Which Tool Is Best Depends on the Question Asked and the System Being Surveyed
While techniques available in the past allowed only a limited number of genes to be examined at one time, genome-based microarray platforms opened the possibility to analyze entire cellular transcriptomes under specific sets of conditions. This global approach enables the visualization of discrete pathways or groups of genes, which can be surveyed under various conditions, such as a specific disease or treatment with a certain therapeutic agent.
Despite their advantages, microarrays have several limitations. “Microarrays are a great tool to start with, but to understand the biology of the system one needs to subsequently conduct more focused experiments,” advises Dr. Stephen Walker, assistant professor at Wake Forest University School of Medicine.
The recent push toward RNA sequencing is being driven not only by the need to learn about changes in the expression of a particular gene, but also by the opportunity to visualize the differential regulation of multiple splice variants for one specific gene.
“By sequencing the transcriptome, rather than labeling RNA and hybridizing on microarrays, there is a higher likelihood to pick up individual splice variants and get a much more comprehensive gene-expression profile,” explains Dr. Walker. “This provides a more comprehensive analysis but adds, at the same time, another layer of complexity, because the size of the files is quite large, and the approach, at the present time, can be cost prohibitive,” he adds.
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