[BioC] KEGG data missing from KEGG.db
Chris Fjell
cfjell at interchange.ubc.ca
Sat Jul 17 01:44:49 CEST 2010
Thanks for the quick replies! You're right, neglected my sessionInfo
(oops - sorry!). From that I see I'm using KEGG.db_2.3.5 .
I'm on R 2.10 and BioC 2.6 needs R 2.11. I'll need to upgrade all.
I reinstalled KEGG.db repeatedly, thinking that would get me the latest
and greatest, but of course I need to update R for that!
I'm surprised KEGG.db 3.5 didn't have NOD-like receptor signaling
pathway hsa04621...
Cheers,
-Chris
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid tools stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] RBGL_1.24.0 KEGGgraph_1.2.2 Rgraphviz_1.24.0
[4] KEGG.db_2.3.5 pls_2.1-0 preprocessCore_1.8.0
[7] limma_3.2.3 SPIA_1.4.0 hopach_2.6.0
[10] cluster_1.13.1 org.Rn.eg.db_2.3.5 org.Mm.eg.db_2.3.6
[13] org.Hs.eg.db_2.3.6 genefilter_1.28.2 annotate_1.24.1
[16] GOstats_2.12.0 graph_1.24.4 Category_2.12.1
[19] GO.db_2.3.5 RSQLite_0.8-4 DBI_0.2-5
[22] AnnotationDbi_1.8.2 CORNA_1.2 XML_2.8-1
[25] GEOquery_2.11.3 RCurl_1.4-1 bitops_1.0-4.1
[28] biomaRt_2.2.0 Biobase_2.6.1
loaded via a namespace (and not attached):
[1] GSEABase_1.8.0 splines_2.10.1 survival_2.35-8 xtable_1.5-6
mcarlson at fhcrc.org wrote:
> 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 that I think your version of KEGG.db is out of date.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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>
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--
-------------------------------------------------
Christopher Fjell, PhD
Postdoctoral Fellow
Centre for Microbial Diseases and Immunity Research
Department of Microbiology and Immunology
University of British Columbia
2259 Lower Mall
Vancouver, British Columbia, Canada, V6T 1Z4
cfjell at interchange.ubc.ca / chris at cmdr.ubc.ca
Fax: (604) 827-5566
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