Amber's research under the guide of Dr. Cuajungco focuses on using big data analytics to study the differential expression of genes in Mucolipidosis Type IV brain samples from mice. Mucolipidosis Type IV is a neurodegenerative disease that is caused by mutations in the mucolipin-1 gene which lead to deleterious affects such as mental and psychomotor retardation. There is currently no viable therapy for this rare disease, but research experiments hope to tackle various aspects of understanding the disease. For instance, my research centers on the use of RNA-seq analysis in order to obtain a more comprehensive understanding of the genetics behind the disease. RNA-seq will be used to quantitatively compare gene expression levels between the two groups: wild-type and knockout. The aim of this experiment to identify specific genes that are significantly upregulated or down-regulated between the two groups. I expect to see a lot of variance between the three sets of wild-type and knockout samples. This data offers many challenges such as the sheer volume of each sample’s file, and the messiness of the raw data. It is necessary to use computational methods in R studio to cleanup the data so that it can easily be compared between samples through coding.
Genomics data is big data and requires appropriate statistical analysis that factors in outliers, and the sheer volume of the data. RNA-seq is the ideal technique for high throughput reading of the entire genome. It involves an intuitive workflow under the TopHat and Cufflinks packages. The Galaxy Project is an open source web interface that allows for the use of these software tools without advanced computer programming knowledge. Genomics data analysis offers its own challenges that are frequently seen in other fields under the umbrella of Big Data Science. RNA-seq requires a minimum of 16gb of RAM in order to conduct the computer processing. Learning techniques for data storage, and data processing are challenges that will arise in this research. At the moment, no data analysis has been conducted due to limitations in machine capabilities, but those problems are in the process of being resolved.
