I am new to GO annotation. I use DAVID to do GO annotation, which calculate the gene overrepresentation by fisher exact test. I have gene list with FDR cutoff, in my point of view, if I choosing FDR <= 10% gene for GO annotation, the matched GO terms should have some overlap with FDR <= 5% ones because the two lists have many gene overlap and the last one is with higher confidence, however, it's totally different, and I doubt the GO annotation result with FDR <= 10% gene is true?
How can the annotation be not robust with the given gene set changed? and is there any ways/paper/packages to permitted this? Thanks!