About DNA arrays
In past, biologists who have been interested in studying gene function have devised methods for studying gene expression. These methods include such well known techniques as Northern blotting, rtPCR, the use of reporter genes, western blotting and many more. However, these techniques are usually applied to studying the expression of a single gene.
The advent of new sequencing technology now allows whole genomes to be sequenced, enabling the sequence of all the potential genes on a organisms genome to be determined. Armed with this knowledge, the traditional techniques of the molecular biologist are now being scaled up to work at the whole genome level instead of the single gene level.
DNA arrays have been devised to allow the transcription of every gene in a genome to be determined simoultaneously by quantifying the levels of mRNA produced from each. A DNA array is simply a collection of immobilised DNA probes that are specific for mRNA from each gene. The probes may be immobilised on a conventional nylon filter (a macroarray) or at high density on glass slide (a microarray).
mRNA is isolated from cells at a particular timepoint or after a particular timepoint, converted to cDNA, labelled and exposed to the probes on the array. In contrast to conventional hybridisation, the probes in a DNA array are immobilised and the target is the labelled cDNA that is free to move in the hybridisation solution.
By analysing the results from a DNA array it is now possible to see at a glance which genes are upregulated or downregulated, for example, at a particular point in the cell cycle or in response to a particular environmental stimulus. Since genes of similar function tend to be co-regulated it is possible to assign putative functions to genes of unknown function by seeing which other genes are expressed in a similar fashion through the process of clustering genes based on their gene expression profiles.
Explore some of the following links to get more background information on DNA arrays before going on to the tutorial.
Alan Robinsons introduction to Microarray technology
A very nice paper on using DNA microarrays
Alan Robinson's excellent Microrray links page
A DNA array web site at Gene-chips.com
What does a DNA array data set look like?
This depends on the experiment type and the array type.
At its simplest level an experiment may simply involve looking at the differences in gene expression between two different conditions at a single time point. e.g. cells grown at 37 after 1 hour compared to cells grown at 42 after 1 hour.
Typically a microarray dataset is more complicated.
A typical microarray dataset contains data derived from a number of arrays. For example we may wish to examine the expression of every gene on a bacterial genome when the bug is grown in a rich medium. This involves taking a number of samples over time and analysing each sample using a new array. So for each time point we get a new set of expression values for each gene. (This is vast oversimplification for the sake of this tutorial!)
Here is a typical set of data taken from a experiment that followed the expression of every yeast gene through the cell cycle by analysing RNA samples taken at various time points.
