ReviewBriefings in bioinformatics2019
An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays.
Review in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers, 7 of them syntheses that pooled 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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
72 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- Epigenetic and blood markers associated with response to electroconvulsive therapy in patients with depressive disorders.Translational psychiatry · 2025Pooled it
- Sex effects on DNA methylation affect discovery in epigenome-wide association study of schizophrenia.Molecular psychiatry · 2024Pooled it
- In utero exposure to diethylstilbestrol and blood DNA methylation in adult women: Results from a meta-analysis of two cohort studies.Environmental research · 2023Pooled it
- Distinct sex-specific DNA methylation differences in Alzheimer's disease.Alzheimer's research & therapy · 2022Pooled it
- Longitudinal associations of DNA methylation and sleep in children: a meta-analysis.Clinical epigenetics · 2022Pooled it
- The applications of DNA methylation as a biomarker in kidney transplantation: a systematic review.Clinical epigenetics · 2022Pooled it
- Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer's disease.Nature communications · 2020Pooled it
- Epigenetic markers of response to psychotherapy in obsessive-compulsive disorder.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- Longitudinal Blood DNA Methylation Changes During Weight-Loss Intervention and Dementia Progression Risk.Research square · 2026Article
- Novel epigenetic loci identified from an epigenome-wide association study underlying brain structural changes in bipolar disorder.Psychological medicine · 2026Article
- DNA methylation signature of cognitive reserve moderates CSF tau pathology in prodromal Alzheimer's disease.Research square · 2026Article
- ReMeDy: A Flexible Statistical Framework For Region-based Detection of DNA Methylation Dysregulation.bioRxiv : the preprint server for biology · 2026Article
- DNA methylation signatures of Life's Essential 8 and their implications for dementia.Alzheimer's research & therapy · 2025Article
- Maternal asthma and newborn DNA methylation.Clinical epigenetics · 2025Article
- DNA methylation signature of a lifestyle-based resilience index for cognitive health.Alzheimer's research & therapy · 2025Article
- Type 2 diabetes impacts DNA methylation in human sperm.Clinical epigenetics · 2025Article
- Blood DNA methylation signature for incident dementia: Evidence from longitudinal cohorts.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Hypermethylation ofJournal of the American Heart Association · 2025Article
- Causality-driven candidate identification for reliable DNA methylation biomarker discovery.Nature communications · 2025Article
- Immediate and durable effects of maternal tobacco consumption on placental DNA methylation: a replication and discovery study.Environmental epigenetics · 2025Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Epigenome-wide association studies (EWASs) have become increasingly popular for studying DNA methylation (DNAm) variations in complex diseases. The Illumina methylation arrays provide an economical, high-throughput and comprehensive platform for measuring methylation status in EWASs. A number of software tools have been developed for identifying disease-associated differentially methylated regions (DMRs) in the epigenome. However, in practice, we found these tools typically had multiple parameter settings that needed to be specified and the performance of the software tools under different parameters was often unclear. To help users better understand and choose optimal parameter settings when using DNAm analysis tools, we conducted a comprehensive evaluation of 4 popular DMR analysis tools under 60 different parameter settings. In addition to evaluating power, precision, area under precision-recall curve, Matthews correlation coefficient, F1 score and type I error rate, we also compared several additional characteristics of the analysis results, including the size of the DMRs, overlap between the methods and execution time. The results showed that none of the software tools performed best under their default parameter settings, and power varied widely when parameters were changed. Overall, the precision of these software tools were good. In contrast, all methods lacked power when effect size was consistent but small. Across all simulation scenarios, comb-p consistently had the best sensitivity as well as good control of false-positive rate.
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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.