[HTML][HTML] Gene set enrichment analysis for genome-wide DNA methylation data
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 …
disease and development. Illumina methylation arrays have been extensively used to …
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
DNA methylation plays key roles in diverse biological processes such as X chromosome
inactivation, transposable element repression, genomic imprinting, and tissue-specific gene …
inactivation, transposable element repression, genomic imprinting, and tissue-specific gene …
[HTML][HTML] DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
JM Gaspar, RP Hart - BMC bioinformatics, 2017 - Springer
Background DNA methylation is an epigenetic modification that is studied at a single-base
resolution with bisulfite treatment followed by high-throughput sequencing. After alignment …
resolution with bisulfite treatment followed by high-throughput sequencing. After alignment …
EWAS Data Hub: a resource of DNA methylation array data and metadata
Abstract Epigenome-Wide Association Study (EWAS) has become an effective strategy to
explore epigenetic basis of complex traits. Over the past decade, a large amount of …
explore epigenetic basis of complex traits. Over the past decade, a large amount of …
MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
M Pelizzola, Y Koga, AE Urban… - Genome …, 2008 - genome.cshlp.org
DNA methylation is an important component of epigenetic modifications that influences the
transcriptional machinery and is aberrant in many human diseases. Several methods have …
transcriptional machinery and is aberrant in many human diseases. Several methods have …
An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays
Epigenome-wide association studies (EWASs) have become increasingly popular for
studying DNA methylation (DNAm) variations in complex diseases. The Illumina methylation …
studying DNA methylation (DNAm) variations in complex diseases. The Illumina methylation …
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation
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 …
the regulation of gene expression during differentiation, but in disease states such as …
CoMeBack: DNA methylation array data analysis for co-methylated regions
Motivation High-dimensional DNA methylation (DNAm) array coverage, while sparse in the
context of the entire DNA methylome, still constitutes a very large number of CpG probes …
context of the entire DNA methylome, still constitutes a very large number of CpG probes …
Comprehensive high-throughput arrays for relative methylation (CHARM)
This study was originally conceived to test in a rigorous way the specificity of three major
approaches to high-throughput array-based DNA methylation analysis:(1) MeDIP, or …
approaches to high-throughput array-based DNA methylation analysis:(1) MeDIP, or …
[HTML][HTML] Probe Lasso: a novel method to rope in differentially methylated regions with 450K DNA methylation data
LM Butcher, S Beck - Methods, 2015 - Elsevier
The speed and resolution at which we can scour the genome for DNA methylation changes
has improved immeasurably in the last 10 years and the advent of the Illumina 450K …
has improved immeasurably in the last 10 years and the advent of the Illumina 450K …