DudleyPheno             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 _D_u_d_l_e_y _e_t _a_l _2_0_0_5

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

     Dudley et al (2005) 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 21 different experimental conditions.

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

     data(DudleyGenelist)
     data(DudleyPhenoFull)
     data(DudleyPhenoM)
     data(DudleySign)

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

     'DudleyGenelist' is a character vector of length 814 genes.
     'DudleyPhenoFull' is a dataframe of 814 genes by 23 elements. The
     column contains the yeast gene name. The 22 remaining columns are
     the experimental conditions (see details). The values obtained in
     the different condition are the fitness defect scores for the 814
     genes sensitive to the experimental condition, as defined by
     Dudley et al (2005). 'DudleyPhenoM' is a 814 by 22 incidence
     matrix with rownames corresponding to the genes names and columns
     to an experimental condition. This matrix contains a 1 in the
     (i,j) position if the i-th gene is sensitive to the experimental
     condition of the j-th column; it contains a 0 otherwise.


     _Y_n_a_m_e Yeast systematic gene name

     _b_e_n_o_m_y_l 15ug/ml benomyl,microtubule function

     _C_a_C_l_2 0.7M calcium chloride, divalent cation

     _C_A_D 55uM Cadmium, heavy metal

     _C_a_f_f 2mg/ml Caffeine

     _c_y_c_l_o_h_e_x 0.18ug/ml cycloheximide, protein synthesis

     _D_T_T unknown

     _E_t_O_H YPD + 6% Ethanol

     _F_e_L_i_m iron limited, nutrient limited condition

     _H_U 11.4mg/ml Hydroxyurea, DNA replication and repair

     _H_y_g_r_o_B 50ug/ml hygromycin B, aminoglycosides

     _l_o_w_P_O_4 Low phosphate, nutrient limited condition

     _M_P_A 20ug/ml mycophenolic acid, transcriptional elongation

     _N_a_C_l 1.2M sodium chloride, general stress condition

     _P_a_r_a_q 1mM paraquat, oxidative stress

     _p_H_3 Low pH, general stress condition

     _r_a_p 0.1ug/ml rapamycin, protein synthesis

     _S_o_r_b 1.2M sorbitol, general stress condition

     _U_V 100J/m2 ultra-violet, DNA replication and repair

     _Y_P_G_a_l 2% galactose, carbon source

     _Y_P_G_l_y 3% glycerol, carbon source

     _Y_P_L_a_c 2% lactate, carbon source

     _Y_P_R_a_f_f 2% raffinose, carbon source

     'DudleySign' is a list of dataframe that summaryzes in which
     complexes the gene related to the phenotype are found, the size of
     the complexes and the associated p-value. This is the result of
     applying a Hypergeometric test (see 'CoHyperGParams-class' for
     more details) and the 'complexStatus' function.

     'Dudleyresult' 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:

     Dudley et al (2005), supplementary information: <URL:
     http://arep.med.harvard.edu/pheno/default.htm>

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

     Aim\'ee Marie Dudley, Daniel Maarten Janse, Amos Tanay, Ron Shamir
     and George McDonald Church. (2005).A global view of pleiotropy and
     phenotypically derived gene function in yeast. Molecular Systems
     Biology doi:10.1038/msb4100004

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

     data(DudleyPhenoFull)
     data(DudleyPhenoM)

