Sentence examples for using the Cytoscape network from inspiring English sources
Networks were visualized using the Cytoscape network visualization tool [ 66].
The bipartite networks, which illustrate the properties of the computed protein networks exemplars with activators of immune cell differentiation, the groups (modules) of coexpressed genes from ImmGen, and the immune cell types, were visualized using the Cytoscape network analysis toolkit [ 32].
As first the network representing the elements common to both the networks was realised, using the Cytoscape plugin Network Analyzer (function "Compute intersection" of "Compare two networks" menu).
To display interactive networks, we use the Cytoscape Web plugin [ 38].
We used the Cytoscape Web [ 42] to display the network on internet browsers.
Clustering with overlap neighborhood expansion (ClusterONE) was used in the Cytoscape network in order to discover densely connected regions in the network with possible overlap.
This allows one later to compute a correlation network using the Cytoscape plugin ExpressionCorrelation (http://www.baderlab.org/Software/ExpressionCorrelation).
In particular, we performed literature mining of the PUBMED database and constructed the herbal monomer-module gene regulatory network using the Cytoscape software.
Enriched gene sets were graphically organised into a network using the Cytoscape (Shannon et al, 2003) plug-in Enrichment Map (Merico et al, 2010), where each gene set was represented as a node and edges represented overlap between sets.
Major network centralities (closeness, betweenness, and node degree) were analyzed with the CP-PPI networks using the Cytoscape plugin CentiScape 2.8.2 [ 43].
First, using the Cytoscape plugin jActiveModules [40], we identified network regions (sub-portions of the full network referred to as "modules") enriched in differentially expressed, interconnected genes (nodes).
