SUPPLEMENTARY TABLE 3. Gene ranking: 277 deregulated genes. overexpressed in the sequence NCF/CAF-PT/CAF-LM mean Log2 normalised expression Fold changes Probe ID gene symbol NCF CAF-PT CAF-LM CAF-PT/NCF CAF-LM/CAF-PT pval qval Gene_description 8114970 C5orf46 4.721 5.843 9.288 1.773 14.845 4.22E-05 0 chromosome 5 open reading frame 46 8130173 RAET1L 7.421 8.139 8.923 1.667 1.665 4.22E-05 0 retinoic acid early transcript 1L 7898413 PADI1 6.316 6.989 7.628 1.535 1.590 4.22E-05 0 peptidyl arginine deiminase, type I 8020455 GATA6 7.902 8.665 9.846 1.598 2.751 4.22E-05 0 GATA binding protein 6 8058450 GPR1 5.420 6.989 8.559 2.921 3.498 4.22E-05 0 G protein-coupled receptor 1 8111387 ADAMTS12 8.507 9.214 10.544 1.663 2.451 4.22E-05 0 ADAM metallopeptidase with thrombospondin type 1 motif, 12 8100382 CHIC2 8.343 9.081 10.723 1.616 3.392 4.22E-05 0 cysteine-rich hydrophobic domain 2 7938485 MICAL2 9.309 10.477 11.568 2.320 2.180 4.22E-05 0 microtubule associated monoxygenase, calponin and LIM domain containing 2 7909789 TGFB2 8.478 10.294 11.406 4.254 1.710 4.22E-05 0 transforming growth factor, beta 2 7953284 NTF3 7.510 8.920 9.474 2.429 1.601 4.22E-05 0 neurotrophin 3 8110932 SEMA5A 8.892 10.081 11.490 2.956 2.526 4.22E-05 0 semaphorin 5A 8122720 ULBP2 6.024 7.831 8.695 3.896 1.531 4.22E-05 0 UL16 binding protein 2 7945245 NTM 7.702 9.005 10.360 1.976 2.891 4.22E-05 0 neurotrimin 8020878 MAPRE2 9.217 9.644 11.028 1.508 2.648 4.22E-05 0 microtubule-associated protein, RP/EB family, member 2 8112007 EMB 4.721 5.986 7.610 1.941 4.055 4.22E-05 0 embigin homolog (mouse) 8114805 FGF1 8.285 8.947 10.377 1.642 2.564 4.22E-05 0 fibroblast growth factor 1 (acidic) 7997504 CDH13 9.137 10.213 11.836 1.624 3.521 4.22E-05 0 cadherin 13, H-cadherin (heart) 7942957 PRSS23 10.003 10.624 11.361 1.725 1.669 4.22E-05 0 protease, serine, 23 8126798 GPR116 5.713 6.832 8.788 1.513 6.179 4.22E-05 0 G protein-coupled receptor 116 8091283 PLOD2 10.341 11.115 11.905 1.829 1.628 4.22E-05 0 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 8083594 PTX3 6.636 7.384 9.315 1.658 3.914 4.22E-05 0 pentraxin-related gene, rapidly induced by IL-1 beta 8112615 ENC1 7.499 8.736 10.119 1.919 3.319 4.22E-05 0 ectodermal-neural cortex (with BTB-like domain) 8075910 RAC2 7.750 8.344 9.316 1.586 1.956 4.22E-05 0 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) 7961532 ARHGDIB 6.378 7.014 10.357 1.687 10.129 4.22E-05 0 Rho GDP dissociation inhibitor (GDI) beta 7922337 TNFSF18 5.058 5.952 7.299 1.551 2.594 4.22E-05 0 tumor necrosis factor (ligand) superfamily, member 18 7912520 NPPB 7.430 8.786 11.781 1.951 21.345 4.22E-05 0 natriuretic peptide precursor B 8022674 CDH2 8.433 9.500 11.151 2.314 3.324 4.22E-05 0 cadherin 2, type 1, N-cadherin (neuronal) 8135069 SERPINE1 10.674 11.720 13.061 2.414 2.124 4.22E-05 0 serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 8104022 PDLIM3 7.661 9.312 10.736 3.207 3.096 4.22E-05 0 PDZ and LIM domain 3 8144786 SLC7A2 6.311 7.254 9.480 2.127 5.056 4.22E-05 0 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 7965094 E2F7 7.265 8.284 9.435 1.793 2.534 4.22E-05 0 E2F transcription factor 