Pathway analysis with Methylation EPIC microarray data

Question

[rasii]

Hi everyone,

I have some methylation microarray data obtained from illumina Methylation EPIC microarray and I wanted to know how I can do some pathway analysis. I have analysed the DMRs and have mean.diff of CpG sites, promoter etc in the form of a table now I want to know what I need to do next and which programs I can use.

Thanks in advance. Rasi

Answer 1

[EagleEye]

1) Make bed file from your list of DMRs and get recent annotation file (preferably GTF, Example GTF). Then use 'annotate peaks' from homer. This will annotate your DMRs to Genes in detailed manner.

Orelse if you have already assigned genes and got the gene lists, proceed with second step.

2) Take those list of genes and check for enriched Pathways. Example using GeneSCF.

WARNING: Do not use outdated tool for gene enrichment analysis.

Check out this recent article Figure 1b for workflow (Instead of peaks, in your case it will be DMRs location).

[rasii]

Thanks heaps for you suggestions! Will try the methods you mentioned a shot :)