Network analysis of differentially-expressed genes using vissE and Cytoscape
An introduction to using vissE and Cytoscape tools for analysing your RNAseq data
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.
Start: Thursday, 29 September 2022 @ 10:30
End: Thursday, 29 September 2022 @ 15:00
Duration: 4.5 hours
Venue: 21 Bedford Street
City: North Melbourne Country: Australia Postcode: 3051Prerequisites:
This is an introductory hands on workshop and no previous experience is required.
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.
- Host institutions
Organiser: Melbourne Bioinformatics
Host institution: University of Melbourne, Melbourne Bioinformatics
Keywords: Cytoscape, vissE, gene lists, NetworksTarget audience:
- Researchers and research students, or anyone who wants to learn intermediate statistical concepts to apply in R.
Capacity: 20Event type:
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)
Cost Basis: Free to all