Table 2

Pathways discriminating patients developing delayed graft function (DGF) from those having early graft function (EGF) at the time of transplantation (T0)
Pathway Number of genes Gene symbol p value
UP-REGULATED IN DGF
NLS bearing substrate import into nucleus 13 CBLB, FYB, KPNA1, KPNA2, KPNA3, KPNA4, KPNA5, KPNA6, KPNB1, NCKIPSD, RANBP5, RERE, TRPS1 <0.001
Nuclear transport 89 AKT1, ALS2CR2, ANP32A, ATXN1, BARD1, BAT1, BCL3, BCL6, CALR, CBLB, CDH1, DDX19B, DDX25, DDX39, DUSP16, EIF5A, F2, F2R, FAF1, FLNA, FYB, GLI3, GSK3B, HNRNPA1, HRB, HTATIP2, KHDRBS1, KPNA1, KPNA2, KPNA3, KPNA4, KPNA5, KPNA6, KPNB1, LYK5, MALT1, MCM3AP, MDFI, MXI1, MYBBP1A, NCBP2, NCKIPSD, NF1, NFKBIE, NFKBIL1, NFKBIL2, NLRP12, NLRP3, NOP5/NOP58, NPM1, NUDT4, NUP107, NUP133, NUP160, NUP205, NUP214, NUP98, NUPL2, NXF5PDIA3, PPIH, PPP1R10, PTTG1IP, RAE1, RANBP2, RANBP5, RERE, RPAIN, SMAD3, SMG1, SMG5, SMG6, SMG7, TBRG1, TGFB1, TNF, TNFSF14, TNPO1, TPR, TRIP6, TRPS1, TSC1, UHMK1, UPF1, UPF2, XPO6, XPO7, ZFYVE9 0.004
Nucleocytoplasmic transport 88 AKT1, ALS2CR2, ANP32A, ATXN1, BARD1, BAT1, BCL3, BCL6, CALR, CBLB, CDH1, DDX19B, DDX25, DDX39, DUSP16, EIF5A, F2, F2R, FAF1, FLNA, FYB, GLI3, GSK3B, HNRNPA1, HRB, HTATIP2, KHDRBS1, KPNA1, KPNA2, KPNA3, KPNA4, KPNA5, KPNA6, KPNB1, LYK5, MALT1, MCM3AP, MDFI, MXI1, MYBBP1A, NCBP2, NCKIPSD, NF1, NFKBIE, NFKBIL1, NFKBIL2, NLRP12, NLRP3, NOP5/NOP58, NPM1, NUDT4, NUP107, NUP133, NUP160, NUP205, NUP214, NUP98, NUPL2, NXF5PDIA3, PPIH, PPP1R10, PTTG1IP, RAE1, RANBP2, RANBP5, RERE, RPAIN, SMAD3, SMG1, SMG5, SMG6, SMG7, TGFB1, TNF, TNFSF14, TNPO1, TPR, TRIP6, TRPS1, TSC1, UHMK1, UPF1, UPF2, XPO6, XPO7, ZFYVE9 0.004
Protein import into nucleus 48 AKT1, BCL3, BCL6, CBLB, CDH1, CEP57, F2, F2R, FAF1, FLNA, FYB, GLI3, KPNA1, KPNA2, KPNA3, KPNA4, KPNA5, KPNA6, KPNB1, MCM3AP, MDFI, MXI1, NCKIPSD, NF1, NFKBIE, NFKBIL1, NFKBIL2, NLRP12, NLRP3, NOP5/NOP58, NUP205, PDIA3, PPIH, PPP1R10, PTTG1IP, RANBP2, RANBP5, RERE, RPAIN, SMAD3, TGFB1, TNF, TNFSF14, TNPO1, TPR, TRIP6, TRPS1, ZFYVE9 0.004
Ribonucleotide metabolic process 16 ACLY, ADK, ADSS, AK5, AMPD3, C16orf7, CMPK, CTNS, CTPS, ENTPD4, FIGNL1, GUK1, NDUFS1, NUDT5, OLA1, UMPS 0.004
