A computational method for differential expression analysis on Thermococcus Onnurineus RNA-Seq data

Abstract

Next-generation sequencing RNA-Seq technology is a powerful tool that creates new possibilities for transcriptome analysis. In our study, the RNA-Seq method was applied to analyze global changes in certain transfer time from adaptation evolution of Thermococcus Onnurineus. We evaluate the performance of two of the most frequently used software tools: DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and unbalanced sequencing depth within transfer times. And taking into account the most restrictive criteria, gene clusters differentially expressed between each transfer times were identified. The functions of the majority of selected genes were consistent with arCOG (archaea Clusters of Orthologus Groups) that classify genes and provide improved functional annotation specific to archaeal genomes. Overall, we provide a pipeline of each step of RNA-seq analysis using bioinformatic approach. We then summarize and discuss the biological insights obtained from the RNA-seq studies in a Thermococcus Onnurineus.ution of Thermococcus Onnurineus. We evaluate the performance of two of the most frequently used software tools: DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and unbalanced sequencing depth within transfer times. And taking into account the most restrictive criteria, gene clusters differentially expressed between each transfer times were identified. The functions of the majority of selected genes were consistent with arCOG (archaea Clusters of Orthologus Groups) that classify genes and provide improved functional annotation specific to archaeal genomes. Overall, we provide a pipeline of each step of RNA-seq analysis using bioinformatic approach. We then summarize and discuss the biological insights obtained from the RNA-seq studies in a Thermococcus Onnurineus.