Supplementary Table I
TNF-inducible genes (360) identified by the microarrays are listed. These genes were identified by the formula M+T/M+M ≥2, and shown is the log2 induction (mean±SD). The Table contains the gene (alphabetical order), the systematic name, and the probe name.
Gene Systematic Name Probe Name log2 induction (mean±SD) 7A5 NM_182762 A_32_P131031 3,06 ± 0,68 ABTB2 NM_145804 A_23_P356616 2,65 ± 0,53 ACSL1 NM_001995 A_23_P110212 2,95 ± 0,36 ACSL5 NM_203380 A_24_P201360 1,97 ± 0,61 ACVR2A NM_001616 A_23_P153930 2,80 ± 0,20 ADA NM_000022 A_23_P210482 1,63 ± 0,30 ADM NM_001124 A_23_P127948 3,15 ± 0,31 ADORA2A NM_000675 A_23_P109436 3,89 ± 0,22 AK3L1 NM_001005353 A_32_P108655 3,81 ± 1,22 AK3L2 NM_001002921 A_23_P200524 3,27 ± 1,40 ALS2CR4 NM_152388 A_23_P370097 1,69 ± 0,40 AMPD3 NM_000480 A_23_P116286 1,77 ± 0,32 AMZ1 NM_133463 A_24_P383649 3,08 ± 0,64 ANKRD15 NM_153186 A_32_P64570 4,34 ± 0,48 ANKRD22 NM_144590 A_23_P161428 1,56 ± 0,65 APOL3 NM_145641 A_24_P416997 2,36 ± 0,69 AQP9 NM_020980 A_23_P106362 2,84 ± 0,94 AREG NM_001657 A_23_P259071 2,62 ± 0,63 ARHGAP20 NM_020809 A_23_P422933 1,69 ± 0,44 ARHGEF7 NM_145735 A_23_P417891 2,01 ± 0,41 ARL5B NM_178815 A_23_P378588 3,64 ± 0,73 ARNTL2 NM_020183 A_23_P53345 2,07 ± 0,40 ARRDC3 NM_020801 A_24_P274615 1,84 ± 0,38 ARRDC4 NM_183376 A_23_P339818 1,89 ± 0,25 ATF5 NM_012068 A_23_P119337 1,66 ± 0,28 ATP2B1 NM_001682 A_23_P128319 2,36 ± 0,20 AXUD1 NM_033027 A_23_P121011 2,03 ± 0,46 B4GALT1 NM_001497 A_24_P103803 2,04 ± 0,20 B4GALT5 NM_004776 A_24_P239731 2,10 ± 0,60 BAZ1A NM_013448 A_23_P76799 1,95 ± 0,33 BCAR3 NM_003567 A_23_P97394 1,35 ± 0,17 BCL2A1 NM_004049 A_23_P152002 3,08 ± 1,08 BCMO1 NM_017429 A_23_P124300 1,37 ± 0,13 BIC NR_001458 A_32_P108156 4,69 ± 1,07 BID NM_197966 A_23_P154929 1,59 ± 0,23 BIRC3 NM_001165 A_23_P98350 2,80 ± 0,55 BLR1 NM_032966 A_24_P252945 2,47 ± 0,83 BRPF3 NM_015695 A_24_P414712 1,31 ± 0,26 BTBD4 NM_025224 A_32_P518489 1,95 ± 0,72
I Supplementary Table I, continued
Gene Systematic Name Probe Name log2 induction (mean±SD) BTG1 NM_001731 A_23_P87560 1,88 ± 0,47 BTG2 NM_006763 A_23_P62901 1,64 ± 0,48 BTG3 NM_006806 A_23_P80068 2,92 ± 0,14 BTNL8 NM_024850 A_23_P7412 1,39 ± 0,20 CCL1 NM_002981 A_23_P49759 1,88 ± 0,65 CCL19 NM_006274 A_23_P123853 1,42 ± 0,48 CCL20 NM_004591 A_23_P17065 7,76 ± 0,50 CCL22 NM_002990 A_24_P313418 1,67 ± 0,26 CCL23 NM_005064 A_24_P319088 4,23 ± 0,33 CCL3 D00044 A_23_P373017 3,11 ± 0,18 CCL3L3 NM_001001437 A_23_P321920 3,33 ± 0,86 CCL4 NM_002984 A_23_P207564 5,22 ± 0,30 CCL5 NM_002985 A_23_P152838 4,59 ± 0,34 CCL8 NM_005623 A_23_P207456 3,55 ± 0,48 CCR7 NM_001838 A_23_P343398 2,91 ± 1,22 CCRL2 NM_003965 A_23_P69310 1,84 ± 0,37 CCRN4L NM_012118 A_24_P213794 2,99 ± 0,85 CD274 NM_014143 A_23_P338479 2,70 ± 0,75 CD40 NM_001250 A_23_P57036 3,00 ± 0,46 CD44 NM_000610 A_23_P24870 1,78 ± 0,25 CD58 NM_001779 A_23_P138308 1,59 ± 0,30 CD6 NM_006725 A_23_P311875 3,17 ± 0,46 CD69 NM_001781 A_23_P87879 4,03 ± 1,04 CD80 NM_005191 A_24_P320033 3,88 ± 0,36 CD83 NM_004233 A_23_P70670 2,80 ± 0,58 CDC42EP2 NM_006779 A_23_P1602 3,91 ± 0,42 CDGAP NM_020754 A_24_P349039 1,88 ± 0,17 CDKN2B NM_078487 A_24_P360674 3,93 ± 0,40 CENTD1 NM_015230 A_32_P83784 1,38 ± 0,22 CGN NM_020770 A_24_P45728 2,10 ± 0,54 CH25H