ecoli: Two versions of an E. Coli network dataset

In statnet/statnet.data: Network Datasets for the Statnet Suite

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.

Format

ecoli1 - Directed network object with 423 nodes and 519 edges. Vertex attributes: self.

ecoli2 - Undirected network object with 418 nodes and 519 edges. Vertex attributes: self.

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.

Licenses and Citation

If the section Source of this page does not specify otherwise, this data set is protected by the Creative Commons License https://creativecommons.org/licenses/by/4.0/.

When publishing results obtained using this data set, the original authors (see sections Source and/or References) should be cited, along with this R package. To cite this package please use the following:

Handcock M, Hunter D, Butts C, Goodreau S, Krivitsky P, Morris M, Bojanowski M (2021). statnet.data: Network Datasets for the Statnet Suite. R package version 0.1-0, <URL: https://statnet.org>.

Source

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

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.

Saul, Z. M., & Filkov, V. (2007). Exploring biological network structure using exponential random graph models. Bioinformatics, 23(19), 2604-2611.

See Also

Other directed networks: emon, faux.desert.high, faux.dixon.high, g4, newcomb, samplk, sampson, tribes

Other undirected networks: davis, faux.magnolia.high, faux.mesa.high, florentine, kapferer, molecule, zach

statnet/statnet.data documentation built on Dec. 16, 2021, 5:54 p.m.