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Supplementary Table S1 Demographic Characteristics Of Supplementary Table S1 Demographic characteristics of HCC patients • Age (year; mean ± SD) 53.950 ± 11.802 • Gender (number; %) Male 79 (79%) Female 21 (21%) • AFP (ng/mL; mean ± SD) 23928.571 ± 79577.084 • Tumor encapsulation (number; %) Absent 61 (63.5%) Present 35 (36.5%) • Cellular differentiation by Edmondson grading I-II 46 (47.9%) III-IV 50 (52.1%) • Tumor microsatellite formation (number, %) Absent 45 (46.9%) Present 51 (53.1%) • Tumor size (cm; mean ± SD) Length 8.3 ± 5.0 Width 7.4 ± 4.3 • Venous invasion (number; %) Absent 42 (43.3%) Present 55 (56.7%) • Direct liver invasion (number; %) Absent 53 (60.2%) Present 35 (39.8%) • pTNM staging (number, %) I-II 37(38.1%) III-IV 60 (61.9%) • Hepatitis B surface antigen (number; %) Absent 22 (23.4%) Present 72 (76.6%) • Background liver disease (number; %) Normal 7 (7.2%) Chronic hepatitis 36 (37.1%) Cirrhosis 54 (55.7%) Supplementary Table S2 Primer sequences used in qRT-PCR study Genes Sequences Forward: cagatcatcggtcaggccaa Human NDUFA4 Reverse: tctgtcccaacaaacatctgga Forward: aaaagacatccggggatcat Human NDUFA4L2 Reverse: tccgggttgttctttctgtc Forward: ctcctccactgcccactcta Human NDUFA4L2 HRE-1 (ChIP) Reverse: gtcactctgtactctgcctt Forward: gagagcaggtccccagaga Human NDUFA4L2 HRE-2 (ChIP) Reverse: ctccttggcccagacttatg Forward: gaggatgaggtggaacgtgt Human 18S Reverse: agaagtgacgcagccctcta Forward: gcactcttccagccttcctt Human ACTB Reverse: aatgccagggtacatggtgg Forward: ctttgctgacctgctggatt Human HPRT Reverse: ctgcattgttttcggagtgt Supplementary Table S3 The target regions of shRNA and siRNA constructs shRNA clones Genebank Target nucleotides shNDUFA4-30 NM_002489 124-144 shNDUFA4-88 NM_002489 353-373 shNDUFA4L2-90 NM_020142 60-80 shHIF-1α NM_181054 2,123-2,141 shHIF-2α NM_001430 1,992-2,012 siRNA clones Genebank Target nucleotides siNDUFA4L2-1 NM_020142 246-264 siNDUFA4L2-3 NM_020142 103-121 siNDUFA4L2-4 NM_020142 146-164 Supplementary Table S4 Clinico-pathological correlation of NDUFA4L2 over-expression in human HCC Clinico-pathological features No. of Cases Mean P value • Tumor size ≤ 5 cm 34 1.516 0.195 > 5 cm 62 2.068 • Cellular differentiation by Edmondson grading I – II 46 2.011 0.411 III – IV 50 1.678 • Tumor encapsulation Absent 61 2.203 *0.039 Present 35 1.346 • Tumor microsatellite formation Absent 45 1.198 *0.002 Present 51 2.402 • Direct liver invasion Absent 53 1.506 0.156 Present 35 2.106 • Hepatitis B surface antigen Absent 22 1.937 0.635 Present 72 1.712 • Venous invasion Absent 42 1.592 0.238 Present 55 2.074 *P<0.05; N=100 Supplementary Table S5 Down Regulated Genes in NDUFA4L2 Knockdown HCC cells Gene NTC (FPKM) shL2-90 (FPKM) Fold change SH3GL1P2 0.761623 0.380601 0.499723617 ADAM8 0.463544 0.231426 0.499253577 SCAMP1-AS1 1.67707 0.837189 0.49919741 SH3YL1 3.37804 1.68605 0.499120792 HIST1H3E 2.81929 1.40268 0.49752952 REREP3 0.647432 0.322092 0.497491628 NR3C2 0.142956 0.0711156 0.497464954 SEC31B 0.184359 0.0917107 0.497457135 MYO7B 0.375316 0.186703 0.497455478 TMEM254-AS1 0.108506 0.0537568 0.495426981 C21orf119 2.80135 1.38549 0.494579399 EXOC3L4 0.380068 0.187964 0.494553606 PRH1 1.68311 0.831699 0.494144174 KLF8 0.393827 