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Cytoscape: a software environment for integrated models of biomolecular interaction networks.
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.
Cytoscape 2.8: new features for data integration and network visualization
- M. Smoot, K. Ono, J. Ruscheinski, Peng-Liang Wang, T. Ideker
- Computer ScienceBioinform.
- 12 December 2010
Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities.
Integration of biological networks and gene expression data using Cytoscape
This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing
A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.
Genome-wide methylation profiles reveal quantitative views of human aging rates.
Network-based classification of breast cancer metastasis
- Han-Yu Chuang, Eunjung Lee, Yu-Tseung Liu, Doheon Lee, T. Ideker
- BiologyMolecular systems biology
- 16 October 2007
A protein‐network‐based approach is applied that identifies markers not as individual genes but as subnetworks extracted from protein interaction databases, which provide novel hypotheses for pathways involved in tumor progression.
A travel guide to Cytoscape plugins
A travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8 and ongoing efforts to distribute, organize and maintain the quality of the collection.
Systematic interpretation of genetic interactions using protein networks
Using a probabilistic model, it is found that 1,922 genetic interactions are significantly associated with either between- or within-pathway explanations encoded in the physical networks, covering ∼40% of known genetic interactions.
Integrated Genomic Characterization of Papillary Thyroid Carcinoma