Question: Reactome Plant to Cytoscape - possible?
gravatar for boczniak767
13 months ago by
boczniak767690 wrote:

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 • 315 views
ADD COMMENTlink modified 13 months ago by xanderpico220 • written 13 months ago by boczniak767690

How did you map your genes against Plant Reactome?

ADD REPLYlink written 7 days ago by Ric300

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

ADD REPLYlink written 6 days ago by boczniak767690
gravatar for xanderpico
13 months ago by
xanderpico220 wrote:

There is a Cytoscape app for Reactome: 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.

ADD COMMENTlink written 13 months ago by xanderpico220

Unfortunately the reactomefi doesn't support plants.

ADD REPLYlink written 13 months ago by boczniak767690
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