Supplemental Table 1 List of genes differentially expressed in normal nasopharyngeal epithelium (N), metaplastic and displastic lesions (R), and carcinoma (T). Parametric Permutation Geom Geom Geom Unique Description Clone UG Gene symbol Map p-value p-value mean mean mean id cluster of of of ratios ratios ratios in in in class class class 1 : N 2 : R 3 : T 1 p < 1e-07 0 0.061 0.123 2.708 169329 secretory leukocyte protease IncytePD:2510171 Hs.251754 SLPI 20q12 inhibitor (antileukoproteinase) 2 p < 1e-07 0 0.125 0.394 1.863 163628 sodium channel, nonvoltage-gated IncytePD:1453049 Hs.446415 SCNN1A 12p13 1 alpha 3 p < 1e-07 0 0.122 0.046 1.497 160401 carcinoembryonic antigen-related IncytePD:2060355 Hs.73848 CEACAM6 19q13.2 cell adhesion molecule 6 (non- specific cross reacting antigen) 4 p < 1e-07 0 0.675 1.64 5.594 165101 monoglyceride lipase IncytePD:2174920 Hs.6721 MGLL 3q21.3 5 p < 1e-07 0 0.182 0.487 0.998 166827 nei endonuclease VIII-like 1 (E. IncytePD:1926409 Hs.28355 NEIL1 15q22.33 coli) 6 p < 1e-07 0 0.194 0.339 0.915 162931 hypothetical protein FLJ22418 IncytePD:2816379 Hs.36563 FLJ22418 1p11.1 7 p < 1e-07 0 1.313 0.645 13.593 162399 S100 calcium binding protein P IncytePD:2060823 Hs.2962 S100P 4p16 8 p < 1e-07 0 0.157 1.445 2.563 169315 selenium binding protein 1 IncytePD:2591494 Hs.334841 SELENBP1 1q21-q22 9 p < 1e-07 0 0.046 0.738 1.213 160115 prominin-like 1 (mouse) IncytePD:2070568 Hs.112360 PROML1 4p15.33 10 p < 1e-07 0 0.787 2.264 3.013 167294 HRAS-like suppressor 3 IncytePD:1969263 Hs.37189 HRASLS3 11q12.3 11 p < 1e-07 0 0.292 0.539 1.493 168221 Homo sapiens cDNA FLJ13510 IncytePD:64451 Hs.37896 2 fis, clone PLACE1005146. 12 p < 1e-07 0 1.816 4.162 5.231 159872 emerin (Emery-Dreifuss muscular IncytePD:1901168 Hs.2985 EMD Xq28 dystrophy) 13 p < 1e-07 0 0.096 0.237 1.251 168256 B-factor, properdin IncytePD:167371 Hs.69771 BF 6p21.3 14 p < 1e-07 0 0.112 0.566 1.205 161755 Incyte EST IncytePD:1507769 15 p < 1e-07 0 0.113 0.366 0.603 161021 zinc finger protein 204 IncytePD:1454640 Hs.8198 ZNF204 6p21.3 16 p < 1e-07 0 0.079 0.575 0.519 168604 amylase, alpha 2B; pancreatic IncytePD:254081 Hs.335493 AMY2B 1p21 17 p < 1e-07 0 0.587 1.038 0.785 168160 zinc finger protein 161 homolog IncytePD:2487368 Hs.156000 ZFP161 18pter- (mouse) p11.2 18 1e-07 0 0.376 0.972 1.84 167971 Meis1, myeloid ecotropic viral IncytePD:1662216 Hs.380923 MEIS3 17p11.2 integration site 1 homolog 3 (mouse) 19 1e-07 0 0.048 0.247 0.388 162648 retinoic acid receptor responder IncytePD:1982324 Hs.82547 RARRES1 3q25.32 (tazarotene induced) 1 20 1e-07 0 0.231 0.783 0.812 164495 hypothetical protein LOC283445 IncytePD:1968776 Hs.234898 LOC283445 12q24.12 21 1e-07 0 0.423 0.975 1.436 163838 family with sequence similarity 13, IncytePD:1458366 Hs.177664 FAM13A1 4q22.1 member A1 22 1e-07 0 0.538 0.644 1.867 166314 LIM domain only 2 (rhombotin- IncytePD:1383888 Hs.184585 LMO2 11p13 like 1) 23 1e-07 0 0.023 0.095 0.53 164946 polymeric immunoglobulin IncytePD:1800114 