[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that I think your version of KEGG.db is out of date.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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