Simply by doing quantitative PCR and western blotting of targetted genes for differential expression.

Hi,

Each cell type qPCR data of Wt or mutant against its own GAPDH or your endogenous control(delta Ct) and then normalise each mutant against either Wt or some control of your choice. I dont think there is any other way to normalize data of all cell types pf Wt Vs mutants all together. Statistically you could have used two-way ANOVA but in qPCR I think you will have to use delta Ct of each type against its own cell type (endogenous control and delta delta Ct of value of your choice). 

Calculate the delta Ct for each cell group. Then divide all values by WT. WT delta Ct divided by WT delta Ct (WT/WT) sets the relative expression of wt to 1. The mutants are also divided by WT and the values of the mutants will be relative to the expression level in WT. You may want to log transform so the values