Answers.Body: <p>mRNA translation is a regulated biological process. There are a number of different factors that need to come together in order for protein translation to take place, and a number of different ways these factors can be blocked from being introduced into the right place at the right time.</p>
  <p>Due to a mixture of enhancers, suppressors, and degredation, it's almost always the case that protein expression is different (and inconsistently different) from mRNA expression. There is some correlation, but it's nowhere near a perfect correlation.</p>
  <hr />
  <p>To add context to the explanation, RNA sequencing (or, more correctly, cDNA sequencing) is most often used as a proxy for protein expression because it's a simpler, cheaper process.</p>
  <p>High-throughput DNA sequencing can be done via observation of current flow (e.g. Nanopore), or via local sequence replication (e.g. Illumina, PacBio). In both cases, the computer output is nearly identical to the input DNA sequence, as long as the input DNA sequence is a string of A/C/G/Ts, and is short enough that the sequencer can handle it (can be up to 600 bases with Illumina sequencers, up to hundreds of kilobases with Nanopore sequencers). The simplicity of the basic DNA sequence makes detection easier, which makes it cheaper, and easier to implement at scale.</p>
  <p>At large scale, protein sequencing is most often done via local assembly of fragmented peptides put through a mass-spectrometer, which is slow and somewhat complicated to analyse. Individual proteins (without sequencing) can be looked at by proxy via antibody binding (as has been used used in Flow Cytometry at single-cell scale for many years), but there aren't really any good, widely used direct analysis methods. Compared to DNA's 4 bases, protein sequences have 20 most commonly-used amino acids, often with additional chemical modifications that alter detection, which adds up to a much higher complexity for detection and sequencing.</p>
  <p>Any techniques for protein sequencing that involve degrading the protein will suffer from the same length/phasing issues that plague short-read sequencing. Any techniques that involve indirect sampling will be sensitive to small changes in protein composition (e.g. carboxylation), and therefore have reduced accuracy. As far as I'm aware, existing methods for protein sequencing are either slow, inaccurate, or don't scale well. We're pretty good at all three for DNA sequencing now.</p>
  <p>[FWIW, I'm less familiar with protein sequencing, because it's been a while since I was working with that data, and things may have changed since then.]</p>
  
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Answers.Text: This may be a very naive question, so forgive me but, why does RNA sequencing seem to be so common for explaining a gene's expression when protein expression may be more truthful? Why is protein sequencing not more common (at least in my limited experience this is the case)?
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Answers.Text: I've added a quick explanation, but this is quite a big topic, and probably better explained and discussed elsewhere.
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Answers.Text: FWIW a paper for reverse translation was released on archive. Maybe in the distant future we will have protein sequencing. https://www.biorxiv.org/content/10.1101/2024.05.31.596913v1
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Answers.Text: As I said, better discussed elsewhere. Comments should not be used for discussion, or for follow-up questions - they should be about how to improve the specific question or answer they are attached to. For discussions, I recommend [reddit](https://www.reddit.com/r/bioinformatics).
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Body: <p>I am finding a levels of gene expression in protein vs rna seq not correlating in protein atlas for a gene of interest. In rna-sequencing there is a high level of expression mainly in the brain, in the protein expression I see higher expression in most tissue across the board.</p>
  <p>Why are the expression levels different if mRNA translates into protein?</p>
  <p>I am mainly not sure why they are not the same. If mRNA translates to proteins would the expression levels be the same?</p>
  <p>I am interested in tissue specificity and I am unsure how to interpret these results.
  See pictures from <a href="https://www.proteinatlas.org/" rel="nofollow noreferrer">https://www.proteinatlas.org/</a> below describing the inconsistency:</p>
  <p><a href="https://i.sstatic.net/JAoRqQ2C.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/JAoRqQ2C.png" alt="protein expression" /></a></p>
  <p><a href="https://i.sstatic.net/wivo9C5Y.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/wivo9C5Y.png" alt="rna expression" /></a></p>
  
Tags: <rna-seq><proteins><public-databases>
Title: Protein atlas rna-seq vs protein expression region missmatch
ThreadText: # Protein atlas rna-seq vs protein expression region missmatch
  
  (Asked by: username_0 on 2024-06-18)
  
  I am finding a levels of gene expression in protein vs rna seq not correlating in protein atlas for a gene of interest. In rna-sequencing there is a high level of expression mainly in the brain, in the protein expression I see higher expression in most tissue across the board.
  
