Assuming that everything was technically well done and the results are fully reliable ,what you find is that mRNAs are more stable/unstable in the different conditions and/or that protein degradation is increased/decreased in the different conditions. Quite often mRNAs expression trends do not correlate with protein epression trends for the above mentioned reasons (but reliability of results is also a major issue)

Assuming that everything was technically well done and the results are fully reliable ,what you find is that mRNAs are more stable/unstable in the different conditions and/or that protein degradation is increased/decreased in the different conditions. Quite often mRNAs expression trends do not correlate with protein epression trends for the above mentioned reasons (but reliability of results is also a major issue)

Dear Justin,

Is pretty usual that there's not a correlation between mRNA levels and protein expression and it's well documented in literature.

For example one of the mechnism of protein expression is miRNA silencing that promotes mRNA decay. Moreover there are different degradation proteins pathways where Ubiquitin plays a central role.

For these and many other reasons qPCR is not gold standard to measure gene and protein expression in Reasearch, but qPCR it's the first step and mRNA levels must be verified with protein quantification method like Western Blot.

In this paper we used qPCR to confirm cell transfection but then we measured protein levels.

https://www.ncbi.nlm.nih.gov/pubmed/?term=peroni+epor

Whereas in this old article is well reported that mRNA and protein expression is not correlated

https://pdfs.semanticscholar.org/0fe3/843ce2b9d5a9afb552fd9910aeb320777f6f.pdf

Good Job

Edoardo

Not sure what you mean by 'better'. If you are interested in protein function, then protein expression should your prime focus. However both are important parameters particular to any gene expression study. While there is a general positive correlation between protein expression and mRNA expression in any steady state system, for reasons mentioned above (and others) this is by no means an obligate relationship; Typical values for correlation are in the order of 0.6 i.e. good but not great!. And perturbing this equilibrium (Overexpression, siRNA, KO etc), can alter mRNA/protein correlations to due complex feedback loops, so I would be particularly careful in using mRNA expression as a proxy for protein expression in that setting. Hopes this helps.

Good luck!