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)

