Suppose I have a list of genes obtained from an experiment using mice. Now I have to perform an enrichment and I can choose to perform it using mouse GO terms, human GO terms, etc...

Is it ok to use human GO terms over mice genes?

If yes, then why bother creating specific mouse GO terms? I understand that mice may be used as a human model for some diseases but then...why are the two set of GO terms different?

If I can apply human GO terms over mice genes, should I perform enrichment analysis using zebrafish GO terms over mice genes (or human genes!), if those genes share a certain degree of similarity (such as homology)?

EDIT: I posted [the same question][1] in stack exchange bioinformatics but no answers there.


  [1]: https://bioinformatics.stackexchange.com/questions/14760/is-it-ok-to-use-gene-sets-from-an-organism-to-enrich-genes-from-a-different-orga
Gene sets such as GO terms are developed by integrating the current scientific knowledge about the function of genes. Even in the case when you use human GO terms in human, many of the functions of those human genes which are "summarized" by the human ontologies, have actually been (at least in part) first discovered in other model organisms such as mouse. Thus, even if you look at them from the human point of view, they may reflect general knowledge which applies to many organisms.

In my opinion, this is a fuzzy characteristic of gene ontologies. All in all, a good strategy can be, when you use gene ontologies in another organism, to assume that the genes that are homologous/orthologous between the organisms share the same functions. This may sometimes not be the case, but I believe that the typical pathway enrichment analyses discover "general trends" which may be not be so impacted by particular exceptions.

Personally I am fond of the [msigdbr][1] package, which provides gene sets from the MSigDB (including GOs, KEGG, Reactome...) for different organisms. It is built by, starting from the human terms containing human genes, translating them to other species by selecting  the orthologs as defined by the HUGO Gene Nomenclature Committee.


  [1]: https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html