Table 2 Core genes contributing to the differential regulation of the critical pathways between HIV, HCV mono- and co-infection identified by GSEA
Pathway | Comparison | Direction | Size | NOM p-val | FDR | Core enrichment genes |
|---|---|---|---|---|---|---|
KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY | HIVvsHH | HH-up | 134 | 0.000 | 0.018 | HLA-G, SHC1, TNFSF10, VAV1, MAP2K2, RAC2, PAK1, KLRD1, VAV3, KLRC2, LCK, PLCG1, PIK3CD, KIR2DS1, PTPN6, PPP3CB, SH2D1B, GZMB, FYN, ICAM2, ITGAL, NCR3, KIR2DL3, ZAP70, MAPK1, PTK2B, PRKCA, NFATC3, KIR2DL4, IFNAR1, PPP3CA, KIR3DL2, KIR2DS5, KIR2DL5A, KIR3DL1, KIR2DL1, PRF1 |
KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY | HCVvsHH | HH-up | 134 | 0.000 | 0.000 | ZAP70, PLCG1, SHC3, ICAM2, PIK3R2, HCST, SH2D1A, KLRC1, SH2D1B, KIR2DS4, KIR2DS1, NCR3, KLRC2, KIR2DS3, PTK2B, NCR1, NFATC3, ITGAL, MAPK1, TNFSF10, PTPN6, FASLG, IFNG, CD244, KIR2DL4, IFNAR1, KIR2DS5, KIR2DL3, HLA-C, VAV3, KLRD1, KLRC3, GZMB, KIR3DL1, KIR3DL2, KIR2DL5A, PRF1, KIR2DL1 |
KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY | HIVvsHCV | HIV-up | 134 | 0.000 | 0.019 | IFNG, HLA-C, KLRC3, IFNB1, TNF, KLRD1, CD244, FASLG, GZMB, VAV3, SH3BP2, SH2D1A, NCR1, CASP3, GRB2, KIR2DS4, HRAS, TNFSF10, KIR3DL2, FAS, HCST, KIR2DL5A, PIK3R2, KRAS, IFNGR2, KIR2DL3, VAV2, SOS2, BID, ULBP1, KIR2DL1, KIR2DS3 |
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION | HIVvsHH | HIV-up | 262 | 0.000 | 0.028 | IL6, OSM, CCL3L1, CCL3, IL1B, CCL2, IL8, CXCL2, CCL3L3, TNF, TNFSF9, IFNG, IL1A, CCL20, CCL4L1, CXCL16, CLCF1, IFNB1, VEGFA, CCL28, CCL7, CCL4L2, IL12A, CXCL1, IL23A, CD70, CXCR3, TNFRSF21, TNFRSF9, IL28RA, CD40, TNFRSF13C, IL21R, IFNGR1, TNFRSF4, CD40LG, IL12RB1, CXCR4, IL15, IFNGR2, LTA, EPOR, CXCL9, FAS, CXCR5, IL10RA, FLT4, PRLR, CCL8 |
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION | HCVvsHH | HCV-up | 262 | 0.000 | 0.003 | OSM, IL6, CXCL2, CCL20, IL1B, IL8, CD40LG, IL1A, VEGFA, CCL3, CCL3L1, CCR4, CXCL1, CXCR5, IL23A, CCL3L3, CXCL16, CXCR4, TNFSF9, TNFRSF4, PRLR, TNFRSF13C, KIT, CXCR3, CXCL6, XCR1, CXCR6, LTA, IL10RA, IFNK, CX3CL1, IL1R2, TNFRSF25, IFNGR1, CLCF1, TNFRSF10A, TNF, CCL28, IL2RA, IL28A, TGFBR2, IL6ST, TGFB3, TNFSF13, FLT3LG, IFNA10, TNFRSF21, CD70, PDGFRA, IL24, CXCL13, TSLP, TNFRSF10C, TNFRSF9, PDGFB, TGFB2, IFNA4, TNFSF4, CCR3, XCL2, EDA, IFNA8, IL7R, IL13RA1, IL4R, CCL7, IFNAR2, TNFSF12 |
KEGG_CELL_CYCLE | HIVvsHCV | HIV-up | 115 | 0.000 | 0.016 | PTTG1, MCM2, GADD45G, TFDP2, CDC20, CCNE2, CDC16, CDK7, CCNB2, FZR1, MCM4, CDK6, E2F5, WEE1, CCNE1, ANAPC10, TTK, CDC23, ANAPC4, E2F3, MDM2, CDKN2C, BUB1, CDKN2A, CCND1, MAD2L1, ANAPC11, MCM7, YWHAQ, CDC27, CHEK1, TGFB1, GADD45B |
KEGG_WNT_SIGNALING_PATHWAY | HIVvsHCV | HCV-up | 148 | 0.000 | 0.006 | WNT5B, NFAT5, CSNK1A1L, CTNNBIP1, CSNK2A2, CUL1, CAMK2A, PLCB1, WNT10A, FZD7, PPP3R1, EP300, PPP3CB, NLK, FOSL1, LRP5, FBXW11, SMAD3, PPP2R1A, DAAM1, TBL1XR1, CAMK2G, DVL2, PLCB2, JUN, PPP3CA, PRICKLE2, SIAH1, TCF7, FZD2, LEF1, AXIN2, PPARD, PRKCA, PRKACG, WNT7A |
KEGG_P53_SIGNALING_PATHWAY | HIVvsHH | HIV-up | 67 | 0.004 | 0.029 | SESN3, CDKN1A, GADD45A, THBS1, PMAIP1, CCNG2, SESN1, CASP9, CCNE1, CCND1, GADD45B, CASP8, CHEK1, CCNE2, CCNB2, FAS, MDM2, MDM4, BID, TP53I3, EI24, CDKN2A, SESN2, RCHY1, SERPINE1, CD82 |
KEGG_RENAL_CELL_CARCINOMA | HCVvsHH | HCV-up | 70 | 0.000 | 0.036 | JUN, VEGFA, HIF1A, EGLN1, GRB2, RAF1, EPAS1, SLC2A1, TGFB3, PIK3CA, NRAS, MAPK3, RAPGEF1, CUL2, PDGFB, TGFB2, KRAS, CREBBP |