*4.4. Di*ff*erential Gene Expression Analysis*

The gene expression levels of all samples were estimated by RSEM version 1.2.15 [56], and the bowtie2 parameter setting mismatch was 0. The R Bioconductor package edgeR [57] was used to identify differentially expressed genes (DEGs) in two samples. DEGs were used for KEGG and GO enrichment analyses, which were performed using the KOBAS version 2.0.12 with default settings and Goatools version 0.5.9 (https://github.com/tanghaibao/Goatools) [58,59].
