Network analysis of differentially-expressed genes using vissE and Cytoscape

29 September 2022 - 10:30am-3pm
21 Bedford St, North Melbourne, VIC 3051


Network analysis of differentially-expressed genes using vissE and Cytoscape

  In biological data, similarity between genes/proteins can be exploited to identify biological functions or pathways. For example, investigating pairwise protein-protein interactions can help us identify protein complexes that have related functions. Such analyses require pairwise interaction or similarity data to be represented as a biological network. Once generated, networks can be used to investigate various structural and topological characteristics to identify key entities in the network. A popular and powerful tool to visualise and analyse biological networks is Cytoscape. This workshop is in two parts. First, using an RNAseq data set from human cancer you will use the vissE tool analyse a list of differentially-expressed (DE) genes and generate a PPI network. In the second half you will be introduced to Cytoscape interface and learn how biological networks can be uploaded and analysed in Cytoscape. Melbourne Bioinformatics + WEHI

Lead trainers:

Dharmesh Bhuva (Davis Laboratory, Bioinformatics division, WEHI) Ahmed Mohamed (Davis Laboratory, Bioinformatics division, WEHI)

Learning objectives

By the end of this training, participants will be able to:
  • Identify functional classes of biological process from a list of differentially expressed (DE) genes.
  • Generate a protein-protein interaction (PPI) network from a list of DE genes.
  • Import a network into Cytoscape.
  • Visualise and annotate networks in Cytoscape.
  • Integrate experimental metadata into networks.
  • Use Network analysis in Cytoscape to identify key molecules in a biological system.


This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section). You must register for this event using an affiliated institutional email address or your registration may be cancelled. Required: This is an introductory hands on workshop and no previous experience is required. Attendees must supply:
  • Laptop computer (we recommend that you bring your charger also)
  • access to the internet/Wifi (UniWireless / Eduroam)
  • Web browser installed (Firefox or Chrome recommended)
  • Cytoscape installed (free to download)
We advise you to begin installation of Cytoscape when registering for the workshop, to allow sufficient time to trouble shoot issues with your own IT support such as permissions and sufficient space for installation. The tool vissE is a web based tool and requires no software installation.


If you require any further information, or have any access requirements in order to participate in this workshop, please contact the workshop organiser Melbourne Bioinformatics as soon as possible to discuss your requirements: