methylGSA

methylGSA performs gene set testing on DNA methylation data by adjusting for the number of CpGs per gene to relate significant CpGs or genes to known biological properties.

Key Features:

• CpG-count bias adjustment: Adjusts for the number of CpGs per gene rather than gene length to correct bias in gene set testing of methylation data.
• Gene set testing for CpGs and genes: Performs enrichment analyses that associate significant CpGs or genes with biological pathways and gene sets.
• Input compatibility: Accepts DNA methylation data derived from Illumina arrays and lists of significant CpGs or genes from differential methylation or RNA-Seq analyses.
• Bias-corrected statistics: Produces more accurate and unbiased p-values for gene set enrichment by accounting for CpG counts.
• Implementation: Implemented as an R package within the Bioconductor ecosystem.

Scientific Applications:

• Functional interpretation of differential methylation: Annotates lists of significant CpGs or genes with enriched biological pathways and gene sets.
• Bias-aware pathway analysis: Provides CpG-count-adjusted enrichment results to reduce false positives due to uneven CpG distribution across genes.
• Integration with downstream analyses: Applicable downstream of differential methylation analyses and RNA-Seq differential expression to connect results to biological function.

Methodology:

Performs gene set testing that adjusts for gene-specific CpG counts to compute bias-corrected p-values for lists of significant CpGs or genes from Illumina methylation arrays.