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Table 4 Examples of modules (hyperedges) in primary and metastatic prostate cancer

From: Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning

miRNAs [exp. levels: up (+), down (−)]

mRNAs [exp. levels: up (+), down (−)]

Primary prostate cancer

     

hsa-miR-330-3p(−)

hsa-miR-133b(+)

hsa-miR-222(−)

MAP1B(−)

WWC3(−)

CAV1(−)

DHX35(−)

TSHZ3(−)

hsa-miR-143(+)

hsa-miR-502-5p(−)

hsa-miR-548c-3p(+)

ZZEF1(−)

C20orf194(−)

TSPYL2(−)

MBD3(+)

GPR132(+)

hsa-miR-19a(+)

hsa-miR-133a(+)

hsa-miR-153(+)

BMPR1B(+)

WWC3(−)

PCBP4(−)

TCEAL4(−)

CUL4A(+)

hsa-miR-130a(+)

hsa-miR-375(+)

hsa-miR-19a(+)

RAP1A(−)

CYLD(−)

SNORA71D(+)

NDUFA6(−)

RGS9BP(−)

hsa-miR-221(−)

hsa-miR-106b(+)

hsa-miR-222(−)

ARSJ(−)

SSPN(−)

C3orf58(+)

PTGDS(−)

RARB(−)

hsa-miR-130a(+)

hsa-miR-133a(+)

hsa-miR-19a(+)

VNN1(−)

FGF5(+)

ELOVL7(+)

PHPT1(−)

RND3(−)

hsa-miR-133a(+)

hsa-miR-222(−)

hsa-miR-130a(+)

C10orf137(+)

FAM108C1(+)

SCRIB(+)

PRKAR1A(−)

MOXD1(−)

hsa-miR-130a(+)

hsa-miR-149*(−)

hsa-miR-26a(+)

RASEF(+)

TPM1(−)

CRB2(−)

TMEM132A(+)

LIX1L(−)

hsa-miR-133b(+)

hsa-miR-23b(+)

hsa-miR-106b(+)

PFAS(+)

UNC5C(−)

HLF(−)

PSEN1(+)

EZH2(+)

hsa-miR-145(+)

hsa-miR-200c(+)

hsa-miR-23b(+)

TTC23(−)

PARM1 (−)

TOPORS(+)

NEBL(−)

RCAN2(−)

Metastatic prostate cancer

     

hsa-miR-221(−)

hsa-miR-29b(−)

hsa-miR-143(−)

SOX4(+)

MMP2(−)

RASEF(−)

SOD2(−)

SCN9A(+)

hsa-miR-29b(−)

hsa-miR-335(−)

hsa-miR-143(−)

SOX4(+)

MPPED1(+)

ERBB3(+)

HOXC4(+)

SMTN(−)

hsa-miR-143(−)

hsa-miR-22*(−)

hsa-miR-23b(−)

CDKN1A(−)

HMGA1(+)

PELO(−)

RAB17(+)

TMEM150(+)

hsa-miR-125b(−)

hsa-miR-616(+)

hsa-miR-143(−)

TSPYL2(−)

ERBB3(+)

ACAD8(−)

PHF15(+)

TMEM16G(−)

hsa-miR-19a(−)

hsa-miR-141(+)

hsa-miR-145(−)

PCDH20(+)

DNAJC3(−)

STAT3(−)

ZNF385(+)

ACTA2(−)

hsa-miR-133b(−)

hsa-miR-145(−)

hsa-miR-218(−)

IRF2(−)

TCF4(−)

STAT5B(−)

RAB2B(−)

WFDC1(−)

hsa-miR-143(−)

hsa-miR-145(−)

hsa-miR-222(−)

ITGA5(−)

MAPK7(+)

MAP3K2(−)

RAB34(−)

S100A1(+)

hsa-miR-143(−)

hsa-miR-145(−)

hsa-miR-214(−)

FEM1A(+)

ITGA5(−)

NAGPA(+)

C1orf142(+)

ERAS(+)

hsa-miR-143(−)

hsa-miR-193b(−)

hsa-miR-145(−)

CLINT1(−)

GJA1(−)

MAPK7(+)

RARRES2(−)

IL28A(+)

hsa-miR-221(−)

hsa-miR-1(−)

hsa-miR-133b(−)

TPM1(−)

NDFIP2(−)

RAD17(−)

VPS28(+)

INPPd5E(+)

  1. miRNAs and their predicted targets are given in bold font. The underlined genes are the cancer genes archived in the Memorial Sloan-Kettering Cancer Center.