Clinical Features CN_CNMF METHLYATION_CNMF MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL MIRSEQ_MATURE_CNMF MIRSEQ_MATURE_CHIERARCHICAL nMutated (%) nWild-Type Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q KRAS 30 (73%) 11 0.53383 1 0.72501 1 1 1 0.26265 1 0.81458 1 0.92132 1 0.50315 1 0.89055 1 TP53 24 (59%) 17 0.31341 1 0.3064 1 0.89317 1 0.96503 1 0.59181 1 0.11269 1 0.22259 1 0.90225 1 C19ORF55 7 (17%) 34 1 1 0.31309 1 0.83812 1 0.14001 1 1 1 0.45774 1 1 1 0.7156 1 B4GALT2 5 (12%) 36 0.28898 1 1 1 0.54401 1 0.63768 1 1 1 1 1 1 1 1 1 CDKN2A 7 (17%) 34 0.0095799 1 0.063609 1 0.70924 1 0.59653 1 0.29922 1 0.01367 1 0.15424 1 0.34959 1 NFIL3 6 (15%) 35 0.50105 1 0.44566 1 1 1 0.35298 1 0.57457 1 0.45951 1 1 1 0.71833 1 OTOF 9 (22%) 32 0.17664 1 0.42223 1 0.85701 1 0.92989 1 0.52865 1 0.73501 1 0.5576 1 0.65663 1 IRS1 6 (15%) 35 0.63426 1 0.53835 1 0.20891 1 0.21898 1 0.0305 1 0.43325 1 0.074409 1 0.51345 1 GAS2L2 6 (15%) 35 0.56367 1 0.84151 1 1 1 1 1 0.84224 1 0.071679 1 0.48502 1 0.51629 1 RBM10 6 (15%) 35 0.5317 1 0.12419 1 0.15441 1 0.12822 1 0.052929 1 0.061079 1 0.04583 1 0.03662 1 APP 6 (15%) 35 0.092379 1 0.74005 1 0.67469 1 0.4908 1 0.39231 1 0.60336 1 1 1 1 1 IPP 5 (12%) 36 0.3386 1 0.39873 1 0.19711 1 0.11762 1 0.4703 1 0.22394 1 0.29067 1 0.25824 1 MAMLD1 7 (17%) 34 0.38139 1 1 1 0.71744 1 0.42362 1 0.79131 1 0.083669 1 0.18536 1 1 1 ARHGAP18 4 (10%) 37 0.39526 1 0.17121 1 1 1 0.87554 1 0.64584 1 0.58592 1 1 1 0.64817 1 PHF8 5 (12%) 36 0.6715 1 0.19471 1 0.13421 1 0.28418 1 0.12019 1 0.33342 1 0.15373 1 0.16029 1 THBS4 6 (15%) 35 0.67247 1 1 1 1 1 1 1 1 1 0.89115 1 0.71545 1 1 1 SMAD4 7 (17%) 34 0.55843 1 0.48793 1 0.32601 1 0.061139 1 0.67875 1 0.074489 1 0.03861 1 0.35038 1 PTPRF 7 (17%) 34 0.40094 1 0.48793 1 0.54194 1 0.64764 1 0.14588 1 0.084739 1 1 1 0.20835 1 MED12 6 (15%) 35 0.40491 1 0.18389 1 0.26302 1 0.7426 1 0.066639 1 0.58591 1 0.71501 1 0.20682 1 BMP2K 4 (10%) 37 0.5523 1 0.80833 1 0.47229 1 0.092269 1 0.36245 1 0.31465 1 1 1 0.5143 1 ZMYM5 4 (10%) 37 0.39442 1 0.66067 1 0.62792 1 0.61509 1 1 1 0.19447 1 0.36344 1 0.79548 1 SYT15 4 (10%) 37 0.81066 1 0.39194 1 1 1 1 1 0.6461 1 0.46629 1 0.10126 1 0.64974 1 PLAU 4 (10%) 37 0.13359 1 0.52127 