This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What is transcriptomics?
Transcriptomics is the study of all of the RNA transcripts in a cell using high-throughput methods (1). Two common transcriptomics techniques are RNA-sequencing and microarray analysis. Transcriptomics can be used to analyze RNA under different experimental conditions. The comparison of transcriptomes allows identification of genes that are differentially expressed in disease vs. non-diseased populations or in response to different drugs/treatments (1).
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The transcriptome is all of the RNA in a cell.
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PINK1 Transcript (RNA) Expression
GEO Datasets
GEO Profiles is a large database containing many datasets. It is a useful tool to show gene expression of one gene from all samples in a dataset (image on right). This specific example shows the decrease in PINK1 gene expression in patients with Parkinson's Disease. Studies have shown that higher expression of PINK1 is linked to lower rates of Parkinson's disease (2). Transcriptomics tools can be used to quantify the level of PINK1 gene expression associated with Parkinson's disease and non-diseased phenotypes. |
The Human Protein Atlas
The Human Protein Atlas (HPA) aims to map proteins in cells, tissues and organs using many different technologies ().
In the image on the left, levels of PINK1 RNA expression and protein expression can be viewed in different tissues. PINK1 is expressed in all tissues, but expression is especially high in the brain, endocrine tissues, muscle tissues, and the gastrointestinal tract. |
Discussion
High-throughput transcriptomics techniques are extremely useful tools for identifying differential levels of gene expression in different treatments and cell types. The microarray analysis showing higher expression of PINK1 in non-diseased postmortem brains could suggest that if Parkinson's disease were caught early, addition of functional PINK1 could be a potential treatment to rescue the disease phenotype. The Human Protein Atlas provides interesting directions for future research. Most research conducted on PINK1 and PD has been about the brain. The high expression in other organ systems could be a source of PD symptoms and provide potential targets for treatment.
References
1. Lowe, R., Shirley, N., Bleackley, M., Dolan, S., & Shafee, T. (2017). Transcriptomics technologies. PLoS Computational Biology, 13(5), e1005457. http://doi.org/10.1371/journal.pcbi.1005457
2. Lang AE, Lozano AM. Parkinson's disease. First of two parts. N Engl J Med. 1998a;339:1044–1053. https://www.ncbi.nlm.nih.gov/pubmed/9761807
2. Lang AE, Lozano AM. Parkinson's disease. First of two parts. N Engl J Med. 1998a;339:1044–1053. https://www.ncbi.nlm.nih.gov/pubmed/9761807