Network analysis of differentially-expressed genes using vissE and Cytoscape

Abstract

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.

Dharmesh D Bhuva

Senior post-doctoral researcher at SAiGENCI

My research interests include cancer systems biology, spatial statistics and computational biology.