ArticleEpigenetics & chromatin2015
De novo identification of differentially methylated regions in the human genome.
Article in Epigenetics & chromatin, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 606 papers, 4 of them syntheses that pooled it.
What it found
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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.
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Who cites it
606 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Road traffic noise exposure and blood DNA methylation at birth and in childhood: An epigenome-wide meta-analysis.Environment international · 2026Pooled it
- Genome- and epigenome-wide association studies identify susceptibility of CpG sites and regions for metabolic syndrome in a Korean population.Clinical epigenetics · 2024Pooled it
- Epigenome-wide meta-analysis of prenatal maternal stressful life events and newborn DNA methylation.Molecular psychiatry · 2023Pooled it
- Sex differences in muscle protein expression and DNA methylation in response to exercise training.Biology of sex differences · 2023Pooled it
- Heat exposure during susceptible windows of spermatogenesis and sperm epigenetic age.Human reproduction (Oxford, England) · 2026Trial
- Medicinal cannabis plant extract (NTI164) modifies epigenetic, ribosomal, and immune pathways in paediatric acute-onset neuropsychiatric syndrome.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2026Trial
- Aberrant DNA methylation within circadian entrainment and clock genes two years after pediatric critical illness is associated with impaired physical and neurocognitive development.Clinical epigenetics · 2025Trial
- An epigenome-wide study of a needs-based family intervention for offspring of trauma-exposed mothers in Kosovo.Brain and behavior · 2024Trial
- Assessment of aberrant DNA methylation two years after paediatric critical illness: a pre-planned secondary analysis of the international PEPaNIC trial.Epigenetics · 2023Trial
- Non-parametric differential methylation analysis characterizes histotype-specific promoter regions in epithelial ovarian cancer.Epigenetics · 2026Article
- Hypertension-associated DNA methylation signatures and multi-generational epigenetic clocks in Korean adults.GeroScience · 2026Article
- DNA methylation signatures in skeletal muscle associated with physical function in healthy older adults.GeroScience · 2026Article
- Epigenetic Insights in Pediatric Multiple Sclerosis: DNA Methylation Highlights an Involvement of Epstein-Barr Virus Infection and Host Immune Networks.Neurology(R) neuroimmunology & neuroinflammation · 2026Article
- Clinical Epigenomics in Rare Diseases: Interpreting DNA Methylation Episignatures.Molecular genetics & genomic medicine · 2026Review
- Investigating the role of CpG islands and DNA methylation at 3'UTRs in cancer.Life science alliance · 2026Article
- DNA methylation variability provides a complementary epigenetic signature of aging heterogeneity: Findings from the Canadian Longitudinal Study on Aging and the Baltimore Longitudinal Study of Aging.bioRxiv : the preprint server for biology · 2026Article
- Cross-Scale Convergence in Epigenetic Gene Regulation: A Perspective on Functional Enrichment Analytics for Cancer.Current issues in molecular biology · 2026Article
- DNA methylation-derived age acceleration reveals neurodevelopmental and stress-linked pathways in depression and suicide.Journal of affective disorders · 2026Article
- The length of the embryo culture in assisted reproductive technology does not have a major impact on newborn DNA methylation.Bioscience reports · 2026Article
- Genome-wide DNA methylation analysis of pediatric medulloblastomas from a Brazilian cohort: an exploratory study.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
546 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe identification and characterisation of differentially methylated regions (DMRs) between phenotypes in the human genome is of prime interest in epigenetics. We present a novel method, DMRcate, that fits replicated methylation measurements from the Illumina HM450K BeadChip (or 450K array) spatially across the genome using a Gaussian kernel. DMRcate identifies and ranks the most differentially methylated regions across the genome based on tunable kernel smoothing of the differential methylation (DM) signal. The method is agnostic to both genomic annotation and local change in the direction of the DM signal, removes the bias incurred from irregularly spaced methylation sites, and assigns significance to each DMR called via comparison to a null model.
resultsWe show that, for both simulated and real data, the predictive performance of DMRcate is superior to those of Bumphunter and Probe Lasso, and commensurate with that of comb-p. For the real data, we validate all array-derived DMRs from the candidate methods on a suite of DMRs derived from whole-genome bisulfite sequencing called from the same DNA samples, using two separate phenotype comparisons.
conclusionsThe agglomeration of genomically localised individual methylation sites into discrete DMRs is currently best served by a combination of DM-signal smoothing and subsequent threshold specification. The findings also suggest the design of the 450K array shows preference for CpG sites that are more likely to be differentially methylated, but its overall coverage does not adequately reflect the depth and complexity of methylation signatures afforded by sequencing. For the convenience of the research community we have created a user-friendly R software package called DMRcate, downloadable from Bioconductor and compatible with existing preprocessing packages, which allows others to apply the same DMR-finding method on 450K array data.
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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.