AFC TNFa/ Published Title QUALIFIER NAME DMSO Rho-related BTB domain containing 2 209441_at RHOBTB2 -2.80 zinc finger 395 218149_s_at ZNF395 -2.12 SLIT and NTRK-like family, member 6 235976_at SLITRK6 -2.07 lunatic fringe homolog (Drosophila) 228762_at LFNG -2.05 zinc finger protein 367 229551_x_at ZNF367 -2.03 early B-cell factor 3 227243_s_at EBF3 -1.90 homeo box B7 204778_x_at HOXB7 -1.90 synaptotagmin-like 5 242093_at SYTL5 -1.88 FLJ41238 protein 229764_at FLJ41238 -1.87 retinoblastoma-like 1 (p107) 205296_at RBL1 -1.86 G protein-coupled receptor 39 208600_s_at GPR39 -1.86 RA-regulated nuclear matrix-associated protein 218585_s_at RAMP -1.85 F-box and leucine-rich repeat protein 16 227641_at FBXL16 -1.85 hypothetical protein FLJ38663 223477_s_at FLJ38663 -1.84 brain-derived neurotrophic factor 206382_s_at BDNF -1.83 UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 211379_x_at B3GALT3 -1.80 MAD, mothers against decapentaplegic homolog 6 (Drosophila) 207069_s_at SMAD6 -1.80 ferredoxin 1 203646_at FDX1 -1.79 CDC10 cell division cycle 10 homolog (S. cerevisiae) 217721_at CDC10 -1.78 SLIT-ROBO Rho GTPase activating protein 2 209794_at SRGAP2 -1.77 Homo sapiens transmembrane protein 201 227617_at TMEM201 -1.76 centrosomal protein 170kDa-like 1552717_s_at CEP170L -1.76 DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae) 209804_at DCLRE1A -1.75 mitogen-activated protein kinase kinase kinase 5 203837_at MAP3K5 -1.75 kelch repeat and BTB (POZ) domain containing 6 226479_at KBTBD6 -1.74 Consensus includes gb:AL109925 /DEF=Human DNA sequence from clone RP4-534K7 on ch226800_at PGM1 -1.74 nuclear factor I/A 224976_at NFIA -1.72 meningioma (disrupted in balanced translocation) 1 205330_at MN1 -1.72 transmembrane protein 53 1554077_a_at TMEM53 -1.72 BCL6 co-repressor 223566_s_at BCOR -1.71 Transcribed sequence with moderate similarity to protein pir:PC4259 (H.sapiens) PC4259 ferr 227941_at LOC339803 -1.71 transcription factor CP2-like 3 219388_at TFCP2L3 -1.70 20 open reading frame 128 1556793_a_at C20ORF128 -1.70 hypothetical protein FLJ12994 222630_at FLJ12994 -1.69 parathyroid hormone-like hormone 211756_at PTHLH -1.69 glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase) 239761_at GCNT1 -1.67 pyridoxal (pyridoxine, vitamin B6) phosphatase 223290_at PDXP -1.66 l(3)mbt-like 2 (Drosophila) 1555815_a_at L3MBTL2 -1.66 hypothetical protein KIAA1434 224826_at KIAA1434 -1.66 Homo sapiens cDNA FLJ11489 232589_at FLJ11489 -1.66 reticulon 4 interacting protein 1 1555679_a_at RTN4IP1 -1.66 autism susceptibility candidate 2 212599_at AUTS2 -1.65 core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase 219439_at C1GALT1 -1.65 synovial sarcoma, X breakpoint 2 interacting protein 203016_s_at SSX2IP -1.65 mutS homolog 6 (E. coli) 202911_at MSH6 -1.65 hypothetical protein FLJ10300 219251_s_at FLJ10300 -1.65 transforming, acidic coiled-coil containing protein 2 211382_s_at TACC2 -1.64 leucine rich repeat containing 17 205381_at LRRC17 -1.64 transmembrane protein 17 1557137_at TMEM17 -1.64 hypothetical protein MGC2827 219142_at RASL11B -1.63 dachshund homolog (Drosophila) 228915_at DACH1 -1.63 hypothetical protein LOC126917 225615_at LOC126917 -1.63 KIAA0941 protein 