org.At.tairENZYME {org.At.tair.db} | R Documentation |
org.At.tairENZYME is an R object that provides mappings between TAIR identifiers and EC numbers.
Each TAIR 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 org.At.tairENZYME2TAIR, 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 TAIR identifiers and enzyme identifiers were obtained using files provided by: Tair ftp://ftp.arabidopsis.org/Pathways/aracyc\_pathways.20110406 With a date stamp from the source of: 2011-May27
ftp://ftp.genome.ad.jp/pub/kegg/pathways
x <- org.At.tairENZYME # Get the TAIR identifiers that are mapped to an EC number mapped_tairs <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_tairs]) if(length(xx) > 0) { # Get the ENZYME for the first five tairs xx[1:5] # Get the first one xx[[1]] }