DEG visualisation with Cytoscape

Question

[gina02]

I performed differential expression analysis and I have a list of DE human genes. I want to visualise these in Cytoscape (showing up and down regulated proteins with different shapes and sizes and size of nodes on base of level of expression) but this requires network and expression data. how to get that files? and how to work with them?

Answer 1

[xanderpico]

You are looking in the right place! You have perfectly described the most common use case for Cytoscape. Fortunately, we have a ton of tutorials cover this at tutorials.cytoscape.org (https://github.com/cytoscape/cytoscape-tutorials/wiki). I'd recommend starting with the three top recommended exercises:

• Basic data visualization
• RNA-seq data analysis
• Differentially expressed genes

This page also has presentations introducing Cytoscape and dozens of resources for network files: https://github.com/cytoscape/cytoscape-tutorials/wiki#introduction

In terms of expression data, you would get those data from the regular places you find expression data: SRA, EBI atlas, TCGA, etc. Cytoscape can read any of the tabular data formats you would download from there. If you are interested in single cell RNA-seq data, there is even an app to help you browse EBI's and CZI's atlases: https://apps.cytoscape.org/apps/scnetviz