CYTOSCAPE APPS SOFTWARE

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.

View a superposition of gene expression ratios and p-values on the network.

Customize network data display using powerful visual styles.

Cytoscape session file includes networks, attributes (for node/edge/network), desktop states (selected/hidden nodes and edges, window sizes), properties, and visual styles.

Load and save state of the cytoscape session in a cytoscape session (.cys) file.

Directly import GO terms and annotations from OBO and Gene Association files.

Import gene functional annotations from the Gene Ontology (GO) and KEGG databases.

For example, input a set of custom annotation terms for your proteins, create a set of confidence values for your proteinвЂ“protein interactions.

Load and save arbitrary attributes on nodes and edges.

Input mRNA expression profiles from tab- or space-delimited text files.

Load and save networks and node/edge attributes in an XML document format called XGMML (eXtensible Graph Markup and Modeling Language).

Load and save previously-constructed interaction networks in GML format (Graph Modelling Language).

User-defined interaction types are also supported. For yeast and other model organisms, large sources of pairwise interactions are available through the BIND and TRANSFAC databases.

Input and construct molecular interaction networks from raw interaction files (SIF format) containing lists of protein-protein and/or proteinвЂ“DNA interaction pairs.

Plugins are developed by core developers and the greater user community.

CYTOSCAPE APPS 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 ProteinвЂ“protein/ProteinвЂ“DNA interaction network visualized by Cytoscape.

Cytoscape apps