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Question: Choosing Hub genes inside a module (WCGNA - COEX NETWORK)
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gravatar for ovariohisterectomia
5 months ago by
ovariohisterectomia • 20
ovariohisterectomia • 20 wrote:

Hi everyone. O Will be brief How You choose the hub genes in a Signed coex network?

I have seen Many posts here, and i have found:

A choosing kME over 0.75 I have My own list with kME of My modules

B Using cytoscape cytohubba For me , did not work in the 3.8 version of cytoscape

C Using a command from WCGNA

chooseTopHubInEachModule

But i think it choose just 1 gene.

I think i'm a little bit Lost, would be great if anyone could help me to clarify this and giveme your experience choosing Hub genes.

Thank You so much!
wcgna rna-seq • 322 views
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modified 5 months ago by Kevin Blighe ♦ 71k • written 5 months ago by ovariohisterectomia • 20
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gravatar for Kevin Blighe
5 months ago by
Kevin Blighe ♦ 71k
Republic of Ireland
Kevin Blighe ♦ 71k wrote:

You can quite easily edit the WGCNA function so that it returns more genes - please see my previous answer, here: A: Hub selection in WGCNA

There are different ways to calculate hub scores. WGCNA's implementation is one way. I allude to others in my tutorial: Network plot from expression data in R using igraph

Kevin
ADD COMMENT • link written 5 months ago by Kevin Blighe ♦ 71k

Thank you Kevin! I will see iT. By the way, what is your opinion about criteria of kME ≥0.85 and the top 10% of the gene list inside the module? Thank you!

ADD REPLY • link written 4 months ago by ovariohisterectomia • 20
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