RNA-Seq of P. pastoris
Differential expression analysis was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate. To assess the transcriptome differences between mutant and parent strain, differentially expressed genes (DEGs) among various samples were compared. The data was analyzed by the DEGseq package in R software. The resulting P-values were adjusted using Benjamini and Hochbergs approach for controlling the false discovery rate. To narrow the research scope, a two-fold or greater change between two samples in expression (fold change (FC), |log2FC| 1) and padj 0.05 was determined as significant.