OsterbergRaw             package:PCpheno             R Documentation

_D_a_t_a _f_r_o_m _O_s_t_e_r_b_e_r_g _a_t _a_l. _2_0_0_6

_D_e_s_c_r_i_p_t_i_o_n:

     Osterberg at al. (2006) report growth phenotypes in yeast for a
     strain collection over-expression ~600 C-terminal tagged integral
     membrane proteins growth both under normal and three different
     stress conditions.

_U_s_a_g_e:

     data(OsterbergRaw)

_F_o_r_m_a_t:

     'OsterbergRaw' is a 17 columns dataframe.


     _S_Y_S_T_E_M_A_T_I_C Systematic gene names of the studied membrane protein

     _C_O_M_M_U_N Commun gene names of the studied membrane protein

     _T_M_H_M_M._C The topology predicted by TMHMM (TransMembrane prediction
          using Hidden Markov Models) using the experimentally assigned
          C-terminal location for the protein as a constraint. The
          topology is represented in the format Location of N-terminus
          TMhelices Location of C-terminus (i and o stand for in and
          out respectively)

     _W_e_s_t_e_r_n_B_l_o_t Protein expression levels (arbitrary units), estimated
          from the band intensity and normalized to the internal
          standard on each Western blot.

     _B_a_n_d_s Proteins detected as two distinct bands with different
          molecular mass on the Western blot analysis. category 1
          indicates that both bands were insensitive to Endo H
          digestion, 2 indicates the higher molecular mass was shifted
          down upon Endo H digestion on SDS/PAGE and one  band was
          predominant compared to the other, and 3 indicates that a
          higher molecular mass band shifted down upon Endo H digestion
          on SDS/PAGE and both bands were equal intensity on Western
          blot

     _T_o_x_i_c_i_t_y Toxicity index from Spoko et al. (2006). The index varies
          between 1 and 5, where 1 means the strain is dead, and 5
          indicates no difference in growth rate compared with the wild
          type strain.

     _s_i_g_n._n_o_r_m Over-expression strains that show a significant
          (P<0.001) growth rate phenotype (LSCrate) in synthetic
          defined medium conditions (Warringer et al., 2003). An
          average of two replicates is given. Strains that do not show
          a significant difference in doubling time compared with the
          wild-type strain are indicated by 0.

     _a_l_l._n_o_r_m Phenotypes (significant or not) of over-expression
          strains (LSCrate) in synthetic defined medium conditions
          (Warringer et al., 2003). An average of two replicates is
          given.

     _s_i_g_n._N_a_C_l Over-expression strains that show a significant
          (P<0.001) growth rate phenotype (LPIrate) in NaCl. An average
          of two replicates is given. Strains that do not show a
          significant difference in doubling time compared with the
          wild-type strain under NACL stress are indicated by 0.

     _a_l_l._N_a_C_l._L_S_C Phenotypes (significant or not) of over-expression
          strains (LSCrate) in NaCl (Warringer et al., 2003). An
          average of two replicates is given.

     _a_l_l._N_a_C_l._L_P_I Phenotypes (significant or not) of over-expression
          strains (LPIrate) in NaCl (Warringer et al., 2003). An
          average of two replicates is given.

     _s_i_g_n._c_a_f_f Over-expression strains that show a significant
          (P<0.001) growth rate phenotype (LPIrate) in caffeine. An
          average of two replicates is given. Strains that do not show
          a significant difference in doubling time compared with the
          wild-type strain under caffeine stress are indicated by 0.

     _a_l_l._c_a_f_f._L_S_C Phenotypes (significant or not) of over-expression
          strains (LSCrate) in caffeine (Warringer et al., 2003). An
          average of two replicates is given

     _a_l_l._c_a_f_f._L_P_I Phenotypes (significant or not) of over-expression
          strains (LPIrate) in caffeine (Warringer et al., 2003). An
          average of two replicates is given.

     _s_i_g_n._p_a_r_a_q. Over-expression strains that show a significant
          (P<0.001) growth rate phenotype (LPIrate) in paraquat. An
          average of two replicates is given. Strains that do not show
          a significant difference in doubling time compared with the
          wild-type strain under paraquat stress are indicated by 0.

     _a_l_l._p_a_r_a_q._L_S_C Phenotypes (significant or not) of overexpression
          strains (LSCrate) in paraquat (Warringer et al., 2003). An
          average of two replicates is given.

     _a_l_l._p_a_r_a_q._L_P_I Phenotypes (significant or not) of overexpression
          strains (LPIrate) in paraquat (Warringer et al., 2003). An
          average of two replicates is given.

_A_u_t_h_o_r(_s):

     N. LeMeur

_S_o_u_r_c_e:

     Osterberg et al (2006), supplementary information: <URL:
     http://www.pnas.org/content/vol0/issue2006/images/data/0604078103/DC1/04078Table1.xls>
     or  <URL:
     ftp://genome-ftp.stanford.edu/pub/yeast/systematic_results/phenotypes>

_R_e_f_e_r_e_n_c_e_s:

     Osterberg M, Kim H, Warringer J, Melen K, Blomberg A, von Heijne
     G. (2006) Phenotypic effects of membrane protein overexpression in
     Saccharomyces cerevisiae. PNAS. 103(30):11148-53. PMID: 16847257

_E_x_a_m_p_l_e_s:

     data(OsterbergRaw)
     str(OsterbergRaw)

