HMSPCI               package:apComplex               R Documentation

_H_i_g_h-_T_h_r_o_u_g_h_p_u_t _M_a_s_s _S_p_e_c_t_r_o_m_i_c _P_r_o_t_e_i_n _C_o_m_p_l_e_x _I_d_e_n_t_i_f_i_c_a_t_i_o_n (_H_M_S-_P_C_I) _D_a_t_a _f_r_o_m _H_o, _e_t _a_l. (_2_0_0_2)

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

     HMS-PCI data published by Ho, et al. (2002).

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

     data(HMSPCI)
     data(HMSPCIgraph)

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

     'HMSPCI' is a matrix of the HMS-PCI data published by Ho, et al.
     (2002). The 493 rows correspond to bait proteins and the 1578
     columns correspond to proteins found as hits in the HMSPCI
     experiment and are named accordingly. The first 493 column names
     are the same as the 493 row names; bait proteins can also be found
     as hits by other baits, hence their inclusion as columns in
     'HMSPCI'.  An entry of "1" in the ith row and jth column of
     'HMSPCI' indicates that bait protein i found protein j as a hit. 
     All other entries are "0".  There are a total of 3687 "1" entries
     in the matrix, corresponding to the 3687 comemberships detected in
     the experiment.

     'HMSPCIgraph' is a 'graphNEL' object in which 1578 nodes represent
     proteins and 3687 directed edges represent comemberships detected
     in the purification.  Each directed edge originates at the bait
     and ends at the hit.  Each edge in 'HMSPCIgraph' corresponds to an
     entry of "1" in the 'HMSPCI' matrix. 

     These data are available at http://www.mdsp.com/yeast.

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

     Ho, et al.  Systematic identification of protein complexes in
     Saccharomyces cerevisiae by mass spectrometry.  Nature 415,
     180-183 (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:

     'MBMEcHMSPCI','SBMHcHMSPCI','UnRBBcHMSPCI','TAP'

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

     data(HMSPCI)
     which(HMSPCI["YAL015C",]==1)

     data(HMSPCIgraph)
     adj(HMSPCIgraph,"YAL015C")

