oxygen {gcExplorer} | R Documentation |
Normalized gene expression microarray data from Escherichia coli (E. coli).
data(oxygen)
oxygen
is a data matrix 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 (arcA,
appY, fnr, oxyR and soxS). The data was
obtained by downloading the corresponding CEL files from the Gene
Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under
accession GDS680
and then normalized using the rma()
function from the affy
package. Following the steps described in
(Castelo and Roverato, 2008) probesets were mapped to Entrez Gene
Identifiers and filtered such that the ExpressionSet
in the
qpgraph
package names EcoliOxygen
contains a total
of p=4205 genes.
Here a subset of the EcoliOxygen data was used containing all genes
where Blattner numbers were available.
This dataset was taken from Bioconductor package qpgraph
and modified
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. 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. Nucleic Acids Res., 36(Database issue):D120-124, 2008.
Castelo, R. and Roverato, A. Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J. Comp. Biol., accepted, 2008.
data(oxygen)