Question: How to find the hub genes in the gene co-expression network constructed by WGCNA
1
gravatar for wangdp123
15 months ago by
wangdp123140
Oxford
wangdp123140 wrote:

Hi there,

I have used WGCNA tool to construct a gene co-expression network and identified several modules. I am keen to discover the hub genes (the gene that has the maximum connections with other genes in a module) in each module. Does anybody know how to pinpoint the hub genes? Via which scripts or functions?

Many thanks,

Regards,

Tom

hub gene wgcna • 2.7k views
ADD COMMENTlink modified 15 months ago by Kevin Blighe41k • written 15 months ago by wangdp123140
0
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe41k
London, England
Kevin Blighe41k wrote:

Easiest way: simply use the chooseTopHubInEachModule function from WGCNA...

Another way: Convert the WGCNA object to an igraph object directly with wgcna2igraph, and then generate hub centrality scores via Kleinberg's metric, part of the igraph package. It does identify nodes/vertices that look like hubs visually when you inspect the graph.

Another way: convert the WGCNA object to Cytoscape and use NetworkAnalyzer plugin to identify hub genes.

Kevin

ADD COMMENTlink modified 3 months ago • written 15 months ago by Kevin Blighe41k
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