Skip to main content

Table 1 Differentially expressed miRNA* and their target genes.

From: Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes

ID fold pval miRNA* target genes (regulation)
mir-374b* 1613 5.44E-01 HMGN2(↓),ZNF362(↑),LRRC8D(↓),NAV1(↑),ENAH(↓),SERBP1(↑),ENSA( ),CDC42BPA(↑),SOCS5(↑),ANXA4(↓),CNNM4(↑),TLK1(↓),TFRC( ),SMAD1(↑),PPARGC1A( ),RCHY1( ),HNRNPD( ),PAM(↑),PURA(↑),RNF138(↑),YIPF5( ),ANKRD6(↑),SCML4(↑),FAM160B2(↑),IKBKB(↑),PLAG1( ),C9orf3(↓),ZFAND5( ),SCD(↑),PTPRE( ),SH3PXD2A( ),SYT9(↑),RCC2(↓),OSBPL5(↑),CALCA(↑),HNRNPA1( ),SIRT4(↑),HECTD1( ),TRIM9(↑),TRMT5(↓),DUT(↑),LRRK1(↑),C15orf38(↓),ZFHX3(↑),FAM64A(↓),SMAD2(↑),SMAD7(↓),ZNF516(↓),MACROD2( ),STX16(↓),ZBTB46(↑),RUNX1(↓)
mir-374a* 1583 1.52E-02 ZBTB40(↑),PTGER3(↑),NEGR1( ),PCYOX1(↓),RANBP2( ),DUSP19( ),MGAT4A( ),TFPI(↑),TNS1(↑),ZNF662(↑),PHLDB2( ),EAF2( ),DCK(↑),BMPR1B(↑),CAMK2D(↑),MTRR( ),AFF4( ),PHACTR2(↑),TULP4(↑),RNGTT(↓),KPNB1(↑),DPY19L4(↑),CCNE2(↑),CDC42(↑),PPP1R16A(↑),DLC1(↑),MTUS1(↑),ANKRD46(↑),TRPS1(↓),SAMD12(↑),ATAD2(↓),NFIB(↑),CUGBP2( ),BCCIP(↑),SH3PXD2A( ),RAG1(↑),RNF141( ),CTSC( ),KDELC2(↑),PARP11(↓),FRYL( ),LYRM5(↓),NFE2( ),XPO4( ),EXOC5(↓),AFF1(↑),NOVA1(↑),SPTLC2( ),CTDSPL2(↓),CCPG1( ),NFAT5( ),SMPD3(↑),STAT3( ),MEX3C( ),VASP(↓),MAPRE1( ),RBL1(↑),REPS2(↓),MED13L( )
mir-126* 1253 4.40E-01 PRDM16(↑),KIF1B(↓),CHD1L(↓),PBX1(↑),ATP1B1( ),PPP1R12B(↑),SNX25(↑),RPS6KC1( ),TBCE(↑),LDLRAD2(↑),TMEM200B(↑),ZMYM6(↑),PTGER3(↑),NEGR1( ),SASS6(↓),CEPT1(↑),ARNT(↓),GATAD2B( ),KIF14(↑),NCOA1(↓),PPM1B( ),ZAK(↑),STAM2(↓),CALCRL(↑),ALS2CR4(↑),ARL4C(↑),PHLDB2( ),EIF2A(↓),MME( ),EIF4A2( ),GMPPB(↑),TMEM33( ),EREG( ),CCDC13( ),BBS12(↓),PPARGC1A( ),BTC(↑),TGFBI(↑),NDFIP1(↓),REEP5(↓),FOXF1( ),UTRN(↑),ICK(↑),SRrp35(↓),AHR(↓),TRIP6(↑),LUC7L2( ),HOXA7(↑),TFEC(↑),CHCHD3(↑),PTPRN2(↑),XKR6(↑),PSD3(↑),PLAG1( ),FABP4( ),MMP16(↑),TRPS1(↓),FAM120A(↓),ZFAND5( ),AKNA(↑),CUGBP2( ),SCD(↑),TRIM8(↓),HIPK3( ),AASDHPPT(↓),PHF21A( ),APOLD1(↑),FRYL( ),LYRM5(↓),GALNT4(↑),XPO4( ),COMMD6( ),POU4F1(↑),C14orf39(↑),TERF2(↓),HS3ST3B1(↑),MLLT6(↓),YPEL2(↓),PRKCA(↑),SEC14L1(↓),GJC1( ),HOXB2(↓),HOXB5(↑),SOCS6(↓),KIAA0355(↑),MYT1(↑),JAG1(↑),C20orf12(↑),ERG(↓),ZNF74(↓),MGAT3(↓),ST13(↓),REPS2(↓),ARMCX3( ),NLGN4X(↑),MED13L( )