203884_s_at RAB11-FIP2 -1.62 E2F transcription factor 2 228361_at E2F2 -1.62 nuclear mitotic apparatus protein 1 214251_s_at NUMA1 -1.61 homeo box A10 213150_at HOXA10 -1.61 hypothetical protein LOC284018 226901_at LOC284018 -1.61 G protein-coupled receptor 48 218326_s_at GPR48 -1.61 replication factor C (activator 1) 4, 37kDa 204023_at RFC4 -1.60 cDNA DKFZp686J23256 230958_s_at UNK_BE67079 -1.60 Ets2 repressor factor 203643_at ERF -1.59 WD repeat and HMG-box DNA binding protein 1 204728_s_at WDHD1 -1.59 KIAA0922 protein 209760_at KIAA0922 -1.59 AT rich interactive domain 1A (SWI- like) 212152_x_at ARID1A -1.58 ras homolog family, member B 212099_at RHOB -1.58 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (CHL1-like homolog, S. cerevisia 208149_x_at DDX11 -1.58 origin recognition complex, subunit 1-like (yeast) 205085_at ORC1L -1.58 M-phase phosphoprotein 9 237158_s_at MPHOSPH9 -1.58 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1 222162_s_at ADAMTS1 -1.57 KIAA1712 228334_x_at KIAA1712 -1.57 deleted in lymphocytic leukemia, 1 205677_s_at DLEU1 -1.57 hypothetical protein FLJ30596 228594_at FLJ30596 -1.57 G protein-coupled receptor kinase interactor 2 225558_at GIT2 -1.57 DKFZP434F091 protein 225730_s_at THUMPD3 -1.56 nuclear receptor subfamily 2, group F, member 2 209120_at NR2F2 -1.55 T-cell immunomodulatory protein 1556151_at CDA08 -1.55 hypothetical protein DKFZp434L0117 227818_at DKFZP434L01 -1.55 Zic family member 2 (odd-paired homolog, Drosophila) 223642_at ZIC2 -1.55 NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa 226209_at NDUFV3 -1.54 potassium channel tetramerisation domain containing 3 217894_at KCTD3 -1.54 activating transcription factor 2 212984_at ATF2 -1.54 arrestin domain containing 3 224797_at ARRDC3 -1.54 cyclin E2 205034_at CCNE2 -1.54 novel C3HC4 type Zinc finger (ring finger) 226360_at FLJ12747 -1.54 dishevelled associated activator of morphogenesis 1 216060_s_at DAAM1 -1.54 discs, large homolog 3 (neuroendocrine-dlg, Drosophila) 207732_s_at DLG3 -1.53 hypothetical protein FLJ11017 219450_at FLJ11017 -1.53 potassium channel tetramerisation domain containing 15 222668_at KCTD15 -1.53 CDNA FLJ26557 fis, clone LNF01992 229004_at ADAMTS15 -1.53 MCM10 minichromosome maintenance deficient 10 (S. cerevisiae) 220651_s_at MCM10 -1.52 mitochondrial tumor suppressor gene 1 212096_s_at MTUS1 -1.52 anaphase-promoting complex subunit 10 241959_at ANAPC10 -1.52 thrombospondin 1 201109_s_at THBS1 -1.52 hypothetical protein FLJ11342 222697_s_at FLJ11342 -1.51 ankyrin repeat domain 15 213005_s_at ANKRD15 -1.51 single-minded homolog 2 (Drosophila) 206558_at SIM2 -1.51 pleckstrin homology domain containing, family E (with leucine rich repeats) member 1 212719_at PLEKHE1 -1.51 FLJ25476 protein 226820_at FLJ25476 -1.51 cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant 212905_at CSTF2T -1.51 zinc finger protein 451 212557_at ZNF451 -1.51 chondroitin sulfate proteoglycan 6 (bamacan) 209257_s_at CSPG6 -1.51 golgi associated, gamma adaptin ear containing, ARF binding protein 2 208915_s_at GGA2 -1.51 erythrocyte membrane protein band 4.1-like 1 212336_at EPB41L1 -1.50 hypothetical protein FLJ12436 218722_s_at FLJ12436 -1.50 DNA (cytosine-5-)-methyltransferase 3 beta 220668_s_at DNMT3B -1.50 death-associated protein kinase 1 203139_at DAPK1 -1.50 ubiquitin specific protease 1 202412_s_at USP1 -1.50

