Basic cell biology and genetics books and dictionaries define gene expression as the whole pathway from gene to the functional gene product (gene is said to be expressed when the protein it encodes functions in an organism). This means that in addition to transcription gene expression includes translation and is affected by mRNA and protein stabilities. Yet, every day ione gets to read advertisements about studying gene expression with cDNA microarrays or quantitative PCR (or PCR arrays). To my knowledge, these methods determine the mRNA level. The mRNA is the template for the protein, as everyone knows. Thus, to say that mRNA level changes give you the functional changes is the same as saying that since we have printed more instructions of how to build a machine indicates to us that more of the product that the machine makes has been made.

mRNA changes give a good picture of how functional protein changes, if the production of protein is only transcriptionally changed. This is true for some proteins but not for others. Unfortunately (or actually luckily for us physiologists) function can only be determined, if the function is measured. I have often wondered what is wrong with the accurate word transcription: if for qPCR one said that one is doing gene transcription analysis (from which it is a long way to gene expression analysis) I would have no quarrel. With the present use of the phrase gene expression for qPCR, if it increases, the true gene expression may increase, remain constant or decrease.