0.194483 0.493828508 DENND2C 0.189965 0.0937807 0.493673571 MAGEC1 0.464209 0.229 0.49331228 C9orf173 0.311722 0.153522 0.492496519 CHSY3 0.30456 0.149903 0.492195298 MRC2 0.17374 0.0855132 0.49219063 RPEL1 0.799184 0.392808 0.491511342 UNC5B-AS1 6.78942 3.33296 0.490904967 KLF3-AS1 0.672482 0.329245 0.489596748 DNAAF3 0.30395 0.148685 0.489175851 LRRC39 0.304849 0.149007 0.488789532 AHRR 0.44304 0.216479 0.488621795 COL11A2 0.234426 0.1144 0.488000478 C1QL1 0.978865 0.476937 0.487234706 KCNMB4 0.856615 0.417361 0.487221214 NFATC1 0.206553 0.100588 0.48698397 NECAB1 0.157432 0.0765264 0.486091773 CCDC150 0.397478 0.193184 0.486024384 FAM160A1 1.31199 0.636949 0.485483121 FAM27E2 0.175755 0.0850939 0.484162044 LDLRAD4 0.17958 0.0867033 0.48281156 APOH 1.73112 0.835328 0.482536162 HSD11B2 1.04178 0.502687 0.482527021 LOC102723385 0.321261 0.154866 0.482056646 PTPN22 0.113555 0.0546526 0.481287482 GPR160 11.0757 5.28357 0.477041632 RXFP1 0.987013 0.467323 0.473471981 RHD 0.162375 0.0766867 0.472281447 SPDYE7P 0.346316 0.163499 0.472109287 ENO1-AS1 0.350972 0.16494 0.469952019 LINC01023 1.45134 0.681979 0.469896096 HIST1H3J 0.314392 0.147728 0.46988473 HIST1H2AH 0.311348 0.146297 0.469882575 LOC101059948 0.300673 0.141281 0.469882563 SPINK13 0.28554 0.134169 0.469878126 LINC00571 0.275742 0.129565 0.469877639 RBAKDN 0.236504 0.111127 0.46987366 LOC102723809 0.989734 0.465049 0.469872713 LINC00539 0.231392 0.108724 0.469869313 CHKB-AS1 0.209275 0.0983317 0.469868355 LOC102467147 0.596706 0.280372 0.469866232 CLLU1OS 0.187297 0.0880038 0.469862304 LOC728228 0.188766 0.0886939 0.469861628 LOC100288911 0.353943 0.166304 0.469860966 LOC101928043 0.183026 0.0859966 0.46986002 CSAG1 0.197675 0.0928795 0.469859618 LOC100507661 0.506705 0.238079 0.469857215 ATP6AP1L 0.657166 0.308774 0.469856931 LOC101927142 0.160727 0.0755185 0.469855718 RASSF1-AS1 0.313603 0.147348 0.469855199 KCNE2 0.152578 0.0716895 0.469854763 ORM1 0.144345 0.0678209 0.469852783 LINC00412 0.138731 0.0651828 0.469850286 CLEC3B 0.141587 0.0665246 0.469849633 LOC101927843 0.398402 0.187189 0.469849549 C1orf162 0.129236 0.0607214 0.469848958 TAS2R46 0.12702 0.0596802 0.469848843 LY6G6C 0.271594 0.127608 0.469848377 ACOT6 0.115725 0.0543729 0.469845755 LOC338694 0.117994 0.0554389 0.469845077 CALML6 0.103644 0.0486965 0.469843889 RAB41 0.107102 0.0503212 0.4698437 MTNR1A 0.2064 0.0969754 0.469842054 LINC00592 0.21858 0.102698 0.469841706 SUGT1P3 0.109789 0.0515834 0.469841241 C11orf42 0.495811 0.232952 0.469840322 IL6 0.666018 0.312922 0.469840154 MRGPRE 0.171333 0.0804984 0.469835934 LOC100630918 0.462935 0.217503 0.469834858 CACNA1G-AS1 0.152721 0.0717536 0.469834535 UBAP1L 0.159026 0.0747159 0.469834492 LOC101928708 0.150337 0.0706334 0.469833773 FLJ26850 0.152359 0.0715833 0.469833092 LYRM9 0.294243 0.138245 0.469832757 CHAD 0.252903 0.118822 0.469832307 SOWAHD 0.203721 0.0957147 0.469832271 FAM19A3 0.323458 0.151971 0.46983225 GPR162 0.143504 0.0674227 0.469831503 LOC344967 0.20047 0.0941871 0.469831396 LOC101927257 0.218851 0.102823 0.469831072 ALKBH3-AS1 0.109737 0.0515578 0.469830595 PCDHGA4 0.380018 0.178544 0.469830376 BIN3-IT1 0.462118 0.217117 0.469830217 OVCH1 0.118593 0.0557185 0.469829585 LOC643770 0.116508 0.0547389 0.46982954 