m10kcodENZYME            package:m10kcod            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:

     m10kcodENZYME is an R environment 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 m10kcodENZYME2PROBE, 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:

     KEGG:<URL:
     ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/pathway.tar.gz>. Built:
     Release 38.1, June 1, 2006

     Entrez Gene:<URL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/>. Built:
     Source data downloaded from Entrez Gene on Fri Sep  8 18:20:31
     2006

     Package built Fri Sep  8 18:49:52 2006

_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:

             # Convert to a list
             xx <- as.list(m10kcodENZYME)
             # Remove probe identifiers that do not map to any enzyme EC number
             xx <- xx[!is.na(xx)]
             if(length(xx) > 0){
             # Gets the enzyme commission numbers for the first five
             #probes
             xx[1:5]
             # Get the first one
             xx[[1]]
     }

