper names GSE32548, GSE13507, GSE188715, GSE32894, GSE31684 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": ["cox_ph"], "assets": ["source:pmid:37637034", "data:geo:GSE13507"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "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": "2026-11-01T18:51:58Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 20953, "completion_tokens": 3063, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37637034", "type": "paper", "label": "pmid:37637034"}, {"id": "source:pmid:37637034", "type": "manuscript", "label": "PMID 37637034 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37637034", "type": "paper", "label": "pmid:37637034"}, {"id": "source:pmid:37637034", "type": "manuscript", "label": "PMID 37637034 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37637034", "type": "extraction", "used": ["source:pmid:37637034"], "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:37637034", "parent_hash": "sha256:f87d6ba2d7d855c609ef256af9d60d081eb8bf08d688b537b51669de54522913", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE188715 licence not read", "asset:data:geo:GSE188715 not downloaded", "asset:data:geo:GSE31684 licence not read", "asset:data:geo:GSE31684 not downloaded", "asset:data:geo:GSE32548 licence not read", "asset:data:geo:GSE32548 not downloaded", "asset:data:geo:GSE32894 licence not read", "asset:data:geo:GSE32894 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["to explore potential therapeutic strategies. Immunohistochemical staining of CD8 and CD68 was performed to va", "Materials and methods Immunohistochemical analysis of EPHB6 and correlation with TME W", "ples (4-µm-thick sections) were subjected to immunohistochemical staining for EPHB6, CD8, CD68 using EPHB6 (a", ", 1:50, Abcam) antibodies, respectively. The immunohistochemical staining method was performed as described p"], "order_basis": "paper_text_order:817", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The univariate Cox regression analysis found 35 genes to be significantly associated with the prognosis of BLCA ( Supplementary Table 2 ). After calculation, the combinational algorithms of RF and Ridge exhibited the best performance ( Figure 9D ), identifying a total of 21 genes enrolled in the EPHB6-related Genes signature (EBGs; Supplementary Table 2 )."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}