Network analysis with cytoscape

Question

[Chris]

Hi Biostars,

I try to use cytoscape on my RNA-seq data. After converting about 1000 DEGs into ENTREZID, I put the list into cytoscape and it makes a very complicated network. Could we use this tool to identify which gene/transcription factor is important from our data? I watch the videos about using cytoscape but not sure what else I can do. Thank you so much!

[Yogi]

A few questions.

1. What does the network represent?
2. Can you insert a high level picture of the network (or pictures) if you want to zoom into certain things?

[Chris]

Sure, the network represents the different expressed genes in my RNA-seq. I choosed string protein query.

Answer 1

[xanderpico]

Hi Chris.

There are dozens of different directions you could go using Cytoscape. There is not just one analysis path. You mention "transcription factors." You can go to the Cytoscape App Store and type that into the search bar to get recommended apps to perform specific analyses: https://apps.cytoscape.org/search?q=transcription+factors. You might try the iRegulon app, for example: https://apps.cytoscape.org/apps/iregulon

From your screenshot, it looks like you are using the stringApp to generate the network. That app comes with it's own enrichment tools. Here's a tutorial about getting more from the stringApp: https://cytoscape.org/cytoscape-tutorials/protocols/stringApp/#/

As another example, you might use the recently integrated enrichment analysis tool: Enrichment Table (see tabs below Table Panel). Here's a manual chapter about it: https://manual.cytoscape.org/en/stable/Enrichment_Table.html?highlight=enrichment. And here's a tutorial: https://cytoscape.org/cytoscape-tutorials/protocols/enrichmenttable-app/#/title

You might want to explore other enrichment apps. See this collection from the App Store: https://apps.cytoscape.org/apps/functionalenrichmentcollection

In general, I'd recommend exploring the App Store and the tutorials site: https://tutorials.cytoscape.org.

[Chris]

Thanks xanderpico! That is great resources. There are many bioinformatics tools now which is hard to choose an appropriate one. I found this one to follow http://iregulon.aertslab.org/tutorial.html and cytoscape said iRegulon and stringApp are in Installed apps but can't find the interface as the tutorial to follow. Would you please have a suggestion?