Figure S1. Comparison of published epithelial senescence expression profiles with the changes >2 fold between normal mucosa and mortal and immortal SCCs identified by SAM analysis (FDR<1%)

Normal mucosa Senescence changes >3 fold versus immortal SCC 3324* 165 in normal oral mucosa (Data from Fig. 3 (Kang et al. 3** Exp Cell Res, 287: 272-281, 2003.) 33 17***

263

Normal mucosa versus mortal SCC

*4 : Down regulated in immortal SCCs but up-regulated in senescent epithelial cells: CEACAM6, DSG3, MMP1 Up-regulated in immortal SCCs but down-regulated in senescent epithelial cells: SMARCA3

**3 genes: Up-regulated both in mortal SCCs and senescent epithelial cells: MMP10 Down-regulated both in mortal SCCs and senescent epithelial cells: BUB1, CDKN3

***17 genes: Up-regulated both in mortal SCCs and senescent epithelial cells: BMPR2, CDKN2B, COL1A1, COL1A2, COL6A1, CXCL3, CYPB1, FN1, IGFBP3, Down-regulated both in mortal SCCs and senescent epithelial cells: BIRC5, CCNA2, CCNB1, CCNB2, CENPF, NRG1, PCNA, SKP2 Table S1 Clinical characteristics of tumours

Biopsy Patient Culture NameSite lesion stage smoking age sex Lifespan (PDs) Normal mucosa FNB3 (N3)BM none N/A n 45 M 25.5 FNB5 (N5)BM none N/A n 40 F 20 FNB6 (N6)BM none N/A n 35 F >24 NB9 (N9)BM normal adjacent N/Ay 53 M >17 Dysplasias D6PT Leukoplakia mod/severe y 55 M 25 D8FOM Leukoplakia mild/mod y 71 M 9 D25FOM Leukoplakia severe y 58 M 28 D30FOM Leukoplakia mild y 52 M 30 D41RM Leukoplakia mild n 55 F 3.5 D47FOM Leukoplakia mod y 82 F 20 D48FOM/VT Leukoplakia mod/severe y 62 F 25.5 D17 (EL)BM Leukoplakia mild/mod y 61 M 61 E1TUU Erythroplakia CIS M 24 E2ALV Erythroplakia CIS U U M 17 E4LT Erythroplakia CIS U 65 F 41 E5LT Erythroplakia severe U 61 M 31 D4 FOM/VTLeukoplakia CIS y 51 M >100 D9VT Leukoplakia mild/mod n 84 M >100 D34LT Leukoplakia mod n 54 F >100 D38LT Leukoplakia mild n 55 F >100 D19LT erythroleukoplakia Severe/CIS y 53 M >100 D20LT Leukoplakia moderate n 50 M >100 D35FOM/VT erythroleukoplakia Severe/CIS y 68 M >100 SCCs BICR 30 (P30)LNX Carcinoma T4N1M0 y U M 17 BICR 66 (P66)RM/T Carcinoma T2N0M0 y 56 M 37 BICR 80 (P80)LNX Carcinoma T4N2CM0 y 71 M 62 BICR 1 (P1)TU68 Carcinoma T2N0M0 M 15 BICR 73 ()Ty49 Carcinoma T2N0M0 M 10 BICR 25 (P25)FOM Carcinoma T2N0M0 y 72 M 15 BICR 3 (P3)ALV Carcinoma T2N0M0 y 56 F >130 BICR 31 (P31)TUU Carcinoma T4N2BM0 M >130 BICR 56 (P56)Ty59 Carcinoma T4N1M0 F >130 BICR 68 (P56)BT Carcinoma T4N0M0 n 75 F >130 T4 (P4)FOM Carcinoma T4N0 U U F >130 T5 (P5)BM Carcinoma T2N2 Y 59 F >130 BICR 78 (P78)ALV Carcinoma T4N1M0 U 68 M >130 BICR 63 (P63)T Carcinoma T2N2BM0 y 70 M >130 BICR 6 (P6)HP Carcinoma T4N1M0 U U M >130 BICR10 (R10)BM Recurrence T4N0M0 n 84 F >130 BICR16 (R16)Ty49 Recurrence T2N0M0 M >130 BICR82 (R82)MX Recurrence N.D. y 48 M >130 BICR 7 (CR7)TY43 Carcinoma T4N2BM0 M 43 (crisis) LN Metastases BICR 37 (M37)Primary:T Metastasis T4N2CM0* U U F 32 BICR 22 (M22)Primary:T Metastasis T4N3M0* U 88 M >130 BICR 18 (M18)Primary:LN Metastasis T4N1M0*UU U >130

