Differential alternative splicing patterns with differential expression to computationally extract plant molecular pathways

Alternative splicing (AS) produces multiple messenger RNAs by combining different regions of the precursor transcript to produce diversity in gene products. Under stress conditions, many genes produce transcripts that are not otherwise produced during normal conditions. Plant growth and development are extensively affected by environmental stresses. In this study, we combine Differentially Alternatively Spliced Genes (DASGs) 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 extracted several molecular pathways associated with temperature stress-response using genes that are either differentially alternatively spliced or differentially expressed. 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. 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 heat stress conditions.