Question: Why is a probe annotated more than one UCSC_RefGene_Group in the same gene?
gravatar for RC
3.6 years ago by
RC0 wrote:

Hi, i'm processing a data from 450K beadchip to identify differentially methylated probes(DMPs) between our case and control. And i get more than 10000 DMPs. When i'm calculating the distribution of DMPs in relation to genes(such as: What percentage of DMPs located in TSS200 region), i face a question: one probe annotated with more than one region to the same gene, sometimes the regions are the same.

For example : 
ID: cg09132215 
UCSC_RefGene_Group: TSS200;TSS200;TSS200;TSS1500;TSS200

What should i do about the location for cg09132215? Should i count as :$num_TSS200=$num_TSS200+4 and $num_TSS1500=$num_TSS1500+1? ($num_TSS200: the number of DMPs located at TSS200; $num_TSS1500: the number of DMPs located at TSS1500)

Any suggestion will be great appreciated!

illumina chip-seq methylation R • 1.3k views
ADD COMMENTlink modified 3.6 years ago by newbiebio80 • written 3.6 years ago by RC0
gravatar for newbiebio
3.6 years ago by
newbiebio80 wrote:

I cited whtat Istvan Albert said under this question "each of them represent different regions of your gene." Maybe this one could help you out. Genes With Multiple Probe Ids

ADD COMMENTlink written 3.6 years ago by newbiebio80

But i still confused about the method to count the distribution of DMPs. if i count as $num_TSS200=$num_TSS200+4 and $num_TSS1500=$num_TSS1500+1, it seems like i count this DMP as 5 probes. Should i took the first annotation as standard annotation (TSS200 in TAS1R1) for cg 09132215 and count as $num_TSS200=$num_TSS200+1?

ADD REPLYlink written 3.6 years ago by RC0

What method did you end up using to account for these multiple locations?

ADD REPLYlink written 3.0 years ago by methylohm0
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