ArticleNucleic acids research2011
QDMR: a quantitative method for identification of differentially methylated regions by entropy.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 126 citations in OpenAlex.
- Decoding coupled epigenetic-fragmentomic signals in circulating cell-free DNA for interpretable cancer diagnosis.Genome medicine · 2026Article
- PlantDeepMeth: A Deep Learning Model for Predicting DNA Methylation States in Plants.Plants (Basel, Switzerland) · 2025Article
- Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer's Disease and Frontotemporal Dementia.International journal of molecular sciences · 2025Review
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- HBCR_DMR: A Hybrid Method Based on Beta-Binomial Bayesian Hierarchical Model and Combination of Ranking Method to Detect Differential Methylation Regions in Bisulfite Sequencing Data.Journal of personalized medicine · 2024Article
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- Differential methylation region detection via an array-adaptive normalized kernel-weighted model.PloS one · 2024Article
- Identification of colon cancer subtypes based on multi-omics data-construction of methylation markers for immunotherapy.Frontiers in oncology · 2024Article
- Age-related promoter-switch regulates Runx1 expression in adult rat hearts.BMC cardiovascular disorders · 2023Article
- The risk model construction of the genes regulated by H3K36me3 and H3K79me2 in breast cancer.Biophysics reports · 2023Article
- Review
- The impact of spatial correlation on methylation entropy with application to mouse brain methylome.Epigenetics & chromatin · 2023Article
- Methylome Imputation by Methylation Patterns.Methods in molecular biology (Clifton, N.J.) · 2023Article
- An evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays.Epigenetics · 2022Article
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- Article
- scMethBank: a database for single-cell whole genome DNA methylation maps.Nucleic acids research · 2022Article
- DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database.Nucleic acids research · 2022Article
- BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation Heterogeneity.Frontiers in bioinformatics · 2022Review
- Heterogeneity Analysis of Bladder Cancer Based on DNA Methylation Molecular Profiling.Frontiers in oncology · 2022Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impact of epigenetic modifications on heritable phenotypic variation. We present a quantitative approach, quantitative differentially methylated regions (QDMRs), to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. QDMR was applied to synthetic methylation patterns and methylation profiles detected by methylated DNA immunoprecipitation microarray (MeDIP-chip) in human tissues/cells. This approach can give a reasonable quantitative measure of methylation difference across multiple samples. Then DMR threshold was determined from methylation probability model. Using this threshold, QDMR identified 10,651 tissue DMRs which are related to the genes enriched for cell differentiation, including 4740 DMRs not identified by the method developed by Rakyan et al. QDMR can also measure the sample specificity of each DMR. Finally, the application to methylation profiles detected by reduced representation bisulphite sequencing (RRBS) in mouse showed the platform-free and species-free nature of QDMR. This approach provides an effective tool for the high-throughput identification of potential functional regions involved in epigenetic regulation.
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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.