Question: WGCNA - focusing on one single gene
0
gravatar for iriswt
8 months ago by
iriswt0
iriswt0 wrote:

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

R rna-seq co-expression wgcna • 245 views
ADD COMMENTlink modified 8 months ago by Kevin Blighe49k • written 8 months ago by iriswt0
0
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe49k
Kevin Blighe49k wrote:

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
ADD COMMENTlink written 8 months ago by Kevin Blighe49k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 754 users visited in the last hour