Exporting Pathway from Pathvisio to Use in Cytoscape

[Ravikiran Komirisetty]

Hello,

I am working on creating a pathway using Pathvisio that includes Glycolysis, TCA, and PPP all combined. I intend to then use this pathway on Cytoscape to display my gene expression data. However, on Cytoscape, I am having trouble importing the .gpml file that I exported from the Pathvisio program. Help?

Thanks,

Ravi

[Kristina Hanspers]

Hi Ravi,

The best option for you would be to upload your pathway to WikiPathways, which makes it easy to import it in Cytoscape via the WikiPathways app. With the app installed you can search for your pathway by WikiPathways ID or title in the Network Search field. See a tutorial here: https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title

It is also possible to import a local gpml file via "File>Import Network from File", although this is currently a bit buggy. Perhaps this is what you tried? Right now importing a local file only works AFTER first importing a pathway directly from WikiPathways (via Network Search), so that is a workaround that you can try.

Regards,

Kristina

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