EcoliOxygen: Preprocessed microarray oxygen deprivation data and filtered...

Description Usage Format Source References Examples


The data consist of two classes of 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.




gds680.eset 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 (arcA, appY, fnr, oxyR and soxS). The data was obtained by downloading the corresponding CEL files from the Gene Expression Omnibus ( under accession GDS680 and then normalized using the rma() function from the affy package. Following the steps described in (Castelo and Roverato, 2009) probesets were mapped to Entrez Gene Identifiers and filtered such that the current ExpressionSet object contains a total of p=4205 genes. The slot featureNames has already the corresponding Entrez Gene IDs.
subset.gds680.eset ExpressionSet object corresponding to a subset of gds680.eset defined by the transcription factor genes that were knocked-out in the experiments by Covert et al. (2004) and their putative targets according to the RegulonDB database version 6.1.
filtered.regulon6.1 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.
subset.filtered.regulon6.1 Subset of filtered.regulon6.1 containing the transcriptional regulatory relationships in RegulonDB version 6.1 that involve the transcription factor genes which were knocked-out in the experiments by Covert et al. (2004).


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., 16(2):213-227, 2009.



qpgraph documentation built on Jan. 10, 2021, 2:01 a.m.