1 0.47277 1 0.36171 1 0.24154 1 0.49332 1 0.03707 1 0.51601 1 MEPCE 4 (10%) 37 1 1 0.66172 1 0.63113 1 0.61034 1 1 1 0.19379 1 1 1 0.79626 1 ZMIZ1 5 (12%) 36 0.17015 1 1 1 0.83348 1 0.80335 1 0.67917 1 0.60233 1 1 1 0.67178 1 SLC39A5 4 (10%) 37 0.55274 1 0.23332 1 0.79846 1 0.092219 1 0.051819 1 0.8114 1 0.80836 1 1 1 GUCY2F 5 (12%) 36 0.34004 1 0.3995 1 1 1 0.40043 1 0.093259 1 0.48362 1 0.28805 1 0.82852 1 EDC4 5 (12%) 36 0.84814 1 0.47643 1 1 1 0.84865 1 0.83896 1 0.26851 1 1 1 0.64696 1 SEH1L 3 (7%) 38 0.86322 1 0.77353 1 0.096879 1 0.58433 1 0.3074 1 0.15979 1 0.057739 1 0.1137 1 SLC4A3 3 (7%) 38 1 1 0.42335 1 0.73784 1 0.58159 1 0.53846 1 0.3681 1 0.10135 1 0.41324 1 CD99L2 4 (10%) 37 0.49773 1 0.52221 1 0.47111 1 0.34046 1 0.3643 1 0.24394 1 0.80839 1 0.5182 1 SBNO1 4 (10%) 37 0.080599 1 0.12092 1 0.6309 1 0.61039 1 0.64324 1 0.33532 1 0.36416 1 0.16125 1 NPNT 3 (7%) 38 0.7526 1 0.03425 1 0.35675 1 0.50423 1 0.5376 1 0.93297 1 0.56447 1 0.57292 1 TMEM175 5 (12%) 36 0.22572 1 0.83892 1 0.54235 1 0.87419 1 1 1 0.10842 1 1 1 0.32145 1 IRX4 4 (10%) 37 0.39491 1 0.23111 1 0.062849 1 0.13279 1 0.31326 1 0.58732 1 0.8079 1 0.21932 1 CLCC1 3 (7%) 38 0.29195 1 0.18733 1 0.53091 1 0.94083 1 0.085289 1 1 1 0.15612 1 0.77338 1 BTNL8 4 (10%) 37 0.73768 1 0.39206 1 0.02251 1 0.067249 1 0.21596 1 0.0051299 1 0.27227 1 0.10761 1 SYNGAP1 5 (12%) 36 0.17243 1 1 1 0.54678 1 1 1 0.68369 1 0.70497 1 0.17536 1 0.82821 1 F8 4 (10%) 37 0.067079 1 0.11857 1 1 1 0.1364 1 0.64344 1 0.056069 1 0.10109 1 0.64537 1 SORBS2 6 (15%) 35 0.099229 1 0.184 1 0.67529 1 0.63798 1 0.47038 1 0.7019 1 0.2842 1 0.56459 1 NR4A3 4 (10%) 37 1 1 0.66029 1 0.63072 1 0.61239 1 1 1 0.33722 1 0.36439 1 0.79598 1 ZNF337 4 (10%) 37 0.60693 1 0.38916 1 0.33953 1 0.16246 1 0.21164 1 0.19438 1 0.01928 1 0.10942 1 TAOK2 4 (10%) 37 0.13104 1 0.22999 1 0.00283 1 0.02771 1 0.00307 1 0.0099799 1 0.058159 1 0.01312 1 UNC5A 4 (10%) 37 1 1 0.80716 1 0.52655 1 0.50292 1 1 1 0.13573 1 0.75001 1 0.77074 1 TNFSF9 4 (10%) 37 0.27529 1 1 1 1 1 0.84724 1 0.84137 1 0.4681 1 0.10035 1 0.64969 1 TEX2 4 (10%) 37 0.443 1 0.52114 1 0.47285 1 0.84974 1 0.16407 1 0.22328 1 0.48503 1 0.51349 1 RBM43 3 (7%) 38 0.3456 1 0.42372 1 NA NA NA NA NA NA NA NA NA