Entering edit mode
5.8 years ago
Baylie_321
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30
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
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.
Please use
ADD REPLY/ADD COMMENTwhen responding to existing posts to keep threads logically organized.SUBMIT ANSWERshould only be used for new answers to original question.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.
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
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.