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. 2017 Mar 9;9(3):823–851. doi: 10.18632/aging.101195

Table 1. Main significant clusters of altered genes in spinal cord of ALS samples.

Cluster Gene names Size Count Odds Ratio p-value Deregulation
Activation of blood coagulation via clotting cascade F3, ANO6 2 2 Inf 0.000574 Up
Antigen processing and presentation of exogenous peptide antigen CTSS, FCER1G, FCGR1A, HLA-A, HLA-B, HLA-C, HLA-DMA, HLA-DMB, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1, HLA-DRB5, HLA-F, HLA-G, NCF2, PSMB8, PSMB9, PSMD5, TAP1, IFI30 165 22 6.58 6.84e-11 Up
Antigen processing and presentation of exogenous peptide antigen via MHC class I CTSS, FCER1G, FCGR1A, HLA-A, HLA-B, HLA-C, HLA-F, HLA-G, NCF2, PSMB8, PSMB9, PSMD5, TAP1, IFI30 75 14 9.66 2.45e-09 Up
Antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent CTSS, HLA-A, HLA-B, HLA-C, HLA-F, HLA-G 9 6 82.7 1.45e-08 Up
Antigen processing and presentation of exogenous peptide antigen via MHC class II CTSS, FCER1G, HLA-DMA, HLA-DMB, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1, HLA-DRB5, IFI30 92 11 5.66 1.24e-05 Up
Antigen processing and presentation of peptide antigen via MHC class I CTSS, FCER1G, FCGR1A, HLA-A, HLA-B, HLA-C, HLA-F, HLA-G, NCF2, PSMB8, PSMB9, PSMD5, TAP1, IFI30 97 14 7.09 7.58e-08 Up
Apoptotic process AHR, APOE, FAS, BCL2A1, BCL6, BMP2, BTK, CAMK2D, CASP1, CASP4, TNFSF8, CDKN1A, CTSC, DAB2, NQO1, ECT2, EDN1, F3, FCER1G, HCK, HGF, HIF1A, HMOX1, ICAM1, IFI16, IL1A, ITGA5, JAK3, LMNB1, LYN, MNDA, MYC, NCF2, NOS3, P2RX4, PLAGL1, PLAUR, PLSCR1, PRLR, PSMB8, PSMB9, PSMD5, PTPN2, CCL2, CCL19, SNAI2, STAT1, TEK, TGFB2, TLR2, TLR3, GPR65, YBX3, NOL3, SOCS3, LY86, IKBKE, CHL1, PPP1R15A, RRM2B, SHISA5, TNFRSF12A, ACSL5, FNIP2, DNASE2B, ZMAT3, NOA1, FGD3, IL33, DEDD2, ANO6 1745 71 1.89 5.22e-06 Up
Apoptotic signaling pathway FAS, BCL2A1, BTK, CASP4, CDKN1A, CTSC, ECT2, HGF, HIF1A, HMOX1, ICAM1, IFI16, IL1A, NOS3, P2RX4, PLAUR, PTPN2, SNAI2, TGFB2, TLR3, YBX3, NOL3, IKBKE, PPP1R15A, RRM2B, SHISA5, TNFRSF12A, ACSL5, FNIP2, FGD3, IL33, DEDD2 596 32 2.43 1.88e-05 Up
Axonemal dynein complex assembly DNAH5, DNAI1, TEKT2, ZMYND10, ARMC4, DNAH7, CCDC114, CCDC151, DNAAF1, CCDC39 21 10 175 8.54e-18 Down
Axoneme DNAH5, DNAH9, SPAG6, DNAI1, DCDC2, HYDIN, CFAP46, ARMC4, MNS1, DNAH7, CFAP74, CCDC114, CCDC151, DNAAF1, CFAP54, DNAH2, SPAG17, CFAP221, CCDC39, RSPH4A 89 20 52.5 1.31e-25 Down
Axoneme assembly DNAH5, DNAI1, TEKT2, ZMYND10, HYDIN, CFAP46, ARMC4, DNAH7, CFAP74, RSPH1, CCDC114, CCDC151, DNAAF1, SPAG17, CCDC39, RSPH4A 42 16 128 5.9e-26 Down
B cell mediated immunity FAS, BCL6, BTK, C1QB, C1QC, C7, FCER1G, HLA-DMA, HLA-DQB1, HLA-DRB1, HLA-DRB5, CFI, IL4R, CD226, TLR8 103 15 7.18 2.28e-08 Up
Cellular protein modification process IL12RB1, INS, KCNE1, MAK, CFP, RASA4, TRAK2, MYLK3, NEK5, C17orf97, PPIAL4A 3527 11 0.473 0.00885 Down
