ItoCore2001BPGraph          package:ppiData          R Documentation

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_d_a_t_a _d_e_t_e_c_t_e_d _b_y _I_t_o _e_t _a_l. _2_0_0_1.

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

     An instance of class graph, ItoCore2001BPGraph is a graphNEL
     object. The nodes are the union of viable baits (VB) and  viable
     prey (VP) of the experiment conducted by Ito et al.  2001 which
     they annotated as the core dataset by having verified  the
     bait-prey interaction at least 3 times. 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 Ito 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 org.Sc.sgdCOMMON2ORF environment of the org.Sc.sgd 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 7 VBs and 12 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(ItoCore2001BPGraph)

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

     The format is: graphNEL "ItoCore2001BPGraph"

_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 two-hybrid analysis to explore the yeast protein
     interactome. Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74.
     Epub 2001 Mar 13.

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

     data(ItoCore2001BPGraph)