Hs.205126 PIGR 1q31-q41 receptor 24 1e-07 0 0.283 0.959 1.196 163419 calmin (calponin-like, IncytePD:1464613 Hs.406099 CLMN 14q32.2 transmembrane) 25 1e-07 0 0.477 1.445 1.307 162175 truncated calcium binding protein IncytePD:1943110 Hs.351621 LOC51149 5q35.3 26 1e-07 0 0.481 0.977 1.168 163378 hypothetical protein IncytePD:2921913 Hs.48219 DKFZp434M033 12q23.2 DKFZp434M0331 27 1e-07 0 0.252 0.233 1.726 166900 likely ortholog of mouse tumor IncytePD:429577 Hs.44208 FLJ23153 7q21.12 necrosis-alpha-induced adipose- related protein 28 1e-07 0 0.572 1.406 1.553 165608 REMOVED_FROM_DATABASE IncytePD:91009 29 1e-07 0 0.379 1.149 1.305 165030 galactosamine (N-acetyl)-6-sulfate IncytePD:2903239 Hs.159479 GALNS 16q24.3 sulfatase (Morquio syndrome, mucopolysaccharidosis type IVA) 30 1e-07 0 0.27 0.949 0.925 160243 iduronate 2-sulfatase (Hunter IncytePD:549290 Hs.172458 IDS Xq28 syndrome) 31 1e-07 0 0.401 0.79 1.775 168767 protein tyrosine phosphatase, IncytePD:2941607 Hs.19718 PTPRU 1p35.3- receptor type, U p35.1 32 1e-07 0 0.032 0.239 1.15 166595 microseminoprotein, beta- IncytePD:3970665 33 1e-07 0 0.653 1.184 1.978 159959 Fanconi anemia, complementation IncytePD:1647354 group A 34 1e-07 0 1.376 0.457 0.853 168559 tripartite motif-containing 16 IncytePD:1996011 Hs.241305 TRIM16 17p11.2 35 1e-07 0 0.682 1.36 1.532 162892 KIAA1228 protein IncytePD:2667106 Hs.306867 KIAA1228 7q36.3 36 2e-07 0 0.261 2.62 3.645 164879 serum amyloid A4, constitutive IncytePD:86390 Hs.1955 SAA4 11p15.1- p14 37 2e-07 0 0.67 1.763 1.345 168694 acylphosphatase 1, erythrocyte IncytePD:1995749 Hs.18573 ACYP1 14q24.3 (common) type 38 2e-07 0 0.962 2.243 2.478 162612 Rho-related BTB domain IncytePD:2095275 Hs.15099 RHOBTB1 10q21.2 containing 1 39 2e-07 0 0.097 0.26 0.515 165530 cytochrome P450, family 2, IncytePD:1597231 Hs.152096 CYP2J2 1p31.3- subfamily J, polypeptide 2 p31.2 40 2e-07 0 0.239 0.683 0.979 165148 Homo sapiens, clone IncytePD:1666815 Hs.72080 21 IMAGE:4766144, mRNA 41 2e-07 0 0.801 0.319 0.361 168279 Homo sapiens, Similar to IncytePD:1987866 Hs.106771 5 hypothetical protein B430208I01, clone IMAGE:5181522, mRNA, partial cds 42 2e-07 0 0.072 0.298 0.917 166593 Wilms tumor associated protein IncytePD:2997479 Hs.251573 WIT-1 11p13 43 2e-07 0 1.298 1.911 5.067 167270 keratin 7 IncytePD:1649959 Hs.23881 KRT7 12q12- q13 44 2e-07 0 0.074 0.428 0.661 166636 ESTs, Weakly similar to neuronal IncytePD:2714867 Hs.436950 11 thread protein [Homo sapiens] [H.sapiens] 45 3e-07 0 0.41 4.837 4.942 164490 carboxylesterase 1 IncytePD:1813269 Hs.76688 CES1 16q13- (monocyte/macrophage serine q22.1 esterase 1) 46 3e-07 0 0.643 2.729 4.235 165666 ribonuclease, RNase A family, 4 IncytePD:1858905 Hs.283749 RNASE4 14q11.1 47 3e-07 0 0.449 1.314 1.636 162294 calcium channel, voltage- IncytePD:2057662 Hs.250712 CACNB3 12q13 dependent, beta 3 subunit 48 3e-07 0 0.132 0.48 0.78 160334 ATPase, Class II, type 9A IncytePD:1942046 Hs.406434 ATP9A 20q13.11- q13.2 49 4e-07 0 0.12 0.591 1.034 161500 