I have a list of 1000 gene names (entrez ID) which is a subset of about 8000 genes expressed in a tumor tissue, and I want to look for GO enrichment and TFBS enrichment and so on.
I know there are a variety of online tools available. However, most of them only take these 1000 subset genes and give a p-value or FDR, which is very biased, because my whole gene set (8000 genes) is obvious enriched for different terms (for example, tumor) by itself. Could anyone suggest an online tool or R package that can take two gene lists (one for interested genes, one for all genes), and query its database and pop out p-values and FDR? Thanks.