Gavin2002BPGraph           package:ppiData           R Documentation

_A _d_i_r_e_c_t_e_d _G_r_a_p_h _f_o_r _t_h_e _A_P-_M_S _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 _G_a_v_i_n _e_t _a_l. _2_0_0_2.

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

     An instance of class graph, Gavin2002BPGraph is a graphNEL object.
     The nodes are the union of viable baits (VB) and  viable prey (VP)
     of the experiment conducted by Gavin et al.  2002. 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.

     One key fact is that Gavin et al. Used the protein common names
     when they recorded the data. As we have chosen to use the gene
     systematic names, we had to map from these common names to 
     systematic names. We used the  YEASTCOMMON2SYSTEMATIC environment
     of the YEAST R-data package to translate from common protein names
     to systematic gene names.

     We encountered two mappings which were not one to one. The VPs
     "Osh1" and "Swh1" both mapped to the  Open Reading Frame (ORF)
     "YAR042W". The VPs "Blm3" and the  alias "YFL006W" both mapped to
     the ORF "YFL007W". When mappings are not one to one, it is
     difficult to reproduce all the  information. 

     The VPs "Osh1" and "Swh1" were found by the same VB "Scs2" while 
     "Blm3" and the alias "YFL006W" were both detected by the VB
     "Scl1".  In creating this graphNEL, we deleted the VPs "Swh1" and
     "YFL006W".

     If, on the other hand, one protein mapped to several different
     ORFs we simple selected the first ORF in the list since there is
     no  definitive process to make the choice un-arbitrary. 

     For example: x -> (a,b), then x -> a in our algorithm.

     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(Gavin2002BPGraph)

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

     The format is: graphNEL "Gavin2002BPGraph"

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

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

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

     Functional organization of the yeast proteome by systematic
     analysis  of protein complexes. Nature. 2002 Jan
     10;415(6868):141-7

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

     data(Gavin2002BPGraph)