NM_003956 A_23_P86470 3,38 ± 1,54 CHML NM_001821 A_23_P46118 2,36 ± 0,52 CHST2 NM_004267 A_23_P40847 3,24 ± 0,48 CIAS1 NM_004895 A_23_P9883 1,83 ± 0,27 CLCF1 NM_013246 A_23_P138760 2,25 ± 0,62 CLEC4D NM_080387 A_23_P25235 2,56 ± 1,00 CLEC4E NM_014358 A_24_P78531 3,20 ± 0,55 CLIC4 NM_013943 A_23_P135494 2,50 ± 0,22 CRIM1 NM_016441 A_23_P51105 3,06 ± 0,77 CSF2 NM_000758 A_23_P133408 4,45 ± 0,52 CSF3 NM_000759 A_23_P501754 4,03 ± 0,46 CSRP2 NM_001321 A_23_P44724 3,06 ± 0,61 CTNND2 NM_001332 A_24_P380196 1,84 ± 0,34 CXCL1 NM_001511 A_23_P7144 6,09 ± 0,70 CXCL2 NM_002089 A_23_P315364 3,58 ± 0,81 CXCL3 NM_002090 A_24_P251764 3,29 ± 0,40 CXCL5 NM_002994 A_23_P110204 3,81 ± 0,82 CXCL6 NM_002993 A_23_P155755 4,29 ± 1,28
II Supplementary Table I, continued
Gene Systematic Name Probe Name log2 induction (mean±SD) CYP7B1 NM_004820 A_23_P169092 3,00 ± 1,01 DC-UbP NM_152277 A_23_P19061 1,89 ± 0,37 DDIT4 NM_019058 A_23_P104318 2,21 ± 0,42 DGKH NM_152910 A_23_P502980 1,90 ± 0,73 DLC1 NM_182643 A_24_P940115 2,00 ± 0,20 DNAJB5 NM_012266 A_23_P112241 2,56 ± 0,22 DOC1 NM_182909 A_23_P252052 2,41 ± 0,27 DOT1L NM_032482 A_23_P408768 2,21 ± 0,33 DSU NM_018000 A_23_P108948 1,51 ± 0,44 DUSP1 NM_004417 A_23_P110712 2,11 ± 0,40 DUSP2 NM_004418 A_24_P37409 2,41 ± 0,61 DUSP5 NM_004419 A_23_P150018 3,44 ± 1,03 DUSP6 NM_001946 A_23_P139704 1,87 ± 0,58 DYRK3 NM_001004023 A_24_P345209 2,45 ± 1,05 E2F7 NM_203394 A_32_P210202 3,16 ± 1,29 EBI3 NM_005755 A_24_P370201 3,20 ± 0,26 ECE1 NM_001397 A_24_P154080 1,72 ± 0,50 EDEM1 NM_014674 A_24_P285768 1,53 ± 0,22 EDN1 NM_001955 A_23_P214821 3,58 ± 0,34 EGR3 NM_004430 A_23_P216225 2,86 ± 1,09 EHD1 NM_006795 A_23_P52647 3,52 ± 0,57 EID3 NM_001008394 A_23_P65068 2,02 ± 0,42 EMP2 NM_001424 A_23_P106682 1,46 ± 0,16 EREG NM_001432 A_23_P41344 5,53 ± 0,71 ESPL1 NM_012291 A_23_P32707 1,84 ± 0,23 ETV3 NM_005240 A_23_P400945 1,96 ± 0,37 EYA3 NM_001990 A_23_P74737 1,60 ± 0,35 EZH2 NM_004456 A_23_P259641 1,73 ± 0,13 F3 NM_001993 A_23_P126782 5,57 ± 1,02 FAM107B NM_031453 A_23_P149975 1,19 ± 0,14 FAM49A NM_030797 A_23_P21560 1,49 ± 0,20 FAM57A NM_024792 A_23_P50000 1,63 ± 0,38 FCAR NM_133280 A_24_P348265 2,15 ± 0,67 FEZ1 NM_005103 A_24_P201552 4,94 ± 0,85 FFAR2 NM_005306 A_23_P397391 1,58 ± 0,20 FJX1 NM_014344 A_23_P150693 1,80 ± 0,49 FMNL3 NM_175736 A_23_P379200 1,73 ± 0,38 FOSL1 NM_005438 A_23_P322519 2,85 ± 0,81 FOSL2 NM_005253 A_23_P348121 2,24 ± 0,59 FPRL1 NM_001462 A_23_P55649 1,46 ± 0,21 FSCN1 NM_003088 A_23_P168532 3,67 ± 0,79 FUT4 NM_002033 A_23_P12965 1,48 ± 0,29 FZD7 NM_003507 A_23_P209449 1,36 ± 0,23 G0S2 NM_015714 A_23_P74609 5,83 ± 0,38 GBP1 NM_002053 A_23_P62890 3,67 ± 0,58 GBP2 NM_004120 A_23_P85693 2,92 ± 0,26 GCH1 NM_000161 A_23_P163079 4,79 ± 0,42 GJB2 NM_004004 A_23_P204947 4,45 ± 0,48
III Supplementary Table I, continued
