Ecoli: Ecoli gene expression and connectivity data from Kao et al....

In plsgenomics: PLS Analyses for Genomics

Ecoli gene expression and connectivity data from Kao et al. (2003)

Description

Gene expression data obtained during Escherichia coli carbon source transition and connectivity data from the RegulonDB data base (Salgado et al., 2001). The experiments and data sets are described in Kao et al. (2003).

Usage

data(Ecoli)

Value

A list with the following components:

CONNECdata	a (100 x 16) matrix containing the connectivity data for 100 genes and 16 regulators. The data are coded as 1 (positive interaction), 0 (no interaction) and -1 (negative interaction).
GEdata	a (100 x 23) matrix containing gene expression data for 100 genes and 23 samples corresponding to differents times during carbon source transition.
timepoint	a numeric vector of length 23 containing the time points (in hours) for the 23 samples.

Source

The data are described in Kao et al. (2004) and can be freely downloaded from http://www.seas.ucla.edu/~liaoj/downloads.html.

References

K. Kao, Y.-L. Yang, R. Boscolo, C. Sabatti, V. Roychowdhury and J. C. Liao (2004). Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis, PNAS 101, 641–646.

H. Salgado, A. Santos-Zavaleta, S. Gama-Castro, D. Millan-Zarate, E. Diaz-Peredo, F. Sanchez-Solano, E. Perez-Rueda, C. Bonavides-Martinez and J. Collado-Vides (2001). RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12, Nucleic Acids Research 29, 72–74.

Examples

# load plsgenomics library
library(plsgenomics)

# load data set
data(Ecoli)

# how many genes and how many transcription factors ?
dim(Ecoli$CONNECdata)

plsgenomics documentation built on Nov. 27, 2023, 5:08 p.m.