hgu133bENZYME            package:hgu133b            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:

     hgu133bENZYME is an R environment that provides mappings between
     manufacturer ids and EC numbers.

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

     Each manufacturer id maps to a named vector containing the EC
     number that corresponds to the enzyme produced by that gene. The
     name corresponds to the manufacturer id. 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 hgu133bENZYME2PROBE, 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 ids and enzyme ids were obtained using
     files provided by:

     KEGG:<URL:
     http://gopher5/compbio/annotationSourceData/kegg/pathways>. Built:
     Release 36.0, October 1, 2005

     Entrez Gene:<URL:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/g
     ene/DATA/>. Built: Source data downloaded from Entrez Gene on Tue
     Oct  4 20:07:35 2005

     Package built Tue Oct  4 20:23:42 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(hgu133bENZYME)
             # 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]]
     }

