Supplementary Table 1: Histopathological data for samples used in study Sample Type WHO Tumor Comments ID histology* stage** N1 Normal NA NA Biopsy Negative Control N2 Normal NA NA Biopsy Negative Control N3 Normal NA NA Biopsy Negative Control N4 Normal NA NA Biopsy Negative Control N5 Normal NA NA Adjacent pair of T18 N6 Normal NA NA Adjacent pair of T20 N7 Normal NA NA Adjacent pair of T7 N8 Normal NA NA Adjacent pair of T10 N9 Normal NA NA N10 Normal NA NA T1 Tumor IIB T1N1 T2 Tumor IIB T2N2 T3 Tumor IIA T3N2 T4 Tumor IIA T2N2 T5 Tumor IIB T2N1 T6 Tumor IIA T1N1 T7 Tumor IIA T1N1 T8 Tumor IIA T1N1 T9 Tumor IIB T1N0 T10 Tumor IIB T2N2 T11 Tumor IIB T1N1 T12 Tumor IIB T2N2 T13 Tumor IIA T2N1 T14 Tumor IIA T1N1 T15 Tumor IIA T1N0 T16 Tumor IIA T1N1 T17 Tumor IIA T1N1 T18 Tumor IIB T1N0 T19 Tumor IIB T1N1 T20 Tumor IIA T3N0 T21 Tumor IIB T2N1 T22 Tumor IIB T2N2 T23 Tumor IIA T2N2 T24 Tumor IIB T1N0 T25 Tumor IIA T2N1 T26 Tumor IIB T3N1 T27 Tumor IIA T1N1 T28 Tumor IIA T1N0 T29 Tumor IIB T1N0 T30 Tumor IIA T2N1 T31 Tumor IIB T3N2 * WHO Histology IIA: Non-Keratinizing Carcinoma and Moderately Differentiated Squamous cell carcinoma IIB: Undifferentiated Carcinoma, Poorly Differentiated Squamous cell carcinoma and Non-Keratinizing Carcinoma, Undifferentiated ** Tumor stage T1: Primary Tumor confined to nasopharynx T2: Tumor extends to nasal fossa, oropharynx, parapharynx, muscles/nerves below base of skull T3: Tumor extends to bone below base of skull, bone at base of skull, cranial nerve, orbit, infratemporal fossa, laryngopharynx N0: No regional lymph node metastasis N1: Metastasis to lymph nodes in upper neck N2: Metastasis to lymph nodes in mid neck NA: Not Applicable Supplementary Table 2: Primers and probes used for Quantitative Real Time PCR (5'→3') Gene Forward Reverse Probe β-actin TCACCCACACTGTGCCCATCTACGA TGAGGTAGTCAGTCAGGTCCCG ATGCCC TCCCCCATGCCATCCTGCGT BARTs GCC TGG CGG ACT TCA TTC T TCT CCT GTA ACC ACC TGG CG ACA GTC CCG AGA CCG GCT CCG BHRF1 GCA GGA CAT TGT GTT GTA ACC AG TAA TGT AGA CCA GCC GCC CT CTA CTC CTT ACT ATG TTG TGG ACC TGT CAG TTC GTG BZLF1 CCC AAG CCT GGA TGT TGA CT GAA GCA GGC GTG GTT TCA AT CAT TAT CCC CCG GAC ACC AGA TGT TTT ACA EBNA1 AGG ATG CGA TTA AGG ACC TTG TT CCA TCG TCA AAG CTG CAC AC TGA CAA AGC CCG CTC CTA CCT GCA ATA EBNA2 CGG CAA CCC CTA ACG TTT C GGG AAG AGA ATG GGA GCC TC CCA ATA CAT GAA CCG GAG TCC CAT AAT AGC C EBNA3A GTG GCA CTT GAG CGA CCA G TAA TGC CAG AAG TTT CCC CG TTA CCC CAA GCC AGT TCG TCC GG EBNA3B GGG CAC ATT CCA TAT CAG CC CTC TCG GTG GTG TCT GCA TG ACC AAC GGG TCC TGC TAC CAT GCT GT EBNA3C CAA GGT GCA TTT ACC CCA CTG GGG CAG GTC CGT GAG AAC T CAT TAA TGC CAC CAC GCC AAA AAG GC LMP1 TCC TCC TGT TTC TGG CGA TTT GGG AGT CAT CGT GGT GGT GT AAT CTG GAT GTA TTA CCA TGG ACA ACG ACA CA LMP2A CCG TCA CTC GGA CTA TCA AC TGA GAT GAG TCA TCC CGT GGA TCA TTC CCG TCG TGT TGC AAT CCC AAG TAC AG HLA -A,F CTG AGA TGG GAG CCG TCT TC AAC CAG GCC AGC AAT GAT G CAG CCC ACC ATC CCC ATC GTG Supplementary Table 3: Genes whose expression is upregulated in tumors Gene Symbol Fold Gene Title Chromosomal Affymetrix Change Location Probeset ID CXCL11 14.31 chemokine (C-X-C