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 ZFPM1 26 (41%) 38 0.18055 1 0.81046 1 0.33521 1 0.81867 1 0.6795 1 0.83823 1 0.49248 1 0.9375 1 LACTB 20 (31%) 44 0.11722 1 0.68193 1 1 1 0.56014 1 0.45392 1 0.74316 1 0.31415 1 0.75608 1 CCDC102A 17 (27%) 47 0.13148 1 0.93564 1 0.91095 1 0.75835 1 0.43869 1 0.4765 1 0.68679 1 0.1451 1 ZNF517 13 (20%) 51 0.6521 1 0.96243 1 0.88407 1 1 1 0.23629 1 0.66739 1 0.79923 1 0.42747 1 TOR3A 12 (19%) 52 0.27292 1 0.02206 1 0.63759 1 0.01515 1 1 1 0.86847 1 0.82756 1 0.66184 1 USP42 16 (25%) 48 0.72527 1 0.04874 1 1 1 0.95951 1 0.56652 1 0.83933 1 0.74837 1 0.28859 1 CLDN23 10 (16%) 54 0.26303 1 0.24679 1 0.02368 1 0.18106 1 0.090519 1 0.18983 1 0.10762 1 0.32206 1 TP53 13 (20%) 51 0.02159 1 0.77532 1 0.02011 1 0.6659 1 0.01804 1 0.63752 1 0.04165 1 0.19199 1 KCNK17 9 (14%) 55 0.10297 1 0.03787 1 0.094449 1 0.0099599 1 1 1 0.52247 1 0.47398 1 0.41669 1 LZTR1 6 (9%) 58 0.22446 1 0.8062 1 0.089449 1 0.19389 1 0.41694 1 0.01375 1 0.44453 1 0.085379 1 APOE 7 (11%) 57 0.16985 1 0.62041 1 0.066919 1 0.45275 1 0.27913 1 0.82243 1 0.027 1 0.82548 1 CCDC105 7 (11%) 57 0.16857 1 0.0085899 1 0.88092 1 0.71391 1 1 1 0.050909 1 0.85899 1 0.32575 1 RINL 8 (12%) 56 0.14617 1 0.70116 1 0.50864 1 0.29372 1 0.882 1 0.16569 1 0.43791 1 0.18693 1 MAL2 12 (19%) 52 0.7821 1 0.30345 1 0.19943 1 0.51765 1 0.12302 1 0.27693 1 0.64433 1 0.32063 1 LRIG1 17 (27%) 47 0.65429 1 0.89431 1 1 1 0.78058 1 0.18568 1 0.49565 1 0.69557 1 0.87421 1 C19ORF10 8 (12%) 56 0.63261 1 0.35487 1 0.23522 1 0.10939 1 0.54989 1 0.8596 1 0.28712 1 0.76091 1 C10ORF95 7 (11%) 57 0.17163 1 0.7071 1 0.55664 1 0.81739 1 0.74993 1 0.49141 1 0.86191 1 0.50452 1 SYT8 9 (14%) 55 0.42757 1 0.40254 1 0.0346 1 0.14721 1 1 1 0.21596 1 1 1 0.64271 1 IDUA 9 (14%) 55 0.54482 1 0.89417 1 0.34512 1 0.53981 1 0.12243 1 0.45663 1 0.1963 1 0.48282 1 HHIPL1 8 (12%) 56 0.12643 1 0.28529 1 0.35778 1 0.20441 1 0.17555 1 0.78622 1 0.28944 1 0.2006 1 ASPDH 8 (12%) 56 0.3061 1 0.6441 1 0.02032 1 0.34379 1 0.47626 1 0.02772 1 0.36772 1 0.079269 1 C1ORF106 9 (14%) 55 0.77036 1 0.43376 1 0.34343 1 0.86068 1 0.47757 1 0.68902 1 0.61644 1 1 1 THEM4 6 (9%) 58 0.00358 1 0.73405 1 0.4368 1 0.88617 1 0.24464 1 0.093829 1 0.25026 1 0.11137 1 CTNNB1 7 (11%) 57 1 1 0.16718 1 0.01942 1 0.01811 1 0.00174 1 0.16881 1 0.02717 1 0.47982 1 GDF1 5 (8%) 59 0.39564 1 0.31217 1 0.3625 1 0.25407 1 0.089629 1 0.53974 1 0.01923 1 0.71349 1 TSC22D2 8 (12%) 56 0.3494 1 0.52755 1 0.81528 1 0.94214 1 0.88263 1 0.42636 1 1 1 0.33405 1 ZAR1 11 (17%) 53 0.17477 1 0.66708 1 0.60218 1 0.80229 