I have a puzzling situation on my hands. I am working with embryonic fibroblasts derived from knockout (KO) mice for a particular gene. These cells showed clear differences in behavior compared to wild-type cells, e.g. they proliferate faster. In order to find out the basis of these differences, I performed microarray analyses to compare wild-type and KO transcriptional profiles. To my big surprise, the target gene for the knockout was not expressed in both wild-type and KO cells. However, I do see distinct differences in the transcriptional profiles between the two types of cells and this is reproducible in a knockout in a different exon created independently in a lab located in another country. If the target gene is not even expressed, what then could account for the differences in transcriptional profiles between wild-type and KO?
If any of you have encountered similar situations, hope you can share some wisdom.
Edited by neuropath, 08 December 2010 - 03:59 AM.