Supplemental Table: Unique decreased by TNFalpha and response to IKI-1. For each cohort, RNA was individually purified from three independently treated cell samples, amplified and hybridized to three independent oligonucleotide arrays. Signal intensity was averaged for each of the treatment groups and reported in columns I to L along with standard of deviation (columns M-P). Average Fold Change and Student tTest (not corrected for false discovery rate) comparing TNFalpha to Vehicle treatments is presented in column D and E. Average Fold Change and Student tTest comparing TNFalpha and IKI-1 cotreatment relative to TNFalpha alone is presented in column F and G. Column H reports percentage of TNFalpha decreased mRNA is reversed by cotreatment with IKI-1. Genes were selected by minimum average fold change decrease greater than -1.5 (P<0.01) with minimum mean signal intensity >50 in vehicle (DMSO) treatment. ttest AFC TNFa ttest TNFa % Mean Mean StDev StDev StDev StDev TNFa/ + IKI-1/ + IKI-1/ Inhibition Mean TNFa 5ng Mean IKI- TNFa + IKI- DMSO TNFa IKI-1 TNFa + DMSO TNFa TNFa by IKI-1 DMSO 3hr 3hr 1 1uM 3hr 1 3hr 3hr 5ng 3hr 1uM 3hr IKI-1 3hr 0.0111 1.83 0.0928 46.2 74 26 81 49 14 10 14 14 0.0052 1.42 0.0679 37.8 114 54 98 77 29 212 0.0002 1.13 0.2579 12.0 284 137 234 154 11 14 11 18 0.0027 -2.24 0.0515 -52.5 136 66 62 30 10 13 10 18 0.0013 1.07 0.4016 7.2 255 125 214 135 20 15 20 3 0.0040 1.18 0.3160 20.5 60 31 51 37 56 5 6 0.0117 1.31 0.0208 35.1 133 70 94 92 14 4 14 7 0.0000 1.11 0.1516 13.1 207 110 152 123 24 210 0.0027 1.02 0.8622 2.8 120 65 83 66 9119 10 0.0007 -1.06 0.4620 -6.8 119 64 70 60 57 5 2 0.0037 -1.00 0.9952 -0.1 90 48 64 48 88 8 5 0.0053 1.89 0.0183 105.0 372 201 502 381 25 5 25 44 0.0038 1.11 0.4873 13.0 73 40 40 44 77 7 7 0.0085 1.62 0.0271 74.4 81 44 81 71 49 410 0.0110 1.45 0.1646 54.6 65 36 86 52 88 813 0.0060 -1.04 0.7408 -5.4 166 92 102 88 16 7 16 17 0.0078 1.07 0.6240 9.0 74 41 55 44 48 4 5 0.0121 -1.30 0.2167 -28.9 265 148 135 114 34 31 34 24 0.0013 1.18 0.3739 23.6 51 29 32 34 43 4 8 0.0119 1.42 0.1272 54.9 56 31 44 45 47 4 9 0.0076 1.88 0.0019 116.1 193 110 246 207 20 10 20 3 0.0021 1.64 0.0730 84.3 52 29 59 48 43 410 0.0131 -1.21 0.1950 -22.9 109 62 80 51 14 10 14 4 0.0123 -1.03 0.8043 -4.5 134 77 81 74 17 14 17 9 0.0005 1.22 0.0406 29.6 209 120 204 146 11 9 11 12 0.0001 -1.21 0.0229 -23.4 60 35 33 29 21 2 2 0.0059 1.08 0.7308 10.9 58 34 49 37 46 411 0.0034 -1.26 0.1993 -29.0 88 51 64 40 68 6 9 0.0005 1.06 0.5711 8.7 51 30 35 32 21 2 5 0.0045 -1.12 0.3665 -15.5 108 63 73 56 8108 5 0.0096 -1.07 0.4676 -9.1 61 36 54 33 74 7 2 0.0022 1.06 0.5860 8.9 363 214 334 227 26 26 26 29 0.0038 -1.37 0.0562 -39.0 68 40 41 29 36 3 3 0.0057 1.14 0.2006 19.6 189 112 153 127 18 12 18 12 0.0001 1.64 0.0004 93.8 1509 894 1921 1471 41 28 41 51 0.0061 -1.03 0.4212 -5.0 71 43 55 41 41 4 2 0.0100 1.13 0.3823 20.3 112 67 73 76 9139 9 0.0017 1.41 0.0155 62.3 115 69 103 98 57 5 9 0.0104 1.31 0.0043 46.9 292 176 262 231 27 9 27 12 0.0143 -1.06 0.7200 -8.0 80 48 38 46 94 910 0.0111 1.21 0.2145 32.1 