1 0.72049 1 1 1 0.51975 1 0.71541 1 RGS9BP 8 (12%) 56 0.29493 1 0.58512 1 1 1 0.88807 1 0.33507 1 0.96156 1 0.88421 1 0.34274 1 OPRD1 12 (19%) 52 0.8238 1 0.38763 1 0.79717 1 0.96058 1 0.33972 1 0.63078 1 0.46877 1 0.46566 1 C16ORF3 6 (9%) 58 0.90367 1 0.00078999 0.784 0.7993 1 0.8305 1 0.59416 1 1 1 0.69799 1 0.71072 1 FPGS 6 (9%) 58 1 1 1 1 0.6135 1 0.61402 1 0.090529 1 0.62384 1 0.67496 1 0.78703 1 PLIN5 5 (8%) 59 0.56098 1 0.69314 1 0.79907 1 0.54247 1 0.35032 1 0.30837 1 0.12864 1 0.32098 1 IRX3 5 (8%) 59 0.33324 1 0.73314 1 0.5197 1 0.19263 1 0.24624 1 0.7785 1 0.25025 1 0.0204 1 TRIOBP 12 (19%) 52 0.82067 1 0.1765 1 1 1 0.12751 1 0.90235 1 0.9301 1 0.66509 1 0.74565 1 KRTAP4-5 5 (8%) 59 0.76911 1 0.31301 1 1 1 0.88608 1 1 1 0.84 1 1 1 0.89362 1 ATXN1 10 (16%) 54 0.40839 1 0.12883 1 0.23438 1 0.6271 1 0.32418 1 0.85185 1 0.41024 1 0.85073 1 ZNF628 7 (11%) 57 0.3054 1 0.89168 1 0.35092 1 0.12178 1 0.12453 1 0.49406 1 0.095299 1 0.72535 1 WDR34 5 (8%) 59 0.67359 1 0.77237 1 0.93077 1 0.83356 1 0.84275 1 0.52263 1 1 1 0.39627 1 BTBD11 6 (9%) 58 1 1 0.23499 1 0.47973 1 1 1 0.49269 1 0.16456 1 0.49067 1 0.21316 1 GARS 21 (33%) 43 0.23647 1 0.068529 1 0.43329 1 0.062989 1 0.23844 1 0.33937 1 0.098939 1 0.34229 1 ZNF598 13 (20%) 51 0.44589 1 0.37703 1 0.5341 1 1 1 1 1 0.21532 1 1 1 0.16226 1 BHLHE22 5 (8%) 59 0.39142 1 0.064129 1 0.10362 1 0.83003 1 0.59521 1 0.88135 1 0.69764 1 0.78544 1 PTPLA 4 (6%) 60 0.44113 1 0.2921 1 0.33154 1 0.47435 1 0.79017 1 1 1 0.20952 1 0.58339 1 CD320 4 (6%) 60 0.93529 1 0.89655 1 0.73707 1 0.68418 1 0.41607 1 0.22088 1 0.17516 1 0.17296 1 KIAA1984 4 (6%) 60 0.25183 1 0.73468 1 0.12576 1 0.04635 1 0.0364 1 0.58018 1 0.061699 1 0.66933 1 TPO 12 (19%) 52 0.53219 1 0.30476 1 0.21362 1 0.15858 1 0.13985 1 0.31852 1 0.27979 1 0.12247 1 AATK 6 (9%) 58 0.11512 1 0.31609 1 0.35973 1 0.25122 1 1 1 0.50562 1 1 1 0.4554 1 PANK2 5 (8%) 59 0.73506 1 0.4283 1 0.11353 1 0.10781 1 0.4412 1 0.34219 1 0.59406 1 0.32284 1 SNED1 6 (9%) 58 0.39386 1 0.59433 1 0.21235 1 0.45542 1 0.04417 1 0.64906 1 0.04589 1 0.32061 1 CCDC150 4 (6%) 60 0.44086 1 0.80766 1 0.26488 1 0.19676 1 0.41741 1 0.18159 1 0.44169 1 0.14295 1 ERCC2 10 (16%) 54 0.75612 1 0.19618 1 0.50999 1 0.14944 1 0.67106 1 0.23917 1 0.2896 1 0.088439 1 RREB1 5 (8%) 59 0.73605 1 0.80672 1 0.61243 1 1 1 0.6749 1 0.5036 1 0.67546 1 0.55363 1 RNF39 5 (8%) 59 0.42685 1 0.31113 1 0.18447 1 0.26744 1 0.16739 1 0.6951 1 0.35136 1 0.55262 1 SEMA5B 8 (12%) 56 0.38973 1 0.35048 1 0.39906 1 0.27377 1 0.85282 1 0.33691 1 0.6367 1 0.66562 1 TAF5 4 (6%) 60 0.93668 1 