How to compare these results? Please comment. - (Apr/22/2012 )
I'm analyzing the expression of one gene after induction of cell death with a drug. I am using a wild type strain as well as a knockout mutant strain (for a cell signaling protein, in order to check if the activation of the gene was dependent on this signaling pathway). For the analysis I use the wild type control-treated sample as a calibrator, meaning the expression is 1 in this sample. I have these levels of expression:
wild type control: 1
wild type drug: 50
mutant control: 10
mutant drug: 50
In the mutant I also have induction of the gene to the same levels as in the wild type. But if I consider that in the mutant control sample I already have 10 times more expression of the gene than in the wild type, the induction caused by the drug is only 5 (50/10 = 5) whereas in the wild type this is 50 (50/1 = 50).
Should I consider that the mutant has a decreased capacity to induce the gene or not?
Please leave your comments.
Your mutant could be deficient in a repressor of gene expression that inhibits action of a separate activating pathway- removing something that keeps gene expression at a basal level might lead to the pattern you're observing.
Thanks for the answer. Yep, that is one possibility.
I don't know if I can conclude that the difference that I observe in the drug-induced expression in the mutant means that the induction of the gene is impaired in this strain... because although there is a significative difference between drug-induced fold change between wild type and mutant, the truth is after the drug the expression reaches the same levels as in the wild type...
Are you doing absolute quantitation or relative?