Boeke                  package:SLGI                  R Documentation

_I_n_c_i_d_e_n_c_e _m_a_t_r_i_x _o_f _S_y_n_t_h_e_t_i_c _L_e_t_h_a_l _i_n_t_e_r_a_c_t_i_o_n _f_r_o_m _t_h_e _B_o_e_k_e _L_a_b

_D_e_s_c_r_i_p_t_i_o_n:

     Data from Pan et al. experiments on DNA integrity Network in the
     Yeast S. cerevisiae.

_U_s_a_g_e:

     data(Boeke2006raw)
     data(Boeke2006)

_F_o_r_m_a_t:

     'Boeke2006raw' is a data frame with 5775 observations on the
     following 6 variables.

     '_Q_u_e_r_y._O_R_F' ORF associated with the query gene.

     '_Q_u_e_r_y._G_e_n_e' Common name of the query gene.

     '_T_a_r_g_e_t._O_R_F' ORF for the array gene.

     '_T_a_r_g_e_t._G_e_n_e' Common name of the array gene.

     '_R_S_A' Random spore analysis

     '_T_e_t_r_a_d' Tetrad dissection

     'Boeke2006' is an incidence matrix is a 74 by 843 adjacency matrix
     of the systematic genetic  interactions identified between 74
     query genes and the deletion gene set in Pan et al.(2004). The row
     names correspond to the systematic (ORF) names for the 74 query
     genes. The column names correspond to the systematic (ORF) names
     of the 843 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.

_D_e_t_a_i_l_s:

     In Pan et al (2006), the authors provide this note. Note: SL -
     synthetically lethal;  SF/SL-very severe synthetic fitness
     defects;  SF-obvious but modest synthetic fitness defects;  SF
     (slight) - slight synthetic fitness defect. Approximately 10% of
     the  positive interactions presented here were not scored as
     positive in the  dSLAM screens.  These were individually tested
     because we wanted to make  sure that they were indeed false
     negatives in the dSLAM screens.  We also  note that there is a
     small chance that the interactions scored as positive in  RSA
     (random spore analysis) might not reflect direct growth defects of
     the  double mutants but rather, the double mutants are defective
     in expressing the  MFA1pr-HIS3 reporter.

_S_o_u_r_c_e:

     The data were extracted from Pan et al (2004) and Table S1 of Pan
     et al. (2006).

_R_e_f_e_r_e_n_c_e_s:

     Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD.  A DNA integrity
     network in the yeast Saccharomyces cerevisiae. Cell. 2006 Mar
     10;124(5):1069-81

     Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS,
     Hieter P, Spencer F, Boeke JD. A robust toolkit for functional
     profiling of the yeast genome. Mol Cell. 2004 Nov 5;16(3):487-96.

_S_e_e _A_l_s_o:

     'dSLAM.GPL1444' 'dSLAM'

