Body: <p>Lets say I performed a single cell RNA sequencing analysis on mice blood samples. Eventually I am able to cluster cells together and get a set of genes of interest for each cell type since I want to study the gene expression of specific cells after a treatment.</p>
  <p>At this point I want to perform an enrichment analysis to get a list of those GO biological processes and/or molecular functions that might be affected by the novel genes that are up or down regulated after the treatment. I can use several tools such as ClusterProfiler, Panther, EnrichR but, and this is the point, should I use gene sets that are compiled for mouse only or can I enrich my genes using gene sets compiled from other organisms too such as, for instance, human gene sets? Is it ok to mix genes and gene sets from different organisms when performing an enrichment?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-10T08:07:40.310Z
Comments.Text: I am not very familiar with those programs but maybe you are searching for the term ortholog? Orthologs are "same" genes/proteins of different species (roughly speaking). So you could convert your genes into the respective ortholog gene of another species (like human) and then perform your analysis on human. You will loose some genes that do not find a counterpart and you have to resolve some ambiguities if your gene is mapped to multiple candidates (choose all/ any/ best).
Comments.UserDisplayName: Paul
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-10T09:44:46.493Z
Comments.Text: @Paul, ok this could be done, of course but is it common practice? also, I need to study the genes in that specific organism not in its ortholog version.
Comments.UserDisplayName: gbt
Tags: <go-enrichment>
Title: is it ok to use gene sets from an organism to enrich genes from a different organism?
ThreadText: # is it ok to use gene sets from an organism to enrich genes from a different organism?
  
  (Asked by: username_0 on 2020-11-09)
  
  Lets say I performed a single cell RNA sequencing analysis on mice blood samples. Eventually I am able to cluster cells together and get a set of genes of interest for each cell type since I want to study the gene expression of specific cells after a treatment.
  
  At this point I want to perform an enrichment analysis to get a list of those GO biological processes and/or molecular functions that might be affected by the novel genes that are up or down regulated after the treatment. I can use several tools such as ClusterProfiler, Panther, EnrichR but, and this is the point, should I use gene sets that are compiled for mouse only or can I enrich my genes using gene sets compiled from other organisms too such as, for instance, human gene sets? Is it ok to mix genes and gene sets from different organisms when performing an enrichment?
  
  **Tags:** go-enrichment
  
  > **Comments:**
  > **username_1**: I am not very familiar with those programs but maybe you are searching for the term ortholog? Orthologs are "same" genes/proteins of different species (roughly speaking). So you could convert your genes into the respective ortholog gene of another species (like human) and then perform your analysis on human. You will loose some genes that do not find a counterpart and you have to resolve some ambiguities if your gene is mapped to multiple candidates (choose all/ any/ best).  
  > **username_0**: @username_1, ok this could be done, of course but is it common practice? also, I need to study the genes in that specific organism not in its ortholog version.  
  
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  ## 0 answers
  
  