[BioC] KEGG pathway

[Marc Carlson]

Yihuan Xu wrote:
> Dear all,
>
> I am interested in a gene pla2g2a, which KEGG entry is 18780. DBGET resurlt 
> for mmu18780 in KEGG website shows there are 9 pathways containning this 
> gene. I checked one of these pathways (mmu00590) using KEGG package, however 
> 18780 didn't show up in the pathway.
>
> my code:
>   
>> library(KEGG)
>> aa <-as.list(KEGGPATHID2EXTID)
>> aa$mmu00590
>>     
>  [1] "106648" "107141" "109857" "11684"  "11685"  "11686"  "11687"  "11688"
>  [9] "12408"  "12409"  "13088"  "13089"  "13090"  "13094"  "13095"  "13096"
> [17] "13097"  "13098"  "13099"  "13106"  "13109"  "13110"  "13117"  "13118"
> [25] "13119"  "13850"  "14598"  "14775"  "14776"  "14778"  "14780"  "16993"
> [33] "17001"  "170716" "18778"  "18781"  "18782"  "18783"  "18784"  "19215"
> [41] "19223"  "19224"  "19225"  "207182" "21391"  "226105" "226143" "23887"
> [49] "26565"  "26970"  "26971"  "28200"  "329502" "404195" "53357"  "54486"
> [57] "64292"  "64385"  "66350"  "67305"  "69836"  "69888"  "70101"  "71519"
> [65] "72054"  "72082"  "72303"  "74519"  "75512"  "96979"
>
> KEGG DBGET resurlt:
> http://www.genome.jp/dbget-bin/www_bget?mmu:18780
>
>
> Do you know what happened here? Thank you very much.
>
> Yihuan
>
> ************************************************
> Yihuan Xu
> Biostatistician
> Division of Biostatistics
> Department of Pharmacology and Experimental Therapeutics
> Thomas Jefferson University
> 1015 Chestnut Street, Suite M100
> Philadelphia, PA19107
> Phone: 215-503-1357
> Fax: 215-503-3804
>
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>
>   

You are correct and there appears to have been something wrong with the
mapping from KEGG pathway ID to external ID for some time.  Thank you
for bringing this problem to my attention.  It will be addressed as soon
as I can reasonably get to it.  Unfortunately, right now we are in a bit
of a crunch for the next release and so my time is quite limited.

But please note that the reverse map appears to be ok.  So you could
also have found that gene associated with the pathway in the KEGG
package by doing the following:
get("18780", KEGGEXTID2PATHID)


As long as you avoid relying on the KEGGPATHID2EXTID, I think you will
be ok.

    Marc