Table 5.
The ten immune-related pathways significantly up-regulated in viremic patients versus BDLs
| Gene set name | GS size | NOM p-val | FDR | Core enrichment genes contributing to the pathway enrichment |
|---|---|---|---|---|
| KEGG_INTESTINAL_IMMUNE_ NETWORK_FOR_IGA_PRODUCTION |
48 |
0.00 |
0.014 |
HLA-DRB5, HLA-DRB1, LTBR, ITGB7, CD40, TNFSF13, HLA-DOA, CCR9 |
| KEGG_ANTIGEN_PROCESSING_ AND_PRESENTATION |
88 |
0.00 |
0.016 |
HLA-DRB5, HLA-DRB1, CD4, HLA-C, IFI30, NFYC, TAPBP, HSPA1B, CD74, HLA-DOA, TAP2, HLA-E, PDIA3, PSME1, HSP90AB1, RFX5, CALR, KIR2DS5, HLA-F |
| KEGG_ADHERENS_JUNCTION |
73 |
0.00 |
0.016 |
ACTN4, EP300, TCF7L2, PTPN6, IQGAP1, CSNK2B, SRC, FYN, RAC1, CSNK2A2, WASF2, PVRL4, PTPN1, BAIAP2, CTNNB1, PVRL2, ACTB |
| KEGG_HEMATOPOIETIC_CELL_ LINEAGE |
87 |
0.00 |
0.016 |
HLA-DRB5, HLA-DRB1, FLT3LG, CD4, TNF, CD37, IL1B, CD9, CD36, EPOR, ANPEP, CD1A, CD19, ITGA2B, FCER2, CD1D, FCGR1A |
| KEGG_CELL_ADHESION_ MOLECULES_CAMS |
134 |
0.00 |
0.017 |
HLA-DRB5, HLA-DRB1, ITGAL, ITGB7, CD40, CD4, HLA-C, SELL, PECAM1, SPN, HLA-DOA, ICAM2, HLA-E, ICAM3, CLDN3, PVRL2, JAM3, HLA-F, CD28, CLDN18, PVR, CD99, ICOS, PDCD1LG2, CD80, CLDN5, NEO1, PDCD1, ITGAM, PTPRF, HLA-DRA, CNTN2, HLA-B, CD58, NLGN3, CTLA4, ITGA4, SIGLEC1 |
| KEGG_LYSOSOME |
119 |
0.00 |
0.023 |
ARSA, ACP2, SGSH, CTSZ, MCOLN1, CTSA, CTSD, SORT1, FUCA1, MAN2B1, GBA, TCIRG1, NAPSA, IDUA, NAGPA, M6PR, ATP6V0D1, NEU1, ACP5, GGA1, LAPTM5, CD63, AP1S1, AP3B1, AP3D1, NAGA, CLN3, IDS, TPP1 |
| KEGG_NEUROTROPHIN_ SIGNALING_PATHWAY |
125 |
0.00 |
0.025 |
YWHAE, ARHGDIA, RPS6KA4, SH2B2, MAP2K2, MAPKAPK2, MAPK7, SORT1, CSK, RELA, SHC1, PIK3CG, KIDINS220, CRK, IRAK1, BAX, SH2B3, RAC1, MAP2K5, AKT1, CALM1, MAP3K3, MAPK9, ABL1, RPS6KA3, SH2B1, IRS1, RAF1, HRAS, MAPK14 |
| KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS |
92 |
0.00 |
0.029 |
MARCKSL1, NCF1, PIP5K1C, VASP, HCK, PIK3CG, DNM2, CRK, SYK, ARPC4, ARPC1A, SPHK1, RAC1, ARPC5L, LYN, AKT1, WASF2, VAV1, ARPC1B, LOC653888, FCGR1A, RAF1, PRKCA, GSN, DNM1, PAK1, VAV2, CFL1, AKT2 |
| KEGG_CHEMOKINE_SIGNALING_ PATHWAY |
185 |
0.00 |
0.038 |
PLCB2, NCF1, GNB2, ELMO1, CX3CR1, GRK6, PPBP, GNAI2, CSK, GNB4, RELA, SHC1, HCK, ARRB1, PIK3CG, CRK, RASGRP2, CCR1, GNGT2, GNG5, GNG3, STAT5B, RAC1, LYN, AKT1, CCL2, JAK2, VAV1, GNG8, CCR2, CCR9, PRKACA, CCR7, XCR1, TIAM2, GNG12, RAF1, ARRB2, HRAS, CXCR5, PTK2B, PAK1, CCR3, VAV2 |
| KEGG_COMPLEMENT_AND_ COAGULATION_CASCADES | 68 | 0.01 | 0.038 | C1QB, C1QC, C5AR1, SERPING1, C1QA, C2, KLKB1, C3AR1, THBD, SERPINA1, C4A, SERPINA5 |
GS size: Gene set size (number of genes in a particular gene set); NOM p-val: nominal p value; FDR: false discovery rate.