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Gene Set Enrichment Analysis

SY Sihui Yu
XL Xi Li
JZ Jiawen Zhang
SW Sufang Wu
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To evaluate the infiltration of immune cells, we performed single-sample gene set enrichment analysis (ssGSEA) using the marker gene set of different immune cells with R package GSVA, which can calculate the normalized enrichment score of immune cell types. Furthermore, GSEA was also conducted with Bioconductor packages clusterProfiler and msigdbr, which can identify hallmark gene sets or immunologic signatures that are activated or suppressed according to their correlation with Immunoscore and immune-related genes. Moreover, we evaluated the correlation between this Immunoscore and specific phenotypes such as epithelial–mesenchymal transition (EMT) and hypoxia via the ssGSEA method. Related gene sets were downloaded from the Molecular Signature Database (MSigDB) via Gene Set Enrichment Analysis tool (GSEA, http://software.broadinstitute.org/gsea/index.jsp).

Copyright and License information:  ©2021 Yu, Li, Zhang and Wu
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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