\name{EcoliOxygen}
\docType{data}
\alias{EcoliOxygen}
\alias{filtered.regulon6.1}
\alias{gds680.eset}

\title{Preprocessed microarray oxygen deprivation data and filtered RegulonDB data}

\description{The data consist of two objects, one containing normalized gene
expression microarray data from Escherichia coli (E. coli) and the other
containing a subset of filtered RegulonDB transcription regulatory relationships
on E. coli.
}

\usage{
data(EcoliOxygen)
}

\format{
  \tabular{ll}{
    \code{gds680.eset}\tab \code{ExpressionSet} object containing n=43 experiments
         of various mutants under oxygen deprivation (Covert et al., 2004). The
         mutants were designed to monitor the response from E. coli during an
         oxygen shift in order to target the a priori most relevant part of the
         transcriptional network by using six strains with knockouts of five
         key transcriptional regulators in the oxygen response (\emph{arcA},
         \emph{appY}, \emph{fnr}, \emph{oxyR} and \emph{soxS}). The data was
         obtained by downloading the corresponding CEL files from the Gene
         Expression Omnibus (\url{http://www.ncbi.nlm.nih.gov/geo}) under
         accession \code{GDS680} and then normalized using the \code{rma()}
         function from the \code{affy} package. Following the steps described in
         (Castelo and Roverato, 2009) probesets were mapped to Entrez Gene
         Identifiers and filtered such that the current \code{ExpressionSet}
         object contains a total of p=4205 genes. The slot \code{featureNames}
         has already the corresponding Entrez Gene IDs.\cr
    \code{filtered.regulon6.1}\tab Data frame object containing a subset of the
         E. coli transcriptional network from RegulonDB 6.1 (Gama-Castro et al,
         2008) obtained through the filtering steps described in (Castelo and
         Roverato, 2009). In this data frame each row corresponds to a
         transcriptional regulatory relationship and the first two columns
         contain Blattner IDs of the transcription factor and target genes,
         respectively, and the following two correspond to the same genes but
         specified by Entrez Gene IDs. The fifth column contains the direction
         of the regulation according to RegulonDB.\cr
  }
}
\examples{
data(EcoliOxygen)
}
\source{
Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J., and Palsson, B.O.
Integrating high-throughput and computational data elucidates bacterial networks.
\emph{Nature}, 429(6987):92-96, 2004.

Gama-Castro, S., Jimenez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A.,
Penaloza-Spinola, M.I., Contreras-Moreira, B., Segura-Salazar, J., Muniz-Rascado,
L., Martinez-Flores, I., Salgado, H., Bonavides-Martinez, C., Abreu-Goodger, C.,
Rodriguez-Penagos, C., Miranda-Rios, J., Morett, E., Merino, E., Huerta, A.M.,
Trevino-Quintanilla, L., and Collado-Vides, J. RegulonDB (version 6.0): gene
regulation model of Escherichia coli K-12 beyond transcription, active
(experimental) annotated promoters and Textpresso navigation.
\emph{Nucleic Acids Res.}, 36(Database issue):D120-124, 2008.
}

\references{
Castelo, R. and Roverato, A. Reverse engineering molecular regulatory
networks from microarray data with qp-graphs. \emph{J. Comp. Biol.},
16(2):213-227, 2009.
}

\keyword{datasets}