GO enrichment analysis. Non-model organism.

Question

[Frogs]

I have a list of differentially expressed genes and the GO terms related to them.

I don't know how to carry out GO enrichment analysis in this non-model organism as any tool I have found wants the list of gene names and the name of the species.

Is there a tool out there which will carry out the analysis with just the list of genes and their GO terms?

Answer 1

[Istvan Albert]

Most tools will allow you to upload custom annotations as long as you have a typically tabular file that lists the gene name and the corresponding GO number.

Agrigo: http://bioinfo.cau.edu.cn/agriGO/

ErmineJ: http://erminej.chibi.ubc.ca/

and many others.

Answer 2

[dago]

I think this problem has been discussed before here. Try to use the search function on the Biostarts home page. I found few posts already, see

Good luck!

[h.mon]

Indeed, discussed many, many times before.

[Frogs]

I searched through them before I posted and none had a good answer and were many years old.

[pablo61991]

Annotation > Go enrichmetn and KEGG pathway enrichment are problematic for non model organism researchers. Even more problematic when most of us are PhD students suddenly involved in to transcriptomics form some reasons.