NA NA NA CIR1 3 (7%) 38 0.86429 1 1 1 0.097579 1 0.58344 1 0.30872 1 0.077089 1 0.75063 1 0.11391 1 TOX4 4 (10%) 37 0.49649 1 0.66153 1 0.47474 1 0.85008 1 0.84098 1 0.13237 1 1 1 0.51602 1 HIBCH 3 (7%) 38 0.8654 1 0.18777 1 0.53026 1 0.33548 1 0.30583 1 1 1 0.75131 1 0.77288 1 CRAT 3 (7%) 38 0.29168 1 0.18877 1 0.02351 1 0.33832 1 0.0032 1 0.2308 1 0.059259 1 0.059809 1 SRP14 3 (7%) 38 0.86456 1 0.57639 1 0.74112 1 0.58199 1 0.30702 1 0.66556 1 1 1 0.77111 1 PDZD7 4 (10%) 37 0.4448 1 1 1 1 1 0.84942 1 0.84 1 0.46422 1 0.48241 1 0.65107 1 POP5 3 (7%) 38 0.65259 1 0.42479 1 0.73819 1 0.5854 1 0.53737 1 0.36648 1 0.74904 1 1 1 UNC5D 3 (7%) 38 0.47742 1 0.42406 1 0.74036 1 0.93988 1 0.54047 1 0.13429 1 0.75225 1 0.41581 1 FAM47C 5 (12%) 36 0.53777 1 1 1 1 1 0.73758 1 1 1 0.96394 1 0.44887 1 0.82813 1 TMEM184A 4 (10%) 37 0.55244 1 0.52269 1 0.0379 1 0.092289 1 0.2445 1 0.054989 1 0.48478 1 0.064279 1 BEGAIN 4 (10%) 37 0.1317 1 0.22914 1 0.80026 1 0.22062 1 0.050929 1 0.49675 1 0.48187 1 0.29942 1 PASD1 5 (12%) 36 0.91335 1 0.56823 1 0.54366 1 0.73576 1 0.46753 1 0.29244 1 0.04692 1 0.3153 1 RBM45 4 (10%) 37 0.27481 1 1 1 0.46907 1 0.49115 1 0.83947 1 0.49647 1 0.2736 1 0.51418 1 POM121 4 (10%) 37 0.4419 1 0.80519 1 0.79834 1 0.22399 1 0.83872 1 0.46351 1 0.48651 1 1 1 EME2 3 (7%) 38 0.291 1 0.57508 1 0.53012 1 0.5049 1 0.084589 1 0.36963 1 0.15593 1 0.7723 1 CUL4B 3 (7%) 38 0.29195 1 0.776 1 0.16207 1 0.33614 1 0.02969 1 0.15953 1 0.15629 1 0.1115 1 DIAPH3 4 (10%) 37 0.39279 1 0.66043 1 0.80128 1 0.44955 1 0.31496 1 0.4642 1 1 1 1 1 IFT46 4 (10%) 37 0.73613 1 1 1 0.52981 1 0.18878 1 0.1996 1 0.37071 1 0.74913 1 0.76997 1 OTUD4 5 (12%) 36 0.62513 1 0.68494 1 0.83186 1 0.02317 1 0.68303 1 0.01774 1 0.44602 1 0.46504 1 GABBR1 4 (10%) 37 0.81119 1 0.3903 1 1 1 0.22084 1 0.64559 1 0.46657 1 1 1 0.6496 1 MYH10 4 (10%) 37 0.44153 1 0.52344 1 0.47202 1 0.84795 1 0.84204 1 0.22635 1 0.27778 1 0.51853 1 ERF 4 (10%) 37 0.43969 1 0.17237 1 0.33888 1 0.70117 1 0.21568 1 0.072129 1 0.27528 1 0.10811 1 OR10A7 4 (10%) 37 0.30795 1 1 1 1 1 0.9403 1 0.36982 1 0.58041 1 0.27081 1 1 1 BRDT 4 (10%) 37 0.27391 1 1 1 0.47279 1 0.48897 1 0.16324 1 0.49773 1 0.27463 1 0.51409 1 CDHR5 4 (10%) 37 0.80416 1 1 1 0.096239 