Table SI. DEmiRNAs and DEIncRNAs expression in A549 and A549‑DDP cell lines.

LINC/miRNA Log2 FC Average expression t P‑value Adjusted P‑value B

LINC01510 ‑3.97070 4.84389 ‑17.35410 0.00000 0.00000 6.72955 LINC01589 2.85377 5.51166 12.83556 0.00000 0.00000 5.22009 LINC00304 ‑2.75795 4.79734 ‑10.53950 0.00001 0.00001 4.08430 OLMALINC ‑1.94510 8.13199 ‑9.74695 0.00002 0.00002 3.60982 HOXC‑AS3 ‑2.41068 4.89131 ‑9.46879 0.00002 0.00002 3.43143 LINC00173 ‑1.70282 6.68825 ‑8.53554 0.00004 0.00004 2.78287 LINC01619 ‑1.85732 6.75041 ‑7.67225 0.00008 0.00008 2.10618 PRKAG2‑AS1 ‑1.48862 4.80181 ‑6.57082 0.00023 0.00023 1.11795 LAMA5‑AS1 1.40434 9.48955 6.35705 0.00028 0.00028 0.90802 PCOLCE‑AS1 ‑1.28159 3.51848 ‑6.25125 0.00032 0.00032 0.80179 LINC01123 1.18057 7.93977 5.97768 0.00042 0.00042 0.51973 PSMB8‑AS1 ‑2.96302 5.98662 ‑5.81762 0.00050 0.00050 0.34967 HOXD‑AS2 1.51247 7.43062 5.76065 0.00053 0.00053 0.28822 LINC01091 ‑1.50634 5.05734 ‑5.72097 0.00056 0.00056 0.24513 LINC00648 1.71835 6.59872 5.68954 0.00058 0.00058 0.21084 CCEPR ‑1.49164 11.64535 ‑5.63872 0.00061 0.00061 0.15507 LINC01152 ‑1.51738 4.80929 ‑5.53917 0.00068 0.00068 0.04469 LINC01006 ‑1.79776 6.49566 ‑5.35044 0.00084 0.00084 ‑0.16877 FIRRE 1.38685 4.82513 5.31448 0.00088 0.00088 ‑0.21007 SPACA6P‑AS ‑1.40943 4.08290 ‑5.26058 0.00093 0.00093 ‑0.27235 LINC01256 1.14013 4.46906 5.16826 0.00104 0.00104 ‑0.38008 RHPN1‑AS1 ‑1.99383 5.07229 ‑5.14184 0.00107 0.00107 ‑0.41117 LINC00950 ‑1.20399 5.51647 ‑5.00702 0.00125 0.00125 ‑0.57150 PRR34‑AS1 1.43324 4.13498 4.98790 0.00128 0.00128 ‑0.59446 ASMTL‑AS1 1.17657 6.91020 4.88177 0.00146 0.00146 ‑0.72305 TOB1‑AS1 ‑1.41673 4.89486 ‑4.83725 0.00154 0.00154 ‑0.77753 LINC00963 ‑1.45696 5.02400 ‑4.81595 0.00158 0.00158 ‑0.80370 LINC00210 2.87044 5.86991 4.79120 0.00163 0.00163 ‑0.83421 LINC00853 ‑1.38307 5.06479 ‑4.72342 0.00177 0.00177 ‑0.91826 TMEM92‑AS1 1.97314 4.88467 4.64015 0.00196 0.00196 ‑1.02253 LINC00920 ‑1.61731 6.15709 ‑4.61573 0.00202 0.00202 ‑1.05331 PWAR6 ‑1.17733 7.41414 ‑4.49971 0.00234 0.00234 ‑1.20091 ZEB1‑AS1 ‑1.01833 5.61408 ‑4.41777 0.00259 0.00259 ‑1.30646 LINC00970 1.09655 6.61802 4.37745 0.00273 0.00273 ‑1.35878 LOXL1‑AS1 ‑1.70424 4.68625 ‑4.34317 0.00285 0.00285 ‑1.40347 LINC01531 1.32027 4.44207 4.30098 0.00301 0.00301 ‑1.45874 LINC00708 1.26089 4.04687 4.28598 0.00307 0.00307 ‑1.47846 LINC00488 ‑1.31352 4.17773 ‑4.25816 0.00319 0.00319 ‑1.51512 VTRNA1‑3 1.18150 6.12458 4.21240 0.00338 0.00338 ‑1.57569 TNRC6C‑AS1 ‑1.49753 3.82328 ‑3.98623 0.00456 0.00456 ‑1.87981 LINC01118 1.01554 6.06101 3.92674 0.00494 0.00494 ‑1.96109 LINC01254 1.18782 5.20876 3.91311 0.00503 0.00503 ‑1.97978 KCNQ5‑AS1 ‑1.13813 4.47585 ‑3.89554 0.00515 0.00515 ‑2.00393 DGCR5 ‑1.16182 5.65765 ‑3.85499 0.00545 0.00545 ‑2.05983 LINC01262 1.15632 4.30354 3.84033 0.00556 0.00556 ‑2.08009 LINC00440 ‑1.41604 4.66126 ‑3.83923 0.00556 0.00556 ‑2.08161 LINC00887 1.75862 6.11678 3.82915 0.00564 0.00564 ‑2.09557 STX17‑AS1 ‑1.05084 5.31559 ‑3.81490 0.00575 0.00575 ‑2.11532 LINC01133 ‑1.22198 7.71154 ‑3.78933 0.00596 0.00596 ‑2.15084 FOXP4‑AS1 ‑1.19111 3.97356 ‑3.72930 0.00647 0.00647 ‑2.23458 PCED1B‑AS1 1.59275 4.16658 3.72439 0.00651 0.00651 ‑2.24145 LINC01588 ‑1.09189 6.31717 ‑3.65885 0.00713 0.00713 ‑2.33350 UBXN10‑AS1 ‑2.78609 6.55237 ‑3.65228 0.00720 0.00720 ‑2.34276 SCARNA20 1.24777 6.13013 3.52574 0.00859 0.00859 ‑2.52222 CASC20 1.38745 9.54750 3.44864 0.00958 0.00958 ‑2.63258 ATP13A5‑AS1 1.19610 5.52011 3.26391 0.01247 0.01247 ‑2.89977 HNF1A‑AS1 ‑1.17902 9.52780 ‑3.26245 0.01250 0.01250 ‑2.90190 LINC00092 1.14610 5.64500 3.25768 0.01259 0.01259 ‑2.90884 LINC00559 ‑1.02585 4.55652 ‑3.25665 0.01260 0.01260 ‑2.91035 Table SI. Continued.

