I'm not an expert in this particular signaling pathway, but unless you have some other results to prove it, the fact that GSK3 absence is reducing NOTCH doesn't mean that they are interacting. It could be attributable to a reduced NOTCH expression in the absence of GSK3. In other words, it could be that GSK3 is mediating NOTCH expression by acting on the transcritption factors involved on its regulation. 

Yes .. Thank you for your answer. But i need some more explanation. There is some inter relation between them... So i need to proof the stabilization of notch by GSK-3

You've found a possible correlation between the two but this is all. Try to overexpress GSK3β and see if you get an increase in Notch expression. This will give you the reciprocal experiment.

Doing an IP and not pulling down Notch suggests that they are not physically interacting with each other. The effect you are seeing with a reduction in Notch after your knock down of shRNA (as said above) is likely down to secondary effects (i.e. GSK3β is regulating transcription factors that regulate Notch expression). GSK3β is a central mediator that regulates many transcription factors including β-catenin.

I would suggest trying to find some good review papers on GSK3β so you can have a better understanding on how this protein regulates different transcription factors. This may help in identifying some candidate proteins to look at and design some future experiments.

Thank you Dr.Jenna ridsdale: I am doing overexpression assay and waiting for the results... I would like to correlate with alpha isoform with notch... I tried lot of paper to find out the solution to move forward my research still I am struggling...

Thank you for your valuable answer...