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Gene Set Variation Analysis (GSVA) and GO/KEGG Annotation

YP Yimin Pan
KX Kai Xiao
YL Yue Li
YL Yuzhe Li
QL Qing Liu
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We downloaded KEGG pathway gene sets, named C2 collection, from the molecular signature database (MsigDB) (https://www.gsea-msigdb.org/gsea/msigdb) for GSVA inputting.29 Next, we performed GSVA using R package “GSVA” on each subgroup to compare relative enrichment level of immune-related KEGG pathways (37). Furthermore, differentially expressed genes (DEGs) among subgroups of distinct m6A modification patterns were utilized for GO and KEGG enrichment analysis based on R package “ClusterProfiler”, which uses hypergeometric distribution tests to annotate DEGs (38).

Copyright and License information:  ©2021 Pan, Xiao, Li, Li and Liu
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