Question: KEGG pathway
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gravatar for Yihuan Xu
11.9 years ago by
Yihuan Xu130
Yihuan Xu130 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$mmu00590 [1] "106648" "107141" "109857" "11684" "11685" "11686" "11687" "11688" [9] "12408" "12409" "13088" "13089" "13090" "13094" "13095" "13096" [17] "13097" "13098" "13099" "13106" "13109" "13110" "13117" "13118" [25] "13119" "13850" "14598" "14775" "14776" "14778" "14780" "16993" [33] "17001" "170716" "18778" "18781" "18782" "18783" "18784" "19215" [41] "19223" "19224" "19225" "207182" "21391" "226105" "226143" "23887" [49] "26565" "26970" "26971" "28200" "329502" "404195" "53357" "54486" [57] "64292" "64385" "66350" "67305" "69836" "69888" "70101" "71519" [65] "72054" "72082" "72303" "74519" "75512" "96979" KEGG DBGET resurlt: http://www.genome.jp/dbget-bin/www_bget?mmu:18780 Do you know what happened here? Thank you very much. Yihuan ************************************************ Yihuan Xu Biostatistician Division of Biostatistics Department of Pharmacology and Experimental Therapeutics Thomas Jefferson University 1015 Chestnut Street, Suite M100 Philadelphia, PA19107 Phone: 215-503-1357 Fax: 215-503-3804
pathways • 612 views
ADD COMMENTlink modified 11.9 years ago by Marc Carlson7.2k • written 11.9 years ago by Yihuan Xu130
Answer: KEGG pathway
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gravatar for Marc Carlson
11.9 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Yihuan Xu wrote: > Dear all, > > I am interested in a gene pla2g2a, which KEGG entry is 18780. DBGET resurlt > for mmu18780 in KEGG website shows there are 9 pathways containning this > gene. I checked one of these pathways (mmu00590) using KEGG package, however > 18780 didn't show up in the pathway. > > my code: > >> library(KEGG) >> aa <-as.list(KEGGPATHID2EXTID) >> aa$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 > > _______________________________________________ > 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 > > 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
ADD COMMENTlink written 11.9 years ago by Marc Carlson7.2k
Answer: KEGG pathway
0
gravatar for Marc Carlson
11.9 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
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_TELE PHONE=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
ADD COMMENTlink written 11.9 years ago by Marc Carlson7.2k
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