Question: Functional analysis of differential methylation regions
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gravatar for tarek_2050
3.8 years ago by
tarek_20500
tarek_20500 wrote:

In Functional analysis of differential methylation regions. how to compute absolute log-fold ?

genome • 1.5k views
ADD COMMENTlink modified 3.2 years ago by hongbo91920 • written 3.8 years ago by tarek_20500

log fold-change doesn't make any sense in the context of methylation.

ADD REPLYlink written 3.8 years ago by Devon Ryan96k
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gravatar for Niraj
3.8 years ago by
Niraj0
India
Niraj0 wrote:

Usually in case of Functional analysis of differential methylation regions, the log-fold change corresponds to log fold change in gene expression associated with DMRs. For the differential methylation regions we only consider the absolute value of methylation difference for the Functional analysis.

ADD COMMENTlink written 3.8 years ago by Niraj0
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gravatar for hongbo919
3.2 years ago by
hongbo91920
hongbo91920 wrote:

Due the methylation data ranges from 0(unmethylated) to 1(fully methylated). Thus, we always don't use log-fold change although it is always used in gene expression analysis. We suggest using the DMR identification software such QDMR (for pre-defined regions) or SMART (for de novo identification of DMRs from BS-Seq data).

Best wishes!

ADD COMMENTlink written 3.2 years ago by hongbo91920
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