Where can I find the "k-value" in my PPI network?

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qlb...@vt.edu

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May 14, 2018, 10:55:33 PM5/14/18
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Dear,
I want to know where can I find the "k-value"of each node in my PPI network?

Thanks a lot!


Qinglai

piet molenaar

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May 15, 2018, 4:44:38 AM5/15/18
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Hi,
I am not sure what you mean with k-value; from what algorithm is this the expected result?
Best regards,
Piet


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Piet Molenaar
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Department of Oncogenomics, M1-131
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qlb...@vt.edu

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May 22, 2018, 12:58:31 PM5/22/18
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Hi,
I want to screen the
major nodes with topological importance, 4 topological,features–“Degree,” “Node betweenness,” “Closeness” and “K value”.
Now, I can't find where the k-value is. Others are done.
Thanks a lot!

Scooter Morris

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May 22, 2018, 3:42:35 PM5/22/18
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I'm not sure what a node K-value is.  I've seen that term used as a
parameter for EIGRP routing, but other than the k used for various
cluster algorithms, I've never seen that as a network topological
parameter.  Do you have a reference?

-- scooter


qlbian

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May 22, 2018, 4:40:10 PM5/22/18
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Hi,
Thanks a lot!
Here is:
For each node i in drug target network, topological features were calculated in four ways: (1) 'Degree': the number of links to node i; (2) 'Node betweenness': the number of shortest paths between pairs of nodes which run through node i; (3) ‘Closeness’: the sum of the distances of node i to all other nodes (the degree, node betweenness and closeness can be used to assess the topological importance of a node in a network, and the larger a node’s degree, node betweenness, and closeness centrality, the more important that node is in the PPI network [3]); and (4) 'K coreness': a measure of the centrality of node i [4].
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------------------ Original ------------------
From: Scooter Morris <sco...@cgl.ucsf.edu>
Date: 周二,5月 22,2018 15:42
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: Re: [cytoscape-helpdesk] Where can I find the "k-value" in my PPInetwork?

 wrote:
> Hi,
> I want to screen the
> major nodes with topological importance, 4 topological,features–“Degree,” “Node betweenness,” “Closeness” and “K value”.
> Now, I can't find where the k-value is. Others are done.
> Thanks a lot!
>
I'm not sure what a node K-value is.  I've seen that term used as a 
parameter for EIGRP routing, but other than the k used for various 
cluster algorithms, I've never seen that as a network topological 
parameter.  Do you have a reference?

-- scooter


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Scooter Morris

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May 22, 2018, 6:02:56 PM5/22/18
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OK, I think I understand now.  As far as I can tell, neither centiscape nor network analyzer calculated the k-coreness of a node, but there are several other centrality measures you can look at.

-- scooter
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