Common Applications of DNA Microarrays

DNA microarrays, believed to be one of the most significant accomplishments in the scientific field, are used for various purposes, each of which possesses its own revolutionary advances in biotechnology. Predominantly used for medical diagnosis and treatment by way of advancements in genetic sequencing, DNA microarrays are also applied for agricultural progression, biological warfare detection, and forensic analysis.

The most common applications of DNA microarrays include gene expression analysis and genotyping, transcription factor binding analysis, and the creation of a digital database that biologists have access to for future research and analyses.

Gene expression levels are measured by extracting RNA and enriching it for messenger RNA to be hybridized. Scanning the microarray after hybridization for the expression of each gene helps determine particular profiles, exhibiting changes in the expression as a response to treatment or a distinct condition. This level of understanding of biochemical pathways lends critical information to be able to diagnose diseases, promote further discoveries of medical science technology, and specifically target biochemical pathways - all of which aid in the expansion and generation of available databases.

With the implementation of DNA microarrays, one of the earliest technologies outside DNA sequencing, biologists have been able to compile expansive amounts of intricate digital data. Having information on previously conducted array studies, plus the protocols and methods used, has proven to be invaluable to reproduce and expand upon further advanced discoveries. Compounding on each of the previous analyses, the exchange of microarray data has evolved into public, experimental standards that are used today by scientists across the globe. Specific research can be filtered out to retrieve only data desired for a particular experiment through various databases made available to the biological community.

FAQs:

What are the types of microarrays based on the probes used? What are the challenges of chromosomal microarrays? What are the types of microarrays based on the mode of preparation? How can I access and analyze a publicly available RNA-seq database?

Genotyping depends on detection of the most minute genetic differences, which can result in significant changes in a phenotypic trait. Genotyping gives the ability to pinpoint the distinct nucleotides and bases creating that change, which allows for associating a particular gene with a specific trait. With the application of a DNA microarray, a better understanding of cellular pathways and processes will allow us to make that association.

Another common application of DNA microarrays is to determine the binding sites of transcription factors (TFs), providing further insight into the regulatory regions of DNA that produce phenotypic differences. Cellular processes and responses can be better understood once we know which TFs are responsible for the changes in DNA. Using a technique called Chromatin immunoprecipitation (ChIP), by crosslinking the DNA with the TF and pulling the protein down by use of a specific antibody, the genomic location of a TF binding site can be established. The ability to calculate which factors are crucially affecting the expression levels of the genes at these sites further advances our regulation of those genes.

Datasets:
Transcription factor AP1 Inhibitors (IC50, Ki) Activating transcription factor 1 Inhibitors (IC50, Ki) Transcription intermediary factor 1-alpha Inhibitors (IC50, Ki)	Transcription initiation factor TFIID subunit 1 Inhibitors (IC50, Ki) Transcription initiation factor IIA alpha and bTranscription initiation factor IIA alpha and beta chains Inhibitors (IC50, Ki)

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References

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Microarray Applications
microarray
DNA microarrays: Types, Applications and their future
The Stanford Microarray Database
Do Transcription Factors Actually Bind DNA? DNA Footprinting and Gel Shift Assays