The tumor names given in brackets are the abbreviations used in the text

Key: ALV, alveolus; BM, buccal mucosa; BT, base of tongue; CIS, carcinoma in situ; FOM, floor of mouth; HP, hypopharynx; LN, lymph node; LNX, larynx; LT, lateral tongue; MX, maxilla; N/A, not applicable; N.D., not determined; normal adjacent, apparently normal mucosa from patient with SCC; PT, posterior tongue; RM, retromolar trigone; T, tongue; U, information not available; VT, ventral tongue; *, staging of primary SCC. Table S2. Gene expression changes common to mortal and immortal SCCs

Average expression levels (AV) are given from the microarray data with standard deviations (SD).

carcinomas normal mortal immortal recurrence Common Genbank Systematic AV SD AV SD AV SD AV SD ASS NM_000050 207076_s_at 138 53 767 424 760 708 794 274 CKB NM_001823 200884_at 99 25 327 104 243 82 347 92 CUGBP2 U69546 202157_s_at 261 34 112 34 76 11 83 5 CYP27B1 NM_000785 205676_at 657 118 306 171 196 86 163 62 FOXQ1 AI676059 227475_at 134 39 280 89 384 199 622 394 ITM2A; E25A; AL021786 202746_at 43 17 16 8 17 19 11 1 MO25 NM_016289 217873_at 1240 191 620 195 696 268 344 114 MTR3 AF131796 231916_at 123 30 54 45 38 15 56 22 PLCD4 BC006355 224505_s_at 187 23 91 32 77 4 82 3 SIX1 N79004 228347_at 58 5 168 73 144 84 147 35 THBS2 NM_003247 203083_at 233 104 92 14 117 69 63 8 Table S3. Genes consistently 5-fold different in expression between mortal and immortal SCCs by SAM (FDR<1%)

