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I am doing a gene enrichment of different clusters obtained by WGCNA, but there are some of them in which I don't get enriched processes, is there any way to find processes to these modules, for example to associate them to orthologues of other organisms. If there are different ways, could you send me links on how to do it?

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  • $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Jun 29 at 12:42
  • $\begingroup$ Hi María José. What kind of gene enrichment are you using? Which databases are you using to infer functionality? What organism are you analyzing? If it is human I doubt there are other organisms more annotated than that. $\endgroup$
    – llrs
    Jun 29 at 14:14

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Well, not all modules will have significant enrichment in gene sets such as GO terms or KEGG pathways. In my experience, the smaller modules are often not significantly enriched. They could be the result of some technical variation, they could contain genes localized to a particular genomic region (do you also calculate enrichment in genomic regions?) or they could be a particular gene family. WGCNA modules often are enriched in known pathways and processes, but that does not mean that all will be.

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  • $\begingroup$ thank you so much for your clarifications @Peter Langfelder , I liked the idea of calculating the enrichment by gene regions, which packages would you recommend for this. $\endgroup$ Jul 2 at 14:04

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