Is it correct to consider the genes of grey module resulted from consensus network analysis (WGCNA) as differential expressed?

Question

[nazaninhoseinkhan]

Dear all,

I have pre and post treatment microarray samples.

I performed differential expression analysis to find list of differential expressed genes.

In parallel I run WGCNA algorithm to find the consensus network between these two conditions.

Approximately 10% of my differential expressed genes were present in the grey module.

Now my question is: Is it correct to consider genes of grey module as differential expressed genes?

I will appreciate any help in advance

Nazanin

Answer 1

[Devon Ryan]

No, the genes in the grey module are those that don't fit anywhere else. Some members will be differentially expressed, most won't be. You might have another module correlating with your groups. That would be a better candidate for its members to all be DE.