A while back I wrote about my favorite Venn Diagram tool. The Venny Venn Diagram Plotter may actually be better. It is a freely available, web accessible Venn plotter that will plot your redundancy for you. For example, if you have an output list of upregulated proteins by gene name from Proteome Discoverer and a list of upregulated genes from a microarray list, you simply copy the column from your Excel file and place it into Venny. It is plotted automatically, saving you tons of time and perhaps even DigDB analysis (necessary if you are comparing lists of 3 or more).
You can use Venny for comparing up to 4 lists at the author's site here.
If you need to compare a 5th list, a modified version of Venny is available at the Genotoul Bioinfo page here.