org.Sc.sgdENZYME        package:org.Sc.sgd.db        R Documentation

_M_a_p _b_e_t_w_e_e_n _O_R_F _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:

     org.Sc.sgdENZYME is an R object that provides mappings between ORF
     identifiers and EC numbers.

_D_e_t_a_i_l_s:

     Each ORF identifier maps to a named vector containing the EC
     number that corresponds to the enzyme produced by that gene. The
     name corresponds to the ORF 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 org.Sc.sgdENZYME2ORF, 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 ORF identifiers and enzyme identifiers were
     obtained using files provided by: KEGG GENOME (
     ftp://ftp.genome.jp/pub/kegg/genomes ) on 2008-Sep2

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

_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 <- org.Sc.sgdENZYME
         # Get the ORF 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 id 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.Sc.sgdENZYME2ORF)
         if(length(xx) > 0){
            # Gets the ORF identifiers for the first five enzyme
            #commission numbers
            xx[1:5]
            # Get the first one
            xx[[1]]
         }

