I hope you’re doing well during this strange and chaotic time.
I conducted WGCNA for my RNAseq data with 18000 genes, and got some nice modules that seemed to have very good eigengene values with the traits I’m interested in. Then I tried to look for hub genes in these modules and also try to visualize the networks. However, since most of my modules of interest are a little big, contained 200-1000 genes, so I have set a high threshold for the weights of the edges when I export the network to Cytoscape, with the idea that to present networks that human eyes can manage to a degree. Here’s an example of a network I have: I think it looks fine, and it revealed a few highly connected genes that are very interesting.
However, while thinking through my method, I’m not entirely sure whether I did it in a correct way. In other words, I’m not sure the highly connected genes in the network graph right now are indeed among the highly connected genes of the entire module. Because I have filtered out most of the edges in the network when exporting data for the graph, it dawned on me that there’s a strong possibility that I actually filtered out the real hub genes. For instance, in a module of 1000 genes, I have three hub genes that are connected with 900, 800, 700 genes, but it seems possible none of their edge met my threshold cutoff then I completely missed.
Do you think my concerns here are real, and I probably have missed a lot of important genes by doing so? If so, do you have any suggestions on how to visualize the networks in a way that human eyes can manage (i.e. not too many genes on the network), but still show the real hubs?
Thanks in advance!