Question: Differential Methylation Interpretation
2
gravatar for stevenlang123
5.5 years ago by
stevenlang123180
United States
stevenlang123180 wrote:

Hey y'all, 

So I have some differential methylation data generated through bisulfite sequencing. I have a only 8 deferentially methylated positions and none of the map to a transcription factor binding site. What are some other ways to interrogate the data? I've used CADD and FATHMM to generate conservation scores, etc. But that does not give me much functional info. I've seen that there is some mapping to histone enhancer regions H3K4Me3, etc. But I honestly do not really understand what that means. Any help is greatly appreciated!!!!! 

Thanks in advance 

-steve

ADD COMMENTlink modified 5.5 years ago by Charles Warden8.0k • written 5.5 years ago by stevenlang123180
1
gravatar for Charles Warden
5.5 years ago by
Charles Warden8.0k
Duarte, CA
Charles Warden8.0k wrote:

With only 8 differentially methylated regions, I think interpretation will be difficult.  Perhaps you can loosen your criteria for differential methylation, which will generally make enrichment analysis easier.

If you know TF binding sites, you could ask if your overlap is more than you expect by chance (but I think it will be hard to currently get a significant result, and you said that there are currently no binding sites).

Alternatively, methylation doesn't need to occur at a transcription factor binding site to be significant, you could check for overlap with CpG islands defined in the UCSC genome browser (or simply check if they are in the transcription start site for any genes).

 

ADD COMMENTlink written 5.5 years ago by Charles Warden8.0k
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