oxygen {gcExplorer}R Documentation

Preprocessed microarray oxygen deprivation data

Description

Normalized gene expression microarray data from Escherichia coli (E. coli).

Usage

data(oxygen)

Format

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.

Note

This dataset was taken from Bioconductor package qpgraph and modified

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. 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.

Examples

data(oxygen)

[Package gcExplorer version 0.9-1 Index]