dSLAM.GPL1444              package:SLGI              R Documentation

_d_S_L_A_M _p_l_a_t_f_o_r_m _u_s_e_d _f_o_r _S_y_n_t_h_e_t_i_c _L_e_t_h_a_l _s_c_r_e_e_n_s _i_n _t_h_e _B_o_e_k_e _L_a_b

_D_e_s_c_r_i_p_t_i_o_n:

     These data are the 21991 probes spotted on the dSLAM array
     (heterozygote diploid-based synthetic lethality analyzed by
     microarray) used to test synthetic lethal interactions by Pan et
     al (2006).

_U_s_a_g_e:

     data(dSLAM.GPL1444)

     data(dSLAM)

_F_o_r_m_a_t:

     dSLAM.GPL1444 is a data frame with 21991 observations on the
     following 10 variables.

     '_I_D' Serial identifier for probe.

     '_R_O_W' Row number in the array as scanned with GenePix scanner.

     '_C_O_L_U_M_N' Column number in the array as scanned with GenePix
          scanner.

     '_T_A_G_T_Y_P_E' Code for whether tag is 5' (Up) or 3' (Dn) relative to
          the open reading frame (ORF).

     '_P_R_O_B_E' Code for singleton probes arrayed in ORF order (ArrA,
          ArrB), five-fold replicate probes arrayed in randomized order
          (Rpts), systematic mutations arrayed across the center of the
          array (Muts), negative controls (NegT), or probes peripheral
          to the array as specified by the manufacturer (Edge)

     '_O_R_F' Systematic ORF name (from SGD, Feb 2003) (<URL:
          http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=>

     '_G_E_N_E' Standard gene name (SGD) (or ORF if not available)

     '_S_E_Q_U_E_N_C_E' DNA sequence of probe (includes custom-designed
          sequences for 193 YA* and YM* ORFs missing DnTags)

     '_S_G_D_I_D' Unique ORF identifier from SGD; 'S000000000' denotes
          missing value

     '_S_P_O_T__I_D' spot identifier; ('YQL' ORFs denote custom-designed
          sequences; 'NegA', 'NegB', 'PosA', 'PosB' denote proprietary
          sequences specified by the manufacturer)

     dSLAM is a character vector of length 5641 that contains the
     unique and valid systematic ORF names.

_D_e_t_a_i_l_s:

     The dSLAM.GPL1444 were directly obtain from parsing the
     GPL1444_family.soft.gz available at <URL:
     http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL1444>

     dSLAM is a vector of length 5641, extracted from the dSLAM.GPL1444
     ORF, and that contains the unique and valid systematic ORF names.
     This vector was built in three steps. First the ORFs with SGDID
     equals to S000000000 in the dSLAM.GPL1444 data frame were removed
     as some correspond to custom sequences and other were dubious ORFs
     that have been  deleted from SGD or merged with other ORFs.
     Secondly, the duplicated names were removed.  Then, the systematic
     ORF names were verified against the YEAST data package.

_S_o_u_r_c_e:

     The data were extracted from the Gene Expression Omnibus (GEO)
     website:  <URL:
     http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL1444>

_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

_S_e_e _A_l_s_o:

     'Boeke2006raw' 'Boeke2006'

