SGD.SL                 package:SLGI                 R Documentation

_I_n_t_e_r_a_c_t_i_o_n _d_a_t_a _f_r_o_m _t_h_e _S_a_c_c_h_a_r_o_m_y_c_e_s _G_e_n_o_m_e _D_a_t_a_b_a_s_e

_D_e_s_c_r_i_p_t_i_o_n:

     The Saccharomyces Genome Database (SGD) provides, for download a
     table listing all known interactions in yeast. This table was
     downloaded on Jan 25, 2007 and three subsets were extracted. The
     synthetic lethal interactions, 'SGD.SL', the synthetic grow defect
     interactions, 'SGD.SynGrowthDefect' and the synthetic rescue
     interactions, 'SGD.SynRescue'. No other processing has been done.

_U_s_a_g_e:

       data(SGD.SL)
       data(SGD.SynRescue)
       data(SGD.SynGrowthDefect)

_F_o_r_m_a_t:

     Each data set is a data frame with  the following 7 variables.

     '_V_1' Factor, indicating the type of data.

     '_V_2' Factor describing the interaction, in particular naming bait
          and prey and interactors.

     '_V_3' Factor indicating whether the cells were viable.

     '_V_4' Factor which is always NA for these data.

     '_V_5' Factor naming the reference for the interaction.

     '_V_6' Factor with levels indicating the PubMed ID for the
          publication in V5.

     '_V_7' Factor with level 'BioGRID', probably indicating the source.

_D_e_t_a_i_l_s:

     SGD says this about the file:


     Contains interaction data.  Tab-separated columns are:
     1) interaction_type (mandatory)
     2) genes involved and their mutation type, in the format: ORF
     (mutation_type, action), with multiples separated by a | 
     3) phenotype (optional, multiples separated by |)
     4) description (optional)
     5) citation (multiples separated by |)
     6) PubMed ID (optional, multiples separated by |)

     This file is updated weekly.


_A_u_t_h_o_r(_s):

     Z. Jiang

_S_o_u_r_c_e:

     The file can be downloaded from, <URL:
     ftp://genome-ftp.stanford.edu/pub/yeast/literature_curation>.

_E_x_a_m_p_l_e_s:

     data(SGD.SL)

