Multilayer network tutorial: Creating a compound-protein-pathway network and visualizing it in 3D
Channel: Lars Juhl Jensen
Date: 2023-01-02

A hands-on tutorial on creation and 3D visualization of multilayer networks in Arena3D by combining two Cytoscape apps, namely stringApp and Arena3DwebApp. I first show how one can use Cytoscape stringApp to retrieve network of chemical compounds (drugs) from the STITCH database. I expand the network with their protein interaction partners from STITCH and protein-protein interactions from STRING, run enrichment analysis on the proteins, and add enriched Reactome pathways to the network. After improving the layout of the network, I use Arena3DwebApp to define a multilayer network with three layers (compounds, proteins, and enriched terms) and send this to the Arena3D web application, where I view it in 3D. Since this tutorial combines many functions from several tools, you may want to first watch my brief introductions to Cytoscape (https://youtu.be/Ohf9IPUJ82w), stringApp (https://youtu.be/MXmzXxNqmnI), Arena3D (https://youtu.be/4qnNBcQb1q8), and Arena3DwebApp (https://youtu.be/c9f427VBU1Q),

0:00 Introduction: Using Cytoscape stringApp and Arena3DwebApp to create a compound-protein-pathway network and visualizing it in Arena3D
1:23 Network creation: STITCH compound query and expansion of network with proteins
2:43 Enrichment analysis: retrieval of enriched terms, filtering of the results, addition of pathway nodes to network
3:28 Network visualization: fixing the 2D layout, defining layers, and sending the network to Arena3Dweb