integrative-DMR-DEG

To integrate DMR and DEG results, the workflow annotates differential methylation regions to gene promoters and calculates the correlation between methylation change and expression fold change. It requires promoter-level methylation data, DMR results, and DEG results to output standardized integrated statistics and plots.

Promoter methylation and gene expression are correlated in epigenetic regulation, often exhibiting patterns like hypermethylation–downregulation or hypomethylation–upregulation. Identifying these coordinated changes helps pinpoint genes under epigenetic control across your datasets.

Yes, you can use metilene DMR results and DESeq2 DEG results for integrative methylation and expression analysis. The workflow specifically preprocesses these differential methylation and expression tables into a standard format to classify coordinated epigenetic regulation patterns.

To annotate DMR regions to gene promoters, the workflow prepares your DMR regions into a 6-column standard BED file for HOMER annotation. This step maps the differential methylation regions directly to their corresponding gene promoter regions.

From integrated methylation and expression data, you can classify patterns of coordinated epigenetic regulation such as hypermethylation–downregulation or hypomethylation–upregulation. The workflow calculates correlations between methylation change and expression fold change to categorize these relationships.

The workflow expects dmr_results.txt and dge_result.csv files as inputs to generate correlation results. It preprocesses these differential methylation and expression tables into a standard format before integrating the data by promoter proximity.