Supplementary Table 3. Ingenuity Pathway Analysis of all predicted mRNA targets of microRNAs with significant differences in expression in all pairwise comparisons of the experimental groups. The top three canonical pathways are listed. VHL: von Hippel-Lindau disease, MEN2: multiple endocrine neoplasia type 2, SB: sporadic benign, NF1: neurofibromatosis type 1.

Group comparison / Top Canonical Pathways / P-value / Predicted targets involved in pathway
VHL vs SB
VHL vs SB
(continued) / 1. Wnt/β-catenin Signaling / 8.89E-08 / ACVR1B, ACVR2A, ACVR2B, AKT1, AKT2, AKT3, APC2, AXIN2, BTRC, CCND1, CD44, CDH3, CDH5, CREBBP, CSNK1D, CSNK1E, CSNK1G1, CSNK1G2, CSNK2A1, CSNK2A2, DVL1, DVL2, DVL3, FZD1, FZD4, FZD5, FZD7, FZD8, FZD10, GNAO1, GSK3A, ILK, KREMEN1, LRP1, LRP6, MAP3K7IP1, MAP4K1, MARK2, MDM2, MMP7, PPARD, PPM1L, PPP2R1A, PPP2R1B, PPP2R2C, PPP2R3CA, PPP2R5B, RAC2, RAC3, RARA, RARG, SFRP2, SFRP5, SOX3, SOX6, SOX7, SOX8, SOX10, SOX11, SOX12, SOX13, SOX17, SOX18, SRC, TCF3, TCF4, TGFB1, TGFBR2, TLE1, TLE3, TLE4, WNT1, WNT4, WNT6, WNT11, WNT10A, WNT10B, WNT2B, WNT3A, WNT5B, WNT7B, WNT8B, WNT9B
2. Axonal Guidance Signaling / 6.49E-06 / ABL1, ABLIM2, ABLIM3, ADAM11, ADAM12, ADAM19, AKT, AKT2, AKT3, ARHGEF11, ARPC4, BDNF, BMP1, BMP2, BMP3, BMP6, BMP7, BMP8A, CDC42, CXCL12, DOCK1, DPYSL2, DPYSL5, EFNA1, EFNA3, EFNA5, EFNB1, EFNB2, EFNB3, EPHA8, EPHA10, EPHB1, EPHB2, FES, FZD1, FZD4, FZD5, FZD7, FZD8, FZD10, GIT1, GLI3, GLIS1, GLIS2, GNA12, GNA14, GNAI2, GNAO1, GNB3, GNB4, GNB5, GNG3, GNG4, GNG7, GNG13, GRB2, HKR1, IGF1, ITGA2, ITGA3, ITGA4, ITSN1, KIF7, KLK1, KLK2, L1CAM, LIMK1, LINGO1, MAP2K2, MAPK1, MAPK3, MRAS, MYL3, NCK2, NFAT5, NFATC1, NFATC3, NFATC4, NGEF, NRP1, NRP2, NTN1, NTN3, NTRK3, PAK2, PAK4, PAK6, PDGFA, PDGFB, PDGFD, PGF, PIK3C2B, PIK3C2G, PIK3CD, PIK3R1, PIK3R2, PLCB3, PLXNA2, PLXNA3, PLXNB1, PLXNB3, PLXND1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCE, PRKCG, PRKCQ, PRKCZ, PTCH2, PXN, RAC2, RAC3, RASSF5, RGS3, RHOD, ROBO3, SDCBP, SEMA3A, SEMA3B, SEMA3E, SEMA3F, SEMA4B, SEMA4D, SEMA4G, SEMA5A, SEMA6A, SEMA6D, SEMA7A, SHANK2, SRGAP1, SRGAP2, SUFU, UNC5A, UNC5B, VEGFA, WAS, WIPF1, WNT1, WNT4, WNT6, WNT11, WNT10A, WNT10B, WNT2B, WNT3A, WNT5B, WNT7B, WNT8B, WNT9B
