I am new to GSEA analysis and i use DAVID for the analysis, so please excuse if these are basic questions. I am currently analyzing WES data, and for that I compare my gene lists to different custom backgrounds. When I looked at the results of the Functional annotation chart I noticed something that I cannot explain in the Count, LT, PH, PT Columns.
It seems like the a gene in my gene list is only counted in the "Count" column, if it also appears in the background. Thus the more background genes I include, the bigger the "Count" gets and the more significant the enrichment is. Is this intentional? And if yes, why? I thought that the background shouldn't play a role in determining what genes of my gene list are in a particular Pathway or GO term.
Furthermore, I noticed that the PT (population total) and LT (List total) are different for each Term. I also have no idea why this is the case, since the number of genes in my gene list and my background shouldn't change.
If somebody could help my understand these observations, I'd be very grateful!