Integrative bioinformatics analysis of miRNA and mRNA expression profiles and identification of associated miRNA-mRNA network in intracranial aneurysms.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38511055", "kind": "science-record", "revision": 4, "content_hash": "sha256:6e364b7a73f3f3602a1572410edc4bb0f565dbfb1387df5f73994a842b29ca94", "created_at": "2026-11-01T19:20:27Z", "updated_at": "2026-11-01T22:11:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative bioinformatics analysis of miRNA and mRNA expression profiles and identification of associated miRNA-mRNA network in intracranial aneurysms.", "doi": "10.1016/j.ncrna.2024.01.004", "pmid": "38511055", "authors": ["Dongxiao Xu", "Ilgiz Gareev", "Ozal Beylerli", "Valentin Pavlov", "Huang Le", "Huaizhang Shi"], "journal": "Non-coding RNA research", "year": 2024, "abstract": "Background: Intracranial aneurysms (IAs) represent protrusions in the vascular wall, with their growth and wall thinning influenced by various factors. These processes can culminate in the rupture of the aneurysm, leading to subarachnoid hemorrhage (SAH). Unfortunately, over half of the patients prove unable to withstand SAH, succumbing to adverse outcomes despite intensive therapeutic interventions, even in premier medical facilities. This study seeks to discern the pivotal microRNAs (miRNAs) and genes associated with the formation and progression of IAs.\nMethods: The investigation gathered expression data of miRNAs (from GSE66240) and mRNAs (from GSE158558) within human aneurysm tissue and superficial temporal artery (STA) samples, categorizing them into IA and normal groups. This classification was based on the Gene Expression Omnibus (GEO) database.\nResults: A total of 70 differentially expressed microRNAs (DEMs) and 815 differentially expressed mRNAs (DEGs) were pinpointed concerning IA. Subsequently, a miRNA-mRNA network was constructed, incorporating 9 significantly upregulated DEMs and 211 significantly downregulated DEGs. Simultaneously, functional enrichment and pathway analyses were conducted on both DEMs and DEGs. Through protein-protein interaction (PPI) network analysis and functional enrichment, 9 significantly upregulated DEMs (hsa-miR-188-5p, hsa-miR-590-5p, hsa-miR-320b, hsa-miR-423-5p, hsa-miR-140-5p, hsa-miR-486-5p, hsa-miR-320a, hsa-miR-342-3p, and hsa-miR-532-5p) and 50 key genes (such as ATP6V1G1, KBTBD6, VIM, PA2G4, DYNLL1, METTL21A, MDH2, etc.) were identified, suggesting their potential significant role in IA. Among these genes, ten were notably negatively regulated by at least two key miRNAs.\nConclusions: The findings of this study provide valuable insights into the potential pathogenic mechanisms underlying IA by elucidating a miRNA-mRNA network. This comprehensive approach sheds light on the intricate interplay between miRNAs and genes, offering a deeper understanding of the molecular dynamics involved in IA development and progression.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) distinguishing between IA and STA samples were identified through the utilization of GEO2R, an interactive web tool accessible at http://www.ncbi.nlm.nih.gov/geo/geo2r.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38511055", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "Differentially expressed genes (DEGs) distinguishing between IA and STA samples were identified through the utilization of GEO2R, an interactive web tool accessible at http://www.ncbi.nlm.nih.gov/geo/geo2r."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray datasets containing miRNA and mRNA expression profiles linked to IAs were acquired from the Gene Expression Omnibus (GEO) database, administered by the National Center for Biotechnology Information (NCBI), and can be accessed at https://www.ncbi.nlm.nih.gov/geo/); accessed in September 2022). 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Notably, the miRNA expression dataset, GSE66240, was conducted on the GPL17303 platform, while the mRNA expression dataset, GSE158558, utilized the GPL20301 platform (Illumina HiSeq 4000)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 70 differentially expressed microRNAs and 815 differentially expressed mRNAs associated with intracranial aneurysm.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38511055", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 70 differentially expressed microRNAs (DEMs) and 815 differentially expressed mRNAs (DEGs) were pinpointed concerning IA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 70 differentially expressed microRNAs and 815 differentially expressed mRNAs associated with intracranial aneurysm.", "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:38511055"], "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:GSE158558"], "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:GSE158558"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38511055", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.ncrna.2024.01.004", "sha256": "sha256:a82c8d819f2ec75c6bb235d1443bf54d24331695606b75f78f301204b3a89578", "bytes": 46943, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.ncrna.2024.01.004", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10950608", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE158558", "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=GSE158558", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE158558", "version": null, "note": "The microarray datasets containing miRNA and mRNA expression profiles linked to IAs were acquired from the Gene Expression Omnibus (GEO) database, administered by the National Center for Biotechnology Information (NCBI), and can be accessed at https://www.ncbi.nlm.nih.gov/geo/); accessed in September 2022). 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