Gavin2006BPGraph           package:ppiData           R Documentation

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_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_6.

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

     An instance of class graph, Gavin2006BPGraph 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.  2006. 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 Gavin et al. 2006 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 3 VBs  and 8 VPs could not be
     mapped to the gene systematic names.

     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(Gavin2006BPGraph)

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

     The format is: graphNEL "Gavin2006BPGraph"

_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:

     Proteome survey reveals modularity of the yeast cell machinery.
     Nature. 2006 Mar 30;440(7084):631-6. Epub 2006 Jan 22.

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

     data(Gavin2006BPGraph)

