org.Hs.egPATH {org.Hs.eg.db}R Documentation

Mappings between Entrez Gene identifiers and KEGG pathway identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. org.Hs.egPATH maps entrez gene identifiers to the identifiers used by KEGG for pathways

Details

Each KEGG pathway has a name and identifier. Pathway name for a given pathway identifier 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 identifiers as keys.

Mappings were based on data provided by: KEGG GENOME ( ftp://ftp.genome.jp/pub/kegg/genomes ) on 2008-Apr1

References

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

Examples

    x <- org.Hs.egPATH
    # Get the entrez gene identifiers that are mapped to a KEGG pathway ID
    mapped_genes <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_genes])
    if(length(xx) > 0) {
      # Get the PATH for the first five genes
      xx[1:5]
      # Get the first one
      xx[[1]]
    }

    # For the reverse map:
    # Convert the object to a list
    xx <- as.list(org.Hs.egPATH2EG)
    # Remove pathway identifiers that do not map to any entrez gene id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The entrez gene identifiers for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    }

[Package org.Hs.eg.db version 2.2.0 Index]