LINC/miRNA Log2 FC Average expression t P‑value Adjusted P‑value B

IGF2‑AS 1.07631 5.04788 3.25068 0.01271 0.01271 ‑2.91905 FREM2‑AS1 1.53847 4.99275 3.18857 0.01391 0.01391 ‑3.00978 NFIA‑AS1 1.61538 6.63913 3.15935 0.01451 0.01451 ‑3.05259 LINC01085 ‑1.16205 3.41785 ‑3.12661 0.01522 0.01522 ‑3.10066 LINC01352 1.47740 7.06471 3.06807 0.01658 0.01658 ‑3.18682 LINC01431 ‑1.18167 5.28320 ‑3.03079 0.01752 0.01752 ‑3.24183 JMJD1C‑AS1 ‑1.09123 6.03985 ‑2.90940 0.02095 0.02095 ‑3.42160 LINC00934 ‑1.20764 5.46744 ‑2.89940 0.02127 0.02127 ‑3.43646 DCTN1‑AS1 1.14361 6.97338 2.87247 0.02213 0.02213 ‑3.47647 LINC01037 1.30705 3.88590 2.86570 0.02236 0.02236 ‑3.48653 ELOVL2‑AS1 ‑1.45694 4.48633 ‑2.85286 0.02279 0.02279 ‑3.50563 PCGEM1 1.24751 4.68658 2.77694 0.02552 0.02552 ‑3.61866 FUT8‑AS1 1.03548 4.68413 2.74356 0.02683 0.02683 ‑3.66842 NRG3‑AS1 1.10444 6.02836 2.73790 0.02706 0.02706 ‑3.67685 LINC00592 ‑1.07269 4.25783 ‑2.73123 0.02733 0.02733 ‑3.68680 LINC01626 ‑2.04524 5.50144 ‑2.65254 0.03076 0.03076 ‑3.80418 THAP9‑AS1 1.27309 6.71712 2.63155 0.03175 0.03175 ‑3.83551 DGUOK‑AS1 1.27184 5.73999 2.58740 0.03393 0.03393 ‑3.90137 LINC00324 ‑1.00842 8.62507 ‑2.55570 0.03560 0.03560 ‑3.94865 LINC01251 ‑1.18512 6.16497 ‑2.51019 0.03814 0.03814 ‑4.01649 GRM7‑AS1 ‑1.58026 5.80487 ‑2.46518 0.04083 0.04083 ‑4.08352 CPEB1‑AS1 ‑1.33023 14.39346 ‑2.46383 0.04091 0.04091 ‑4.08554 ZNF385D‑AS2 ‑1.09988 4.60585 ‑2.44207 0.04228 0.04228 ‑4.11790 NRIR ‑1.17691 5.36938 ‑2.41947 0.04376 0.04376 ‑4.15151 ZNF503‑AS2 1.03737 4.96642 2.41768 0.04388 0.04388 ‑4.15417 RUVBL1‑AS1 ‑1.30957 7.83602 ‑2.41300 0.04419 0.04419 ‑4.16111 LINC00602 ‑1.47903 8.05841 ‑2.40940 0.04443 0.04443 ‑4.16646 LINC01416 ‑1.55774 6.18549 ‑2.40792 0.04453 0.04453 ‑4.16866 HTR5A‑AS1 ‑1.22051 6.92105 ‑2.39250 0.04559 0.04559 ‑4.19155 LINC01324 1.13801 4.25345 2.37245 0.04700 0.04700 ‑4.22130 FGF12‑AS2 ‑1.58819 5.84287 ‑2.35822 0.04803 0.04803 ‑4.24240 hsa‑mir‑146a ‑1.33395 ‑0.38704 ‑11.41869 0.00000 0.00000 6.25071 hsa‑mir‑886 ‑1.58844 ‑0.33372 ‑10.36467 0.00000 0.00000 5.50071 hsa‑mir‑574 1.19605 2.91744 8.57531 0.00001 0.00001 4.00292 hsa‑mir‑106b ‑1.39495 2.64603 ‑7.02495 0.00005 0.00005 2.42426 hsa‑miR‑194‑star 1.22352 0.22878 6.99981 0.00005 0.00005 2.39616 hsa‑miR‑194 1.21343 6.98141 6.95402 0.00006 0.00006 2.34476 hsa‑mir‑31 ‑1.06803 5.45538 ‑6.23245 0.00013 0.00013 1.49632 hsa‑mir‑152 ‑1.68437 0.42166 ‑5.93408 0.00019 0.00019 1.12348 hsa‑miR‑138‑ 1.11963 2.07105 5.63684 0.00028 0.00028 0.73876 1‑star hsa‑miR‑125b‑ 1.04687 ‑0.47476 5.53097 0.00032 0.00032 0.59846 2‑star hsa‑miR‑138 1.42706 5.79066 5.34313 0.00041 0.00041 0.34532 hsa‑mir‑1231 ‑1.07837 ‑0.06926 ‑4.15205 0.00229 0.00229 ‑1.38493 hsa‑mir‑762 ‑1.02037 5.22909 ‑3.71978 0.00448 0.00448 ‑2.06189 hsa‑mir‑1469 ‑1.09446 5.26306 ‑3.50287 0.00632 0.00632 ‑2.40926 hsa‑mir‑4298 1.10370 5.86823 3.49882 0.00637 0.00637 ‑2.41580 hsa‑mir‑935 ‑1.09231 1.51172 ‑3.36159 0.00794 0.00794 ‑2.63769 v11_hsa‑miR‑ 1.07276 4.82606 3.05229 0.01318 0.01318 ‑3.14171 768‑3p hsa‑mir‑2861 ‑1.05140 6.55989 ‑3.04015 0.01344 0.01344 ‑3.16155

DE, differentially expressed; miRNA, microRNA; lncRNA, long non‑coding RNA; FC, fold change. Table SII. Survival‑associated DEmRNAs in A549‑DDP cell lines.

Symbol Log‑rank P‑value Low median High median

MT1A 0.00151 2.54521 NDST3 0.00264 2.52603 EDEM1 0.00652 2.85753 HSPA2 0.01063 4.15343 2.54521 DBP 0.01093 2.86575 NCAM1 0.01160 2.85753 ADRA1D 0.01161 4.15343 2.54521 STAC3 0.01166 2.60000 ZNF417 0.01305 2.60000 ID4 0.01660 4.15343 2.60000 CEACAM6 0.01712 4.15343 2.54521 VGF 0.01765 4.15343 2.54521 RHBG 0.01935 4.15343 2.85753 KIF26A 0.01990 2.54521 FAM117A 0.02281 2.85753 DIRAS3 0.02317 2.60000 RAB9B 0.02360 2.86575 GJA1 0.02632 4.15343 2.21370 ELOVL2 0.02707 2.86575 PHOSPHO2 0.02930 2.85753 ARC 0.03251 2.54521 DPP4 0.03395 2.85753 4.15343 SIRT4 0.03502 2.86575 FKBP1B 0.03636 4.15343 2.60000 SLC17A9 0.03801 2.85753 SH2B2 0.03920 2.85753 TXN 0.04021 4.15343 2.60000 PER1 0.04283 2.85753 SARM1 0.04304 2.85753 4.15343 MED12 0.04438 2.52603 4.15343 MAGEH1 0.04509 2.60000 NR1D1 0.04612 2.86575 ARF4 0.04794 2.85753 RTN4RL2 0.05395 2.86575 HAPLN3 0.05597 2.86575 PCDH7 0.05666 4.15343 2.86575 COX4I2 0.05668 2.60000 RNF128 0.05678 2.85753 FAM173B 0.05749 4.15343 2.60000 REEP6 0.05911 2.60000 POLR3G 0.05972 2.86575 PPBP 0.06293 3.46575 2.26301 PER3 0.06806 2.86575 4.15343 MAP6D1 0.07797 4.15343 2.86575 PPP1R3C 0.08052 2.60000 4.15343 PTP4A3 0.08071 2.85753 ZNF140 0.08080 2.85753 4.15343 C12orf75 0.08170 2.60000 CD40 0.08354 2.85753 4.15343 BARHL1 0.08390 2.86575 3.46575 PDK4 0.08530 3.46575 MMP11 0.08700 4.15343 2.52603 CRISP3 0.08780 4.15343 2.85753 TMEM121 0.09036 4.15343 2.85753 GPR141 0.09183 2.85753 4.15343 CDH16 0.09193 2.85753 RHOB 0.09281 2.60000 C4orf17 0.09604 4.15343 2.52603 GPR37 0.09853 2.86575 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

CATSPERG 0.09988 3.46575 4.15343 LCP1 0.09994 2.85753 4.15343 PYCARD 0.10080 2.86575 4.15343 PRM3 0.10088 3.46575 1.57260 ARG2 0.10220 2.85753 4.15343 ABCB1 0.10329 2.85753 AZU1 0.10531 2.54521 GORASP2 0.10599 3.46575 RAB20 0.10612 2.60000 AGR3 0.10652 4.15343 3.46575 CDH4 0.10756 2.86575 GPC2 0.10841 4.15343 2.85753 POU2F2 0.10902 2.85753 4.15343 SGCZ 0.11029 4.15343 2.19178 CLEC2D 0.11094 2.60000 4.15343 SOX17 0.11150 4.15343 2.60000 GAL 0.11178 4.15343 2.85753 LTB 0.11426 2.85753 4.15343 PPP1R14C 0.11451 4.15343 2.85753 HIVEP3 0.11595 4.15343 SLC4A8 0.11721 2.85753 TNFRSF10D 0.11993 2.85753 CA8 0.12059 4.15343 2.85753 GPATCH2 0.12314 4.15343 2.85753 PLD5 0.12353 4.15343 2.52603 CCR2 0.12452 2.85753 4.15343 WNT4 0.12479 4.15343 2.86575 PMCH 0.12932 3.46575 MAGI1 0.12961 2.85753 4.15343 C10orf90 0.13004 4.15343 2.85753 ODF3 0.13057 2.86575 BCHE 0.13185 4.15343 3.46575 SMC6 0.13490 4.15343 2.86575 TGIF2 0.13748 2.85753 EIF1AY 0.13821 4.15343 2.86575 ZFY 0.13821 4.15343 2.86575 UTY 0.13821 4.15343 2.86575 TM4SF20 0.14018 4.15343 2.85753 SENP7 0.14031 2.85753 4.15343 EFNB1 0.14191 2.86575 HIST1H3H 0.14204 2.60000 4.15343 SOX7 0.14633 2.86575 FGF18 0.14825 2.85753 4.15343 GSTO2 0.14999 2.86575 4.15343 EPC2 0.15017 3.46575 TRIM54 0.15062 3.46575 4.15343 OPRK1 0.15094 4.15343 2.60000 CRIP1 0.15158 4.15343 2.60000 GOSR2 0.15229 2.85753 GAS2L2 0.15528 2.60000 DSEL 0.16030 4.15343 2.60000 DJC10 0.16033 2.85753 ALDOC 0.16620 2.85753 4.15343 PIK3CD 0.16622 2.85753 4.15343 PLXNC1 0.17104 2.85753 4.15343 IL6 0.17188 4.15343 2.85753 ZNF778 0.17434 2.86575 4.15343 PARD6G 0.17635 4.15343 3.46575 RPIA 0.17689 3.46575 4.15343 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

