ArticleNucleic acids research2022
MethReg: estimating the regulatory potential of DNA methylation in gene transcription.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it, 26 citations in OpenAlex.
- DNA methylation signatures of bilateral hippocampal volume, asymmetry and atrophy: a cross-omics analysis in the general population.EBioMedicine · 2026Pooled it
- Prenatal PMNature communications · 2026Article
- MeDReaders 2.0: an updated database for modified DNA readers.BMC genomics · 2026Article
- Epigenomic study of the lower airway reveals COPD-associated methylation patterns and potential microbiota links.BMJ open respiratory research · 2025Article
- Systematic identification of regions where DNA methylation is correlated with transcription refines regulatory logic in normal and tumour tissues.Nucleic acids research · 2025Article
- Gradual DNA methylation changes reveal transcription factors implicated in metabolic dysfunction-associated steatotic liver disease progression and epigenetic age acceleration.Clinical epigenetics · 2025Article
- GAIN-BRCA: a graph-based AI-net framework for breast cancer subtype classification using multiomics data.Bioinformatics advances · 2025Article
- Dust mite antigens endow dendritic cells with the capacity to induce a Th2 response by regulating their methylation profiles.Cell communication and signaling : CCS · 2024Article
- Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays.Epigenetics · 2024Article
- Article
- Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays.Research square · 2023Article
- Distinct CSF biomarker-associated DNA methylation in Alzheimer's disease and cognitively normal subjects.Alzheimer's research & therapy · 2023Article
- Distinct CSF biomarker-associated DNA methylation in Alzheimer's disease and cognitively normal subjects.Research square · 2023Article
- CanMethdb: a database for genome-wide DNA methylation annotation in cancers.Bioinformatics (Oxford, England) · 2023Article
- Cancer stem/progenitor signatures refine the classification of clear cell renal cell carcinoma with stratified prognosis and decreased immunotherapy efficacy.Molecular therapy oncolytics · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Epigenome-wide association studies often detect many differentially methylated sites, and many are located in distal regulatory regions. To further prioritize these significant sites, there is a critical need to better understand the functional impact of CpG methylation. Recent studies demonstrated that CpG methylation-dependent transcriptional regulation is a widespread phenomenon. Here, we present MethReg, an R/Bioconductor package that analyzes matched DNA methylation and gene expression data, along with external transcription factor (TF) binding information, to evaluate, prioritize and annotate CpG sites with high regulatory potential. At these CpG sites, TF-target gene associations are often only present in a subset of samples with high (or low) methylation levels, so they can be missed by analyses that use all samples. Using colorectal cancer and Alzheimer's disease datasets, we show MethReg significantly enhances our understanding of the regulatory roles of DNA methylation in complex diseases.
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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.