S. cerevisiae transcriptional regulation network
Dataset information
This is a transcriptional regulation network for S. cerevisiae, a yeast. In the network, each node is an operon (a group of genes in a mRNA molecule), and a directed edge from operon i to operon j means that i is regulated by a transcriptional factor encoded by j. Furthermore, edges are signed to represent activation and repression. Coherent feedforward loops (FFLs) are a particular signed motif formed between three nodes, and such motifs are known to have particular functional roles. We include a list of coherent FFLs for this dataset along with their functional roles.
| Dataset statistics | |
|---|---|
| Nodes | 690 |
| Edges | 1094 |
| Nodes in largest WCC | 664 (0.962) |
| Edges in largest WCC | 1078 (0.985) |
| Nodes in largest SCC | 3 (0.004) |
| Edges in largest SCC | 5 (0.005) |
| Average clustering coefficient | 0.0470 |
| Number of triangles | 72 |
| Fraction of closed triangles | 0.005467 |
| Diameter (longest shortest path) | 15 |
| 90-percentile effective diameter | 7 |
Source (citation)
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For the network:
- Ron Milo, et al. "Network motifs: simple building blocks of complex networks." Science 298.5594 (2002): 824-827.
- Shmoolik Mangan and Uri Alon. "Structure and function of the feed-forward loop network motif." Proceedings of the National Academy of Sciences 100.21 (2003): 11980-11985.
For the coherent feedforward loops:
Files
| File | Description |
|---|---|
| S-cerevisiae.txt.gz | Directed transcriptional regulation network |
| S-cerevisiae-names.csv.gz | Names of operons |
| S-cerevisiae-coherent-FFLs.csv.gz | Coherent feedforward loops and functionality |