Super-enhancers (SE) have become a popular concept and are widely used as a 
feature defining key identity genes. Here, we provide perspectives on the use of 
SE to define and identify cell/tissue-identity genes. By mining SE and their 
associated genes using murine functional genomics data, we highlight and discuss 
current limitations and open questions regarding both the sensitivity and 
specificity of identity genes/transcription factors predicted by SE. In this 
context, we point to cell/tissue-specific promoters as an important additional 
level of information, which we propose to combine with SE when aiming to define 
potential identity genes.