Cagney2001BPGraph          package:ppiData          R Documentation

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_d_a_t_a _d_e_t_e_c_t_e_d _b_y _C_a_g_n_e_y _e_t _a_l. _2_0_0_1.

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

     An instance of class graph, Cagney2001BPGraph is a graphNEL
     object. The nodes are the union of viable baits (VB) and  viable
     prey (VP) of the experiment conducted by Cagney et al.  2001. A
     viable bait is a node that has at least one directed  edge for
     which this node serves as the source. A viable prey  is a node
     that has at least one directed edge for which this  node serves as
     a sink.

     The data from Cagney et al. 2001 were obtained via the Intact
     repository. The Intact repository assigns an Intact specific code
     for each VB and each VP. Each Intact ID is mapped to  the a SGD ID
     (if available) and then mapped to the gene  systematic name via
     the YEASTCOMMON2SYSTEMATIC environment of the YEAST R-data
     package. If the mapping is one to many  at any point, the first
     entry of the mapping is selected.

     For example: x -> (a,b); a -> (c,d); b -> (e,f),  in our
     algorithm, x ---> c  

     While this selection is arbitrary, there is no definitive  way to
     select from the mappings without more information. If more
     information concerning the experiment is given, the  non-arbitrary
     choice can be made.

     If no proper mapping could be achieved in this manner,  the Intact
     ID's were kept so that other methods can be employed  for
     translation in the future. In all 0 VBs and 0 VPs could not be
     mapped to the gene systematic names, and so retain the Intact ID's
     for Cagney 2001.

     These graphs are not simple. While we chose not to present data
     with multiple edges between nodes (i.e. if bait b found prey p
     with multiplicity k, we do not assign k directed edges from b to
     p, only a single edge). We do, however, allow self loops to detail
     homodimer relationships.

_U_s_a_g_e:

     data(Cagney2001BPGraph)

_F_o_r_m_a_t:

     The format is: graphNEL "Cagney2001BPGraph"

_S_o_u_r_c_e:

     The sparse matrix adjacency matrix for this graph can be found in
     the bioconductor R-package ppiStats.

_R_e_f_e_r_e_n_c_e_s:

     Two-hybrid analysis of the Saccharomyces cerevisiae 26S
     proteasome.      Physiol Genomics. 2001 Oct 10;7(1):27-34.

_E_x_a_m_p_l_e_s:

     data(Cagney2001BPGraph)