PTGS2 0.18056 4.15343 2.86575 NPTX1 0.18112 4.15343 2.60000 CLCN1 0.18314 2.85753 PLXND1 0.18387 2.85753 4.15343 HS3ST6 0.18429 4.15343 2.52603 ZNF836 0.18518 2.86575 NRN1L 0.18691 3.46575 NTS 0.18822 4.15343 2.86575 ZNF510 0.18874 2.86575 STXBP5L 0.18899 4.15343 2.85753 HERC5 0.18989 3.46575 2.86575 PLA2G4A 0.19021 4.15343 2.86575 KISS1 0.19058 3.46575 HOXC11 0.19107 4.15343 2.85753 SLC2A1 0.19262 4.15343 2.86575 APOH 0.19299 3.46575 GRB7 0.19502 4.15343 3.46575 NOX1 0.19568 3.46575 2.60000 CTH 0.19733 3.46575 4.15343 OR51E2 0.19882 3.46575 2.52603 FOXF2 0.20203 4.15343 2.85753 CUL2 0.20356 3.46575 PDZK1IP1 0.20768 2.85753 4.15343 TMEM47 0.20876 4.15343 2.54521 EM 0.20932 3.46575 4.15343 JUN 0.20953 2.60000 RERG 0.21172 2.85753 4.15343 PTPRCAP 0.21323 2.85753 4.15343 C5 0.21475 4.15343 3.46575 ZNF396 0.21715 4.15343 2.60000 BAIAP2 0.21888 2.85753 AVEN 0.22072 3.46575 2.86575 KLF14 0.22140 2.85753 KIF5A 0.22265 4.15343 3.46575 F2 0.22271 3.46575 CD72 0.22510 2.86575 TMEM173 0.22517 2.60000 SNCG 0.22602 4.15343 3.46575 SIGLEC9 0.22616 2.86575 GLCE 0.22648 3.46575 ARHGAP22 0.23272 4.15343 3.46575 SLITRK5 0.23460 4.15343 2.60000 NT5DC3 0.23501 2.86575 CNKSR3 0.23960 3.46575 4.15343 XKRX 0.24062 2.60000 PROCR 0.24476 2.85753 SLC4A1 0.24506 3.46575 CDCA4 0.24619 4.15343 3.46575 BCL2 0.24919 2.86575 4.15343 SCARA5 0.24920 4.15343 3.46575 GALNT14 0.25139 4.15343 2.86575 FLT3LG 0.25205 2.86575 C1orf21 0.25325 2.60000 NEGR1 0.25591 4.15343 2.54521 PRRX2 0.25622 4.15343 2.85753 MYO1D 0.26281 2.86575 CCDC138 0.26479 4.15343 2.86575 ZG16B 0.26499 2.86575 PAX7 0.26517 2.86575 4.15343 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

CD28 0.26536 2.86575 4.15343 ADHFE1 0.26593 2.85753 4.15343 DJC12 0.26918 2.86575 RPS6KL1 0.26948 2.86575 3.46575 GALNT13 0.27112 4.15343 3.46575 FAM47E 0.27160 2.86575 4.15343 ZNF622 0.27273 4.15343 2.85753 RUNDC3B 0.27351 4.15343 3.46575 MBOAT2 0.27535 2.86575 HDAC5 0.27605 2.86575 3.46575 SLC43A2 0.27939 2.86575 DLGAP3 0.28077 4.15343 2.60000 OR2F1 0.28178 3.46575 1.57260 USP42 0.28206 2.60000 3.46575 CDH19 0.28403 3.46575 TNNI3 0.28405 2.85753 CRP 0.28427 4.15343 2.60000 NUDT11 0.28502 4.15343 2.86575 NKPD1 0.28601 3.46575 UCN2 0.28911 4.15343 2.86575 PIP 0.28936 4.15343 3.46575 GPD1L 0.28968 3.46575 4.15343 ZNF264 0.28975 3.46575 LSAMP 0.29027 4.15343 IGDCC3 0.29035 4.15343 3.46575 HS3ST1 0.29040 2.85753 3.46575 PGF 0.29276 2.86575 EPHX4 0.29301 3.46575 RASGEF1B 0.29303 3.46575 ZNF879 0.29428 2.86575 JPH3 0.29593 2.86575 TMEFF2 0.29706 4.15343 2.85753 DJC15 0.29860 2.85753 4.15343 FAM162B 0.29912 3.46575 SLC6A14 0.29953 2.86575 ZP3 0.30058 4.15343 3.46575 SP5 0.30167 2.86575 KLF17 0.30432 4.15343 3.46575 HLA‑DQB2 0.30600 3.46575 4.15343 STMN3 0.30616 4.15343 2.60000 SLC25A29 0.30626 3.46575 TPPP3 0.30910 4.15343 3.46575 MAP1A 0.31059 3.46575 2.86575 ERAP1 0.31172 3.46575 GLP2R 0.31174 3.46575 GNG2 0.31252 4.15343 LRRC4B 0.31311 2.85753 RPRM 0.31489 4.15343 2.85753 TM7SF2 0.31655 3.46575 HEY1 0.31902 2.86575 4.15343 IL4I1 0.31922 3.46575 4.15343 HMGA2 0.31972 2.85753 4.15343 GAL3ST4 0.32080 2.86575 TMTC2 0.32265 3.46575 OCLN 0.32271 2.86575 4.15343 UPK1A 0.32358 4.15343 3.46575 IL22RA1 0.32385 4.15343 2.86575 CREB3L1 0.32420 2.86575 4.15343 RGS16 0.32584 3.46575 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

IMMP2L 0.32652 3.46575 ALDH1A3 0.32746 4.15343 3.46575 GALNT5 0.32780 2.86575 4.15343 FABP1 0.33115 3.46575 4.15343 FN1 0.33159 4.15343 2.86575 GLUL 0.33161 2.86575 UPK2 0.33271 4.15343 2.86575 TSRE1 0.33316 2.86575 ESPNL 0.33537 2.85753 CCDC114 0.33595 4.15343 3.46575 COBL 0.33597 3.46575 VANGL2 0.33909 4.15343 3.46575 C2CD4A 0.34482 2.85753 4.15343 MAP1B 0.35371 4.15343 3.46575 MAPKAPK3 0.35443 3.46575 LGI3 0.35703 3.46575 SIGLEC12 0.35820 4.15343 3.46575 CLEC11A 0.35903 2.86575 GPX7 0.35926 2.86575 TMEM174 0.35938 3.46575 DGAT2 0.36109 3.46575 I 0.36580 2.86575 S100P 0.36656 3.46575 PCDH1 0.36697 4.15343 3.46575 CHAD 0.36820 2.86575 3.46575 HK2 0.36826 3.46575 EHF 0.36875 2.86575 4.15343 COX6B2 0.36923 3.46575 CYP2J2 0.37186 4.15343 2.86575 PABPC4L 0.37322 3.46575 SPRY2 0.37336 3.46575 2.60000 TXNIP 0.37604 3.46575 4.15343 FITM1 0.37651 3.46575 CLEC4E 0.37694 4.15343 2.85753 PTPRG 0.37762 2.86575 4.15343 TRIM46 0.37790 3.46575 LGALS4 0.37888 3.46575 CHEK2 0.37920 2.86575 OR4A16 0.38015 3.46575 FZD8 0.38021 3.46575 YIPF2 0.38151 2.86575 4.15343 SLC4A7 0.38177 3.46575 BAHCC1 0.38222 3.46575 4.15343 PCDH10 0.38312 4.15343 2.85753 MYF6 0.38421 4.15343 3.46575 PI3 0.38436 4.15343 2.85753 NHLH2 0.38504 4.15343 3.46575 TMEM45B 0.38767 3.46575 4.15343 NKX3‑2 0.38841 4.15343 3.46575 MUC5B 0.38887 2.85753 4.15343 DYNLRB2 0.38931 3.46575 0.38984 2.86575 LGI1 0.38988 2.86575 4.15343 PHLDA1 0.39036 4.15343 3.46575 OR5K3 0.39343 3.46575 STXBP6 0.39359 3.46575 ZNF280A 0.39415 4.15343 3.46575 MSC 0.39567 3.46575 CCDC134 0.39585 2.86575 4.15343 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

