[BioC] KEGG data missing from KEGG.db

[Chao-Jen Wong]

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