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.
1 |
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 (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, 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.
1 2 | data(EcoliOxygen)
ls()
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.