Uetz2000BPGraph2           package:ppiData           R Documentation

_A _d_i_r_e_c_t_e_d _G_r_a_p_h _f_o_r _t_h_e _Y_2_H _B_a_i_t _t_o _P_r_e_y _I_n_t_e_r_a_c_t_i_o_n
_d_a_t_a _d_e_t_e_c_t_e_d _b_y _U_e_t_z _e_t _a_l. _2_0_0_0.

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

     An instance of class graph, Uetz2000BPGraph2 is a graphNEL object.
     The nodes are the union of viable baits (VB) and  viable prey (VP)
     of the experiment conducted by Uetz et al.  2000. 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 Uetz et al. 2000 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. 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.

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

     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 2 VPs could not be
     mapped to the gene systematic names, and so retain the Intact
     ID's.

     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(Uetz2000BPGraph2)

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

     The format is: graphNEL "Uetz2000BPGraph2"

_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:

     A comprehensive analysis of protein-protein interactions in
     Saccharomyces cerevisiae. Nature. 2000 Feb 10;403(6770):623-7.

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

     data(Uetz2000BPGraph2)

