Gene list preparing for overrepresentation test

[hubentu]

For the GO overrepresentation test, when preparing the reference gene list (background), should I remove foreground genes from reference genes for overrepresentation test before uploading? Thanks!

Given, foreground list (List) and reference list (Population):
List Hits (LH)
List Total (LT)
Population Hits (PH)
Population Total (PT)

It seems panther did the fisher exact test directly. If this is true, we should remove foreground list from reference first, right?

L	P
LH	PH
LT - LH	PT - PH

However, for DAVID, the reference list should always include foreground list and it will do the subtraction in the contingency table.

L	P-L
LH	PH - LH
LT - LH	PT - LT - (PH-LH)