Table 3.
GO analysis of 2388 annotations; the immune-related terms have been chosen based on FDR p < 0.05.
| Biological Process | No. of Genes | Genes Involved | Raw p-Value | FDR |
|---|---|---|---|---|
| regulation of toll-like receptor 3 signaling pathway | 9 | TIRAP, F2RL1, WDFY1, FLOT1, PELI1, CAV1, TNFAIP3, Ptpn22, UBQLN1 | 6.14 × 10−05 | 7.16 × 10−04 |
| regulation of interferon-gamma secretion | 12 | Nr1h4, HMHB1, Cd160, Cd2, ZC3H12A, Ptpn22, App, Il36rn, CD244, Rasgrp1, ABL1, Lgals9 | 3.74 × 10−16 | 1.28 × 10−14 |
| response to triacyl bacterial lipopeptide | 3 | Tlr1, TLR2, Cd14 | 6.14 × 10−05 | 7.15 × 10−04 |
| type I interferon production | 5× | Trex1, myd88, Irf3, Irf7, TBK1 | 1.21 × 10−06 | 1.83 × 10−05 |
| MyD88-independent toll-like receptor signaling pathway | 32 | Cd300lf, CD14, TICAM2, PRKCE, BIRC2, TLR3, IKBKB, UBB, TANK, tlr6, Irf3, UBE2D2, CHUK, TRAF3, Irf7, UBC, Tnip3, UBE2D1, CASP8, UBA52, UBE2D3, IKBKE, IKBKG, TLR4, TBK1, RPS27A, FADD, TICAM1, LY96, RIPK1, RAB11FIP2, BIRC3 | 5.93 × 10−42 | 5.69 × 10−40 |
| toll-like receptor 2 signaling pathway | 5 | TLR2, IRAK1, RIPK2, TNIP2, PIK3AP1 | 1.60 × 10−07 | 2.73 × 10−06 |
| positive regulation of antigen processing and presentation of peptide antigen via MHC class II | 2 | TREM2, PYCARD | 1.27 × 10−03 | 1.14 × 10−02 |
| regulation of MyD88-dependent toll-like receptor signaling pathway | 4 | CD300LF, IRF7, CD300A, IRF1 | 1.27 × 10−03 | 1.14 × 10−02 |
| macrophage apoptotic process | 2 | IRF3, CTSL | 1.27 × 10−03 | 1.14 × 10−02 |
| regulation of interleukin-4 biosynthetic process | 2 | Cd86, IRF-4 | 1.27 × 10−03 | 1.14 × 10−02 |
| macrophage activation involved in immune response | 13 | TREM2, TREX1, PRKCE, IL33, TYROBP, Syk, DYSF, GRN, SUCNR1, TICAM1, LBP, SBNO2, HAVCR2 | 1.06 × 10−17 | 3.97 × 10−16 |
| regulation of interleukin-18 production | 5 | TLR9, TLR2, IL10, NLRP9, Cd84 | 4.91 × 10−07 | 7.86 × 10−06 |
| detection of diacyl bacterial lipopeptide | 2 | TLR6, TLR2 | 1.27 × 10−03 | 1.12 × 10−02 |
| interferon-gamma secretion | 9 | TCIRG1, VTCN1, LILRB1, ISG15, TRIM27, BTN3A2, GATA3, F2RL1, BTN3A1 | 1.27 × 10−12 | 3.46 × 10−11 |
| interleukin-10 secretion | 2 | ISG15, F2RL1 | 1.27 × 10−03 | 1.12 × 10−02 |
| regulation of interleukin-1 beta biosynthetic process | 6 | JAK2, AGER, IFNG, App, TYROBP, AZU1 | 1.54 × 10−08 | 2.97 × 10−07 |
| interleukin-1 beta secretion | 7 | TLR6, AIM2, CD36, TLR4, NLRC4, F2RL1, TMEM106A | 1.45 × 10−09 | 3.09 × 10−08 |
| positive regulation of interleukin-18 production | 3 | TLR9, TLR2, NLRP9 | 1.06 × 10−04 | 1.19 × 10−03 |
