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)

