Week 8- Data Analysis Continued

Arnab M -

Hi guys, It’s Arnab and this is my eight weekly update on my senior research project: Exploring the Genomic Effects of PNPLA7 Mutations on Cerebral Palsy through RNA Sequencing.

This week we took a deep dive into the other part of Downstream Data Analysis in RNA Seq: Gene Set Enrichment Analysis (GSEA). GSEA serves as another statistical method of conducting bioinformatics data analysis, used to identify biological pathways or gene sets that are significantly enriched in a gene expression dataset. GSEA functions by comparing the distribution of genes in predefined gene sets or pathways against the observed gene expression changes between two or more experimental conditions. As opposed to Overrepresentation Analysis (ORA), from last week, GSEA utilizes the entire gene list to observe pathways and gene sets that may be related to PNPLA7. This data yielded plenty of interesting results specifically pertaining to the functional pathways that they listed. Out of our 3 genome databases we utilized to run GSEA (GO, KEGG, and REACTOME) 2 of them, GO and REACTOME, showed that numerous cell replication and division pathways were listed as the most pertinent to PNPLA7 through GSEA. This is exciting yet, it could be a false eureka moment, because yes Cell Division and Replication can impact a child and cause a movement disorder, but it can also impact nearly everything else in the body too. The information is not specific enough to draw direct correlation to PNPLA7 mutation causing CP. However, when other experiments and analysis are carried out for PNPLA7 it will be useful to have this data in the back of the researchers mind. Now that all the brute force coding work is complete it is time to put together a coherent Research Paper, Presentation, Github Account (to track coding script), and shadow even more people at the lab. The future is exciting and stressful simultaneously and I can’t wait to see what happens!

More Posts

Leave a Reply

Your email address will not be published. Required fields are marked *