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: 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...

Video Tip of the Week: yEd Graph Editor for visualizing pathways and networks: This week's video tip of the week closes out a series that began last month. I started to explore one gene co-expression tool, which led me to another tool for visualization, and so on. This week's too...

Video Tip of the Week: GeneFriends: It was just a little tweet, with hardly any information about the function or purpose of the resource mentioned. But the cute name drove a lot of people to take a look at GeneFriends from our blog rece...

Video Tip of the Week: InnateDB, Systems Biology of the Innate Immune Response: The immune system is challenging to study. Different people may mount different responses to assaults on their system--and sometimes the systems go into overdrive on stuff they shouldn't. Cracking the ...

Video Tip of the Week: Integrative Multi-species Prediction (IMP) Network Analysis Resource: A while back Mary saw the following tweet go by & collected it as a possible topic for one of our weekly tips: RT @moorejh: #bioinformatics #genomics RT @GreeneScientist Interactive and video tutorials...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Mills D James et al., High expression of long intervening non-coding RNA OLMALINC in the human cortical white matter is associated with regulation of oligodendrocyte maturation. Molecular Brain (2015) doi:10.1186/s13041-014-0091-9

Hsu Sheng-Da et al., Integrated analyses to reconstruct microRNA-mediated regulatory networks in mouse liver using high-throughput profiling Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Genomics The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Genomics (2015) doi:10.1186/1471-2164-16-S2-S12

Ke Tao et al., ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. BMC Plant Biology (2015) doi:10.1186/s12870-014-0399-8

Jeong Hyun-hwan et al., Investigating the utility of clinical outcome-guided mutual information network in network-based Cox regression Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Systems Biology The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Systems Biology (2015) doi:10.1186/1752-0509-9-S1-S8

Tseng Yu-Ting et al., IIIDB: a database for isoform-isoform interactions and isoform network modules Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Genomics The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Genomics (2015) doi:10.1186/1471-2164-16-S2-S10