Question

Hub gene analyses

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7.5 years ago

saj98 ▴ 140

Hello everyone

I have RNA seq data and I would like to find hub gene in my data set. Do you have any idea which package or software I should use?

Thanks for helping

RNA-Seq R • 3.4k views

ADD COMMENT • link updated 7.5 years ago by Jean-Karim Heriche 27k • written 7.5 years ago by saj98 ▴ 140

score 0 · Answer 1 · 2017-07-05

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7.5 years ago

WouterDeCoster 47k

You can identify modules and their hub genes using WGCNA

ADD COMMENT • link 7.5 years ago by WouterDeCoster 47k

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Hello Wouter

I have six samples. Can I use WGCNA to find hub gene.

ADD REPLY • link 7.5 years ago by saj98 ▴ 140

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That's probably not enough.

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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I have one more query, in WGCA, I need to prepare clinical trait. I do not have the clinical trait, I have RNA seq value for each sample. How I should prepare CSV file for clinical trait.

ADD REPLY • link 7.5 years ago by saj98 ▴ 140

score 0 · Answer 2 · 2017-07-05

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7.5 years ago

Jean-Karim Heriche 27k

By definition a hub is a high-degree node. You find them by looking at the distribution of node degrees for your graph. If working with the adjacency matrix, node degrees are easily obtained by summing over the rows/columns.

ADD COMMENT • link 7.5 years ago by Jean-Karim Heriche 27k