regulatory factor X, 2 (influences IncytePD:2674796 Hs.100007 RFX2 19p13.3- HLA class II expression) p13.2 50 4e-07 0 0.124 0.079 0.726 160357 coagulation factor III IncytePD:2061594 Hs.62192 F3 1p22-p21 (thromboplastin, tissue factor) 51 4e-07 0 0.225 0.531 0.869 160168 kinesin family member 13B IncytePD:2708596 Hs.15711 KIF13B 8p12 52 5e-07 0 0.496 0.83 0.872 160625 myeloid/lymphoid or mixed- IncytePD:1887185 Hs.114765 MLLT2 4q21 lineage leukemia (trithorax homolog, Drosophila); translocated to, 2 53 5e-07 0 0.753 1.526 1.27 162298 hypothetical protein LOC90410 IncytePD:1552481 Hs.4187 LOC90410 17q11.1 54 5e-07 0 0.112 0.193 0.311 160654 B-cell CLL/lymphoma 6 (zinc IncytePD:1569189 Hs.155024 BCL6 3q27 finger protein 51) 55 6e-07 0 0.25 0.915 1.585 159838 aldehyde dehydrogenase 3 family, IncytePD:2610218 Hs.83155 ALDH3B1 11q13 member B1 56 6e-07 0 0.104 0.771 1.25 160072 solute carrier family 22 (organic IncytePD:1308162 Hs.77239 SLC22A4 5q31.1 cation transporter), member 4 57 6e-07 0 0.092 0.417 0.466 166685 KIAA0675 gene product IncytePD:1794725 Hs.165662 KIAA0675 3q13.12 58 7e-07 0 0.295 0.505 0.693 165716 complement component 5 receptor IncytePD:1447909 Hs.2161 C5R1 19q13.3- 1 (C5a ligand) q13.4 59 7e-07 0 0.669 1.017 2.773 169559 E74-like factor 3 (ets domain IncytePD:1988412 Hs.166096 ELF3 1q32.2 transcription factor, epithelial- specific ) 60 7e-07 0 0.736 1.472 1.208 169562 CDC16 cell division cycle 16 IncytePD:1413704 Hs.1592 CDC16 13q34 homolog (S. cerevisiae) 61 8e-07 0 0.099 0.766 5.296 165371 trefoil factor 3 (intestinal) IncytePD:2242817 Hs.82961 TFF3 21q22.3 62 8e-07 0 0.587 1.254 1.723 164531 Homo sapiens cDNA: FLJ22050 IncytePD:2868216 Hs.173705 4 fis, clone HEP09454. 63 8e-07 0 0.175 0.465 0.618 163376 ESTs IncytePD:2818878 Hs.32135 20 64 8e-07 0 0.21 0.664 0.872 163828 mucin 5, subtype B, IncytePD:1737280 Hs.102482 MUC5B 11p15 tracheobronchial 65 8e-07 0 0.327 0.686 0.7 164891 paired box gene 2 IncytePD:194662 Hs.155644 PAX2 10q22.1- q24.3 66 8e-07 0 0.114 0.079 0.535 160506 UDP glycosyltransferase 1 family, IncytePD:86450 Hs.278896 UGT1A1 2q37 polypeptide A1 67 9e-07 0 0.656 1.628 1.865 168674 Homo sapiens, clone IncytePD:1964852 Hs.427683 10 IMAGE:5587702, mRNA 68 9e-07 0 0.414 0.326 1.223 166348 epidermal growth factor receptor IncytePD:1395088 Hs.28907 EPS8R1 19q13.42 pathway substrate 8-related protein 1 69 9e-07 0 0.127 0.349 0.64 166331 Arg/Abl-interacting protein IncytePD:1495766 Hs.379795 ARGBP2 4q35.1 ArgBP2 70 9e-07 0 1.011 2.238 2.34 169526 transducin-like enhancer of split 2 IncytePD:1236828 Hs.332173 TLE2 19p13.3 (E(sp1) homolog, Drosophila) 71 9e-07 0 0.103 0.574 0.967 169644 hypothetical protein MGC27085 IncytePD:1256859 Hs.120277 MGC27085 3q26.31 72 9e-07 0 0.01 0.039 0.431 161792 tetraspan 1 IncytePD:2989680 Hs.38972 TSPAN-1 1p33 73 1e-06 0 0.17 0.872 1.348 163423 Incyte EST IncytePD:2279991 74 1e-06 0 0.238 0.485 0.47 159850 Homo sapiens cDNA FLJ34315 IncytePD:1734634 Hs.376655 14 fis, clone FEBRA2008341.