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Map between SomaScan SeqIds and Enzyme Commission (EC) numbers

SomaScanENZYME.Rd

SomaScanENZYME is an R object that provides mappings between SeqIds and EC numbers. SomaScanENZYME2PROBE is an R object that maps Enzyme Commission (EC) numbers to SeqIds.

Details

When the SomaScanENZYME mapping 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 correspond to the SeqIds. If this information is unknown, the vector will contain an NA.

For the SomaScanENZYME2PROBE object, each EC number maps to a named vector containing all of the SeqIds that correspond to the gene that produces that enzyme. The name of the vector corresponds to the EC number.

EC 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 EC number is of the format EC x.y.z.w, where x, y, z, and w are numeric values. In SomaScanENZYME2PROBE, the "EC" prefix is dropped from the Enzyme Commission numbers.

EC 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 SeqIds 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

Value

A Bimap object of the ProbeAnnDbBimap class.

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 <- SomaScanENZYME
# 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][1:3])
if(length(xx) > 0) {
    # Get the ENZYME for the first five probes
    xx[1:5]
    # Get the first one
    xx[[1]]
}
#> [1] "2.7.11.1"

# Now convert SomaScanENZYME2PROBE to a list to see inside
x <- SomaScanENZYME2PROBE
mapped_probes <- mappedkeys(x)
## convert to a list
xx <- as.list(x[mapped_probes][1:3])
if(length(xx) > 0){
    # Get the probe identifiers for the first five enzyme
    #commission numbers
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#> [1] "12632-14"