\HeaderA{ath1121501ENZYME}{Map Between Manufacturer IDs and Enzyme Commission (EC) Numbers}{ath1121501ENZYME}
\keyword{datasets}{ath1121501ENZYME}
\begin{Description}\relax
ath1121501ENZYME is an R environment that provides mappings between
manufacturer ids and EC numbers.
\end{Description}
\begin{Details}\relax
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 \code{NA}.

Enzyme Commission numbers are assigned by the Nomenclature Committee
of the International Union of Biochemistry and Molecular Biology
\url{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 ath1121501ENZYME2PROBE, 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
\url{http://www.chem.qmul.ac.uk/iupac/jcbn/index.html#6} 

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

Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Pathways/aracyc_dump_20050412}
Built: N/A

Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Genes/gene_aliases.20041105}
Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes}
Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Genes/Gene_Anatomy/ATH_Anatomy.20040209.txt}
Built: N/A

Package built Tue May 17 18:45:34 2005
\end{Details}
\begin{References}\relax
\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}
\end{References}
\begin{Examples}
\begin{ExampleCode}
        # Convert to a list
        xx <- as.list(ath1121501ENZYME)
        # 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]]
}
\end{ExampleCode}
\end{Examples}

