Network visualization tutorial: PPI import, data import, coloring, network clustering, and layout
Channel: Lars Juhl Jensen
Date: 2021-12-13

A bioinformatics tutorial on network visualization of omics data using Cytoscape and several Cytoscape apps. I first show how to retrieve a large physical protein interaction network from STRING by using stringApp to query with the proteins from an omics spreadsheet and adjust the graphical view of the network. I then show how to import the omics data itself and visualize it on the network before performing clustering and layout. I recommend that you watch my brief introductions to Cytoscape (https://youtu.be/Ohf9IPUJ82w) and stringApp (https://youtu.be/MXmzXxNqmnI) before watching this tutorial.

0:00 Introduction: network visualization of omics data and overview of the tutorial
0:59 Dataset: Overview of the omics dataset and retrieval of physical interaction network through stringApp
1:45 Network graphics: show graphics detail and network styling via the STRING panel
2:10 Data import: importing the omics data and visualizing it on the network using a color palette
3:00 Clustering and layout: MCL clustering of the network with clusterMaker2 and improving its layout with yFiles Layout Algorithms

Hands-on exercises on Cytoscape stringApp are available at https://jensenlab.org/training/stringapp/