ArticleBMC genomics2017
Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it, 42 citations in OpenAlex.
- Association of vitamin D receptor TaqI and ApaI genetic polymorphisms with nephrolithiasis and end stage renal disease: a meta-analysis.BMC medical genetics · 2019Pooled it
- Vitamin D and Acute Kidney Injury: A Reciprocal Relationship.Biomolecules · 2025Review
- Vitamin D Receptor Regulates the Expression of the Grainyhead-Like 1 Gene.International journal of molecular sciences · 2024Article
- Potential treatment of squamous cell carcinoma by targeting heparin-binding protein 17/fibroblast growth factor-binding protein 1 with vitamin DIn vitro cellular & developmental biology. Animal · 2024Review
- VDR is a potential prognostic biomarker and positively correlated with immune infiltration: a comprehensive pan-cancer analysis with experimental verification.Bioscience reports · 2024Article
- Vitamin D status associates with skeletal muscle loss after anterior cruciate ligament reconstruction.JCI insight · 2023Article
- Role of Vitamin D in Head and Neck Cancer-Immune Function, Anti-Tumour Effect, and Its Impact on Patient Prognosis.Nutrients · 2023Review
- Vitamin D and Systems Biology.Nutrients · 2022Review
- Nongenomic Activities of Vitamin D.Nutrients · 2022Review
- Pleiotropic Effects of Vitamin D in Patients with Inflammatory Bowel Diseases.Journal of clinical medicine · 2022Review
- [Identification of microRNAs targeting vitamin D receptor and their effect on parathyroid hormone secretion in secondary hyperparathyroidism].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2022Article
- Progress in the Relationship between Vitamin D Deficiency and the Incidence of Type 1 Diabetes Mellitus in Children.Journal of diabetes research · 2022Review
- Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci.Science immunology · 2021Article
- Influence of Vitamin D on Islet Autoimmunity and Beta-Cell Function in Type 1 Diabetes.Nutrients · 2019Review
- Ancient Nuclear Receptor VDR With New Functions: Microbiome and Inflammation.Inflammatory bowel diseases · 2018Review
- Nuclear receptors in cancer - uncovering new and evolving roles through genomic analysis.Nature reviews. Genetics · 2018Review
- Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D.Journal of molecular endocrinology · 2018Article
- Regulation of Microbiota by Vitamin D Receptor: A Nuclear Weapon in Metabolic Diseases.Nuclear receptor research · 2018Article
- Genomic Effects of the Vitamin D Receptor: Potentially the Link between Vitamin D, Immune Cells, and Multiple Sclerosis.Frontiers in immunology · 2018Review
- Vitamin D Receptor Signaling and Cancer.Endocrinology and metabolism clinics of North America · 2017Review
Corrections and comments
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Authors and funding
12 authors at 6 institutions in 4 countries.
Funding
Abstract
backgroundThe nuclear hormone receptor superfamily acts as a genomic sensor of diverse signals. Their actions are often intertwined with other transcription factors. Nuclear hormone receptors are targets for many therapeutic drugs, and include the vitamin D receptor (VDR). VDR signaling is pleotropic, being implicated in calcaemic function, antibacterial actions, growth control, immunomodulation and anti-cancer actions. Specifically, we hypothesized that the biologically significant relationships between the VDR transcriptome and phenotype-associated biology could be discovered by integrating the known VDR transcription factor binding sites and all published trait- and disease-associated SNPs. By integrating VDR genome-wide binding data (ChIP-seq) with the National Human Genome Research Institute (NHGRI) GWAS catalog of SNPs we would see where and which target gene interactions and pathways are impacted by inherited genetic variation in VDR binding sites, indicating which of VDR's multiple functions are most biologically significant.
resultsTo examine how genetic variation impacts VDR function we overlapped 23,409 VDR genomic binding peaks from six VDR ChIP-seq datasets with 191,482 SNPs, derived from GWAS-significant SNPs (Lead SNPs) and their correlated variants (r
conclusionsThese analyses showed that VDR peaks are enriched for SNPs associated with immune phenotypes suggesting that VDR immunomodulatory functions are amongst its most important actions. The enrichment of genetic variation in non-DR3 motifs suggests a significant role for the VDR to bind in multimeric complexes containing other transcription factors that are the primary DNA binding component. Our work provides a framework for the combination of ChIP-seq and GWAS findings to provide insight into the underlying phenotype-associated biology of a given transcription factor.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.