interactome_yeast — Jeong yeast interactome (2001)

Description

Protein-protein interactions in yeast (Saccharomyces cerevisiae), studied by H. Jeong, S. P. Mason, A.-L. Barabási and Z. N. Oltvai (2001), who found that highly connected proteins are more likely to be essential (lethal if removed) than proteins of lower degree; later studies (e.g. S. Coulomb et al., 2005) argued that this result could be an artifact of the incompleteness of the data. The interactions were distributed by the Barabási lab at the University of Notre Dame (no longer online), from which this version was obtained via the Internet Archive. The protein names and lethalities were distributed, together with the same interactions, by L. C. Freeman on his network data page at the University of California, Irvine (no longer online), also obtained via the Internet Archive.

An undirected edge (i, j) indicates an interaction between proteins i and j. The data contain self-loops. The protein list of L. C. Freeman contains 244 additional proteins without any interaction, which are not included.

The network has the following properties:

(Node) protein_id: the number of the protein in the source files.
(Node) orf: the systematic (ORF) name of the gene (missing for 35 proteins).
(Node) name: the standard gene name.
(Node) lethality: whether the deletion of the gene is lethal ("Lethal", "Non-Lethal" or "Unknown").

Tags

Biological Protein interactions Unweighted Metadata

Added

2020-08-11

Citation

H. Jeong, S. P. Mason, A.-L. Barabási, Z. N. Oltvai, "Lethality and centrality in protein networks." Nature 411, 41-42 (2001) 10.1038/35075138 Sci-Hub
S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005). 10.1098/rspb.2005.3128 Sci-Hub

Upstream URL [Errno 111] Connection refused

https://web.archive.org/web/20060812145625/http://www.nd.edu/~networks/resources.htm
https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#pro-pro

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

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
interactome_yeast	1,870	2,277	2.44	3.16	5.84	133.86	-0.15	0.06	19	0.78	Undirected	Unipartite			34 KiB	46 KiB	46 KiB	38 KiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.