1 0.091949 1 0.84141 1 0.4966 1 0.48521 1 1 1 EPS8L3 3 (7%) 38 0.47946 1 0.57647 1 NA NA NA NA NA NA NA NA NA NA NA NA GPR25 3 (7%) 38 1 1 0.42265 1 0.73769 1 0.58455 1 0.53732 1 0.19809 1 0.40757 1 0.41574 1 PPARGC1B 3 (7%) 38 0.86545 1 0.77527 1 0.16456 1 0.33907 1 0.02923 1 0.15932 1 0.057609 1 0.11393 1 FGF10 3 (7%) 38 0.1491 1 0.28786 1 1 1 0.93863 1 0.36993 1 0.57842 1 0.2703 1 1 1 SALL1 5 (12%) 36 0.53597 1 1 1 1 1 0.85022 1 0.84059 1 0.46209 1 0.48387 1 0.64787 1 VEPH1 4 (10%) 37 0.39385 1 0.66019 1 1 1 1 1 1 1 0.27249 1 1 1 0.64995 1 ATRX 3 (7%) 38 0.47973 1 0.42587 1 0.74039 1 0.9393 1 0.53592 1 0.36801 1 0.10154 1 0.41512 1 ST6GALNAC5 4 (10%) 37 0.27236 1 0.80507 1 0.63022 1 0.13361 1 0.8413 1 0.19443 1 1 1 0.79698 1 DHX57 3 (7%) 38 0.75014 1 1 1 1 1 0.50304 1 1 1 0.28369 1 0.75054 1 1 1 GNL3L 3 (7%) 38 0.092139 1 1 1 0.25876 1 0.70227 1 0.8102 1 0.47431 1 0.26867 1 0.28638 1 MST1 5 (12%) 36 0.78086 1 1 1 0.54346 1 0.45777 1 0.47052 1 0.094489 1 0.44537 1 0.19973 1 GRB7 4 (10%) 37 0.73642 1 0.11688 1 1 1 1 1 0.6461 1 0.26742 1 0.36269 1 0.64574 1 TMC4 5 (12%) 36 0.34097 1 1 1 1 1 0.49063 1 0.24277 1 0.19539 1 0.48372 1 0.51981 1 MED9 3 (7%) 38 0.75419 1 1 1 0.53104 1 0.50615 1 0.19773 1 0.13641 1 0.75169 1 0.77132 1 WASF3 3 (7%) 38 0.5612 1 1 1 0.52992 1 0.50332 1 0.19842 1 0.13612 1 0.74986 1 0.57394 1 GIT1 3 (7%) 38 0.48265 1 0.42356 1 0.73882 1 0.93895 1 0.53596 1 0.13673 1 0.74931 1 0.4161 1 SV2A 3 (7%) 38 0.34384 1 0.42522 1 1 1 1 1 0.81264 1 0.93496 1 0.39889 1 1 1 UGP2 4 (10%) 37 0.55078 1 0.80559 1 0.1633 1 0.18728 1 0.084969 1 0.03474 1 0.15553 1 0.060909 1 ERCC3 3 (7%) 38 0.2928 1 0.1251 1 0.096429 1 0.27139 1 0.057899 1 0.03466 1 0.059379 1 0.02615 1 ARMCX3 3 (7%) 38 0.65151 1 1 1 0.35639 1 0.70388 1 0.80852 1 0.93443 1 1 1 0.57388 1 TMCO1 3 (7%) 38 0.64955 1 0.28821 1 0.73847 1 0.94075 1 0.80999 1 0.19941 1 0.40749 1 0.41432 1 HMX2 3 (7%) 38 0.29186 1 0.77595 1 0.16259 1 0.33698 1 0.03085 1 0.15861 1 0.15587 1 0.11394 1 AARS2 4 (10%) 37 0.44203 1 1 1 0.4727 1 0.49062 1 0.16348 1 0.49881 1 0.48202 1 0.51748 1 ALS2CR11 3 (7%) 38 0.86553 1 0.77254 1 0.74112 1 0.93963 1 0.30453 1 0.36771 1 0.059409 1 0.41393 1 ARFGAP3 3 (7%) 38 0.86355 1 0.7731 1 0.7406 1 0.58524 