Question: What does 'distance to cpg' mean? And what is it used for?
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gravatar for aishsiva03
5.0 years ago by
aishsiva0310
United States
aishsiva0310 wrote:

Hi, I'm a bioinformatics intern and I have a data set that shows deferentially methylated DNA genes. I have the index number, gene name, level of methylation...etc. 

I have also been provided the transcription start site (TSS) (a co-ordinate), the strand (+ or -), CPG ID (cpg island ID) and something called 'Dist2CPG' which I believe is the distance to CPG island.

I don't know if this dist2cpg means it is the distance between the CPG and the TSS or the distance of the methylation from the CPG island. I would be grateful if someone could answer this and explain its significance.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by aishsiva0310

Thank you for your help h.mon!

Do you know if I would be able to find out whether the site is upstream or downstream from the CpG island? I have been given a column titled 'strand' which tells me whether it is the plus or minus strand. Do I need to use that information or do I always assume its downstream of that CpG island?

ADD REPLYlink written 5.0 years ago by aishsiva0310
2
gravatar for R. Taylor Raborn
5.0 years ago by
Tempe, AZ | Biodesign Institute at ASU
R. Taylor Raborn290 wrote:

I think h.mon provided the likely correct answer for what the 'Dist2CPG' value signifies. I'll just add that the association between the TSS and CpG Island is valuable because a prominent number of mammalian promoters are located near CpG Islands. This class of promoter (CpG Island Promoters) isn't as well characterized as the canonical 'TATA-containing' class. Lenhard et al. (2012) is an excellent review on the topic. 

As recent work by Piero Carninci, Boris Lenhard (both FANTOM) and Roger Hoskins (modENCODE) (and many, many others) has shown that the distribution of TSSs at a promoter reflects the underlying promoter architecture, knowledge of the proximity of a given TSS (ideally TSS distribution from a CAGE experiment) to CpG islands is valuable, especially on a genome scale. The methylation status (and dynamics, depending on the experiment you have) will be informative and should be consistent with the proximity to a given CpG Island.

The above may be more background than you were looking for, but I hope you (and potentially others) find this additional context informative.

ADD COMMENTlink written 5.0 years ago by R. Taylor Raborn290
1

Thank you so much for the information you provided Taylor! I really appreciate it!

ADD REPLYlink written 5.0 years ago by aishsiva0310

You're welcome! If it was helpful give it a 'thumbs up' so others can (possibly) evaluate it down the road.

ADD REPLYlink written 5.0 years ago by R. Taylor Raborn290
1
gravatar for h.mon
5.0 years ago by
h.mon29k
Brazil
h.mon29k wrote:

This paper defines dist2cpg as:

"dist2CpG is defined as the distance between the nearest point of a given site and the nearest CpG island; dist2CpG = 0 when a site overlaps any CpG island."

ADD COMMENTlink written 5.0 years ago by h.mon29k

Hello h.mon,

Thank you so much for your reply! 

I apologize for the silly question but could you please clarify what you mean by 'site'. Do you mean the methylation site on the DNA? 

 

ADD REPLYlink written 5.0 years ago by aishsiva0310

Any site, in case one refers to a methylation site, yes.

ADD REPLYlink written 5.0 years ago by h.mon29k
0
gravatar for aishsiva03
5.0 years ago by
aishsiva0310
United States
aishsiva0310 wrote:

Thank you so much for the information you provided Taylor! I really appreciate it!

ADD COMMENTlink written 5.0 years ago by aishsiva0310
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