Mappings between ORF identifiers and KEGG pathway identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. org.Sc.sgdPATH maps ORF identifiers to the identifiers used by KEGG for pathways. The reverse map org.Sc.sgdPATH2ORF maps back from KEGG pathway IDs to the ORF identifiers.

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 With a date stamp from the source of: 2011-Mar15

References

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

Examples

    x <- org.Sc.sgdPATH
    # Get the ORF 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]]
    }
    # Convert the object to a list
    xx <- as.list(org.Sc.sgdPATH2ORF)
    # Remove pathway identifiers that do not map to any ORF id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The ORF identifiers for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    }