Table 2

Summary of the DAVID pathway analysis results in the five time windows

Time windowPathway term (DAVID)FDR (%)P valueGenes
Before seroconversionhsa03010:Ribosome8.840.011911RPL26, RPS27L, RSL24D1
At seroconversionNo pathways
6–18 months after seroconversionhsa04610:Complement and coagulation cascades0.490.000477C3AR1, F5, SERPING1, C4BPA, C2, CFD
hsa03010:Ribosome0.030.000024RPL17, MRPL13, RPL7, RPL31, RPS3A, RPL9, RPL26, RPS15A, RPS27L, RPL39, RPS23
REACT_17015:Metabolism of proteins0.190.000210RPL17, RPL26, VBP1, RPS15A, RPL39, PIGK, PIGF, RPL7, RPS3A, RPL31, RPL9, PFDN5, RPS14, DPM1, RPS23, PIGA
REACT_1762:3′-UTR-mediated translational regulation1.060.001189RPL17, RPL7, RPL31, RPS3A, RPL9, RPS14, RPL26, RPS15A, RPL39, RPS23
h_DNAfragmentPathway:Apoptotic DNA fragmentation and tissue homeostasis1.480.001414HMGB1, HMGB2, CASP3, TOP2A
REACT_6167:Influenza infection4.210.004784RPL17, RPL7, RPL31, RPS3A, RPL9, RPS14, RPL26, RPS15A, RPL39, RPS23, SNRPG
hsa05012:Parkinson's disease9.000.008457NDUFA4, CASP3, COX7A2, NDUFS4, UBE2J1, COX7C, NDUFA1, UQCRQ, COX6C
1 to 2 years before T1D diagnosishsa05332:Graft-versus-host disease0.730.000710PRF1, HLA-A, HLA-C, KIR2DL3, HLA-DQA1
hsa05330:Allograft rejection6.360.006311PRF1, HLA-A, HLA-C, HLA-DQA1
REACT_6900:Signaling in immune system5.480.007180SELP, LY96, HLA-A, HLA-C, TLR5, C2, KIR2DL3, PROS1, HLA-DQA1
hsa04940:Type I diabetes mellitus9.630.009703PRF1, HLA-A, HLA-C, HLA-DQA1
hsa03010:Ribosome0.000.000002RPL36A, MRPL13, RPL31, RPS3A, RPL9, RPL26, RPS15A, RPS27L, RPL39, RPS23
REACT_1762:3′-UTR-mediated translational regulation0.440.000519RPL36A, RPL31, RPS3A, RPL9, RPL26, RPS15A, RPL39, RPS23
REACT_6167:Influenza infection0.850.001011RPL36A, RPL31, RPS3A, RPL9, RPL26, RPS15A, RPL39, EIF2AK2, RPS23
REACT_17015:Metabolism of proteins1.730.002063RPL36A, RPL31, RPS3A, RPL9, RPL26, RPS15A, RPL39, PROS1, RPS23, PIGA
REACT_6900:Signaling in immune system3.360.004040THBD, LY96, CD160, C1R, TREM1, KIR2DL3, CFD, KLRD1, PROS1, HLA-DOB, TLR8
At T1D diagnosishsa05332:Graft-versus-host disease0.160.000178HLA-A, GZMB, HLA-C, KLRD1
hsa05330:Allograft rejection4.250.004829HLA-A, GZMB, HLA-C
hsa04650:Natural killer cell mediated cytotoxicity5.530.006321HLA-A, GZMB, HLA-C, KLRD1
hsa04940:Type I diabetes mellitus5.720.006533HLA-A, GZMB, HLA-C
hsa05320:Autoimmune thyroid disease8.240.009527HLA-A, GZMB, HLA-C
hsa03010:Ribosome0.030.000027RPS26, RPL31, RPL9, RPL26, RPS15A, RSL24D1, RPL39, RPS23
hsa05310:Asthma0.210.000206FCER1A, HLA-DRB4, MS4A2, HLA-DOB, HLA-DQA1
hsa05330:Allograft rejection0.480.000484HLA-A, HLA-DRB4, HLA-C, HLA-DOB, HLA-DQA1
REACT_1762:3′-UTR-mediated translational regulation0.370.000493RPS26, RPL31, RPL9, RPL26, RPS15A, RPL39, RPS23
hsa05332:Graft-versus-host disease0.660.000661HLA-A, HLA-DRB4, HLA-C, HLA-DOB, HLA-DQA1
hsa04940:Type I diabetes mellitus0.870.000878HLA-A, HLA-DRB4, HLA-C, HLA-DOB, HLA-DQA1
hsa05320:Autoimmune thyroid disease1.810.001830HLA-A, HLA-DRB4, HLA-C, HLA-DOB, HLA-DQA1
REACT_6167:Influenza infection2.610.003467RPS26, RPL31, RPL9, RPL26, RPS15A, RPL39, RPS23
hsa05416:Viral myocarditis5.930.006104HLA-A, HLA-DRB4, HLA-C, HLA-DOB, HLA-DQA1
  • Pathways with FDR <10% are presented. See Supplementary Table 4 for further details. Boldface text indicates pathways enriched among the upregulated genes; italicized text indicates pathways enriched among the downregulated genes.

  • COX, cytochrome c oxidase; GZMB, granzyme B; RP, ribosomal protein; VBP, von Hippel-Lindau binding protein.