I'm new to the field of gene network/pathway analysis, thus I have little concept of it. Thank you all to help me in advance.
I've heard about some regression models or WGCNA for gene network analysis, but, as I understand, those are all based on differentially expressed genes. Because of it, those methods can only give us differentially active pathways that may contribute to the specific condition/cell type of interest.
Then, how can I get whole gene networks in the normal tissue or tumor tissue solely? In the situation where I want to construct each gene network of normal colon tissue and colorectal cancer tissue respectively, is there any way, or isn't?
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maximal_life •
1 answer
WGCNA does not depend on differential genes. In fact, the manual of WGCNA even recommends against using DEGs as input. Please read the manual and FAQ to see what the input is. What WGCNA does is to infer modules of correlated genes, so yes, you can run that separately on groups.
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