Map between Entrez Gene IDs and Enzyme Commission (EC) Numbers

Description

org.Mm.egENZYME is an R object that provides mappings between entrez gene identifiers and EC numbers.

Details

Each entrez gene identifier maps to a named vector containing the EC number that corresponds to the enzyme produced by that gene. The name corresponds to the entrez gene 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.Mm.egENZYME2EG, 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 entrez gene identifiers and enzyme identifiers were obtained using files provided by: KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15

For the reverse map, each EC number maps to a named vector containing the entrez gene identifier that corresponds to the gene that produces that enzyme. The name of the vector corresponds to the EC number.

References

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

See Also

• AnnotationDb-class for use of the select() interface.

Examples

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

## Bimap interface:
x <- org.Mm.egENZYME
# Get the entrez gene identifiers that are mapped to an EC number 
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the ENZYME for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}
# For the reverse map:
# Convert to a list
xx <- as.list(org.Mm.egENZYME2EG)
if(length(xx) > 0){
   # Gets the entrez gene 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.Mm.eg.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.Mm.eg.db/org.Mm.egENZYME.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Mm.egENZYME
> ### Title: Map between Entrez Gene IDs and Enzyme Commission (EC) Numbers
> ### Aliases: org.Mm.egENZYME org.Mm.egENZYME2EG
> ### 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:
> x <- org.Mm.egENZYME
> # Get the entrez gene identifiers that are mapped to an EC number 
> mapped_genes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_genes])
> if(length(xx) > 0) {
+   # Get the ENZYME for the first five genes
+   xx[1:5]
+   # Get the first one
+   xx[[1]]
+ }
[1] "2.3.1.87"
> # For the reverse map:
> # Convert to a list
> xx <- as.list(org.Mm.egENZYME2EG)
> if(length(xx) > 0){
+    # Gets the entrez gene identifiers for the first five enzyme
+    #commission numbers
+    xx[1:5]
+    # Get the first one
+    xx[[1]]
+ }
[1] "11298"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>