[HTML][HTML] Methods in DNA methylation array dataset analysis: A review

K Sahoo, V Sundararajan - Computational and Structural Biotechnology …, 2024 - Elsevier
Understanding the intricate relationships between gene expression levels and epigenetic
modifications in a genome is crucial to comprehending the pathogenic mechanisms of many …

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 …

A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling

H Meng, AR Joyce, DE Adkins, P Basu, Y Jia, G Li… - BMC …, 2010 - Springer
Background High-throughput DNA methylation arrays are likely to accelerate the pace of
methylation biomarker discovery for a wide variety of diseases. A potential problem with a …

DBCAT: database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells

HC Kuo, PY Lin, TC Chung, CM Chao… - Journal of …, 2011 - liebertpub.com
DBCAT (database of CpG islands and analytical tools, http://dbcat. cgm. ntu. edu. tw/),
developed to characterize comprehensive DNA methylation profiles in human cancers, is a …

Genome-scale DNA methylation analysis

SD Fouse, RP Nagarajan, JF Costello - Epigenomics, 2010 - Taylor & Francis
The haploid human genome contains approximately 29 million CpGs that exist in a
methylated, hydroxymethylated or unmethylated state, collectively referred to as the DNA …

coMethDMR: accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies with continuous phenotypes

L Gomez, GJ Odom, JI Young, ER Martin… - Nucleic acids …, 2019 - academic.oup.com
Recent technology has made it possible to measure DNA methylation profiles in a cost-
effective and comprehensive genome-wide manner using array-based technology for …

An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays

S Mallik, GJ Odom, Z Gao, L Gomez… - Briefings in …, 2019 - academic.oup.com
Epigenome-wide association studies (EWASs) have become increasingly popular for
studying DNA methylation (DNAm) variations in complex diseases. The Illumina methylation …

computational methods for analysis of DNA methylation data

P Di Lena, C Nardini, M Pellegrini - Frontiers in Bioinformatics, 2022 - frontiersin.org
DNA methylation is among the most studied epigenetic modifications in eukaryotes. The
interest in DNA methylation stems from its role in development, as well as its wellestablished …

Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array

L Yang, K Zhang, W Dai, X He, Q Zhao, J Wang… - BMC genomics, 2011 - Springer
Background Recent progress in high-throughput technologies has greatly contributed to the
development of DNA methylation profiling. Although there are several reports that describe …

High-throughput DNA methylation profiling using universal bead arrays

M Bibikova, Z Lin, L Zhou, E Chudin… - Genome …, 2006 - genome.cshlp.org
We have developed a high-throughput method for analyzing the methylation status of
hundreds of preselected genes simultaneously and have applied it to the discovery of …