Question: WGCNA gene significance
0
gravatar for rebekah_321
28 days ago by
rebekah_32120
rebekah_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 • 144 views
ADD COMMENTlink modified 28 days ago • written 28 days ago by rebekah_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 28 days ago • written 28 days ago by rebekah_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 28 days ago by genomax64k

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 28 days ago by Kevin Blighe39k

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 27 days ago by rebekah_32120

Great, and I already answered:

I would just do the enrichment on all genes found in each module.

ADD REPLYlink written 27 days ago by Kevin Blighe39k
0
gravatar for Kevin Blighe
28 days ago by
Kevin Blighe39k
Republic of Ireland
Kevin Blighe39k wrote:

Hey rebekah,

Here is my moment to be blunt on this Friday night: the type of analysis that you are doing should not normally warrant the level of concern that you are raising. Indeed, I believe WGCNA and GO / KEGG enrichment should not form part of your main conclusions in any project - so, don't waste time on them. Among the more experienced of us, these tools are not held in high regard. The use of these tools sends a shudder down my spine because they have somehow found their way into bioinformatics 'folklore' yet nobody ever really gets much useful information out of them.

I would just do the enrichment on all genes found in each module.

If you wanted a better enrichment tool, then take a look at GSEA / GSVA, which utilises gene signatures from MSigDB

Kevin

ADD COMMENTlink written 28 days ago by Kevin Blighe39k
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