Nuclear import 50 AKT1, BCL3, BCL6, CBLB, CDH1, CEP57, F2, F2R, FAF1, FLNA, FYB, GLI3, HNRNPA1, HTATIP2, KPNA1, KPNA2, KPNA3, KPNA4, KPNA5, KPNA6, KPNB1, MCM3AP, MDFI, MXI1, NCKIPSD, NF1, NFKBIE, NFKBIL1, NFKBIL2, NLRP12, NLRP3, NOP5/NOP58, NUP205, PDIA3, PPIH, PPP1R10, PTTG1IP, RANBP2, RANBP5, RERE, RPAIN, SMAD3, TGFB1, TNF, TNFSF14, TNPO1, TPR, TRIP6, TRPS1, ZFYVE9 0.006
Pyrimidine nucleotide metabolic process 10 AK5, CMPK, CTPS, DCK, DCTD, ENTPD4, NT5C, NT5M, TYMP, UMPS 0.006
Macromolecule localization 237 ABCA1, ABCG1, ACHE, AGXT, AIP, AKAP10, AKT1, ALS2CR2, ANG, ANGPTL3, AP1G1, AP1GBP1, AP1M2, AP3B1, AP3D1, AP3M1, AP3S2, APBA1, APOA1, APOA2, APPBP2, ARCN1, ARFGAP3, ARFIP1, ARL4D, ATG4A, ATG4B, ATG4C, ATG4D, BACE2, BARD1, BAT1, BCL3, BCL6, BIN3, BIRC5, C3orf31, CADM1, CALR, CANX, CARD8, CBLB, CBY1, CD24, CD3G, CD74, CD81, CDC37, CDH1, CEP290, CEP57, CIDEA, CKAP5, COG2, COG3, COG7, COLQ, COX18, CRTAM, CTSA, CUTA, DDX19B, DDX25, DDX39, DERL1, DERL2, DNAJC1, DPH3, DUSP16, EGFR, EIF5A, ERCC3, ERP29, F2, F2R, FAF1, FLNA, FOXP3, FYB, GABARAP, GGA1, GGN, GLI3, GLMN, GSK3B, HNRNPA2B1, HOMER3, HPS4, HRB, ICMT, INS, KDELR1, KDELR2, KHDRBS1, KIF13B, KLHL2, KPNA1, KPNA2, KPNA3, KPNA4, KPNA5, KPNA6, KPNB1, LGTN, LMAN2L, LRP1B, LTBP2, LYK5, MAL, MCM3AP, MDFI, MFN2, MIPEP, MXI1, MYH9, MYO6, NAGPA, NCBP2, NCKIPSD, NF1, NFKBIE, NFKBIL1, NFKBIL2, NLGN1, NLRC4, NLRP12, NLRP2, NLRP3, NOD2, NOP5/NOP58, NPM1, NUDT4, NUP107, NUP133, NUP160, NUP205, NUP214, NUPL2, NXF5, OPTN, PDIA2, PDIA3, PDIA4, PEX1, PEX10, PEX12, PEX13, PEX14, PEX16, PEX19, PEX26, PEX3, PEX6, PEX7, PPIH, PPP1R10, PPT1, PPY, PTTG1IP, PYCARD, PYDC1, RAB35, RAB3GAP2, RAE1, RANBP2, RANBP5, REEP1, RERE, RPAIN, RPGR, RPL11, RTP1, RTP2, RTP3, RTP4, SCG2, SCG5, SEC23IP, SEC63, SELS, SERGEF, SHROOM2, SHR 0.008
DOWN-REGULATED IN DGF
Vasculature development 55 ACVRL1, AGGF1, AMOT, ANG, ANGPTL3, ANGPTL4, ATPIF1, BTG1, C1GALT1, CANX, CCM2, CDH13, CHRNA7, COL4A2, COL4A3, CUL7, EGF, EGFL7, EMCN, EPGN, ERAP1, FOXC2, FOXO4, GLMN, HTATIP2, IL17F, IL18, IL8, MYH9, NCL, NF1, NOTCH4, NPPB, NPR1, PDPN, PF4, PLG, PML, PROK2, RASA1, RHOB, RNH1, ROBO4, RUNX1, SCG2, SERPINF1, SHH, SPHK1, SPINK5, STAB1, TGFB2, THY1, TNFSF12, TNNI3, VEGFA 0.005
