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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).