BioMethyl

BioMethyl is an R package that provides biological interpretation of DNA methylation data, mainly when corresponding gene expression data is not available. Key features of BioMethyl include:

1. It utilizes a given cancer type's complete DNA methylation data to reflect corresponding gene expression profiles.

2. It performs pathway enrichment analyses on the DNA methylation data, providing unique biological insights.

3. Using breast cancer as an example, BioMethyl shows high consistency in identifying enriched biological pathways from DNA methylation data compared to the results calculated from RNA sequencing data.

4. For estrogen receptor (ER) positive breast cancer samples, 12 out of 14 pathways identified by BioMethyl are shared with those identified using RNA-seq data, with a Jaccard score of 0.8.

5. For ER-negative samples, three pathways are shared between the two enrichment methods, with a slightly lower similarity (Jaccard score = 0.6).

6. BioMethyl can successfully identify hidden biological pathways in DNA methylation data when gene expression profiles are lacking.