Comprehensive analysis of lncRNA-miRNA-mRNA ceRNA network in ischemic stroke.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38698974", "kind": "science-record", "revision": 3, "content_hash": "sha256:1f7811f05a94f5c282b68097d22241f1f52319512c45517968afed115e4e42f9", "created_at": "2026-11-01T19:20:39Z", "updated_at": "2026-11-01T21:33:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis of lncRNA-miRNA-mRNA ceRNA network in ischemic stroke.", "doi": "10.1016/j.heliyon.2024.e29651", "pmid": "38698974", "authors": ["Lin Cheng", "Yun Zhao", "Hong Ke"], "journal": "Heliyon", "year": 2024, "abstract": "Objective: Competitive endogenous RNA (ceRNA) networks have uncovered a novel mode of RNA interaction, and are implicated in various biological processes and the pathogenesis of IS. This study aimed to explore the potential mechanisms underlying the ceRNA network in IS.\nMethods: Four public datasets containing lncRNA and mRNA (GSE22255 and GSE16561) and miRNA (GSE55937 and GSE43618) expression profiles from the GEO database were systematically analyzed to explore the role of RNAs in ischemic stroke (IS). Differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs), and miRNAs (DEmiRNAs) between IS and normal control samples were identified. LncRNA-miRNA and miRNA-mRNA interactions were predicted, and the competing endogenous RNA (ceRNA) regulatory network was constructed using the Cytoscape software. The correlation between the RNAs in the ceRNA network and the clinical features of the samples was evaluated. Finally, principal component analysis was performed on the RNAs that constitute the ceRNA regulatory network, and their differential expression and principal component relationships among different types of samples were observed.\nResults: A total of 224 DEmRNAs, 7 DEmiRNAs, and four DElncRNAs related to IS in four datasets were identified. Then, through target gene prediction, a lncRNA-miRNA-mRNA ceRNA network that contained 3 DElncRNAs, 2 DEmiRNAs, and 24 DEmRNAs was constructed. Correlations of the clinical characteristics showed that PART1 and SERPINH1 were related to clinical diseases, WNK1 was related to lifestyle, and seven RNAs were related to age. PCA results indicate that three principal components of PC1, PC2, and PC3 can clearly distinguish between control and IS samples.\nConclusion: Overall, we constructed a ceRNA network in IS, which could offer insights into the molecular mechanism and potential prognostic biomarkers for further research.", "claims": [{"id": "claim-method", "statement": "The R3.6.1 language psychology software package version 1.7.8 was used to perform PCA on the intersecting DElncRNA, DEmiRNA, and DEmRNA in the ceRNA network.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38698974", "locator": "sections[8] \"Principal component analysis for the ceRNAs network\" paragraph 2", "quote": "The R3.6.1 language psychology software package version 1.7.8 was used to perform PCA on the intersecting DElncRNA, DEmiRNA, and DEmRNA in the ceRNA network."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are publicly available in the 10.13039/100000085GEO database (https://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE22255, GSE16561, GSE55937 and GSE43618.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38698974", "locator": "sections[22] \"Data accessibility\" paragraph 2", "quote": "The data that support the findings of this study are publicly available in the 10.13039/100000085GEO database (https://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE22255, GSE16561, GSE55937 and GSE43618."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PCA results indicate that three principal components of PC1, PC2, and PC3 can clearly distinguish between control and IS samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38698974", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "PCA results indicate that three principal components of PC1, PC2, and PC3 can clearly distinguish between control and IS samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PCA results indicate that three principal components of PC1, PC2, and PC3 can clearly distinguish between control and IS samples.", "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:38698974"], "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:GSE16561"], "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:GSE16561"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38698974", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e29651", "sha256": 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