Can anyone please help me to perform Gene ontology analysis on my differentially expressed genes? My organism (Pichia pastoris) is a non model organism and thus many online portals and tools like QUICKGO, AMIGO does not support analysis of gene ontology terms of Pichia pastoris.
Is it a good idea to convert gene IDs of my organism into a model organism gene IDs like Saccharomyces cerevisiae. If yes, then can anyone please tell me how to convert the Gene/protein Ensembl fungi IDs of pichia pastoris into Saccharomyces IDs readable by the online available portals?
A lot of researchers perform GO with human/mouse/zebrafish orthologs of their study organism's genes because those are species for which a significant amount of biological information is available. So I guess it is acceptable in your case too. However, when doing so, we assume that the orthologs are involved in the same functional networks in both species (your's & the one for which GO is available). I think the validity of using orthologs for GO essentially comes down to how closely evolutionarily related the species are.
You can get Pichia -> Saccharomyces orthologs from OMA Genome Pair Orthology tool. Enter YEAST for species 1 & KOMPG for species 2, and preferred ID as Ensembl gene ID. You should get a table with yeast ensembl IDs mapped to orthologous Pichia (Komagataella phaffii) genes. You can choose to keep only the 1:1 orthologs as 1:m (one to many) can be a bit of pain to deal with. You can then join the yeast IDs to your list of genes, and move on to GO analysis.
