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Why is the y-axis labeled 'relative gene expression'?


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#1 Ahrenhase

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Posted 29 January 2010 - 05:53 PM

In a publication showing qRT-PCR data, they typically label the y-axis 'relative gene expression', why is that? Gene expression assumes that the gene is translated. Reverse Transcription qRT-PCR data shows the amount of polyadenylated transcript present but says nothing about the amount of which is translated into protein.

#2 Ahrenhase

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Posted 31 January 2010 - 02:46 PM

In a publication showing qRT-PCR data, they typically label the y-axis 'relative gene expression', why is that? Gene expression assumes that the gene is translated. Reverse Transcription qRT-PCR data shows the amount of polyadenylated transcript present but says nothing about the amount of which is translated into protein.


so i guess it's just a misnomer

#3 HomeBrew

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Posted 31 January 2010 - 11:34 PM

Are rRNA genes or tRNA genes not expressed? The expression of a gene does not assume that the gene is translated, though many experimental designs often try to draw a direct correlation between expression levels and translation levels...

#4 Mighty Mouse

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Posted 01 February 2010 - 06:56 PM

I agree with Homebrew..."expression" does not imply translation. IMO expression implies transcription. I think by now we're beyond the traditional "dogma of molecular biology" in which RNA primarily exists as a messenger between the genome and protein translation. There is plenty of documentation for functional ncRNA.

MM
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#5 Ahrenhase

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Posted 02 February 2010 - 01:38 PM

very good points, but expression does imply a functional gene product. If what's being describe in the data must be translated into a protein before it's functional, then the label "relative gene expression" would not work. It would simply be 'relative transcript abundance'.

#6 Mighty Mouse

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Posted 02 February 2010 - 05:01 PM

This is an interesting point, although I tend to disagree. Perhaps the problem we're running into is with the word "gene" and talking about "gene expression". For what exactly is a gene? Does a gene imply protein? If so, then perhaps the problem isn't with the word expression itself but only when it follows "gene". I'm no molecular biologist, but I've always found the term "gene" to be a bit difficult to understand.

According to wikipedia a gene is "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions . So perhaps gene does not imply protein? Doesn't really clear up the term "gene expression" though as a gene appears to refer to a "unit of inheritance", whatever that means.

But back to your point about a functional product, I don't know that we can say any mRNA, even if not translated into a protein, is not associated with some sort of functional product (what about all those introns spliced out?! Seems like a waste to me if it's not used for something!)...I'm of the persuasion that the cell does not run around making stuff for no reason.

But anyway, I digress....

MM
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