xenopuslaevisENZYME {xenopuslaevis}R Documentation

Mappings between probe identifiers and the enzyme commission numbers, to which the products of the genes represented by the probe ids correspond

Description

Genes code for proteins/enzymes that take part in various biological processes. xenopuslaevisENZYME maps probe ids to Enzyme Commission numbers for the enzymes the genes represented by the probe ids code for. 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.

Details

Each probe id is mapped to one or more Enzyme Commission numbers. An Enzyme Commission number is of the format EC x.y.z.w, where x, y, z, and w are numeric numbers. In xenopuslaevisENZYME, 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

xenopuslaevisENZYME only provides mappings to EC numbers. 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: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 16, 2004

Package built Fri Sep 17 09:04:28 2004

References

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

Examples

        # Convert to a list
        xx <- as.list(xenopuslaevisENZYME)
        # 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]]
}

[Package xenopuslaevis version 1.6.5 Index]