![]() 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 protein–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 protein–DNA interaction pairs.Plugins are developed by core developers and the greater user community. 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.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |