[BioC] Question about 'annFUN.db' in topGO ....

[Joern Toedling]

Hi ALok,
you could use the function 'annFUN.gene2GO' instead. Then you have to
supply a list that contains the GO identifiers mapped to each gene,
which, for example, you can create using the biomaRt package.

Here's an example:

- suppose we have a list "mm9.gene2GO", which maps Ensembl gene
identifiers to GO identifiers:

head(mm9.gene2GO)
$ENSMUSG00000000001
[1] "GO:0003924" "GO:0005515" "GO:0005737" "GO:0005794" "GO:0005834"
[6] "GO:0007186"

$ENSMUSG00000000003
[1] "GO:0005549"

$ENSMUSG00000000049
[1] "GO:0005615" "GO:0030193"
...

- we have a vector of genes of interest:

selGenes <- c("ENSMUSG00000000003","ENSMUSG00000000049")


- then the way to find GO identifiers enriched for these genes of
interest is like this:

inGenes <- factor(as.integer(names(mm9.gene2GO) %in% selGenes))
names(inGenes) <- names(mm9.gene2GO)
GOdata <- new("topGOdata", ontology="BP", allGenes=inGenes,
              annot=annFUN.gene2GO, gene2GO=mm9.gene2GO)

...

See the topGO vignette for more details on these steps.
Hope this helps,
Joern


ALok wrote:
> Dear all,
>
> I have a question about using the function 'annFUN.db' in topGO. for which i
> have converted my gene symbols to probe id (by using annotation package
> hgu133plus2) and used the function
>
> GOdata <- new("topGOdata", ontology = "MF", allGenes = geneList,geneSel =
> myInterestedGenes,description = "GO analysis of my data.", annot =
> annFUN.db, affyLib = affyLib)
> to create the GOdata object and find enriched GO
> terms.
>
> Is there a direct way to find enriched GO terms by using the gene symbols
> without converting them to probe Id's.
>
> Thanks in advance!
> ALok
>