strange RT-PCR expression - (Aug/16/2006 )

My question actually is not related to molecular biology technique, but I just couldn'y find a proper place to paste it.

Recently I found several cases like this: gene A is significantly upregulated when gene B is knocked out OR over-expressed. I'm sure the RT-PCR result is repeatable.

Certainly gene B influences the expression of gene A, but why the outcome is same?

I just couldn't find any previously published paper dealing with such situation, could anyone share some opinions?

Thanks a lot

Maybe upregulation of gene A is a consequence of something in the KO/OE protocol that is the same (ie: transfection upregulates gene A) and that is why it goes up regardless of gene B being KO or OE...