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GO, KEGG, GSEA, Venn diagram, and heatmap analysis

YC Yan-Hong Cui
SY Seungwon Yang
JW Jiangbo Wei
CS Christopher R. Shea
WZ Wen Zhong
FW Fang Wang
PS Palak Shah
MK Muhammad G. Kibriya
XC Xiaolong Cui
HA Habibul Ahsan
CH Chuan He
YH Yu-Ying He
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To understand the function of the differentially expressed genes, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using Metascape and Networkanalyst. P < 0.05 was considered to indicate a significantly enriched DEG. Metascape (https://metascape.org/) is a free gene annotation and analysis resource that helps biologists make sense of one or multiple gene lists67. Gene Set Enrichment Analysis (GSEA) and the heatmap of relative significant genes were performed using Networkanalyst and WebGestalt (http://www.webgestalt.org/106. Venn diagrams were generated using the following web tool: https://bioinfogp.cnb.csic.es/tools/venny/index.html107, with the following statistical cutoff: p-value <0.05 in combination with log2 (fold change) >0.5 or < −0.5 for human cuSCC/CHR and mouse cuSCC/NS (GSE84292, GSE84293), or log2 (TPM) > 0.5 or < −0.5 for As-T cells/Control cells.

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