Gene Systematic Name Probe Name log2 induction (mean±SD) GPR109A NM_177551 A_23_P329924 2,15 ± 0,54 GPR109B NM_006018 A_23_P64721 4,33 ± 0,72 GPR132 NM_013345 A_24_P201994 2,66 ± 0,51 GPR35 NM_005301 A_23_P154245 1,51 ± 0,34 GPR84 NM_020370 A_23_P25155 2,76 ± 0,20 GRAMD1A NM_020895 A_23_P56213 2,97 ± 0,54 GRAMD3 NM_023927 A_23_P22350 2,55 ± 0,07 HEY1 NM_012258 A_32_P83845 5,81 ± 1,20 HIVEP1 NM_002114 A_23_P19619 2,38 ± 0,30 HIVEP2 NM_006734 A_23_P214766 3,45 ± 0,34 HSA251708 AJ251708 A_24_P932084 2,80 ± 0,30 HSD11B1 NM_181755 A_23_P63209 2,27 ± 0,77 IBRDC2 NM_182757 A_24_P406060 3,87 ± 0,31 IBRDC3 NM_153341 A_23_P321388 2,54 ± 0,51 ICAM1 NM_000201 A_23_P153320 3,34 ± 0,56 IER3 NM_003897 A_23_P42257 3,30 ± 0,39 IFNB1 NM_002176 A_23_P71774 2,54 ± 0,76 IFNGR2 NM_005534 A_23_P29036 1,69 ± 0,28 IGSF21 NM_032880 A_32_P78101 2,14 ± 0,54 IL12B NM_002187 A_23_P7560 4,53 ± 0,97 IL15RA NM_172200 A_23_P138680 2,90 ± 0,48 IL18 NM_001562 A_23_P104798 2,75 ± 0,16 IL18R1 NM_003855 A_24_P208567 2,58 ± 1,29 IL1A NM_000575 A_23_P72096 8,19 ± 0,63 IL1B NM_000576 A_23_P79518 6,16 ± 0,53 IL1F9 NM_019618 A_23_P17053 4,12 ± 0,90 IL20 NM_018724 A_23_P46482 2,58 ± 1,63 IL23A NM_016584 A_23_P76078 3,91 ± 0,76 IL28A NM_172138 A_23_P409438 1,72 ± 0,25 IL2RA NM_000417 A_23_P127288 4,22 ± 1,10 IL32 NM_001012631 A_23_P15146 1,82 ± 0,19 IL4I1 NM_172374 A_23_P502520 1,59 ± 0,27 IL6 NM_000600 A_23_P71037 6,54 ± 0,50 IL7R NM_002185 A_23_P404494 4,47 ± 0,97 IL8 NM_000584 A_32_P87013 5,80 ± 1,08 INHBA NM_002192 A_23_P122924 2,65 ± 1,38 INSIG1 NM_198336 A_23_P22027 3,08 ± 0,40 IRAK2 NM_001570 A_23_P80635 2,79 ± 0,88 IRAK3 NM_007199 A_23_P162300 2,00 ± 0,20 ITGB8 NM_002214 A_24_P273599 2,93 ± 0,73 JAG1 NM_000214 A_23_P210763 5,20 ± 0,38 JUNB NM_002229 A_23_P4821 1,72 ± 0,25 KCNA3 NM_002232 A_23_P201138 3,68 ± 0,34 KCNJ2 NM_000891 A_23_P329261 3,45 ± 0,45 KCNN4 NM_002250 A_23_P67529 2,14 ± 0,40 KMO NM_003679 A_23_P200838 2,17 ± 0,47 KRT23 NM_015515 A_23_P78248 2,50 ± 0,66 KYNU NM_003937 A_24_P11506 2,24 ± 0,31
IV Supplementary Table I, continued
Gene Systematic Name Probe Name log2 induction (mean±SD) LAD1 NM_005558 A_23_P415510 2,98 ± 0,88 LAMB3 NM_001017402 A_23_P86012 3,36 ± 0,52 LAMP3 NM_014398 A_23_P29773 2,38 ± 1,03 LCT NM_002299 A_23_P79217 1,86 ± 0,29 LENG9 NM_198988 A_32_P493225 3,08 ± 0,55 LIMS3 NM_033514 A_23_P365685 1,69 ± 0,50 LINCR NM_001080535 A_23_P328740 3,15 ± 0,61 LITAF NM_004862 A_23_P3532 1,45 ± 0,47 LONRF1 NM_152271 A_23_P94216 1,90 ± 0,39 LRFN5 NM_152447 A_23_P163195 3,11 ± 0,78 LRP12 NM_013437 A_23_P8906 1,92 ± 0,62 LRRC32 NM_005512 A_24_P389916 4,24 ± 1,02 LSS NM_002340 A_24_P110799 1,88 ± 0,29 MAFF NM_012323 A_23_P103110 2,27 ± 0,56 MAP2K3 NM_145109 A_23_P118427 2,28 ± 0,40 MAP3K8 NM_005204 A_23_P23947 3,09 ± 0,46 MARCH3 NM_178450 A_23_P321511 1,92 ± 0,32 MCL1 NM_021960 A_24_P319635 1,92 ± 0,53 MCOLN2 NM_153259 A_23_P23639 2,75 ± 0,55 MCTP1 NM_024717 A_24_P212481 1,79 ± 0,47 MESDC1 NM_022566 A_23_P99891 1,42 ± 0,25 MET NM_000245 A_23_P359245 3,66 ± 1,39 MFSD2 NM_032793 A_23_P43820 2,81 ± 0,33 MN1 NM_002430 A_23_P6381 2,27 ± 0,73 MOBKL2C NM_145279 A_24_P225339 1,87 ± 0,31 MSC NM_005098 A_23_P256948 4,29 ± 0,31 MTF1 NM_005955 A_23_P74241 2,36 ± 0,18 MYC NM_002467 A_23_P215956 2,70 ± 0,87 MYO1G NM_033054 A_23_P257542 1,37 ± 0,37 N4BP3 NM_015111 A_23_P58747 2,03 ± 0,38 NAB1 NM_005966 A_23_P209805 1,80 ± 0,31 NBN NM_002485 A_23_P251480 2,75 ± 0,33 NFE2L3 NM_004289 A_23_P42718 2,20 ± 0,32 NFKB1 NM_003998 A_23_P30024 3,00 ± 0,27 NFKB2 NM_002502 A_23_P202156 2,56 ± 0,25 NFKBIA NM_020529 A_23_P106002 2,45 ± 0,28 NFKBIE NM_004556 A_23_P30655 1,26 ± 0,12 NFKBIZ NM_031419 A_23_P212089 3,19 ± 0,82 NUMB NM_001005743 A_23_P88381 1,50 ± 0,16 OASL NM_003733 A_23_P139786 2,62 ± 0,56 OGFRL1 NM_024576 A_23_P7791 1,89 ± 0,30 OLR1 NM_002543 A_24_P124624 1,99 ± 0,61 OPTN NM_001008211 A_23_P1461 1,45 ± 0,28 OR11H12 NM_001013354 A_23_P128868 2,06 ± 0,63 OSM NM_020530 A_23_P166408 2,38 ± 0,23 OTUD1 AB188491 A_32_P60459 1,55 ± 0,39 P2RX7 NM_002562 A_23_P25354 1,66 ± 0,17 PBEF1 NM_005746 A_24_P408772 2,87 ± 0,40