Activation of protein kinase activity 28 ALS2CR2, ANG, AZU1, CARD10, CARTPT, CCDC88A, CHRM1, EDN2, GADD45B, GADD45G, GAP43, IRAK1, LYK5, MALT1, MAP3K13, MAP3K4, MAP3K7, MAP3K7IP1, PARD3, PICK1, PPAP2A, PRKD3, TAOK2, TNFSF15, TRAF2, TRAF6, TRAF7, ZAK 0.006
Regulation of angiogenesis 26 AGGF1, AMOT, ANGPTL3, ANGPTL4, BTG1, CHRNA7, COL4A2, COL4A3, FOXO4, HTATIP2, IL17F, NF1, NPPB, NPR1, PF4, PLG, PML, RHOB, RNH1, RUNX1, SERPINF1, SPHK1, SPINK5, STAB1, TNFSF12, TNNI3 0.006
G PROTEIN Signaling coupled to IP3 phospholipase C activating 45 AGTR1, ANG, AVPR1A, AVPR1B, AZU1, C5AR1, CALCA, CCKAR, CCKBR, CHRM1, CHRM2, DRD1, DRD2, EDG2, EDG4, EDG6, EDN2, EDNRA, EDNRB, EGFR, F2RL3, GAP43, GNA15, GNAQ, GRM5, HOMER1, HRH1, HTR2B, IL8RB, LTB4R, MC3R, NMBR, NMUR1, NMUR2, P2RY1, P2RY11, P2RY2, P2RY4, P2RY6, PARD3, PICK1, PLCB2, PPAP2A, PRKD3, TACR1 0.007
Phosphoinositide mediated signaling 48 AGTR1, ANG, AVPR1A, AVPR1B, AZU1, C5AR1, CALCA, CCKAR, CCKBR, CHRM1, CHRM2, DRD1, DRD2, EDG2, EDG4, EDG6, EDN2, EDNRA, EDNRB, EGFR, F2RL3, GAP43, GNA15, GNAQ, GRM5, HOMER1, HRH1, HTR2B, IL8RB, LTB4R, MC3R, NMBR, NMUR1, NMUR2, P2RY1, P2RY11, P2RY2, P2RY4, P2RY6, PARD3, PICK1, PLCB2, PLCE1, PLCH1, PPAP2A, PRKD3, PTAFR, TACR1 0.007
Phospholipase C activation 14 ANG, AVPR1A, AVPR1B, C5AR1, CCKBR, EDG2, EDG4, EDG6, EDNRA, EGFR, GNA15, GNAQ, NMUR1, PLCB2 0.008
Regulation of myeloid cell differentiation 19 ACIN1, ACVR1B, ACVR2A, CALCA, CARTPT, CDK6, ETS1, FOXO3, IL4, INHA, INHBA, LDB1, MAFB, PF4, RUNX1, SCIN, SPI1, ZBTB16, ZNF675 0.009

P value, calculated by using an empirical phenotype-based permutation test procedure, represents the degree to which the pathway is over-represented at the extremes (top or bottom) of the entire ranked list of the total 825 pathways analyzed after comparison DGF versus EGF (for details about the statistical methodology see Subramanian et al. [22]).

Zaza et al.

Zaza et al. BMC Medical Genomics 2014 7:14   doi:10.1186/1755-8794-7-14

Open Data