yeast_transcription — Yeast transcription network (2002)
- Description
Transcriptional regulation network of the yeast Saccharomyces cerevisiae, from the collection of networks of U. Alon's lab used by R. Milo et al. to identify network motifs, compiled from the Yeast Proteome Database (Costanzo et al., 2001). Nodes are genes (including the genes of transcription factors) and a directed edge $i \to j$ indicates that the transcription factor encoded by gene $i$ regulates the transcription of gene $j$. The upstream adjacency matrix also includes 226 genes without any regulatory interaction, which appear as isolated nodes.
The network has the following properties:
- (Node)
name: the name of the gene. - (Edge)
regulation: the type of regulation, coded as 1, 2 or 3. In the networks of this collection these codes denote activation, repression, and dual (both) regulation, respectively, but the codes are not documented in the upstream file.
- (Node)
- Tags
- Biological Gene regulation Unweighted
- Added
- 2020-08-11
- Citation
-
- R. Milo et al., "Network Motifs: Simple Building Blocks of Complex Networks." Science 298, 824-827 (2002). 10.1126/science.298.5594.824 Sci-Hub
- Upstream URL 404
- http://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks
- Networks
-
Tip: hover over a column header 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
- Ridiculograms*
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