Integrative analysis of prognostic long non-coding RNAs with copy number variation in bladder cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34414701", "kind": "science-record", "revision": 3, "content_hash": "sha256:4f436b11ed194bd24ca105d52bc21027774e4aa7b9cf927df750d92fef9dc16b", "created_at": "2026-11-01T17:35:57Z", "updated_at": "2026-11-01T21:26:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative analysis of prognostic long non-coding RNAs with copy number variation in bladder cancer.", "doi": "10.1631/jzus.B2000494", "pmid": "34414701", "authors": ["Wenwen Zhong", "Dejuan Wang", "Bing Yao", "Xiaoxia Chen", "Zhongyang Wang", "Hu Qu", "Bo Ma", "Lei Ye", "Jianguang Qiu"], "journal": "Journal of Zhejiang University. Science. B", "year": 2021, "abstract": "Copy number variations (CNVs), which can affect the role of long non-coding RNAs (lncRNAs), are important genetic changes seen in some malignant tumors. We analyzed lncRNAs with CNV to explore the relationship between lncRNAs and prognosis in bladder cancer (BLCA). Messenger RNA (mRNA) expression levels, DNA methylation, and DNA copy number data of 408 BLCA patients were subjected to integrative bioinformatics analysis. Cluster analysis was performed to obtain different subtypes and differently expressed lncRNAs and coding genes. Weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression gene and lncRNA modules. CNV-associated lncRNA data and their influence on cancer prognosis were assessed with Kaplan-Meier survival curve. Multi-omics integration analysis revealed five prognostic lncRNAs with CNV, namely NR2F1-AS1, LINC01138, THUMPD3-AS1, LOC101928489,and TMEM147-AS1,and a risk-score signature related to overall survival in BLCA was identified. Moreover, validated results in another independent Gene Expression Omnibus (GEO) dataset, GSE31684, were consistent with these results. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway, focal adhesion pathway, and Janus kinase-signal transducers and activators of transcription (JAK-STAT) signaling pathway were enriched in a high-risk score pattern, suggesting that imbalance in these pathways is closely related to tumor development. We revealed the prognosis-related lncRNAs by analyzing the expression profiles of lncRNAs and CNVs, which can be used as prognostic biomarkers for BLCA.", "claims": [{"id": "claim-method", "statement": "CNV-associated lncRNA data and their influence on cancer prognosis were assessed with Kaplan-Meier survival curve.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34414701", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "CNV-associated lncRNA data and their influence on cancer prognosis were assessed with Kaplan-Meier survival curve."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Moreover, validated results in another independent Gene Expression Omnibus (GEO) dataset, GSE31684, were consistent with these results.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34414701", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Moreover, validated results in another independent Gene Expression Omnibus (GEO) dataset, GSE31684, were consistent with these results."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Multi-omics integration identified five CNV-associated prognostic lncRNAs and an overall-survival risk-score signature in bladder cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34414701", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Multi-omics integration analysis revealed five prognostic lncRNAs with CNV, namely NR2F1-AS1, LINC01138, THUMPD3-AS1, LOC101928489,and TMEM147-AS1,and a risk-score signature related to overall survival in BLCA was identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Multi-omics integration identified five CNV-associated prognostic lncRNAs and an overall-survival risk-score signature in bladder cancer.", "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:34414701"], "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. 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