MadSci Network: Molecular Biology

Re: why is log2 ratio ,a measure of gene induction / repression in microarray

Date: Mon Jul 21 18:04:59 2003
Posted By: Matthew Champion, Staff Scientist
Area of science: Molecular Biology
ID: 1058574768.Mb

     I am not entirely certain what you mean by "Why is Log2 a 
Measure...?" but I think you are asking why is it used as opposed to some 
other form of measuring the differences in a Gene Array.

     First some background.  Gene arrays are not quantitative.  As far as 
I know Real Time PCR is the only way to actually quantitate the amount of 
mRNA in a cell absolutely in any manner appraoching high throughput.  As 
for gene arrays, they essentially measure *relative* increases/decreases 
in the amount of transcribed message within a cell.  

     The reason we use a log scale to compare them is for two reasons. 

1.) We do not obtain an amount of RNA (Indirectly via cDNA) produced by 
any given gene (See above). Therefore, our data has to be expressed in 
terms of relative amounts, i.e. Two (2) fold higher in the test sample 
over the control.  Logs are very good at displaying relativistic data

2.) The range of change in mRNA levels in a cell as a function of gene 
expression is on the order of a few fold, so a log2 scale fits nicely 
within this range.  Although absolute levels of protein produced from any 
gene in induced versus uninduced state can span more than 6 orders of 
magnitude, the corresponding amount of mRNA needed for this is 
considerably less.  One of the standards for the veracity of a gene array 
is that it is at least two fold above or below background (0).  This 
corresponds to one Log2 (or 1).  What this means is that even if you take 
the same sample and run it repeatedly, you will often find variation in 
the same sample that ranges between +/- two fold.  In modern chip based 
array approaches, the stringency for such identifications are getting 
better, and lower standards may now be possible, but this does not change 
the relative display of the data.

Virtually any arithmatic scale could be employed for gene arrays.  By 
convention, ease of having the numbers to manipulate, as well as other reasons, 
Log2 was chosen.  In traditional mRNA quantitation/detection experiments 
the levels of mRNA induction were measured by Northern blots and often 
expressed in fold difference based on the number of radioactive counts 
incorporated into the nascent mRNA.  These values are rarely more than 10 
fold above baseline, which is consistent with the values we see on gene 
arrays.  Thank you for your question.


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