text: user4905: It is almost common sense that local amplification of gene increase the its mRNA expression . I recently heard that large scale SCNA (such as arm-level amplification) does not increase the mRNA expression level of gene within the region. I did some analysis (SCNA is determined by SNP array and NGS, mRNA expression is measured by RNA-Seq) and found that this is indeed the case. I further did some research and did not found any explanations. it seems like a common acknowledgement. Is there any technical bias or biological explanation that I am missing here? Or is it something that has not have a answer yet?
  I have no clue about this at all. Can you recommend this papers on this?
  
  user73: Answer from @devon-ryan, converted from comments:
  The common presumption in such cases is that there's a feedback loop on most genes to control their expression level. It doesn't have to be specific to arm-level expression.
  
original_text: 4905: <p>It is almost common sense that local amplification of gene increase the its mRNA expression . I recently heard that large scale SCNA (such as arm-level amplification) does not increase the mRNA expression level of gene within the region. I did some analysis (SCNA is determined by SNP array and NGS, mRNA expression is measured by RNA-Seq) and found that this is indeed the case. I further did some research and did not found any explanations. it seems like a common acknowledgement. Is there any technical bias or biological explanation that I am missing here? Or is it something that has not have a answer yet?</p>
  <p>I have no clue about this at all. Can you recommend this papers on this?</p>
   73: <p><em>Answer from @devon-ryan, converted from comments:</em></p>
  <p>The common presumption in such cases is that there's a feedback loop on most genes to control their expression level. It doesn't have to be specific to arm-level expression.</p>
  