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Reactome Plant to Cytoscape - possible?

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
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updated by Biostar Biostar • written by boczniak767 boczniak767

How did you map your genes against Plant Reactome?

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written by Ric Ric

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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written by boczniak767 boczniak767

1 answer

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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written by xanderpico xanderpico

Unfortunately the reactomefi doesn't support plants.

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written by boczniak767 boczniak767

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