Many people use Gene Ontology analyses to look for enrichment of specific terms, and some of them further include GO Slim results to get "higher rank" terms.
- whether the GO Slim approach is meaningful, given that we can provide the specific terms that we want to slim for
- how can we choose these specific terms ("transcription factor", etc.) before even doing the analysis
- which program (web or not) to use
I know this is kind of a broad question but I haven't seen any recent post related to GO Slim (this one is quite old) on Biostars and thought this could be useful not only to me but to others. Many thanks!