Entering edit mode
9 months ago
Mamatha Y S
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I have gene-level methylation data and identified genomic areas with a GTF file. I used the GenomicRanges program to calculate the sum of methylation counts within these identified gene ranges. This method was carried out individually for both diseased and healthy states.
I am thinking about doing a differential expression analysis comparing these two groups with gene-level methylation data. However, I am uncertain about the biological validity of this approach. If anyone has knowledge in this field, I'd like to know whether this analysis is biologically valid or not.
Thank you in advance
That is a biologically valid approach if a little weak. There is plenty of literature showing DNA modifications such as methylation is important in regulating gene expression.
As a result, correlations between methylation state and expression are common in the literature. However, inferences only drawn from correlations and not the strongest, but are still very useful in exploring potential mechanisms on a genomic scale.
Thank you so much for your response. Can you please provide me if there is any reference regarding this it will be very helpful for me..
I would look up "DNA methylation gene expression" on something like Google scholar. There are hundreds of papers and reviews. Some likely in the organism you work on too.
Regarding the quality of correlative interferences, I don't have a paper, but I understand the limitations of such analyses. I'm sure there are papers out there discussing them, but I've not read many.
I have seen "DNA methylation gene expression" that papers in that actually they take CpG sites and find the DMRs then they connect with gene expression . my question if I have data something like
is it valid to use edger and do differential analysis for this data. I don't want to do gene expression analysis.
I have seen differential analysis for gene promoter region but not the whole gene.is it any problem if i take whole region.