V Supplementary Table I, continued
Gene Systematic Name Probe Name log2 induction (mean±SD) PBX4 NM_025245 A_23_P90419 2,76 ± 0,61 PDE4B NM_002600 A_24_P325333 4,44 ± 0,47 PDE4DIP NM_022359 A_23_P149153 1,60 ± 0,28 PDGFA NM_002607 A_23_P113701 2,84 ± 0,82 PDGFB NM_002608 A_24_P339944 2,32 ± 0,44 PDSS1 NM_014317 A_23_P161152 1,97 ± 0,47 PELI1 NM_020651 A_23_P120345 1,85 ± 0,46 PHLDA2 NM_003311 A_23_P47614 3,00 ± 1,07 PHLDB1 NM_015157 A_23_P24555 2,80 ± 0,49 PHLPPL NM_015020 A_23_P418234 1,36 ± 0,16 PIK3AP1 NM_152309 A_23_P104445 1,38 ± 0,22 PIM2 NM_006875 A_24_P379104 2,64 ± 0,29 PIM3 NM_001001852 A_23_P61398 1,75 ± 0,39 PLAGL2 NM_002657 A_23_P6151 1,89 ± 0,20 PLAUR NM_001005377 A_23_P16469 1,56 ± 0,52 PLCB4 NM_000933 A_23_P28898 1,77 ± 0,52 PLEK NM_002664 A_23_P209678 2,69 ± 0,36 PLEKHC1 NM_006832 A_23_P88347 3,32 ± 1,51 PLK3 NM_004073 A_23_P51646 2,13 ± 0,39 PMAIP1 NM_021127 A_23_P207999 2,97 ± 0,28 PNPLA1 NM_173676 A_32_P526255 3,04 ± 0,95 PNRC1 NM_006813 A_23_P145074 2,57 ± 0,26 PPP1R15B NM_032833 A_23_P160449 2,68 ± 0,47 PPP3CC NM_005605 A_23_P157495 1,71 ± 0,09 PRDM11 NM_020229 A_23_P13057 2,09 ± 0,42 PRPF3 NM_004698 A_23_P97573 1,33 ± 0,26 PSTPIP2 NM_024430 A_23_P208119 2,74 ± 0,51 PTGER2 NM_000956 A_23_P151710 2,64 ± 0,45 PTGER4 NM_000958 A_23_P435394 2,91 ± 0,46 PTGIR NM_000960 A_23_P340848 1,87 ± 0,47 PTGS2 NM_000963 A_24_P250922 6,05 ± 0,61 PTPN1 NM_002827 A_23_P338890 1,93 ± 0,27 PTPN12 NM_002835 A_23_P8763 1,32 ± 0,11 PTPRJ NM_002843 A_24_P282434 1,55 ± 0,25 PTX3 NM_002852 A_23_P121064 4,46 ± 1,13 PVR NM_006505 A_24_P65616 1,94 ± 0,44 RAB6IP1 NM_015213 A_23_P321201 1,78 ± 0,27 RABGEF1 NM_014504 A_23_P250825 1,83 ± 0,43 RAP2C NM_021183 A_24_P374319 1,57 ± 0,42 RAPGEF2 XM_944412 A_24_P912587 3,18 ± 0,68 RASGEF1B NM_152545 A_23_P331186 1,79 ± 0,44 RASL11A NM_206827 A_23_P14124 1,96 ± 0,43 REL NM_002908 A_23_P56938 2,48 ± 0,66 RELB NM_006509 A_23_P55706 1,94 ± 0,42 RHOF NM_019034 A_24_P104115 2,06 ± 0,37 RIPK2 NM_003821 A_24_P124032 1,79 ± 0,28 RND1 NM_014470 A_23_P53370 2,37 ± 0,54 RRAD NM_004165 A_24_P262127 3,81 ± 0,38
VI Supplementary Table I, continued
Gene Systematic Name Probe Name log2 induction (mean±SD) SAMD14 NM_174920 A_24_P185186 2,99 ± 0,48 SDC4 NM_002999 A_24_P373976 2,56 ± 0,55 SEC24A BC019341 A_23_P329593 1,53 ± 0,26 SERPINB2 NM_002575 A_24_P245379 3,24 ± 0,45 SERPINB8 NM_198833 A_23_P4561 2,02 ± 0,27 SERPINB9 NM_004155 A_23_P30687 4,31 ± 0,48 SERPINE1 NM_000602 A_24_P158089 1,56 ± 0,46 SESN3 NM_144665 A_23_P361448 1,58 ± 0,35 SGPP2 NM_152386 A_23_P153971 4,92 ± 0,21 SH2D2A NM_003975 A_23_P160618 1,67 ± 0,35 SKIL NM_005414 A_23_P351215 1,71 ± 0,33 SLAMF7 NM_021181 A_24_P353638 2,43 ± 0,64 SLC1A2 NM_004171 A_23_P162068 2,68 ± 1,02 SLC2A6 NM_017585 A_23_P169249 2,87 ± 0,43 SLC35F2 NM_017515 A_23_P339098 1,69 ± 0,30 SLC39A8 NM_022154 A_23_P41424 3,18 ± 0,39 SLC43A3 NM_199329 A_23_P358548 1,62 ± 0,35 SLC7A5 NM_003486 