SCOC-AS1 0.156577 0.0735644 0.469828902 ZNF77 0.206199 0.0968782 0.469828661 LOC100507501 1.50383 0.706542 0.469828372 DLX6 0.113088 0.0531319 0.469827922 STK4-AS1 0.148604 0.0698183 0.469827865 FAAH 0.350529 0.164688 0.469827033 LINC00501 0.152769 0.071775 0.469826994 CHRNA3 0.12244 0.0575255 0.469826037 C19orf57 0.342693 0.161006 0.469825762 LOC100128361 0.291304 0.136862 0.469825337 SLC16A9 0.151454 0.0711566 0.469823181 WNT4 0.128984 0.0605996 0.469822614 ROBO4 0.105102 0.0493792 0.469821697 GNN 0.110843 0.0520763 0.469820377 GPR133 0.110861 0.0520846 0.469818962 BEGAIN 0.269196 0.126472 0.469813816 PDC 0.189156 0.088868 0.469813276 TMOD2 0.194677 0.0914606 0.469806911 LOC100132529 0.190634 0.0895539 0.469768772 C4B_2 0.17881 0.083828 0.468810469 LOXL1 2.29853 1.07474 0.467577104 NEURL1B 14.8661 6.94447 0.467134622 LOC101927811 0.818921 0.382264 0.466789837 NBPF11 3.29108 1.52877 0.464519246 CDKN2B-AS1 1.11798 0.517799 0.46315587 PDE5A 0.875884 0.404448 0.461759776 SIRPB1 0.503763 0.232441 0.461409433 MRPL42P5 1.27122 0.58609 0.461045295 YPEL1 0.894964 0.412066 0.460427459 RORC 0.54904 0.252755 0.46035808 RAET1E-AS1 0.132074 0.0607946 0.460307101 SNHG21 1.88131 0.865421 0.46000978 OAZ1 264.986 121.621 0.458971417 ZNF773 0.513736 0.235754 0.45890107 GDPD3 1.0658 0.488542 0.458380559 OSCP1 0.601027 0.274812 0.457237362 FYN 1.11284 0.506793 0.45540509 ARMC12 0.102323 0.0465853 0.455276917 JAZF1 1.4475 0.65765 0.45433506 DRD4 1.09236 0.494223 0.45243601 GKAP1 0.776409 0.351116 0.452230719 HOXC5 0.10029 0.0452748 0.451438827 UCN 2.49897 1.12314 0.44944117 LINC00854 1.39452 0.626722 0.449417721 USP27X-AS1 0.522854 0.23497 0.449398876 PRODH 51.7476 23.2366 0.44903725 GUSBP3 0.476315 0.213876 0.449022181 AGER 1.24434 0.558654 0.448956073 ANKRD16 2.48992 1.11587 0.448154961 TMEM200B 0.307683 0.137875 0.448107305 LINC00035 3.35578 1.50175 0.447511458 NAPSA 0.414363 0.185412 0.447462732 PCDHGB6 0.220671 0.09874 0.447453449 MOB3B 0.159164 0.0712172 0.447445402 RYR2 0.18139 0.0810289 0.446710954 SULT2B1 0.578977 0.257859 0.445370023 MARCH1 0.350718 0.1561 0.445086936 C7orf63 0.193633 0.0861464 0.44489524 GPR161 1.77598 0.789736 0.444676179 FGF13 0.979771 0.434695 0.44367 IQUB 0.147545 0.065389 0.443180047 SLAIN1 0.430705 0.190134 0.441448323 LOC100289580 0.203496 0.0896847 0.440719719 ZMYND15 0.684168 0.30139 0.440520457 PLXNC1 0.221024 0.0972151 0.439839565 CYP4V2 1.27494 0.55906 0.438499067 RFESD 0.28061 0.122854 0.437810484 INHA 1.64436 0.718676 0.437055146 CA11 2.9746 1.29828 0.436455322 AKAP7 2.91843 1.26941 0.434963319 STAM-AS1 0.508268 0.220428 0.433684592 ID4 0.168992 0.0732889 0.43368266 ELFN1 0.175335 0.0760397 0.433682379 CLCNKB 0.156194 0.067579 0.432660666 TP73 0.716315 0.309883 0.432607163 PCDHGC5 0.175796 0.0758945 0.431719152 SOX2-OT 0.128938 0.055615 0.431331338 ENDOU 0.13769 0.0593478 0.431024766 LOC101929696 0.19855 0.0855091 0.430667842 KCNQ1 0.851664 0.366275 0.43006984 TSC22D1-AS1 0.21402 0.0918467 0.429150079 C6orf201 0.236836 0.101233 0.427439241 DFNB59 0.391718 0.167311 0.427121041 TMLHE-AS1 0.173076 0.0739239 0.427118145 TMLHE-AS1 0.173076 0.0739239 0.427118145 EFCAB6 0.120402 0.051424 0.42710254 TNFRSF10C 0.258494 0.110062
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