I've read papers which contain statements such as "control of gene expression is critical in biological processes".
How exactly does one quantify "gene expression"? Isn't gene expression an umbrella term describing all of the mechanism by which DNA is synthesized into an organism's phenotype?
The primary product of protein coding genes are mRNAs. When we talk about measuring gene expression we want to assay the steady-state levels of a specific mRNA within a cell. This is usually accomplished by starting with a large number of cells and harvesting all of the mRNAs from all of the cells. One way to measure the expression level of just one gene's mRNA is to perform a Northern Blot. Other sensitive methods include: an S1 nuclease protection assay, an RNAse protection assay, and a primer extension assay.
Microarrays have also been used extensively to measure expression levels of thousands of genes at the same time in a single experiment.
With the advent of RNA-Seq methodology it is possible to count the number of transcripts in an experiment (if you have a sequenced reference genome)
According to next generation data:
I was never working directly with mRNA but what I got from the bioinformatician was something like this: you extract your mRNA, sequence it, filter it according to the quality & length, assemble it and what you then have is something like "transcripts". Those you are counting: xy of transcript1 & yx of transcript2. You are further looking for isoforms and in the end you are correcting this counts according to the initial reads which you computed. Comparing the transcripts to a control you can measure if its up or downregulated (setting the reads of the control as "zero" like 1234 reads of one transcript are normal..... in sample 2 you have 5000 reads of this transcript... the gene seems to be upregulated). As far as I know is is approximately the way how gene expression approximations / quantifications are made.
