Identification of immune-related genes that predict prognosis and risk of bladder cancer: bioinformatics analysis of TCGA database.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34329197", "kind": "science-record", "revision": 8, "content_hash": "sha256:42943e0e9a12e45518a6ee08210089767703515182dbfa7caa7866cfd2dbd67f", "created_at": "2026-11-01T15:41:45Z", "updated_at": "2026-11-01T22:04:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of immune-related genes that predict prognosis and risk of bladder cancer: bioinformatics analysis of TCGA database.", "doi": "10.18632/aging.203333", "pmid": "34329197", "authors": ["Liqiang Guo", "Qiong Wu", "Zhen Ma", "Mingzhen Yuan", "Shengtian Zhao"], "journal": "Aging", "year": 2021, "abstract": "BACKGROUND: Bladder cancer (BLCA) is the major tumor of the urinary system, and immune-related genes (IRGs) contribute significantly to its initiation and prognosis.\nRESULTS: A total of 51 prognostic IRGs significantly associated with overall survival were identified. Functional enrichment analysis revealed that these genes were actively involved in tumor-related functions and pathways. Using multivariate Cox regression analysis, we detected 11 optimal IRGs (ADIPOQ, PPY, NAMPT, TAP1, AHNAK, OLR1, PDGFRA, IL34, MMP9, RAC3, and SH3BP2). We validated the prognostic value of this signature in two validation cohorts: GSE13507 (n = 165) and GSE32894 (n = 224). Furthermore, we performed a western blot and found that the expression of these IRGs matched their mRNA expression in TCGA. Moreover, correlations between risk score and immune-cell infiltration indicated that the prognostic signature reflected infiltration by several types of immune cells.\nCONCLUSION: We identified and validated an 11-IRG-based risk signature that may be a reliable tool to evaluate the prognosis of BLCA patients and help to devise individualized immunotherapies.\nMETHODS: Bioinformatics analysis was performed using TCGA and ImmPort databases. Cox regression was used to identify prognostic signatures. Two external GEO cohorts and western blotting of samples were performed to validate the IRG signature.", "claims": [{"id": "claim-method", "statement": "Using multivariate Cox regression analysis, we detected 11 optimal IRGs (ADIPOQ, PPY, NAMPT, TAP1, AHNAK, OLR1, PDGFRA, IL34, MMP9, RAC3, and SH3BP2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34329197", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using multivariate Cox regression analysis, we detected 11 optimal IRGs (ADIPOQ, PPY, NAMPT, TAP1, AHNAK, OLR1, PDGFRA, IL34, MMP9, RAC3, and SH3BP2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Clinical and transcriptome RNA-seq data of 433 BLCA samples, including 414 BLCA patients and 19 matched normal samples, downloaded from the TCGA cohort.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34329197", "locator": "sections[15] \"Clinical samples and data collection\" paragraph 2", "quote": "Clinical and transcriptome RNA-seq data of 433 BLCA samples, including 414 BLCA patients and 19 matched normal samples, downloaded from the TCGA cohort."}], "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:34329197"], "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:34329197", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.203333", "sha256": 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