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nazia
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@nazia-15800
Last seen 6.7 years ago
Hello Everyone,
I am seeking help in regards to performing WGCNA analysis on four different tissues datasets. I have been successful to achieve the gene dendrogram, modules for each and every tissue but I am not sure how to go ahead with further analysis. My objective is to identify 1.identify modules in each tissue which are relevant. 2. a particular gene which is being expressed across all the tissue. I am not sure on what basis should Identify the relevant modules of my interest .I do not have any clinical trait data that would help me shortlist a particular module.Any suggestion would be really appreciated.
You need to be more specific in your questions. How do you define "relevant" modules? Enrichment analysis in functional sets (GO, KEGG) etc could help you identify modules that may have some functional interpretation. I am not sure what you mean by gene "expressed in all 4 tissues" - if it's really just expression, it has nothing to do with WGCNA. Simply choose a threshold for being expressed and find all genes whose expression (mean, median, perhaps minimum) is above that threshold in all 4 tissues.