Hub gene analyses

Question

[saj98]

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

Answer 1

[WouterDeCoster]

You can identify modules and their hub genes using WGCNA

[saj98]

Hello Wouter

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

[WouterDeCoster]

That's probably not enough.

[saj98]

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.

Answer 2

[Jean-Karim Heriche]

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.