AF1Q 211071_s_at NM_006818 ALDH1A3 203180_at NM_000693 ANLN 222608_s_at NM_018685 ASNS 205047_s_at NM_133436 ASPM 219918_s_at NM_018123 AURKB 209464_at NM_004217 BF 202357_s_at NM_001710 BIRC5 202095_s_at NM_001168 BPGM 203502_at NM_001724 BUB1B 203755_at NM_001211 C10orf3 218542_at NM_018131 C1orf10 220090_at NM_016190 C3 217767_at NM_000064 CCL20 205476_at NM_004591 CCNA2 203418_at NM_001237 CCNB1 214710_s_at NM_031966 CCNB2 202705_at NM_004701 CD24 209772_s_at NM_013230 CDC2 203214_x_at NM_001786 CDC20 202870_s_at NM_001255 CDC6 203968_s_at NM_001254 CDCA7 224428_s_at NM_031942 CDKN2B 236313_at NM_078487 CDKN3 209714_s_at NM_005192 CDSN 206193_s_at NM_001264 CEACAM1 209498_at NM_001712 CEACAM5 201884_at NM_004363 CEACAM6 203757_s_at NM_002483 CENPF 207828_s_at NM_005196 CKS1B 201897_s_at NM_001826 CKS2 204170_s_at NM_001827 COL1A1 202310_s_at NM_000088 COL1A2 202403_s_at NM_000089 COL6A3 201438_at NM_004369 CSPG2 221731_x_at NM_004385 CXCL1 204470_at NM_001511 CXCL5 214974_x_at NM_002994 CXCL6 206336_at NM_002993 DEFB1 210397_at NM_005218 DHRS9 224009_x_at NM_005771 DLG7 203764_at NM_014750 DSC2 204751_x_at NM_004949 ECG2 223720_at NM_032566 ECM1 209365_s_at NM_004425 EHF 225645_at NM_012153 EPS8L1 221665_s_at NM_133180 FAP 209955_s_at NM_004460 FEN1 204768_s_at NM_004111 FKBP1B 206857_s_at NM_054033 FLJ32029 229256_at NM_173582 FN1 216442_x_at NM_002026 FOXM1 202580_x_at NM_021953 FYB 227266_s_at NM_001465 G0S2 213524_s_at NM_015714 GABRP 205044_at NM_014211 HEC 204162_at NM_006101 HES2 231928_at AK091122 HIST2H2AA 214290_s_at NM_003516 HMGB2 208808_s_at NM_002129 HOP 211597_s_at NM_032495 HOXD10 229400_at NM_002148 HSD11B1 205404_at NM_181755 IL1RN 212657_s_at NM_173843 IL8 202859_x_at NM_000584 INSR 227432_s_at NM_000208 IVL 214599_at NM_005547 KIAA0101 202503_s_at NM_014736 KIAA0186 206102_at NM_021067 KIAA1359 231941_s_at AB037780 KLK5 222242_s_at AF243527 KLK6 204733_at NM_002774 KLK7 239381_at NM_005046 KRT13 207935_s_at NM_153490 KRT19 201650_at NM_002276 KRT23 218963_s_at NM_015515 KRT4 213240_s_at NM_002272 KRT7 209016_s_at NM_005556 LCN2; NGAL 212531_at NM_005564 LIPG 219181_at NM_006033 MAC30 212279_at NM_014573 MAD2L1 203362_s_at NM_002358 MAL 204777_s_at NM_002371 MAP17 219630_at NM_005764 MCM2 202107_s_at NM_004526 MCM4 222037_at NM_005914 MCM5 216237_s_at NM_006739 MCM7 208795_s_at NM_182776 MKI67 212022_s_at NM_002417 MMP1 204475_at NM_002421 MMP10 205680_at NM_002425 MMP7 204259_at NM_002423 MYL9 201058_s_at NM_006097 NICE-1 220620_at NM_019060 NMES1 223484_at NM_032413 NTN4 223315_at NM_021229 NUSAP1 218039_at NM_016359 OSF-2 210809_s_at NM_006475 PCNA 201202_at NM_002592 Pfs2 221521_s_at NM_016095 PI3 203691_at NM_002638 PIGR 226147_s_at AA838075 PLAB 221577_x_at NM_004864 PLAT 201860_s_at NM_000930 PMSCL1 213226_at NM_005033 PPBP 214146_s_at NM_002704 PRC1 218009_s_at NM_003981 PTGS1 215813_s_at NM_000962 PTGS2 204748_at NM_000963 RAMP 218585_s_at NM_016448 RARRES1 206391_at NM_002888 RBPMS 209488_s_at NM_006867 RCP 225177_at NM_025151 RFC3 204127_at NM_002915 RFC4 204023_at NM_002916 RHCG 219554_at NM_016321 RPS4Y 201909_at NM_001008 RRM2 209773_s_at NM_001034 S100A7 205916_at NM_002963 S100A8 202917_s_at NM_002964 203535_at NM_002965 S100P 204351_at NM_005980 SAA2 208607_s_at NM_030754 SAT 213988_s_at NM_002970 SCEL 206884_s_at NM_144777 SCGB1A1 205725_at NM_003357 SDP35 222958_s_at NM_017779 SERPINA3 202376_at NM_000624 SERPINB1 212268_at NM_030666 SERPINB3 209719_x_at NM_006919 SIAT7A 227725_at NM_018414 SLC6A14 219795_at NM_007231 SLPI 203021_at NM_003064 SMC2L1 204240_s_at NM_006444 SMC4L1 201664_at NM_005496 SNRPN 201522_x_at NM_022807 SPINK5 205185_at NM_006846 SPRR1A 213796_at NM_005987 SPRR1B 205064_at NM_003125 SPRR2B 208539_x_at NM_006945 SPRR3 232082_x_at NM_005416 STK6 208079_s_at NM_003158 TAGLN 205547_s_at NM_015996 TCN1 205513_at NM_001062 TGFB2 228121_at NM_003238 TOP2A 201292_at NM_001067 TOPK 219148_at NM_018492 TP53I3 210609_s_at NM_004881 TPX2 210052_s_at NM_012112 TRIM22 213293_s_at NM_006074 TRIP13 204033_at NM_004237 TTK 204822_at NM_003318 TUBA3 209118_s_at NM_006009 TYMS 202589_at NM_001071 UBE1C 229831_at NM_003968 UBE2C 202954_at NM_181802 UHRF1 225655_at NM_013282 UPK1B 210064_s_at NM_006952 VRK1 203856_at NM_003384 ZNF367 229551_x_at NM_153695 ZWINT 204026_s_at NM_032997 Table S4. Gene expression changes associated with dysplasia and SCC immortality

