Question: WGCNA gene significance
0
gravatar for Baylie_321
8 months ago by
Baylie_32120
London
Baylie_32120 wrote:

Hi,

I have used WGCNA to find gene modules relating to two traits - I see that many people have carried out functional analysis (KEGG/GO) on the modules - does it make more sense to carry out such enrichments on those genes with high significance (p<0.05) rather than on the module as a whole? I have tried both and a lot of the GO terms are dropped when looking at the significant genes for the associated trait only - so I feel it would make more sense to focus on these?

Best wishes

B

rna-seq wgcna gene • 765 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by Baylie_32120

Many thanks for your reply, but I don't think this software is appropriate as I am working on a non-model organism and many of the genes do not have a gene-symbol annotation compatible with the human-gene-symbol. I already carried out DE analysis, and this is in addition to that.

ADD REPLYlink modified 8 months ago • written 8 months ago by Baylie_32120

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized. SUBMIT ANSWER should only be used for new answers to original question.

ADD REPLYlink written 8 months ago by genomax73k

Enrichment for a non-model organism is a frequent topic here. Take a look here: GO enrichment analysis. Non-model organism.

You could also do a search via a search engine.

ADD REPLYlink written 8 months ago by Kevin Blighe51k

Hi, I already know how I to do the GO enrichment part, I was seeking opinions on which WGCNA gene list made more sense to pass to my GO enrichment. Many thanks, B

ADD REPLYlink written 8 months ago by Baylie_32120

Hey, I just happened to be going over old posts about WGCNA. I think that it makes more sense to use all genes in the module, and not just the ones that are differentially expressed.

ADD REPLYlink written 10 weeks ago by Kevin Blighe51k
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