DNA methylation analysis techniques

C Dahl, P Guldberg - Biogerontology, 2003 - Springer
DNA methylation contributes to the control of gene expression and plays an essential role in
cellular physiology. Well-defined patterns of DNA methylation are established and fixed …

Review of processing and analysis methods for DNA methylation array data

CS Wilhelm-Benartzi, DC Koestler, MR Karagas… - British journal of …, 2013 - nature.com
The promise of epigenome-wide association studies and cancer-specific somatic DNA
methylation changes in improving our understanding of cancer, coupled with the decreasing …

An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies

K McGregor, S Bernatsky, I Colmegna, M Hudson… - Genome biology, 2016 - Springer
Background Many different methods exist to adjust for variability in cell-type mixture
proportions when analyzing DNA methylation studies. Here we present the result of an …

Introduction to single-cell DNA methylation profiling methods

J Ahn, S Heo, J Lee, D Bang - Biomolecules, 2021 - mdpi.com
DNA methylation is an epigenetic mechanism that is related to mammalian cellular
differentiation, gene expression regulation, and disease. In several studies, DNA …

Tools and strategies for analysis of genome-wide and gene-specific DNA methylation patterns

A Chatterjee, EJ Rodger, IM Morison… - Oral biology: molecular …, 2017 - Springer
DNA methylation is a stable epigenetic mechanism that has important roles in the normal
function of a cell and therefore also in disease etiology. Accurate measurements of normal …

MethylMix 2.0: an R package for identifying DNA methylation genes

PL Cedoz, M Prunello, K Brennan, O Gevaert - Bioinformatics, 2018 - academic.oup.com
DNA methylation is an important mechanism regulating gene transcription, and its role in
carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a …

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation

MD Robinson, C Stirzaker, AL Statham… - Genome …, 2010 - genome.cshlp.org
DNA methylation is an essential epigenetic modification that plays a key role associated with
the regulation of gene expression during differentiation, but in disease states such as …

DNA methylation landscapes: provocative insights from epigenomics

MM Suzuki, A Bird - Nature reviews genetics, 2008 - nature.com
The genomes of many animals, plants and fungi are tagged by methylation of DNA cytosine.
To understand the biological significance of this epigenetic mark it is essential to know …

Gene set enrichment analysis for genome-wide DNA methylation data

J Maksimovic, A Oshlack, B Phipson - Genome Biology, 2021 - Springer
DNA methylation is one of the most commonly studied epigenetic marks, due to its role in
disease and development. Illumina methylation arrays have been extensively used to …

Hunting for the 5th base: Techniques for analyzing DNA methylation

O Ammerpohl, JI Martín-Subero, J Richter… - … et Biophysica Acta (BBA …, 2009 - Elsevier
BACKGROUND: In the recent past large progress has been made in the analysis of the
epigenome, the entirety of epigenetic modifications, and its meaning for the implementation …