Mean SD CV AFFY ID Gene Symbol N (n=4) MD (n=11) MC (n=4) ID (n=7) IC (n=11) N (n=4) MD (n=11) MC (n=4) ID (n=7) IC (n=11) N (n=4) MD (n=11) MC (n=4) ID (n=7) IC (n=11) 222162_s_at ADAMTS1 388 409 638 159 165 68 97 195 46 104 18 24 31 29 63 211071_s_at AF1Q 307 419 1186 101 152 85 132 980 48 96 28 32 83 48 63 203180_at ALDH1A3 1542 4102 4537 538 518 852 1337 2724 376 836 55 33 60 70 162 203722_at ALDH4A1 306 404 243 136 154 43 159 99 34 53 14 39 41 25 34 203404_at ALEX2 151 124 181 50 59 8 28 46 23 52 6 23 26 46 89 206385_s_at ANK3 88 106 92 45 53 24 37 24 16 22 27 35 26 37 41 204244_s_at ASK 36 32 19 77 90 4 8 3 24 47 12 27 18 30 52 202095_s_at BIRC5 290 235 90 540 540 65 95 29 160 152 22 40 32 30 28 219555_s_at BM039 125 96 52 243 260 24 24 9 74 91 19 24 17 31 35 227850_x_at CDC42EP5 328 311 489 141 130 68 104 148 89 113 21 34 30 63 87 203967_at CDC6 40 39 18 90 122 8 14 4 38 58 21 37 22 42 47 223307_at CDCA3 226 191 99 462 433 41 53 23 124 182 18 28 23 27 42 209714_s_at CDKN3 260 167 59 485 531 59 65 19 134 194 23 39 33 28 37 203757_s_at CEACAM6 772 1124 2742 265 115 341 855 2150 204 137 44 76 78 77 119 207828_s_at CENPF 199 139 74 396 396 40 41 25 96 108 20 30 34 24 27 219363_s_at CGI-12 41 38 31 94 94 4 7 4 42 21 10 19 14 45 22 217783_s_at CGI-127 422 486 742 237 229 65 124 56 76 101 15 26 8 32 44 201897_s_at CKS1B 471 383 190 1083 963 67 68 47 370 172 14 18 25 34 18 219529_at CLIC3 510 500 624 206 165 93 313 298 249 340 18 63 48 121 206 227961_at CTSB 386 518 985 206 216 131 223 287 117 120 34 43 29 57 55 206336_at CXCL6 41 97 322 14 15 22 51 431 1 3 53 52 134 9 21 226632_at CYGB 394 273 418 119 151 152 206 177 62 170 39 75 42 52 113 220431_at DESC1 181 129 138 61 59 57 39 91 14 36 31 30 66 23 61 213279_at DHRS1 826 808 528 333 245 158 210 332 98 196 19 26 63 29 80 226281_at DNER 34 34 45 112 91 2 3 23 63 55 6 9 50 56 60 209365_s_at ECM1 1486 1222 1925 487 321 335 1009 1894 212 132 23 83 98 44 41 219787_s_at ECT2 35 28 24 72 117 6 4 7 22 98 17 16 28 30 84 91826_at EPS8L1 447 471 641 228 163 120 203 208 69 52 27 43 32 30 32 213524_s_at G0S2 1942 1252 2073 113 94 781 492 441 99 151 40 39 21 88 161 205483_s_at G1P2 141 257 262 674 637 21 76 79 267 650 15 30 30 40 102 201348_at GPX3 1201 1681 1284 143 306 592 633 293 130 762 49 38 23 91 249 204162_at HEC 67 54 33 145 179 11 18 5 50 94 17 34 15 35 53 231928_at HES2 831 934 1408 422 279 151 214 329 111 108 18 23 23 26 39 209709_s_at HMMR 120 105 65 257 233 17 29 14 126 44 14 28 21 49 19 227566_at HNT 154 130 196 60 51 20 28 121 16 5 13 21 62 27 9 211597_s_at HOP 857 454 962 105 67 160 480 1527 94 41 19 106 159 89 62 223687_s_at HSJ001348 142 135 155 698 582 12 25 100 355 400 9 19 64 51 69 202718_at IGFBP2 1566 1479 930 311 274 699 221 960 209 223 45 15 103 67 81 212657_s_at IL1RN 2860 1906 2656 747 320 467 1137 1203 513 275 16 60 45 69 86 214599_at IVL 823 771 676 165 106 133 431 302 65 41 16 56 45 39 38 206102_at KIAA0186 100 82 36 254 243 20 26 7 70 85 20 31 19 27 35 209408_at KIF2C 236 194 112 473 504 32 49 28 94 137 14 25 25 20 27 205470_s_at KLK11 735 724 815 266 169 152 422 490 161 140 21 58 60 61 83 205783_at KLK13 273 197 194 59 53 82 139 150 13 19 30 71 77 22 36 222242_s_at KLK5 3971 3149 3583 1343 533 285 1096 623 1229 543 7 35 17 92 102 239381_at KLK7 1622 2335 2654 589 305 226 639 850 373 105 14 27 32 63 34 209800_at KRT16 3214 2109 2697 954 588 597 1784 2442 783 483 19 85 91 82 82 218963_s_at KRT23 179 1217 3094 45 35 151 855 2970 10 7 84 70 96 22 