after isolation of my cells can i make characterization for these cells using gel electrophoresis after doing conventional PCR for certain genes known from literature that they are overexpressed by these cells ?
Yes you can. If your gel electrophoresis showing band at specific position with reference to ladder and the primer you have used than that gene is present in the cell you have isolated.
Is it bacterial or eukaryotic cells? For the former colony PCR is very straight forward. For the latter it is sometimes less easy (in my experience with yeast, I need to extract DNA prior PCR).