ArticleNucleic acids research2017
Modeling complex patterns of differential DNA methylation that associate with gene expression changes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis 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
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of genome-wide DNA methylation and integrative omics of age in human skeletal muscle.Journal of cachexia, sarcopenia and muscle · 2021Pooled it
- Integration of DNA methylation and gene expression analysis in Gephyrocapsa huxleyi provides insight into genes related to calcification.G3 (Bethesda, Md.) · 2026Article
- Comprehensive Exploration of NOTCH2NLA Across Cancers and Its Potential Roles in Prognosis and Immune System Interactions.Current medicinal chemistry · 2026Article
- Systematic identification of regions where DNA methylation is correlated with transcription refines regulatory logic in normal and tumour tissues.Nucleic acids research · 2025Article
- ETV2/ER71 regulates hematovascular lineage generation and vascularization through an H3K9 demethylase, KDM4A.iScience · 2025Article
- Article
- Development of an epigenetic clock resistant to changes in immune cell composition.Communications biology · 2024Article
- MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer data.Nature communications · 2024Article
- Article
- Large-scale integration of DNA methylation and gene expression array platforms identifies bothEpigenetics · 2022Article
- Making sense of the ageing methylome.Nature reviews. Genetics · 2022Review
- Skeletal muscle methylome and transcriptome integration reveals profound sex differences related to muscle function and substrate metabolism.Clinical epigenetics · 2021Article
- Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM.Nucleic acids research · 2021Article
- Single-nucleotide methylation specifically represses type I interferon in antiviral innate immunity.The Journal of experimental medicine · 2021Article
- DNA methylation and cancer incidence: lymphatic-hematopoietic versus solid cancers in the Strong Heart Study.Clinical epigenetics · 2021Article
- Cellular Heterogeneity-Adjusted cLonal Methylation (CHALM) improves prediction of gene expression.Nature communications · 2021Article
- Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data.Genome biology · 2020Article
- ICGEC: a comparative method for measuring epigenetic conservation of genes via the integrated signal from multiple histone modifications between cell types.BMC genomics · 2020Article
- Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members.Nucleic acids research · 2020Article
- Resistin expression in human monocytes is controlled by two linked promoter SNPs mediating NFKB p50/p50 binding and C-methylation.Scientific reports · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Numerous genomic studies are underway to determine which genes are abnormally regulated by DNA methylation in disease. However, we have a poor understanding of how disease-specific methylation changes affect expression. We thus developed an integrative analysis tool, Methylation-based Gene Expression Classification (ME-Class), to explain specific variation in methylation that associates with expression change. This model captures the complexity of methylation changes around a gene promoter. Using 17 whole-genome bisulfite sequencing and RNA-seq datasets from different tissues from the Roadmap Epigenomics Project, ME-Class significantly outperforms standard methods using methylation to predict differential gene expression change. To demonstrate its utility, we used ME-Class to analyze 32 datasets from different hematopoietic cell types from the Blueprint Epigenome project. Expression-associated methylation changes were predominantly found when comparing cells from distantly related lineages, implying that changes in the cell's transcriptional program precede associated methylation changes. Training ME-Class on normal-tumor pairs from The Cancer Genome Atlas indicated that cancer-specific expression-associated methylation changes differ from tissue-specific changes. We further show that ME-Class can detect functionally relevant cancer-specific, expression-associated methylation changes that are reversed upon the removal of methylation. ME-Class is thus a powerful tool to identify genes that are dysregulated by DNA methylation in disease.
Indexed as
Identifiers
What OpenQuestion holds
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.