3. Molecular Mechanism of Cancer
3. Molecular Mechanism of Cancer
(continued) / 8.26E-06
8.26E-06 / ABL1, ADCY1, ADCY9, AKT1, AKT2, AKT3, ARHGEF1, ARHGEF11, ARHGEF16, ARHGEF17, BAD, BAK1, BAX, BBC3, BCL2, BCL2L1, BCL2L11, BMP1, BMP2, BMP3, BMP6, BMP7, BMP8A, BMPR1A, BRCA1, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CASP6, CASP8, CASP9, CASP10, CBL, CCND1, CCND2, CCND3, CCNE2, CDC42, CDC25B, CDK2, CDK4, CDK6, CDKN1A, CDKN2B, CREBBP, CTNND1, CYCS, DAXX, DIABLO, DVL1, E2F3, E2F4, E2F6, ELK1, FNBP1, FOS, FZD1, FZD4, FZD5, FZD7, FZD8, FZD10, GAB2, GNA12, GNA14, GNAI2, GNAO1, GRB2, GSK3A, HIPK2, IRS1, JAK1, JAK3, JUN, LRP1, LRP6, MAP2K2, MAP2K3, MAP2K4, MAP3K7IP1, MAPK1, MAPK3, MAPK10, MAPK11, MAPK12, MAPK13, PK14, MAX, MDM2, MRAS, NAIP, NF1, NFKBIE, PA2G4, PAK2, PAK4, PAK6, PIK3C2B, PIK3C2G, PIK3CD, PIK3R1, PIK3R2, PLCB3, PRKACA, PRKACB, PRKACG, PRKCA, PRKCE, PRKCG, PRKCQ, PRKCZ, PRKDC, PTCH2, RAC2, RAC3, RALGDS, RAP2B, RAPGEF1, RASGRF1, RASGRP1, RHOD, RHOF, RHOG, RHOH, RHOT2, RHOU, RND2, SMAD2, SMAD3, SRC, SUFU, SUV39H1, SYNGAP1, TCF3, TCF4, TGFB1, TGFBR2, TYK2, WNT1
MEN2 vs VHL
MEN2 vs SB
MEN2 vs recurring
MEN2 vs NF1 / 1. Breast Cancer Regulation By Stathmin1 / 1.28E-03 / ARHGEF1, ARHGEF7, ARHGEF10, ARHGEF18, CAMK4,CAMK2A, CAMK2G, CDC42, E2F1, E2F2, GNAI2, GNAI3, GNB2, GNB4, GNG2, GNG12, GRB2, MAPK1,MRAS, PIK3CG, PLCB2, PPP1R11, PPP1R12A, PPP1R3D, PPP2CA, PPP2R1A, PPP2R2A, PRKCA, RAC1, ROCK2, RRAS2, SOS1, STMN1, TUBA1A, TUBA3C, TUBA3E, TUBB1
2. Molecular Mechanism of Cancer / 1.16E-02 / APAF1, APH1A, ARHGEF1, ARHGEF7, ARHGEF10, ARHGEF18, BCL2, BCL2L11, BMP3, BMPR2, CAMK2A, CAMK2G, CASP3, CCND1, CDC42, CDK6, CDKN2B, CFLAR, CTNNA2, CTNNB1, E2F1, E2F2, FADD, FOXO1, FZD5, FZD10, GAB2, GNA14, GNAI2, GNAI3, GRB2 LRP5, LRP6, MAPK1, MRAS, NBN, NF1, NLK, PAK7, PIAS2, PIK3CG, PLCB2, PRKCA, PTCH1, PTPN11, RABIF, RAC1, RASGRP1, RRAS2, SMAD2, SMAD4, SOS1, TCF4, TGFBR1, WNT5A
3. Myc-Mediated Apoptosis Signaling / 1.35E-02 / CASP3, BCL2, IGF1R, YWHAH, YWHAE, SOS1, RRAS2, RAC1, PIK3CG, MRAS, IGF1, GRB2, APAF1, FADD
