PT  - JOURNAL ARTICLE
AU  - Jovana Maksimovic
AU  - Alicia Oshlack
AU  - Belinda Phipson
TI  - Gene set enrichment analysis for genome-wide DNA methylation data
AID  - 10.1101/2020.08.24.265702
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2020.08.24.265702
4099  - http://biorxiv.org/content/early/2021/04/27/2020.08.24.265702.short
4100  - http://biorxiv.org/content/early/2021/04/27/2020.08.24.265702.full
AB  - 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 StatementThe authors have declared no competing interest.TCGAThe Cancer Genome AtlasMSigDBMolecular Signatures DatabaseRNA-SeqRNA sequencingFDRfalse discovery rateDMPdifferentially methylated probeDMRdifferentially methylated region