[BioC] KEGG pathway

[mcarlson at fhcrc.org]

Quoting Yihuan Xu <Yihuan.xu at jefferson.edu>:

> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 

Hi everyone,
It would appear that I may have spoken too soon.  I am afraid that you'll have
to forgive me, as I am still new to this whole Q/A forum.

It seems that this problem does not occur in the latest version of KEGG.  Here
is my session info. so that you too can get this result:

> sessionInfo()
R version 2.6.0 alpha (2007-09-13 r42838)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] KEGG_1.99.10

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15

Please update your packages to what is in devel and give it a whirl.

    Marc