interactome_pdz — PDZ-domain interactome (2005)

Description

A network of protein–protein interactions mediated by PDZ domains, from PDZBase, a manually curated database of PDZ-domain-mediated interactions extracted from the literature (about 300 interactions from over 200 articles at the time of publication). The data were obtained from the network collection of the Ma'ayan Laboratory (Mount Sinai School of Medicine), which distributed a version of PDZBase in its SIG flat file format; PDZBase itself is no longer online. Nodes are proteins, identified by their gene symbols, and an edge represents a binding interaction between a PDZ-domain-containing protein and its partner. All interactions are of type "Binding" with neutral effect. Self-loops denote proteins that bind to themselves.

The network has the following properties:

Nodes: name, the gene symbol; uniprot_human and uniprot_mouse, the Swiss-Prot/UniProt accessions of the human and mouse proteins (empty if not available); type, the molecule types assigned to the protein (e.g. Adapter, Kinase, Receptor, Channel); location, its cellular localizations (Cytosol, Membrane, Extracellular, Vesicles). A few proteins are assigned different types or locations in different interactions, hence the last two are lists.
Edges: pubmed, the PubMed ID of the article reporting the interaction.

Tags

Biological Protein interactions Unweighted Metadata

Citation

T. Beuming, L. Skrabanek, M. Y. Niv, P. Mukherjee, H. Weinstein, "PDZBase: a protein–protein interaction database for PDZ-domains." Bioinformatics 21(6), 827-828 (2005) 10.1093/bioinformatics/bti098 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_pdz	212	244	2.30	2.64	4.03	50.97	-0.36	0.00	10	0.76	Undirected	Unipartite	name uniprot_human uniprot_mouse type location	pubmed	8 KiB	10 KiB	10 KiB	8 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.