text: user4413: I have a list of mutated genes from a VCF. Does it make sense to perform a pathway enrichment analysis using PANTHER or STRING as examples to know which pathway is affected?
  EDIT: to reply to @terdon
  We sequence mostly human genome data using Illumina sequencers. As for the type of data, we perform mostly Whole-Exome Sequencing (WES), Whole-Genome Sequencing (WGS).
  At the end, after performing all pre-processing, we obtain the VCF files from HaplotypeCaller using GATK. Then we proceed to annotate using VEP.
  
  user235: The concept of looking for enriched pathways makes sense, but you can't do it using the same tools you would use for gene expression data because the biases are different - longer genes are far more likely to contain variants by chance than short ones, and this needs to be accounted for in any enrichment analysis.
  
original_text: 4413: <p>I have a list of mutated genes from a VCF. Does it make sense to perform a pathway enrichment analysis using <a href="http://www.pantherdb.org/" rel="nofollow noreferrer">PANTHER</a> or <a href="https://string-db.org/" rel="nofollow noreferrer">STRING</a> as examples to know which pathway is affected?</p>
  <p>EDIT: to reply to @terdon</p>
  <p>We sequence mostly human genome data using Illumina sequencers. As for the type of data, we perform mostly Whole-Exome Sequencing (WES), Whole-Genome Sequencing (WGS).</p>
  <p>At the end, after performing all pre-processing, we obtain the VCF files from HaplotypeCaller using GATK. Then we proceed to annotate using VEP.</p>
   235: <p>The concept of looking for enriched pathways makes sense, but you can't do it using the same tools you would use for gene expression data because the biases are different - longer genes are far more likely to contain variants by chance than short ones, and this needs to be accounted for in any enrichment analysis.</p>
  