How To Represent A Complex In Cytoscape

Question

[Lyco]

Is there a preferred way to represent a multi-protein complex in a cytoscape layout? I am not thinking of an internal data-representation but rather of a graphical one, i.e. is there a way to draw a box around a collection of nodes?

Answer 1

[Keiichiro Ono]

Actually, there are several ways to represent protein complexes (or any collection of objects).

• Metanode Plugin - Represents collection of nodes as a node. Since this collapses/expands nodes in the same network, all nodes representing proteins should be in a same network:

http://www.cgl.ucsf.edu/cytoscape/groups/index.html

• Nested Network - adds references to a network from a node. This means you need to define protein complexes as small, individual networks. The following diagram is not the one for protein complexes, but the basic idea is big nodes representing complexes have reference to other networks. This is a built-in feature in Cytoscape core. You can just right-click a node and add reference to other network.

http://www.cytoscape.org/images/top_slides/network1.png

Kei

Cytoscape Core Developer Team

[Boboppie]

Wondering if CytoscapeWeb will implement this

[Keiichiro Ono]

Next version of Cytoscape Web do support this type of features (nested network/grouping). I've watched demo by U Toronto team and looks it was already working. You can ask them the release schedule.

[Lyco]

Thank you! I had been thinking of something simpler, like e.g. the possibility to draw rectangles on the cytoscape canvas. Most likely, this idea would not fit well into the cytoscape philosophy. Anyway, one of the two answers given above should work for me.

[Boboppie]

Thanks Kei, that's great news!

Answer 2

[Michael Kuhn]

AFAIK there's no way to group nodes with a box, but I'm not sure. Something you could do is to make edges within a complex in a special type (wider, different color) to make it clear that these are complexes. If they form a clique, then the layout algorithms should also put the nodes close together.