Question: WGCNA heatmap modules-trait relationship
gravatar for debitboro
2.6 years ago by
debitboro110 wrote:

Hi everyone,

By using WGCNA for inference of coexpression networks I have generated the following values (heatmap) of correlation and significance of modules (10 modules), I mean the correlation between the modules and the trait of interest, the significance is measured by p_value enter image description here

From the heatmap, we can say that the most three significant modules are: blue, black, and salmon modules. But, what about the green modules for example for the yellow module which is negatively correlated with the trait, is it also among the most significant modules like the red modules ?

ADD COMMENTlink written 2.6 years ago by debitboro110

So your question essentially is whether anti-correlation is also of interest?

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k

yeah, this is my question

ADD REPLYlink written 2.6 years ago by debitboro110

I don't know your research hypothesis, but from a biological point of view a module which is anti-correlated with a trait is as interesting as a module which is correlated.

Say that your trait is weight, both modules which are overexpressed and those underexpressed with increasing weight are biologically interesting: which pathways are upregulated and which are repressed when you start devouring your 16th big mac of the day?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by WouterDeCoster39k


in this image a trait such as Aortic.lession with red module has correlation 1 and p.value -0.019, but I can't figure out if correlation is 1 then why the color is not red (red color is correspond to positive correlation between module and trait).

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by F3.4k

The p-value is 1, the correlation coefficient is -0.019.

As far as I know, p-value can't be negative. That doesn't make sense since it's a probability.

ADD REPLYlink written 2.5 years ago by WouterDeCoster39k

thank you. so helpful.

ADD REPLYlink written 2.5 years ago by F3.4k
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