Map Between Manufacturer IDs and Enzyme Commission (EC) Numbers

Description

rgu34aENZYME is an R environment that provides mappings between manufacturer ids and EC numbers.

Details

Each manufacturer id maps to a named vector containing the EC number that corresponds to the enzyme produced by that gene. The name corresponds to the manufacturer id. If this information is unknown, the vector will contain an NA.

Enzyme Commission numbers are assigned by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology http://www.chem.qmw.ac.uk/iubmb/enzyme/ to allow enzymes to be identified.

An Enzyme Commission number is of the format EC x.y.z.w, where x, y, z, and w are numeric numbers. In rgu34aENZYME2PROBE, EC is dropped from the Enzyme Commission numbers.

Enzyme Commission numbers have corresponding names that describe the functions of enzymes in such a way that EC x is a more general description than EC x.y that in turn is a more general description than EC x.y.z. The top level EC numbers and names are listed below:

EC 1 oxidoreductases

EC 2 transferases

EC 3 hydrolases

EC 4 lyases

EC 5 isomerases

EC 6 ligases

The EC name for a given EC number can be viewed at http://www.chem.qmul.ac.uk/iupac/jcbn/index.html#6

Mappings between probe ids and enzyme ids were obtained using files provided by:

KEGG:http://gopher5/compbio/annotationSourceData/kegg/pathways. Built: Release 34.0 (April 2005)

Entrez Gene:http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Tue May 17 16:25:58 2005

Package built Tue May 17 16:31:20 2005

References

ftp://ftp.genome.ad.jp/pub/kegg/pathways

Examples

        # Convert to a list
        xx <- as.list(rgu34aENZYME)
        # Remove probe ids that do not map to any enzyme EC number
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
        # Gets the enzyme commission numbers for the first five
        #probes
        xx[1:5]
        # Get the first one
        xx[[1]]
}