Construction of a circRNA-miRNA-mRNA network based on competitive endogenous RNA reveals the function of circRNAs in osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32063749", "kind": "science-record", "revision": 6, "content_hash": "sha256:be5348fdbfe47b0eb2b678a7b8d0c060ce16437ecd3e716f12c3be6a7cdd11f6", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T21:22:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of a circRNA-miRNA-mRNA network based on competitive endogenous RNA reveals the function of circRNAs in osteosarcoma.", "doi": "10.1186/s12935-020-1134-1", "pmid": "32063749", "authors": ["Yu Qiu", "Chao Pu", "Yanchao Li", "Baochuang Qi"], "journal": "Cancer cell international", "year": 2020, "abstract": "BACKGROUND: Osteosarcoma (OS) is a common primary malignant bone tumour. Growing evidence suggests that circular RNAs (circRNAs) are closely related to the development of tumours. However, the function of circRNAs in OS remains unknown. Here, we aimed to determine the regulatory mechanisms of circRNAs in OS.\nMETHODS: The expression profiles of OS circRNA (GSE96964), microRNA (GSE65071) and mRNA (GSE33382) were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed circRNAs, miRNAs and mRNAs in OS. A ceRNA network was constructed based on circRNA-miRNA pairs and miRNA-mRNA pairs. MRNAs with significant prognostic differences were identified by the TARGET database in the network. Functional and pathway enrichment analyses were performed, and interactions between proteins were predicted using Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to elucidate the possible functions of these differentially expressed circRNAs.\nRESULTS: A total of 15 downregulated circRNAs, 136 upregulated miRNAs and 52 downregulated mRNAs were identified in OS. Finally, a circRNA-miRNA-mRNA network was constructed in OS based on 14 circRNAs, 24 miRNAs, and 52 mRNAs. GO and KEGG pathway analyses suggested that the mRNAs in the network may be involved in the pathogenesis and progression of OS. Four mRNAs identified by the TARGET database were significantly associated with OS survival prognosis. A circRNA-miRNA-mRNA subnetwork was constructed based on these four mRNAs.\nCONCLUSION: Our results provide a deeper understanding of the regulatory mechanisms by which circRNAs compete for endogenous RNAs in OS.", "claims": [{"id": "claim-method", "statement": "The log-rank test was used for statistical analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32063749", "locator": "sections[7] \"Survival analysis\" paragraph 2", "quote": "The log-rank test was used for statistical analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We declare that the data and materials in this study are provided free of charge to scientists for non-commercial purposes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32063749", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "We declare that the data and materials in this study are provided free of charge to scientists for non-commercial purposes."}], "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:32063749"], "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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"structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We declare that the data and materials in this study are provided free of charge to scientists for non-commercial purposes.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM825623", "GSM825624", "GSM825625", "GSM825626", "GSM825627", "GSM825628", "GSM825629", "GSM825630", "GSM825631", "GSM825632", "GSM825633", "GSM825634", "GSM825635", "GSM825636", "GSM825637", "GSM825638", "GSM825639", "GSM825640", "GSM825641", "GSM825642", "GSM825643", "GSM825644", "GSM825645", "GSM825646", "GSM825647", "GSM825648", "GSM825649", "GSM825650", "GSM825651", "GSM825652", "GSM825653", "GSM825654", "GSM825655", "GSM825656", "GSM825657", "GSM825658", "GSM825659", "GSM825660", "GSM825661", "GSM825662", "GSM825663", "GSM825664", "GSM825665", "GSM825666", "GSM825667", "GSM825668", "GSM825669", "GSM825670", "GSM825671", "GSM825672", "GSM825673", "GSM825674", "GSM825675", 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"access_route": "GEO accession URL", "access_statement_verbatim": "We declare that the data and materials in this study are provided free of charge to scientists for non-commercial purposes.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2546888", "GSM2546889", "GSM2546890", "GSM2546891", "GSM2546892", "GSM2546893", "GSM2546894", "GSM2546895"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "19978", "taxon": "Homo sapiens", "title": "Microarray expression profile and functional analysis of circular RNAs in osteosarcoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32063749:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7836d1ebc02ccdc16e9e5b8b146640338d6bf37508787a4f3849247c6e2b37a8", 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["hsa_circ_0001910", "chrX:10031484–10066619", "35,135", "+", "NM_015691", "WWC3"]], "row_count": 16, "column_count": 6, "numeric_cells": 60, "header_rows": 1, "locator": "section[9]/table-wrap[2]#Tab2"}}], "gaps": ["asset:data:geo:GSE33382 not downloaded", "asset:data:geo:GSE33382 licence not read", "asset:data:geo:GSE65071 not downloaded", "asset:data:geo:GSE65071 licence not read", "asset:data:geo:GSE96964 not downloaded", "asset:data:geo:GSE96964 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The log-rank test was used for statistical analysis."}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / 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