Abstract
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 measure methylation across the human genome. Methylation array analysis has primarily focused on preprocessing, normalisation and identification of differentially methylated CpGs and regions. GOmeth and GOregion are new methods for performing unbiased gene set testing following differential methylation analysis. Benchmarking analyses demonstrate GOmeth outperforms other approaches and GOregion is the first method for gene set testing of differentially methylated regions. Both methods are publicly available in the missMethyl Bioconductor R package.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Email addresses: Jovana Maksimovic: Jovana.Maksimovic{at}petermac.org, Alicia Oshlack: Alicia.Oshlack{at}petermac.org
https://www.bioconductor.org/packages/release/bioc/html/missMethyl.html
Abbreviations
- TCGA
- The Cancer Genome Atlas
- MSigDB
- Molecular Signatures Database
- RNA-Seq
- RNA sequencing
- FDR
- false discovery rate
- DMR
- differentially methylated region