[BioC] KEGG data missing from KEGG.db
Chao-Jen Wong
cwon2 at fhcrc.org
Sat Jul 17 01:17:06 CEST 2010
Which version of KEGG.db are you using? If you can upgrade your KEGG.db
to the current version 2.4.1, then you should be able to find the
information.
> mget( "hsa04621" , revmap(KEGGEXTID2PATHID) )
$hsa04621
[1] "10392" "10454" "10910" "114548" "1147" "1432" "22861" "22900"
[9] "23118" "257397" "260434" "29108" "2919" "2920" "329" "330"
[17] "331" "3320" "3326" "3551" "3553" "3569" "3576" "3606"
[25] "4210" "4671" "4790" "4792" "4793" "55914" "5594" "5595"
[33] "5599" "5600" "5601" "5602" "5603" "58484" "59082" "5970"
[41] "6300" "6347" "6352" "6354" "6355" "6356" "6357" "64127"
[49] "64170" "6885" "7124" "7128" "7184" "7189" "7205" "834"
[57] "838" "841" "84674" "8517" "8767" "9051"
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-05-17 r52025)
x86_64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] KEGG.db_2.4.1 RSQLite_0.9-1 DBI_0.2-5
[4] AnnotationDbi_1.11.3 Biobase_2.9.0
loaded via a namespace (and not attached):
[1] tools_2.12.0
On 07/16/10 15:44, Chris Fjell wrote:
> I'm using KEGG.db and org.Hs.egPATH to find the genes in KEGG pathways
> and the reverse.
> It seems to me some pathways are not found in the annotation packages,
> for example hsa04621.
>
> Can someone correct me? Anyone know where to get the equivalent in, say,
> a tab-delimited file instead?
>
> For example, when I look up the gene 10392 on the KEGG web site I get
> pathways
> (http://www.genome.jp/dbget-bin/www_bget?hsa:10392)
> hsa04621 NOD-like receptor signaling pathway
> hsa05120 Epithelial cell signaling in Helicobacter pylori infection
> hsa05131 Shigellosis
>
> But using KEGGEXTID2PATHID I get no entry for that pathway
>
>> mget( "hsa04621" , revmap(KEGGEXTID2PATHID) )
>>
> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
> value for "hsa04621" not found
>
> And the gene just gives me one pathway:
>
>> mget( "10392" , org.Hs.egPATH )
>>
> $`10392`
> [1] "05120"
>
> I think I'm doing this correctly as for "hsa04620":
>
>
>> mget( "hsa04620" , revmap(KEGGEXTID2PATHID) )
>>
> $hsa04620
> [1] "10000" "10333" "10454" "114609" "1147" "1326" "1432"
> "148022"
> [9] "207" "208" "23118" "2353" "23533" "23643" "29110"
> "3439"
> [17] "3440" "3441" "3442" "3443" "3444" "3445" "3446"
> "3447"
> [25] "3448" "3449" "3451" "3452" "3454" "3455" "3456"
> "353376"
> [33] "3551" "3553" "3569" "3576" "3592" "3593" "3627"
> "3654"
> [41] "3661" "3663" "3665" "3725" "3929" "4283" "4615"
> "4790"
> [49] "4792" "51135" "51284" "51311" "5290" "5291" "5293"
> "5294"
> [57] "5295" "5296" "54106" "54472" "5594" "5595" "5599"
> "5600"
> [65] "5601" "5602" "5603" "5604" "5605" "5606" "5608"
> "5609"
> [73] "5879" "5970" "6300" "6348" "6351" "6352" "6373"
> "6416"
> [81] "6696" "6772" "6885" "7096" "7097" "7098" "7099"
> "7100"
> [89] "7124" "7187" "7189" "841" "8503" "8517" "8737"
> "8772"
> [97] "929" "941" "942" "958" "9641"
>
>
>> mget( "10000" , org.Hs.egPATH )
>>
> $`10000`
> [1] "04010" "04012" "04062" "04150" "04210" "04370" "04510" "04530" "04620"
> [10] "04630" "04660" "04662" "04664" "04666" "04722" "04910" "04920" "05200"
> [19] "05210" "05211" "05212" "05213" "05214" "05215" "05218" "05220" "05221"
> [28] "05222" "05223"
>
> Cheers,
> -Chris
>
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--
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M1-B514
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org
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