Affordable Access

deepdyve-link
Publisher Website

Biological network exploration with Cytoscape 3.

Authors
Type
Published Article
Journal
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]
Volume
47
Identifiers
DOI: 10.1002/0471250953.bi0813s47
Source
Ideker Lab
License
Unknown

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.

Report this publication

Statistics

Seen <100 times