[BioC] KEGG: gene ids for nodes in a pathway

Sim, Fraser Fraser_Sim at URMC.Rochester.edu
Tue May 5 20:16:18 CEST 2009

KEGGgraph is part of R2.9.0 not 2.8.1. You will need to upgrade to the latest version of R.


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Tim Smith
Sent: Tuesday, May 05, 2009 2:03 PM
To: bioc
Subject: Re: [BioC] KEGG: gene ids for nodes in a pathway

Hi David,

Thanks for the suggestion. That sounds exactly like what I want. I tried to install KEGGgraph, but got some errors:

> source("http://www.bioconductor.org/biocLite.R")
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
>     biocLite(KEGGgraph)
Running biocinstall version 2.3.13 with R version 2.8.1 Your version of R requires version 2.3 of Bioconductor.
Error in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  : 
  object "KEGGgraph" not found

Am I doing something wrong?


PS: My session info is:

> sessionInfo()
R version 2.8.1 (2008-12-22) 

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RankAggreg_0.3-1    gplots_2.6.0        gmodels_2.14.1      gtools_2.5.0-1      gdata_2.4.2         Rgraphviz_1.14.1   
 [7] EBImage_2.6.0       KEGGSOAP_1.16.0     SSOAP_0.4-8         RCurl_0.94-0        geneplotter_1.20.0  lattice_0.17-20    
[13] XML_1.99-0          biomaRt_1.16.0      GOstats_2.8.0       Category_2.8.4      RBGL_1.18.0         annotate_1.20.1    
[19] xtable_1.5-4        graph_1.20.0        PFAM.db_2.2.5       GO.db_2.2.5         KEGG.db_2.2.5       org.Mm.eg.db_2.2.6 
[25] org.Hs.eg.db_2.2.6  RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.4.3 genefilter_1.22.0   survival_2.34-1    
[31] affy_1.20.2         Biobase_2.2.2      

loaded via a namespace (and not attached):
[1] affyio_1.10.1        cluster_1.11.12      grid_2.8.1           GSEABase_1.4.0       KernSmooth_2.22-22   MASS_7.2-45         
[7] preprocessCore_1.4.0 RColorBrewer_1.0-2  

From: Jitao David Zhang <davidvonpku at gmail.com>

Sent: Tuesday, May 5, 2009 1:21:04 PM
Subject: Re: [BioC] KEGG: gene ids for nodes in a pathway

Hi Tim,

  Using KEGGgraph package may solve the problem. As an example:

    // use human MAPK pathway as an example
    xfile <- system.file("/extdata/hsa04010.xml", package="KEGGgraph")
    p <- parseKGML(xfile)
    pNodes <- nodes(p)

    displayNames <- sapply(pNodes, getDisplayName)
    geneids <- sapply(pNodes, function(x) translateKEGG2GeneID(getName(x)))

    The displayNames now contain the labels (the visible names of the nodes), while the geneids are the EntrezGeneID (in human case) of the genes contained in that node.

    To install KEGGgraph, just type


    Best wishes,


I wanted a list of genes for a particular pathway arranged nodewise. For example, if I select the Jak-stat pathway ("http://www.genome.jp/kegg/pathway/hsa/hsa04630.html"), how do I get the entrez ids of genes associated with the node 'STAT' ? Currently, I use the following code:

x <- toTable(org.Hs.egPATH)

and then select genes associated with a particular pathway (e.g. for Jak-stat: "04630") . But this gives the entire set of genes associated with the pathway. Is there a way to get the entrez ids of the genes associated with each of the nodes ('JAK', 'STAT', 'STAM','PIAS' etc.) in the pathway?


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Jitao David Zhang
Computational Biology Ph.D.
Division of Molecular Genome Analysis
DKFZ, Heidelberg D-69120, Germany


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