7 8108905 KCTD16 7.252 8.329 9.164 2.206 1.815 4.22E-05 0 potassium channel tetramerisation domain containing 16 7990054 UACA 7.406 8.688 11.202 2.204 7.039 4.22E-05 0 uveal autoantigen with coiled-coil domains and ankyrin repeats 8081219 ST3GAL6 6.097 6.795 7.875 1.836 2.220 4.22E-05 0 ST3 beta-galactoside alpha-2,3-sialyltransferase 6 7955637 KRT18 9.486 10.448 11.824 2.563 2.516 4.22E-05 0 keratin 18 8102831 C4orf49 9.015 10.000 11.522 2.078 3.194 4.22E-05 0 chromosome 4 open reading frame 49 8163149 PTPN3 6.790 7.252 8.034 1.551 1.557 4.22E-05 0 protein tyrosine phosphatase, non-receptor type 3 8006736 DUSP14 9.066 9.541 10.164 1.590 1.510 4.22E-05 0 dual specificity phosphatase 14 8077441 BHLHE40 9.092 9.735 10.862 1.988 2.030 4.22E-05 0 basic helix-loop-helix family, member e40 7942941 CCDC81 6.520 7.211 9.082 1.528 4.529 4.23E-05 0 coiled-coil domain containing 81 8058849 MARCH4 8.489 9.367 9.981 2.000 1.598 4.23E-05 0 membrane-associated ring finger (C3HC4) 4 7934979 ANKRD1 6.930 8.770 11.579 4.973 7.189 4.23E-05 0 ankyrin repeat domain 1 (cardiac muscle) 8107673 GRAMD3 9.299 10.131 11.070 1.824 1.929 4.23E-05 0 GRAM domain containing 3 8130674 PDE10A 7.184 7.675 8.920 1.724 2.311 4.23E-05 0 phosphodiesterase 10A 8140534 SEMA3C 8.333 9.010 10.736 1.795 3.222 4.23E-05 0 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C 7927964 SRGN 7.730 8.652 12.309 1.830 17.546 4.23E-05 0 serglycin 8097058 CEP170L 6.689 7.465 8.384 1.591 1.827 4.24E-05 0 centrosomal protein 170kDa-like 8149574 CSGALNACT1 6.226 6.956 8.307 1.519 2.838 4.24E-05 0 chondroitin sulfate N-acetylgalactosaminyltransferase 1 8103630 SH3RF1 8.949 9.557 10.397 1.564 1.763 4.25E-05 0 SH3 domain containing ring finger 1 7995838 MT1X 8.504 9.170 10.824 1.550 2.897 4.25E-05 0 metallothionein 1X 8139207 INHBA 10.513 11.390 12.265 1.939 1.824 4.26E-05 0 inhibin, beta A 7922343 TNFSF4 5.800 8.691 10.041 9.118 2.465 4.28E-05 0 tumor necrosis factor (ligand) superfamily, member 4 7922807 GLT25D2 6.545 7.324 8.141 2.091 1.868 4.28E-05 0 glycosyltransferase 25 domain containing 2 7964733 RPSAP52 4.814 5.687 7.396 1.943 4.516 4.29E-05 0 ribosomal protein SA pseudogene 52 8057898 HECW2 7.069 7.389 9.173 1.532 2.827 4.30E-05 0 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 8154245 PDCD1LG2 9.131 9.834 10.982 1.623 2.198 4.32E-05 0 programmed cell death 1 ligand 2 8139087 SFRP4 6.370 6.677 9.818 1.771 9.160 4.34E-05 0 secreted frizzled-related protein 4 8109830 CCDC99 7.865 8.597 9.604 1.603 2.189 4.43E-05 0 coiled-coil domain containing 99 7983478 C15orf48 6.224 7.293 9.997 2.059 11.537 4.44E-05 0 chromosome 15 open reading frame 48 8007363 WNK4 7.332 8.488 9.390 2.507 1.811 4.45E-05 0 WNK lysine deficient protein kinase 4 8056491 SCN9A 8.756 9.567 10.418 1.915 1.886 4.67E-05 0 sodium channel, voltage-gated, type IX, alpha subunit 7995697 LPCAT2 7.923 8.676 9.327 1.557 1.650 4.80E-05 0 lysophosphatidylcholine acyltransferase 2 7975459 SIPA1L1 9.643 10.214 10.703 1.504 1.549 4.92E-05 0 signal-induced proliferation-associated 1 like 1 8149749 TNFRSF10D 9.306 9.921 10.559 1.518 1.641 5.09E-05 0 tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain 