Table 2 Enriched biological processes and pathways from upregulated genes. Results from gene enrichment analysis with Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). All differentially expressed genes with FDR < 0.01 and positive fold change were included in the analysis. Percent is the percentage of differentially expressed genes belonging to the pathway. P value is the significance level of the enrichment. Genes are the gene symbol of the differentially expressed genes belonging to the pathway. FDR is the significance level after correction for multiple testing with false discovery rate
Category | Term | Percent | P value | Genes | FDR |
|---|---|---|---|---|---|
Upregulated GO terms (top 3) | |||||
BIOLOGICAL PROCESS | Adaptive immune response | 11% | 8.01E-16 | EOMES, TRAT1, SH2D1A, TARM1, CAMK4, ZNF683, ZAP70, KLRD1, CD3D, CD3E, LAX1, CD3G, ITK, SKAP1, CD247, JCHAIN, THEMIS, CD6, CD7, CD8A, CD8B, TXK, LAG3 | 9.88E-13 |
BIOLOGICAL PROCESS | T cell activation | 7% | 1.45E-14 | DPP4, CD28, NLRC3, RASGRP1, ZAP70, CD2, CD3E, CD3G, ITK, CD7, CD8A, LAG3, CD8B, LY9 | 8.98E-12 |
BIOLOGICAL PROCESS | T cell receptor signaling pathway | 8% | 4.45E-14 | GATA3, CD28, ZNF683, ZAP70, BTN3A3, CD3D, CD3E, CD3G, ITK, PLCG1, CD247, SKAP1, THEMIS, LCK, CD8A, CD8B, TXK | 1.83E-11 |
Upregulated KEGG pathways (top 3) | |||||
PATHWAY | T cell receptor signaling pathway | 7% | 6.45E-10 | NFATC2, CD28, RASGRP1, ZAP70, CARD11, CD3D, CD3E, CD3G, ITK, PLCG1, CD247, LCK, CD8A, CD8B | 1.20E-07 |
PATHWAY | Th1 and Th2 cell differentiation | 6% | 1.44E-09 | RUNX3, GATA3, NFATC2, IL2RB, ZAP70, CD3D, CD3E, CD3G, PLCG1, CD247, STAT4, TBX21, LCK | 1.34E-07 |
PATHWAY | Th17 cell differentiation | 6% | 9.73E-09 | GATA3, NFATC2, IL2RB, ZAP70, RORA, RORC, CD3D, CD3E, CD3G, PLCG1, CD247, TBX21, LCK | 6.04E-07 |