WGCNA - focusing on one single gene

Question

[iriswt]

Hi everyone!

I am absolutely new to R but I need to construct gene networks based on co-expression. The problem is that I only want to look at the genes that are co-expressed with one single gene of interest across different RNA-seq datasets from tumors. I've read through the tutorials but realized that this package is usually used for exploring networks of all the genes present in the datasets. Is there a way to just focus on one particular gene of interest as the 'hub gene' already from the begining? Or is there any other software/program that can serve this purpose better?

(sorry if this sounds ignorant but any help would be appreciated!)

Iris

Answer 1

[Kevin Blighe]

You likely are referring to the 'first nearest neighbours' [of a node/vertex]. In WGCNA, you can use this function: nearestNeighborConnectivity.

As you imply, checking the vertex hub score can help too. Other metrics include

• vertex degree
• betweenness centrality
• closeness centrality