  Why are the expression levels different if mRNA translates into protein?
  
  I am mainly not sure why they are not the same. If mRNA translates to proteins would the expression levels be the same?
  
  I am interested in tissue specificity and I am unsure how to interpret these results.
  See pictures from <https://www.proteinatlas.org/> below describing the inconsistency:
  
  [![protein expression](https://i.sstatic.net/JAoRqQ2C.png)](https://i.sstatic.net/JAoRqQ2C.png)
  
  [![rna expression](https://i.sstatic.net/wivo9C5Y.png)](https://i.sstatic.net/wivo9C5Y.png)
  
  **Tags:** rna-seq, proteins, public-databases
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-06-19. Score: 1 | Accepted answer
  
  mRNA translation is a regulated biological process. There are a number of different factors that need to come together in order for protein translation to take place, and a number of different ways these factors can be blocked from being introduced into the right place at the right time.
  
  Due to a mixture of enhancers, suppressors, and degredation, it's almost always the case that protein expression is different (and inconsistently different) from mRNA expression. There is some correlation, but it's nowhere near a perfect correlation.
  
  ---
  
  To add context to the explanation, RNA sequencing (or, more correctly, cDNA sequencing) is most often used as a proxy for protein expression because it's a simpler, cheaper process.
  
  High-throughput DNA sequencing can be done via observation of current flow (e.g. Nanopore), or via local sequence replication (e.g. Illumina, PacBio). In both cases, the computer output is nearly identical to the input DNA sequence, as long as the input DNA sequence is a string of A/C/G/Ts, and is short enough that the sequencer can handle it (can be up to 600 bases with Illumina sequencers, up to hundreds of kilobases with Nanopore sequencers). The simplicity of the basic DNA sequence makes detection easier, which makes it cheaper, and easier to implement at scale.
  
  At large scale, protein sequencing is most often done via local assembly of fragmented peptides put through a mass-spectrometer, which is slow and somewhat complicated to analyse. Individual proteins (without sequencing) can be looked at by proxy via antibody binding (as has been used used in Flow Cytometry at single-cell scale for many years), but there aren't really any good, widely used direct analysis methods. Compared to DNA's 4 bases, protein sequences have 20 most commonly-used amino acids, often with additional chemical modifications that alter detection, which adds up to a much higher complexity for detection and sequencing.
  
  Any techniques for protein sequencing that involve degrading the protein will suffer from the same length/phasing issues that plague short-read sequencing. Any techniques that involve indirect sampling will be sensitive to small changes in protein composition (e.g. carboxylation), and therefore have reduced accuracy. As far as I'm aware, existing methods for protein sequencing are either slow, inaccurate, or don't scale well. We're pretty good at all three for DNA sequencing now.
  
  [FWIW, I'm less familiar with protein sequencing, because it's been a while since I was working with that data, and things may have changed since then.]
  
  > **Comments:**
  > **username_0**: This may be a very naive question, so forgive me but, why does RNA sequencing seem to be so common for explaining a gene's expression when protein expression may be more truthful? Why is protein sequencing not more common (at least in my limited experience this is the case)?  
  > **username_1**: I've added a quick explanation, but this is quite a big topic, and probably better explained and discussed elsewhere.  
  > **username_0**: FWIW a paper for reverse translation was released on archive. Maybe in the distant future we will have protein sequencing. https://www.biorxiv.org/content/10.1101/2024.05.31.596913v1  
  > **username_1**: As I said, better discussed elsewhere. Comments should not be used for discussion, or for follow-up questions - they should be about how to improve the specific question or answer they are attached to. For discussions, I recommend [reddit](https://www.reddit.com/r/bioinformatics).  
  
  ---
  
  