ArticleBioinformatics (Oxford, England)2019
Differential methylation values in differential methylation analysis.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-treatment DNA Methylation From Peripheral Blood.International journal of radiation oncology, biology, physics · 2023Trial
- SOPA and SIMPA: normalized single-sample integrated multiomics pathway analysis of tumor heterogeneity in solid cancers.Briefings in bioinformatics · 2026Article
- Continuous DNA methylation deconvolution-based surrogate for B-cell differentiation state in chronic lymphocytic leukemia.Communications medicine · 2026Article
- Epigenetic biomarkers in inflammatory bowel diseases-computational challenges and opportunities.Journal of Crohn's & colitis · 2026Review
- The genetic basis for DNA methylation variation across tissues and development.Nature communications · 2026Article
- Global impact of germline structural variation on the cancer proteome.Nature communications · 2026Article
- Differential DNA Methylation of the Brain-Derived Neurotrophic Factor Gene is Observed after Pediatric Traumatic Brain Injury Compared with Orthopedic Injury.Journal of neurotrauma · 2026Article
- Interplay of the nasal microbiome and epigenome among adolescents.Clinical epigenetics · 2026Article
- Preliminary insights into methylation patterns in Agent Orange exposed thyroid cancers: a pilot study.Environmental pollution (Barking, Essex : 1987) · 2026Article
- Associations of arsenic exposure and folate in maternal leukocyte DNA methylation: a case-control study of mothers with spina-bifida affected children.Environmental health : a global access science source · 2026Article
- Article
- Continuous DNA Methylation Deconvolution-Based Surrogate for B-Cell Differentiation State in CLL.bioRxiv : the preprint server for biology · 2025Article
- DNA methylation associations with cognitive function in early-stage hormone receptor-positive breast cancer patients.Epigenomics · 2025Article
- Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors.Nature communications · 2025Article
- Differential DNA methylation 7 months after SARS-CoV-2 infection.Clinical epigenetics · 2025Article
- Deciphering FOXM1 regulation: implications for stemness and metabolic adaptations in glioblastoma.Medical oncology (Northwood, London, England) · 2025Article
- Epigenetic signatures of phthalate exposure and potential risks: a DNA methylation analysis using Infinium MethylationEPIC BeadChip.Environmental epigenetics · 2025Article
- DNA Methylation Biomarker Discovery for Colorectal Cancer Diagnosis Assistance Through Integrated Analysis.Cancer informatics · 2025Article
- Profiling Genome-Wide Methylation Patterns in Cattle Infected withInternational journal of molecular sciences · 2024Article
- Prenatal exposure to genocide and subsequent adverse childhood events are associated with DNA methylation of SLC6A4, BDNF, and PRDM8 in early adulthood in Rwanda.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationBoth β-value and M-value have been used as metrics to measure methylation levels. The M-value is more statistically valid for the differential analysis of methylation levels. However, the β-value is much more biologically interpretable and needs to be reported when M-value method is used for conducting differential methylation analysis. There is an urgent need to know how to interpret the degree of differential methylation from the M-value. In M-value linear regression model, differential methylation M-value ΔM can be easily obtained from the coefficient estimate, but it is not straightforward to get the differential methylation β-value, Δβ since it cannot be obtained from the coefficient alone.
resultsTo fill the gap, we have built a bridge to connect the statistically sound M-value linear regression model and the biologically interpretable Δβ. In this article, three methods were proposed to calculate differential methylation values, Δβ from M-value linear regression model and compared with the Δβ directly obtained from β-value linear regression model. We showed that under the condition that M-value linear regression model is correct, the method M-model-coef is the best among the four methods. M-model-M-mean method works very well too. If the coefficients α0, α2,…αp are not given (as 'MethLAB' package), the M-model-M-mean method should be used. The Δβ directly obtained from β-value linear regression model can give very biased results, especially when M-values are not in (-2, 2) or β-values are not in (0.2, 0.8). AVAILABILITY AND IMPLEMENTATION: The dataset for example is available at the National Center for Biotechnology Information Gene Expression Omnibus repository, GSE104778. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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