How to find the hub genes in the gene co-expression network constructed by WGCNA

Question

[wangdp123]

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

Answer 1

[Kevin Blighe]

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

[Arindam Ghosh]

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?

[Kevin Blighe]

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