Answers.Body: <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-07-02T14:04:27.647Z
Answers.Text: 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.
Answers.UserDisplayName: María José
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-06-29T16:24:56.127Z
Answers.LastActivityDate: 2022-06-29T16:24:56.127Z
Answers.UserDisplayName: Peter Langfelder
Body: <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-29T12:42:33.067Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-29T14:14:56.190Z
Comments.Text: 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.
Comments.UserDisplayName: llrs
Tags: <r><rna-seq><wgcna>
Title: Find enriched processes in modules obtained by WGCNA
ThreadText: # Find enriched processes in modules obtained by WGCNA
  
  (Asked by: username_0 on 2022-06-29)
  
  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?
  
  **Tags:** r, rna-seq, wgcna
  
  > **Comments:**
  > **username_1**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_2**: Hi username_0 username_0. 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.  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2022-06-29. Score: 2
  
  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.
  
  > **Comments:**
  > **username_0**: thank you so much for your clarifications @username_3 , I liked the idea of calculating the enrichment by gene regions, which packages would you recommend for this.  
  
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