|MadSci Network: Molecular Biology|
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. -Matt-
Try the links in the MadSci Library for more information on Molecular Biology.