ArticleBioinformatics (Oxford, England)2016
seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Effects of alcohol on the transcriptome, methylome and metabolome of in vitro gastrulating human embryonic cells.Disease models & mechanisms · 2025Article
- Genome-wide DNA methylation and gene expression in human placentas derived from assisted reproductive technology.Communications medicine · 2024Article
- MethylCallR : a comprehensive analysis framework for Illumina Methylation Beadchip.Scientific reports · 2024Article
- Gbdmr: identifying differentially methylated CpG regions in the human genome via generalized beta regressions.BMC bioinformatics · 2024Article
- A novel approach toward optimal workflow selection for DNA methylation biomarker discovery.BMC bioinformatics · 2024Article
- Article
- Chromatin modifier developmental pluripotency associated factor 4 (DPPA4) is a candidate gene for alcohol-induced developmental disorders.BMC medicine · 2022Article
- Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses.Bioinformatics (Oxford, England) · 2022Article
- Maternal haemoglobin levels in pregnancy and child DNA methylation: a study in the pregnancy and childhood epigenetics consortium.Epigenetics · 2022Article
- Article
- Blood lead levels in Peruvian adults are associated with proximity to mining and DNA methylation.Environment international · 2021Article
- Identification of two methylated fragments of an SDC2 CpG island using a sliding window technique for early detection of colorectal cancer.FEBS open bio · 2021Article
- Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization.Experimental & molecular medicine · 2021Review
- Article
- MADA: a web service for analysing DNA methylation array data.BMC bioinformatics · 2020Article
- Identification of methylation states of DNA regions for Illumina methylation BeadChip.BMC genomics · 2020Article
- Genome-Wide DNA Methylation Patterns in Children Exposed to Nonpharmacologically Treated Prenatal Depressive Symptoms: Results From 2 Independent Cohorts.Epigenetics insights · 2020Article
- coMethDMR: accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies with continuous phenotypes.Nucleic acids research · 2019Article
- Genome-wide DNA methylation profiling in ectopic and eutopic of endometrial tissues.Journal of assisted reproduction and genetics · 2019Article
- Association of dietary folate and vitamin B-12 intake with genome-wide DNA methylation in blood: a large-scale epigenome-wide association analysis in 5841 individuals.The American journal of clinical nutrition · 2019Article
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Authors and funding
5 authors.
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Abstract
motivationOne of the main goals of large scale methylation studies is to detect differentially methylated loci. One way is to approach this problem sitewise, i.e. to find differentially methylated positions (DMPs). However, it has been shown that methylation is regulated in longer genomic regions. So it is more desirable to identify differentially methylated regions (DMRs) instead of DMPs. The new high coverage arrays, like Illuminas 450k platform, make it possible at a reasonable cost. Few tools exist for DMR identification from this type of data, but there is no standard approach.
resultsWe propose a novel method for DMR identification that detects the region boundaries according to the minimum description length (MDL) principle, essentially solving the problem of model selection. The significance of the regions is established using linear mixed models. Using both simulated and large publicly available methylation datasets, we compare seqlm performance to alternative approaches. We demonstrate that it is both more sensitive and specific than competing methods. This is achieved with minimal parameter tuning and, surprisingly, quickest running time of all the tried methods. Finally, we show that the regional differential methylation patterns identified on sparse array data are confirmed by higher resolution sequencing approaches. AVAILABILITY AND IMPLEMENTATION: The methods have been implemented in R package seqlm that is available through Github: https://github.com/raivokolde/seqlm CONTACT: rkolde@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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