Skip to content

Edward Sukarto (SURF STEM)

Analysis of RNA-Sequencing Data Methods to Understand Quorum Sensing in Candida albicans

Edward Sukarto, Deepika Gunasekaran, and Clarissa J. Nobile, PhD

RNA-Sequencing (RNA-Seq) is a technique used to determine the transcriptional profile of cells under specific conditions. Different methods exist to analyze RNA-Seq data, especially in terms of determining differentially expressed genes in the conditions of interest. We have found that RNA-Seq data using different RNA-Seq analysis methods has generated very different results in terms of the differentially expressed genes identified. The goal of my project is to understand the limitations of these different methods in identifying differentially expressed genes. We are comparing two widely used methods, DESeq2 and Limma, to determine the extent of the differences observed between the differentially expressed genes identified using the two tools. We are looking at differences in Log2 fold change values, adjusted P values, and CPM values, to understand the sensitivity and precision of the different tools. Our results are revealing the utility of these tools and identifying the best-practices for analyzing RNA-Seq data in the field. These findings are being applied to existing RNA-Seq data for Candida albicans in the presence of the quorum sensing compound, farnesol. Analysis of this RNA-seq data will lead to the identification of the transcriptional profile of C. albicans during exposure to farnesol. This work will ultimately shed new light on how cells of this important human fungal pathogen communicate with one another.


Mobile device: Open PDF to view the document in a new browser window.




Email Scholar - Provide Feedback - Return to Showcase Gallery