Answers.Body: <p>Looking at this resource, these data are microarray data rather than RNAseq data. Thus the "signal" in question is the intensity of florescent light being emitted from the the probe associated with your gene.  The relationship between intensity and quantity of RNA is different for every probe because each probe will have a different affinity for complementary fragments dependent on the sequence in question (not least the melting temperature). </p>
  
  <p>Affy intensities are usually presented as log values going up to around 12, but the raw number is next to meaningless and usually only means something as a normalized (e.g. RMA) log fold change. </p>
  
  <p>I've never come across RefExA before, and it appears to be undocumented and unmaintained. I wouldn't rely on it for usable data if I were you. A more modern database of expression data is the <a href="https://www.ebi.ac.uk/gxa/home/" rel="noreferrer">EBI Expression Atlas</a>. It presents data from a wide range of different studies, processed and normalised on a unified pipeline and expressed as TPMs. </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-16T09:01:19.277Z
Answers.LastActivityDate: 2018-04-16T09:01:19.277Z
Answers.UserDisplayName: Ian Sudbery
Body: <p>I'm exploring gene expression on public available databases. <a href="http://sbmdb.genome.rcast.u-tokyo.ac.jp/refexa/main_search.jsp" rel="nofollow noreferrer">RefExa</a> is one of the databases I've been studying.</p>
  
  <p>When I searched something there, the website reported the expression value unit as "signal". See screenshot where I highlighted:</p>
  
  <p><a href="https://i.sstatic.net/znUEJ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/znUEJ.png" alt="enter image description here"></a></p>
  
  <p>I'm not able to find anywhere what that really mean. TPM? RPKM? Raw counts? Normalizated for gene length?</p>
  
  <p>My question is that how to interpret gene expression "signal"? What does signal 100 mean?</p>
  
Tags: <gene><database>
Title: What's "signal" in gene expression?
ThreadText: # What's "signal" in gene expression?
  
  (Asked by: username_0 on 2018-04-16)
  
  I'm exploring gene expression on public available databases. [RefExa](http://sbmdb.genome.rcast.u-tokyo.ac.jp/refexa/main_search.jsp) is one of the databases I've been studying.
  
  When I searched something there, the website reported the expression value unit as "signal". See screenshot where I highlighted:
  
  [![enter image description here](https://i.sstatic.net/znUEJ.png)](https://i.sstatic.net/znUEJ.png)
  
  I'm not able to find anywhere what that really mean. TPM? RPKM? Raw counts? Normalizated for gene length?
  
  My question is that how to interpret gene expression "signal"? What does signal 100 mean?
  
  **Tags:** gene, database
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-04-16. Score: 4 | Accepted answer
  
  Looking at this resource, these data are microarray data rather than RNAseq data. Thus the "signal" in question is the intensity of florescent light being emitted from the the probe associated with your gene. The relationship between intensity and quantity of RNA is different for every probe because each probe will have a different affinity for complementary fragments dependent on the sequence in question (not least the melting temperature).
  
  Affy intensities are usually presented as log values going up to around 12, but the raw number is next to meaningless and usually only means something as a normalized (e.g. RMA) log fold change.
  
  I've never come across RefExA before, and it appears to be undocumented and unmaintained. I wouldn't rely on it for usable data if I were you. A more modern database of expression data is the [EBI Expression Atlas](https://www.ebi.ac.uk/gxa/home/). It presents data from a wide range of different studies, processed and normalised on a unified pipeline and expressed as TPMs.
  
  
  ---
  
  