Identification of a potentially functional circRNA-miRNA-mRNA ceRNA regulatory network in bladder cancer by analysis of microarray data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33532293", "kind": "science-record", "revision": 8, "content_hash": "sha256:112af00db6f169ecf85fb93fc283d49cb02a39d6c8197bbc551afdc6f1dc083e", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:03:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a potentially functional circRNA-miRNA-mRNA ceRNA regulatory network in bladder cancer by analysis of microarray data.", "doi": "10.21037/tau-20-660", "pmid": "33532293", "authors": ["Lei Du", "Xin Wang", "Yuewei Yin", "Yanping Zhang", "Jianghua Jia", "Baosai Lu", "Wenyong Xue", "Changbao Qu", "Jinchun Qi"], "journal": "Translational andrology and urology", "year": 2021, "abstract": "BACKGROUND: Circular RNAs (circRNAs) have received increasing attention in cancer development. However, a substantial number of circRNAs still require characterization. The purpose of this study is to uncover novel circRNAs and their molecular mechanism in bladder cancer (BCa).\nMETHODS: A combinative strategy of extensive data mining and computational biology was employed to identify BCa-related circRNAs and explore their potential mechanisms of action.\nRESULTS: Three differentially expressed circRNAs (has_circ_0023642, has_circ_0047322, has_circ_0041151) were obtained from the microarray dataset (GSE92675). Four miRNAs (miR-616, miR-515-5p, miR-647, miR-1178) with potential binding sites with these three circRNAs were identified. Pathway analysis demonstrated that all four miRNAs were closely associated with some cancer-related pathways. Survival analysis indicated that these miRNAs might potentially play a role in tumor-suppressive functions in BCa. Subsequently, 181 overlapping genes were identified from 472 up-regulated genes in BCa (TCGA database), and 10,017 predicted target genes of the four miRNAs obtained. A circRNA-miRNA-mRNA network was constructed on the identified three circRNAs, four miRNAs, and 181 overlapping genes. Besides, six hub genes (CENPA, HIST1H2BJ, HIST1H2BO, HIST1H3H, HIST1H3B, HIST1H3F) were identified from establishing a protein-protein interaction (PPI) network on the same overlapping genes. Furthermore, a circRNA-miRNA-hub gene sub-network was built to delineate the links among the differential circRNAs, miRNA, and hub genes.\nCONCLUSIONS: Our study provided significant insights into the molecular mechanisms that regulate the progression of BCa from the circRNA-miRNA-mRNA network view.", "claims": [{"id": "claim-method", "statement": "The correlation between miRNA expression and patients’ survival was assessed by Kaplan-Meier method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33532293", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "The correlation between miRNA expression and patients’ survival was assessed by Kaplan-Meier method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The circRNA expression profile of GSE92675 was obtained from the GEO database, including 4 pairs of matched BCa (GSM2434319, GSM2434321, GSM2434323, GSM2434325) and para-cancer tissues (GSM2434320, GSM2434322, GSM2434324, GSM2434326).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33532293", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "The circRNA expression profile of GSE92675 was obtained from the GEO database, including 4 pairs of matched BCa (GSM2434319, GSM2434321, GSM2434323, GSM2434325) and para-cancer tissues (GSM2434320, GSM2434322, GSM2434324, GSM2434326)."}], "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:33532293"], "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:GSE92675"], "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:GSE92675"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33532293", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tau-20-660", "sha256": "sha256:aa45f1dfab1ad17fc98b19e5eeabe0a399cf3bbd494eb468f7511fa3e5572b92", "bytes": 24470, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tau-20-660", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7844515", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE92675", "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=GSE92675", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE92675", "version": null, "note": "The circRNA expression profile of GSE92675 was obtained from the GEO database, including 4 pairs of matched BCa (GSM2434319, GSM2434321, GSM2434323, GSM2434325) and para-cancer tissues (GSM2434320, GSM2434322, GSM2434324, GSM2434326).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The circRNA expression profile of GSE92675 was obtained from the GEO database, including 4 pairs of matched BCa (GSM2434319, GSM2434321, GSM2434323, GSM2434325) and para-cancer tissues (GSM2434320, GSM2434322, GSM2434324, GSM2434326).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2434319", "GSM2434320", "GSM2434321", "GSM2434322", "GSM2434323", "GSM2434324", "GSM2434325", "GSM2434326"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "19978", "taxon": "Homo sapiens", "title": "Expression profiles of circular RNAs in bladder cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE92675 not downloaded", "asset:data:geo:GSE92675 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The correlation between miRNA expression and patients’ survival was assessed by Kaplan-Meier method."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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