\HeaderA{Ecoli}{Ecoli gene expression and connectivity data from Kao et al. (2003)}{Ecoli}
\keyword{datasets}{Ecoli}
\begin{Description}\relax
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).
\end{Description}
\begin{Usage}
\begin{verbatim}
data(Ecoli)
\end{verbatim}
\end{Usage}
\begin{Value}
A list with the following components:
\begin{ldescription}
\item[\code{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).
\item[\code{GEdata}] a (100 x 23) matrix containing gene expression data for 100 genes and 23 samples corresponding
to differents times during carbon source transition.
\item[\code{timepoint}] a numeric vector of length 23 containing the time points (in
hours) for the 23 samples.
\end{ldescription}
\end{Value}
\begin{Source}\relax
The data are described in Kao et al. (2004) and can be freely downloaded from 
\url{http://www.seas.ucla.edu/~liaoj/downloads.htm}.
\end{Source}
\begin{References}\relax
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
\bold{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 \bold{29},
72--74.
\end{References}
\begin{Examples}
\begin{ExampleCode}
# load plsgenomics library
library(plsgenomics)

# load data set
data(Ecoli)

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

\end{ExampleCode}
\end{Examples}

