Map between Enzyme Commission Numbers and TAIR Identifiers

Description

org.At.tairENZYME2TAIR is an R object that maps Enzyme Commission (EC) numbers to TAIR identifiers.

Details

Each EC number maps to a named vector containing all of the TAIR identifiers that correspond to the gene that produces that enzyme. The name of the vector corresponds to the EC number.

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 were based on data provided by: Tair ftp://ftp.plantcyc.org/Pathways/Data_dumps/PMN10_June2015/aracyc_pathways.20150608 With a date stamp from the source of: 2015-Apr07

References

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

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
# Convert to a list
xx <- as.list(org.At.tairENZYME2TAIR)
if(length(xx) > 0){
    # Gets the tair identifiers for the first five enzyme
    #commission numbers
    xx[1:5]
    # Get the first one
    xx[[1]]
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(org.At.tair.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/org.At.tair.db/org.At.tairENZYME2TAIR.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.At.tairENZYME2TAIR
> ### Title: Map between Enzyme Commission Numbers and TAIR Identifiers
> ### Aliases: org.At.tairENZYME2TAIR
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## select() interface:
> ## Objects in this package can be accessed using the select() interface
> ## from the AnnotationDbi package. See ?select for details.
> 
> ## Bimap interface:
> # Convert to a list
> xx <- as.list(org.At.tairENZYME2TAIR)
> if(length(xx) > 0){
+     # Gets the tair identifiers for the first five enzyme
+     #commission numbers
+     xx[1:5]
+     # Get the first one
+     xx[[1]]
+ }
[1] "AT1G01050" "AT1G15690" "AT1G16780" "AT2G18230" "AT2G46860" "AT3G53620"
[7] "AT4G01480" "AT5G09650"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>