LRP3 0.39603 3.46575 ABCC8 0.39845 2.86575 3.46575 FGB 0.39972 3.46575 ACACB 0.40206 4.15343 3.46575 RASSF4 0.40338 3.46575 HSPA1L 0.40693 3.46575 YBX2 0.40714 2.86575 NUP35 0.40865 3.46575 4.15343 C11orf86 0.40880 3.46575 UBE2NL 0.41085 3.46575 THNSL1 0.41098 3.46575 2.86575 ASGR1 0.41189 4.15343 3.46575 CRIP3 0.41486 2.86575 4.15343 COL4A1 0.41523 3.46575 LHFPL4 0.41746 2.86575 4.15343 FOXA3 0.41796 2.86575 3.46575 TIGD7 0.41807 3.46575 2.85753 VTN 0.41822 3.46575 NEFL 0.41974 4.15343 2.85753 KRT15 0.42204 2.86575 CEACAM5 0.42281 2.86575 HBB 0.42296 3.46575 TNFAIP6 0.42403 4.15343 3.46575 PSMB8 0.42506 3.46575 4.15343 NMB 0.42719 4.15343 2.86575 GALNT12 0.42892 3.46575 CPE 0.43403 4.15343 3.46575 MYO1F 0.43432 3.46575 RHOV 0.43457 4.15343 2.86575 SLC9A1 0.43654 4.15343 PRSS8 0.43970 4.15343 3.46575 CFB 0.44279 3.46575 4.15343 LPAR3 0.44574 2.85753 3.46575 MT1F 0.44855 3.46575 CA2 0.44956 3.46575 CCDC106 0.44975 2.86575 AGFG2 0.45104 4.15343 MMP28 0.45534 2.60000 IL17D 0.45607 2.86575 4.15343 PLLP 0.45709 2.85753 ITIH5 0.45761 2.86575 4.15343 PCDH17 0.45890 3.46575 AK7 0.46064 4.15343 3.46575 HUS1B 0.46070 3.46575 4.15343 HS3ST3B1 0.46112 4.15343 3.46575 IGFN1 0.46512 3.46575 GPR153 0.46720 4.15343 3.46575 PILRA 0.46792 2.86575 B3GALT4 0.46912 4.15343 3.46575 CCL2 0.46916 4.15343 2.86575 SLCO4A1 0.46982 4.15343 3.46575 WASL 0.47025 3.46575 VMAC 0.47129 2.86575 3.46575 TFPI 0.47426 3.46575 ZNF569 0.47468 3.46575 4.15343 GC 0.47745 4.15343 2.86575 KLF2 0.47843 3.46575 S100A12 0.47996 3.46575 LGALS3BP 0.48132 2.86575 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

BARX1 0.48181 2.86575 3.46575 C19orf25 0.48196 4.15343 3.46575 PELI1 0.48225 2.86575 EXOC3L2 0.48338 4.15343 3.46575 KCNG1 0.48408 4.15343 3.46575 LPCAT1 0.48573 4.15343 3.46575 PALMD 0.48676 4.15343 3.46575 SLC17A4 0.48689 3.46575 RFTN1 0.48948 2.86575 4.15343 IL12A 0.49011 4.15343 3.46575 ZNF671 0.49020 3.46575 GBGT1 0.49140 3.46575 MMD 0.49155 4.15343 3.46575 S100A9 0.49361 3.46575 TSPAN33 0.49417 2.85753 4.15343 C2CD4B 0.49439 4.15343 2.86575 CRABP1 0.49649 4.15343 3.46575 SHROOM3 0.49894 3.46575 LAMA1 0.49937 3.46575 4.15343 RNF186 0.50124 2.86575 3.46575 DEGS2 0.50269 3.46575 TRIM31 0.50301 3.46575 SERPINB7 0.50326 3.46575 D2HGDH 0.50416 4.15343 3.46575 FEZ1 0.50482 4.15343 3.46575 BTG2 0.50596 2.85753 IFI27 0.50598 3.46575 SLC25A35 0.50992 4.15343 3.46575 TRPM2 0.51061 3.46575 2.86575 DUSP27 0.51121 4.15343 2.85753 C5orf47 0.51161 2.86575 AP1S1 0.51443 4.15343 3.46575 HEATR5B 0.51469 4.15343 3.46575 GRTP1 0.51600 3.46575 STAT5A 0.51826 2.86575 4.15343 G0S2 0.51830 3.46575 TSPAN12 0.52168 4.15343 3.46575 APBA3 0.52346 4.15343 3.46575 FBXL7 0.52352 4.15343 3.46575 HRCT1 0.52504 2.85753 PAX4 0.52651 3.46575 CYP2E1 0.52772 3.46575 OR10G3 0.52944 3.46575 MEGF6 0.53191 2.86575 4.15343 RIT2 0.53359 4.15343 2.86575 GREM1 0.53483 4.15343 2.86575 CXCL5 0.53654 3.46575 EPHB6 0.53859 3.46575 KCNJ6 0.53881 3.46575 ATRNL1 0.54005 4.15343 2.85753 PPP1R14D 0.54180 4.15343 3.46575 LPGAT1 0.54290 3.46575 2.86575 SLC16A13 0.54291 4.15343 2.86575 CLDN7 0.54365 4.15343 3.46575 DNER 0.54468 2.86575 SEC22B 0.54549 3.46575 2.86575 NMUR2 0.54554 4.15343 3.46575 C1orf115 0.54582 2.86575 CD274 0.54745 4.15343 2.85753 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

CA9 0.54951 3.46575 HLA‑DMA 0.55045 4.15343 TSPAN7 0.55147 3.46575 FAM120C 0.55198 3.46575 4.15343 VIL1 0.55200 3.46575 COL9A3 0.55236 4.15343 3.46575 FAM83F 0.55260 4.15343 3.46575 SCN11A 0.55374 3.46575 CFH 0.55481 2.85753 4.15343 BST1 0.55686 4.15343 2.86575 CEACAM1 0.55735 4.15343 3.46575 CXCR2 0.55925 3.46575 2.86575 TNNT1 0.56024 4.15343 2.85753 FAM83A 0.56079 4.15343 3.46575 IQGAP2 0.56114 2.86575 THEM5 0.56134 3.46575 NECAB2 0.56375 4.15343 3.46575 SLC22A14 0.56393 4.15343 3.46575 ITGBL1 0.56733 2.86575 GCHFR 0.56836 2.86575 4.15343 PRSS23 0.57118 2.86575 CRIP2 0.57143 4.15343 3.46575 UBQLNL 0.57205 3.46575 4.15343 ERMP1 0.57320 4.15343 2.86575 DUSP23 0.57402 3.46575 4.15343 LRG1 0.57513 3.46575 SYT7 0.57516 4.15343 2.86575 NFE2L3 0.57523 2.86575 4.15343 CCDC83 0.57668 4.15343 2.60000 DACT2 0.58248 2.86575 4.15343 SLCO1B1 0.58335 3.46575 NUDT13 0.58339 3.46575 4.15343 SLC38A11 0.58434 3.46575 ZNF404 0.58852 3.46575 IGFBP7 0.59002 2.86575 CCDC33 0.59100 4.15343 2.86575 BCL2L15 0.59212 3.46575 ADCY1 0.59239 2.86575 4.15343 SPEG 0.59295 2.86575 3.46575 PRR15L 0.59634 3.46575 THAP9 0.59644 3.46575 FAM43B 0.59935 3.46575 PEX11A 0.59945 3.46575 LRRK2 0.59968 3.46575 PON3 0.60155 4.15343 TRIP6 0.60340 2.86575 4.15343 CA13 0.60342 3.46575 4.15343 VASN 0.60535 2.86575 MED10 0.60696 4.15343 3.46575 CHGB 0.60784 4.15343 3.46575 PKDCC 0.60799 4.15343 3.46575 SLC6A1 0.60805 3.46575 4.15343 HIST1H2BF 0.60838 4.15343 3.46575 SEMA3A 0.61079 2.86575 HABP2 0.61140 2.86575 4.15343 DAB2 0.61175 4.15343 PTGER2 0.61258 3.46575 TUBB2B 0.61320 4.15343 3.46575 CNNM1 0.61646 3.46575 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

