Question

CpG site not annotated with annotatr

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soli5 • 0

@soli5-17849

Last seen 6.2 years ago

Hi,

I am using annotatr to annotate differentially methylated cytosines and I have a list of CpGs not included in the exons, promoters, introns or intergenic results. Where could they be classified if it's not in one of those regions. I checked one of the non annotated CpGs and I found it 4Kb downstream a gene. Is there an explanation for CpGs not being present in those regions?

Thanks

Sol

annotatr cpg • 1.6k views

ADD COMMENT • link updated 6.2 years ago by rcavalca ▴ 140 • written 6.2 years ago by soli5 • 0

score 0 · Answer 1 · 2018-10-17

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rcavalca ▴ 140

@rcavalca-7718

Last seen 5.9 years ago

United States

Hi,

Thanks for using annotatr. If it were 4kb upstream of a gene, I would answer that it falls in the 1to5kb regions, which is distinct from the promoters. However, you said 4kb downstream which suggests that it should probably be intergenic. To help me figure this out, could you give me the location of the CpG and what genome it's with respect to, and I'll have a look on the Genome Browser to see what could be going on.

Thanks,

Raymond

ADD COMMENT • link 6.2 years ago rcavalca ▴ 140

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Hi Raymond,

Thanks for your reply and help. I actually meant upstream. In any case, in the list I got there are different situations. For example chr12:9818891 falls in a region that to me could be promoter, 1to5Kb or intergenic, but it was not annotated as promoter or intergenic, would it be in a 1to5Kb region?. I did not perform that annotation.
I give you a small list of examples (from this particular comparison I got 1195 CpGs not in those 4 categories), it would really help understand where these CpGs would go.

Another question, I see overlaps between exon and promoter lists for example, I understand that this is due to isoform configuration (one cytosine could be in the exon of an isoform and in the promoter of another isoform). But other than exon, promoter and intron annotations, are the other categories supposed to be mutually exclusive?

chr1,10487953
chr1,1070681
chr1,109641692

chr12,70094442
chr12,8818948
chr12,9818891
chr13,101245080
chr13,112717043

chr2,55744587

chrX,100351769

I hope my questions are clear. Thank you

Sol

ADD REPLY • link 6.2 years ago soli5 • 0

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Hi Sol,

Since it is upstream, my guess would be that it would show up in the 1to5kb annotation. The promoter annotation only extends 1kb upstream from the TSS. I verified in the UCSC Genome Browser for hg19.

As for the list of other CpGs, I looked at a handful at random and they seem to primarily be in that 1to5kb region upstream of a TSS. I would recommend adding that annotation and seeing if that does the trick.

Thanks,

Raymond

ADD REPLY • link 6.2 years ago rcavalca ▴ 140