Hi,
I am comparing CNA data with mRNA expression level. For some genes there is no correlation between copy number and mRNA expression level and even for some there is negative relation (low copy number yet high mRNA expression). I found some papers stating same situation but I could not find any paper discussing it in a deeper manner. I will appreciate if one can help me to understand this.
thank you
3 answers
This paper might help, it deals with CNA, mRNA and proteome, and presents an 'attenuation expression signature' for genes that are unaffected by CNV, possibly due to degradation of a rate-limiting complex-partner. Probably goes beyond your scope, but some useful ideas (at least for me!).
First of all, there is no linear correlation between CNA and mRNA or, mRNA and protein expressions. That is why biology is challenging, there are many other parameters like post transcriptional modification, post translational modification, epigenetics etc.. (some of them we know, some of them are still missing) that we have to take into account.
There are papers that might be interesting for you.
Check this previous discussion on this topic: CNV detection from RNA-seq data
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