0.73292 1 1 1 0.88371 1 0.02122 1 0.12113 1 0.01946 1 0.19726 1 SARM1 7 (11%) 57 0.03013 1 0.43528 1 0.27521 1 0.02852 1 0.11292 1 0.75418 1 0.04596 1 0.91705 1 PRSS27 3 (5%) 61 0.79659 1 0.90882 1 0.60941 1 0.1085 1 0.14053 1 1 1 0.20649 1 1 1 TMEM189 4 (6%) 60 0.16191 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NOXA1 5 (8%) 59 0.14971 1 0.42644 1 0.21945 1 0.47551 1 0.30178 1 0.34113 1 0.31362 1 0.32778 1 LRP11 7 (11%) 57 0.04064 1 0.072719 1 0.79851 1 0.54098 1 0.59265 1 0.93604 1 0.69506 1 0.94988 1 RNF149 4 (6%) 60 0.37564 1 0.0356 1 0.35995 1 0.61618 1 0.32863 1 0.35255 1 0.34287 1 0.44358 1 DMKN 3 (5%) 61 0.80071 1 0.29152 1 0.61112 1 0.47394 1 0.0083099 1 0.5601 1 0.01009 1 0.82309 1 FANK1 4 (6%) 60 0.93616 1 0.34953 1 0.85465 1 0.32792 1 0.7897 1 0.2267 1 1 1 0.17158 1 MUC5B 22 (34%) 42 1 1 0.57224 1 0.67625 1 0.73062 1 0.81659 1 0.6309 1 0.59053 1 0.84633 1 PABPC1 4 (6%) 60 0.41488 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA GLTPD2 6 (9%) 58 0.071439 1 0.84394 1 0.88299 1 0.45342 1 0.55283 1 0.51017 1 0.85754 1 0.5965 1 MEN1 5 (8%) 59 0.095519 1 0.04326 1 0.01267 1 0.0061299 1 0.21546 1 0.0387 1 0.35144 1 0.0088899 1 SRPX 3 (5%) 61 0.89373 1 0.12546 1 0.46813 1 1 1 0.78949 1 0.78856 1 1 1 0.82242 1 MAP1S 5 (8%) 59 0.27558 1 0.38386 1 0.34911 1 1 1 1 1 0.88159 1 0.84164 1 1 1 SCRT1 3 (5%) 61 0.79861 1 0.42484 1 0.60894 1 0.63901 1 0.44056 1 0.70975 1 0.59239 1 0.87509 1 OBSCN 20 (31%) 44 0.65718 1 0.26103 1 0.45769 1 0.62428 1 0.094529 1 0.7802 1 0.1956 1 0.73022 1 IER5 3 (5%) 61 0.36916 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNIP2 5 (8%) 59 0.67281 1 0.62526 1 0.73473 1 0.8865 1 1 1 0.40158 1 1 1 0.23453 1 NOTCH2 7 (11%) 57 0.30407 1 0.79783 1 0.35037 1 0.03381 1 0.0083499 1 0.41721 1 0.0089299 1 0.3251 1 RASIP1 7 (11%) 57 0.62976 1 0.67612 1 0.03912 1 0.15934 1 0.02197 1 0.68638 1 0.03768 1 0.74793 1 NMU 5 (8%) 59 0.82142 1 1 1 0.04848 1 0.6393 1 1 1 0.50642 1 1 1 0.45531 1 VARS 6 (9%) 58 0.44486 1 0.43726 1 0.18523 1 0.081819 1 0.85447 1 0.86074 1 0.34017 1 0.7617 1 SHOX2 3 (5%) 61 0.33425 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA HSD17B1 4 (6%) 60 1 1 0.10804 1 1 1 0.01275 1 1 1 0.83984 1 1 1 0.76189 1 COQ2 5 (8%) 59 0.2959 1 0.76505 1 0.36106 1 0.61626 1 1 1 0.66905 1 1 1 0.76161 1 KNDC1 10 (16%) 54 0.78477 1 0.12943 1 0.14061 1 0.37179 1 0.28835 1 0.35721 1 0.22846 1 0.74873 1 AR 4 (6%) 60 0.31961 1 0.42628 1 0.61023 1 0.47192 1 0.44463 1 1 1 0.59577 1 1 1 KCTD3 4 (6%) 60 0.41358 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA FZD1 3 (5%) 61 0.4066 