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
In the revised version of our manuscript, we have added the analysis of two new methylation datasets, including a dataset that has matched gene expression data. We have repeated our analyses using the new implementation of the ebGSEA methods and have incorporated these into our results and modified the figures accordingly. In addition, we have added text to clarify how the statistical framework in GOmeth is implemented.
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
- DMP
- differentially methylated probe
- DMR
- differentially methylated region
