Question: How to find the hub genes in the gene co-expression network constructed by WGCNA
1
gravatar for wangdp123
3.0 years ago by
wangdp123250
Oxford
wangdp123250 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 • 7.3k views
ADD COMMENTlink modified 3.0 years ago by Kevin Blighe69k • written 3.0 years ago by wangdp123250
7
gravatar for Kevin Blighe
3.0 years ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k 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 2.0 years ago • written 3.0 years ago by Kevin Blighe69k

Regarding the third method, if I am not wrong, NetworkAnalyzer simply counts the number of edges connected to a node as degree. The weights are ignored. For weighted network the degree is instead the sum of edge weights a node is connected with. So will that be the correct thing to do?

ADD REPLYlink written 13 months ago by Arindam Ghosh340

Sorry, not sure. Only seeing this now because somebody upvoted my answer.

ADD REPLYlink written 9 months ago by Kevin Blighe69k
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