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZC3H12D 3 (5%) 61 0.0033 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA KRTAP5-5 5 (8%) 59 0.36199 1 1 1 0.21875 1 0.21558 1 0.44371 1 0.17993 1 0.5933 1 0.055969 1 AKAP2 4 (6%) 60 0.074529 1 0.47489 1 0.73825 1 0.31557 1 0.67308 1 0.46833 1 0.34089 1 0.64663 1 KBTBD13 9 (14%) 55 0.58425 1 0.10709 1 0.7341 1 0.13518 1 1 1 0.35795 1 1 1 0.78026 1 SPIRE2 3 (5%) 61 0.30162 1 0.02675 1 1 1 0.82439 1 1 1 0.70773 1 1 1 0.87463 1 NPTX1 3 (5%) 61 0.33661 1 1 1 1 1 0.82507 1 0.58677 1 0.70816 1 0.43003 1 0.65669 1 ADAD2 4 (6%) 60 0.25126 1 0.57383 1 0.73819 1 0.31749 1 0.02058 1 0.5399 1 0.01958 1 0.83675 1 SEZ6L2 8 (12%) 56 0.35475 1 0.59835 1 0.882 1 1 1 0.45913 1 0.58435 1 0.4558 1 0.80766 1 NEFH 7 (11%) 57 0.03617 1 0.15719 1 0.02364 1 0.0082499 1 0.16761 1 0.52123 1 0.34961 1 0.15789 1 DLEU7 3 (5%) 61 0.56802 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA AMDHD1 11 (17%) 53 0.02665 1 0.72113 1 0.56926 1 0.18475 1 0.23603 1 0.88811 1 0.062549 1 0.95415 1 GLTSCR2 5 (8%) 59 0.21973 1 0.80584 1 0.26412 1 0.19682 1 1 1 0.62317 1 0.25072 1 0.5891 1 PLEC 13 (20%) 51 0.61249 1 0.71264 1 0.19417 1 0.68085 1 0.67273 1 0.60395 1 0.39595 1 0.47141 1 MAP7 3 (5%) 61 1 1 0.69664 1 1 1 0.82529 1 0.58797 1 0.70841 1 0.42907 1 0.65491 1 DSPP 10 (16%) 54 0.92834 1 0.063989 1 1 1 0.51567 1 0.51474 1 0.57392 1 0.31267 1 0.32966 1 CRIPAK 10 (16%) 54 0.20062 1 0.92806 1 0.47354 1 0.83613 1 0.80664 1 0.35859 1 0.71864 1 0.28701 1 PRKAR1A 6 (9%) 58 0.48718 1 1 1 0.27675 1 0.45697 1 0.086499 1 0.564 1 0.17361 1 0.15055 1 CYP4A22 4 (6%) 60 0.11348 1 0.62155 1 0.1627 1 0.50734 1 0.24569 1 0.20715 1 0.24918 1 0.83682 1 NOM1 6 (9%) 58 1 1 0.2328 1 0.93021 1 1 1 1 1 0.74204 1 0.8399 1 0.27569 1 RNF135 3 (5%) 61 0.89448 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA C12ORF65 3 (5%) 61 0.37142 1 0.03538 1 0.11298 1 0.062299 1 0.44495 1 0.56347 1 0.59267 1 0.73537 1 HLA-B 6 (9%) 58 0.29302 1 0.77461 1 0.88291 1 1 1 0.65349 1 0.27381 1 0.53529 1 0.3192 1 CSGALNACT2 3 (5%) 61 0.89466 1 0.02558 1 0.69111 1 0.82337 1 0.58427 1 0.87607 1 0.42958 1 0.93325 1 UQCRFS1 5 (8%) 59 0.50825 1 0.50185 1 1 1 0.8849 1 0.48961 1 0.18738 1 0.49365 1 0.050789 1 PDCD6 3 (5%) 61 0.30169 1 0.69939 1 NA NA NA NA 1 1 0.63181 1 1 1 0.69614 1 PTX4 3 (5%) 61 0.56751 1 1 1 0.61215 1 0.21699 1 0.44354 1 1 1 0.59514 1 0.39209 1 SGK223 3 (5%) 61 0.89549 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA POLRMT 4 (6%) 60 0.50821 1 0.03631 1 0.32719 1 0.073749 1 0.18898 1 0.3534 1 0.12538 1 0.44339 1 CACNA1D 3 (5%) 61 