Table 4

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

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.

Kim et al.

Kim et al. BMC Systems Biology 2013 7:47   doi:10.1186/1752-0509-7-47

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