Cellular response to interferon-gamma CAMK2D, EDN1, FCGR1A, GBP1, HCK, HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1, HLA-DRB5, HLA-F, HLA-G, ICAM1, IRF8, OAS2, PTPN2, CCL2, CCL19, STAT1, SOCS3, IFI30, TRIM38, TRIM5 126 27 11.9 1.95e-18 Up
Clathrin-coated endocytic vesicle membrane FCGR1A, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1, HLA-DRB5 49 7 7.32 0.000108 Up
Copper ion import ATP7B, SLC31A1, STEAP4 7 3 30.7 0.000446 Up
Cytokine production involved in immune response BCL6, BTK, FCER1G, HLA-A, HMOX1, JAK3, SLC11A1, TEK, TGFB2, TLR2, TLR3, TREM1 69 12 8,81 7,87E-08 Up
Endolysosome membrane TLR3, TLR7, TLR8 4 3 131 4.51e-05 Up
Fc receptor mediated stimulatory signaling pathway FCER1G, FCGR1A, FCGR2A, FGR, HCK, ITPR3, LYN, PLSCR1, CD226, MYO1G 77 10 6.21 1.47e-05 Up
Humoral immune response mediated by circulating immunoglobulin C1QB, C1QC, C7, HLA-DQB1, HLA-DRB1, HLA-DRB5, CFI 46 7 7.42 0.000103 Up
Igg binding FCER1G, FCGR1A, FCGR2A, FCGR2B 10 4 28.3 5.42e-05 Up
Immunoglobulin production FAS, BCL6, CD37, HLA-DQB1, HLA-DRB1, HLA-DRB5, IL4R, TNFSF13B, POLM, IL33 87 10 5.4 4.34e-05 Up
Inner dynein arm assembly TEKT2, ZMYND10, DNAH7, DNAAF1, CCDC39 10 5 182 1.44e-09 Down
Integral component of lumenal side of endoplasmic reticulum membrane HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1, HLA-DRB5, HLA-F, HLA-G 28 11 28.8 1.04e-11 Up
Interferon-alpha production TLR3, NMI, TLR7, TLR8 18 4 11.7 0.000764 Up
Interferon-beta biosynthetic process TLR3, NMI, TLR7, TLR8 8 4 41.1 2.12e-05 Up
Interferon-gamma biosynthetic process TLR3, EBI3, TLR7, TLR8 16 4 13.7 0.000472 Up
Interleukin-10 production FCER1G, HLA-DRB1, HLA-DRB5, JAK3, TLR2, PDCD1LG2 42 6 6.87 0.000463 Up
Intrinsic apoptotic signaling pathway BCL2A1, CASP4, CDKN1A, HIF1A, HMOX1, IFI16, PLAUR, PTPN2, SNAI2, YBX3, NOL3, IKBKE, PPP1R15A, RRM2B, SHISA5, FNIP2 284 16 2.49 0.00143 Up
Macrophage activation IL4R, SLC11A1, TLR1, SBNO2, CD93, TLR7, TLR8, IL33 48 8 8.29 1.66e-05 Up
Mast cell cytokine production BCL6, FCER1G, HMOX1 7 3 30.7 0.000446 Up
MHC class II receptor activity HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1 11 5 35.4 2.73e-06 Up
MHC protein complex HLA-A, HLA-B, HLA-C, HLA-DMA, HLA-DMB, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1, HLA-DRB5, HLA-F, HLA-G 25 13 48.4 1.34e-15 Up
Microtubule bundle formation DNAH5, DNAI1, TEKT2, ZMYND10, HYDIN, CFAP46, ARMC4, DNAH7, CFAP74, RSPH1, CCDC114, CCDC151, DNAAF1, SPAG17, CCDC39, RSPH4A 63 16 70.7 1.18e-22 Down
Monocyte chemotaxis CCR1, LYN, CCL2, CCL19, PLA2G7, ANO6 49 6 5.75 0.00107 Up
Outer dynein arm assembly DNAH5, DNAI1, ZMYND10, ARMC4, CCDC114, CCDC151, DNAAF1 11 7 325 5.6e-14 Down
Peptide antigen binding HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB5, HLA-F, HLA-G, TAP1 26 10 26.9 1.57e-10 Up
Platelet-derived growth factor receptor binding TYMP, ITGA5, ITGB3, LYN 12 4 21.2 0.000123 Up
