Hi Isla

Down-regulated is a relative term, means the transcription level of your gene in one sample is lower than another one. Although some times this "lower" means very very low transcription. It depends on the degree of down-regulation.

Hi Isla Nair

I agree with Ali's answer, it's a relative term which tells us that due to ur intervention, the particular gene expression reduced compared to ur untreated/control condition.

Every gene has significance in the cell processes, now it depends on the regulation and function, when and how much any gene should up/down or epigenetically silenced.

In this situation, you can silence or knockdown that particular gene in your condition to understand that to what extent it can be downregulated and what is its functional effect upon on silence or knockdown. The same opposite principle goes with overexpression.

Regards,

Saurabh

Hi Isla,

I agree with Ali and Saurabh. Moreover, gene expression does not necessarly represent the build and functional protein in the cell. As an example, we compared Nox2 levels in peritoneal and bone marrow macrophages and, while mRNA levels (measured by qRT-PCR) showed no differences between these cell types, the Nox2 protein levels were much lower in bone marrow macrophages (see Article The β2 Integrin Mac-1 Induces Protective LC3-Associated Phag...

mRNA can be stored by the cell without building the protein. I would recommend to make cell lysates of untreated cells and cells were your gene is knocked down and the look at the protein that it encodes via Western Blot.

All the best,

Marc