Cell Miner is a good way to compare gene expression and drug response across the NCI-60 cell panel. Ref: Cancer Res. 2012 July 15; 72(14): 3499–3511. doi:10.1158/0008-5472.CAN-12-1370. I tried, but could not attach a pdf on Cell Miner.
Flow cytometry will be a valuable tool for the analysis of differential expression of cellular CD marker. however if u r looking for molecular markers, real time pcr can measure the differntial expression of genes & mRNAs.