Learn to use Cytoscape, an open-source software platform used for visualization and analysis of molecular interaction and network data. Cytoscape uses a graphical user interface with floatable panels to easily manage your network data. Graphical data displays and text attributes provide detailed information about interactions of interest. Customizable features enable extensive visualization and manipulation opportunities. This platform also offers plugin capability to increase functionality, and has an active user community developing and maintaining the software.
Note: This tutorial corresponds to Cytoscape 2.x versions. We are monitoring the releases of the 3.x software and will provide updates in the future.
You will learn:
This tutorial is a part of the tutorial group Interaction resources. You might find the other tutorials in the group interesting:
Pathway Interaction Database: A resource of pathway and network data and displays
MINT: Molecular Interaction Database
BiologicalNetworks: Analyze and visualize molecular interaction networks
BioSystems: Database of Biological Systems
Reactome Legacy: Older version of the current Reactome knowledgebase of biological processes.
Reactome: Knowledgebase of biological processes
GeneMANIA: GeneMANIA: Fast Gene Function Predictions
GenMAPP: A freely available open source software application for visualizing microarray data in the context of biological pathways.
VisANT: A web-based or downloadable software platform used for visualization and analysis of networks and interaction pathways
InterPro: A comprehensive protein signature resource
IntAct protein interaction database: IntAct is an open source database and analysis resource for protein interaction data
KEGG: KEGG, The Kyoto Encyclopedia of Genes and Genomes
Pathways and Interactions : Tools that are involved with protein interactions and pathway features. Some tools are primarily repositories and some offer analysis options.
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Recent BioMed Central research articles citing this resource
Landeghem Van Sofie et al., Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks Networks analysis. BMC Bioinformatics (2016) doi:10.1186/s12859-015-0863-y
Huang Kai-Yao et al., A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. BMC Systems Biology (2016) doi:10.1186/s12918-015-0244-1
Azevedo Hátylas et al., Intragraft transcriptional profiling of renal transplant patients with tubular dysfunction reveals mechanisms underlying graft injury and recovery. Human Genomics (2016) doi:10.1186/s40246-015-0059-6
Huang Chien-Hung et al., Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory. BMC Bioinformatics (2016) doi:10.1186/s12859-015-0845-0
de Souza-Cruz Soriane et al., Liver and blood cytokine microenvironment in HCV patients is associated to liver fibrosis score: a proinflammatory cytokine ensemble orchestrated by TNF and tuned by IL-10 Microbe-host interactions and microbial pathogenicity. BMC Microbiology (2016) doi:10.1186/s12866-015-0610-6