A novel circRNA-miRNA-mRNA network reveals hsa-circ-0040039 as a biomarker for intervertebral disc degeneration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34939437", "kind": "science-record", "revision": 5, "content_hash": "sha256:d27af8e018f244f7e8116cc798d4629ae820dd7540560e75f9860caee9fe6436", "created_at": "2026-11-01T17:36:39Z", "updated_at": "2026-11-01T22:48:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A novel circRNA-miRNA-mRNA network reveals hsa-circ-0040039 as a biomarker for intervertebral disc degeneration.", "doi": "10.1177/0300060520960983", "pmid": "34939437", "authors": ["Jianhua Tang", "Chenlin Zhang", "Shengru Wang", "Jianfeng Chen"], "journal": "The Journal of international medical research", "year": 2021, "abstract": "OBJECTIVE: Alterations in the structure and function of intervertebral discs by multifaceted chronic processes can result in intervertebral disc degeneration (IDD). The mechanisms involved in IDD are still unknown.\nMETHODS: We investigated the possible mechanisms underlying IDD using a bioinformatics analysis of publicly available microarray expression datasets and built a circular RNA-microRNA-mRNA (circRNA-miRNA-mRNA) network based on the results. Datasets GSE67566 and GSE116726 were downloaded from the Gene Expression Omnibus (GEO) and analyzed using the limma package in R. The CircInteractome database was used to detect miRNAs related to circRNA, and TargetScan, miRDB, and miRTarBase were used to predict target mRNAs. Key target genes were annotated using Gene Ontology terms.\nRESULTS: The circRNA hsa-circ-0040039 was found to have the top log fold-change score. Analysis using Metascape showed that the associated genes were enriched mainly in the cell cycle. The Cytoscape plugin MCODE predicted that two members of the RAS oncogene family-RAB1A and RAB1B-and multiple coagulation factor deficiency (MCFD2) may play key roles in IDD.\nCONCLUSION: Our results suggested that hsa-circ-0040039 and the related network may be potential biomarkers for IDD.", "claims": [{"id": "claim-method", "statement": "The Bioconductor affy package (https://www.bioconductor.org/packages/release/bioc/html/affy.html) was used to analyze the annotation files for log2 conversion, standardization, and background correction of the raw data, and the limma package in R (https://www.R-project.org/) was used to screen the DEGs in the IDD tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34939437", "locator": "sections[5] \"Data analysis to detect DEGs in the IDD tissues\" paragraph 2", "quote": "The Bioconductor affy package (https://www.bioconductor.org/packages/release/bioc/html/affy.html) was used to analyze the annotation files for log2 conversion, standardization, and background correction of the raw data, and the limma package in R (https://www.R-project.org/) was used to screen the DEGs in the IDD tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this study, we used the microarray expression profile datasets GSE67566 and GSE116726 from the Gene Expression Omnibus (GEO) to obtain circRNAs, miRNAs, and mRNAs related to IDD.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34939437", "locator": "sections[1] \"Introduction\" paragraph 5", "quote": "In this study, we used the microarray expression profile datasets GSE67566 and GSE116726 from the Gene Expression Omnibus (GEO) to obtain circRNAs, miRNAs, and mRNAs related to IDD."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 970 DEMs were detected in GSE116726 and 105 DECs were detected in GSE67566 using the limma package.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34939437", "locator": "sections[10] \"Identification of DEGs in IDD tissues\" paragraph 2", "quote": "A total of 970 DEMs were detected in GSE116726 and 105 DECs were detected in GSE67566 using the limma package."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 970 DEMs were detected in GSE116726 and 105 DECs were detected in GSE67566 using the limma package.", "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:34939437"], "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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