text: user3575: 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:
  
  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)
  
  user3631: 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
  
original_text: 3575: <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.stack.imgur.com/4gnnA.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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>
   3631: <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>
  