How to create a network of multiple clusters in co-expression network?

Question

[newbie]

Hello everyone,

I have used WGCNA for co-expression analysis between coding genes and non-coding genes. This gave me 48 modules. Among these I'm very much interested in 13 clusters and want to create a network out of these 13 clusters.

I wanted the plot to be looked like below. I took this plot from this paper Figure 5a

Which information from WGCNA I have to use to make the above network and could you please give me an example how to make such network in R?

Answer 1

[ashish]

You will need the correlation values between the genes from your module of interest. See part 6 of the WGCNA tutorial, the package has function to export your network into cytoscape input format. Import it into cytoscape and choose the desired layout. You can also try igraph which is a R package. Here is a nice tutorial.

[newbie]

Thanq. For igraph What should be the input from WGCNA? From which step I should use the input for igraph?

[ashish]

For igraph also you would need correlation values. If you start with gene expression matrix then you can calculate the correlation matrix yourself and convert it into igraph object. This is explained in step two of the igraph tutorial I linked. You can also convert the WGCNA network directly to igraph object using the wgcna2igraph function. See here for instructions.

The input to wgcna2igraph conversion function will be the wgcna network which you created using the blockwiseModules function.