Question: How to export molecular action between nodes from String PPI network?
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gravatar for miky.zo
3 months ago by
miky.zo40
Italy / Busto Arsizio / University of Insubria
miky.zo40 wrote:

Hi everybody. I am using the online version of STRING (https://string-db.org) to build a PPI network using DEGs from RNAseq analysis. In the settings, I checked the "molecular action" box to visualize the predicted mode of action for the interaction between different nodes. But when I export the .tsv file from the site to load the network on cytoscape, this information is not present. I checked all the files that can be exported and there is no trace of "molecular action". Do you know how can I export this type of info to load it into other software like cytoscape? Or is there any other way to do this? Or other software/tools/websites? The STRING app in cytoscape do not allow to visualize the "molecular action".

Thank you for your help!

ps here's a picture of a network as an example of what I can see on STRING (with "molecular action" turned on). The different edges that you can see are what I want to export (e.g. green arrow for activation, red line for inhibition, etc). STRING molecular action example

ADD COMMENTlink modified 3 months ago by Jean-Karim Heriche23k • written 3 months ago by miky.zo40
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gravatar for Jean-Karim Heriche
3 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

This information is in the protein.actions file in the download section.

ADD COMMENTlink written 3 months ago by Jean-Karim Heriche23k

Thank you for your answer! I am trying to export the network in cytoscape; is there a way to then import this information (molecular action) into the network inside cytoscape?

ADD REPLYlink written 3 months ago by miky.zo40

File → Import → Table from File…. and selecting appropriate options or if this doesn't work, just pre-process the file, for example replacing the gene IDs to match those you already have. To reproduce the STRING visualization, you'll also need to play with styles.

ADD REPLYlink written 3 months ago by Jean-Karim Heriche23k
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