mir-106a* 1176 3.36E-02 CAMTA1( ),MIER1( ),HIPK1( ),ENAH(↓),LUZP1(↓),GATAD2B( ),CDC42BPA(↑),EPC2(↓),ARL4C(↑),HEG1( ),ZFYVE28(↑),SGTB(↓),PURA(↑),SH3TC2(↑),RANBP9( ),ICK(↑),KPNB1(↑),UBE2W(↑),RBM12B(↑),COL5A1(↓),ANKS6(↑),YME1L1( ),PTPRE( ),SEPHS1(↓),PLEKHA7(↑),MBD6(↓),KRAS(↓),SLAIN1(↑),XPO4( ),GNPTG(↓),GINS3(↓),SSH2(↓),C18orf1(↑),HNRNPM(↑),NFIX(↑),ZNF473(↑),RBM39( ),C22orf13(↓),RAC2( )
mir-10a* 1134 3.43E-01 PRDM16(↑),PBX1(↑),DBT(↑),CNNM4(↑),ARPP21(↑),TAPT1( ),CYFIP2( ),VDAC1( ),DBN1(↑),C7orf58(↑),C7orf31(↑),MAGI2( ),UQCRB(↓),NFIB(↑),RAG1(↑),DENR(↓),KRAS(↓),ACOX1(↓),SMCHD1( ),STX16(↓),REPS2(↓),XK(↑),COL4A5(↑)
mir-598** 733 1.92E-01 PHF21A( )
mir-20b* 672 1.00E-01 STX12(↓),LEPR( ),MAN1A2( ),ANP32E(↓),PREPL(↑),SPTBN1(↓),TOP2B( ),TBL1XR1(↓),BBS12(↓),UBE2D2(↓),FBXL17(↑),RANBP9( ),BACH2(↑),DMTF1(↓),INPP5F(↑),AMOTL1(↑),PAFAH1B2(↓),PIP4K2C(↓),PACS2(↑),HECTD1( ),TRIM9(↑),CTDSPL2(↓),TBC1D2B( ),GINS3(↓),DNAJA2( ),ANKRD11(↓),CDC6(↑),TWSG1(↑),NUMBL(↓),RP5-1022P6.2( )
mir-195* 557.6 2.50E-02 PPP1R12B(↑),SERBP1(↑),NEGR1( ),RSBN1(↓),ARNT(↓),CDC42BPA(↑),C1orf96(↑),CENPO(↑),BCL2L11(↓),RAB1A( ),WDR33(↓),ACVR1( ),TLK1(↓),PPP2R5C(↓),ATP2C1(↑),MME( ),KCNMB2(↑),LRIG1(↑),SUCLG2( ),RAB6B(↑),DGKG(↑),HIGD1A( ↑) ,C4orf29(↑),PPP1R14B(↓),UBE2B( ),SEC24A( ),PURA(↑),FYB(↓),SEMA6A(↓),VDAC1( ),TUBB(↓),NCOA7(↑),ZNF323( ),ICK(↑),AHR(↓),SEMA3C(↑),FAM133B(↑),EPHB4(↑),TFEC(↑),PAXIP1(↑),PLAG1( ),PAG1( ),TRPS1(↓),SLC31A1(↓),LINGO2( ),AKNA(↑),HSPA5( ),C10orf119(↑),AMOTL1(↑),AASDHPPT(↓),PHF21A( ),MRE11A(↓),BTG1( ),CUL4A(↑),GNG2( ),DACT1(↑),MPP5( ),CFL2(↓),C14orf39(↑),ATP10A(↑),CCPG1( ),GJC1( ),SFRS2( ),YES1(↓),OAZ1( ),SIN3B(↑),BTG3( ),ZNF280B(↑),CSNK1E( ),ZFX( ),STAG2( ),BCOR(↓),ODZ1(↓),MED13L( )
