Q:

I was wondering if you could help me.

I read your interesting article " The Importance of Bottlenecks in

Protein Networks: Correlation with Gene Essentiality and Expression

Dynamics".

I have trouble understanding the definition of hubs and bottlenecks (We

defined hubs as all proteins that are in the top 20% of the degree

distribution (i.e., proteins that have the 20% highest number of neighbors).

Accordingly, we defined

bottlenecks as the proteins that are in the top 20% in terms of

betweenness.. )

For example: if we want to calculate proteins that are in top 10% of degree

distributions, in a PPI network with 1000 nodes, we consider 100 highest

degree nodes?

or

we calculate 10% of the highest degree, which is for example 700 and

proteins with degree above 630 are the hubs?

Which one of these interpretations are correct?

A:

Your first interpretation is correct, i.e., if there are 1000 proteins in the network, we consider the top 100 proteins with the highest degrees.

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