20 213240_s_at KRT4 1356 2155 1483 573 224 617 1214 1386 677 286 46 56 93 118 127 209016_s_at KRT7 597 2450 2550 230 72 258 1051 1600 392 67 43 43 63 170 92 208029_s_at LAPTM4B 569 609 569 1269 1528 38 83 75 498 296 7 14 13 39 19 212531_at LCN2 826 2547 5721 200 317 856 1971 2559 174 655 104 77 45 87 207 228080_at LOC143903 211 251 432 100 113 88 67 127 47 43 42 27 29 48 38 225673_at LOC91663 487 640 805 246 207 62 111 194 169 157 13 17 24 68 76 225283_at LOC91947 797 735 999 225 216 350 524 307 92 112 44 71 31 41 52 211747_s_at LSM5 295 250 128 567 550 47 52 15 179 174 16 21 12 32 32 202107_s_at MCM2 335 289 125 694 841 53 103 20 238 271 16 36 16 34 32 222036_s_at MCM4 148 130 55 361 379 31 46 8 107 137 21 35 15 30 36 221020_s_at MFTC 115 114 89 260 288 21 20 28 88 103 19 18 32 34 36 231736_x_at MGST1 1648 3255 2746 663 592 667 713 474 1212 1004 41 22 17 183 170 205680_at MMP10 123 248 951 81 61 22 108 151 68 106 18 44 16 84 173 200875_s_at NOL5A 357 368 176 751 723 45 62 22 225 276 13 17 12 30 38 201860_s_at PLAT 211 733 1067 90 98 37 465 701 30 90 18 63 66 33 93 204284_at PPP1R3C 132 148 211 59 83 30 120 185 9 55 23 81 88 15 66 228582_x_at PRO1073 132 98 188 42 51 53 92 173 12 30 40 94 92 28 59 225177_at RCP 855 928 1692 410 255 307 312 295 205 109 36 34 17 50 43 219554_at RHCG 889 858 1514 164 103 436 659 761 77 76 49 77 50 47 73 202917_s_at S100A8 5023 6488 7686 2122 429 1168 1183 1485 1356 371 23 18 19 64 87 203535_at S100A9 3976 5330 6248 1378 444 974 1610 1842 858 386 25 30 29 62 87 204351_at S100P 1276 3119 4791 409 317 604 1862 2628 331 268 47 60 55 81 85 210592_s_at SAT 2559 3355 5031 1298 1164 272 865 1655 470 347 11 26 33 36 30 227949_at SCAPIN1 28 23 37 111 105 3 3 23 118 97 11 13 61 106 92 206884_s_at SCEL 479 522 721 168 106 186 227 517 135 97 39 44 72 80 91 212268_at SERPINB1 1650 1337 1669 395 310 52 491 221 311 266 3 37 13 79 86 213572_s_at SERPINB1 381 344 427 96 70 44 137 102 65 56 12 40 24 68 79 209720_s_at SERPINB3 50 187 272 24 23 35 158 175 7 11 69 85 64 31 50 209719_x_at SERPINB3 254 1005 1595 127 114 164 789 917 66 80 65 79 57 52 70 201312_s_at SH3BGRL 224 251 394 106 81 31 54 81 58 57 14 21 20 55 71 219795_at SLC6A14 213 513 753 30 16 64 338 172 18 12 30 66 23 59 74 201663_s_at SMC4L1 222 169 132 443 640 68 54 80 73 188 31 32 61 16 29 205185_at SPINK5 675 494 1059 195 112 150 483 1723 147 31 22 98 163 75 28 232082_x_at SPRR3 2644 1746 2271 944 195 107 1299 1540 927 118 4 74 68 98 61 204542_at STHM 540 538 794 224 235 53 122 233 74 100 10 23 29 33 42 208079_s_at STK6 299 221 97 725 686 61 69 17 241 150 20 31 18 33 22 209278_s_at TFPI2 2954 2819 2654 406 859 824 485 488 482 945 28 17 18 119 110 206008_at TGM1 906 877 751 383 258 292 392 643 249 213 32 45 86 65 83 201292_at TOP2A 141 107 38 284 331 23 46 9 73 120 16 43 24 26 36 226071_at TSRC1 432 382 699 174 143 138 277 429 95 92 32 73 61 54 64 209118_s_at TUBA3 261 419 1005 115 83 129 193 532 148 62 49 46 53 129 76 202954_at UBE2C 456 366 186 1095 1027 62 108 52 321 151 14 30 28 29 15 238542_at ULBP2 654 727 1036 268 261 49 357 200 96 62 7 49 19 36 24 210064_s_at UPK1B 509 660 1044 69 62 110 213 877 17 12 22 32 84 24 19 202412_s_at USP1 74 58 34 169 153 18 26 12 54 69 24 44 36 32 45 223642_at ZIC2 14 15 15 71 64 2 2 1 38 37 13 10 6 53 58 203585_at ZNF185 1350 1005 888 478 347 153 257 522 241 202 11 26 59 51 58 231148_at 402 259 304 100 85 174 298 237 53 21 43 115 78 53 24 225834_at 173 116 61 427 359 30 40 21 157 88 17 35 34 37 24

