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Differentially expressed genes (DEGs) and their functional enrichment analysis

LL Linhui Lai
YL Yaohang Long
ML Meng Luo
BT Bo Tu
ZW Zailin Wu
JL Jinling Liu
ZW Zhixian Wan
GW Guangyin Wang
XW Xianyi Wang
HL Hongmei Liu
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The expression level of genes was estimated by counting the sequences located in the genomic region or gene exon region, and functional annotation of transcripts was performed using seven databases, including Nr28, Pfam29, Uniprot, KEGG30, Gene Ontology (GO)31, KOG/COG32, and PATHWAY30. The number of reads that were mapped to each transcript in all samples was obtained using RSEM33, and FPKM conversion was performed. Double-ended sequences from the same fragment were counted as one fragment, and the expression levels of genes and transcripts were determined. The quantitative expression levels of the genes in each sample were used for differential expression analysis using DESeq2 software34. The screening threshold was Padj < 0.05 and |log2FoldChange|> 1, and the main metabolic pathways or signaling pathways associated with the DEGs were determined.

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