How to perform GO enrichment in non-model organisms?

Question

[CaERu]

Hello

I am a beginner using RNA-seq data for analysis. I would like to use GO enrichment analysis to infer the functions of genes that are upregulated by DEG analysis. However, since my analysis target is a non-model plant, there are no annotation files available, so I have to create them myself. Fortunately, I obtained the whole genome sequence and the GFF file describing the positions of the gene sequences. If I were to annotate all genes myself, what tools would be optimal? I personally plan to use eggNOG-mapper.

Answer 1

[lieven.sterck]

In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed.

Other options are Interpro2GO (first run an interpro analysis, then 'convert' the results to GO-terms) or even Blast2GO . All approach have the strengths and weaknesses so it is a bit of a trade-off between precision and recall for all them. You might consider running all approaches and combine the results afterwards to get a more complete view. Keep in mind that these can be quite heavy analyses (eg. Interproscan running) so you ideally have access to serious compute resources (and even then they might run for a while).

In any you will in the end get more useful info than only the GO-terms, Interpro will give you info on the protein domains present which to itself can also indicate function (even when lacking GO-terms). Just to say that these are valuable analyses to do anyway.

You should also have a look at GOslim: this is a kind of higher level GO annotation and might prove more useful for DEG analysis