Reactome Plant to Cytoscape - possible?
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21 months ago
boczniak767 ▴ 740

Hi, are there pathway files (Reactome Plant) which can be loaded to cytoscape to recreate the shapes and arrangement of nodes and edges? Similarly as for animals with reactomefi app. I can recall seeing something like that some time ago but now I can't find it. I'm aware of existing biopax and sbgn files at the pathway subpage, but its not what I'm searching for.

Best Regards, Maciej

cytoscape network • 553 views
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How did you map your genes against Plant Reactome?

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I'm working on maize and Plant Reactome has maize IDs (version 4). So I don't have to map my genes.

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21 months ago
xanderpico ▴ 350

There is a Cytoscape app for Reactome: http://apps.cytoscape.org/apps/reactomefiplugin. I'm not sure if it supports Plant Reactome or not, but it is worth a try. Otherwise, as you already mentioned, Cytoscape can directly read BioPAX or SBML files, which you can download from Plant Reactome.

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Unfortunately the reactomefi doesn't support plants.

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