You don't need R, just two lists of genes, one list for unregulated and one list for your other category. You can paste each set into BioVenn to make a roughly proportional circular Venn diagram. If you want a list of overlaps, just use
grep between the two lists:
$ grep -fF listA listB > answer
Here are three simple methods using R. Thomas Girke has a lot of useful R stuff. FInd it and use it.
# generate two random lists
a <- sample(LETTERS,20)
b <- sample(LETTERS,20)
# grab Thomas Girke's Venn Diagram functions
# draw a diagram
qlist <- venndiagram(x=a, y=b, unique=T, title="2-Way Venn Diagram", labels=c("Sample1", "Sample2")
,plot=T, lines=c(2,3), lcol=c(2,3), lwd=3, cex=1.3, type="2")
You'll find that qlist is a list containing the elements of each Venn diagram region. e.g.
 "M" "J" "F" "U" "O" "K" "S" "T" "G" "Q" "Y" "Z" "L" "W" "A"
However, if you just need simple counts, you can use the %in% operator:
# count the common elements of a and b
sum(a %in% b)
# get the elements themselves
a[a %in% b]
# or use other functions for sets
Note: if you examine the code at the URL above (just load it into your browser) he says he has replaced that Venn Diagram function with something better. Might be worth examining.