yeast_exosome — Yeast nuclear exosome protein interactions (2006)
- Description
Weighted network of physical interactions among the proteins of the nuclear exosome, the 3'-5' exonuclease complex, of the budding yeast Saccharomyces cerevisiae. The data were compiled by M. Cantor and collaborators for a study of nestedness across levels of biological organization, and are distributed in the repository of that study (file
mol_yeast_nuclearexosome.txt). They retrieved the interactions among 44 exosome proteins from the IMEx consortium databases, mostly from the large-scale affinity purification and mass spectrometry study of protein complexes of N. J. Krogan and collaborators. Nodes are proteins, and an undirected edge connects two proteins with evidence of a physical association between them, weighted by the reliability score of the interaction, which combines the available experimental evidence and ranges from 0 (no evidence) to 1 (strong support), i.e. an estimate of the probability that the interaction is correct. The source lists each interaction in both directions, with the same score; here each appears once.The network has the following properties:
- Nodes:
name, the UniProt accession of the protein (e.g. "P38792"). - Edges:
weight, the reliability score of the interaction.
- Nodes:
- Tags
- Biological Protein interactions Weighted Metadata
- Citation
-
- N. J. Krogan et al., "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae." Nature 440, 637-643 (2006) 10.1038/nature04670 Sci-Hub
- S. Orchard et al., "Protein interaction data curation: the International Molecular Exchange (IMEx) consortium." Nature Methods 9, 345-350 (2012) 10.1038/nmeth.1931 Sci-Hub
- M. Cantor, M. M. Pires, F. M. D. Marquitti, R. L. G. Raimundo, E. Sebastián-González, P. P. Coltri, S. I. Perez, D. R. Barneche, D. Y. C. Brandt, K. Nunes, F. G. Daura-Jorge, S. R. Floeter, P. R. Guimarães Jr., "Nestedness across biological scales." PLoS ONE 12(2), e0171691 (2017) 10.1371/journal.pone.0171691 Sci-Hub
- Upstream URL OK
- https://bitbucket.org/maucantor/unodf_analyses
- 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