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Gene expression profiling is a way of measuring the activity levels of thousands of genes at the same time. Identifying gene expression patterns in an organism is the next step after the genome of an organism has been sequenced. Gene expression profiling experiments are usually carried out on the entire genome of an organism at once. Measuring gene expression levels in an organism provides a picture of how the organism’s cells function during the cell cycle, or in response to specific stimuli.
The genes of an organism can be in one of two states: switched on or switched off. When a gene is switched on, it is being transcribed into messenger RNA, which provides the instructions for making the protein which is coded for by the gene. When genes are switched on, they are said to be being expressed. When a gene is switched off, it is not being transcribed into mRNA and is not being expressed.
The DNA of even a single-celled organism contains thousands of genes, but only a fraction of those genes are switched on at any time. The pattern of gene expression within a cell at a particular point in time is referred to as its gene profile. Looking at the types of genes switched on in a cell can provide large amounts of significant information about cells and organisms.
In a gene expression profiling experiment, DNA microarray technology is used to obtain a measurement of relative activity of previously sequenced genes. These experiments typically involve measuring amounts of mRNA in a control setting and in an experimental setting, to determine the effects of one or more variables on gene expression. Using a control is important because it establishes baseline mRNA levels for normal cellular conditions.
Looking at how mRNA levels change in response to stimuli shows how cellular needs for proteins change in response to new environmental conditions. This information is useful for pure research purposes, but can also be important in medicine. For example, if breast cancer cells are used in DNA microanalysis, a profile might show that in cancerous breast cells a certain type of receptor is active which is normally inactive. If the receptor is shown to be cancer-specific, it may prove to be an effective drug target.
Gene expression profiling has, in fact, been used as a prognostic measure for breast cancer. This is useful because women at the same stage of disease can respond very differently to treatment, and have very different prognoses. Using DNA microanalysis to build up gene expression profiles has shown in at least one study that a certain gene expression profile in breast cancer cells correlates with poor prognosis. This application of gene expression profiling technology helps identify women who may benefit from more aggressive treatment.