Table 3 Enriched biological processes and pathways from downregulated genes. Results from gene enrichment analysis with Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). All differentially expressed genes with a cut off FDR < 0.01 and negative 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 |
|---|---|---|---|---|---|
Downregulated GO terms (significant) | |||||
Biological process | Apoptotic process | 12% | 7.82E + 08 | IL1B, RNF144B, STK3, DRAM1, CASP5, MAP2K6, DDIT4, PLK3, GADD45Α, PLSCR1, MARCKS, HIP1, KLLN, BMX, BCL2A1, NLRP3, KIF1B, NFKBIA, TNFAIP3, TNFRSF10D, NR2E1, NAIP | 0.001037 |
Biological process | Positive regulation of T helper 1 cell cytokine production | 2% | 5.62E + 10 | ARID5A, IL1B, IL18R1, IL1R1 | 0.03726 |
Downregulated KEGG pathways (significant) | |||||
PATHWAY | NF-kappa B signaling pathway | 5% | 7.17E-06 | IL1B, TNFSF13B, IL1R1, BCL2A1, CXCL1, ICAM1, TNFAIP3, NFKBIA, TRIM25, GADD45Α | 0.001147 |