| regulation of interleukin-12 production | 27 | ARRB2, TLR9, AGER, FOXP1, TLR3, IRAK3, IFNG, CD36, LILRB1, TLR2, TRAF6, IL12B, SYK, RIPK2, HSPD1, THBS1, SCIMP, TLR4, RELA, IL10, cd40, HMGB1, IRF1, TLR8, Lgals9, SLAMF1, TIRAP | 4.05 × 10−29 | 2.62 × 10−27 |
| positive regulation of granzyme B production | 2 | PTPN22, CD244 | 2.10 × 10−03 | 1.75 × 10−02 |
| regulation of gamma-delta T cell differentiation | 2 | SYK, PTPRC | 3.13 × 10−03 | 2.45 × 10−02 |
| iron ion transport | 7 | TCIRG1, TFR2, TFRC, ATP6V1G2, LTF, TF, SLC11A1 | 1.53 × 10−04 | 1.66 × 10−03 |
| regulation of inflammatory response to wounding | 2 | AGER, Grn | 3.13 × 10−03 | 2.43 × 10−02 |
| positive regulation of type I interferon-mediated signaling pathway | 6 | IRF3, IRF7, WNT5A, IKBKE, TBK1, FADD | 2.26 × 10−07 | 3.79 × 10−06 |
| regulation of epithelial cell apoptotic process | 17 | ARRB2, JAK2, IL6, Il4, CD160, PDPK1, FGB, IL13, Tnf, TNFAIP3, FGA, THBS1, cd40, GATA3, TNIP2, FGG, ABL1 | 6.20 × 10−14 | 1.88 × 10−12 |
| negative regulation of inflammatory response to antigenic stimulus | 4 | FCGR2B, IL12B, NLRP6, IL10 | 9.48 × 10−05 | 1.07 × 10−03 |
| negative regulation of interferon-beta production | 4 | PYCARD, LILRB1, CACTIN, PTPRS | 1.20 × 10−04 | 1.33 × 10−03 |
| cellular response to interferon-beta | 6 | TREX1, TLR3, AIM2, IFNB, IRF1, ACOD1 | 2.80 × 10−06 | 4.02 × 10−05 |
| interleukin-12-mediated signaling pathway | 6 | JAK2, IFNG, IL12B, MIF, IL10, IL12A | 1.13 × 10−04 | 1.24 × 10−03 |
| interferon-gamma-mediated signaling pathway | 8 | JAK2, IFNGR1, IRF4, IFNG, IRF3, Ifngr2, b2m, IRF1 | 3.02 × 10−06 | 4.30 × 10−05 |
| macrophage activation involved in immune response | 50 | Csf2, SNCA, JAK2, AGER, TREM2, TREX1, ITGB2, PRKCE, FOXP1, TLR3, C1QA, TRPV1, MAPT, IFNGR1, JUN, IL33, ITGAM, IFNG, TLR6, CX3CL1, TLR2, TLR7, CRTC3, CLU, IL13, App, SLC7A2, CD93, TYROBP, Tnf, SYK, DYSF, EDN2, FPR2, SUCNR1, AIF1, JMJD6, GRN, NAMPT, TLR4, AZU1, TICAM1, Ifngr2, TLR1, LBP, TLR8, TMEM106A, SLC11A1, SBNO2, HAVCR2, C5AR1 | 1.06 × 10−17 | 3.97 × 10−16 |
| regulation of macrophage cytokine production | 7 | Irak3, CD36, LILRB1, WNT5A, CD74, TLR4, RTN4 | 6.92 × 10−08 | 1.23 × 10−06 |
| macrophage chemotaxis | 5 | CX3CL1, SFTPD, AZU1, EDN2, CCL3 | 6.62 × 10−06 | 8.87 × 10−05 |
| negative regulation of macrophage apoptotic process | 2 | CLU, LDLR | 5.72 × 10−03 | 4.13 × 10−02 |
| Total genes | 166 | |||
| immune system process | 28 | |||
| regulation of immune system process | 18 | |||