I have a lot of protein clusters. I want to perform an enrichment analysis of their functional annotations, against reference datasets or list of genes I select.
More precisely: a method yields cluster of proteins. I want to decide, for each cluster (which is a set of proteins identifiers), if it holds meaning regarding the proteins it contains, by comparing the annotations found in the cluster and the annotations found in common or specific datasets.
Initially, I used DAVID, which compute the GO annotations from the protein list, then perform the enrichment analysis against common datasets.
However, DAVID suffer of the following drawbacks:
- since I didn't find any other way to use it, I'm limited by the web interface and its limitations (number of genes, url size, number of request/day).
- automation over the web interface is a hacky script.
The team behind seems to offer a way to run DAVID in-house (allowing, hopefully, to relax the limitations), but I can't find any way to download the database from their website.
What are the alternative ways to get enrichment analysis over proteins in a reliable and automated way ?