agENZYME                package:ag.db                R Documentation

_M_a_p _b_e_t_w_e_e_n _M_a_n_u_f_a_c_t_u_r_e_r _I_D_s _a_n_d _E_n_z_y_m_e _C_o_m_m_i_s_s_i_o_n (_E_C) _N_u_m_b_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     agENZYME is an R object that provides mappings between
     manufacturer identifiers and EC numbers.

_D_e_t_a_i_l_s:

     Each manufacturer 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 <URL: 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 agENZYME2PROBE, 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 <URL:
     http://www.chem.qmul.ac.uk/iupac/jcbn/index.html#6> 

     Mappings between probe identifiers and enzyme identifiers were
     obtained using files provided by: Tair (
     ftp://ftp.arabidopsis.org/Pathways/aracyc_dump_20070703 ) on
     2007-Oct04

_R_e_f_e_r_e_n_c_e_s:

     <URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways>

_E_x_a_m_p_l_e_s:

             x <- agENZYME
             # 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]]
             }

