ArticleNucleic acids research2013
Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 2 of them syntheses that pooled it.
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Who cites it
64 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes.Acta neuropathologica · 2023Pooled 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
- The interaction between a leflunomide-response methylation site (cg17330251) and variant (rs705379) on response to leflunomide in patients with rheumatoid arthritis.Frontiers in pharmacology · 2025Article
- Article
- The contribution of DNA methylation to the (dys)function of oligodendroglia in neurodegeneration.Acta neuropathologica communications · 2023Review
- Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts.Clinical epigenetics · 2023Article
- Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli.G3 (Bethesda, Md.) · 2023Article
- Large-scale integration of DNA methylation and gene expression array platforms identifies bothEpigenetics · 2022Article
- Making sense of the ageing methylome.Nature reviews. Genetics · 2022Review
- Article
- Review
- Epigenome-Wide DNA Methylation Profiling of Normal Mucosa Reveals HLA-F Hypermethylation as a Biomarker Candidate for Serrated Polyposis Syndrome.The Journal of molecular diagnostics : JMD · 2022Article
- Testing differentially methylated regions through functional principal component analysis.Journal of applied statistics · 2022Article
- Neurodegenerative movement disorders: An epigenetics perspective and promise for the future.Neuropathology and applied neurobiology · 2021Review
- Skeletal muscle methylome and transcriptome integration reveals profound sex differences related to muscle function and substrate metabolism.Clinical epigenetics · 2021Article
- Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in aCancer research · 2021Article
- MOBP and HIP1 in multiple system atrophy: New α-synuclein partners in glial cytoplasmic inclusions implicated in the disease pathogenesis.Neuropathology and applied neurobiology · 2021Article
- DNA methylation and cancer incidence: lymphatic-hematopoietic versus solid cancers in the Strong Heart Study.Clinical epigenetics · 2021Article
- Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling.Epigenetics & chromatin · 2021Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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4 authors.
Funding
Abstract
Methylation of the CpG-rich region (CpG island) overlapping a gene's promoter is a generally accepted mechanism for silencing expression. While recent technological advances have enabled measurement of DNA methylation and expression changes genome-wide, only modest correlations between differential methylation at gene promoters and expression have been found. We hypothesize that stronger associations are not observed because existing analysis methods oversimplify their representation of the data and do not capture the diversity of existing methylation patterns. Recently, other patterns such as CpG island shore methylation and long partially hypomethylated domains have also been linked with gene silencing. Here, we detail a new approach for discovering differential methylation patterns associated with expression change using genome-wide high-resolution methylation data: we represent differential methylation as an interpolated curve, or signature, and then identify groups of genes with similarly shaped signatures and corresponding expression changes. Our technique uncovers a diverse set of patterns that are conserved across embryonic stem cell and cancer data sets. Overall, we find strong associations between these methylation patterns and expression. We further show that an extension of our method also outperforms other approaches by generating a longer list of genes with higher quality associations between differential methylation and expression.
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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.