How to construct circRNA-miRNA-mRNA network using cytoscape

Question

[Babita Pruseth]

Hi,

If I have a selected set of circRNAs, miRNAs, mRNAs, then how can I construct an interaction network among them through Cytoscape. Is there any Cytoscape plugin for that and what should be the input file format? Please guide me to perform that.

Thank you

[Hyper_Odin]

1. Do you already have the relationship between them ? or you want to find those out?
2. Which species are you analyzing?

[Babita Pruseth]

Yes, I have and this is the human dataset. Here I have gone through a few papers (PMCID: PMC7011443 and PMCID: PMC5878900).

[Hyper_Odin]

That's great!

• For miRNA-mRNA you can try this plugin https://apps.cytoscape.org/apps/cytargetlinker
• For mRNA-mRNA https://apps.cytoscape.org/apps/stringapp
• And for circ-mRNA relationship you have to do it manually, I am not sure if any plugin exists for that https://circinteractome.nia.nih.gov/

[Babita Pruseth]

Thank you. But using these plugins I can get a complex biological network and here I want a subnetwork only for a selected set of data.

[Hyper_Odin]

Use the selected list of genes/miRNA while analyzing, and the plugins will draw the relationship between them

Answer 1

[Babita Pruseth]

ok, I'll go through accordingly. I appreciate your help so much. Thank you.