Question: How to find the hub genes in the gene co-expression network constructed by WGCNA
1
gravatar for wangdp123
2.7 years ago by
wangdp123240
Oxford
wangdp123240 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 • 6.5k views
ADD COMMENTlink modified 2.7 years ago by Kevin Blighe65k • written 2.7 years ago by wangdp123240
7
gravatar for Kevin Blighe
2.7 years ago by
Kevin Blighe65k
Kevin Blighe65k 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 20 months ago • written 2.7 years ago by Kevin Blighe65k

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 9 months ago by Arindam Ghosh300

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

ADD REPLYlink written 5 months ago by Kevin Blighe65k
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