[BioC] KEGG data missing from KEGG.db

mcarlson at fhcrc.org mcarlson at fhcrc.org
Sat Jul 17 01:32:14 CEST 2010


Hi Chris,

I suspect that there are a couple of things going on here.  The 1st is  
that I think your version of KEGG.db is out of date.  I get many genes  
for the pathway you checked on the latest version.  But I can't be  
100% sure because you did not share your sessionInfo() with us.  :(

The other issue you are likely facing is that the KEGG website is  
updated continuously, while the annotation packages are updated (and  
versioned) biannually.  The web site will give you the very most  
current information, whereas the package will allow you to reproduce  
your results several months from now when you finally get that paper  
written up or even later when someone demands that you demonstrate how  
you got that result two years ago etc.  Both of these approaches are  
valuable in their own way.  But the difference between them means that  
a few annotations may not be in the latest annotation packages till  
they are updated again in the fall.

Anyhow I hope that this helps you.


   Marc



Quoting Chris Fjell <cfjell at interchange.ubc.ca>:

> 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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