interactome_figeys — Figeys human interactome (2007)

Description

A network of interactions between human proteins, from the first large-scale study of protein–protein interactions in human cells using mass spectrometry, by Ewing et al. (2007). Flag-tagged versions of 338 bait proteins, selected for known or suspected disease and functional associations, were expressed in HEK293 cells and immunoprecipitated, and the co-purified proteins were identified by LC-ESI-MS/MS. Of the 24,540 potential interactions identified, false positives and redundant hits were removed using empirical criteria and a computed confidence score, giving 6,463 interactions between 2,235 proteins. The data were obtained from the network collection of the Ma'ayan Laboratory (Mount Sinai School of Medicine), which distributed them in its SIG flat file format, with proteins identified by gene symbols.

Nodes are proteins, and a directed edge points from a bait protein to a protein co-purified with it (the 338 nodes with outgoing edges are the baits). Twenty pairs of proteins are connected in both directions.

The network has the following properties:

(Node) name: the gene symbol of the protein.

Tags

Biological Protein interactions Unweighted

Added

2020-08-11

Citation

R. M. Ewing et al., "Large-scale mapping of human protein–protein interactions by mass spectrometry." Molecular Systems Biology 3, 89 (2007) 10.1038/msb4100134 Sci-Hub

Upstream URL OK

https://web.archive.org/web/20180916202441/http://research.mssm.edu/maayan/datasets/qualitative_networks.shtml

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_figeys	2,239	6,452	2.88	17.01	27.83	16.04	-0.33	0.01	10	0.99	Directed	Unipartite			45 KiB	63 KiB	63 KiB	52 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.