126 76 87 92 8148 12 0.0013 -1.04 0.7371 -6.1 63 38 51 37 44 4 6 0.0028 1.17 0.1403 26.6 175 106 144 124 14 11 14 13 0.0002 1.03 0.4890 4.5 169 103 123 106 64 6 6 0.0002 1.18 0.1256 27.1 635 386 487 453 24 18 24 49 0.0125 1.02 0.8759 3.5 80 49 63 50 27 2 9 0.0015 1.34 0.0146 52.6 246 149 240 200 12 16 12 14 0.0004 1.43 0.0377 66.8 107 65 118 93 55 512 0.0092 -1.54 0.0214 -54.8 79 48 35 31 85 8 2 0.0085 1.35 0.0485 55.4 62 38 51 51 46 4 5 0.0013 -1.03 0.8312 -5.4 96 59 65 57 25 214 0.0027 1.54 0.0064 86.0 331 203 540 313 22 13 22 25 0.0149 -1.03 0.8462 -4.8 96 59 65 57 29 212 0.0088 -1.04 0.7520 -6.2 114 70 81 68 10 12 10 6 0.0009 1.39 0.2103 63.9 64 40 53 55 21 215 0.0040 -1.04 0.6398 -5.9 362 225 254 217 26 13 26 24 0.0056 1.03 0.8135 4.7 173 107 120 110 15 14 15 15 0.0149 -1.08 0.4865 -11.8 463 289 305 268 39 6 39 42 0.0108 -1.58 0.0047 -61.5 430 269 192 170 41 18 41 23 0.0102 1.36 0.1548 60.0 108 67 118 91 12 9 12 20 0.0064 1.05 0.7178 8.9 233 146 165 154 7177 29 0.0117 1.09 0.6051 15.9 131 82 116 90 8148 19 0.0022 1.05 0.6587 8.1 83 52 76 55 35 3 7 0.0102 1.17 0.2488 29.1 202 127 158 149 19 9 19 24 0.0042 2.10 0.0196 189.2 311 197 534 413 18 25 18 67 0.0148 1.01 0.8889 1.8 137 86 114 87 15 8 15 7 0.0081 1.16 0.1401 28.4 213 135 210 157 21 17 21 12 0.0126 1.56 0.0216 97.3 58 37 55 57 46 4 7 0.0011 1.49 0.0037 86.0 685 436 926 650 34 38 34 18 0.0137 -1.68 0.0101 -70.8 75 48 22 28 85 8 5 0.0055 -1.20 0.0820 -29.4 198 126 129 105 4134 8 0.0079 1.16 0.4173 27.5 182 116 129 134 17 9 17 31 0.0128 1.15 0.2647 26.0 135 86 119 99 13 14 13 5 0.0027 1.36 0.0185 64.9 174 112 165 152 11 12 11 4 0.0005 -1.07 0.2548 -12.6 1036 667 810 621 10 26 10 51 0.0127 -1.13 0.5876 -20.6 857 552 402 489 87 86 87 158 0.0141 1.17 0.1496 31.3 186 120 160 140 20 12 20 15 0.0022 1.05 0.5983 8.5 187 121 156 127 6116 13 0.0124 1.22 0.2491 39.8 72 47 64 57 58 510 0.0009 1.07 0.2543 12.9 157 102 127 109 78 7 2 0.0121 1.76 0.0174 141.3 105 68 100 120 10 5 10 14 0.0004 -1.27 0.0155 -39.2 203 132 123 104 78 7 4 0.0004 1.41 0.0023 75.2 349 227 355 319 14 13 14 6 0.0091 1.53 0.0280 99.2 135 88 128 135 10 3 10 15 0.0052 -1.36 0.0129 -49.9 764 498 418 365 11 41 11 28 0.0018 1.15 0.1098 28.2 121 79 109 91 63 6 8 0.0049 -1.15 0.2601 -24.2 92 60 71 52 77 7 8 0.0007 1.07 0.0892 13.3 253 165 241 177 11 7 11 4 0.0011 1.24 0.0345 45.9 157 103 170 128 37 311 0.0082 1.33 0.0080 64.2 373 246 358 327 20 1 20 13 0.0000 1.11 0.0722 21.1 368 243 316 269 46 415 0.0047 1.71 0.0182 138.2 63 42 73 72 24 2 9 0.0000 1.05 0.6467 9.0 1380 910 1139 952 14 11 14 137 0.0033 1.22 0.0568 43.3 242 159 219 195 14 17 14 16 0.0078 1.23 0.0260 44.7 101 67 91 82 61 6 5 0.0001 -1.10 0.4529 -17.4 57 38 37 34 11 1 6 0.0020 1.30 0.0644 57.9 133 88 107 114 86 814 0.0008 1.14 0.1304 27.9 207 137 207 156 10 8 10 14 0.0067 1.14 0.1993 27.2 126 84 116 95 8118 6 0.0055 1.57 0.0050 112.6 111 73 136 115 84 8 8 0.0065 1.21 0.4245 42.1 183 121 148 147 15 14 15 45 0.0084 1.45 0.1525 88.0 144 95 151 138 11 4 11 33 0.0027 1.45 0.2959 88.4 147 98 129 141 84 854 0.0084 -1.09 0.3440 -16.4 386 257 277 235 12 29 12 16 0.0085 1.09 0.5054 17.8 70 47 47 51 56 5 8 0.0138 1.07 0.5533 14.8 102 68 89 73 9119 8 0.0030 1.07 0.4538 14.2 252 168 204 180 17 14 17 20