Atong                  package:SLGI                  R Documentation

_S_y_s_t_e_m_a_t_i_c _g_e_n_e_t_i_c _a_n_a_l_y_s_i_s _w_i_t_h _o_r_d_e_r_e_d _a_r_r_a_y_s _o_f _y_e_a_s_t _d_e_l_e_t_i_o_n
_T_o_n_g _e_t. _a_l. (_2_0_0_4).

_D_e_s_c_r_i_p_t_i_o_n:

     Data from Tong et. al. (2004) buffering experiments using ordered
     arrays of yeast deletion design by Tong et. al. (2001).

_U_s_a_g_e:

         data(Atong)
         data(tong2004raw)

_F_o_r_m_a_t:

     'tong2004Raw' is dataframe extracted from Table S1 of Tong et al.
     (2004) online supporting material.  We added an extra column,
     queryGene.sysName, which is the  systematic names of the query
     genes.


     _q_u_e_r_y_G_e_n_e._g_e_n_e_N_a_m_e Column indicates the gene used as query in the
          synthetic genetic array screen (SGA).

     _I_n_t._g_e_n_e_N_a_m_e Column indicates the gene identified as an interactor
          with a particular query.

     _I_n_t._s_y_s_N_a_m_e Column indicates the systematic  name of the open
          reading frame (ORF) that corresponds to the interactor gene.

     _S_c_o_r_e An interaction scored three times in the three runs by
          visual inspection received a scored of 3. An interaction
          scored twice in the three in the runs by  visual inspection
          received a scored of 2. An interaction scored by the
          computer-based image analysis but not visual inspection
          received a scored of 1. For interactions that scored once in
          the three runs by visual inspection confirmation was
          attempted only for those genes pairs related functions. Such
          confirmed interactions received a score of 0.

     _R_S_A Column identifies an interaction that was confirmed by random
          spore analysis.

     _T_e_t_r_a_d Column identifies an interaction confirmed by tetrad
          analysis.

     _S_S Refers to synthetic sick interaction.

     _S_L Refers to synthetic lethal interaction.

     _F_u_n_c_t_i_o_n_a_l._R_o_l_e Column indicates the assigned GO functional
          annotation from their defined subset of annotations.All the
          interactions are identified in this study unless otherwise
          stated.

     _R_e_f_e_r_e_n_c_e_s Genetic Interactions that have been previously
          described.

     _q_u_e_r_y_G_e_n_e._s_y_s_N_a_m_e Column indicates the systematic (ORF) name of
          the gene used as query in a SGA screen.

     'Atong' is a 132 by 1008 adjacency matrix of the systematic
     genetic  interactions identified between 132 query genes and the
     deletion gene set (Tong et al. 2001; see 'SGA' for more details). 
     The row names correspond to the systematic (ORF) names for the 132
     query genes. The column names correspond to the systematic (ORF)
     names of the 1011 reporter genes, which showed a synthetic lethal
     or synthetic sick  interaction with at least one query genes.
     Values are 0 or 1, with a 1 indicating the occurrence of the
     genetic interaction between the gene pairs.

_S_o_u_r_c_e:

     Tong et al, Science. Vol.303, 2004.

_R_e_f_e_r_e_n_c_e_s:

     Global Mapping of the Yeast Genetic Interaction Network, Tong et
     al, Science Vol.303, 2004.

     <URL: http://www.sciencemag.org/cgi/data/303/5659/808/DC1/1>

_S_e_e _A_l_s_o:

     'SGA'

_E_x_a_m_p_l_e_s:

      data(Atong)
      dim(Atong)
      

