This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What is transcriptomics?
The central dogma of molecular biology explains how our genetic messages are expressed: DNA is transcribed into RNA and RNA is translated into proteins. Transcriptomics is the study of the transcriptome, which means investigating this pathway at the RNA level. The transcriptome consists of all of the RNA transcripts expressed from a given sample. The transcripts present in the sample are dependent on what genes are expressed at that time. This is dependent on a variety of factors, including the tissue type, environmental conditions, and even the time of day.
Figure 1. The Central Dogma [1]. Transcriptomics is the study of the transcriptome, which consists of exploring genetic messages at the RNA level.
What is SNRPN expression like in cases of epilepsy?
The NCBI database, GEO DataSets,can be used to examine gene expression recorded from past experiments that are included in the database. Below is an example of a study with epileptic mice. Mice lines with cystatin B knockouts were epileptic and had decreased Snrpn expression. This decreased expression is displayed below on the heat map.Genes with high expression in a particular genotype are displayed in pink, no difference in expression in black, and decreased expression in green compared to other samples.
Figure 2. Cystatin B knockout model of progressive myoclonus epilepsy: cultured cerebellar granule cells. Knockouts were epileptic and had differential expression compared to non epileptic lines [2].
From the GEO DataSets, an additional databade called PANTHER can be used to determine the gene ontology of larger collections of genes. Specifically, the genes involved in the particular GEO DataSet study can be analyzed at once. Below is the PANTHER gene ontology profile for a set of genes that were analyzed in the Cystatin B knockout model of progressive myoclonus epilepsy: cultured cerebellar granule cells. The pie chart for this study reveals genes implicated in response to stimulus and locomotion undergo differential expression, which are also ontology groups involved in epileptic phenotypes.
Figure 3. PATHER gene ontology analysis of Cystatin B knockout model of progressive myoclonus epilepsy: cultured cerebellar granule cells.
Analysis
By determining what transcripts are present in a sample, it can be determined what genes are required under certain conditions. This method can also be used to compare healthy and diseased samples to identify the difference in gene expression between the two. These differences may indicate which genes/gene products contribute to disease.
References
[1] Personome <http://www.personome.com/transcriptomics.html>
[2] GEO DataSet of Cystatin B knockout model of progressive myoclonus epilepsy: cultured cerebellar granule cells <https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS5091>
[3] PANTHER analysis of Cystatin B knockout model of progressive myoclonus epilepsy: cultured cerebellar granule cells <http://pantherdb.org/geneListAnalysis.do>
[2] GEO DataSet of Cystatin B knockout model of progressive myoclonus epilepsy: cultured cerebellar granule cells <https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS5091>
[3] PANTHER analysis of Cystatin B knockout model of progressive myoclonus epilepsy: cultured cerebellar granule cells <http://pantherdb.org/geneListAnalysis.do>