1 1 1 0.47215 1 0.75129 1 0.77211 1 SMG7 3 (7%) 38 0.65272 1 0.28629 1 0.73793 1 0.94003 1 0.8108 1 0.20069 1 0.40591 1 0.41395 1 CHGA 3 (7%) 38 0.47783 1 0.1252 1 0.097259 1 0.27322 1 0.058039 1 0.076619 1 0.10198 1 0.02609 1 FAM63B 3 (7%) 38 0.86527 1 1 1 0.16503 1 0.3366 1 0.02952 1 0.075639 1 0.75191 1 0.113 1 VPS36 3 (7%) 38 0.86399 1 1 1 0.73812 1 0.70465 1 1 1 0.13809 1 0.75306 1 0.77214 1 MAP3K7 3 (7%) 38 0.2887 1 0.77414 1 0.16263 1 0.33712 1 0.30819 1 0.15997 1 0.15623 1 0.11288 1 OTX1 4 (10%) 37 0.19428 1 0.11917 1 1 1 1 1 0.64745 1 0.27171 1 0.36533 1 0.64791 1 THBS1 3 (7%) 38 0.7512 1 1 1 0.52967 1 0.50482 1 0.19841 1 0.36994 1 0.75035 1 0.7715 1 INTS7 3 (7%) 38 0.75465 1 0.4227 1 0.73888 1 0.93702 1 0.53183 1 0.13682 1 0.10062 1 0.4133 1 ZNF644 3 (7%) 38 0.75424 1 1 1 0.52961 1 0.50267 1 0.19811 1 0.13504 1 0.74867 1 0.77239 1 NFAT5 3 (7%) 38 0.75198 1 0.57439 1 1 1 0.50377 1 1 1 0.28364 1 0.75169 1 1 1 WHSC1L1 3 (7%) 38 1 1 0.12596 1 0.73793 1 0.74646 1 0.54112 1 0.47698 1 0.74839 1 0.41499 1 KIAA1211 3 (7%) 38 0.28983 1 0.57466 1 0.53167 1 0.18704 1 0.084489 1 0.15978 1 0.15652 1 0.061529 1 NAGPA 3 (7%) 38 0.55927 1 0.28727 1 1 1 0.50287 1 0.81212 1 0.01946 1 0.40822 1 1 1 PPIG 3 (7%) 38 0.29027 1 0.1262 1 NA NA NA NA NA NA NA NA NA NA NA NA SLITRK5 4 (10%) 37 0.39417 1 0.80543 1 1 1 0.61175 1 1 1 0.46576 1 1 1 1 1 MBD3 3 (7%) 38 0.29291 1 0.77685 1 0.16315 1 0.336 1 0.02883 1 0.16005 1 0.059019 1 0.11425 1 FOXP2 5 (12%) 36 0.4273 1 0.83839 1 0.33815 1 0.33925 1 0.84214 1 0.31231 1 0.27514 1 0.10704 1 NAPSA 3 (7%) 38 0.29215 1 0.77523 1 NA NA NA NA NA NA NA NA NA NA NA NA EIF3C 3 (7%) 38 0.48186 1 1 1 1 1 0.18907 1 1 1 0.28408 1 0.75058 1 1 1 GTF2F1 3 (7%) 38 0.75281 1 0.5726 1 0.52815 1 0.50418 1 1 1 0.1367 1 0.75302 1 0.77411 1 CCKAR 3 (7%) 38 0.75128 1 0.77456 1 NA NA NA NA NA NA NA NA NA NA NA NA MMP14 3 (7%) 38 0.75067 1 1 1 0.16415 1 0.33765 1 0.1992 1 0.075589 1 0.75116 1 0.11266 1 ATM 3 (7%) 38 1 1 0.42399 1 NA NA NA NA NA NA NA NA NA NA NA NA CCDC28B 3 (7%) 38 0.18835 1 0.28644 1 0.7399 1 0.58576 1 0.80953 1 0.66661 1 0.40861 1 0.41424 1 IFFO1 3 (7%) 38 1 1 0.28751 1 1 1 0.064079 1 0.81139 1 0.28387 1 0.40648 1 1 1 TWISTNB 3 (7%) 38 0.74971 1 0.57252 1 1 1 