Edit Data mining and learning analytics tools: Cytoscape

FREE TEXT:

== '''Features ( from Wikipedia):''' == '''Input''' * Input and construct molecular interaction networks from raw interaction files (SIF format) containing lists of protein-protein and/or protein-DNA interaction pairs. For yeast and other model organisms, large sources of pairwise interactions are available through the BIND and [[TRANSFAC]] databases. User-defined interaction types are also supported. * Load and save previously-constructed interaction networks in [[Graph Modelling Language|GML]] format (Graph Modelling Language). * Load and save networks and node/edge attributes in an XML document format called [[XGMML]] (eXtensible Graph Markup and Modeling Language). * Input mRNA expression profiles from tab- or space-delimited text files. * Load and save arbitrary attributes on nodes and edges. For example, input a set of custom annotation terms for your proteins, create a set of confidence values for your protein-protein interactions. * Import gene functional annotations from the [[Gene Ontology]] (GO) and [[KEGG]] databases. * Directly import GO Terms and annotations from OBO and Gene Association files. * Load and save state of the Cytoscape session in a Cytoscape Session (.cys) file. Cytoscape Session file includes networks, attributes (for node/edge/network), Desktop states (selected/hidden nodes and edges, window sizes), Properties, and Visual Styles. '''Visualization''' * Customize network data display using powerful visual styles. * View a superposition of gene expression ratios and p-values on the network. Expression data can be mapped to node color, label, border thickness, or border color, etc. according to user-configurable colors and visualization schemes. * Layout networks in two dimensions. A variety of layout algorithms are available, including cyclic and [[Force-based algorithms (graph drawing)|spring-embedded layouts]]. * Zoom in/out and pan for browsing the network. * Use the network manager to easily organize multiple networks. And this structure can be saved in a session file. * Use the bird's eye view to easily navigate large networks. * Easily navigate large networks (100,000+ nodes and edges) by efficient rendering engine. '''Analysis''' * Plugins available for network and molecular profile analysis. For example: ** Filter the network to select subsets of nodes and/or interactions based on the current data. 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. ** Find active subnetworks/pathway modules. The network is screened against gene expression data to identify connected sets of interactions, i.e. interaction subnetworks, whose genes show particularly high levels of differential expression. The interactions contained in each subnetwork provide hypotheses for the regulatory and signaling interactions in control of the observed expression changes. ** Find clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families.