A_24_P335620 2,86 ± 0,38 SLCO4A1 NM_016354 A_23_P5903 3,17 ± 0,57 SNFT NM_018664 A_23_P160720 2,28 ± 0,72 SNX10 NM_013322 A_24_P98109 1,46 ± 0,32 SOCS1 NM_003745 A_24_P48014 1,53 ± 0,60 SOCS3 NM_003955 A_23_P207058 4,30 ± 0,62 SOD2 NM_000636 A_23_P134176 2,70 ± 0,21 SPHK1 NM_021972 A_23_P38106 1,61 ± 0,56 SPSB1 NM_025106 A_23_P200096 2,04 ± 0,48 SQLE NM_003129 A_23_P146284 1,70 ± 0,21 SRC NM_005417 A_23_P308603 2,60 ± 0,20 SRrp35 NM_080743 A_23_P110903 4,01 ± 1,88 SRXN1 NM_080725 A_23_P320113 1,86 ± 0,16 STAT4 NM_003151 A_23_P305198 3,30 ± 0,84 STX11 NM_003764 A_23_P156788 2,06 ± 0,31 SYNPO2 AL833294 A_23_P310094 3,14 ± 1,04 TACR1 NM_015727 A_24_P148590 2,23 ± 0,41 TANK NM_133484 A_24_P257108 1,76 ± 0,31 TARP NM_001003799 A_23_P59543 3,72 ± 1,46 TBC1D9 NM_015130 A_23_P41487 1,78 ± 0,36 TCEB3 NM_003198 A_23_P74097 1,17 ± 0,09 THBS1 NM_003246 A_23_P206212 3,41 ± 0,44 THRAP1 NM_005121 A_23_P27247 1,50 ± 0,23 TICAM1 NM_182919 A_23_P90311 1,70 ± 0,27 TIFA NM_052864 A_24_P350686 2,45 ± 0,42 TINAG NM_014464 A_23_P168329 1,63 ± 0,66 TJP2 NM_201629 A_24_P201153 1,91 ± 0,41 TLR2 NM_003264 A_23_P92499 2,20 ± 0,10 TMEM88 NM_203411 A_23_P77859 2,52 ± 0,18 TNF NM_000594 A_24_P50759 3,61 ± 0,32 TNFAIP2 NM_006291 A_23_P421423 2,76 ± 0,46
VII Supplementary Table I, continued
Gene Systematic Name Probe Name log2 induction (mean±SD) TNFAIP3 NM_006290 A_24_P166527 3,73 ± 0,79 TNFAIP6 NM_007115 A_23_P165624 5,69 ± 0,55 TNFAIP8 NM_014350 A_32_P219520 2,79 ± 0,29 TNFRSF10B NM_003842 A_23_P169030 1,78 ± 0,35 TNFRSF18 NM_148901 A_24_P411121 2,66 ± 0,29 TNFRSF4 NM_003327 A_32_P26092 2,57 ± 0,45 TNFRSF9 NM_001561 A_23_P51936 3,74 ± 0,47 TNFSF15 NM_005118 A_24_P167012 1,99 ± 0,41 TNFSF9 NM_003811 A_23_P67224 1,95 ± 0,44 TNIP1 NM_006058 A_23_P30435 2,48 ± 0,39 TNIP2 NM_024309 A_23_P258418 2,30 ± 0,48 TNIP3 NM_024873 A_23_P386478 7,63 ± 0,90 TP53BP2 NM_005426 A_23_P12526 1,75 ± 0,37 TP53INP2 NM_021202 A_24_P357465 2,16 ± 0,47 TRAF1 NM_005658 A_24_P89891 5,71 ± 0,33 TRAF3 NM_145725 A_23_P37068 1,35 ± 0,17 TRIM36 NM_018700 A_23_P110569 2,32 ± 0,11 TRIP10 NM_004240 A_23_P50349 2,51 ± 0,38 UAP1 NM_003115 A_23_P160460 1,52 ± 0,44 UPB1 NM_016327 A_23_P120822 2,53 ± 0,29 USP12 NM_182488 A_24_P237613 3,29 ± 0,51 USP13 NM_003940 A_23_P40989 1,33 ± 0,31 UXS1 NM_025076 A_23_P67829 1,53 ± 0,21 VCAM1 NM_001078 A_23_P34345 3,11 ± 0,42 WNT5A NM_003392 A_23_P211926 3,29 ± 1,08 WTAP NM_152858 A_23_P215037 3,55 ± 0,23 YRDC NM_024640 A_23_P62840 1,93 ± 0,19 ZBTB10 NM_023929 A_24_P64071 3,79 ± 0,95 ZC3H12A NM_025079 A_23_P326160 3,63 ± 0,53 ZHX2 NM_014943 A_23_P168951 2,07 ± 0,30 ZNF140 NM_003440 A_23_P150841 1,23 ± 0,09 ZNF697 NM_001080470 A_23_P322076 2,10 ± 0,51 ZNFX1 NM_021035 A_24_P23034 1,63 ± 0,37
VIII Supplementary Table II
Summary of genes affected by absolute tolerance in human monocytes. The 51 genes induced by preincubation with the high TNF dose (Figure 3A; 400+T/M+T ≤0.25) and the 24 genes induced by the low TNF preincubation dose (Figure 3C; 40+T/M+T ≤0.25) are summarized according to their function. A regulation by NF-ĸB and/or AP-1 is indicated (extracted from http://www.genecards.org). Genes affected by the high dose (normal font), by the low dose (italic), and under both conditions (bold) are indicated accordingly.
