Dataset EV3. Comparison of differentially expressed and AS transcripts in Vector and 2Flag-eIF4E overexpressing cells. U2OS_AS: Alternative Splicing targets of eIF4E in U2OS U2OS_DE: Differentially expressed genes upon eIF4E overexpression in U2OS Names elements U2OS_AS U2OS_DE 13 FAN1 ATAD3B LTBR PIGF CATSPER1 ETV4 ITPR1 EDIL3 COQ6 AGRN TUBB6 SPTB ERCC2 U2OS_AS 751 DPM2 CD44 COBLL1 DLG1 MAP4 ACTR3 GPHN TUBD1 POLR2G APBB2 GCSH DFFB MEF2D LINC01547 ARRB2 COX5A CEP70 HERPUD2 SLC7A6 EIF6 SLC10A7 SOS1 IFT122 UBE2G1 POLK LRRC6 C1RL ATP9B TPX2 AGFG1 CCNI KANSL2 GPSM2 PAIP1 DDX11 ZEB1 SMARCC2 PTPN18 HLTF AP1G1 RNF170 HMG20B SMARCC1 C9orf85 GPR180 SYNE2 FHL3 RNF14 SEMA4D COX6C ZNF248 INIP PDLIM2 PIKFYVE USP20 DUSP22 ANP32E TEAD1 PCYT2 AC026412.1 SUGCT METTL8 DHRS11 ARHGAP17 PCBP1-AS1 STK25 PSMA3 LAMP1 GINS1 LYRM1 EIF4G3 NFATC4 ACTR10 ACSL3 CDK11A LIN54 NR1H3 INTS14 PALLD STAG2 CCDC66 ENOX2 LARP7 FOXK2 BIN3 DGUOK FGGY ZNF197 CSGALNACT2 PRDM2 TMCO3 CMIP CTDSPL2 TMEM267 GNAS PLP2 DDB2 SHROOM1 GFPT2 DAP3 DDX47 PHF3 BCLAF1 ITGB4 YTHDF3 CCNY NPC2 LPGAT1 CTIF FOXM1 HENMT1 TAF1B VAMP1 YWHAE RIC1 EMC1 TRIM41 LCOR PI4KA SLC15A4 PTK2 COQ9 TRAPPC9 DNM1 MARF1 THBS3 PGAP2 EXD2 MGAT5 SKP2 ZNF75A TNFRSF11B GMPPA EXO5 DENND1A SEC14L1 RACGAP1 CLPTM1 NCF2 SEC31B PCGF6 MRPL48 POLR2J4 DNMT3B PSMD11 MTMR14 PACRGL ZNF774 PPP2R5A ZIM2 COMMD7 RICTOR RAI14 MROH8 OGFOD2 DDX49 CD40 DYNC1LI2 SEPTIN4 TRIP12 ZMYND8 UQCC1 RGL1 ATG10 CASP8 RCOR3 CROCCP3 ABI2 CACNB1 FAM135A SETMAR QKI FGFR3 TCF12 MFAP5 ASNSD1 PPP2R1B WDR62 RNF144A ZNF655 ZWILCH PRKCD CCDC18 CBFA2T2 RBMS2 PICALM MARK3 SERPINA1 MED14 HP1BP3 C11orf58 BRD8 TCF4 SMC4 PSG4 ATP2C1 RGS19 DBF4 AURKA FAM86DP SF3A3 AHI1 COP1 SYTL1 PBRM1 PPP1R12A STRADA LINC01535 PLAGL1 BICRAL VAPA ARIH2 SH3PXD2A FAM169A PIK3C2A RBBP6 ARNTL2 GNAO1 PFN2 CHCHD7 ASPH TARS UIMC1 ATP7B YIPF6 CLTCL1 PAX8-AS1 TIPIN UBR5 ETFA WT1 SLC2A8 VMP1 TXNRD2 DDX42 AKIRIN1 DTNB SLC25A13 SVIL AKAP10 CADPS2 MEIS1 TPTEP1 DLST LINC00960 BLM ANK2 SH3KBP1 ITGB1 AKR7A2 CFAP44 HPS1 SAMD8 MPI XRCC3 RSPO4 SLC50A1 LDHA BICD1 AC005394.2 DENND4B TPCN2 TRIM26 GLI1 TNNT2 BARD1 PARPBP HAUS4 XRRA1 MAD1L1 NEK1 USP25 NAA60 RAD51C ZNF614 AGER ATXN3 ZNF561 PRPS1 