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The gene with the highest intramodular connectivity was considered the "hub gene" (most connected gene).
TNF was the 13th most connected gene in the entire network with a total network connectivity (k.total) of 29.0 (max k.total = 35.2).
It was the 6th most connected gene in the blue module with a k.in = 27.6 (max blue module k.in = 30.8).
The unfiltered gene set indicated that the most connected gene network represented genes mostly involved in the ribosome which is not particularly associated with prostate cancer.
For the single most connected gene in each network, we verified its implied interactions by querying genes against the Drosophila Interaction Database (DroID version 2013_02 database, http://www.droidb.org).
Precisely BCL2L1 (B-Cell CLL/Lymphoma 2 like 1), a member of the BCL2 family, is the second most connected gene in the module.
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Table 1 also shows the number of connections of the nine most connected genes (central genes) in the network from Figure 2B.
The number of connections of the nine most connected genes (central genes) is presented in Table 1 IFN-γ and TNFα had the greatest number of connections (35 and 32, respectively).
Among the top 660 (10%) most connected genes in the Always correlated Landscape, there were 70 TF, implying an over-representation hypergeometric test p-value of 8.66E-6 8.66E-6
The next most connected genes are CDC2 (58 edges), CCNB1 (49 edges), LGALS1 (48 edges), and MYBL2 (42 edges).
Within this new network, the component with most connected genes was identified and considered as biologically important regulation module.
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