GO Enrichment Analysis of Differentially Expressed Genes

For GO enrichment analysis on the biological processes domain, the hypergeometric test in the GOstats package (version 2.56.0) was applied. The analysis was restricted to gene sets containing 5–1,000 genes. Significant pathways were filtered by applying P value <0.05 and gene count/term >10. Further selection of relevant GO terms was based on sorting terms on their OddsRatios (the ratio of a GO term in the differently expressed genes list to the occurrence of this GO term in a universal gene list, obtained from org.Mm.eg.db [version 3.13.0]). In addition, GO term results were screened for enrichment of terms related to immune regulation. Selected top pathways were visualized using ggplot2 (version 3.3.5).
A web application for data searching and visualization was generated using the shiny package of Rstudio (https://shiny.rstudio.com), and the package ShinyCell for database creation (Ouyang et al., 2021 (link)).