GROUPS N normal mucosa FNB3 FNB5 FNB6 NB9 MD mortal dysplasias D41 D48 D6 D8 D25 D30 D47 E1 E2 E4 E5 MC mortal SCCs P30 P66 P80 M37 ID immortal dysplasias D38 D4 D9 D34 D19 D20 D35 IC immortal SCCs P68 P3 P31 P56 P4 P5 M18 R16 R82 R10 M22

CV: coefficient of variance x 100 [(SD/Mean)x100] SD: standard deviation Table S5. Citations of -regulated genes.

CDKN1A/p21WAF1 (1); BTG2(2); SERPINE 1/PAI-1 (3);TGFA (3); CCNG2(4); GADD45 (5); PERP (6); LGALS7/PIG1 (7); CLIC4 (8); TP53I3/PIG3 (9, 10); PLAB (2, 3); ALDH1A3 (11), TUBA3 (11); MM7 (12); MMP9 (12); CSPG2 (9); IGFBP3 (13); TMSB4X (2); CTSD (14); DDR1 (15); TGS2/COX-2 (16); WIG1/PAG608 (17); BIRC5 (18); RRM2 (19); PRC1 (20); PCNA (9);TGFBR2 (12); DDB2 (2); PPM1D/WIP1 (21); FDXR (10); BAX (22); MDM2 (9, 10); NINJ1 (2, 10); OPN3 (23); CCNE2 (2); TNFRSF6/FAS (24); BAK1 (2, 25); SMTN (2, 10); ATF3 (2); LISCH7 (2); NHL2 (2); TNFRSF10B/KILLER (26); PRG1 (27); GLIPR1/mRVP-1 (28);TSAP6 { Passer, 2003 #1141}; RGS16 (29); P53AIP1 (30); EI24 (31); SFN/14-3-3σ (32); NOXA (33); BBC3/PUMA (34); LRDP/PIDD (35); SCN3B (36); DDA3 (37);

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TABLE S6. GENES EXPRESSION CHANGES IN HNSCCS ASSOCIATED WITH LYMPH NODE INVOLVEMENT

