Differential expression analysis and Functional enrichment
To identify DEGs (differential expression genes) between two different
samples, the expression level of each transcript was calculated
according to the fragments per kilobase of exon per million mapped reads
(FRKM) method. RSEM (http:// deweylab. biostat.wisc.edu/rsem/) (B. Li &
Dewey, 2011) was used to quantify gene and isoform
abundances. R statistical package
software EdgeR (Empirical analysis of Digital Gene Expression in
R,http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html)
(Robinson, McCarthy, & Smyth, 2010) was utilized
for differential expression
analysis. In addition, functional-enrichment analysis include- ing GO
and KEGG were performed to identify which DEGs were significantly
enriched in GO terms and metabolic pathways at Bonferroni-corrected
P-value ≤0.05 compared with the whole-transcriptome background. GO
functional enrichment and KEGG pathway analysis were carried out by
Goatools (https://github.com/tanghaibao/ Goatools) and KOBAS
(http://kobas.cbi.pku.edu.cn/home.do) (Xie et al., 2011).