YEASTENZYME              package:YEAST              R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _p_r_o_b_e _i_d_e_n_t_i_f_i_e_r_s _a_n_d _t_h_e _e_n_z_y_m_e _c_o_m_m_i_s_s_i_o_n
_n_u_m_b_e_r_s, _t_o _w_h_i_c_h _t_h_e _p_r_o_d_u_c_t_s _o_f _t_h_e _g_e_n_e_s _r_e_p_r_e_s_e_n_t_e_d _b_y _t_h_e _p_r_o_b_e
_i_d_s _c_o_r_r_e_s_p_o_n_d

_D_e_s_c_r_i_p_t_i_o_n:

     Genes code for proteins/enzymes that take part in various
     biological processes. YEASTENZYME maps probe ids to Enzyme
     Commission numbers for the enzymes the genes represented by the
     probe ids code for. 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.

_D_e_t_a_i_l_s:

     Each probe id is mapped to one or more Enzyme Commission numbers.
     An Enzyme Commission number is of the format EC x.y.z.w, where x,
     y, z, and w are numeric numbers. In YEASTENZYME, 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

     YEASTENZYME only provides mappings to EC numbers. 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 ids and enzyme ids were obtained using
     files provided by:

     KEGG:<URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways>. Built: Yeast
     Genome data are built at various time  intervals. Sources used
     were downloaded  Fri Jan  7 14:56:44 2005 

     Yeast Genome:<URL:
     http://www.yeastgenome.org/DownloadContents.shtml>. Built: Yeast
     Genome data are built at various time  intervals. Sources used
     were downloaded  Fri Jan  7 14:56:40 2005 

     Package built Fri Jan  7 16:12:38 2005

_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(YEASTENZYME)
             # Remove probe ids 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]]
     }

