Answers.Body: <p>You add 1 to the count of each COG category. You are looking for over represented <em>COG categories</em> so you must count them all. Many genes will be assigned to multiple categories. In fact, a majority of human genes are given multiple GO cellular function annotations. I have worked considerably in this field and one of the surprises I found is how common protein multifunctionality is. But I digress. </p>
  
  <p>The point here is that you want to see whether any COG categories are over represented in your test set. Whether a gene is annotated to one or to a hundred categories is irrelevant. You are counting genes per COG, so you need to count each of the COGs assigned to a gene separately. </p>
  
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Answers.CreationDate: 2017-07-07T12:48:31.647Z
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Body: <p>I am dealing with a list of genes which have been selected from a gene enrichment analysis. In order to see what kind of genes are overrepresented, I ran <a href="https://github.com/jhcepas/eggnog-mapper" rel="nofollow noreferrer">eggnog-mapper</a> to do an orthology assignment of each gene against a bacterial database (provided in eggnog). </p>
  
  <p>After running eggnog you get a .csv file containing for each gene which is the closest ortholog, and a list of GO, KEGG and COG terms associated. </p>
  
  <p>From there, I would like to do a Fisher-test (also considering Bonferroni correction) to highlight COG categories overrepresented in our dataset compared to our reference genome. </p>
  
  <p>Finally my question: How do you deal with genes assigned to multiple COG categories (same would apply for GO terms). You count +1 to each of the COG categories assigned? Do you just choose one category per gene? </p>
  
Tags: <sequence-annotation>
Title: COG Annotation - Dealing with genes assigned to two or more COG categories
ThreadText: # COG Annotation - Dealing with genes assigned to two or more COG categories
  
  (Asked by: username_0 on 2017-07-07)
  
  I am dealing with a list of genes which have been selected from a gene enrichment analysis. In order to see what kind of genes are overrepresented, I ran [eggnog-mapper](https://github.com/jhcepas/eggnog-mapper) to do an orthology assignment of each gene against a bacterial database (provided in eggnog).
  
  After running eggnog you get a .csv file containing for each gene which is the closest ortholog, and a list of GO, KEGG and COG terms associated.
  
  From there, I would like to do a Fisher-test (also considering Bonferroni correction) to highlight COG categories overrepresented in our dataset compared to our reference genome.
  
  Finally my question: How do you deal with genes assigned to multiple COG categories (same would apply for GO terms). You count +1 to each of the COG categories assigned? Do you just choose one category per gene?
  
  **Tags:** sequence-annotation
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2017-07-07. Score: 3 | Accepted answer
  
  You add 1 to the count of each COG category. You are looking for over represented *COG categories* so you must count them all. Many genes will be assigned to multiple categories. In fact, a majority of human genes are given multiple GO cellular function annotations. I have worked considerably in this field and one of the surprises I found is how common protein multifunctionality is. But I digress.
  
  The point here is that you want to see whether any COG categories are over represented in your test set. Whether a gene is annotated to one or to a hundred categories is irrelevant. You are counting genes per COG, so you need to count each of the COGs assigned to a gene separately.
  
  
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