centrality scores in network

Question

[hennet.lauriane]

Hi,

I have two questions regarding the different scores of centralities and the way to calculate them.

First one is, every one uses connectivity (or degree), is that that simple to identify hub genes ? Why not using other scores such as closeness and betweeness ?

Second question is, is it meaningflu to calculate centrality scores in subnetworks (for instance in highly correlated genes networks ie setting a threshold of correlation and only considering this subnetwork).

Thank you !

Answer 1

[Jean-Karim Heriche]

1- By definition, a hub is a node with high degree (how high is defined by the user). So if that's what you are interested in, that's what you look for. Nodes with high betweenness or closeness centrality can have a low degree and so may not meet the requirement for being a hub.
2- It depends on the question you want to address.

Answer 2

[hennet.lauriane]

Thank you Jean-Karim,

I don't understand how different the biological question can be between the full network and a subnetwork of higly correlated genes. I only work with highly correlated genes to be more certain of the link between the genes...