hgu133aPATH {hgu133a}R Documentation

Mappings between probe identifiers and KEGG pathway identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. hgu133aPATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved

Details

Each KEGG pathway has a name and id. Pathway name for a given pathway id can be obtained using the KEGG data package that can either be built using AnnBuilder or downloaded from Bioconductor http://www.bioconductor.org.

Graphic presentations of pathways are searchable at url{http://www.genome.ad.jp/kegg/pathway.html} by using pathway ids as keys.

Mappings were based on data provided by:

KEGG:ftp://ftp.genome.ad.jp/pub/kegg/pathways. Built: Release 31.0 (July 2004)

LocusLink:ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Built: September 15, 2004

Package built Wed Sep 15 18:48:08 2004

References

http://www.genome.ad.jp/kegg/

Examples

    # Convert the environment to a list
    xx <- as.list(hgu133aPATH)
    # Remove probe ids that do not map to any pathway id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The pathway ids for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    } 

[Package hgu133a version 1.6.5 Index]