Category Gene Gene Name Regulation
Inflammation IL18R1 interleukin 18 receptor 1 NF-κB
IL1A interleukin 1 alpha AP-1
IL6 interleukin 6 NF-κB
IL8 interleukin 8 NF-κB
MAP3K8 mitogen-activated protein kinase kinase kinase 8 NF-κB
OLR1 oxidized low density lipoprotein receptor 1 AP-1
PTGS2 prostaglandin-endoperoxide synthase 2 AP-1
PTX3 pentraxin 3 NF-κB
TNF tumor necrosis factor NF-κB, AP-1
TNFSF15 tumor necrosis factor superfamily member 15 NF-κB
Growth/ IL12B interleukin 12B Differentiation
AREG amphiregulin NF-κB, AP-1
CSF2 colony stimulating factor 2
CSF3 colony stimulating factor 3 AP-1
STAT4 signal transducer and activator of transcription 4
HEY1 hairy/enhancer-of-split related with YRPW motif 1 NF-κB, AP-1
EGR3 early growth response 3 AP-1
PDGFA platelet-derived growth factor alpha AP-1
PDGFB platelet-derived growth factor beta pleckstrin homology-like domain family A member PHLDA2 2
IX Supplementary Table II, continued
Category Gene Gene Name Regulation
Growth/ TMEM88 transmembrane protein 88 AP-1 Differentiation Chemotaxis/ CCL20 C-C motif chemokine ligand 20 Migration
CCL4 C-C motif chemokine ligand 4
CXCL1 C-X-C motif chemokine ligand 1 NF-κB
CXCL2 C-X-C motif chemokine ligand 2 NF-κB
CXCL3 C-X-C motif chemokine ligand 3
CXCL6 C-X-C motif chemokine ligand 6 NF-κB
FEZ1 fasciculation and elongation protein zeta 1
THBS1 thrombospondin 1 pleckstrin homology-domain containing protein family C PLEKHC1 member 1 CD6 CD6 molecule NF-κB, AP-1
Signaling/ GPR35 G protein-coupled receptor 35 AP-1 Transcription ARL5B ADP-ribosylation factor-like 5B AP-1
ARRDC3 arrestin domain containing 3
DOT1L DOT1-like histone H3 methyltransferase AP-1
RASGEF1B RasGEF domain family member 1B
Metabolism CHML Rab escort protein 2 NF-κB, AP-1
INSIG1 insulin induced gene 1 major facilitator superfamily domain-containing MFSD2A protein 2A UAP1 UDP-N-acteylglucosamine pyrophosphorylase 1 AP-1
potassium voltage-gated channel shaker-related Transport KCNA3 subfamily member 3 solute carrier organic anion transporter family SLCO4A1 member 4A1 Cell Cycle/ ESPL1 extra spindle pole bodies homolog 1 NF-κB, AP-1 Proliferation TRIM36 tripartite motif containing 36
IL20 interleukin 20 AP-1
CD69 CD69 molecule NF-κB, AP-1
X Supplementary Table II, continued
Category Gene Gene Name Regulation
Cell Cycle/ INHBA inhibin beta A AP-1 Proliferation
Procoagulation F3 Tissue factor NF-κB, AP-1
SERPINB2 serpin peptidase inhibitor member 2 NF-κB, AP-1
Vasoconstrictive EDN1 endothelin 1 NF-κB
v-maf musculoaponeurotic fibrosarcoma oncogene Oncogene MAFF AP-1 homolog F
Unknown ANKRD15 KN motif and ankyrin repeat domains 1
LENG9 leukocyte receptor cluster member 9 AP-1
LIMS3 LIM and senescent cell antigen-like domains 3
BIC MIR155 host gene
FAM57A family with sequence similarity 57 member A NF-κB
XI Supplementary Table III
Summary of 99 genes affected by low-dose-induced tolerance applying less stringent criteria. Genes were selected using the formula: 40+T/M+T ≤0.5.
CSF2 EDN1 DNAJB5 CSF3 DUSP2
F3 IL12B MAP2K3 CXCL3 IFNB1
IL6 LENG9 MYC CXCL2 BTBD4
PTGS2 ARL5B PPP1R15B KCNA3 LRP12
CCL20 IL23A REL TNF PHLDB1
IL1A USP12 ATP2B1 CD69 DUSP6
HEY1 IL1F9 EID3 SERPINB2 STX11
SERPINB9 IL18R1 LRFN5 RAPGEF2 SDC4
ANKRD15 MFSD2 P2RX7 PMAIP1 PIM2
IL8 INHBA EDEM1 THBS1 OGFRL1
CXCL1 TNFSF15 TICAM1 ARRDC3 BIC
JAG1 PHLDA2 CD83 ESPL1 STAT4
IL1B EGR3 RASGEF1B DOT1L UAP1
EREG CXCL6 CHML OLR1 FAM57A
INSIG1 PDGFB TRIM36 TMEM88 DDIT4
MAP3K8 SPSB1 AREG PLEKHC1 CCRN4L
CLCF1 LCT
XII Supplementary Table IV
List of genes affected by induction tolerance in human monocytes. The table shows the list of 227 genes inhibited by TNF induction tolerance (400+T/400+M ≤1.25) depicted in Figure 5A. Again, the genes are summarized into functional groups, and NF-ĸB- and/or AP-1-dependent genes were identified by monitoring online database genecards.
Category Gene Gene Name Regulation
Signaling/ RRAD Ras-related associated with diabetes NF-κB, AP-1 Transcription PLCB4 phospholipase C beta 4
GPR109B hydroxycarboxylic acid receptor 3
ADORA2A adenosine A2a receptor NF-κB
OASL 2'-5'-oligoadenylate synthetase-like
PDE4B phosphodiesterase 4B human immunodeficiency virus type I HIVEP1 NF-κB, AP-1 enhancer binding protein 1 human immunodeficiency virus type I HIVEP2 AP-1 enhancer binding protein 2 PTGER4 prostaglandin E receptor 4
ARRDC4 arrestin domain containing 4
OPTN optineurin NF-κB
GPR132 G protein-coupled receptor 132 AP-1
FZD7 frizzled family receptor
TJP2 tight junction protein 2 AP-1
PTGER2 prostaglandin E receptor 2
MCOLN2 mucolipin 2
GJB2 gap junction protein, beta 2 AP-1
RABGEF1 RAB guanine nucleotide exchange factor 1 NF-κB
RAPGEF2 Rap guanine nucleotide exchange factor 2 AP-1
TICAM1 toll-like receptor adaptor molecule 1 NF-κB
GPR35 G protein-coupled receptor 35 AP-1
CD83 CD83 molecule NF-κB
XIII Supplementary Table IV, continued
Category Gene Gene Name Regulation
