The dark side of STRING visualization: Bad network figures in omics papers and how to do better
Channel: Lars Juhl Jensen
Date: 18/10/2021

A look at the dark side of how the STRING database is used to create network figures in omics publications. The presentation covers how some omics researchers use STRING to create network visualizations with zero effort and how others do invest effort into visualizing their data on networks but nonetheless end up with pointless hairballs. I give some suggestions for solutions to what one can do to produce more meaningful STRING network visualizations and pointers to free training material.

0:00 Introduction: omics data visualization and the STRING database
0:22 Zero effort figures: publishing networks as-is in evidence or confidence view
1:29 Pointless figures: Cytoscape, network layout, data import and visualization, but still hairballs
2:29 Solutions: functional vs. physical networks, confidence cutoff, network clustering, ideas for improving figures, and training material

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