TAP                package:apComplex                R Documentation

_T_a_n_d_e_m _A_f_f_i_n_i_t_y _P_u_r_i_f_i_c_a_t_i_o_n (_T_A_P) _D_a_t_a _f_r_o_m _G_a_v_i_n _e_t _a_l. (_2_0_0_2)

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

     TAP data published by Gavin, et al. (2002).

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

     data(TAP)
     data(TAPgraph)

_D_e_t_a_i_l_s:

     'TAP' is a matrix of the TAP data published by Gavin, et al.
     (2002).  The 455 rows correspond to bait proteins and the 1364
     columns correspond to proteins found as hits in the TAP experiment
     and are named accordingly. The first 455 column names are the same
     as the 455 row names; bait proteins can also be found as hits by
     other baits, hence their inclusion as columns in 'TAP'.  An entry
     of "1" in the ith row and jth column of 'TAP' indicates that bait
     protein i found protein j as a hit.  All other entries are "0". 
     There are a total of 3420 "1" entries in the matrix, corresponding
     to the 3420 comemberships detected in the experiment.

     'TAPgraph' is a 'graphNEL' object in which 1364 nodes represent
     proteins and 3420 directed edges represent comemberships detected
     in the purification.  Each directed edge originates at the bait
     and ends at the hit.  Each edge in 'TAPgraph' corresponds to an
     entry of "1" in the 'TAP' matrix. 

     These data are available in Supplementary Table S1 of Gavin et al.
     at http://www.nature.com.

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

     Gavin, et al.  Functional organization of the yeast proteome by
     systematic analysis of protein complexes.  Nature 415, 141-147
     (2002).

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

     Scholtens D and Gentleman R.  Making sense of high-throughput
     protein-protein interaction data.  Statistical Applications in
     Genetics and Molecular Biology 3, Article 39 (2004).

     Scholtens D, Vidal M, and Gentleman R.  Local modeling of global
     interactome networks.  Bioinformatics 21, 3548-3557 (2005).

_S_e_e _A_l_s_o:

     'yTAP','MBMEcTAP','SBMHcTAP','UnRBBcTAP','HMSPCI'

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

     data(TAP)
     which(TAP["Abd1",]==1)

     data(TAPgraph)
     adj(TAPgraph,"Abd1")