Signaling/ SOCS3 suppressor of cytokine signaling 3 Transcription protein phosphatase 3 catalytic subunit PPP3CC gamma MSC musculin NF-κB, AP-1
ZNF140 zinc finger protein 140
DOT1L DOT1-like histone H3 methyltransferase AP-1
NAB1 EGR1 binding protein 1
EZH2 enhancer of zeste homolog 2
ZHX2 zinc fingers and homeoboxes 2 bromodomain adjacent to zinc finger BAZ1A domain 1A bromodomain and PHD finger containing BRPF3 protein 3 ATF5 activating transcription factor 5 NF-κB, AP-1 protein phosphatase 1 regulatory PPP1R15B subunit 15B transcription elongation factor B TCEB3 polypeptide 3 PLAGL2 pleiomorphic adenoma gene-like 2
NFE2L3 nuclear factor (erythroid-derived 2)-like 3 NF-κB
THRAP1 mediator complex subunit 13
CTNND2 catenin delta 2
EYA3 eyes absent homolog 3
tumor necrosis factor alpha-induced Inflammation TNFAIP2 protein 2 TLR2 toll-like receptor 2 NF-κB, AP-1 CIAS1 NLR family pyrin domain containing protein 3 (NLRP3) NFKB2 NF-κB 2 NF-κB receptor-interacting serine-threonine RIPK2 NF-κB kinase 2 FCAR Fc fragment of IgA receptor NF-κB
LITAF lipopolysaccharide-induced TNF factor
IL18 interleukin 18 NF-κB, AP-1
XIV Supplementary Table IV, continued
Category Gene Gene Name Regulation
Inflammation MAP2K3 mitogen-activated protein kinase kinase 3 NF-κB, AP-1 mitogen-activated protein kinase kinase MAP3K8 NF-κB kinase 8 OLR1 oxidized low density lipoproteinreceptor 1 AP-1
IL18R1 interleukin 18 receptor 1 NF-κB
EBI3 Epstein-Barr virus induced 3 NF-κB v-rel reticuloendotheliosis viral oncogene RELB NF-κB, AP-1 homolog B FPRL1 formyl peptide receptor 2
IL32 interleukin 32 NF-κB
NFKBIA NF-κB inhibitor alpha NF-κB, AP-1 TRAF family member-associated NFKB TANK NF-κB activator NFKB1 NF-κB 1 NF-κB
TRAF1 TNF receptor-associated factor 1 NF-κB, AP-1
TRAF3 TNF receptor-associated factor 3 NF-κB, AP-1
PLEK pleckstrin NF-κB
CLCF1 cardiotrophin-like cytokine factor 1
IL2RA interleukin 2 receptor alpha NF-κB
CLEC4D C-type lectin domain family 4 member D
LAMP3 lysosomal-associated membrane protein 3
MYO1G myosin IG
CD80 CD80 molecule AP-1 PIK3AP1 phosphoinositide-3-kinase adaptor PIK3AP1 NF-κB protein 1 SH2D2A SH2 domain containing protein 2A NF-κB, AP-1 tumor necrosis factor receptor superfamily TNFRSF9 NF-κB member 9 DNAJB5 DnaJ homolog subfamily B member 5
SRXN1 sulfiredoxin 1
MTF1 metal-regulatory transcription factor 1 NF-κB, AP-1
XV Supplementary Table IV, continued
Category Gene Gene Name Regulation
Inflammation DUSP1 dual specificity phosphatase 1
GBP1 guanylate binding protein 1
IL28A interleukin 28A AP-1
IFNGR2 interferon gamma receptor 2
Metabolism PBEF1 nicotinamide phosphoribosyltransferase acyl-CoA synthetase long-chain family ACSL1 AP-1 member 1 acyl-CoA synthetase long-chain family ACSL5 member 5 AMZ1 AMZ1 archaelysin family metallopeptidase 1 AP-1
PDSS1 prenyl diphosphate synthase subunit 1
GCH1 GTP cyclohydrolase 1 AP-1 UDP-Gal:betaGlcNAc beta 1,4- B4GALT1 galactosyltransferase polypeptide 1 KMO kynurenine 3-monooxygenase UDP-Gal:betaGlcNAc beta 1,4- B4GALT5 galactosyltransferase polypeptide 5 cytochrome P450 family 7 subfamily B CYP7B1 polypeptide 1 KYNU kynureninase
AK3L1 Adenylate kinase 3 alpha-like 1
MARCH3 membrane-associated ring-CH finger 3
UPB1 ureidopropionase beta
OTUD1 OTU domain containing protein 1
ADA adenosine deaminase NF-κB, AP-1
FUT4 fucosyltransferase 4 AP-1
LSS lanosterol synthase
NBN nibrin NF-κB, AP-1
GBP2 guanylate binding protein 2
ECE1 endothelin converting enzyme 1 AP-1
LCT lactase NF-κB, AP-1
XVI Supplementary Table IV, continued
Category Gene Gene Name Regulation
UDP-N-acteylglucosamine Metabolism UAP1 AP-1 pyrophosphorylase 1 major facilitator superfamily domain MFSD2A containing protein 2A splA/ryanodine receptor domain and SOCS SPSB1 box containing 1 ER degradation enhancer, mannosidase EDEM1 alpha-like 1 SQLE squalene epoxidase
CHST2 carbohydrate sulfotransferase 2
HSD11B1 hydroxysteroid 11-beta dehydrogenase 1
INSIG1 insulin induced gene 1 IBRDC2 ring finger protein 144B (RNF144B) IBRDC3 ring finger protein 19B (RNF19B) Growth/ signal transducer and activator of STAT4 Differentiation transcription 4 CSRP2 cysteine and glycine-rich protein 2 AP-1 cysteine rich transmembrane BMP CRIM1 AP-1 regulator 1 ACVR2A activin A receptor type IIA protein tyrosine phosphatase non-receptor PTPN1 type 1 JUNB jun B proto-oncogene NF-κB, AP-1
DUSP5 dual specificity phosphatase 5
FOSL2 FOS-like antigen 2 NF-κB, AP-1
DSU MREG melanoregulin
PDGFA platelet-derived growth factor alpha AP-1
PDGFB platelet-derived growth factor beta
IL20 interleukin 20 AP-1
CSF2 colony stimulating factor 2
INHBA inhibin, beta A AP-1
BTG1 B-cell translocation gene 1 NF-κB, AP-1
BTG3 B-cell translocation gene 3 NF-κB
XVII Supplementary Table IV, continued
Category Gene Gene Name Regulation
Growth/ NUMB numb homolog Differentiation
