Ecoli              package:plsgenomics              R Documentation

_E_c_o_l_i _g_e_n_e _e_x_p_r_e_s_s_i_o_n _a_n_d _c_o_n_n_e_c_t_i_v_i_t_y _d_a_t_a _f_r_o_m _K_a_o _e_t _a_l. (_2_0_0_3)

_D_e_s_c_r_i_p_t_i_o_n:

     Gene expression data obtained during Escherichia coli carbon
     source transition and connectivity data from the RegulonDB data
     base (Salgado et al., 2001).  The experiments  and data sets are
     described in Kao et al. (2003).

_U_s_a_g_e:

     data(Ecoli)

_V_a_l_u_e:

     A list with the following components: 

CONNECdata: a (100 x 16) matrix containing the connectivity data for
          100 genes and 16 regulators. The data are coded as 1
          (positive interaction), 0 (no interaction) and -1 (negative
          interaction).

  GEdata: a (100 x 23) matrix containing gene expression data for 100
          genes and 23 samples corresponding to differents times during
          carbon source transition.

timepoint: a numeric vector of length 23 containing the time points (in
          hours) for the 23 samples.

_S_o_u_r_c_e:

     The data are described in Kao et al. (2004) and can be freely
     downloaded from  <URL:
     http://www.seas.ucla.edu/~liaoj/downloads.htm>.

_R_e_f_e_r_e_n_c_e_s:

     K. Kao, Y.-L. Yang, R. Boscolo, C. Sabatti, V. Roychowdhury and J.
     C. Liao (2004). Transcriptome-based determination of multiple
     transcription regulator activities in Escherichia coli by using
     network component analysis, PNAS *101*, 641-646. 

     H. Salgado, A. Santos-Zavaleta, S. Gama-Castro, D. Millan-Zarate,
     E. Diaz-Peredo, F. Sanchez-Solano, E. Perez-Rueda, C.
     Bonavides-Martinez and J. Collado-Vides (2001). RegulonDB (version
     3.2): transcriptional regulation and operon organization in
     Escherichia coli K-12, Nucleic Acids Research *29*, 72-74.

_E_x_a_m_p_l_e_s:

     # load plsgenomics library
     library(plsgenomics)

     # load data set
     data(Ecoli)

     # how many genes and how many transcription factors ?
     dim(Ecoli$CONNECdata)