CHUNG et al. CROMER et al ROEPMANN et al O'DONNELL et al. Up regulated Down regulated Up regulated Down regulated Up regulated Down regulated Up regulated Down regulated ACP1 ARG2 APOL3 ATP6IP2 ADPRT ACTA1 ABCA12 ADCY8 AP1S1 AR ATF2 APOL1 ATP6V1H ARHGDIB ALDOA ADAM12 ALOX12B ARHGEF7 ARL6IP ATF7 AHR AXL ATRX ATP5A1 APM2 ATP6V1C1 ACADSB ATF3 AIM2 AIM1 ALDH4A1 AKAP1 ATP2B4 AP2S1 ACP5 ATP5D ANXA1 ATP6AV0A2 ATIC AP3S1 AFG3L2 AP1S2 APC10 AP2S1 AMD1 ARPP-19 ALDH1A1 ALCAM ALDH3A2 ANP32A APPBP2 ATAD2 ATP6V0B APRT BMP7 BTN3A3 B4GALT6 BMI1 BAIAP2 BAL BBC3 BDH BID BF BLVRA BUB3 BENE BASP1 BAP1 BTN3A3 BMP1 BENE BCDO1 BACH1 CENPA C14orf170 CASP1 CALR C10orf10 CUL1 CKTSF1B1 C10orf26 C14orf118 CCDC2 CNAP1 C1D CANX CCND3 CKB COL5A1 C4.4A CA6 CCKAR CROT CUTC CCL13 CD164 COL17A1 COL5A3 C9orf5 COL2A1 CHAF1B C2orf3 CNAP1 CXCL9 CCT5 CDH11 CELSR1 CTDSP1 CAPNS2 CORO2B CALM2 COX7A2L CXCL10 CD163 CNN3 CEBPA CIDE-3 CASP3 CXorf40 CXCL11 CD47 CNOT2 CLIC3 CACNB4 CD83 CHERP C1R CDC42 COL4A1 COPG CG018 CD9 C1QBP C1S CDH3 CRI1 CNNM2 CDC14A CENPB CTNNB1 CDC7L1 CHST2 CLECSF2 CXCR4 CDKN1B COPEB CSNK1A1 CEACAM1 CAP C2orf17 CHES1 CRSP9 c10orf99 CLASP1 CTSD CALD1 CLDN4 CALU CAPG COPS4 C1orf8 CASP4 CRY1 CYP1B1 CAPN2 COQ7 CTSO CYB5 CAP350 CRSP2 DAAM2 DKFZ566F212DDOST DKFZP564G092DEK DUSP7 D2S448 DNAH11 DRG2 DUT DNAJC3 DMD DECR1 DAP3 DP1 DDB2 DAPK3 DSG3 DKFZP566F0546 DNMT1 DAZAP2 DFNA5 DSTN DSIPI DTX2 DKK3 DLG3 DGKD DDX42 DEGS1 DCTN3 DGUOK DDX18 DUSP14 DS4S234E DYRK1A DLEU1 DEDD ECT2 ELF3 ETF1 ETS2 ENPP2 EPAS1 ERBB4 ETV2 EGR2 ERCC3 EVA1 EXT1 eIF3k ECG2 ENIGMA ENSA EGR3 ECE2 EEG1 EDG2 ECM1 ED1 ETV6 EZH2 EIF2AK4 EXOSC9 EFNB2 EPPK1 FEN1 FABP5 FLJ10134 FADS1 FLNB FAP FLJ20073 FLJ10922 FIGNL1 FCGR2B FLJ10904 FADS2 FXYD3 FTH1 FLJ22582 FOXA1 FNBP1 FCGRT FLJ11362 FZD7 FURIN FAT FBX021 FXYD3 FGF1 FOS FXYD5 FLJ22527 FHL1 FCGR1A GCA GTF3A G1P3 GALNT1 GTSE1 GSTP1 GATA2 GPRK6 G1P2 GJA1 GJB3 GRF2 GGA3 GUK1 GJB2 GABRB3 GPR48 GPR34 GJB6 GRB2 GNAI1 GALNTL4 GTF3C3 GAS1 GNB2L1 GPX2 GOCAP1 GRN HCFC1 HLA-G HCCS HOP/LAGY HOXC8 HLA-DOB HPCA HLA-C HLA-A HPCAL1 HLF HSPA1L HLA-DPB1 HIF1A HMGB1 HLA-DQB1 HRH1 HNRPH3 HFC-2 HNRPR HHEX HINT1 HEXB HSPA1A HAX1 HLA-DRB1 HSPA5 IGLJ3 IL7 IK ID2 ITGB4 IER3 IDI1 IFNA4 ISG20 INSIG1 IL18 IL8 ITGA3 INSL5 ITM2A IF135 IL27W IMPA2 IL22RA1 IL9R ILF2 IGF1R ITM1 IGSF3 IVL IGL@ ITGB1 JUP KIF23 KNS2 KIAA0092 KIAA0368 KIAA0010 KIAA0350 KIAA1052 KRT13 KIF11 KLHL13 KLK7 KIAA0483 KLF5 KLK12 KCNJ5 KCNS3 KIAA0528 KLK8 KIAA0830 KLK10 KRT23 KIAA1277 KRT8 KRT1 KLF6 KSR KRT13 KRT16 KLF10 KLF12 KRT18 KRT2A KCNJ15 KIAA0963 KUB3 KCTD12 KIPAP3 KIAA0485 LMO4 LOC151162 LAPTM4A