ecoli_transcription — E. coli transcription network (2002)
- Description
The transcriptional regulation network of the bacterium Escherichia coli, compiled by S. S. Shen-Orr, R. Milo, S. Mangan and U. Alon to study network motifs. Nodes are operons (groups of genes transcribed together), and a directed edge connects a transcription factor to an operon whose transcription it regulates (a transcription factor is itself encoded by an operon, so it is represented by the corresponding node; self-loops represent autoregulation). The interactions were assembled from the RegulonDB database (version 3.2, excluding interactions of unknown type and interactions supported only by ChIP experiments), complemented by a literature search.
There are two versions of the data:
v1.0: the original data set used in the publication;v1.1: an updated version with 578 interactions, in which three errors were corrected (the misspelled operon moaABDE renamed to maoABDE; hycA merged into the autoregulated operon hycABCDE; and a missing interaction of ArcA added).
The networks have the following properties:
- (Node)
name: the name of the operon (e.g.crp). - (Edge)
regulation_type: the kind of regulation (1: activation, 2: repression, 3: dual, i.e. both activation and repression depending on conditions).
- Tags
- Biological Gene regulation Unweighted
- Added
- 2020-08-11
- Citation
-
- Shen-Orr et. al, "Network motifs in the transcriptional regulation network of Escherichia coli." Nature Genetics 31, 64-68 (2002). 10.1038/ng881 Sci-Hub
- Upstream URL 404
- http://www.weizmann.ac.il/mcb/UriAlon/e-coli-transcription-network
- Networks
-
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
- $\left<k\right>$
- Mean degree
- $\sigma_k$
- Standard deviation of the degrees
- $\lambda_h$
- Largest eigenvalue of the Hashimoto (non-backtracking) matrix
- $\tau$
- Random walk mixing time
- $r$
- Degree assortativity
- $c$
- Global clustering coefficient
- $\oslash$
- (Pseudo-) diameter
- $S$
- Relative size of the largest component
- NPs
- Node properties
- EPs
- Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv v1.0 424 577 1.36 4.88 6.12 141.95 -0.19 0.02 13 0.78 Directed Unipartite name regulation_type 8 KiB 12 KiB 11 KiB 9 KiB v1.1 423 578 1.37 4.90 6.20 141.96 -0.19 0.02 13 0.78 Directed Unipartite name regulation_type 8 KiB 12 KiB 12 KiB 9 KiB - Ridiculograms*