HSD17B7 0.61857 3.46575 CFI 0.62782 3.46575 SLC36A1 0.62882 4.15343 2.86575 GRIN2D 0.63003 4.15343 2.86575 MATN3 0.63040 4.15343 3.46575 SPOCD1 0.63122 3.46575 C15orf62 0.63157 2.86575 4.15343 MUC13 0.63171 2.86575 SCFD2 0.63250 3.46575 2.86575 CDH11 0.63490 4.15343 3.46575 HSD11B2 0.63591 3.46575 4.15343 PDX1 0.63700 4.15343 3.46575 CCL8 0.63725 3.46575 FAM107B 0.64192 3.46575 GLDC 0.64544 3.46575 ZNF747 0.64963 3.46575 TRNP1 0.65005 2.86575 CREB3L4 0.65022 2.86575 TTC39A 0.65093 3.46575 FGA 0.65169 4.15343 3.46575 SLC16A7 0.65236 4.15343 SGSH 0.65322 2.86575 4.15343 TM4SF5 0.65329 4.15343 GDA 0.65444 4.15343 2.86575 FHIT 0.65528 3.46575 4.15343 ZNF215 0.65614 2.86575 4.15343 KCNK3 0.65663 3.46575 ADAM28 0.65706 3.46575 HCN4 0.65777 3.46575 APOBEC3C 0.66160 4.15343 ANKRD24 0.66225 3.46575 ACSM3 0.66383 3.46575 SHROOM2 0.66411 3.46575 ADAM30 0.66473 3.46575 GATA6 0.66493 3.46575 ANKRD22 0.66649 4.15343 LINGO2 0.66759 3.46575 PRKCG 0.66787 4.15343 3.46575 CD52 0.66836 3.46575 MYEF2 0.66869 4.15343 3.46575 WDR62 0.66940 3.46575 PSMB9 0.67387 3.46575 4.15343 CHPF 0.67597 2.86575 0.67707 4.15343 2.86575 EBI3 0.67740 3.46575 KRT19 0.67921 4.15343 3.46575 CXCL3 0.67929 4.15343 2.86575 GPRC5B 0.68130 3.46575 FOXL2 0.68139 4.15343 3.46575 RARRES3 0.68655 3.46575 LIPC 0.68664 3.46575 TLE4 0.68704 3.46575 4.15343 SLITRK4 0.68984 4.15343 SAA2 0.69254 3.46575 2.86575 ASB4 0.69307 2.85753 4.15343 BCL2A1 0.69912 3.46575 LIN7A 0.70139 4.15343 3.46575 LIPI 0.70313 4.15343 2.85753 BIK 0.70461 2.86575 3.46575 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

COL5A3 0.70597 4.15343 3.46575 NTF4 0.70794 3.46575 BMP7 0.70804 2.86575 4.15343 SLC25A6 0.70820 2.86575 4.15343 DCDC2 0.71364 2.86575 3.46575 AQP11 0.71533 4.15343 3.46575 LCN2 0.71626 3.46575 RASL11B 0.71658 3.46575 TMEM120A 0.71841 3.46575 4.15343 MESP2 0.71990 2.86575 MDFIC 0.72397 3.46575 CA11 0.72474 4.15343 3.46575 MFAP5 0.72621 4.15343 3.46575 CXCL16 0.72720 3.46575 HOXB13 0.72801 4.15343 3.46575 PLAU 0.72844 3.46575 EID3 0.72969 3.46575 SH3RF2 0.73021 3.46575 KAZALD1 0.73106 3.46575 RAB33A 0.73269 3.46575 4.15343 KRT222 0.73278 4.15343 3.46575 SCARA3 0.73590 3.46575 HMSD 0.73616 4.15343 2.85753 LGI4 0.73631 4.15343 2.86575 TUBGCP5 0.73660 3.46575 ANXA10 0.73680 3.46575 C8orf48 0.73817 3.46575 EDIL3 0.73874 3.46575 BOD1 0.73972 2.86575 4.15343 ADAMTSL4 0.74078 3.46575 FAM50B 0.74115 3.46575 4.15343 B4GALT1 0.74235 3.46575 2.86575 MFF 0.74256 4.15343 2.86575 RARRES1 0.74443 4.15343 3.46575 PTPN22 0.74592 4.15343 MICB 0.74643 2.86575 4.15343 ITGAM 0.74901 3.46575 IL33 0.75022 4.15343 PTGDS 0.75080 4.15343 PON1 0.75127 3.46575 FGG 0.75145 2.85753 3.46575 FAAH2 0.75265 3.46575 4.15343 PCYOX1L 0.75281 3.46575 F5 0.75305 3.46575 RFX6 0.75400 3.46575 TNNC1 0.75451 4.15343 2.86575 DUOXA1 0.75874 2.86575 4.15343 SH3TC1 0.76088 3.46575 LHX8 0.76210 3.46575 TBC1D2 0.76346 4.15343 3.46575 C1QL4 0.76516 4.15343 2.86575 ZNF853 0.76532 2.86575 4.15343 OR5C1 0.76618 3.46575 LYZL6 0.76777 3.46575 2.85753 CITED4 0.76867 3.46575 CCDC85A 0.76896 2.86575 3.46575 C17orf67 0.76971 4.15343 3.46575 TSPAN1 0.77099 3.46575 4.15343 SSC5D 0.77198 3.46575 2.60000 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

DIRAS1 0.77318 3.46575 FHOD1 0.77488 3.46575 SOX8 0.77490 3.46575 TUBA4A 0.77563 3.46575 ZNF606 0.77656 3.46575 CLEC2B 0.77664 3.46575 4.15343 MPZL2 0.77935 3.46575 SLC2A4 0.77935 2.86575 4.15343 SCT 0.77965 4.15343 3.46575 ZNF675 0.78101 3.46575 PPM1J 0.78163 3.46575 LPAR4 0.78192 3.46575 SULT1E1 0.78288 3.46575 LUM 0.78487 3.46575 C4BPA 0.78525 3.46575 NFIX 0.78702 2.86575 4.15343 RSBN1L 0.79095 3.46575 ZNF22 0.79245 3.46575 CLDN15 0.79274 2.86575 3.46575 CXCL1 0.79282 3.46575 CD38 0.79493 3.46575 PLIN2 0.79601 3.46575 KCNN1 0.79780 3.46575 SYT13 0.79817 3.46575 PEX1 0.79862 2.86575 3.46575 CLDN23 0.79950 3.46575 4.15343 ZNF469 0.80754 4.15343 3.46575 CSF1R 0.80908 3.46575 2.86575 QPCT 0.80977 2.86575 4.15343 RHBDL2 0.81448 3.46575 2.86575 SRCIN1 0.81453 4.15343 3.46575 GBP2 0.81495 3.46575 4.15343 TRIM38 0.81709 4.15343 2.86575 RNF152 0.81741 3.46575 TSPYL5 0.82048 4.15343 2.86575 MYO15A 0.82135 4.15343 3.46575 HES1 0.82284 4.15343 3.46575 APLP1 0.83286 4.15343 2.86575 LOXL1 0.83357 4.15343 3.46575 RSPO3 0.83386 3.46575 HIP1 0.83593 3.46575 CRTAC1 0.83986 2.86575 4.15343 SEMA3B 0.84048 4.15343 3.46575 TMPRSS5 0.84561 4.15343 3.46575 NR2E3 0.84654 3.46575 CTLA4 0.84669 2.86575 4.15343 CRLF1 0.84705 4.15343 3.46575 GKN1 0.84870 3.46575 FUT4 0.84988 4.15343 3.46575 B2 0.85004 4.15343 3.46575 WDR86 0.85549 4.15343 3.46575 TSPAN8 0.85746 2.86575 4.15343 OR51E1 0.85748 3.46575 UPK1B 0.85785 3.46575 ZNF488 0.85985 4.15343 3.46575 CYBB 0.86357 3.46575 2.86575 CTSB 0.86563 4.15343 SERPINB5 0.86622 3.46575 DAP 0.86778 3.46575 4.15343 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

ZNF784 0.86835 3.46575 TMEM168 0.86993 4.15343 3.46575 TMTC1 0.87217 3.46575 INHA 0.87352 3.46575 CALCB 0.87425 3.46575 TIMM13 0.87488 3.46575 CXXC5 0.87620 3.46575 TMEM52 0.87659 3.46575 TCTA 0.88008 3.46575 4.15343 CHST1 0.88062 4.15343 3.46575 KCNMB4 0.88116 3.46575 FAM155A 0.88168 4.15343 RAB3IL1 0.88494 3.46575 4.15343 HBQ1 0.88500 4.15343 3.46575 CHST6 0.88624 3.46575 LBP 0.88768 3.46575 2.85753 KCNJ8 0.88913 3.46575 PIWIL4 0.89011 4.15343 3.46575 TAP1 0.89044 3.46575 2.86575 SLC45A3 0.89077 3.46575 CNKSR2 0.89097 3.46575 CHDH 0.89160 2.86575 3.46575 PYROXD2 0.89253 4.15343 3.46575 PPIC 0.89315 3.46575 2.86575 GOLT1A 0.89388 3.46575 IL1RL2 0.89440 3.46575 CIB4 0.89456 4.15343 3.46575 ARHGEF16 0.89565 4.15343 2.85753 SLC23A1 0.89576 3.46575 2.86575 SERPINB11 0.89740 3.46575 NEU2 0.89888 4.15343 3.16164 EFNB3 0.89957 4.15343 3.46575 OAS2 0.90131 3.46575 DZIP3 0.90288 3.46575 4.15343 FOXQ1 0.90512 3.46575 CHPF2 0.90568 2.85753 4.15343 SH3YL1 0.91002 3.46575 IFITM1 0.91010 3.46575 4.15343 FAM84B 0.91120 2.86575 APCS 0.91163 3.46575 ASCL1 0.91212 3.46575 PAQR7 0.91225 4.15343 3.46575 KDELR3 0.91292 3.46575 JOSD2 0.91631 4.15343 3.46575 KCNT2 0.91761 4.15343 3.46575 XYLT1 0.91773 4.15343 3.46575 ADK 0.91967 3.46575 BCL11A 0.92049 2.86575 3.46575 SRPRB 0.92149 2.85753 4.15343 CSMD2 0.92228 4.15343 ST6GALC2 0.92274 4.15343 2.85753 OLFM2 0.92290 3.46575 2.86575 PF4 0.92507 3.46575 4.15343 C5orf38 0.92524 3.46575 RAB3B 0.92737 3.46575 RAB5B 0.92833 4.15343 2.85753 AQP6 0.92925 3.46575 4.15343 PAQR8 0.92961 3.46575 TBX6 0.93112 3.46575 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

