Ok, back to the basics. I need another break from raw data.
I've briefly discussed the basics of DNA and RNA in previous posts. I've also introduced transcription. So what's the big deal? As it turns out, although every cell in an organism has the same DNA, different tissues, have different genes expressed at a given time, resulting in their unique characteristics. So that is why a plant leaf looks different from a flower a root. Whether a gene is expressed (turned on) or not (turned off) depends on available transcription factors. The availability of these transcription factors again depends on whether the genes encoding these transcription factors are turned on and so on. As you can see it can get rather complicated.
In general there are different levels of regulation in the pathway from DNA to final product. This list is not intended to be complete, but should give an idea of what can happen.
1. Transcriptional regulation (is the gene turned on or off?)
2. Transcript processing orpost-transcriptional regulation (changes to the transcript can affect subsequent steps)
3. Translational regulation (is protein made from the available RNA?)
4. Post-translational regulation (sugars or lipids can be attached to proteins)
Protein activity is regulated on a number is different levels, which warrants an entire post, so we'll leave that for another time. For the purposes of this discussion, it is enough to know that different cell express different genes at any time.
Now that we know that, we can ask: so which genes are turned on/off in this cell, but not in that. This is also referred to as "differential expression." And in a nutshell, that is what microarrays do. For the entire genome in one single experiment (with more controls than experimental treatments, but that is the nature of the beast).
Differential expression will be covered in a future post (hopefully soon).