Example gene set: GO:0000002
When I use different tools, I get different lists of genes! g:Profiler vs gageData and more. The thing is I have not yet been able to find an up to date list of genes for this gene set.
I want to do it in R preferably, and just get a vector of all the genes from geneontology.org officially, not through any of the 3rd party sites. I tried downloading some of their tables but the results gave bad gene sets. I did not manage to find an up to date .gmt file, the mSigDB gmt files for GO terms are from 2016
EDIT: I have been able to find the list of genes here http://amigo.geneontology.org/amigo/term/GO:0000002 by setting the correct parameters, 22 genes in human. However, I am still unable to find a download of up to date annotation files/gmt files that give the same results.