CTNNB1 NDUFB5 OXR1 ATXN7 FIS1 ELF4 ATG4D FOXN2 TPM1 CRIM1 SLC35G1 FLNB PRKDC CEP164 ADD1 RBX1 MYO18A ODF2L SYT7 LINC00667 KIAA0232 CDK4 SUMF2 SELENOM GPR157 AMDHD2 RNF168 MELK DPY19L2 ACOT9 MTMR10 PPIA CSNK1D TOM1 PHF12 CENPN MAP2K4 UBE2K TPD52L1 TXNL4A SLC4A7 SEMA3B FKBP1B PPP6R2 TRERF1 KIF9 MFAP3L LIPT1 AP2S1 SENP3 ZNF530 OSBPL6 ZNF18 PFDN5 BCL11B PHYH CCNT2 UNKL BCL2L13 PIGK NUP50 SNX14 WASF3 LONP2 TTC27 TRAPPC10 TXLNA RAB31 NIPA2 UBAP1 GTF3C2 MR1 SLC25A39 VPS35L CCDC62 SPIN1 PIGT EMC7 DROSHA CHD1L NAA40 TRIP10 SLC9B2 TMEM134 ZNF611 CCND3 SPATA7 NCOA6 PPP4R1 ANXA5 ANAPC10 TK2 STYXL1 ZMAT3 TRIM16 KARS LIX1L MED23 SNX7 SEC31A FAM131A HSD11B1L CHMP4C KANSL1L PROCA1 MMP24 EIF4G1 HMBS GADD45B ZBTB14 ARHGAP8 TNRC6B ZNF608 FAAP20 NAP1L1 GLCCI1 DEPDC1 ADGRG1 KIAA1109 CCDC74A PODNL1 CLOCK DALRD3 IFT74 VPS29 PSMA4 PNISR PLPP4 CD34 INPP5F IQGAP3 NEK11 GAPVD1 DPH5 CDC27 ADARB1 LINC01128 CLSTN1 EPB41 ATP11B NUCKS1 MED4 TMEM255B TNC PPARA KRIT1 PUM2 AKR1E2 NFASC CACNB4 ENTPD6 HDX ELP5 ST7L MAPKAPK5 GMPPB CTNNBIP1 KLF7 METTL9 HMGN2 MFGE8 DMKN IFI6 FRMD8 MSH5 RPS20 GOLGB1 MYRF HNRNPA2B1 WDFY3 RPL21 PHF6 XPNPEP1 JKAMP DDX31 IQCA1 SEM1 MDM2 SPOP LRRC23 RREB1 IKBKB BOK UBE2C POLL ANXA8L1 EEF1D EIF4A1 CHD2 HTT TRAPPC8 LEPROTL1 SEMA6C PRC1 NIN ATP6V1H HPCAL1 STAG1 OSBPL7 IQGAP1 LAT DBI LATS1 ZBTB21 ZDHHC20 FADS3 PFDN1 RPL34 MARK2 RPS12 MED1 PABPC4 HNRNPM D2HGDH AP3M1 HM13 TBL1XR1 SP140 OS9 ZNF346 KHDRBS3 ADGRL3 MICAL2 CAPRIN2 SF3B1 TRA2A GNPDA2 ABCC5 FANCI SNAPC5 PRDM10 AFDN PAQR5 SYTL2 RETREG3 RAD54L SNRPN CDC45 PLEC NRDC IL6ST XPNPEP3 LRRCC1 ANK1 PAFAH1B2 LMBR1L WASHC2A IKZF4 GLYR1 SPATA20 GUF1 FER CDK7 PC GSDMB STEAP2 SLC25A33 MON2 TMEM234 WDHD1 SLC30A6 TRRAP ACAD10 ZDHHC13 SCAMP1 PTS BANP CEP192 CCDC169 EGLN2 MRPS36 RAB34 ROBO3 STAU1 DDX21 AP3S1 FAM76A HDAC11 FKBP15 DHX29 MTO1 ADSL NFATC2 SLC15A3 REPS1 SLC29A1 MTA1 UNC50 TENT2 ATP5F1C INTS2 MLLT10 RRM1 NDUFAF5 CROCCP2 TMEM218 TMEM14B SOX6 RAD17 H2AFV ZSCAN31 PHTF1 CDC16 KCNC4 UBA2 PEG3 SBDS MPDZ ZC3H11A ZNF532 ZNF185 AZIN1 RNPS1 EIF2AK1 LIN37 THAP9-AS1 ATAT1 IL4R PRMT9 CUL9 SEC11A DDHD1 PPP6R3 NAV3 NUDT13 BICD2 PPP6C SLC29A2 PLEKHH3 MFSD14C PRPSAP2 EXOG PLGRKT MED15P9 NT5C2 NAF1 