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]]
     }

