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Bioinformatics of the Brain

FIGURE 8.1

A simplified A. Microarray B. RNA-seq workflow.

There are various types of microarrays with DNA microarrays being the

most widely used one. The other microarray technologies include protein, pep-

tide, antibody, transfection, cell, and tissue microarrays [9]. Making use of mi-

croarray technology, one can investigate the concurrent gene expression pat-

terns of thousands of different genes, determine transcription factor binding

sites or genotype single-nucleotide-polymorphism (SNP) [10]. The most impor-

tant purpose of using this technology is to identify a pattern in the investigated

areas. Subsequently, qPCR (quantitative polymerase chain reaction) is used to

validate the microarray findings. There are different microarray platforms such

as Affymetrix (https://www.thermofisher.com/tr/en/home/brands/applied-

biosystems.html), Illumina (https://www.illumina.com) and Agilent

(https://www.agilent.com). Various characteristics set these microarray tech-

nologies apart. For instance, while Illumina arrays use multiple copies of a

single 50-nucleotide probe attached to microbeads to quantify target levels

and Agilent uses a single 60-nucleotide probe per gene on the microarray,

Affymetrix arrays characterize gene expression using a set of different 25-

nucleotide probes synthesized in situ [11, 12].

There are quite a few benefits to using microarray technology. Microar-

rays have well defined protocols for hybridization and the data submission is

standardized. They are also low cost compared to RNA-seq. However, since

microarrays use hybridization techniques prior knowledge of a sequence is re-

quired. There also have been several problems identifying very low and highly

expressed genes using this technique. Background noise can be high. Further-

more, microarrays generally do not identify splice variants and they do not

give paralogue information. Most commonly used microarray platforms use a

single set of manufacturer-designed probes, resulting in an absence of over-

sight over the collection of analyzed transcripts. Another major drawback of