topGO: How to create gene2GO annotation for mouse?
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Brian Smith ▴ 120
@brian-smith-6197
Last seen 9 months ago
United States

Hi,

I was trying to use topGO to find over-representation of some selected genes. I don't have probe ids, just the gene symbols for both the selected genes and the gene universe. For the topGO object, I have:

sampleGOdata <- new("topGOdata",
                      description = "Simple session", ontology = "BP",
                      allGenes = mygeneUniverse, geneSel = myselectedGenes,
                      nodeSize = 10,
                      annot = annFUN.db)

 

How can I create the annot object so that I can create my topGO object?

thanks!!

topgo • 4.2k views
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Entering edit mode
Bernd Klaus ▴ 590
@bernd-klaus-6281
Last seen 2.7 years ago
Germany

Hi Brian,

this is a bit complicated, you need to define something like:

annot=annFUN.org, mapping="org.Mm.eg.db", ID = "ensembl"

in the call of "new" (for ENSEMBL IDs in this case). You can find a worked example in some teaching material of mine:

http://www-huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html#gene-ontology-enrichment-analysis

Here are  the link to the source of this html:

http://www-huber.embl.de/users/klaus/teaching.html#differential-expression-analysis-of-rna-seq-predoc-course-2014

Cheers.

 

Bernd

 

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