WTAP Wilms tumor 1 associated protein 7A5 metastasis associated in colon cancer 1 (MACC1) PIM3 pim-3 oncogene
BTG2 BTG family member 2 NF-κB, AP-1
PTPRJ protein tyrosine phosphatase receptor type J v-src sarcoma (Schmidt-Ruppin A-2) viral SRC AP-1 oncogene homolog v-myc myelocytomatosis viral oncogene MYC homolog EID3 EP300 interacting inhibitor of differentiation 3 NF-κB
PBX4 pre-B-cell leukemia homeobox 4
TMEM88 transmembrane protein 88 AP-1
Chemotaxis/ RHOF ras homolog gene family member F Migration
RAP2C member of RAS oncogene family NF-κB
CCRL2 C-C motif chemokine receptor-like 2 NF-κB CDGAP (ARHGAP3 Rho GTPase activating protein 31 1) RND1 Rho family GTPase 1 NF-κB
ITGB8 integrin, beta 8
FMNL3 formin-like 3
CD58 CD58 molecule AP-1
CD44 CD44 molecule NF-κB protein tyrosine phosphatase non-receptor PTPN12 type 12 CCR7 C-C motif chemokine receptor 7 NF-κB
CCL22 C-C motif chemokine ligand 22 NF-κB, AP-1
ICAM1 intercellular adhesion molecule 1 NF-κB
PLEKHC1 fermitin family member 2 ArfGAP with RhoGAP domain, ankyrin CENTD1 repeat, and PH domain 2
XVIII Supplementary Table IV, continued
Category Gene Gene Name Regulation
Chemotaxis/ LAMB3 laminin beta 3 NF-κB Migration
BLR1 C-X-C motif chemokine receptor 5
PVR poliovirus receptor NF-κB
FEZ1 fasciculation and elongation protein zeta 1
CCL19 C-C motif chemokine ligand 19 NF-κB
potassium inwardly-rectifying channel Transport KCNJ2 AP-1 subfamily J member 2 potassium intermediate/small conductance KCNN4 calcium-activated channel subfamily N AP-1 member 4 SLC7A5 solute carrier family 7 member 5 AP-1
ATP2B1 plasma membrane Ca(2+) ATPase
SEC24A SEC24 family member A AP-1 solute carrier organic anion transporter SLCO4A1 family member 4A1 SLC39A8 solute carrier family 39 member 8
APOL3 apolipoprotein L 3 AP-1
AQP9 aquaporin 9
AMPD3 adenosine monophosphate deaminase 3
SLC43A3 solute carrier family 43 member 3 AP-1
SLC1A2 solute carrier family 1 NF-κB, AP-1
CLIC4 chloride intracellular channel 4
tumor necrosis factor alpha-induced Apoptosis TNFAIP8 protein 8 MCL1 myeloid cell leukemia sequence 1 NF-κB, AP-1
BID BH3 interacting domain death agonist NF-κB, AP-1
IL15RA interleukin 15 receptor alpha AP-1
BIRC3 baculoviral IAP repeat containing 3 NF-κB, AP-1 TNFRSF10 tumor necrosis factor receptor superfamily NF-κB, AP-1 B member 10b TP53BP2 tumor protein p53 binding proteim 2 NF-κB
Antiinflammatory IRAK3 interleukin-1 receptor-associated kinase 3 NF-κB, AP-1
XIX Supplementary Table IV, continued
Category Gene Gene Name Regulation
Antiinflammatory P2RX7 purinergic receptor P2X NF-κB
NFKBIE NF-κB inhibitor epsilon NF-κB, AP-1 tumor necrosis factor alpha-induced TNFAIP3 protein 3 ETV3 ets variant 3 NF-κB
Oncogene BCAR3 breast cancer anti-estrogen resistance 3
PIM2 pim-2 oncogene NF-κB v-rel reticuloendotheliosis viral oncogene REL AP-1 homolog MET met proto-oncogene AP-1 v-maf musculoaponeurotic fibrosarcoma MAFF AP-1 oncogene homolog F
Coagulation SERPINB9 serpin peptidase inhibitor clade B member 9
SERPINB2 serpin peptidase inhibitor member 2 NF-κB, AP-1 aryl hydrocarbon receptor nuclear ARNTL2 AP-1 translocator-like 2 PTGIR prostaglandin I2 receptor NF-κB
Cell Cycle/ PH domain and leucine rich repeat protein PHLPPL Proliferation phosphatase 2 ESPL1 extra spindle pole bodies homolog 1 NF-κB, AP-1 mRNA processing SRrp35 serine/arginine-rich splicing factor 12 PRP3 pre-mRNA processing factor 3 PRPF3 homolog
Unknown SYNPO2 synaptopodin 2 AP-1
LAD1 ladinin 1 AP-1
USP13 ubiquitin specific peptidase 13
TARP TCR gamma alternate reading frame protein
GRAMD3 GRAM domain containing 3
ALS2CR4 transmembrane protein 237
TP53INP2 tumor protein p53 inducible nuclear protein 2 AP-1
FJX1 four jointed box 1
MESDC1 mesoderm development candidate 1 AP-1
XX Supplementary Table IV, continued
Category Gene Gene Name Regulation
ankyrin repeat and BTB domain containing Unknown ABTB2 NF-κB protein 2 LON peptidase N-terminal domain and ring LONRF1 AP-1 finger 1 CGN cingulin NF-κB multiple C2 domains transmembrane MCTP1 protein 1 FAM49A family with sequence similarity 49 member A
ZNFX1 zinc finger NFX1-type containing protein 1 DOC1 filamin A interacting protein 1-like (FILIP1L) RAB6IP1 DENN/MADD domain containing 5A (DENND5A) proline-serine-threonine phosphatase PSTPIP2 NF-κB interacting protein 2 PDE4DIP phosphodiesterase 4D interacting protein AP-1
EMP2 epithelial membrane protein 2
SLC35F2 solute carrier family 35 member F2
IL4I1 interleukin 4 induced 1 NF-κB, AP-1 LIM and senescent cell antigen-like LIMS3 domains 3 leucine rich repeat and fibronectin type III LRFN5 domain containing protein 5 OGFRL1 opioid growth factor receptor-like 1
FAM57A family with sequence similarity 57 member A NF-κB
BIC MIR155 host gene family with sequence similarity 107 FAM107B member B GRAMD1A GRAM domain containing 1A NF-κB, AP-1
BTNL8 butyrophilin-like 8
MN1 meningioma 1
ARRDC3 arrestin domain containing 3
XXI