Positive regulation of Fc receptor mediated stimulatory signaling pathway LYN, CD226 2 2 Inf 0.000574 Up
Positive regulation of interleukin-6 production FCER1G, TLR1, TLR2, TLR3, TLR7, IL33 55 6 5.05 0.00197 Up
Positive regulation of interleukin-8 production TLR2, TLR3, TLR5, TLR7, TLR8 42 5 5.56 0.00318 Up
Positive regulation of tumor necrosis factor production FCER1G, CCL2, CCL19, TLR1, TLR2, TLR3 51 6 5.5 0.00133 Up
Protection from natural killer cell mediated cytotoxicity HLA-A, HLA-B, TAP1 5 3 61.5 0.000132 Up
Regulated secretory pathway ANXA3, FCER1G, FGR, HCK, HMOX1, IL4R, LYN, STX11, CD300A, RAB11FIP2, RAB11FIP1 73 11 7.4 1.23e-06 Up
Regulation of apoptotic process APOE, FAS, BCL2A1, BCL6, BMP2, BTK, CAMK2D, CASP1, CASP4, CDKN1A, CTSC, DAB2, NQO1, ECT2, EDN1, F3, FCER1G, HCK, HGF, HIF1A, HMOX1, ICAM1, IL1A, ITGA5, JAK3, LYN, MNDA, MYC, NCF2, NOS3, PLAUR, PRLR, PSMB8, PSMB9, PSMD5, PTPN2, CCL2, CCL19, SNAI2, STAT1, TEK, TGFB2, TLR3, YBX3, NOL3, SOCS3, CHL1, RRM2B, TNFRSF12A, ACSL5, ZMAT3, FGD3, DEDD2, ANO6 1344 54 1.82 0.000117 Up
Regulation of B cell apoptotic process BCL6, BTK, LYN 16 3 9.45 0.00608 Up
Regulation of coagulation APOE, EDN1, F3, FCER1G, LYN, NOS3, PLAU, PLAUR, THBD, HPSE, ADAMTS18, ANO6 85 12 6.87 8.31e-07 Up
Regulation of cytokine biosynthetic process CD86, HMOX1, IL1A, TLR1, TLR2, TLR3, NMI, EBI3, TLR7, TLR8 93 10 5.01 7.72e-05 Up
Regulation of extrinsic apoptotic signaling pathway FAS, HMOX1, ICAM1, IL1A, NOS3, SNAI2, TGFB2, NOL3, TNFRSF12A, ACSL5, DEDD2 155 11 3.17 0.0013 Up
Regulation of Fc receptor mediated stimulatory signaling pathway LYN, PLSCR1, CD226 5 3 61.5 0.000132 Up
Regulation of hemostasis APOE, EDN1, F3, FCER1G, LYN, NOS3, PLAU, PLAUR, THBD, HPSE, ADAMTS18, ANO6 81 12 7.27 4.87e-07 Up
Regulation of leukocyte apoptotic process BCL6, BTK, FCER1G, HIF1A, JAK3, LYN, CCL19, TGFB2 74 8 5.02 0.000386 Up
Regulation of lipid kinase activity FGR, LYN, CCL19, TEK, NRBF2 47 5 4.89 0.0052 Up
Regulation of mast cell activation FCER1G, FGR, HMOX1, IL4R, LYN, PLSCR1, CD226, CD300A 31 8 14.4 4.96e-07 Up
Regulation of mast cell degranulation FCER1G, FGR, HMOX1, IL4R, LYN, CD300A 24 6 13.8 1.71e-05 Up
Regulation of microtubule movement DNAH11, ARMC4, DNAAF1, CCDC39 18 4 51.3 3.03e-06 Down
Regulation of natural killer cell mediated immunity HLA-A, HLA-B, PVR, TAP1, CD226 27 5 9.36 0.000405 Up
Regulation of protein metabolic process FOXJ1, INS, CFP, RASA4, NEK5, DTHD1 2448 6 0.381 0.00803 Down
Regulation of protein modification process INS, RASA4 1641 2 0.192 0.00288 Down
Regulation of T-helper 1 cell differentiation HLX, IL4R, JAK3, CCL19 9 4 32.9 3.74e-05 Up
T cell costimulation CD86, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1, HLA-DRB5, LYN, CCL19, TNFSF13B, PDCD1LG2 71 11 7.65 9.25e-07 Up
TAP binding HLA-A, HLA-B, HLA-C, HLA-F, TAP1 7 5 106 1.34e-07 Up
T-helper 2 cell differentiation BCL6, CD86, HLX, IL4R 14 4 16.4 0.00027 Up