UNIT 8.13 Biological Network Exploration with Cytoscape 3. Issue 1 (8th September 2014)

• Record Type: Journal Article
• Authors: Su, Gang; Morris, John H.; Demchak, Barry; Bader, Gary D.
• Is Part Of: Current protocols in bioinformatics. Volume 47:Issue 1(2014)
• Page Start: 8.13.1
• Page End: 8.13.24
• Publication Date: 2014-09-08
• Subjects: Cytoscape -- interactive network visualization -- network analysis; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/0471250953.bi0813s47
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: Cytoscape is one of the most popular open‐source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface, and performance relative to previous versions. This protocol aims to jump‐start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the networks, visualizing network associated data (attributes), and identifying clusters. It also highlights new features that benefit experienced users. Curr. Protoc. Bioinform . 47:8.13.1‐8.13.24. © 2014 by John Wiley & Sons, Inc.