GO analysis and KEGG analysis
Gene Ontology (GO) is an internationally standardized gene function
classification system that comprehensively describes the properties of
any biological gene and its products by using a dynamically updated
controlled vocabulary and strictly defined concepts. In this study,
significant DE genes between different groups of samples were subjected
to GO terms for the three parts, molecular function (MF), biological
process (BP), and cell component(CC) through the standard vocabulary
provided by Gene Ontology (http://www.geneontology.org).) enrichment
analysis to calculate the hypergeometric distribution relationship
between DE genes and several specific branches in the GO classification
to explore which gene function changes may be related to DE genes in
different samples. The Kyoto Encyclopedia of Genes and Genomes (KEGG) is
a database that systematically analyzes gene functions, links genomic
information and functional information, and the pathway database is the
most widely used. Pathway analysis of DE genes was used to find the
metabolic pathways enriched in DE genes, and to clarify which metabolic
pathways may lead to the differential expression of genes between
different groups of samples. GO analysis and pathway analysis utilized
hypergeometric tests to calculate P-values, which represent the
importance of condition-related pathways or GO terms enriched in DE
genes. The lower the P value, the more significant the GO term or
pathway (recommended cutoff value 0.05).