EME1 PHF13 FNTA GUCD1 CIT RAD51 ZNF615 PPIP5K2 RGP1 NIT2 AGAP3 CNOT8 RNF10 PATJ FAM219B NOLC1 NRBP2 P2RX4 ATP10D SNHG12 UGP2 ZMIZ2 NPTN ABCA7 NUTM2A-AS1 COL6A3 SNHG6 RABGAP1L SYT14 TCF20 TTC14 MAPK8IP3 SRM PPM1G HEMK1 BOC TXNRD3 HDAC10 RALGAPA1 ELMOD3 RPARP-AS1 SNRPB RUFY3 ABCC1 SUN3 IL1B EEF1AKMT2 RBM27 AFTPH SAE1 METTL27 LARP4 DSN1 RPS25 GIPC1 ELL2 RPN2 ITGA7 CBX5 TSPAN4 ZNF592 IDE CNIH3 SCMH1 MAP4K4 TMEM185A ZNF266 ALKBH6 TBCD KHDRBS1 AKR1A1 SRSF5 MORF4L1 CLNS1A PVT1 SEPTIN10 CHN1 TMLHE FAM120B BNC2 PARD3 CCDC7 QTRT2 NF2 PGS1 TECPR1 PPARGC1B DGCR2 GLP2R SETD4 MYO18B ATXN2L EPB41L5 OGDHL ANKS3 BAX PTPN13 FDPS AKT3 NCOA4 GOLT1B MROH1 ITGB5 SIN3B ARHGAP11B RPL23AP82 EMSY SATB1 SCN5A PPM1D SMAD5 FAM49B YPEL2 PCNT LETMD1 APC2 STT3B USP3 SPART FNBP1 NSUN4 RDM1 CYP2R1 DCAF17 PUM1 CERS4 TNNT1 CCDC88A LINC00847 ZNF519 SLC2A11 HELQ TRAPPC6B EIF2D CDC25A CTSC U2OS_DE 389 CREB3L1 MMP2 TFIP11 KIF26B CTC-564N23.2 PMPCA AEN CXCL14 GDF15 STARD4-AS1 AC239868.1 ZBED3 CTC-459F4.1 ABALON RP11-135A24.4 LRRN1 RP11-57H14.2 AC015971.2 RP11-350N15.6 ITGA3 CTD-2384B11.2 PTPRG-AS1 TGM2 EFNB1 RP11-223P11.3 RP11-50E11.2 AC093690.1 EPHA2 C15orf52 ST3GAL1 DYSF HLA-DQB1-AS1 SCUBE3 RP11-701H16.4 SSU72 RP11-1069G10.2 MSH6 RP4-735C1.4 C3 WDFY3-AS1 SLCO4A1-AS1 RP11-732A19.5 CCDC137 NFKB2 TMEM120B SYNC CH507-513H4.6 RPL13AP20 CTC-428H11.2 MAFK NUP153 ID1 PPP6R1 FANCL BCAM CPSF3L NOP2 CTD-2269F5.1 LRRC8A RP11-244F12.3 LTBP1 ZMAT5 FANCD2OS SDC2 ZNF395 PTPRB NCAM1 LINC00987 CADM3-AS1 NQO2 LINC00565 PKIB STBD1 MEIS1-AS2 TBC1D9B RP5-1021I20.1 C11orf68 KRT15 RP4-678D15.1 LINC01465 LOXL1 RP11-290O12.2 PAGE2B SPINK5 FAM83H ARHGEF16 ARNTL2-AS1 TRAF2 IMPDH1P4 RP11-2E11.9 SEMA3F-AS1 ST7-AS1 LAMB3 MAP3K7CL PDAP1 RP11-295I5.4 RPUSD1 PIEZO2 CDK6 SYTL4 LARGE RP11-15L13.4 ZXDA PPHLN1 RP11-166N17.1 WWC1 NEDD4L AF230666.2 UNC13D RP11-728F11.4 LA16c-366D1.3 SDC4 COL5A2 RP11-1151B14.4 RBBP4 RP3-323A16.1 RP11-488C13.6 KRT8 RP4-665N4.8 AURKAIP1 MRPL20 CMC1 AC025165.8 RP11-19P22.8 ATG7 CCDC86 RAB15 AC007308.7 FAM212B TRPA1 RP13-895J2.3 SVIL-AS1 GLIPR2 PTCHD3P1 RNF150 FAM129B RP11-500G22.5 RP11-363J20.2 RP11-269F20.1 NOC2L MTIF3 RP4-758J18.2 RP11-681H18.2 TTC28-AS1 PIGCP1 SEMA3B-AS1 