Question: Filtering DMRs
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gravatar for niutster
2.4 years ago by
niutster80
niutster80 wrote:

Hi,

I get a large number of DMRs by seqlm package in comparison between two tissues after filtering by p-value <0.05 , it is near 115000 regions which contains one bp differentially methylated sites,too. Does anyone of you have recommendations for filtering these regions to get some meaningful sites and regions? I have features like number of probes have changed, CpG islands, different regions in genome such as body, UTR,... and beta value.

genome • 747 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.4 years ago by niutster80

Are you doing WGBS, array, MBD or other profiling protocol? That's a lot of DMRs. Try using GREAT (http://bejerano.stanford.edu/great/public/html/) to annotate DMRs with gene names. GREAT also does a reasonable job at GO enrichment. Alternatively, you can annotate DMRs with gene names using a BedTools with an bed file of gene/TSS coordinates. Once annotated with gene names, a pathway analysis using GSEA would be insightful.

ADD REPLYlink written 2.4 years ago by mark.ziemann1.2k
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