LIPA LAD1 LLGL2 LIM2 LOC130502 LCP2 LTBP1 LOC139202 LGALS3BP LMAN1 LMNA LOR LOC51236 MAD2L1 MLLT6 MX1 MRC1 MAGED1 MINK MAN1B1 MAL2 MGC40499 MAPK13 MCM3 MPHOSPH10 MAF MTMR6 MAGED2 MBD2 MICAL2 MAP17 MYO7A MYCN MCM7 MRPL19 MAP3K5 MYO1B MCP MRPS12 MMD MYO1B MGC3731 MGC12197 MTHFD2 MGC3067 MICB MGC3113 MGC24665 MGC4796 MESDC2 MYH10 MTMR2 MEIS1 MYH2 MAGOH MT1E MKRN1 MYO5C MMP3/12 ? M96 MYOD1 MTMR1 MGC3101 MSH6 MVP MMP1 MCTP2 NUP107 NEDD4L NFIL3 NFYC NOL1 NCOR2 NALP1 NTRK2 NXT1 NTS NUP155 NCK1 NDUFB4 NNAT NR4A1 NDUFA9 NDEL1 NT5C3 NR4A1 NIFUN NEDD4 NPHP4 NOX1 NXPH3 ODAG OPRS1 OSF-2 ODC-p OPRK1 OVOL1 OSBP2 ONECUT1 PAK2/3 PIGH PSMB10 PAM PLCG1 PKP1 P4HA1 PALM2 PCDHB6 PAXIP1L PDLIM3 PGAM1 PSMB8 ? PLEKHC1 PLEC1 PLAU PARVB PSG6 PCBP1 PINK1 PPID PHLDA2 PSMD2 PGBD5 PSG2 PCNT1 PPIC PPIH PA2G4 PI3 P101-PI3K PIAS1 PRNP PPT1 PSMD8 PLA2G4B PKD1 POLB PTEN PRB1 PRSS3 PLK PARK2 PPM1B PTGS1 PSMB9 PRODH PPL PMP2 PPM1D PVRL2 PTPRK PFKP PPT2 PRKCBP1 PPP1CC PDIA3 PPP4C PTCH2 PSIP1/2 PPGB PDE6A PTMA PRNP PRO2958 PISD P4HB PVR POLB PRSS11 PLCB4 RFC5 RBMX2 RAB38 RNH RPL26L1 RAB31 RAD17 RPH3AL RPL35A RDBP RSRC1 RARS RPA1 RPN2 REN RGS5 R29124_1 REV1L REA RNF14 RPS14 RPL37A RAI1 RFP2 REG4 RNU2 RNF130 RNF103 REPIN1 RXRA RUNX1 RHEB RBMX RFK RNF5 RAB40B STK6 SERPINB1 SP100 SDC4 SH3BGRL S100A11 SPOCK S100A7 SLC22A2 SCNN1A SP110 SDFR1 SH3BP5 SH3GL1 SERPINE1 S100A9 SPINLW1 SLAM STAT1 SEC22L1 SLC2A3 SERPINB5 SLPI SHANK2 SLC25A4 S100A7 SEC22L2 SMC1L1 SFN SMC5L1 SLC28A2 SOCS2 S100A8 SEC23B SMTN SPINK5 SNX26 SPARCL1 SC4MOL SFN SVIL SRP19 STARD13 SH3MD2 SCAMP1 SHC1 SDC4 SSH2 SOX10 SET8 SCARB2 SLC31A2 SLC20A2 SEZ6L SFRS9 STOML2 SLC1A2 SF3B1 SERPING1 SLC39A6 ST3GAL5 SF3B2 SSR2 SMARCD2 SMYD2 SERPINI1 SQLE Sep-08 TMPO TOP2A TRIM22 TLR2 TBCE TPBG TNFAIP3 TGM3 THSD1 TGM3 TAF4B TSC22D1 TPBG TCF12 TRIM29 TPM2 TNFRSF5 TDRD1 TTC9 TAF7 TAF13 TPST2 TFAP2C TUBA1 TRGV9 TLL2 TGDS TCEB1 TRIO TUBB TUBA3 TAF1 TM4SF6 TCERG1 TUBA1 TRIM16 TSN THBD T1A-2 TNNT3 TMEM38B THBS2 TM7SF3 TNFRSF10B TIA1 TRAM1 TUBB2 TACC1 TIEG TTC1 TP73L TRAP1 TRA1 UBE2C USP8 UBE2L6 USP31 UBD UBE2M UBA52 UPK1B UNG2 UBR2 UBXD2 VRK2 VRK1 VAV3 VDAC3 VSNL1 VBP1 VDAC3 VDP VSNL1 WRNIP1 WTAP WARS WAS WDR45L XPO1 YEATS4/GAS41 ZNF268 ZNF195 ZBTB24 ZBED4 ZWINT ZNF161 ZNF169 ZNF138 ZNF145 ZDHHC18

Data obtained from: Chung et al (2004) Supplementary Figure S2. Cromer et al. (2004). Tables 5 and 6. Roepman et al. (2005). Supplementary Table 2. O'Donnell et al. (2005). Supplementary Figure 1.

The GeneCards encyclopedia was used to identify gene names where necessary. Rebhan et al. http://bioinformatics.weizmann.ac.il/cards