Merging networks or creating a gene-interactions in a already established network - Cytoscape

Question

[be.bielikova]

Hello everyone, I've been tasked with creating a lncRNA-mRNA network where, if possible, also the interactions between the coding genes should be shown. Is there an app to make protein-protein interactions between the protein coding genes in a already established lncRNA-mRNA network?

I haven't found such an app that would allow me to do so yet, so I tried merging two networks - lncRNA-mRNA network created by me and mRNA-mRNA network made by putting in Entrez gene IDs into STRING app. I'm not able to merge them by using - I get an error saying: Index 0 out of bounds for length. When I tried to look into advanced options, there was a red Matching.Attribute in the Merged Network column of the nodes section. If I hover my mouse over the red Matching.Attribute it says Change me!. How do I merge the networks then?

Thank you in advance.

Answer 1

[xanderpico]

The Merge Tool is indeed difficult to use when the default setting don't work and when there are many columns, like with STRING networks. You might have a simpler option, however.

If you start with your lncRNA-mRNA network, you could then use the stringApp to add edges to the network. If it's not a STRING network to begin with, then first run Apps>STRING>STRINGify network. Then run Apps>STRING>Change confidence or type. Set the cutoff to 0.4 and click OK. This should add new edges connecting any of the recognized nodes, e.g., mRNA-mRNA interactions.

You can adjust the cutoff higher if you want fewer interactions.

[be.bielikova]

Hi, thank you very much for your answer. Changing confidence or type, unconnected my lncRNA from the other mRNA, but it inspired me to try Query for additional nodes in the STRING app. It allowed me to put in the EntrezIDs of the mRNAs that were already in the network and when I clicked re-layout network on the pop up window, it did exactly what I was looking for.

Again thank you very much and have a wonderful day.