Reactome Plant to Cytoscape - possible?

Question

[boczniak767]

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

[Ric]

How did you map your genes against Plant Reactome?

[boczniak767]

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

Answer 1

[xanderpico]

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.

[boczniak767]

Unfortunately the reactomefi doesn't support plants.