Evidence map›Paper›PMID 20736230›Full record

ArticleGenome research2010

A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution.

Sreeram V Ramagopalan, Andreas Heger, Antonio J Berlanga, Narelle J Maugeri, Matthew R Lincoln, Amy Burrell, Lahiru Handunnetthi, Adam E Handel, Giulio Disanto, Sarah-Michelle Orton and 6 more

Registry-linked trialOpen access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT02803476 (Is There An Association Between Vitamin D Levels And Insulin Resistance In Polycystic Ovary Syndrome?), which is not on this map. Cited by 399 papers, 7 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
399citing papers in PubMed, 7 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

NCT02803476 unknown statusnot on this mapstarted 2016, after this paper: background citation

Is There An Association Between Vitamin D Levels And Insulin Resistance In Polycystic Ovary Syndrome?

TypeobservationalSponsorAin Shams Maternity HospitalRan2016 to 2016Enrolled166ConditionsPolycystic Ovary Syndrome, Insulin Resistance, Vitamin D Deficiency
3 · Its place in the literature

Who cites it

399 citing papers in PubMed, 7 syntheses or guidelines pooled it, 876 citations in OpenAlex.

  1. Polymorphisms inNutrients · 2023
    Pooled it
  2. Pooled it
  3. Pooled it
  4. Pooled it
  5. Pooled it
  6. Pooled it
  7. Pooled it
  8. Trial
  9. Trial
  10. Trial
  11. Trial
  12. Trial
  13. Trial
  14. Trial
  15. Vitamin DBMC cardiovascular disorders · 2017
    Trial
  16. High-Dose Vitamin DAmerican journal of respiratory and critical care medicine · 2017
    Trial
  17. Vitamin DObesity surgery · 2017
    Trial
  18. Trial
  19. Review
  20. Review

339 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors at 4 institutions in 2 countries.

Sreeram V RamagopalanWellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom. sreeramr@well.ox.ac.uk
Andreas Heger
Antonio J Berlanga
Narelle J Maugeri
Matthew R Lincoln
Amy Burrell
Lahiru Handunnetthi
Adam E Handel
Giulio Disanto
Sarah-Michelle Orton
Corey T Watson
Julia M Morahan
Gavin Giovannoni
Chris P Ponting
George C Ebers
Julian C Knight
Centre for Human Genetics · GBUniversity of Oxford · GBQueen Mary University of London · GBSimon Fraser University · CA

Funding

Medical Research Council MC_U137761446Multiple Sclerosis Society 875Wellcome Trust 074318Wellcome Trust 075491/Z/04
6 · The paper itself

Abstract

Initially thought to play a restricted role in calcium homeostasis, the pleiotropic actions of vitamin D in biology and their clinical significance are only now becoming apparent. However, the mode of action of vitamin D, through its cognate nuclear vitamin D receptor (VDR), and its contribution to diverse disorders, remain poorly understood. We determined VDR binding throughout the human genome using chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq). After calcitriol stimulation, we identified 2776 genomic positions occupied by the VDR and 229 genes with significant changes in expression in response to vitamin D. VDR binding sites were significantly enriched near autoimmune and cancer associated genes identified from genome-wide association (GWA) studies. Notable genes with VDR binding included IRF8, associated with MS, and PTPN2 associated with Crohn's disease and T1D. Furthermore, a number of single nucleotide polymorphism associations from GWA were located directly within VDR binding intervals, for example, rs13385731 associated with SLE and rs947474 associated with T1D. We also observed significant enrichment of VDR intervals within regions of positive selection among individuals of Asian and European descent. ChIP-seq determination of transcription factor binding, in combination with GWA data, provides a powerful approach to further understanding the molecular bases of complex diseases.

Indexed as

Chromatin ImmunoprecipitationEvolution, MolecularGenome-Wide Association StudyAutoimmune DiseasesBinding SitesCrohn DiseaseDiabetes Mellitus, Type 1HumansInterferon Regulatory Factor-8Interferon Regulatory FactorsMultiple SclerosisProtein BindingProtein Tyrosine Phosphatase, Non-Receptor Type 2Receptors, CalcitriolSequence Analysis, DNAVitamin DInterferon Regulatory Factor-8Interferon Regulatory FactorsProtein Tyrosine Phosphatase, Non-Receptor Type 2PTPN2 protein, humanReceptors, CalcitriolVitamin D

Identifiers

PMID20736230
PMCPMC2945184
OpenAlexW2138258120

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.