[BioC] TopGO: How to retrieve the gene list related to a GO ID ?

[Ricardo]

Hi Jean-Pierre,

I assume you were using TopGO from the message header,
so you can do the following:

# sample are your candidate genes and allgenes all other genes
# you included in your analysis

universe = factor(as.integer(allgenes %in% sample))
names(universe) = allgenes

# you created an GOdata object for TopGO
# "GO" would be your annotation Gene2GOid list

GOdata = new('topGOdata',ontology="BP",allGenes=universe,  
annot=annFUN.gene2GO,gene2GO=GO)

# retrieve genes2GO list from the "expanded" annotation in GOdata

allGO = genesInTerm(GOdata)

#allGO["GO:0000109"]
#$`GO:0000109`
#[1] "ENSG00000012061" "ENSG00000104472" "ENSG00000175595"

SAM_ANOTATION = lapply(allGO,function(x) x[x %in% sample] )

# Your significant genes for GO:0051427
SAM_ANOTATION[["GO:0051427"]]

Hope it was helpful.
Best wishes,
Ricardo


Jean-Pierre Desvignes wrote:
> Hello,
>
> I would known if it was possible to retrieve the genes related to a GO term ?
>
> If yes, how to do that ?
>
> GO.ID  Term  Level  Annotated  "Significant"  Expected  classicFisher
>
> GO:0051427  hormone receptor binding  5  16  17  "2"  0.12  0.00583
>
> For example, what are the 2 Significant genes here ?
>
>
>
> Thanks a lot.
>
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