Table 3

Pathways discriminating patients developing delayed graft function (DGF) from those having early graft function (EGF) 24 hours after transplantation (T24)
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
Regulation of small GTpase mediated signal transduction 24 ABRA, ALS2, ARF6, ARHGAP27, CDC42BPA, CDC42BPB, CDC42BPG, CENTD2, CENTD3, DMPK, FGD1, FGD2, FGD3, FGD4, FGD5, FGD6, MFN2, NF1, NOTCH2, PLCE1, RAC1, RALBP1, RASGRP4, TSC1 0.005
RNA 3 end processing 10 CPSF1, CPSF3, CSTF1, CSTF2, CSTF3, GRSF1, NCBP1, PABPC1, SLBP, TRNT1 0.006
Regulation of RAS protein signal transduction 19 ABRA, ALS2, ARF6, ARHGAP27, CENTD2, CENTD3, FGD1, FGD2, FGD3, FGD4, FGD5, FGD6, MFN2, NF1, NOTCH2, PLCE1, RAC1, RALBP1, RASGRP4, TSC1 0.009
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 0.009
DOWN-REGULATED IN DGF
Positive regulation of epithelial cell proliferation 10 EGFR, EPGN, ERBB2, FGF10, LAMA1, LAMB1, LAMC1, NME1, NME2, TGFA 0.003
Rhythmic process 29 AANAT, ARNTL, BMPR1B, CARTPT, CLOCK, CRY1, EGR3, EIF2B2, EIF2B4, EIF2B5, ENOX2, EREG, FOXL2, HEBP1, HTR7, MTNR1A, OPN4, PER1, PER2, PTGDS, SOD1, SPRR2A, SPRR2B, SPRR2C, SPRR2D, SPRR2E, SPRR2F, SPRR2G, TIMELESS 0.004
Negative regulation of translation 23 APBB1, BCL3, EIF2AK1, EIF2AK3, EIF4A3, ELA2, FOXP3, FURIN, GHRL, GHSR, IL10, IL6, INHA, INHBA, INHBB, NDUFA13, NLRP12, PAIP2, PAIP2B, PRG3, SFTPD, SIGIRR, TSC1 0.006
Keratinocyte differentiation 15 ANXA1, CSTA, DSP, EREG, EVPL, IL20, IVL, LOR, NME2, SCEL, SPRR1A, SPRR1B, TGM1, TGM3, TXNIP 0.006
Negative regulation of cytokine biosynthetic process 12 BCL3, ELA2, FOXP3, GHRL, GHSR, IL6, INHA, INHBA, INHBB, NLRP12, SFTPD, SIGIRR 0.008
Negative regulation of biosynthetic process 30 APBB1, BACE2, BCL3, BRCA1, EIF2AK1, EIF2AK3, EIF4A3, ELA2, FOXP3, FURIN, GCK, GHRL, GHSR, GLA, GRM8, IL10, IL6, INHA, INHBA, INHBB, NDUFA13, NLRP12, PAIP2, PAIP2B, PDZD3, PRG3, SFTPD, SIGIRR, SOD1, TSC1 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

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