Integrating machine learning for the identification of ubiquitination-associated genes in moyamoya disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41036271", "kind": "science-record", "revision": 4, "content_hash": "sha256:c575cccc3c5b63777d36aa236213e99f08e502ad64eadb8bbdcefeb77386570e", "created_at": "2026-11-01T20:31:06Z", "updated_at": "2026-11-01T22:57:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrating machine learning for the identification of ubiquitination-associated genes in moyamoya disease.", "doi": "10.3389/fneur.2025.1653433", "pmid": "41036271", "authors": ["Hongchuan Niu", "Xilong Wang", "Zhenyu Zhou", "Yutong Liu", "Shihao He", "Yuanli Zhao"], "journal": "Frontiers in neurology", "year": 2025, "abstract": "Introduction: Moyamoya disease (MMD) is an infrequent cerebrovascular disorder typified by bilateral internal carotid artery obstruction, yet its pathogenic mechanism remains elusive. This study examines the role of epigenetic ubiquitination-related genes in MMD.\nMethods: We utilized two datasets (GSE157628 and GSE141024) from the GEO database and sourced ubiquitination-related genes from the GeneCards database. Differentially expressed genes were identified, followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) to elucidate key gene functions. Machine learning techniques, including LASSO logistic regression and support vector machine, helped identify crucial genes. Immune characteristics were analyzed using single-sample gene set enrichment analysis, while transcription factors and miRNA-gene regulatory networks were constructed with the Citrome and Mircode databases.\nResults: We identified three key ubiquitination-related genes-ANAPC11, UCHL1, and USP41-that may be involved in the pathogenesis of MMD. Further, we found that the serum UCHL1 expression level in MMD was significantly reduced, and knocking down UCHL1 could enhance the migration ability of human brain vascular smooth muscle cells (HBVSMCs), as verified by In vitro experiments. Immune infiltration analysis demonstrated significant correlations between these genes and various immune factors. Furthermore, we constructed a miRNA-gene network involving 30 miRNAs and identified secondary genes EXO1 and ISG15.\nDiscussion: Potential therapeutic drugs, including benzohydroxamic acid and PKC-beta inhibitors, were predicted to target these key genes, suggesting new avenues for MMD treatment.", "claims": [{"id": "claim-method", "statement": "The “limma” package in R software was used to examine the distinctions in molecular mechanisms between MMD and control samples, with the objective of pinpointing DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41036271", "locator": "sections[4] \"Batch effect correction and analysis of differentially expressed genes (DEGs)\" paragraph 2", "quote": "The “limma” package in R software was used to examine the distinctions in molecular mechanisms between MMD and control samples, with the objective of pinpointing DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author/s.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41036271", "locator": "sections[25] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author/s."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the limma package, 1,632 differentially expressed genes were identified, comprising 794 upregulated and 838 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41036271", "locator": "sections[14] \"DEGs identification and functional enrichment analysis\" paragraph 5", "quote": "Using the “limma” package, we identified 1,632 differentially expressed genes (Figures 1B,C). Based on the criteria of |logFoldChange(FC)|exceeding 0.585 and a p-value below 0.05, the expression levels of 794 genes were found to be upregulated, while those of 838 genes were downregulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the limma package, 1,632 differentially expressed genes were identified, comprising 794 upregulated and 838 downregulated genes.", "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:41036271"], "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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(B) The Western Blot experiment resul"], "order_basis": "paper_text_order:3817", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e the medium the next day. On the day before transfection, approximately 2.5 × 105 cells were seeded i", "pproximately 60–70%. Use Lipofectamine 3,000 transfection reagent (L3000150) (Thermo Fisher Scientific", "fresh medium and incubate for 3 days. After transfection, prepare each group as a cell suspension and", "e Western Blot experiment results showed the transfection efficiency of si-RNAs in HBVSMC. 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The cells are cultured in a 37°C, 5% CO2 cell culture incubator accord", "lture medium per well is 2 mL. The cells are cultured in a 37°C, 5% CO2 cell culture incubator acc"], "order_basis": "paper_text_order:10717", "id": "assay:4"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["serum were measured by ELISA assay. (B) The Western Blot experiment results showed the transfection e", "validated the transfection efficiency using Western Blot experiments and PCR (Figures 3B–D). 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