Supplementary Table S4 - Genes downregulated by anti-MYCN PNA ProbeID Symbol Description RH30ctrl_SignalRH30mut__SignalRH30pna_Signalpna vs mut pna vs ctrl 210842_at NRP2 neuropilin 2 109.8 83.2 3.4 -4.613 -5.013 219239_s_at ZNF654 zinc finger protein 654 155.9 140.8 6.8 -4.372 -4.519 220786_s_at SLC38A4 solute carrier family 38, member 4 91.8 135.1 17.7 -2.932 -2.375 206205_at MPHOSPH9 M-phase phosphoprotein 9 208.2 235.7 39.2 -2.588 -2.409 201171_at ATP6V0E ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e 93.5 105 19.1 -2.459 -2.291 204732_s_at TRIM23 tripartite motif-containing 23 132.9 126.3 31 -2.027 -2.100 221079_s_at METTL2B methyltransferase like 2B 141.8 236.9 58.8 -2.010 -1.270 216971_s_at PLEC1 plectin 1, intermediate filament binding protein 500kDa 170 176.3 44.7 -1.980 -1.927 221703_at BRIP1 BRCA1 interacting protein C-terminal helicase 1 137 200.4 52.6 -1.930 -1.381 213647_at DNA2L DNA2 DNA replication helicase 2-like (yeast) 180.5 226.1 61.4 -1.881 -1.556 217547_x_at ZNF675 zinc finger protein 675 89.6 93.3 26 -1.843 -1.785 209865_at SLC35A3 solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 191.6 171.3 50.4 -1.765 -1.927 AFFX-M27830_5_atSOX18 SRY (sex determining region Y)-box 18 755.4 982.7 295.8 -1.732 -1.353 212177_at C6orf111 chromosome 6 open reading frame 111 453.6 484.7 147.8 -1.713 -1.618 211088_s_at PLK4 polo-like kinase 4 (Drosophila) 174.6 122.1 37.4 -1.707 -2.223 213880_at LGR5 leucine-rich repeat-containing G protein-coupled receptor 5 172 178 56.2 -1.663 -1.614 201534_s_at UBL3 ubiquitin-like 3 948 900.4 287.1 -1.649 -1.723 219787_s_at ECT2 epithelial cell transforming sequence 2 oncogene 590.7 640.6 205.5 -1.640 -1.523 206852_at EPHA7 EPH receptor A7 287.7 292.6 97 -1.593 -1.569 201083_s_at BCLAF1 BCL2-associated transcription factor 1 338.7 405.8 135.5 -1.582 -1.322 204873_at PEX1 peroxisome biogenesis factor 1 349.9 487.7 164.2 -1.571 -1.091 214429_at MTMR6 myotubularin related protein 6 1213.5 830.9 291.5 -1.511 -2.058 200733_s_at PTP4A1 protein tyrosine phosphatase type IVA, member 1 1139.7 1289.3 457.9 -1.493 -1.316 201437_s_at EIF4E eukaryotic translation initiation factor 4E 1195.8 1312 466.3 -1.492 -1.359 40612_at DOPEY1 dopey family member 1 77.1 107.5 38.6 -1.478 -0.998 218772_x_at TMEM38B transmembrane protein 38B 489.4 505.1 181.4 -1.477 -1.432 221568_s_at LIN7C lin-7 homolog C (C. elegans) 1105.3 1300.6 468.9 -1.472 -1.237 204525_at PHF14 PHD finger protein 14 189.1 241 86.9 -1.472 -1.122 212930_at ATP2B1 ATPase, Ca++ transporting, plasma membrane 1 777.7 868.4 313.3 -1.471 -1.312 203078_at CUL2 cullin 2 166.1 155.6 56.2 -1.469 -1.563 213118_at KIAA0701 271 231.6 83.7 -1.468 -1.695 222250_s_at C1orf73 chromosome 1 open reading frame 73 355.3 397.8 144.4 -1.462 -1.299 215385_at FTO 175.8 214.3 78 -1.458 -1.172 205964_at ZNF426 zinc finger protein 426 267.5 242.9 88.7 -1.453 -1.593 214155_s_at LARP4 La ribonucleoprotein domain family, member 4 404 494 182.5 -1.437 -1.146 218649_x_at SDCCAG1 serologically defined colon cancer