Choosing Hub genes inside a module (WCGNA - COEX NETWORK)

Question

[ovariohisterectomia]

Hi everyone

I will be brief

How can I 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 give me your experience choosing hub genes.

Thank you so much!

Answer 1

[Kevin Blighe]

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

[ovariohisterectomia]

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!