YEASTGO2ALLPROBES           package:YEAST           R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _G_O _i_d_e_n_t_i_f_i_e_r_s _a_n_d _a_l_l _t_h_e _p_r_o_b_e _i_d_i_f_i_e_r_s
_r_e_p_r_e_s_e_n_t_i_n_g _g_e_n_e_s _a_s_s_o_c_i_a_t_e_d _w_i_t_h _t_h_e _G_O _i_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     The Gene Ontology (GO) Consortium maintains a controlled
     vocabulary of defined terms to describe gene products. Each of the
     terms is assigned a GO id that can be associated with a group of
     genes directly or indirectly through the children GO ids of the GO
     id. YEASTGO2ALLPROBES maps GO ids to genes (represented by probe
     identifiers) that are directly or indirectly mapped to the GO ids
     by traversing the GO tree.

_D_e_t_a_i_l_s:

     GO terminologies are presented as a directed acyclic graph with
     root nodes having more general terms than their children nodes.
     Therefore, a GO id can be mapped to genes corresponding to the
     term of that particular GO id as well as genes corresponding to
     the terms of all the children GO ids.

     YEASTGO2ALLPROBES maps a GO id to all the probe ids representing
     genes mapped by traversing the GO tree. The mapped probe ids are
     named vectors. Names of the vectors are the evidence codes
     indicating what kind of evidence is found to support the
     association between GO ids and genes.

     The evidence codes in use include: 

     IMP - inferred from mutant phenotype  

     IGI - inferred from genetic interaction

     IPI - inferred from physical interaction  

     ISS - inferred from sequence similarity  

     IDA - inferred from direct assay  

     IEP - inferred from expression pattern  

     IEA - inferred from electronic annotation  

     TAS - traceable author statement  

     NAS - non-traceable author statement  

     ND - no biological data available  

     IC - inferred by curator

     A GO id may be mapped to the same probe id more than once but the
     evidence code can be different. Mappings between Gene Ontology ids
     and Gene Ontology terms and other information are available in a
     separate data package named GO.  

     Mappings were based on data provided:

     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.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>

_E_x_a_m_p_l_e_s:

         # Convert to a list
         xx <- as.list(YEASTGO2ALLPROBES)
         if(length(xx) > 0){
             # Gets the probe ids for the top 2nd and 3nd GO ids
             goids <- xx[2:3]
             # Gets all the probe ids for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