0.5657 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NF1 7 (11%) 57 0.15156 1 0.90395 1 0.4105 1 0.26839 1 0.34214 1 0.85268 1 0.099859 1 0.5271 1 RGMB 6 (9%) 58 0.58126 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA ADAMTS7 4 (6%) 60 0.13955 1 0.57498 1 0.073199 1 0.46532 1 0.060999 1 0.35139 1 0.038 1 0.28841 1 CLIC6 6 (9%) 58 0.96218 1 1 1 0.66525 1 0.19282 1 0.2457 1 0.57929 1 0.24793 1 0.75949 1 EMR2 4 (6%) 60 0.37495 1 0.31374 1 0.47341 1 0.61423 1 0.67446 1 0.20684 1 0.6758 1 0.83861 1 PCDHB13 5 (8%) 59 0.51296 1 0.13865 1 0.1074 1 0.25597 1 0.54227 1 0.056569 1 0.80135 1 0.01259 1 MTFMT 3 (5%) 61 1 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA SPTAN1 3 (5%) 61 0.24435 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA HLA-A 3 (5%) 61 1 1 1 1 0.85411 1 0.21867 1 1 1 0.44475 1 1 1 0.21533 1 ASB16 6 (9%) 58 0.74346 1 0.94537 1 0.61418 1 0.88529 1 0.54311 1 0.77811 1 0.80198 1 0.95925 1 GPRIN2 9 (14%) 55 0.59114 1 0.37047 1 0.64955 1 0.42754 1 0.58162 1 0.80077 1 0.381 1 0.64671 1 HNRNPCL1 3 (5%) 61 0.33568 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA BTNL9 4 (6%) 60 0.41581 1 0.096209 1 0.14139 1 0.061799 1 0.14222 1 1 1 0.20851 1 1 1 KCNJ11 4 (6%) 60 0.0135 1 0.62438 1 0.43373 1 0.14002 1 0.13209 1 0.04984 1 0.17415 1 0.21103 1 JMJD4 3 (5%) 61 0.8003 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRRC4B 6 (9%) 58 0.18804 1 0.18901 1 0.0133 1 0.070819 1 0.17356 1 0.0299 1 0.17172 1 0.0097399 1 OPLAH 3 (5%) 61 0.56625 1 0.8536 1 0.60805 1 0.47224 1 0.4435 1 0.34205 1 0.59389 1 0.39449 1 BAGE2 3 (5%) 61 0.89508 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA MADCAM1 3 (5%) 61 0.48054 1 0.69606 1 NA NA NA NA 1 1 0.1994 1 1 1 0.13571 1 CTBP2 3 (5%) 61 0.89455 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA MSH3 4 (6%) 60 0.01762 1 0.70014 1 0.33472 1 1 1 0.3001 1 0.4425 1 0.3141 1 0.49462 1 ATN1 4 (6%) 60 0.13022 1 0.85314 1 0.85539 1 1 1 0.79082 1 0.79018 1 1 1 0.82251 1 FAM46A 3 (5%) 61 0.89679 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA UTS2R 3 (5%) 61 0.16223 1 0.69864 1 0.68975 1 0.82399 1 0.58611 1 0.7908 1 0.42823 1 0.82306 1 SMG1 3 (5%) 61 0.16446 1 0.12517 1 0.1435 1 0.062079 1 0.30478 1 0.02561 1 0.31573 1 0.18792 1 FUCA1 3 (5%) 61 0.40436 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA FEZ2 3 (5%) 61 0.47655 1 0.34752 1 0.17902 1 0.82481 1 0.20914 1 0.70909 1 0.13261 1 0.6576 1 GLI3 5 (8%) 59 0.73674 1 0.40683 1 1 1 0.88541 1 0.13374 1 0.39937 1 0.17551 1 0.091939 1 NOL9 4 (6%) 60 0.00202 1 1 1 1 1 1 1 0.78882 1 0.55872 1 1 1 0.73293 1