Cytoscape's plugin 'stringApp' error

Question

[anu014]

Hello Biostars,

Today, I'm doing network analysis using Cytoscape. I installed 'stringApp' plugin for getting STRINGDb network. After adding 'gene symbol' list in it, I ran strinApp. As a result, got node, edge and network text files. The node file I got contains those genes also which I never entered in input!

Has anyone faced such problem? or is it something very obvious?

Please help me out. Thanks in advance!

Answer 1

[xanderpico]

In Cytoscape, the stringApp installs into the network search bar at the top of the Control Panel. I think this is where you are pasting/typing your list of gene symbols, which is correct. Before clicking on search (the magnifying glass icon), however, you will want to click on settings (the three line icon). Here you can specify how many "additional interactors" you want. Set it to zero and then you'll just get interactions between you original input.

[anu014]

Yes, that's it! Thanks xanderpico.