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:

  • how to navigate and use the graphical user interface
  • to import network data from different sources
  • how to create a network layout and import attributes for your network
  • how to find and load plugins to add functionality to your network analysis
TUTORIAL RELATED CONTENT

TUTORIALS

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

CATEGORIES

Pathways and Interactions : Tools that are involved with protein interactions and pathway features. Some tools are primarily repositories and some offer analysis options.

BLOG POSTS

Video Tip of the Week: GenomeSpace Orientation: "Frictionless connection of bioinformatics tools" The GenomeSpace site has been highlighted before in our "tips of the week". We appreciated this site that pulled together a lot of different useful ty...

Video Tip of the Week: Weave, Web-based Analysis and Visualization Environment: At the recent Discovery On Target conference, a workshop on data and analytics for drug discovery contained several informative talks. This week's Video Tip of the Week was inspired by the first speake...

Video Tip of the Week: PANDA (Pathway AND Annotation) Explorer for lists of genes: This week's Video Tip of the Week demonstrates PANDA, a tool for generating and examining annotations that are available for a list of genes, and evaluating them in the context of pathways. Two great t...

Video Tip of the Week: PhenogramViz for evaluating phenotypes and CNVs: As I've mentioned before, once I start looking over some new tools I'm often led to others in the same arena that offer related but different features. That's what happened when I looked at the Proband...

Video Tip of the Week: PhosphoSitePlus, protein post-translational modifications : Nucleotide sequence data and analysis commands the bulk of my attention on most days. But certainly post-translational modification of proteins has a lot of influence on the ultimate function (or dysfu...

BIOMED CENTRAL

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