Integrative Methylation–Expression Correlation Analysis

Overview

This skill integrates differential methylation and differential expression datasets to reveal coordinated epigenetic regulation patterns.

Refer to Inputs & Outputs to verify necessary files.
Always prompt user for genome assembly used.
Prepare the DMR regions into 6-column standard format BED file received by HOMER.
Annotate the differential methylation regions to the gene promoter.
Preprocess differential methylation and expression tables into a standard format.
Integrate methylation and expression data by promoter proximity.
Calculate correlation between methylation change and expression fold change.
Classify patterns such as hypermethylation–downregulation or hypomethylation–upregulation.