MBOAT1 0.93119 4.15343 3.46575 MBD5 0.93143 3.46575 HES2 0.93192 3.46575 COL8A1 0.93217 2.86575 4.15343 EFHD2 0.93388 3.46575 2.85753 CPNE4 0.93406 2.86575 4.15343 ARMS2 0.93503 3.46575 2.85753 FBXL16 0.93626 3.46575 LMBRD2 0.93628 3.46575 2.86575 DCST2 0.93685 4.15343 3.46575 TMEM97 0.93685 3.46575 4.15343 EPCAM 0.93769 3.46575 4.15343 TIPARP 0.93775 3.46575 HELZ 0.93798 4.15343 3.46575 IGFBPL1 0.93898 3.46575 SPAG4 0.94063 3.46575 DUS4L 0.94284 4.15343 3.46575 SFRP5 0.94321 4.15343 HORMAD1 0.94467 3.46575 ZNF277 0.94591 3.46575 EFCAB10 0.94792 3.46575 4.15343 SPINK8 0.95023 3.46575 HSPB1 0.95059 2.86575 3.46575 MTNR1A 0.95108 3.46575 4.15343 P4HA3 0.95234 3.46575 THSD7A 0.95320 4.15343 3.46575 DOC2A 0.95643 3.46575 SRRM3 0.95662 4.15343 3.46575 HLA‑DMB 0.95664 3.46575 HBE1 0.95798 3.46575 4.15343 PROCA1 0.95934 4.15343 3.46575 PRAME 0.95955 4.15343 3.46575 PPM1N 0.95996 3.46575 2.85753 NRCAM 0.96030 3.46575 CYB561D2 0.96050 3.46575 4.15343 S100A8 0.96213 4.15343 3.46575 ELK3 0.96451 3.46575 ZNF25 0.96569 3.46575 FERMT3 0.96671 3.46575 C2orf70 0.96819 4.15343 3.46575 TBX20 0.97176 4.15343 3.46575 ANXA13 0.97326 3.46575 CLIP3 0.97367 4.15343 3.46575 PLEKHG2 0.97441 2.86575 3.46575 ZNF251 0.97486 3.46575 AZGP1 0.97568 2.85753 4.15343 CPNE7 0.97595 2.86575 4.15343 BAMBI 0.97915 3.46575 SLC25A41 0.97957 3.46575 4.15343 PITX1 0.97963 4.15343 3.46575 APPL2 0.98173 3.46575 B3GNT7 0.98175 3.46575 MDH1B 0.98179 3.46575 OR51B6 0.98213 3.46575 SLC11A1 0.98236 4.15343 2.86575 CCR10 0.98249 3.46575 HOXB8 0.98290 2.86575 3.46575 TWIST1 0.98395 3.46575 2.86575 ALX1 0.98614 3.46575 Table SII. Continued.

Symbol Log‑rank P‑value Low median High median

ZNF287 0.98646 4.15343 3.46575 CNRIP1 0.98985 3.46575 CNNM3 0.99147 2.86575 SDSL 0.99271 3.46575 RNF112 0.99284 4.15343 3.46575 CCL5 0.99416 4.15343 3.46575 RHOD 0.99609 3.46575 DEFB1 0.99745 3.46575 ZNF544 0.99877 3.46575 4.15343 S100A14 0.99908 3.46575 NR2F1 0.99930 4.15343 3.46575 LXN 0.99983 4.15343 3.46575

DE, differentially expressed. Table SIII. Functional enrichment of the survival‑associated DEmRNAs.

List Pop Pop Fold Category Term Count % P‑value Total Hits Total enrichment Bonferroni Benjamini FDR

GOTERM_ GO:0005615~ 7 23.33333 0.017562 GC, SFRP5, KISS1, 30 1,347 18,224 3.15684 0.68945 0.68945 16.56954 CC_DIRECT extracellular APOH, C4BPA, space DEFB1, HABP2 GOTERM_ GO:0072562~ 3 10 0.024216 GC, HSPA2, C4BPA 30 152 18,224 11.98947 0.80169 0.55468 22.17005 CC_DIRECT blood microparticle GOTERM_ GO:0043651~ 2 6.666667 0.027985 CYP2J2, ELOVL2 29 17 16,792 68.12170 0.99677 0.99677 29.97683 BP_DIRECT linoleic acid metabolic process GOTERM_ GO:0005576~ 7 23.33333 0.03827 GC, KISS1, COL4A1, 30 1,610 18,224 2.64116 0.92388 0.57619 32.89919 CC_DIRECT extracellular APOH, C4BPA, DEFB1, region HABP2

GO, Ontology; FDR, false discovery rate; DE, differentially expressed. Table SIV. Co‑expression of DElncRNAs and survival‑associated DEmRNAs.

