ergm (version 3.1.3)

ecoli: Two versions of an E. Coli network dataset

Description

This network data set comprises two versions of a biological network in which the nodes are operons in Escherichia Coli and a directed edge from one node to another indicates that the first encodes the transcription factor that regulates the second.

Usage

data(ecoli)

source

The data set is based on the RegulonDB network (Salgado et al, 2001) and was modified by Shen-Orr et al (2002).

Licenses and Citation

When publishing results obtained using this data set, the original authors (Salgado et al, 2001; Shen-Orr et al, 2002) should be cited, along with this R package.

Details

The network object ecoli1 is directed, with 423 nodes and 519 arcs. The object ecoli2 is an undirected version of the same network, in which all arcs are treated as edges and the five isolated nodes (which exhibit only self-regulation in ecoli1) are removed, leaving 418 nodes.

References

Salgado et al (2001), Regulondb (version 3.2): Transcriptional Regulation and Operon Organization in Escherichia Coli K-12, Nucleic Acids Research, 29(1): 72-74.

Shen-Orr et al (2002), Network Motifs in the Transcriptional Regulation Network of Escerichia Coli, Nature Genetics, 31(1): 64-68.