Gaurav Kandoi, a BCB Ph.D. candidate in Julie Dickerson’s lab will be presenting a paper at a November 13-16 conference in Kansas City, Missouri. The paper is entitled, “Differential alternative splicing patterns with differential expression to computationally extract plant molecular pathways”.
The conference is the IEEE International Conference on Bioinformatics and Biomedicine, and Gaurav will present at one of the workshops associated with the conference entitled The 8th Integrative Data Analysis in Systems Biology.
Their analysis of Arabidopsis thaliana RNA-Seq data suggest that using differentially alternatively spliced genes in addition to differentially expressed genes can supplement our understanding of biological pathways. Their abstract is below.
Abstract—Alternative splicing (AS) produces multiple messenger RNAs by combining different regions of the precursor transcript to produce diversity in gene products. Plant growth and development are extensively affected by environmental disturbances. Under stress conditions, many genes produce transcripts that are not otherwise produced during normal conditions. In this study, we use Differentially Alternatively Spliced Genes (DASGs) along with Differentially Expressed Genes (DEGs) to discover important metabolic networks in the presence of environmental stress. Using publicly available RNA-Seq datasets from Arabidopsis thaliana (Col-0) subjected to heat stress conditions, we extract several molecular pathways associated with temperature stress-response using differentially alternatively spliced and differentially expressed genes. Increased numbers of AS events are seen under stress conditions. Most DASGs are linked with biological processes such as splicing, circadian rhythm, and metabolic processes. In contrast, most DEGs are linked with cell cycle and division, and transport (of water, fluid, and polyol etc.). These differences in the biological processes highlight the importance of integrating differential splicing information along with differential expression to extract important metabolic pathways. Our analysis suggests that the exon/intron usage of the transcripts involved in key metabolic pathways significantly changes during extreme temperature conditions.