Question: Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
gravatar for inschigu
2.5 years ago by
inschigu10 wrote:

I tried to use HORMER to identify TF binding sites on differentially methylated regions (DMRs), but I have no idea about the following three parameters.

Strand information There is not the strand information in DMRs. Is the BED file without the strand information acceptable for HOMER?

Size parameter (-size) Unlike ChIP-seq data, DMRs don't have a certain peak. In this case, is the "-size given" appropriate as "-size" parameter?

Sequence normalization options Since DMRs are basically CpG rich regions, is the “-cpg” option appropriate to normalize sequence?

Thank you

next-gen • 1.3k views
ADD COMMENTlink modified 13 months ago by Charles Warden7.6k • written 2.5 years ago by inschigu10

I am also having the same question, as I am trying to develop a workflow from DMR multiple sequence alignment and clustering to de novo motif discovery and enrichment.

ADD REPLYlink written 2.3 years ago by pepinme10
gravatar for Charles Warden
13 months ago by
Charles Warden7.6k
Duarte, CA
Charles Warden7.6k wrote:

You bring up a nice question about the -cpg option (in HOMER).

I there there are some common GC-rich motifs that HOMER tries to place less emphasis on. However, you specifically want to know about the CpG sites within the region (and sequence outside CpG motifs would not be as relevant).

If you are going to try and do some motif analysis, I think you would need to be able to find differential methylation across CpG-overlapping motifs at multiple genes.

So, you probably need to get site-centric transcription factor binding information. I think ENCODE would be a popular, but I can't precisely vouch for it's use in this application.

If you have that, I can think of at least two possibilities (methods-wise):

1) I believe methylSig performs such a test with ENCODE Motifs (section 6.3 in the linked PDF)

2) If you use an annotation-based strategy that doesn't take proximity into consideration, you could also do something similar (with your own set of annotations). Again, I don't have a success story about defining the "region" as CpG sites within motifs in different genes, but you can use the default COHCAP region analysis (without re-defining boundaries) to test this sort of thing (with the extra effort of defining your own "custom" annotation with platform="custom" in COHCAP.annotate())

ADD COMMENTlink modified 13 months ago • written 13 months ago by Charles Warden7.6k
gravatar for luisjavierleandrogarcia
13 months ago by

Hi, same questions here. Did any of you solve them? Thank you.

ADD COMMENTlink written 13 months ago by luisjavierleandrogarcia0
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