A Cytoscape plug-in for calculating network centralities with numerical and graphical output
Complex biological networks, such as intracellular signaling
networks, are modeled by the evolution
to accomplish a
variety of different regulatory functions. This is achieved
by controlling the overall topology of the network which, then,
affects its dynamic behavior. Biological networks are
hierarchichal, scale-free,
modular structure in which few nodes,
the hubs,
play a particularly relevant
topological role and this may
reflect a critical role at biological level. However, also
nodes with no or lower hub role may have critical regulatory
role in certain biological phenomena. This could reflect
node-specific topological properties. Thus, it is of
interest to categorize every nodes in a network by means of
topological parameters allowing scoring of the nodes
according to their individual topological relevance.
Computation of centrality indexes may accomplish this goal.
The centrality indexes are topological parameters allowing a
node-by-node quantification of the reciprocal relationship
between the nodes. This provides a classification of the
nodes according to their capability to influence the
function of other nodes in the network. Combination of this
analysis with experimental data (node attributes) may help
to identify critical nodes and regulatory circuits in a
context-specific manner.
The most complete Centralities Cytoscape plugin! CentiScaPe computes:
-
Network parameters:
- Diameter
-
Average Distance
-
Node parameters and their min, max and average
values:
- Eccentricity
- Closeness
- Betweenness
- Stress
- Centroid
- Radiality
Several kind of graphical output
- Plot by centrality: Identify the nodes with high centrality values and integrate the analysis with biological attributes from lab experiment.
- Plot by node: Analyze single node centrality values
- Boolean highlight: Highlight nodes by their centrality values
More about CentiScaPe
- Documentation: CentiScaPe userguide, Centralities tutorial with definitions and biological meaning.
- How does people use CentiScaPe? See a list of publications using CentiScaPe.
Support CentiScaPe project!
If you publish result using CentiScaPe please cite:
"Analyzing biological network parameters with CentiScaPe"
Giovanni Scardoni; Michele Petterlini; Carlo Laudanna.
Bioinformatics 2009;
doi:10.1093/bioinformatics/btp517
This is really important for us!