zebrafishENZYME {zebrafish} | R Documentation

## Map Between Manufacturer IDs and Enzyme Commission (EC) Numbers

### Description

zebrafishENZYME is an R environment that provides mappings between manufacturer identifiers and EC numbers.

### Details

Each manufacturer identifier maps to a named vector containing the EC number that corresponds to the enzyme produced by that gene. The name corresponds to the manufacturer identifier. 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 zebrafishENZYME2PROBE, 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 identifiers and enzyme identifiers were obtained using files provided by:

KEGG:ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/pathway.tar.gz. Built: Release 41.1, February 1, 2007

Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Thu Mar 15 18:13:35 2007

Package built Thu Mar 15 18:18:58 2007

### References

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

### Examples

            # Convert to a list
            xx <- as.list(zebrafishENZYME)
            # Remove probe identifiers 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 zebrafish version 1.16.0 Index]