interactome_vidal — Vidal human interactome (2005)

Description

Networks of interactions between human proteins from the first version of a proteome-scale map of human binary protein–protein interactions by Rual et al. (2005), from the Center for Cancer Systems Biology (CCSB) at the Dana-Farber Cancer Institute. In that study, pairwise interactions among the products of about 8,100 open reading frames (the "Space-I" of the human ORFeome) were tested with a stringent high-throughput yeast two-hybrid (Y2H) system, detecting 2,754 interactions among 1,549 proteins (the CCSB-HI1 data set, later called HI-I-05). The collection contains two versions of the data:

HI-I-05: the CCSB-HI1 interactions, as released by the CCSB in its Interactome Database (file HI-I-05.tsv, with the gene identifiers of the original publication), with proteins identified by their Entrez Gene IDs.
maayan: the network distributed by the network collection of the Ma'ayan Laboratory (Mount Sinai School of Medicine), in its SIG flat file format, as protein–protein interactions extracted from the paper, with proteins identified by gene symbols and, where available, UniProt accessions. This network is larger than CCSB-HI1: of its 6,726 interactions, only 2,509 match (by gene symbol) the 2,754 interactions of HI-I-05; the origin of the others is not documented.

In both networks, nodes are proteins (identified by the genes that encode them), and an undirected edge represents an interaction. Self-loops denote proteins that interact with themselves.

The networks have the following properties:

HI-I-05: Nodes: entrez_id, the Entrez Gene ID; name, the HGNC gene symbol.
maayan: Nodes: name, the gene symbol of the protein; uniprot_human and uniprot_mouse, the UniProt accessions of the human protein and of its mouse orthologue (empty if not available).

Other data sets of the CCSB Interactome Database are in the entries human_interactome_2014 (the later human maps HI-II-14 and Lit-BM-13), yeast_interactome_ccsb (the yeast binary Y2H maps CCSB-YI1, Ito core and Uetz screen, and literature-curated and gold-standard reference sets), collins_yeast (the yeast co-complex associations of Collins et al.) and celegans_interactomes (the C. elegans interactome networks).

Tags

Biological Protein interactions Unweighted Metadata

Citation

J.-F. Rual et al., "Towards a proteome-scale map of the human protein–protein interaction network." Nature 437(7062), 1173-1178 (2005) 10.1038/nature04209 Sci-Hub

Upstream URL OK

https://web.archive.org/web/20150511224913/http://interactome.dfci.harvard.edu/H_sapiens/index.php?page=download
https://web.archive.org/web/20180916202441/http://research.mssm.edu/maayan/datasets/qualitative_networks.shtml

Networks

Tip: click on a column header to sort the list, or hover over it 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
maayan	3,133	6,726	4.29	6.88	13.91	39.11	-0.10	0.04	13	0.89	Undirected	Unipartite	name uniprot_human uniprot_mouse		44 KiB	62 KiB	62 KiB	60 KiB
HI-I-05	1,549	2,754	3.56	7.45	13.37	31.84	-0.18	0.02	12	0.84	Undirected	Unipartite	entrez_id name		16 KiB	24 KiB	23 KiB	23 KiB