Question: Correlation MeDip-seq data with gene expression data
gravatar for florian.noack
6.0 years ago by
florian.noack20 wrote:

Hi everybody,

Iam quite new in the field of bioinformatics and epigenetics and right now iam stucked with my analysis. I want to analysis if we see any correlation between changes of DNA methylation at certain loci (promotor, exons, introns ... ) and the expression of the corresponding gene (unfortunately i dont have the raw file but only log2fold changes) between two cell types.

The first question is should I work with peaks ( i have already peaksets of both MeDip-seq samples which i generated with SICER) or the whole readcount of Input and IP sample for a given gene region (for example -5kb from the TSS)?

If I go for the whole readcount I have to calculate somehow a methylation level. I tried to calculate such value using this formula:

(unique_reads / total_readcount)*region_length

My idea was to use this formula in both IP and Input sample and subtract the input value from the IP value. Unfortunately i got a lot of negative values and therefor its not really possible to calculate a log2 value to correlate with gene expression data. Is there another way to subtract the background noise from my IP sample using the Input control?

Any other ideas how i could correlate this two datasets with each other ?


Thanks for any kind of suggestion.





chip-seq • 2.7k views
ADD COMMENTlink modified 6.0 years ago by ayyappakumar.s20 • written 6.0 years ago by florian.noack20
gravatar for ayyappakumar.s
6.0 years ago by
ayyappakumar.s20 wrote:

If you are interested in analyzing the correlation between near by CpG's, in this case you can use RnBeads a R package by using a Fishers method.


ADD COMMENTlink written 6.0 years ago by ayyappakumar.s20
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