Answers.Body: <p>What is "click here for details" saying? That link should contain an explanation of what happened.</p>
  
  <p>GSEA usually requires <code>entrez_id</code> to run. If your list contains <code>gene_symbols</code>, then before enrichment, you need to convert the genes names. This can and is (always) tricky as genes are known with different names. For example, by googling I couldn't find any <code>AASS3</code> gene, but I found <code>AASS</code>, which is also named <code>LKRSDH</code>,<code>LORSDH</code>, and <code>LKR/SDH</code>. Depending on the software you are using for conversion, and the genome version used some genes will be missed. I usually run (in R) a combination of <code>geneSynonym</code> and <code>biomaRt</code> to fill the gaps in the lists.  </p>
  
  <p>Even better, would be to use <code>ensembl_id</code> or even better <code>entrez_id</code> directly</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-18T17:27:22.643Z
Answers.Text: Hi thank you, you solved it! (1) The blue table in the picture is revealed after clicking on *click here*. (2) These interfaces work usually well with gene symbols. (3) Do you know if there are less gene with an entrez_id than specific in GENCODE? (4) Actually you pointed out right that AASS3 does not exist. It turns out I used the wrong column in my table to select the genes: AASS3 was just a unique row name for AASS
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Answers.CreationDate: 2019-11-18T08:32:30.330Z
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Body: <p>When I enter a list of gene names into common gene ontology (GO) term enricher (e.g. MsigDB or ToppGene) only a small fraction of genes is actually used for the enrichment:</p>
  
  <p><a href="https://i.sstatic.net/4gnnA.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/4gnnA.png" alt="msigdb gene restriction"></a></p>
  
  <p><strong>I am struggling to understand why precisely only such a small number of genes is mapped here.</strong></p>
  
  <p>My dataset is mapped with the GENCODE annotation. What annotation is the base of gene ontology? (The picture mentions entrez genes)</p>
  
Tags: <gene-ontology><functional-annotation><go-enrichment><sequence-annotation><gencode>
Title: Why are my genes filtered for Gene Ontology term enrichment?
ThreadText: # Why are my genes filtered for Gene Ontology term enrichment?
  
  (Asked by: username_0 on 2019-11-18)
  
  When I enter a list of gene names into common gene ontology (GO) term enricher (e.g. MsigDB or ToppGene) only a small fraction of genes is actually used for the enrichment:
  
  [![msigdb gene restriction](https://i.sstatic.net/4gnnA.png)](https://i.sstatic.net/4gnnA.png)
  
  **I am struggling to understand why precisely only such a small number of genes is mapped here.**
  
  My dataset is mapped with the GENCODE annotation. What annotation is the base of gene ontology? (The picture mentions entrez genes)
  
  **Tags:** gene-ontology, functional-annotation, go-enrichment, sequence-annotation, gencode
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-11-18. Score: 1 | Accepted answer
  
  What is "click here for details" saying? That link should contain an explanation of what happened.
  
  GSEA usually requires `entrez_id` to run. If your list contains `gene_symbols`, then before enrichment, you need to convert the genes names. This can and is (always) tricky as genes are known with different names. For example, by googling I couldn't find any `AASS3` gene, but I found `AASS`, which is also named `LKRSDH`,`LORSDH`, and `LKR/SDH`. Depending on the software you are using for conversion, and the genome version used some genes will be missed. I usually run (in R) a combination of `geneSynonym` and `biomaRt` to fill the gaps in the lists.
  
  Even better, would be to use `ensembl_id` or even better `entrez_id` directly
  
  > **Comments:**
  > **username_0**: Hi thank you, you solved it! (1) The blue table in the picture is revealed after clicking on *click here*. (2) These interfaces work usually well with gene symbols. (3) Do you know if there are less gene with an entrez_id than specific in GENCODE? (4) Actually you pointed out right that AASS3 does not exist. It turns out I used the wrong column in my table to select the genes: AASS3 was just a unique row name for AASS  
  
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