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Table 3 Transcription factors (TFs) and microRNAs (miRNAs) identified by the analyses of PrCa-associated modules (M1-M5)

From: Key regulators in prostate cancer identified by co-expression module analysis

  No. Module genes TF symbol p a Module genes miRNA symbol p
Module M1 1 CEBPB CXCR4 CTGF PPP1R15A SELE CCL4 EREG SERPINE1 FOS THBD TATA 1.23 × 10−5 BTG2 GAP43 ADM SMAD7 hsa-miR-25 2.70 × 10−3
2 GADD45A CTGF HIF1A GADD45B CCL4 GAP43 SGK1 ERRFI1 FOS IL5 ADM NFAT[79] 2.20 × 10−5 CEBPB GAP43 hsa-miR-191 4.00 × 10−3
3 CEBPB NLRP3 GAP43 EREG HMGB2 ERRFI1 IL5 DUSP1 UNKNOWN 5.19 × 10−5 HMGB2 FOS ADM SMAD7 hsa-miR-181a 6.10 × 10−3
4 ATM HIF1A FOS CCL20 EREG TCF1P 7.40 × 10−5 SGK1 BCL3 CTGF EREG hsa-miR-19a[82] 6.10 × 10−3
5 BCL3 CTGF CCL20 GADD45B ERN1 CREL 7.40 × 10−5 ERRFI1 GADD45A GAP43 hsa-miR-148a 1.19 × 10−2
Module M2 1 DOPEY1 CARTPT RIMS1 CDH1 TLK1 STEAP2 ANP32A TOMM22 CADM1 ADRB2 COG3 XPO7 COPG2 KDELR2 PDIA4 UNKNOWN 6.27 × 10−5 BET1 AP1G1 ARCN1 SEC62 hsa-miR-409-3p 3.50 × 10−2
2 TMEM48 SEC62 CADM1 SYNRG AP3M1 DOPEY1 COPZ1 RIMS1 ARFIP1 ANP32A ARFGAP3 GSK3B COG3 TIMM17B LMAN1 AP1G1 SNAPIN SP1[80] 4.00 × 10−4 RAB14 AP1G1 ATP2C1 hsa-miR-302b 3.80 × 10−3
3 SEC23IP ARFIP1 ATP2C1 TLK1 TOMM22 AP3B1 COG3 UHMK1 SYNRG MTX2 ELK1 1.50 × 10−3 RAB14 ARCN1 AP3M1 RERE hsa-miR-211 4.70 × 10−3
4 COPZ1 CARTPT ATP2C1 STEAP2 ANP32A CADM1 UHMK1 AP1G1 SYNRG ARCN1 MTX2 RERE NFAT 2.60 × 10−3 STRADB CADM1 ADRB2 SYNRG ARCN1 TLK1 hsa-miR-15a[83] 4.70 × 10−3
5 DOPEY1 CARTPT ERGIC1 AP1M2 CDH1 MIPEP SEC22A ANP32A CADM1 ADRB2 SHROOM2 AP3M1 RPAIN E12 5.90 × 10−3 BET1 AP1G1 ARCN1 SEC62 hsa-miR-1 1.14 × 10−2
Module M3 1 SMAD3 KPNA4 KPNA3 LMAN2L REEP1 FLNA PEX14 OPTN TRPS1 SP1 1.20 × 10−3 SMAD3 MXI1 LRP1B KPNA4 TRPS1 hsa-miR-524 1.00 × 10−4
2 RTP4 KPNA3 OPTN STAT1 4.80 × 10−3 SMAD3 NLGN1 LRP1B KPNA4 LMAN2L hsa-miR-15a 3.00 × 10−4
3 MXI1 KPNA3 TRPS1 CEBPA 4.80 × 10−3 NLGN1 KPNA4 REEP1 TRPS1 hsa-miR-493 3.00 × 10−4
4 SMAD3 BIN3 LMAN2L PITX2 4.80 × 10−3 MXI1 KPNA3 REEP1 hsa-miR-24 2.40 × 10−3
5 GLI3 MXI1 TRPS1 CDC5L 4.80 × 10−3 SMAD3 KPNA3 hsa-miR-302b 3.70 × 10−3
Module M4 1 CALR EIF5A UNC13B IGF1R TBX3 SOCS2 GLO1 BCL2L1 VEGFA PSEN1 SP1 3.00 × 10−4 BCL2L1 VEGFA DHCR24 hsa-miR-377 3.00 × 10−3
2 EIF5A BCL2L1 PPP1R13B SOCS2 UNKNOWN 6.00 × 10−4 PPP2CA SOCS2 hsa-miR-139 9.00 × 10−3
3 BCL2L1 VEGFA NME5 BIK RFX1 6.00 × 10−4 PPP2CA VEGFA CBX4 hsa-miR-200b[84] 9.00 × 10−3
4 PPP2CA CALR EIF5A PPP1R13B SFN VSX1 1.90 × 10−3 VEGFA TBX3 hsa-miR-140 9.00 × 10−3
5 PPP2CA EIF5A SOCS2 RORA 1.90 × 10−3 PPP2CA VEGFA PPP1R13B hsa-miR-29a 9.60 × 10−3
Module M5 1 TNF BTG1 GADD45A CCL2 IL6 GADD45B PIM1 CDKN1A RELA RHOB IER3 NFAT 3.59 × 10−7 GADD45A RHOB SOCS3 hsa-miR-527 3.50 × 10−3
2 BCL3 TNFRSF9 TNFSF18 ERN1 GADD45B IER3 RELA 3.59 × 10−7 BTG1 BCL3 RHOB SOCS3 hsa-miR-19a 3.50 × 10−3
3 BCL3 TNFRSF9 TNFSF18 ERN1 GADD45B IER3 REL 3.59 × 10−7 NLRP3 RHOB hsa-miR-223 8.40 × 10−3
4 TNF BCL3 TNFRSF9 TNFSF18 ERN1 GADD45B NFKB 3.59 × 10−7 BTG1 PIM1 hsa-miR-183 2.14 × 10−2
  5 TNFRSF9 GADD45A IL6 PPP1R15A GADD45B CDKN1A PIM1 RELA SERPINB2 JUN 4.86 × 10−7 CUL1 SOCS3 hsa-miR-203 2.89 × 10−2
  1. TFs and miRNAs in italics were those shared between modules and associated with prostate cancer.
  2. ap values were adjusted by FDR method.