DVL1 CEBPZ RP3-416H24.1 SLC5A9 SFN COMTD1 SEMA6A-AS1 DQX1 AC010136.2 CEP68 MYC CTD-2002J20.1 PRICKLE2-AS3 RRM1-AS1 PYROXD1 ZNF503-AS1 ABT1 LASP1 AL022476.2 KLHDC2 ATAD3A FUT8 COL13A1 RP11-521C20.3 AP000619.5 LINC00662 AGAP2-AS1 SLC2A1 AC007906.1 TRIM47 ISG15 ZP3 DAAM2 MOCS1 NNT-AS1 MT-TE RP11-53B2.3 RP5-1172A22.1 TRIP6 STK24 RP11-27M24.1 DHFRL1 RP3-430N8.10 PRICKLE2-AS1 RP11-47I22.2 C9orf142 BRD9 MSC-AS1 AC006116.27 FAM207A GGACT AC000068.9 RP4-724E13.2 HOTAIR PTPN1 RP11-575L7.8 PPP1R12B AC007098.1 PRKCZ AC068134.8 RP11-477D19.2 RP11-498B4.5 PLXNA2 MN1 CTD-2196E14.7 SGK223 PCNXL4 CTA-221G9.12 AC009480.3 RP11-244F12.2 RP11-712B9.2 SEPP1 KIAA0196-AS1 GADD45A RP11-481J2.4 PERM1 RP11-484D2.2 SDF4 UTS2 AC007620.3 DENND6A-AS1 RP11-423P10.2 RP11-287D1.3 BBOF1 AFAP1 TTC28 MCM7 TBPL1 CTD-2047H16.5 HIST1H4D SAMD11 SDC1 PALM3 FOS HCG4 RP11-218E20.5 RP11-278A23.4 RP11-3L21.2 NEMF CTC-241F20.4 SKI RP11-488C13.5 RP11-9N12.2 AC007563.5 CTPS1 IAH1 CDR1 THBS1 BCL2L1 LOXL1-AS1 CTB-175E5.7 NFE2L1 CTA-125H2.2 RP11-517I3.1 CTD-2154I11.2 EXTL3 KRT18 RP11-586K2.1 RP11-270M14.5 AC002116.7 TNFRSF14 RP11-145A3.1 TRIM28 RP11-471B22.2 B3GALT6 COL16A1 TNIP1 INHBE FSIP2 MLF2 RBPMS-AS1 ITFG1-AS1 SURF6 MTCL1 CTB-43P18.1 RSPH10B RP11-328C8.4 RPL12P14 SERPINE1 RP11-61I13.3 AC006116.24 GLB1L3 ARG2 RP13-895J2.6 RP3-395M20.8 RP11-589M4.1 EPS8L2 C14orf119 CPTP CTBP2 TLDC2 ANKRD18EP RP11-632L2.2 RP11-256L6.2 RP11-856M7.2 PTGFRN CTA-373H7.7 IL32 PLPP1 SFTA1P PKM MARCH4 RP11-211G3.2 RP13-270P17.2 APOBEC3B-AS1 CFLAR TOR4A MAF RBM5-AS1 ASPHD2 PTGR2 SH3BP5-AS1 RP3-430N8.11 KLHL17 FDXR RP11-300E4.2 YBX3 CCDC121 RP11-344N10.2 CGN CAPN15 GNB1 RFFL BTD SIAE ZNF503-AS2 CBR3-AS1 ST13P12 WRNIP1 RP11-34A14.3 RP11-334E6.3 LMNA CTD-2319I12.2 RP11-388M20.2 PRICKLE1 AC104134.2 CCDC152 ZXDB RP11-264B14.2 NCAM1-AS1 RP11-651K21.1 HMGA1 NBAT1 RBP1 CCDC73 AP006621.9 RP4-613B23.1 KCNN4 COL27A1 MAP2K3 IL10RB-AS1 FLII AC005330.2 AC007899.3 HSPG2 RP11-538I12.2 NOTCH1 PCSK7 GALNT16 CYP24A1 MYBBP1A RP11-632F7.3 FOSL1 RP11-73M7.6 ZNF503 ATP8B1 C10orf142 CTA-407F11.9 MISP AC004510.3 SDHA SPHK2 ABLIM1 DACT1 CTA-363E6.7 MAGEB17 PVR AC107081.5 HECW1 CASK-AS1 PPP3CB-AS1 PIK3IP1 BAIAP2L1