motif) ligand 11 4q21.2 211122_s_at CXCL11 13.31 chemokine (C-X-C motif) ligand 11 4q21.2 210163_at FN1 9.21 fibronectin 1 /// fibronectin 1 2q34 /// 2q34 211719_x_at PTGS2 8.69 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 1q25.2-q25.3 204748_at FN1 7.61 fibronectin 1 2q34 212464_s_at CXCL10 7.56 chemokine (C-X-C motif) ligand 10 4q21 204533_at OSF-2 7.37 osteoblast specific factor 2 (fasciclin I-like) 13q13.3 210809_s_at --- 7.16 Homo sapiens mRNA; cDNA DKFZp686G12112 (from clone DKFZp686G12112) --- 227921_at LAMB1 6.53 laminin, beta 1 7q22 201505_at FN1 6.52 fibronectin 1 2q34 210495_x_at FLJ12505 6.34 hypothetical protein FLJ12505 1q32.3 235343_at FN1 6.25 fibronectin 1 2q34 216442_x_at --- 6.21 Homo sapiens clone 23688 mRNA sequence --- 213808_at --- 6.16 --- --- 1556499_s_at COL1A2 5.93 collagen, type I, alpha 2 7q22.1 202404_s_at --- 5.63 Homo sapiens cDNA FLJ11041 fis, clone PLACE1004405. --- 227140_at CHI3L1 5.55 chitinase 3-like 1 (cartilage glycoprotein-39) 1q32.1 209395_at CXCL9 5.48 chemokine (C-X-C motif) ligand 9 4q21 203915_at RAMP 5.37 RA-regulated nuclear matrix-associated protein --- 218585_s_at COL4A1 5.24 collagen, type IV, alpha 1 13q34 211980_at C6orf141 5.07 chromosome 6 open reading frame 141 6p12.3 1554314_at HOXC6 5.04 homeo box C6 12q13.3 206858_s_at PTGS2 4.95 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 1q25.2-q25.3 1554997_a_at --- 4.93 Homo sapiens cDNA FLJ45482 fis, clone BRTHA2001953 --- 230312_at TNFAIP6 4.89 tumor necrosis factor, alpha-induced protein 6 2q24.1 206026_s_at --- 4.81 --- --- 211161_s_at GAD1 4.77 glutamate decarboxylase 1 (brain, 67kDa) 2q31 205278_at SULF1 4.73 sulfatase 1 8q13.2 212353_at DKFZp434C0631 4.70 hypothetical protein DKFZp434C0631 12p11.22 228245_s_at PIR51 4.69 RAD51-interacting protein 12p13.2-p13.1 204146_at NID 4.69 nidogen (enactin) 1q43 202007_at TOPK 4.66 T-LAK cell-originated protein kinase 8p21.2 219148_at TYMS 4.65 thymidylate synthetase 18p11.32 202589_at COL5A2 4.59 collagen, type V, alpha 2 2q14-q32 221729_at COL4A2 4.58 collagen, type IV, alpha 2 13q34 211964_at GZMB 4.53 granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1) 14q11.2 210164_at CCNE2 4.52 cyclin E2 8q22.1 205034_at --- 4.51 Homo sapiens transcribed sequences --- 238852_at SYNPO2 4.45 synaptopodin 2 4q27 225895_at COL3A1 4.45 collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) 2q31 215076_s_at CCL2 4.39 chemokine (C-C motif) ligand 2 17q11.2-q21.1 216598_s_at PRO2000 4.22 PRO2000 protein 8q24.13 222740_at ANAPC7 4.19 anaphase-promoting complex subunit 7 12q13.12 204709_s_at CDCA1 4.17 cell division cycle associated 1 1q23.2 223381_at --- 4.10 Human full-length cDNA 5-PRIME end of clone CS0DK007YB08 of HeLa cells of H. sapiens --- 242881_x_at PMCH 4.09 pro-melanin-concentrating hormone 12q23-q24 227928_at MAD2L1 4.06 MAD2 mitotic arrest deficient-like 1 (yeast) 4q27 203362_s_at --- 4.01 Homo sapiens cDNA FLJ11381 fis, clone HEMBA1000501. --- 227350_at PMAIP1 3.95 phorbol-12-myristate-13-acetate-induced protein 1 18q21.32 204286_s_at HEC 3.91 highly expressed in cancer, rich in leucine heptad repeats 18p11.31 204162_at NPL 3.88 