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Table 2 Core genes contributing to the differential regulation of the critical pathways between HIV, HCV mono- and co-infection identified by GSEA

From: Differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection identified by transcriptome profiling of PBMCs

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
  1. Size: Gene set size (number of genes in a particular gene set); NOM p-val: nominal p value; FDR: false discovery rate.