Elucidating the Associated Biological Function and Clinical Significance of RHOJ Expression in Urothelial Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37762382", "kind": "science-record", "revision": 2, "content_hash": "sha256:0890c981a96ea2dae129e87c3c582c7f00119842f4fb43eec1e62727569cf029", "created_at": "2026-11-01T19:02:36Z", "updated_at": "2026-11-01T21:31:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Elucidating the Associated Biological Function and Clinical Significance of RHOJ Expression in Urothelial Carcinoma.", "doi": "10.3390/ijms241814081", "pmid": "37762382", "authors": ["Xin-Jie Lu", "Hsing-Fan Lai", "Sheng-Cheng Wu", "Chin-Li Chen", "Yi-Lin Chiu"], "journal": "International journal of molecular sciences", "year": 2023, "abstract": "Urothelial cancer, a common urinary system malignancy, often presents treatment challenges due to metastasis and chemotherapy side effects. Angiogenesis, crucial for tumor growth, has become a target for drug development. This study explores the expression, prognostic value, and clinical correlation of RHOJ in the TCGA BLCA, GSE31684, and GSE32894 datasets. We identify common differentially expressed genes across these databases and utilize g:Profiler and Cytoscape ClueGO for functional assessment. Further, we perform a gene set enrichment analysis (GSEA) using Hallmark gene sets and use the imsig package for immune cell infiltration analysis. Our analysis indicates that RHOJ expression levels significantly impact survival rates, tumor progression, and immune response in urothelial tumors. High RHOJ expression correlated with poor prognosis, advanced disease stages, and an increase in monocyte population within the tumor microenvironment. This aligns with current literature indicating a key role of immune infiltration in bladder cancer progression and treatment response. Moreover, the GSEA and imsig results further suggest a potential mechanistic link between RHOJ expression and immune-related pathways. Considering the increasing emphasis on immunotherapeutic strategies in bladder cancer management, our findings on RHOJ's potential as a diagnostic biomarker and its association with immune response open new avenues for therapeutic interventions.", "claims": [{"id": "claim-method", "statement": "We applied R survival (v3.5-5) and survminer (v0.4.9) packages to conduct a Kaplan–Meier survival analysis on RHOJ expression data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37762382", "locator": "sections[13] \"4.2. Survival Analysis\" paragraph 2", "quote": "We applied R survival (v3.5-5) and survminer (v0.4.9) packages to conduct a Kaplan–Meier survival analysis on RHOJ expression data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Availability StatementPublicly available datasets were analyzed in this study. These data can be found here: GSE31684 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31684 (acessed on 16 November 2022)); GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 (accessed on 16 November 2022)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37762382", "locator": "sections[23] \"notes\" paragraph 1", "quote": "Data Availability StatementPublicly available datasets were analyzed in this study. These data can be found here: GSE31684 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31684 (acessed on 16 November 2022)); GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 (accessed on 16 November 2022))."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This highlights a poorer prognosis and significantly lower survival rates in bladder cancer patients with elevated RHOJ expression (Figure 1).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37762382", "locator": "sections[3] \"2.1. Correlation of RHOJ Expression and Prognosis in Patients with Urothelial Tumors\" paragraph 2", "quote": "This highlights a poorer prognosis and significantly lower survival rates in bladder cancer patients with elevated RHOJ expression (Figure 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This highlights a poorer prognosis and significantly lower survival rates in bladder cancer patients with elevated RHOJ expression (Figure 1).", "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:37762382"], "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:GSE31684"], "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:GSE31684"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37762382", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms241814081", "sha256": "sha256:3b00fa3547da35f4707b651ab589ca16d4c657a2d365416eaceed95e94c9ed3a", "bytes": 38655, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms241814081", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10531362", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"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": "Data Availability StatementPublicly available datasets were analyzed in this study. These data can be found here: GSE31684 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31684 (acessed on 16 November 2022)); GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 (accessed on 16 November 2022)).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability StatementPublicly available datasets were analyzed in this study. These data can be found here: GSE31684 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31684 (acessed on 16 November 2022)); GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 (accessed on 16 November 2022)).", "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": "Data Availability StatementPublicly available datasets were analyzed in this study. These data can be found here: GSE31684 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31684 (acessed on 16 November 2022)); GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 (accessed on 16 November 2022)).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability StatementPublicly available datasets were analyzed in this study. These data can be found here: GSE31684 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31684 (acessed on 16 November 2022)); GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 (accessed on 16 November 2022)).", "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:GSE31684 not downloaded", "asset:data:geo:GSE31684 licence not read", "asset:data:geo:GSE32894 not downloaded", "asset:data:geo:GSE32894 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Kaplan–Meier survival analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We applied R survival (v3.5-5) and survminer (v0.4.9) packages to conduct a Kaplan–Meier survival analysis on RHOJ expression data."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Kaplan–Meier survival analysis), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE31684", "GSE32894"], "resolved_accessions": ["GSE31684", "GSE32894"], "statements": ["Data Availability StatementPublicly available datasets were analyzed in this study. These data can be found here: GSE31684 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31684 (acessed on 16 November 2022)); GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894 (accessed on 16 November 2022))."], "basis": "The paper names GSE31684, GSE32894 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:37762382", "data:geo:GSE31684"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE31684"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:54:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10675, "completion_tokens": 2148, "cached_tokens": 264}}, "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:37762382", "type": "paper", "label": "pmid:37762382"}, {"id": "source:pmid:37762382", "type": "manuscript", "label": "PMID 37762382 full text"}, {"id": "data:geo:GSE31684", "type": "dataset", "label": "GEO GSE31684"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37762382", "type": "paper", "label": "pmid:37762382"}, {"id": "source:pmid:37762382", "type": "manuscript", "label": "PMID 37762382 full text"}, {"id": "data:geo:GSE31684", "type": "dataset", "label": "GEO GSE31684"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37762382", "type": "extraction", "used": ["source:pmid:37762382"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE31684", "type": "accession_resolution", "used": ["data:geo:GSE31684"], "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:37762382", "parent_hash": "sha256:9010fd1da531460c4400c949d412c5da1ea0e490b06cb3ed18ffaa96c2a01be6", "fork_of": null, "generation": 1}, "gaps": ["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", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["cellular proliferation, differentiation, and apoptosis. SLRPs and TGF-beta are renowned for their c"], "order_basis": "paper_text_order:8416", "id": "assay:1"}]}