7962212 PKP2 7.166 8.248 9.109 2.453 1.689 5.13E-05 0 plakophilin 2 8078529 STAC 5.682 6.424 7.998 1.932 2.874 5.14E-05 0 SH3 and cysteine rich domain 7995797 MT1E 8.076 8.603 11.006 1.995 5.331 5.15E-05 0 metallothionein 1E 7976012 NRXN3 7.610 9.305 10.582 5.443 1.909 5.36E-05 0 neurexin 3 8085138 OXTR 8.975 9.877 10.647 1.922 1.860 5.93E-05 0 oxytocin receptor 7906919 RGS4 7.442 8.834 10.929 1.803 7.067 6.34E-05 0 regulator of G-protein signaling 4 7972750 COL4A1 10.058 10.646 11.258 1.510 1.536 6.37E-05 0 collagen, type IV, alpha 1 8120654 KCNQ5 6.591 7.502 8.119 1.860 1.745 6.96E-05 0 potassium voltage-gated channel, KQT-like subfamily, member 5 7918869 NGF 8.711 9.270 10.270 1.584 2.044 8.15E-05 0 nerve growth factor (beta polypeptide) 7963567 KRT8 7.958 9.015 9.665 1.714 2.181 8.95E-05 0 keratin 8 8098006 GLRB 6.240 6.880 7.250 1.647 1.506 9.21E-05 0 glycine receptor, beta 8177732 HLA-A 9.001 9.928 10.572 1.640 1.777 9.73E-05 0 major histocompatibility complex, class I, A 7909503 SERTAD4 5.565 6.616 7.365 2.557 1.556 1.01E-04 0 SERTA domain containing 4 7984259 RNU5B-1 5.061 6.371 7.402 1.580 5.525 1.16E-04 0 RNA, U5B small nuclear 1 8054479 MALL 7.714 8.847 9.245 1.940 1.654 1.52E-04 0 mal, T-cell differentiation protein-like 7946983 SAA2 7.550 9.144 10.278 2.910 2.545 1.68E-04 0 serum amyloid A2 8015268 KRT34 7.660 9.128 10.109 4.600 1.551 2.58E-04 2.96E-05 keratin 34 7995793 MT1L 9.747 10.224 11.137 1.549 1.963 2.68E-04 2.96E-05 metallothionein 1L (gene/pseudogene) 8063458 DOK5 7.566 8.253 9.540 2.092 2.492 3.54E-04 2.96E-05 docking protein 5 8092726 CLDN1 7.804 8.688 9.540 1.870 2.406 3.63E-04 2.96E-05 claudin 1 7934570 KCNMA1 8.416 9.089 9.918 1.804 2.183 4.07E-04 2.96E-05 potassium large conductance calcium-activated channel, subfamily M, alpha member 1 8145793 SNORD13 9.170 9.982 10.912 1.693 2.595 4.60E-04 7.80E-05 small nucleolar RNA, C/D box 13 8174201 BEX1 7.443 8.478 9.762 2.133 4.555 1.82E-03 1.40E-04 brain expressed, X-linked 1 8147049 FABP5L1 7.644 8.204 9.164 1.881 1.928 2.05E-03 2.93E-04 fatty acid binding protein 5-like 1 (pseudogene) 8114572 HBEGF 8.038 8.592 9.400 1.761 1.610 2.25E-03 2.93E-04 heparin-binding EGF-like growth factor 8005955 SNORD42A 5.488 7.085 7.362 1.686 3.452 3.74E-03 5.78E-04 small nucleolar RNA, C/D box 42A 8105267 ITGA2 8.882 9.456 10.403 2.207 2.435 4.16E-03 5.78E-04 integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) 7981996 SNRPN 6.023 6.930 7.348 1.730 1.640 5.15E-03 5.78E-04 small nuclear ribonucleoprotein polypeptide N 8135218 LRRC17 7.751 8.722 9.688 1.710 2.989 5.90E-03 5.78E-04 leucine rich repeat containing 17 7971077 POSTN 7.991 9.617 10.518 3.413 3.003 1.03E-02 1.10E-03 periostin, osteoblast specific factor 7926545 PLXDC2 8.599 9.571 9.907 2.363 1.576 1.20E-02 1.99E-03 plexin domain containing 2 7990345 SEMA7A 8.578 9.107 9.576 1.630 1.740 1.24E-02 1.99E-03 semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group) 8145361 NEFM 7.462 8.308 8.786 1.593 1.908 4.00E-02 5.59E-03 neurofilament, medium polypeptide 8180303 SAA2 8.081 9.114 9.758 2.134 2.315 1.05E-01 1.89E-02 serum amyloid A2 infraexpressed