ReactomeFIVIz

Manually curated reactions in Reactome can be transformed into protein-protein interaction networks. For example, two inputs of a reaction can be safely assumed to interact with each other. Since this interaction is derived from the function of the protein, we call this functional interaction (FI).

Reactome Functional Interaction Visualization (ReactomeFIVIz) allows you to analyse the FI networks from Reactome. Unlike other analysis tools, ReactomeFIVIz is not available to use from the website. It is an app in the network visualization platform, Cytoscape. In addition to Reactome, this tool also uses other external resources to build the interaction networks. A detailed tutorial of ReactomeFIVIz is beyond the scope of this course and we shall limit this section to an overview. More information can be found on our website here (Figure 37).

Overview

The ReactomeFIViz app is designed to find pathways and network patterns related to cancer and other types of diseases. The app can access the Reactome (FI) network and allows you to:

• Construct a FI sub-network based on a set of genes
• Query the FI data source for the underlying evidence for the interaction
• Build and analyse network modules of highly-interacting groups of genes
• Perform functional enrichment analysis to annotate the modules
• Expand the network by finding genes related to the experimental data set
• Display pathway diagrams and overlay with a variety of information sources such as cancer gene index annotations
• Visualize FDA-approved cancer drugs in the contexts of the FI networks
• Build Boolean network models directly from Reactome pathways to investigate potential functional impacts of displayed cancer drugs