You might also find GeneMania useful in this context, especially to get a sense about the functions of genes of interest to you. I suggest having a look at the paper to have a sense of the functionality: http://nar.oxfordjournals.org/content/38/suppl_2/W214.short

The website uses CytoscapeWeb to visualize the networks and there is also a Cytoscape plug-in if you want to work within Cytoscape environment.

Hi William,

In general, at least as a starting point, you can BLAST your sequences and translate your problem to Arabidopsis. Cytoscape is mostly a network visualization tool (it will be useful eventually, but first you need to define your "network" or "pathway").

For this, go to this link: http://www.arabidopsis.org/portals/proteome/proteinInteract.jsp

Here, you will find several arabidopsis protein interaction resources. This should be useful to reconstruct small networks around your genes of interest.

Since you mentioned KEGG pathways, you can also take a look at KEGG Automatic Annotation Server to get functional annotations