Analysis of Biological Networks using Cytoscape

Workshop Information

  • Wednesday 12th June 09:30 - 16:30 (approx)
  • Bartolome House, Seminar Room EG03 or ONLINE

Please book your place using this link


The workshop is designed to give you an introduction to using Cytoscape, which is a network-based software application to perform bioinformatics data and pathway enrichment analysis. The particular use-case in this course is that of RNA-seq data, but many of the concepts are used for other types of omics-analysis.

Who should attend this course?

Researchers in life sciences who want to get an appreciation for the computational network biology steps involved in RNA-seq analysis, and how to execute best-practice Cytoscape workflows.

Objectives:- After this course you should be able to:

  • Have more detailed understanding of terms used in network biology.
  • Use Cytoscape to better visualise enriched terms from an RNA-seq dataset
  • Know what tools are available in App Store for RNA-seq, miRNA data and pathway analysis.

Aims:- During this course you will learn about:

  • Cytoscape and specific plugins used for RNA-Seq data analysis.
  • Sources for integrating differentially expressed genes within pathway modules.
  • Hierarchical clustering using String and FunctionalEnrichment apps.

Software installation

You will need to bring an internet-enabled laptop to the course and install the latest versions of Cytoscape before coming to the course

1) Install Cytoscape

2) Install the Cytoscape packages/Apps required for the course

  • Go to ClueGO and CluePedia
  • Click Download or Install (if your cytoscape application is already open)
  • More on installation, documentation and how to integrate the package with R or Python is described here:

3) Download and unzip this file containing the data for the course

4) (Optional) Watch these short introductory videos

Timetable (Provisional)

  • Session 1 Wednesday 12th June 9:30 - 13:00
    • Importing example cancer RNA-seq counts into Cytoscape
    • Querying pathway and interaction sources using Cytoscape - App.
    • Styling the network and saving for publication.
  • Session 2 Wednesday 12th June 13:00 - 15:00
    • Using diffrential expressed gene-lists, perform protein-protein interactions or gene-regulatory networks.
    • Manipulating and filtering gene-lists, pathways and clustered modules.
    • Creating sub-networks of specific derived clustered modules.
    • Enriching gene-list into pathways using FunctionalEnrichment - App.
  • Session 3 Thursday 12th June 15:00 - 16:30
    • Pathway clustering using ClueGO - Functional Enrichment
    • Using ClueGO’s features for integrating and querying multiple pathway database sources.
    • Use CluePedia (sister-software for ClueGO) to map gene regulatory information within specific pathways.

For queries relating to collaborating with the Bioinformatics Core team on projects:

Join our mailing list so as to be notified when we advertise talks and workshops by subscribing to this Google Group. You can also connect with us on Linkedin.

Requests for a Bioinformatics support clinic can be made via the Research Software Engineering (RSE) code clinic system. This is monitored by Bioinformatics Core staff, so we will ensure the appropriate expertise (which may involve individuals from multiple teams) will be available to help you

Queries regarding sequencing and library preparation provision at The University of Sheffield should be directed to the Multi-omics facility in SITraN or the Genomics Laboratory in Biosciences.