Best way to evaluate the relationship between protein and RNA abundance

Question

[haasroni]

Hi everyone,

I have samples for which RNA and protein abundances are given for about 7,000 genes (3 replicas for each group). I want to test the relationship between the RNA and protein abundance (e.g. high RNA abundance means high protein abundance for a given gene?)

I was wondering what would be the best way to evaluate it.

Would it be Pearson correlation, effect sizes using Cohen's d? Or maybe something that I haven't thought about.

Thank you!

Answer 1

[Nitin Narwade]

I guess correlation analysis should be fine for this task, but before doing the analysis you need to normalise your data. I would suggest transform the expression data (gene and protein) on the same scale, for example by using min-max normalisation. After this normalisation your data will be ranging from 0(minimum) to 1(maximum).

BTW,

the high RNA abundance means high protein abundance for a given gene?

Is not always true. I mean of course you are talking in terms of abundance so you can exclude other possibilities like post transcriptional, post translation modification and other regulatory mechanisms. But they are there.

[haasroni]

Thank you very much!

Is not always true. I mean of course you are talking in terms of abundance so you can exclude other possibilities like post transcriptional, post translation modification and other regulatory mechanisms. But they are there.

Sure, you are right. It was just an example of a finding that may be, not necessarily true. This is why I want to do the testing - to find out for which genes it is true.