GiaeverPheno             package:PCpheno             R Documentation

_L_i_s_t _o_f _f_i_t_n_e_s_s _d_e_f_e_c_t _s_c_o_r_e _g_e_n_e_r_a_t_e_d _f_r_o_m _G_i_a_e_v_e_r _e_t _a_l _2_0_0_2

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

     Giaever et al (2002) create a  collection of gene-deletion mutants
     to determine genes that contribute to a  particular phenotype in
     specific environmental conditions. This list is generated from a
     fitness analysis under six different experimental conditions.

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

     data(GiaeverPheno)
     data(GiaeverGene)
     data(GiaeverExpCdt)

_F_o_r_m_a_t:

     'GiaeverPheno' is a list with 31 elements. The name of each
     element is a experimental condition (see details). The value of
     each element are the fitness defect scores for the genes sensitive
     to the experimental condition, as defined by Giaever et al (2002).

     'GiaeverGene' Vector of the systematic gene names of the 5898
     tested genes. Note that some updates have been made for the list
     to be consistent with _Saccharomyces Genome Database_.

     'GiaeverExpCdt' is a 3 columns dataframe with fileID from which
     the data were extracted, the generation time (growth time) and the
     condition (media).


     _g_e_n. generations

     _r_e_p. replicate

     _y_p_g_5_a,_y_p_g_5_b yeast/peptone/galactose 5 gen. rep. a and b  ==>
          carbone source

     _y_p_g_1_5_a _y_p_g_1_5_b yeast/peptone/galactose 15 gen. rep.  a and b ==>
          carbone source

     _s_o_r_b_i_t_o_l_5_a _s_o_r_b_i_t_o_l_5_b 1.5M Sorbitol 5 gen. rep. a and b ==> sugar,
          osmotic stress

     _s_o_r_b_i_t_o_l_2_0_a _s_o_r_b_i_t_o_l_1_5_b 1.5M Sorbitol 20  and 15 gen. rep. a and b
          respectively==> sugar, osmotic stress

     _N_a_C_l_5_a _N_a_C_l_5_b 1M NaCl 5 gen. rep.  a and b ==> salt, osmotic
          stress

     _N_a_C_l_1_5_a _N_a_C_l_1_5_b 1M NaCl 15 gen. rep. a and b ==> salt, osmotic
          stress

     _l_y_s_M_5_a _l_y_s_M_5_b lysine minus 5 gen. rep. a and b ==> lack of
          required AA

     _t_h_M_5_a threonine minus 5 gen. rep. a ==> lack of required AA

     _t_r_p_M_5_a _t_r_p_M_5_b tritophanee minus 5 gen. rep. a ==> lack of required
          AA

     _m_i_n_i_m_a_l_P_l_u_s_5_a _m_i_n_i_m_a_l_P_l_u_s_5_b minimal + histidine/leuvine/uracile 5
          gen. rep. a and b

     _m_i_n_i_m_a_l_P_l_u_s_1_5_a _m_i_n_i_m_a_l_P_l_u_s_1_5_b minimal + histidine/leuvine/uracile
          15 gen. rep. a and b

     _m_i_n_i_m_a_l_C_5_a _m_i_n_i_m_a_l_C_5_b minimal complete 5 gen. rep. a and b

     _n_y_s_t_a_t_i_n_5_a _n_y_s_t_a_t_i_n_5_b Nystatin 5 gen. rep. a and b ==> antifungal
          drug

     _n_y_s_t_a_t_i_n_1_5_a _n_y_s_t_a_t_i_n_1_5_b Nystatin 5 gen. rep. a and b ==>
          antifungal drug

     _p_H_8_g_5_a _p_H_8_g_5_b pH 8 5 gen. rep. a and b ==> alkali stress

     _p_H_8_g_1_5_a _p_H_8_g_2_0_b pH 8 15 and 20 gen. rep. a and b respectively ==>
          alkali stress

     Note: in their study they confound the 15 and 20 generations.

     'Giaeverresult' is a data.frame that summaryzes the number of
     sensitive genes per condition, how many of those genes are present
     in the ScISI interactome and the associated p-value. This is the
     result of applying a Hypergeometric test (see
     'CoHyperGParams-class' for more details) and the 'complexStatus'
     function.

_A_u_t_h_o_r(_s):

     N. LeMeur

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

     Giaever et al (2002), supplementary information: <URL:
     http://genomics.lbl.gov/YeastFitnessData/websitefiles/cel_index.html>
     Saccharomyces Genome Database (last update 03/17/06): <URL:
     http://www.yeastgenome.org/>

_R_e_f_e_r_e_n_c_e_s:

     Giaever G et al (2002) Functional profiling of the Saccharomyces
     cerevisiae genome. Nature. 418(6896):387-91. PMID: 12140549

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

     data(GiaeverPheno)
     data(GiaeverExpCdt)
     data(GiaeverGene)

