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
| Â | 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 |