Nodes and attributes in Cytoscape NA

Question

[chan.cordeiro]

I have mapped in CS a network of different classes of foods possessing pharmaceutical-grade natural compounds and their in silico-inferred gene-targets.

Centrality measures shows no food class is significantly different in hierarchy, considering each class' individual foods as the source targets.

But I have found that, considering each food's natural compounds as attributes of the target genes, there is a correlation between the gene targets with most relevance in the network (mostly degree, betweenness and closeness) and a particular class.

Is this valid?

[scooter]

I'm not sure I can answer the question of "validity" with just the description you've given us. Some additional information might help:

1. It sounds like you are creating a bi-partide network, with food classes as one type of node and gene-targets as another. Is that right?
2. I'm not clear how you are calculating your correlation -- are you creating a table of centrality measures and compounds and calculating that outside of Cytoscape? How are you feeding that back to the food class?

A lot of my intuition of network centrality measures sort of breaks down when I'm dealing with a bipartide graph, so I don't have a good intuition about what a "high degree" node would represent beyond the obvious (this gene is targeted by many food classes). If a class has multiple natural products, and it's the natural product that is actually targeting the gene, then you are certainly removing a lot of the confusing aspects of the network by looking at just the natural product, but I'm certainly not expert in that area.

-- scooter