Recurring vs SB / 1. Colorectal Cancer Metastasis Signaling / 2.64E-05 / ADCY1, ADCY7, ADCY9, ADRBK1, ADRBK2, AKT2, ARRB1, BIRC5, CDH1, FZD1, FZD5, GNB4, GNG7, GNG12, IL6R, JAK3, KRAS, MAPK1, MAPK12, MMP14, MMP15, MMP24, MMP25, MRAS, PIK3R5, PRKACA, PRKACG, PRKAR1B, PRKAR2A, RAC2, RHOA, RHOF, RHOG, RHOT2, RND2, RRAS, SRC, TLR4, TLR7, TNFRSF1A, TP53, WNT4, WNT3A, WNT5A, WNT7B, WNT8B, WNT9A
2. Notch Signaling / 3.12E-05 / APH1A, DLL4, DTX2, DTX4, HES1, HES5, HES7, LFNG, MAML1, MAML3, MFNG, NUMBL, RFNG, FURIN
3. G-Protein Coupled Receptor Signaling / 5.14E-05 / ADCY1, ADCY7, ADCY9, ADRA2C, ADRBK1, AKT2, CREB3, DRD2, DUSP1, DUSP6, DUSP9, EDNRA, GNAO1, GRM2, GRM4, GRM6, IKBKG, KRAS, MAPK1, MRAS, P2RY2, PDE11A, PDE1B, PDE4C, PDE7B, PDPK1, PIK3R5, PLCB2, PRKACA, PRKACG, PRKAR1B, PRKAR2A, PRKCE, PTK2B, RAC2, RASGRP1, RGS12, RGS16, RPS6KA1, RRAS, SRC, SYNGAP1
Recurring vs VHL
Recurring vs VHL
(continued) / 1. Basal Cell Carcinoma Signaling / 1.76E-05 / APC2, BMP1, BMP2, BMP6, BMP8A, DVL1, DVL3, FZD5, FZD10, GLI3, GLIS1, GLIS2, HKR1, KIF7, PTCH2, SUFU, WNT1, WNT4, WNT6, WNT11, WNT3A
2. Natural Killer Cell Signaling / 1.16E-04 / AKT2, AKT3, GRB2, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DL5B, KIR2DS2, KIR2DS4, KIR2DS5, KIR3DL1, KIR3DL2, KIR3DL3, LAT, LCK, MAP2K2, MRAS, PAK2, PAK4, PAK6, PIK3C2G, RAC3, SH2D1B, SH3BP2, TYROBP
3. Human Embryonic Stem Cell Pluripotency / 1.14E-03 / AKT2, AKT3, BDNF, BMP1, BMP2, BMP6, BMP8A, BMPR1A, DVL1, FGFR1, FZD5, FZD10, GSK3A, KLK2, MRAS, NODAL, NTRK3, PIK3C2G, RAC3, SMAD2, SMAD3, TGFB1, TGFBR2, WNT1, WNT4, WNT6, WNT11, WNT3A
NF1 vs VHL / 1. Apoptosis Signaling / 4.52E-05 / BAD, CASP6, CASP8, CASP9, CASP10, CDK1, CYCS, DFFA, DIABLO, MAP2K2, MAP4K4, MAPK1, NAIP, NFKBIE, PLCG1, PRKCQ, SPTAN1
2. HGF Signaling / 2.88E-04 / AKT1, CCND1, CDC42, CDKN1A, DOCK1, FOS, GRB2, IL6, MAP2K2, MAP3K4, MAPK1, MAPK10, PIK3R1, PIK3R2, PLCG1, PRKCQ, PRKCZ
3. PTEN Signaling / 3.19E-04 / AKT1, BAD, CASP9, CCND1, CDC42, CDKN1A, GRB2, ILK, ITGA4, MAGI2, MAP2K2, MAPK1, PDPK1, PIK3R1, PIK3R2, PRKCZ