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Functional and pathway enrichment analysis

SH Sen-Yuan Hong
QX Qi-Dong Xia
JX Jin-Zhou Xu
CL Chen-Qian Liu
JS Jian-Xuan Sun
YX Yang Xun
SW Shao-Gang Wang
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Following the steps above, two gene lists were obtained, one for the DEGs, the other one for the most KSD-related gene modules. Subsequently, the intersection of these two gene lists was taken to identify the KSD-related genes and a Venn diagram was constructed via the “VennDiagram” package (version 1.7.1). The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis were conducted to define the potential functions and pathways between these genes using the “org.Hs.eg.db” (version 3.10.0), “clusterProfiler” (version 3.14.3), “enrichplot” (version 1.6.1), and the “ggplot2” (version 3.3.5) packages in the R software [17, 18]. The GO terms of biological processes (BP), molecular functions (MF), and cellular components (CC) were respectively evaluated. Significant results were determined under the condition of adjusted P value < 0.05. The top ten terms were visualized if there were more than ten terms.

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