ArticleBioinformatics (Oxford, England)2014
PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.The Journal of clinical investigation · 2022Article
- BCurve: Bayesian Curve Credible Bands Approach for the Detection of Differentially Methylated Regions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Epigenetic Silencing of STAT3-Targeted miR-193a, by Constitutive Activation of JAK/STAT Signaling, Leads to Tumor Progression Through Overexpression of YWHAZ in Gastric Cancer.Frontiers in oncology · 2021Article
- Environmental Factor-Mediated Transgenerational Inheritance ofFrontiers in immunology · 2020Article
- A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction.BMC bioinformatics · 2019Article
- TET1 reprograms the epithelial ovarian cancer epigenome and reveals casein kinase 2α as a therapeutic target.The Journal of pathology · 2019Article
- cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.Nucleic acids research · 2017Article
- Statistical methods for detecting differentially methylated regions based on MethylCap-seq data.Briefings in bioinformatics · 2016Review
- Statistical challenges in analyzing methylation and long-range chromosomal interaction data.Statistics in biosciences · 2016Article
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Authors and funding
12 authors.
Funding
Abstract
motivationDNA methylation is an epigenetic change occurring in genomic CpG sequences that contribute to the regulation of gene transcription both in normal and malignant cells. Next-generation sequencing has been used to characterize DNA methylation status at the genome scale, but suffers from high sequencing cost in the case of whole-genome bisulfite sequencing, or from reduced resolution (inability to precisely define which of the CpGs are methylated) with capture-based techniques.
resultsHere we present a computational method that computes nucleotide-resolution methylation values from capture-based data by incorporating fragment length profiles into a model of methylation analysis. We demonstrate that it compares favorably with nucleotide-resolution bisulfite sequencing and has better predictive power with respect to a reference than window-based methods, often used for enrichment data. The described method was used to produce the methylation data used in tandem with gene expression to produce a novel and clinically significant gene signature in acute myeloid leukemia. In addition, we introduce a complementary statistical method that uses this nucleotide-resolution methylation data for detection of differentially methylated features.
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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.