What is transcriptomics?
Transcriptomics refers to the study of transcriptomes and their function. A transcriptome is a collection of all of the RNA transcripts in a cell. Analysis of the transcriptome allows researchers to determine when and where each gene is expressed (or not expressed) in the cells of an organism. In addition, because most cells contain the same genes, different cells show different patterns of gene expression. This is true for many other organisms as well. Therefore, by comparing transcriptomes of different types of cells, researchers are able to gain a deeper understanding of cell differentiation, cell function, and how changes in gene activity contribute to disease [1].
Examples of Transcriptomics: TP53 Expression
GEO Profiles is a useful database, derived from GEO Datasets, for exploring gene expression profiles from past research studies. Below is an example of a gene expression profile found when searching the TP53 datasets. This expression panel shows TP53 expression across various normal tissues in humans [2]. This allows for direct comparison between tissue types. It not only gives us the opportunity to gain an understanding of the role of TP53 in different cell types, but also in how it might influence diseases in these different tissues.
Another interesting way to utilize GEO Profiles and GEO Datasets is to look at previous studies in cancer drug testing. Due to the high prevalence of TP53 mutations in many cancers (like ovarian cancer), there have been several studies that look at cancer drug effects on TP53 expression. Below is an example of how the anticancer drug NSC319726 affects TP53 expression in ovarian cancer cells. The shorter red bars indicate decreased gene expression [3].
References:
[1]National Human Genome Research Institute. (2015). Transcriptome Fact Sheet. Retrieved March 9, 2017. https://www.genome.gov/13014330/
[2] https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS1096:201746_at
[3] https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS4877:201746_at
[1]National Human Genome Research Institute. (2015). Transcriptome Fact Sheet. Retrieved March 9, 2017. https://www.genome.gov/13014330/
[2] https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS1096:201746_at
[3] https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS4877:201746_at