I am working on cancer project. I have made my small molecule which kills cancer cells and trying to figure out the mechanism of its action, i.e. its protein target. Besides affinity purification, I am thinking to perform a global gene expression analysis ,using Affy chips, after treatment of cancer cells with my compound. I know I gonna get thousands of data points. Did you ever try something like that? If you know change in mRNA expresion can you find out the target?