2003/11/01 by Paul Shannon, Andrew Markiel, Owen Ozier +6 · 27 citations
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #Microbial Metabolic Engineering and Bioproduction #Gene Regulatory Network Analysis
paper · pdf · doi:10.1101/gr.1239303
openalex publication_date 2003/11/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.