antigen 1 605.4 575.4 213 -1.434 -1.507 203791_at DMXL1 Dmx-like 1 188.6 145.4 53.9 -1.432 -1.807 32723_at CSTF1 cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa 657.5 805.5 298.7 -1.431 -1.138 206770_s_at SLC35A3 solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 280.9 282.6 104.9 -1.430 -1.421 215143_at FLJ36166 119.9 104.1 38.7 -1.428 -1.631 212927_at SMC5L1 SMC5 structural maintenance of chromosomes 5-like 1 (yeast) 475.4 534.7 199.8 -1.420 -1.251 203049_s_at KIAA0372 KIAA0372 711.6 769.9 288 -1.419 -1.305 215936_s_at KIAA1033 KIAA1033 433.1 333.5 125 -1.416 -1.793 212388_at USP24 ubiquitin specific peptidase 24 733.9 770.1 292.4 -1.397 -1.328 213049_at GARNL1 GTPase activating Rap/RanGAP domain-like 1 372.5 377 143.5 -1.394 -1.376 214306_at OPA1 optic atrophy 1 (autosomal dominant) 433.2 419.2 159.7 -1.392 -1.440 213225_at PPM1B protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform 663.3 940.4 359.8 -1.386 -0.882 209314_s_at HBS1L HBS1-like (S. cerevisiae) 328.2 298.4 114.5 -1.382 -1.519 213372_at PAQR3 progestin and adipoQ receptor family member III 842.2 1211.4 466.3 -1.377 -0.853 212984_at ATF2 activating transcription factor 2 302.8 266.2 102.9 -1.371 -1.557 209551_at YIPF4 Yip1 domain family, member 4 383.1 367.1 142.7 -1.363 -1.425 218196_at OSTM1 osteopetrosis associated transmembrane protein 1 618 612.2 238.9 -1.358 -1.371 212060_at SR140 731.8 696.7 272.7 -1.353 -1.424 206555_s_at THUMPD1 THUMP domain containing 1 981.4 967.3 379.2 -1.351 -1.372 216609_at TXN thioredoxin 466.4 521.4 204.5 -1.350 -1.189 219439_at C1GALT1 core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 389.1 501.4 197.4 -1.345 -0.979 205430_at BMP5 bone morphogenetic protein 5 567.9 552.6 217.7 -1.344 -1.383 209657_s_at HSF2 heat shock transcription factor 2 684.2 780.2 309.2 -1.335 -1.146 208653_s_at CD164 CD164 antigen, sialomucin 725.1 737.2 292.5 -1.334 -1.310 201151_s_at MBNL1 muscleblind-like (Drosophila) 343.1 385.9 153.3 -1.332 -1.162 210281_s_at ZNF198 zinc finger protein 198 220.9 200.5 80.2 -1.322 -1.462 215629_s_at KIAA1799 1369.5 1290.3 522 -1.306 -1.392 208883_at EDD1 E3 ubiquitin protein ligase, HECT domain containing, 1 316.1 338.6 137.2 -1.303 -1.204 218352_at RCBTB1 regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1 528.6 586.9 239.1 -1.296 -1.145 212569_at SMCHD1 structural maintenance of chromosomes flexible hinge domain containing 1 468.8 430.9 176.6 -1.287 -1.408 219625_s_at COL4A3BP collagen, type IV, alpha 3 (Goodpasture antigen) binding protein 391.7 334.4 137.4 -1.283 -1.511 210293_s_at SEC23B Sec23 homolog B (S. cerevisiae) 1138.4 878.3 362.2 -1.278 -1.652 220295_x_at DEPDC1 DEP domain containing 1 360.3 464.3 191.8 -1.275 -0.910 218578_at CDC73 cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) 322.9 307.7 127.2 -1.274 -1.344 204342_at SLC25A24 solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24 1658.1 2225.4 924.6 -1.267 -0.843 212917_x_at FLJ22028 648.7 714.3 297.2 -1.265 -1.126 200841_s_at EPRS glutamyl-prolyl-tRNA