Maps between Manufacturer IDs and Enzyme Commission (EC) Numbers

Description

indacENZYME is an R object that provides mappings between manufacturer identifiers and EC numbers. indacENZYME2PROBE is an R object that maps Enzyme Commission (EC) numbers to manufacturer identifiers.

Details

When the indacENZYME maping viewed as a list, each manufacturer identifier maps to a named vector containing the EC number that corresponds to the enzyme produced by that gene. The names corresponds to the manufacturer identifiers. If this information is unknown, the vector will contain an NA.

For the indacENZYME2PROBE, each EC number maps to a named vector containing all of the manufacturer 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 indacENZYME2PROBE, 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 GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15

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 <- indacENZYME
# Get the probe identifiers that are mapped to an EC number 
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
  # Get the ENZYME for the first five probes
  xx[1:5]
  # Get the first one
  xx[[1]]
}

# Now convert indacENZYME2PROBE to a list to see inside
xx <- as.list(indacENZYME2PROBE)
if(length(xx) > 0){
   # Get the probe 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)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(indac.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

Loading required package: org.Dm.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/indac.db/indacENZYME.Rd_%03d_medium.png", width=480, height=480)
> ### Name: indacENZYME
> ### Title: Maps between Manufacturer IDs and Enzyme Commission (EC) Numbers
> ### Aliases: indacENZYME indacENZYME2PROBE
> ### 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 <- indacENZYME
> # Get the probe identifiers that are mapped to an EC number 
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+   # Get the ENZYME for the first five probes
+   xx[1:5]
+   # Get the first one
+   xx[[1]]
+ }
[1] "2.1.1.43"
> 
> # Now convert indacENZYME2PROBE to a list to see inside
> xx <- as.list(indacENZYME2PROBE)
> if(length(xx) > 0){
+    # Get the probe identifiers for the first five enzyme
+    #commission numbers
+    xx[1:5]
+    # Get the first one
+    xx[[1]]
+ }
[1] "1000031286" "1000034675" "1000031238" "1000035824"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>