I will be adding methods to this section as they come up in the papers.

A microarray is a way of looking at changes in gene expression for an entire genome.  The way it works is that a small chip (called a gene chip) is created that has a series of small spots of DNA, one for each gene.  Chips already exist for the genomes of the main animal models, so all you have to do is buy one.

During the process of gene expression, a gene which is made up of DNA is transcribed into mRNA.  The RNA sequence is complimentary to the DNA sequence (you can think of the RNA as a copy of the DNA sequence).  Not all genes are transcribed, so if you want to see which genes are being expressed, you can look at the types of RNAs that are being made.  If you find RNA-A and RNA-C, then you know that Gene-A and Gene-C are actively being transcribed and expressed.  The RNAs will go on to direct synthesis of Protein-A and Protein-C. 

For microarray, once you have your gene chip, you need to extract RNA from cells or an organism, and label it with a dye.  Technically speaking, the extracted RNA is first converted back into DNA and then labeled with the dye.  Then you mix all the labeled DNA (from the RNA) with the gene chip.  Remember that the chip has spots of DNA, which can bind to this complimentary DNA.  In our example where Gene-A and Gene-C are being expressed, they will make the corresponding RNAs, which will then bind two spots of DNA on the gene chip, one for Gene-A and one for Gene-C.  In other words, the chip will have two fluorescent spots on it.  The researchers know from the position of those spots that Gene-A and Gene-C are being expressed. 

In this example, they are seeing how gene expression is altered in cancer cells

In practice, microarrays are usually used to compare two different conditions.  For instance, let’s say you think that pesticides cause changes in gene expression.  You could expose one group of mice to the pesticide and the other group will be the controls.  Then you isolate the RNAs from both sets, label one set in red and other with a green dye.  When you put them on the gene chip, if a spot is very green, then you know that that particular gene is expressed more in the green group.  In this way you can see how gene expression changes in response to pesticide exposure.

Microarray = changes in gene expression on a whole genome scale