[BioC] Annotating yeast ORFs with GO and KEGG
Ken Simpson
ksimpson at wehi.edu.au
Mon Nov 17 06:53:08 MET 2003
Hi Shih-Te,
Use the lookUp function (devel version of the annotate package) or
multiget (older version) to obtain the quantities of interest.
e.g.
> lookUp("YAL001C","YEAST","GO")
<NA> <NA> <NA>
"GO:0000127" "GO:0003709" "GO:0006384"
> multiget(c("YAL001C","YAL002W"),envir=YEASTGO)
$YAL001C
<NA> <NA> <NA>
"GO:0000127" "GO:0003709" "GO:0006384"
$YAL002W
<NA> <NA> <NA>
"GO:0045324" "GO:0005554" "GO:0005624"
KEGG information is available for some organisms, but not (IIRC) yeast,
yet. Do help(package=YEAST) to see the available annotation data.
Cheers,
Ken
On Mon, 17 Nov 2003, Shih-Te Yang wrote:
> Dear all:
>
> I am wondering to annotate each of Yeast genes or ORFs with GO and KEGG
> pathway. As you had known, the package of "AnnBuilder" and metadata of
> "GO"/"KEGG" can provide the functions about what are genes involved in the
> specific GO category and KEGG pathway.
>
> However, I am interested in what are the GO terms or KEGG belong to the
> genes I want!! Please see the format below:
>
> ORF GO KEGG
> YAL001C .. ..
> YAL002W .. ..
> YAL003W .. ..
> YAL004W .. ..
> .. .. ..
>
> How can I annotate these kind of information?
>
> Regards,
> Shih-Te
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