The Effect of Vitamin D Deficiency on Immune-Related Hub Genes: A Network Analysis Associated With Type 1 Diabetes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39371824", "kind": "science-record", "revision": 3, "content_hash": "sha256:dce3902b29efa249f4bcf0e2e0398e18b0c8038920cba70da06cd0ba16b13c6e", "created_at": "2026-11-01T20:29:35Z", "updated_at": "2026-11-01T22:12:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Effect of Vitamin D Deficiency on Immune-Related Hub Genes: A Network Analysis Associated With Type 1 Diabetes.", "doi": "10.7759/cureus.68611", "pmid": "39371824", "authors": ["Safin Hussein", "Fatemeh Bandarian", "Najmeh Salehi", "Ali Mosadegh Khah", "Elahe Motevaseli", "Zahra Azizi"], "journal": "Cureus", "year": 2024, "abstract": "Background Type 1 diabetes (T1D) is an autoimmune disorder that results in the destruction of pancreatic beta cells, causing a shortage of insulin secretion. The development of T1D is influenced by both genetic predisposition and environmental factors, such as vitamin D. This vitamin is known for its ability to regulate the immune system and has been associated with a decreased risk of T1D. However, the specific ways in which vitamin D affects immune regulation and the preservation of beta cells in T1D are not yet fully understood. Gaining a better understanding of these interactions is essential for identifying potential targets for preventing and treating T1D. Methods The analysis focused on two Gene Expression Omnibus (GEO) datasets, namely, GSE55098 and GSE50012, to detect differentially expressed genes (DEGs). Enrichr (Ma'ayan Laboratory, New York, NY) was used to perform enrichment analysis for the Gene Ontology (GO) biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The Search Tool for the Retrieval of Interacting Genes 12.0 (STRING) database was used to generate a protein-protein interaction (PPI) network. The Cytoscape 3.10.1 (Cytoscape Team, San Diego, CA) was used to analyze the PPI network and discover the hub genes. Results The DEGs in both datasets were identified using the GEO2R tool, with a particular focus on genes exhibiting contrasting regulations. Enrichment analysis unveiled the participation of these oppositely regulated DEGs in processes relevant to the immune system. Cytoscape analysis of the PPI network revealed five hub genes, MNDA, LILRB2, FPR2, HCK, and FCGR2A, suggesting their potential role in the pathogenesis of T1D and the response to vitamin D. Conclusion The study elucidates the complex interaction between vitamin D metabolism and immune regulation in T1D. The identified hub genes provide important knowledge on the molecular pathways that underlie T1D and have the potential to be targeted for therapeutic intervention. This research underscores the importance of vitamin D in the immune system's modulation and its impact on T1D development.", "claims": [{"id": "claim-method", "statement": "The GEO2R tool was utilized to identify DEGs in both datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39371824", "locator": "sections[2] \"Materials and methods\" paragraph 8", "quote": "The GEO2R tool was utilized to identify DEGs in both datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE55098, based on the GPL570 platform, was composed of newly diagnosed 12 T1D samples and 10 normal control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39371824", "locator": "sections[2] \"Materials and methods\" paragraph 6", "quote": "The GSE55098, based on the GPL570 platform, was composed of newly diagnosed 12 T1D samples and 10 normal control samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Cytoscape analysis of the PPI network revealed five hub genes, MNDA, LILRB2, FPR2, HCK, and FCGR2A, suggesting their potential role in the pathogenesis of T1D and the response to vitamin D.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39371824", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "Cytoscape analysis of the PPI network revealed five hub genes, MNDA, LILRB2, FPR2, HCK, and FCGR2A, suggesting their potential role in the pathogenesis of T1D and the response to vitamin D."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Cytoscape analysis of the PPI network revealed five hub genes, MNDA, LILRB2, FPR2, HCK, and FCGR2A, suggesting their potential role in the pathogenesis of T1D and the response to vitamin D.", "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:39371824"], "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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