kinophosphatome — Human protein interactome and kino-phosphatome (2009)

Description

Networks of interactions among human proteins, from the supplementary data of the article by G. Scardoni, M. Petterlini and C. Laudanna introducing CentiScaPe, a Cytoscape plugin for computing node centralities. Nodes represent human proteins (identified by their HGNC gene symbols), and an undirected edge means that the two proteins are known to interact, according to the public protein interaction databases HPRD, BIND, DIP, IntAct, MINT and BioGRID, from which the data were compiled. There are two networks:

global: the global human protein interactome compiled by the authors (the file GLOBAL-HGNC.sif), with 11,120 proteins and 84,776 interactions, including 2,500 self-interactions.
kinophosphatome_core: a sub-network of the human kino-phosphatome, i.e. of the network of interactions among human protein kinases and phosphatases, containing the 97 proteins (82 kinases and 15 phosphatases) whose values of all the centralities computed by CentiScaPe (degree, betweenness, closeness, eccentricity, radiality, stress and centroid value) are above the average of the kino-phosphatome network, and the 962 interactions among them.

The kino-phosphatome network analyzed in the article, with 549 proteins (406 kinases and 143 phosphatases, listed in its Table S4) and 3,844 interactions, is not included in the supplementary data; it can be approximated as the sub-network of the global interactome induced by the proteins marked as kinases or phosphatases, but that sub-network has 3,777 interactions (including 244 self-interactions), and 6 of the 549 proteins do not occur in the global interactome.

The networks have the following properties:

Nodes: name, the HGNC symbol of the gene encoding the protein; kind, kinase or phosphatase for the 549 proteins of the kino-phosphatome network (Table S4 of the article), empty otherwise (LMTK2, which is marked both as a kinase and as a phosphatase in the table, is given as a phosphatase, consistent with the counts of the article).¹

Description obtained in part from the ICON project. ↩

Tags

Biological Protein interactions Unweighted Metadata

Citation

G. Scardoni, M. Petterlini, C. Laudanna, "Analyzing biological network parameters with CentiScaPe." Bioinformatics 25(21), 2857-2859 (2009) 10.1093/bioinformatics/btp517 Sci-Hub

Upstream URL OK

https://doi.org/10.1093/bioinformatics/btp517

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
global	11,120	84,776	15.25	28.56	102.13	22.54	0.04	0.23	11	0.98	Undirected	Unipartite	name kind		197 KiB	342 KiB	362 KiB	321 KiB
kinophosphatome_core	97	962	19.84	8.97	23.34	1.99	0.09	0.36	3	1.00	Undirected	Unipartite	name kind		2 KiB	4 KiB	4 KiB	4 KiB