Table 3 Predicted miRNA regulators of upregulated genes (only miRNAs predicted to target three or more significantly upregulated genes are listed; for angiosarcoma, only the top 10 miRNAs are listed)

Angiosarcoma

miR-541-3p/miR-654-5p

ADAMTS7, ANO9, ARHGAP29, ATP11A, CHST15, CXorf36, FAM163A, FGD5, FLT4, GRAP, HID1, JUP, KCTD17, LIMD2, MAF, MGST2, PLXND1, PPM1F, RAMP2, ROBO4, 100A16, SCAMP5, SCGB3A1, SH2B3, SLC7A1, TSPAN15

miR-128-3p

ADAM19, APOLD1, CDH5, DLL4, DTX1, DUSP5, FAM126A, GIMAP8, MESDC1, MYCT1, NETO2, PEAK1, PLXND1, RELN, SH2D3C, SHE, SLC7A1, SOX7, TAL1

miR-1-3p

ARHGAP29, CREM, EFNB2, ETS1, FAM107B, FAM126A, GIMAP6, KANK3, MAF, MAP4K2, NETO2, NOL4L, NR1H3, PEAK1, PPP2R5A, TAL1

miR-485-5p

ADAMTS4, ARHGAP25, ARHGEF15, CARD8, CCL21, CXorf36, FAM163A, GRPEL2, IKBKE, KIAA1671, LIMD2, NID1, PEAR1, PPM1F, SLC41A1, TIE1

miR-370-3p

ADAM19, AFAP1L1, ATP11A, CCL21, CHST15, CHST7, GRB10, GYPC, KDR, MAGI1, PEAR1, PODXL, SHE, SLC7A1

miR-381-3p

ARHGAP29, B3GNT2, COL4A1, DLL4, EFNB2, ETS1, FAM107B, FAM126A, FSCN1, JUP, MAGI1, RAPGEF5, SH2B3, SLC7A1

miR-193a-3p

ARHGEF15, CDH5, EFNB2, ETS1, FLI1, IKBKE, N4BP3, NOL4L, PPM1F, PPP1R16B, RAPGEF5, TNFAIP1, UACA

miR-377-3p

ADAMTS4, APOLD1, ARHGAP29, ARRB1, COL4A1, ETS1, LIMK2, NOL4L, NOVA2, NTS, PPP1R16B, SHE, TAL1

miR-153-3p

ADAM19, CD69, CD93, CHST15, CREM, DLL4, EFNB2, GNG11, MAGI1, NOL4L, SCAMP5, SH2B3

miR-504-5p

AKAP2, CCM2L, CDH5, F2RL3, GIMAP6, LIMD2, LYVE1, MYCT1, RPP25, SLC7A1, UACA, UBTD1

Epithelioid sarcoma

miR-344d-3p

ADIPOR2, CCDC6, CPNE8, ERG, ESR1, FOXP2, IRS1, KDM7A, LPCAT4, LRRFIP2, MTMR12, MYLIP, NRIP1, PARD6G, PPAP2B, RHEB, RPS6KA3, ST6GAL2, TMEM100, TRIM9, UBE2H, WNT5B

miR-136-5p

ABI3BP, ARHGEF4, B3GALNT1, CPD, CTTNBP2, GDF6, IGSF1, KDM7A, MAMDC2, MDM1, MOSPD1, MTPN, NR4A3, PLEKHA5, RIMKLB, SLC16A9, SOCS7, SYTL4, UNC5D, ZNF516

miR-376a-3p

ABI3BP, ARHGAP26, ARMC10, COPS7A, EFCAB14, FAM131B, HELLS, MTMR12, MYOCD, PLEKHA5, PUS7, RAPGEFL1, SALL1, SATB1, TMEM100, SLC16A1

miR-196a-5p

AKNA, CDKN1B, CPD, ERG, EYA4, FAM110B, FOXP2, GDNF, MAMDC2, SCUBE2, ST6GAL2, TGFBR3, TUB, ZNF516

miR-542-5p

ARHGEF4, CA12, CMTM4, CUL4B, EPHB4, ERMP1, FBLN5, MARVELD1, PEX5, PLXNB1, SOCS2, TMEM229B, VIPR2

miR-654-3p

BTG1, CDH10, ESYT2, FAM115A, FOXL2NB, KCNIP4, MBOAT1, MYLIP, NT5E, SLC16A1, ST6GAL2, TUB

miR-452-5p

ARMC10, CDKN1B, CST2, CST5, EPS8, IMMP2L, MBOAT1, RPS6KA3, SLC18A2, ST6GAL2, ZNF516

Ewing’s sarcoma

miR-204-5p

ARX, BCL11B, CEACAM6, DKK2, IRF6, SLC17A7, ZDHHC21

miR-146a-5p

KRT80, PGLYRP2, RBM11, SYNPR

miR-938

CAMK1G, FAM84B, GPR64, PRKCB

miR-574-5p

CAMK1G, DLG2, SOX2

Fibromatosis

miR-135a-5p

ADAM12, ADRA2A, ANGPTL2, CERCAM, COL5A1, EDIL3, LRRN1, MAN1A1, MAN2A1, MXRA5, PSD3, RUNX1, THBS2, VCAN, XPNPEP2

miR-141-3p

ATRN, CCDC80, FAP, GOLM1, LGR4, LOXL1, RUNX1, VCAN

miR-149-5p

ADAM12, ATRN, FAM198A, FBLN1, NAV1, PSD3, STAC, XPNPEP2

miR-182-5p

CD55, COL5A1, FBN1, GXYLT2, HMCN1, SH3PXD2B, THBS2, WISP1

miR-130a-3p

ADAM12, ATRN, CERCAM, COL6A3, MAFB, SH3D19, TIMP2

miR-17-5p

ADAMTS5, CERCAM, GALNT10, LAMP5, MMP2, RUNX1, TIMP2

miR-33-5p

ADAM12, ADRA2A, GALNT10, PIEZO2, POSTN, STAC, VCAN

miR-92a-3p

ANGPTL2, COL5A1, FBN1, MAN2A1, SH3D19, VSNL1, ZNF469

miR-203a-3p

ADAMTS5, GALNT10, MAFB, SPARC, VSNL1

miR-183-5p

ATRN, COL12A1, PSD3, SH3D19

miR-200b-3p

LRP1, RUNX1, TIMP2, TMOD3

Schwannoma

miR-663

ABLIM3, ALAD, ATP1B2, CD37, CERS1, CMTM5, CNTNAP2, CORO2B, DDR1, EXTL1, GAS7, IL34, ITGB4, JUNB, NAT8L, NCDN, NR4A1, NRXN3, PLD4, RASGEF1C, S100B, SHISA9, SMIM5, SOX10, SPOCK2, ST6GAL1, SYNGR1, TMBIM1, TRAF1, TRIM58, TRIM9, WBSCR17, ZCCHC24

miR-582-5p

ARHGAP12, CLEC7A, EPB41L3, FGF2, GPR34, SHC4, ZNRF2

miR-483-3p

ANGPTL7, CLDN11, LY86, QKI, SPATA13, TANC1

miR-1290

GPR176, GPR34, GRIA4, KLHDC8A, SORCS1, SORL1

miR-483-5p

CHST3, FN3K, TMCC2

Synovial sarcoma

miR-330-5p

BNC2, BTBD11, CRHR1, DLX1, FGF11, HOXC10, NAV3

miR-150-5p

C5orf58, CYP4X1, HOXC9, RPRM

miR-185-5p

DLX6, FAM163B, SIX1

miR-221-3p

CYP4X1, HOXC10, ZIC1