mir-16-1* 533.7 4.53E-02 SPEN(↓),KIAA0495(↑),COL24A1(↑),PTPN22( ),CD34(↑),FAM84A(↓),SLC5A7(↑),BCL2L11(↓),ARL6IP6(↓),UBE2E3(↓),COQ10B( ),ABI2( ),RAB1A( ),SPRED2(↑),SCN2A(↑),STK39(↓),ALS2CR4(↑),TNS1(↑),ARL4C(↑),CDV3( ),KCNMB2(↑),ANKRD28(↓),CDC25A(↑),KPNA1(↓),TBL1XR1(↓),KLF3(↓),FRAS1(↑),PPARGC1A( ),EBF1(↑),MAPK14( ),ZNF323( ),BACH2(↑),CBX3(↓),NOD1(↑),RNF133( ),CCNE2(↑),PAG1( ),TP53INP1( ),UQCRB(↓),SAMD12(↑),PALM2(↑),FUBP3( ),PTEN(↓),HSPA5( ),CUGBP2( ),SUV39H2(↑),DDX21(↓),SCD(↑),RASSF4(↑),PDE3B(↓),CUL5(↓),ETS1(↑),FRYL( ),KLF5( ),FOXO1(↓),WDR76(↑),CCPG1( ),SMPD3(↑),USP6(↑),MLLT6(↓),HLF(↑),SEC14L1(↓),TOP2A(↑),C18orf1(↑),ZCCHC2(↑),SMAD2(↑),ZNF516(↓),OAZ1( ),MYT1(↑),JAG1(↑),RUNX1(↓),ZFX( ),ZFY( ),RBM3( ),STARD8(↓),ODZ1(↓),NLGN4Y(↑)
mir-503** 453 4.84E-03 DBT(↑),MCL1( ),ARHGEF2(↓),NCOA1(↓),SOCS5(↑),WDR33(↓),HIGD1A( ),DHX15( ),SLC12A2(↑),FNIP1( ),SH3TC2(↑),GPR85(↑),TACC1( ),MMP16(↑),UBR5( ),TRPS1(↓),ZFAND5( ),SUV39H2(↑),KBTBD3(↑),SLC43A1(↑),BACE1(↑),SUOX(↑),MON2( ),DYRK2(↑),FRYL( ),SENP1(↓),MLL2(↓),PCDH9(↑),CCNK( ),IQGAP1( ),AKT1S1(↓),MACROD2( ),RP5-1022P6.2( ),ZNF512B(↓),HSPA13( ), STAG2( ),NLGN4X(↑)
  1. List of ten miRNA* (see Additional file 6 Table S4 for folding information) that were detected with the largest fold changes in control and low-grad cells. We show the fold change, p-value (measuring if the number of down regulated target genes is greater than expected by chance) and target genes with regulation (bold arrows mark significant and italic non-significant regulation). We assessed the significantly down regulated genes for functional enrichment and pathways. The top five enriched biological functions included RNA Post-Transcriptional Modification (pval:1.2E-04), Cellular Growth and Proliferation (pval:1.25E-04), Cell Death (pval:5.79E-04) and Cancer (pval:5.95E-04-). The top six enriched canonical pathways included IL-22 Signaling (pval:2.63E-04), p53 Signaling (pval: 8.32E-04), IL-15 Signaling (pval:2.95E-03), B Cell Receptor Signaling (pval:4.47E-03) and FLT3 Signaling in Hematopoietic Progenitor Cells (pval:4.68E-03).