Question: GO enrichment analysis. Non-model organism.
0
gravatar for Frogs
23 months ago by
Frogs0
Frogs0 wrote:

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?

non-model go • 2.5k views
ADD COMMENTlink modified 23 months ago by dago2.5k • written 23 months ago by Frogs0
3
gravatar for Istvan Albert
23 months ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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.

ADD COMMENTlink written 23 months ago by Istvan Albert ♦♦ 80k
2
gravatar for dago
23 months ago by
dago2.5k
Germany
dago2.5k wrote:

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 here

test

Good luck!

ADD COMMENTlink modified 23 months ago • written 23 months ago by dago2.5k

Indeed, discussed many, many times before.

ADD REPLYlink written 23 months ago by h.mon25k

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

ADD REPLYlink written 23 months ago by Frogs0

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.

ADD REPLYlink written 14 months ago by pablo6199170
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