Hi, I have developed a signed hybrid gene co-expression network using WGCNA and constructed module based on TOM followed by hierarchical clustering. I selected a module which gave a positive correlation of the eigen gene module with immune score. When I look at the hub genes based on module membership >0.8, most of these have negative correlations with the immune score range correlation range (-0.23-0.028). Would somebody be able to explain why I get negative correlations with the hub genes, but a positive correlation of the eigen gene of this particular module. Thanks

It is possible that the hub genes are not directly related to the immune score but are instead related to other factors that are negatively correlated with the immune score. Alternatively, it is possible that the hub genes are involved in complex regulatory networks that are not captured by simple correlation analysis. You can reference: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04179-4 uno online