synthetase 343.6 347.5 144.6 -1.265 -1.249 202259_s_at PFAAP5 778.2 821.2 343.3 -1.258 -1.181 203510_at MET met proto-oncogene (hepatocyte growth factor receptor) 2448.9 2994.1 1253.9 -1.256 -0.966 202034_x_at RB1CC1 RB1-inducible coiled-coil 1 357.2 391.2 164.1 -1.253 -1.122 59644_at BMP2K BMP2 inducible kinase 307.2 302.3 127.1 -1.250 -1.273 221749_at YTHDF3 YTH domain family, member 3 1406.8 1386 588.4 -1.236 -1.258 205122_at TMEFF1 transmembrane protein with EGF-like and two follistatin-like domains 1 739.3 1184.6 503.2 -1.235 -0.555 200685_at SFRS11 splicing factor, arginine/serine-rich 11 359.1 386.4 164.2 -1.235 -1.129 205091_x_at RECQL RecQ protein-like (DNA helicase Q1-like) 367.4 430.5 184.2 -1.225 -0.996 212417_at SCAMP1 secretory carrier membrane protein 1 311.2 292.9 125.8 -1.219 -1.307 203525_s_at APC adenomatosis polyposis coli 263.6 286.1 122.9 -1.219 -1.101 218311_at MAP4K3 mitogen-activated protein kinase kinase kinase kinase 3 700.3 892 383.9 -1.216 -0.867 214658_at TMED7 transmembrane emp24 protein transport domain containing 7 601 566.3 244.6 -1.211 -1.297 218875_s_at FBXO5 F-box protein 5 849.8 1005.6 435.9 -1.206 -0.963 202933_s_at YES1 v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 3271.6 3247.5 1412 -1.202 -1.212 208296_x_at TNFAIP8 tumor necrosis factor, alpha-induced protein 8 509.4 559.1 243.4 -1.200 -1.065 215245_x_at FMR1 fragile X mental retardation 1 3125.6 4346.9 1901.8 -1.193 -0.717 203651_at ZFYVE16 zinc finger, FYVE domain containing 16 575.9 824.4 361.1 -1.191 -0.673 212179_at C6orf111 chromosome 6 open reading frame 111 1048.5 874.6 383.9 -1.188 -1.450 203970_s_at PEX3 peroxisomal biogenesis factor 3 335.8 347.5 152.6 -1.187 -1.138 214804_at FSHPRH1 FSH primary response (LRPR1 homolog, rat) 1 393.7 439.7 193.6 -1.183 -1.024 203276_at LMNB1 lamin B1 1675.9 2259.4 998.1 -1.179 -0.748 204832_s_at BMPR1A bone morphogenetic protein receptor, type IA 368.2 378.5 167.4 -1.177 -1.137 209681_at SLC19A2 solute carrier family 19 (thiamine transporter), member 2 763.5 901.4 398.9 -1.176 -0.937 221596_s_at DKFZP564O0523 257.2 249.7 110.6 -1.175 -1.218 209004_s_at FBXL5 F-box and leucine-rich repeat protein 5 1104.2 1251.6 557.3 -1.167 -0.986 212636_at QKI quaking homolog, KH domain RNA binding (mouse) 909.1 1235.2 550.1 -1.167 -0.725 213817_at 520.5 534 238.6 -1.162 -1.125 219631_at LRP12 low density lipoprotein-related protein 12 353.5 399.8 179.1 -1.159 -0.981 207719_x_at CEP170 centrosomal protein 170kDa 849.6 1085.7 487 -1.157 -0.803 203830_at C17orf75 chromosome 17 open reading frame 75 410.4 500.4 226.2 -1.145 -0.859 212138_at SCC-112 1312.7 1107.1 500.9 -1.144 -1.390 212526_at SPG20 spastic paraplegia 20, spartin (Troyer syndrome) 1076.8 1338.9 606.5 -1.142 -0.828 218490_s_at ZNF302 zinc finger protein 302 576.3 582.8 264.9 -1.138 -1.121 220327_at VGLL3 vestigial like 3 (Drosophila) 345.4 343 156.1 -1.136 -1.146 212420_at ELF1 E74-like factor 1 (ets domain transcription factor) 271.8 272.5 124.2 -1.134 -1.130 221931_s_at SEH1L SEH1-like (S.