Adjusted Cluster lncRNA ID Description P‑value P‑value Count

ASMTL‑AS1 ASMTL‑AS1 hsa05031 Amphetamine addiction 0.01868 0.03176 1 ASMTL‑AS1 ASMTL‑AS1 hsa04919 Thyroid hormone signaling pathway 0.03176 0.03176 1 CASC20 CASC20 hsa04141 processing in endoplasmic reticulum 0.02277 0.02277 1 CCEPR CCEPR hsa01040 Biosynthesis of unsaturated fatty acids 0.00744 0.03718 1 CCEPR CCEPR hsa00062 Fatty acid elongation 0.00826 0.03718 1 CCEPR CCEPR hsa01212 Fatty acid metabolism 0.01457 0.04372 1 CPEB1‑AS1 CPEB1‑AS1 hsa04978 Mineral absorption 0.00704 0.00704 1 FGF12‑AS2 FGF12‑AS2 hsa04710 Circadian rhythm 0.00428 0.00428 1 FIRRE FIRRE hsa05031 Amphetamine addiction 0.01868 0.03176 1 FIRRE FIRRE hsa04919 Thyroid hormone signaling pathway 0.03176 0.03176 1 GRM7‑AS1 GRM7‑AS1 hsa04978 Mineral absorption 0.00704 0.00704 1 HOXD‑AS2 HOXD‑AS2 hsa05020 Prion diseases 0.00964 0.02891 1 HOXD‑AS2 HOXD‑AS2 hsa04919 Thyroid hormone signaling pathway 0.03176 0.03935 1 HOXD‑AS2 HOXD‑AS2 hsa04514 Cell adhesion molecules (CAMs) 0.03935 0.03935 1 HTR5A‑AS1 HTR5A‑AS1 hsa04710 Circadian rhythm 0.00428 0.00428 1 IGF2‑AS IGF2‑AS hsa04141 Protein processing in endoplasmic reticulum 0.02277 0.02277 1 LAMA5‑AS1 LAMA5‑AS1 hsa05020 Prion diseases 0.00483 0.00966 1 LAMA5‑AS1 LAMA5‑AS1 hsa04514 Cell adhesion molecules (CAMs) 0.01987 0.01987 1 LINC00092 LINC00092 hsa04621 NOD‑like signaling pathway 0.02318 0.02318 1 LINC00440 LINC00440 hsa01040 Biosynthesis of unsaturated fatty acids 0.00744 0.01457 1 LINC00440 LINC00440 hsa00062 Fatty acid elongation 0.00826 0.01457 1 LINC00440 LINC00440 hsa04978 Mineral absorption 0.01403 0.01457 1 LINC00440 LINC00440 hsa01212 Fatty acid metabolism 0.01457 0.01457 1 LINC00488 LINC00488 hsa05162 Measles 0.01821 0.01821 1 LINC00559 LINC00559 hsa04710 Circadian rhythm 0.00428 0.00428 1 LINC00592 LINC00592 hsa04710 Circadian rhythm 0.00428 0.00428 1 LINC00602 LINC00602 hsa04978 Mineral absorption 0.00704 0.00704 1 LINC00648 LINC00648 hsa04141 Protein processing in endoplasmic reticulum 0.02277 0.02277 1 LINC00853 LINC00853 hsa05162 Measles 0.01821 0.01821 1 LINC00934 LINC00934 hsa04710 Circadian rhythm 0.00428 0.00428 1 LINC00963 LINC00963 hsa04970 Salivary secretion 0.01242 0.03030 1 LINC00963 LINC00963 hsa04270 Vascular smooth muscle contraction 0.01670 0.03030 1 LINC00963 LINC00963 hsa04261 Adrenergic signaling in cardiomyocytes 0.01987 0.03030 1 LINC00963 LINC00963 hsa04022 cGMP‑PKG signaling pathway 0.02249 0.03030 1 LINC00963 LINC00963 hsa04020 Calcium signaling pathway 0.02525 0.03030 1 LINC00963 LINC00963 hsa04080 Neuroactive ligand‑receptor interaction 0.03822 0.03822 1 LINC01118 LINC01118 hsa04919 Thyroid hormone signaling pathway 0.01601 0.01601 1 LINC01123 LINC01123 hsa05020 Prion diseases 0.00964 0.02891 1 LINC01123 LINC01123 hsa04919 Thyroid hormone signaling pathway 0.03176 0.03935 1 LINC01123 LINC01123 hsa04514 Cell adhesion molecules (CAMs) 0.03935 0.03935 1 LINC01133 LINC01133 hsa04978 Mineral absorption 0.00704 0.00704 1 LINC01251 LINC01251 hsa04978 Mineral absorption 0.00704 0.00704 1 LINC01256 LINC01256 hsa05031 Amphetamine addiction 0.01868 0.03176 1 LINC01256 LINC01256 hsa04919 Thyroid hormone signaling pathway 0.03176 0.03176 1 LINC01352 LINC01352 hsa04141 Protein processing in endoplasmic reticulum 0.02277 0.02277 1 LINC01416 LINC01416 hsa04978 Mineral absorption 0.00704 0.00704 1 LINC01431 LINC01431 hsa04540 Gap junction 0.01214 0.01214 1 LINC01589 LINC01589 hsa05020 Prion diseases 0.01442 0.04326 1 LINC01626 LINC01626 hsa04978 Mineral absorption 0.00704 0.00704 1 LOXL1‑AS1 LOXL1‑AS1 hsa01040 Biosynthesis of unsaturated fatty acids 0.00744 0.01138 1 LOXL1‑AS1 LOXL1‑AS1 hsa00062 Fatty acid elongation 0.00826 0.01138 1 LOXL1‑AS1 LOXL1‑AS1 hsa04710 Circadian rhythm 0.00854 0.01138 1 LOXL1‑AS1 LOXL1‑AS1 hsa01212 Fatty acid metabolism 0.01457 0.01457 1 NRIR NRIR hsa04710 Circadian rhythm 0.00428 0.00428 1 PCOLCE‑AS1 PCOLCE‑AS1 hsa04710 Circadian rhythm 0.00854 0.04269 1 PCOLCE‑AS1 PCOLCE‑AS1 hsa04713 Circadian entrainment 0.02632 0.04682 1 PCOLCE‑AS1 PCOLCE‑AS1 hsa04722 Neurotrophin signaling pathway 0.03257 0.04682 1 PCOLCE‑AS1 PCOLCE‑AS1 hsa04910 Insulin signaling pathway 0.03745 0.04682 1 Table SIV. Continued.

Adjusted Cluster lncRNA ID Description P‑value P‑value Count

PWAR6 PWAR6 hsa04710 Circadian rhythm 0.00428 0.01283 1 PWAR6 PWAR6 hsa04713 Circadian entrainment 0.01325 0.01987 1 PWAR6 PWAR6 hsa05168 Herpes simplex infection 0.02553 0.02553 1 RHPN1‑AS1 RHPN1‑AS1 hsa04974 Protein digestion and absorption 0.01242 0.01242 1 RUVBL1‑AS1 RUVBL1‑AS1 hsa04978 Mineral absorption 0.00704 0.00704 1 SPACA6P‑AS SPACA6P‑AS hsa04710 Circadian rhythm 0.00428 0.01283 1 SPACA6P‑AS SPACA6P‑AS hsa04713 Circadian entrainment 0.01325 0.01987 1 SPACA6P‑AS SPACA6P‑AS hsa05168 Herpes simplex infection 0.02553 0.02553 1 THAP9‑AS1 THAP9‑AS1 hsa04141 Protein processing in endoplasmic 0.02277 0.02277 1 reticulum UBXN10‑AS1 UBXN10‑AS1 hsa04978 Mineral absorption 0.00704 0.00704 1 VTRNA1‑3 VTRNA1‑3 hsa05031 Amphetamine addiction 0.00938 0.00938 1

DE, differentially expressed; lncRNA, long non‑coding RNA. Table SV. Target gene prediction for DEmiRNA. miRNA MIMATid Gene EntrezID hsa‑miR‑106b‑5p MIMAT0000680 GJA1 2697 hsa‑miR‑106b‑5p MIMAT0000680 FAM117A 81558 hsa‑miR‑106b‑5p MIMAT0000680 EDEM1 9695 hsa‑miR‑1231 MIMAT0005586 GJA1 2697 hsa‑miR‑1231 MIMAT0005586 ARF4 378 hsa‑miR‑1231 MIMAT0005586 NCAM1 4684 hsa‑miR‑1231 MIMAT0005586 SARM1 23098 hsa‑miR‑138‑5p MIMAT0000430 KIF26A 26153 hsa‑miR‑138‑5p MIMAT0000430 GJA1 2697 hsa‑miR‑138‑5p MIMAT0000430 EDEM1 9695 hsa‑miR‑138‑5p MIMAT0000430 RAB9B 51209 hsa‑miR‑146a‑5p MIMAT0000449 EDEM1 9695 hsa‑miR‑146a‑5p MIMAT0000449 NCAM1 4684 hsa‑miR‑146a‑5p MIMAT0000449 PER1 5187 hsa‑miR‑146a‑5p MIMAT0000449 CEACAM6 4680 hsa‑miR‑146a‑5p MIMAT0000449 KIF26A 26153 hsa‑miR‑152‑3p MIMAT0000438 ELOVL2 54898 hsa‑miR‑152‑3p MIMAT0000438 ARF4 378 hsa‑miR‑152‑3p MIMAT0000438 MED12 9968 hsa‑miR‑152‑3p MIMAT0000438 DPP4 1803 hsa‑miR‑152‑3p MIMAT0000438 EDEM1 9695 hsa‑miR‑152‑3p MIMAT0000438 NCAM1 4684 hsa‑miR‑152‑3p MIMAT0000438 RAB9B 51209 hsa‑miR‑152‑3p MIMAT0000438 SIRT4 23409 hsa‑miR‑194‑5p MIMAT0000460 EDEM1 9695 hsa‑miR‑194‑5p MIMAT0000460 ELOVL2 54898 hsa‑miR‑194‑5p MIMAT0000460 ARF4 378 hsa‑miR‑194‑5p MIMAT0000460 PER1 5187 hsa‑miR‑2861 MIMAT0013802 NCAM1 4684 hsa‑miR‑2861 MIMAT0013802 DPP4 1803 hsa‑miR‑2861 MIMAT0013802 SARM1 23098 hsa‑miR‑31‑5p MIMAT0000089 KIF26A 26153 hsa‑miR‑31‑5p MIMAT0000089 SARM1 23098 hsa‑miR‑31‑5p MIMAT0000089 RAB9B 51209 hsa‑miR‑31‑5p MIMAT0000089 CEACAM6 4680 hsa‑miR‑4298 MIMAT0016852 EDEM1 9695 hsa‑miR‑4298 MIMAT0016852 SARM1 23098 hsa‑miR‑4298 MIMAT0016852 PER1 5187 hsa‑miR‑762 MIMAT0010313 VGF 7425 hsa‑miR‑762 MIMAT0010313 SARM1 23098 hsa‑miR‑762 MIMAT0010313 NCAM1 4684 hsa‑miR‑762 MIMAT0010313 PER1 5187 hsa‑miR‑762 MIMAT0010313 FAM117A 81558 hsa‑miR‑762 MIMAT0010313 RHBG 57127 hsa‑miR‑762 MIMAT0010313 SLC17A9 63910 hsa‑miR‑935 MIMAT0004978 GJA1 2697 hsa‑miR‑935 MIMAT0004978 CEACAM6 4680 hsa‑miR‑935 MIMAT0004978 DPP4 1803 hsa‑miR‑935 MIMAT0004978 ELOVL2 54898 hsa‑miR‑935 MIMAT0004978 EDEM1 9695 hsa‑miR‑935 MIMAT0004978 RHBG 57127

DEmiRNA, differentially expressed microRNA. Table SVI. DEmiRNA functional enrichment analysis.

