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Construction of the Protein-Protein Interaction (PPI) Network and GO/KEGG Enrichment Analysis

YW Yan Wang
LQ Liwei Qiu
YC Yu Chen
XZ Xia Zhang
PY Peng Yang
FX Feng Xu
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Top 300 gene pairs in the two modules screened by WGCNA with the highest GS in each module were selected to construct the PPI network using the “Cytoscape” software (Version 3.8.0). The immune infiltration key genes finally screened were analyzed by inputting the names into the “STRING” website (https://STRING-db.org/) (30). The minimum required interaction score was set as 0.4 during the STRING PPI analysis, while the max number of interactions was set as no more than 10, the line color was set to indicate the type of interaction and the node color was set to indicate the gene ontology (GO) terms to which the gene belongs. The “ClusterProfiler” R package was used to perform GO and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis (31). Three aspects were mainly investigated by the GO analysis: biological process, molecular function, and cellular component.

Copyright and License information:  ©2021 Wang, Qiu, Chen, Zhang, Yang and Xu
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