HiveR

Summary of E coli files in inst/extdata/E_coli

Part of HiveR package by Bryan Hanson.  Files provided by Martin Krzywinski of the Genome Sciences Center and used with permission.

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The main source of data for the regulatory network is:

Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muniz-Rascado
L, Solano-Lira H et al (2011). RegulonDB version 7.0: transcriptional
regulation of Escherichia coli K-12 integrated within genetic sensory
response units (Gensor Units). Nucleic Acids Research 39: D98-D105.

http://www.ncbi.nlm.nih.gov/pubmed/21051347?dopt=Abstract

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The files Ecoli_P.dot, EdgeInst_P.csv, NodeInst_P.csv and NodeLabels_P.csv pertain to the gene regulatory network of E. coli as discussed in:

Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. 2010. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proc Natl Acad Sci U S A 107(20): 9186-9191.

This data set has been extended by Martin Krzywinski by the addition of persistence and edge classifiers as described below.

Nodes are classified as 'persistent' or 'nonpersistent' according to the definition in the original paper (Yan et al). Edges are classified using a type=N label where N=0,1,2,3 defined as follows. For E. coli

type=0  - E. coli gene names share 0 common start characters (crp acea)
type=1  - E. coli gene names share 1 common start characters (arca acee)
type=2  - E. coli gene names share 2 common start characters (argr arti)
type=3  - E. coli gene names share 3 common start characters (acrr acrb)

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The files Ecoli_TF.dot and EdgeInst_TF.csv are from an more recent version of RegulonDB; the edges are coded according to whether the transcription factor is an activator, repressor, or dual function protein.  There are no node instructions for the transcription factor data set.