[BioC] KEGG data missing from KEGG.db

Chris Fjell cfjell at interchange.ubc.ca
Sat Jul 17 00:44:16 CEST 2010


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



More information about the Bioconductor mailing list