0.70646 1 1 1 0.1373 1 0.74935 1 0.77394 1 RASGRF2 3 (7%) 38 0.6512 1 0.42466 1 0.74007 1 0.94022 1 0.53672 1 0.36764 1 0.10218 1 0.41255 1 SPAG9 3 (7%) 38 0.75318 1 1 1 1 1 0.5027 1 1 1 0.28388 1 0.75141 1 1 1 SMCR7 3 (7%) 38 0.75063 1 1 1 0.74188 1 0.02759 1 0.30777 1 0.36696 1 0.10007 1 0.41334 1 PSAT1 4 (10%) 37 0.60973 1 0.39154 1 1 1 0.50216 1 0.81174 1 0.93388 1 0.40766 1 1 1 PDILT 3 (7%) 38 0.48056 1 1 1 1 1 0.5061 1 1 1 0.28418 1 0.40582 1 1 1 CCDC8 3 (7%) 38 0.2917 1 0.57656 1 1 1 0.02763 1 0.30618 1 0.28493 1 0.15526 1 1 1 HIST1H2BK 3 (7%) 38 0.55932 1 1 1 0.53248 1 0.1886 1 0.19857 1 1 1 0.75155 1 0.77176 1 METAP1 3 (7%) 38 0.4792 1 1 1 0.5292 1 0.50575 1 1 1 0.36751 1 0.74779 1 0.77112 1 SCRIB 3 (7%) 38 0.75404 1 1 1 0.16251 1 0.02812 1 0.02874 1 0.16038 1 0.057889 1 0.11422 1 STAU1 3 (7%) 38 0.47793 1 1 1 0.16191 1 0.02729 1 0.02954 1 0.0039 1 0.058869 1 0.77414 1 GOLGA6B 3 (7%) 38 1 1 0.28592 1 0.73802 1 0.58372 1 0.81173 1 0.19976 1 0.40445 1 0.41625 1 IRS4 4 (10%) 37 0.39408 1 0.6585 1 0.46988 1 0.13542 1 0.16775 1 0.49677 1 0.27443 1 0.51432 1 PDZD2 4 (10%) 37 1 1 1 1 0.47105 1 0.84807 1 0.84005 1 0.22553 1 0.2721 1 0.51744 1 CCDC135 3 (7%) 38 0.86463 1 1 1 0.73787 1 0.062949 1 1 1 0.37011 1 0.75069 1 0.7729 1 CEP72 3 (7%) 38 0.75179 1 1 1 1 1 0.18577 1 1 1 0.28396 1 0.40592 1 1 1 SMARCA2 3 (7%) 38 0.2894 1 0.5725 1 0.02341 1 0.02818 1 0.30751 1 0.03531 1 0.15887 1 0.061619 1 UBXN6 3 (7%) 38 0.3469 1 1 1 1 1 0.50773 1 0.81111 1 0.28345 1 0.40521 1 1 1 YIPF2 3 (7%) 38 1 1 0.28579 1 0.098519 1 0.088059 1 0.80869 1 0.1997 1 0.40608 1 0.41669 1 GNAS 7 (17%) 34 0.58368 1 0.3119 1 0.26135 1 0.32465 1 0.10742 1 0.40427 1 0.62489 1 0.54214 1 TGFBR2 3 (7%) 38 0.28917 1 0.57608 1 0.53195 1 0.50579 1 0.084469 1 0.36909 1 0.15676 1 0.7717 1 PARVB 3 (7%) 38 0.56248 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA PTPN21 3 (7%) 38 0.64996 1 0.28688 1 0.097779 1 0.087119 1 0.059299 1 0.00138 1 0.10169 1 0.41611 1 TSC22D1 3 (7%) 38 1 1 0.28623 1 0.73941 1 0.58458 1 0.81012 1 0.20035 1 0.40791 1 0.41484 1 ZNF184 4 (10%) 37 0.73563 1 0.1197 1 0.34 1 0.31275 1 0.64564 1 0.27038 1 0.36267 1 0.65008 1 ANK3 5 (12%) 36 0.36717 1 1 1 0.62863 1 0.61247 1 0.84098 1 0.46224 1 0.48436 1 1 1