[BioC] Annotating yeast ORFs with GO and KEGG

[Ken Simpson]

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