Question: Length of differentially methylated regions
1
gravatar for niutster
2.7 years ago by
niutster90
niutster90 wrote:

Hi,

I want to identify significant differentially methylated regions from a set of DMRs which has DMRs with length from 1 bp to 200 bp, which numbers of bps define a regions in biology? i need a threshold.

dmrs length genome • 861 views
ADD COMMENTlink modified 2.7 years ago by Devon Ryan94k • written 2.7 years ago by niutster90
1
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

Well, pretty much by definition a region will need to be more than one CpG, so 4 bases. In practice, most people use a minimum of 3 or more CpGs, meaning at least 6 bases.

ADD COMMENTlink written 2.7 years ago by Devon Ryan94k

Do you mean DMRs must contains at least 3 CpGs with any length or at Least 6 bp length and contain any desired CpG numbers?

ADD REPLYlink written 2.7 years ago by niutster90

3 CpG with any length (this is obviously never less than 6 bases) is a common usage. Using length as a threshold for definition isn't terribly useful without also setting some sort of CpG number threshold.

ADD REPLYlink written 2.7 years ago by Devon Ryan94k

and by 3 CpGs you mean they must be consecutive/end to end? or we can have some distance in between? like 3 differentially methylated Cs but having 2kb distance in between. I am trying to search some papers as a reference to this ideally 3CpG thing. please let me know if you have any reference.

Thank you :)

ADD REPLYlink written 5 weeks ago by Binte.farooq0

One normally allows distance in between, though 2kb would be biologically excessive. You will not find a reference to 3 CpGs in any paper, it's not something people write down.

ADD REPLYlink written 5 weeks ago by Devon Ryan94k

Any ideal distance you can suggest ?

ADD REPLYlink written 4 weeks ago by Binte.farooq0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1474 users visited in the last hour