N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) 1q25 240440_at ZNF367 3.85 zinc finger protein 367 9q22 229551_x_at COL3A1 3.83 collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) 2q31 201852_x_at CENPF 3.82 centromere protein F, 350/400ka (mitosin) 1q32-q41 209172_s_at C20orf42 3.81 chromosome 20 open reading frame 42 20p12.3 60474_at LAMB1 3.79 laminin, beta 1 /// laminin, beta 1 7q22 /// 7q22 211651_s_at KIAA0186 3.76 KIAA0186 gene product 20p11.21 206102_at BUB1B 3.76 BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) 15q15 203755_at COL8A1 3.75 collagen, type VIII, alpha 1 3q12.3 226237_at TOP2A 3.75 topoisomerase (DNA) II alpha 170kDa 17q21-q22 201292_at C6orf141 3.73 chromosome 6 open reading frame 141 6p12.3 1552575_a_at C10orf3 3.73 chromosome 10 open reading frame 3 10q23.33 218542_at ANLN 3.70 anillin, actin binding protein (scraps homolog, Drosophila) 7p15-p14 222608_s_at BRIP1 3.63 BRCA1 interacting protein C-terminal helicase 1 17q22-q24 235609_at SPARC 3.61 secreted protein, acidic, cysteine-rich (osteonectin) 5q31.3-q32 200665_s_at ADAM23 3.59 a disintegrin and metalloproteinase domain 23 2q33 244463_at XTP1 3.56 HBxAg transactivated protein 1 5q12.1 226980_at ATP11C 3.55 ATPase, Class VI, type 11C Xq27.1 226785_at COL5A2 3.52 collagen, type V, alpha 2 2q14-q32 221730_at --- 3.50 Homo sapiens cDNA FLJ11397 fis, clone HEMBA1000622. --- 232797_at HCAP-G 3.50 chromosome condensation protein G 4p16-p15 218662_s_at --- 3.43 Homo sapiens transcribed sequences --- 236251_at KIAA0286 3.43 KIAA0286 protein 12q13.2 212621_at STAR 3.43 steroidogenic acute regulatory protein 8p11.2 204548_at KIAA0101 3.42 KIAA0101 gene product 15q22.1 202503_s_at CSPG2 3.41 chondroitin sulfate proteoglycan 2 (versican) 5q14.3 204619_s_at CALD1 3.40 caldesmon 1 7q33 212077_at PRO2000 3.39 PRO2000 protein 8q24.13 228401_at FLJ14813 3.38 hypothetical protein FLJ14813 10p12.1 228468_at KLIP1 3.38 KSHV latent nuclear antigen interacting protein 1 4q35.1 229305_at LOC147463 3.37 hypothetical protein LOC147463 18q11.2 238332_at KIF11 3.37 kinesin family member 11 10q24.1 204444_at NUSAP1 3.34 nucleolar and spindle associated protein 1 15q14 218039_at MCM8 3.32 MCM8 minichromosome maintenance deficient 8 (S. cerevisiae) 20p12.3 224320_s_at RRM2 3.31 ribonucleotide reductase M2 polypeptide 2p25-p24 201890_at HELLS 3.31 helicase, lymphoid-specific 10q24.2 242890_at CSPG2 3.29 chondroitin sulfate proteoglycan 2 (versican) 5q14.3 221731_x_at TRAG3 3.26 taxol resistance associated gene 3 Xq28 220445_s_at FZD7 3.25 frizzled homolog 7 (Drosophila) 2q33 203706_s_at NFE2L3 3.25 nuclear factor (erythroid-derived 2)-like 3 7p15-p14 204702_s_at FLJ11029 3.25 hypothetical protein FLJ11029 17q23.2 228273_at CALD1 3.24 caldesmon 1 7q33 201617_x_at CDC2 3.24 cell division cycle 2, G1 to S and G2 to M 10q21.1 203213_at KLIP1 3.24 KSHV latent nuclear antigen interacting protein 1 4q35.1 218883_s_at HELLS 3.21 helicase, lymphoid-specific 10q24.2 220085_at --- 3.20 Homo sapiens transcribed sequences --- 243299_at ADAM22 3.19 a disintegrin and metalloproteinase domain 22 7q21 213411_at PAPSS2 3.17 3'-phosphoadenosine