Question

Length of differentially methylated regions

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7.5 years ago

niutster ▴ 110

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 genome length • 2.2k views

ADD COMMENT • link updated 7.5 years ago by Devon Ryan 104k • written 7.5 years ago by niutster ▴ 110

score 1 · Answer 1 · 2017-06-08

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7.5 years ago

Devon Ryan 104k

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 COMMENT • link 7.5 years ago by Devon Ryan 104k

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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 REPLY • link 7.5 years ago by niutster ▴ 110

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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 REPLY • link 7.5 years ago by Devon Ryan 104k

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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 REPLY • link 4.8 years ago by Binte.farooq ▴ 20

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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.