@inbook{cad9db9985e844878a2a8d75dfb6cb18,
title = "Integrated Analysis of DNA Methylation, Hydroxymethylation, and Gene Expression Data Using ME-Class2",
abstract = "There is increasing interest in understanding the pathological role of DNA methylation changes in disease by profiling genome-wide methylation changes. This includes both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). The typical profiling study is designed to measure 5mC and/or 5hmC levels alongside gene expression in a set of samples and controls to determine a list of candidate genes whose 5mC and/or 5hmC changes are associated with expression changes. We recently showed that ME-Class2 substantially outperforms other bioinformatic approaches at accurately identify genes with highly associated methylation and expression changes. ME-Class2 further illuminated how synergistic changes in 5mC and 5hmC potentially contribute to gene silencing and activation. Here we present a detailed protocol for using ME-Class2 to analyze genome-wide methylation (5mC and/or 5hmC) and expression data. Further, we provide advice about extending ME-Class2 to study the relationships between other epigenetic marks.",
keywords = "5-Hydroxymethylcytosince, 5-Methylcytosine, DNA methylation, Epigenetics, Epigenomics, ME-Class, ME-Class2, Transcription regulation",
author = "Singh, {Manoj K.} and Edwards, {John R.}",
note = "Funding Information: This work was supported by NIH grants R01 LM013096 and R01 GM108811 to J.R.E. Publisher Copyright: {\textcopyright} 2021, The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2021",
doi = "10.1007/978-1-0716-0876-0_34",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "467--489",
booktitle = "Methods in Molecular Biology",
}