Question: Pathway analysis with Methylation EPIC microarray data
0
gravatar for rasii
2.9 years ago by
rasii0
rasii0 wrote:

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

ADD COMMENTlink modified 2.9 years ago by EagleEye6.4k • written 2.9 years ago by rasii0
0
gravatar for EagleEye
2.9 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

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WARNING: Do not use outdated tool for gene enrichment analysis.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

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by EagleEye6.4k

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

ADD REPLYlink written 2.9 years ago by rasii0
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