Cluster miRNA ID Description P‑value Adjusted P‑value Count hsa‑miR‑106b‑5p hsa‑miR‑106b‑5p hsa04540 Gap junction 0.02414 0.04502 1 hsa‑miR‑106b‑5p hsa‑miR‑106b‑5p hsa04141 Protein processing in 0.04502 0.04502 1 endoplasmic reticulum hsa‑miR‑1231 hsa‑miR‑1231 hsa05020 Prion diseases 0.00964 0.02891 1 hsa‑miR‑1231 hsa‑miR‑1231 hsa04540 Gap junction 0.02414 0.03621 1 hsa‑miR‑1231 hsa‑miR‑1231 hsa04514 Cell adhesion molecules (CAMs) 0.039348 0.03935 1 hsa‑miR‑146a‑5p hsa‑miR‑146a‑5p hsa04710 Circadian rhythm 0.01278 0.04326 1 hsa‑miR‑146a‑5p hsa‑miR‑146a‑5p hsa05020 Prion diseases 0.01442 0.04326 1 hsa‑miR‑194‑5p hsa‑miR‑194‑5p hsa01040 Biosynthesis of unsaturated 0.01114 0.02982 1 fatty acids hsa‑miR‑194‑5p hsa‑miR‑194‑5p hsa00062 Fatty acid elongation 0.01237 0.02982 1 hsa‑miR‑194‑5p hsa‑miR‑194‑5p hsa04710 Circadian rhythm 0.01278 0.02982 1 hsa‑miR‑194‑5p hsa‑miR‑194‑5p hsa01212 Fatty acid metabolism 0.02178 0.03812 1 hsa‑miR‑2861 hsa‑miR‑2861 hsa05020 Prion diseases 0.00964 0.02891 1 hsa‑miR‑2861 hsa‑miR‑2861 hsa04974 Protein digestion and absorption 0.02469 0.03703 1 hsa‑miR‑2861 hsa‑miR‑2861 hsa04514 Cell adhesion molecules (CAMs) 0.03935 0.03935 1 hsa‑miR‑31‑5p hsa‑miR‑31‑5p hsa05162 Measles 0.01821 0.01821 1 hsa‑miR‑4298 hsa‑miR‑4298 hsa04710 Circadian rhythm 0.00854 0.03415 1 hsa‑miR‑762 hsa‑miR‑762 hsa04710 Circadian rhythm 0.00854 0.02409 1 hsa‑miR‑762 hsa‑miR‑762 hsa05020 Prion diseases 0.00964 0.02409 1 hsa‑miR‑762 hsa‑miR‑762 hsa04713 Circadian entrainment 0.02632 0.04387 1 hsa‑miR‑762 hsa‑miR‑762 hsa04514 Cell adhesion molecules (CAMs) 0.03935 0.04919 1 hsa‑miR‑935 hsa‑miR‑935 hsa01040 Biosynthesis of unsaturated 0.01482 0.04938 1 fatty acids hsa‑miR‑935 hsa‑miR‑935 hsa00062 Fatty acid elongation 0.01646 0.04938 1

DEmiRNA, differentially expressed microRNA. Table SVII. Competing endogenous RNA regulatory network. Table SVII. Continued.

Node 1 Node 2 Type Net type Node 1 Node 2 Type Net type hsa‑miR‑106b‑5p FAM117A mi‑m ce LINC01123 hsa‑miR‑762 lnc‑m ce hsa‑miR‑106b‑5p EDEM1 mi‑m ce TNRC6C‑AS1 hsa‑miR‑762 lnc‑m ce hsa‑miR‑106b‑5p GJA1 mi‑m ce HOXC‑AS3 SARM1 lnc‑m co hsa‑miR‑1231 NCAM1 mi‑m ce PCOLCE‑AS1 SARM1 lnc‑m co hsa‑miR‑1231 SARM1 mi‑m ce LINC01006 SARM1 lnc‑m co hsa‑miR‑1231 GJA1 mi‑m ce LINC01123 NCAM1 lnc‑m co hsa‑miR‑1231 ARF4 mi‑m ce HOXD‑AS2 NCAM1 lnc‑m co hsa‑miR‑138‑5p RAB9B mi‑m ce LINC01123 MED12 lnc‑m co hsa‑miR‑138‑5p KIF26A mi‑m ce HOXD‑AS2 MED12 lnc‑m co hsa‑miR‑138‑5p GJA1 mi‑m ce FIRRE MED12 lnc‑m co hsa‑miR‑138‑5p EDEM1 mi‑m ce HOXC‑AS3 PER1 lnc‑m co hsa‑miR‑146a‑5p EDEM1 mi‑m ce PCOLCE‑AS1 PER1 lnc‑m co hsa‑miR‑146a‑5p KIF26A mi‑m ce PWAR6 PER1 lnc‑m co hsa‑miR‑146a‑5p NCAM1 mi‑m ce PCOLCE‑AS1 VGF lnc‑m co hsa‑miR‑146a‑5p PER1 mi‑m ce LINC01006 VGF lnc‑m co hsa‑miR‑146a‑5p CEACAM6 mi‑m ce LINC01123 ARF4 lnc‑m co hsa‑miR‑152‑3p DPP4 mi‑m ce FIRRE ARF4 lnc‑m co hsa‑miR‑152‑3p ARF4 mi‑m ce HOXC‑AS3 FAM117A lnc‑m co hsa‑miR‑152‑3p MED12 mi‑m ce LINC01091 FAM117A lnc‑m co hsa‑miR‑152‑3p NCAM1 mi‑m ce DGCR5 FAM117A lnc‑m co hsa‑miR‑152‑3p ELOVL2 mi‑m ce LINC01123 RHBG lnc‑m co hsa‑miR‑152‑3p EDEM1 mi‑m ce FIRRE RHBG lnc‑m co hsa‑miR‑152‑3p RAB9B mi‑m ce HOXC‑AS3 SIRT4 lnc‑m co hsa‑miR‑152‑3p SIRT4 mi‑m ce DGCR5 SIRT4 lnc‑m co hsa‑miR‑194‑5p PER1 mi‑m ce PWAR6 CEACAM6 lnc‑m co hsa‑miR‑194‑5p EDEM1 mi‑m ce HNF1A‑AS1 CEACAM6 lnc‑m co hsa‑miR‑194‑5p ELOVL2 mi‑m ce LINC01085 CEACAM6 lnc‑m co hsa‑miR‑194‑5p ARF4 mi‑m ce LINC00648 EDEM1 lnc‑m co hsa‑miR‑2861 SARM1 mi‑m ce hsa‑miR‑2861 NCAM1 mi‑m ce miRNA, microRNA; lncRNA, long non‑coding RNA; net type, hsa‑miR‑2861 DPP4 mi‑m ce regulatory network. hsa‑miR‑4298 EDEM1 mi‑m ce hsa‑miR‑4298 SARM1 mi‑m ce hsa‑miR‑4298 PER1 mi‑m ce hsa‑miR‑762 VGF mi‑m ce hsa‑miR‑762 SARM1 mi‑m ce hsa‑miR‑762 NCAM1 mi‑m ce hsa‑miR‑762 SLC17A9 mi‑m ce hsa‑miR‑762 PER1 mi‑m ce hsa‑miR‑762 FAM117A mi‑m ce hsa‑miR‑762 RHBG mi‑m ce HNF1A‑AS1 hsa‑miR‑106b‑5p lnc‑m ce FIRRE hsa‑miR‑106b‑5p lnc‑m ce LINC01085 hsa‑miR‑106b‑5p lnc‑m ce PWAR6 hsa‑miR‑106b‑5p lnc‑m ce FIRRE hsa‑miR‑1231 lnc‑m ce LINC00963 hsa‑miR‑1231 lnc‑m ce LINC01531 hsa‑miR‑1231 lnc‑m ce DGUOK‑AS1 hsa‑miR‑138‑5p lnc‑m ce LINC01091 hsa‑miR‑138‑5p lnc‑m ce PWAR6 hsa‑miR‑146a‑5p lnc‑m ce HOXD‑AS2 hsa‑miR‑152‑3p lnc‑m ce LINC01123 hsa‑miR‑152‑3p lnc‑m ce HNF1A‑AS1 hsa‑miR‑194‑5p lnc‑m ce LINC01006 hsa‑miR‑194‑5p lnc‑m ce DGCR5 hsa‑miR‑2861 lnc‑m ce PCOLCE‑AS1 hsa‑miR‑2861 lnc‑m ce HOXC‑AS3 hsa‑miR‑2861 lnc‑m ce LINC00648 hsa‑miR‑4298 lnc‑m ce