
For instance, clusters in a protein–protein interaction network have been shown to be protein complexes and parts of pathways. Depending on the type of network, clusters may mean different things. Find clusters (highly interconnected regions) in any network loaded into Cytoscape.The interactions contained in each subnetwork provide hypotheses for the regulatory and signaling interactions in control of the observed expression changes. interaction subnetworks, whose genes show particularly high levels of differential expression. The network is screened against gene expression data to identify connected sets of interactions, i.e. Find active subnetworks/pathway modules.For instance, users may select nodes involved in a threshold number of interactions, nodes that share a particular GO annotation, or nodes whose gene expression levels change significantly in one or more conditions according to p-values loaded with the gene expression data. Filter the network to select subsets of nodes and/or interactions based on the current data.Plugins are available for network and molecular profile analysis.Easily navigate large networks (100,000+ nodes and edges) by an efficient rendering engine.Use the bird's eye view to easily navigate large networks.And this structure can be saved in a session file. Use the network manager to easily organize multiple networks.Zoom in/out and pan for browsing the network.A variety of layout algorithms are available, including cyclic and spring-embedded layouts. according to user-configurable colors and visualization schemes. Expression data can be mapped to node color, label, border thickness, or border color, etc.

Cytoscape klay software#
A vital aspect of the software architecture of Cytoscape is the use of plugins for specialized features.

Cytoscape can visualize and analyze network graphs of any kind involving nodes and edges (e.g., social networks). While Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage. Yeast Protein–protein/Protein–DNA interaction network visualized by Cytoscape.
