StringApp error

[Anupriya Verma]

Hello all,

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!

[Alex Pico]

Hi Anupriya,

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.

 - Alex

[Anupriya Verma]

Hi Alex. Thanks a lot. Now I'm getting it.
But what are these additional interactions?

[Scooter Morris]

Those allow you to add additional strongly interacting proteins in addition to the terms you provided.  Essentially it allows you to "enrich" your network with known strongly interacting proteins.

-- scooter

[Anupriya Verma]

Thanks a lot Scooter! There's one more thing I have noticed. I had list of 147 genes ,after adding interactors I got a network with 242 genes with 2367 interactions. Whereas if I add 5 more genes to the gene list n then create network with interactors then I am getting 247 genes with 2363 interactions. I'm assuming the interactors are adding between randomly selected proteins. Am I right? If yes, can we select the proteins for which interactors to be added?

[Scooter Morris]

Hi Anupriya,

   The best way to look at "adding interactors" is that you are adding additional edges with high confidence values >= your confidence cutoff such that an additional node is brought in.  You can select a set of nodes and the additional interactors should tend to interact with those nodes.

--- scooter