Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35645614", "kind": "science-record", "revision": 5, "content_hash": "sha256:fe0a9c660fd2a792564f557dbf99f9118dcda8e697c9ebc85de32672058636e5", "created_at": "2026-11-01T18:14:33Z", "updated_at": "2026-11-01T22:49:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy.", "doi": "10.1155/2022/9792913", "pmid": "35645614", "authors": ["Bing-Zhe Huang", "Yang Jing-Jing", "Xiao-Ming Dong", "Zhuan Zhong", "Xiao-Ning Liu"], "journal": "Genetics research", "year": 2022, "abstract": "Background: We aimed to construct the lncRNA-associated competing endogenous RNA (ceRNA) network and distinguish feature lncRNAs associated with tendinopathy.\nMethods: We downloaded the gene profile of GSE26051 from the Gene Expression Omnibus (GEO), including 23 normal samples and 23 diseased tendons. Differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) were identified, and functional and pathway enrichment analyses were performed. Protein-protein interaction (PPI) network was constructed and further analyzed by module mining. Moreover, a ceRNA regulatory network was constructed based on the identified lncRNA-mRNA coexpression relationship pairs and miRNA-mRNA regulation pairs.\nResults: We identified 1117 DEmRNAs and 57 DElncRNAs from the GEO data. The downregulated DEmRNAs were particularly associated with muscle contraction and muscle filament, while the upregulated ones were linked to extracellular matrix organization and cell adhesion. From the PPI network, 11 modules were extracted. Genes in MCODE 2 (such as TPM4) were significantly involved in cardiomyopathy, and genes in MCODE 4 (such as COL4A3 and COL4A4) were involved in focal adhesion, ECM-receptor interaction, and PI3K-Akt signaling pathway. The ceRNA network contained 7 lncRNAs (MIR133A1HG, LINC01405, PRKCQ-AS1, C10orf71-AS1, MBNL1-AS1, HOTAIRM1, and DNM3OS), 63 mRNAs, and 41 miRNAs. Downregulated lncRNA MIR133A1HG could competitively bind with hsa-miR-659-3p and hsa-miR-218-1-3p to regulate the TPM3. Meanwhile, MIR133A1HG could competitively bind with hsa-miR-1179 to regulate the COL4A3. Downregulated C10orf71-AS1 could competitively bind with hsa-miR-130a-5p to regulate the COL4A4.\nConclusions: Seven important lncRNAs, particularly MIR133A1HG and C10orf71-AS1, were found associated with tendinopathy according to the lncRNA-associated ceRNA network.", "claims": [{"id": "claim-method", "statement": "The Bayes method in the limma package (version 3.34.7, https://bioconductor.org/packages/release/bioc/html/limma.html) was used to conduct the differential expression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35645614", "locator": "sections[5] \"2.3. Differential Expression Analysis\" paragraph 2", "quote": "The Bayes method in the limma package (version 3.34.7, https://bioconductor.org/packages/release/bioc/html/limma.html) was used to conduct the differential expression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset used and/or analyzed during the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35645614", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The dataset used and/or analyzed during the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 1117 DEmRNAs and 57 DElncRNAs from the GEO data.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35645614", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 1117 DEmRNAs and 57 DElncRNAs from the GEO data."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 1117 DEmRNAs and 57 DElncRNAs from the GEO data.", "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:35645614"], "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:GSE26051"], "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:GSE26051"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35645614", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/9792913", "sha256": 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