truenet: The known intreactions of E.coli from RegulonDB database.

In Ac3net: Inferring Directional Conservative Causal Core Gene Networks

Description

This true interactions of E.coli from RegulonDB database.

Usage

data("truenet")

Details

These true interactions are mainly from RegulonDB database. We compiled the one from (Faith, 2007), and the RegulonDB database (TF-TF and TF-gene).We removed the links where the gene names is not evailable in our example E.coli dataset. See the references for the usage information of the data.

Source

This data was downloaded from http://regulondb.ccg.unam.mx/menu/download/datasets/index.jsp and m3d.mssm.edu/network_inference.html .

References

Gama-Castro S, et.al., RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond., Nucleic Acids Res. 2016 Jan 4;44(D1):D133-43.

Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 2007 Jan;5(1):e8

Examples

data(truenet)

Ac3net documentation built on May 2, 2019, 6:54 a.m.