E-learning in analysis of genomic and proteomic data 2. Data analysis 2.2. Analysis of high-density genomic data 2.2.1. DNA microarrays Types of microarrays

There are different types of microarrays that can be divided according to the type of the manufacturing technology, length of the probes on the microarray or type of the organism the microarray is designed for.

According to the length and type of the probes, microarray can be divided into cDNA microarrays and oligonucleotide microarrays.

cDNA microarrays

     The probes at this type of array are 500-5000 base pair long cDNA clones of a target gene or a known sequence. Usually, they are synthetised prior to the immobilization onto the solid surface using a spotting robot.

     The advantage of such a long probes is that they are more specific to individual target gene and in case of a successful hybridization with a target sample DNA, we can almost certainly assume a match with the gene.

     However, because the amount of the hybridization in these arrays is dependent on the length of the probes, and because the exact number of clones in each spot is unknown (in comparison to oligonucleotide chips), the hybridization level for each spot have to be compared with some reference (control). This relative information is much more robust than absolute information about intensity in each spot. This is why cDNA array experiments are usually performed in two-channel format. One channel (e.g. red) is used for the DNA of interest and second channel (e.g. green) is used for the reference DNA.

Oligonucleotide microarrays

     Here the probes are represented by oligonucleotides, very short sequences (usually not more than 25 base pairs) designed to match parts of the sequence of known or predicted open reading frames. They are synthetised either in situ (most often) or conventionally followed by the immobilization on the surface. The most common are GeneChip arrays (producer: Affymetrix Inc., GeneChip-->®), called simply Affymetrix arrays.

       In contrast to long cDNA probes, the shorter oligonucleotide probes may be spotted in higher density across the array and are cheaper to manufacture.