Table 5.

Predicted Upstream Regulators of Twist1-Low (Tertile 1) vs Twist1-High (Tertile 3)

Upstream Regulator	Molecule Type	Predicted Activation State	Activation z-score	−log (p-value of overlap)	Target molecules in dataset
IFNG	cytokine	Activated	2.431	12.66	ACTB,ADGRG2,AGT,ALDH1A3,AVPR1A,B2M,BATF2,BST2,BTN3A1,C1R,CASP1,CCL11,CD2,CHST7,CHST8,CLIC5,CX3CR1,CXCL11,CXCL9,FHL2,GBP1,GBP4,GCH1,GJB2,GLIS1,GRM8,HIF1A,HMGCR,IDO1,IFI44L,IFIH1,IGF1,IGFBP4,IL23R,ITGAL,KLRC4-KLRK1/KLRK1,LOX,MMP11,MMP3,OAS2,OAS3,PCSK1,PLA2G2A,PRDX2,PSMB9,SCG5,SMAD1,TACR2,TBX21,TIMP1,TLR3,TLR7,TMEM158,TNFAIP6,TNFSF11,TRPC4,WARS
TNF	cytokine		0.767	10.34	ACTB,ADRB2,AGT,ALDH1A3,APC,AVPR1A,B2M,BDKRB1,BDKRB2,BST2,CASP1,CCL11,COL15A1,COL3A1,CX3CR1,CXCL11,CXCL9,FERMT1,FIGF,FST,FZD5,GADD45A,GBP1,GCH1,HIF1A,HMGCR,IDO1,IFIH1,IGF1,IGFBP4,IGFBP5,IGFBP6,ITGAL,LOX,MMP3,NGFR,NME1,NPPA,NUMB,OAS2,OAS3,OSMR,PLA2G2A,PPAP2A,PSMB9,RBPMS,SERPINF1,SLC2A4,SMAD1,TBX21,TDRD7,TGFB3,TIMP1,TLR3,TLR7,TNC,TNFAIP6,TNFSF11,TPST1,VIP
lipopolysaccharide	chemical drug		−0.073	9.05	ADRB2,AGT,AK4,AVPR1A,BDKRB1,CASP1,CCL11,CD160,CHST7,COL3A1,COX4I1,CX3CR1,CXCL11,CXCL9,DIO2,DRD5,EHHADH,FBLN2,FST,GADD45A,GBP1,GBP4,GCH1,GJB2,HIF1A,HMGCR,IDO1,IFI44L,IFIH1,IGF1,IGFBP4,IGFBP5,IL23R,ITGAL,LGALS1,MMP3,NGFR,NPPA,OAS2,OAS3,OSMR,PLA2G2A,PSMB9,RNF19A,RXRG,SERPINF1,SLC39A14,TBX21,TIMP1,TLR3,TLR7,TNC,TNFAIP6,TNFSF11,TP53BP2,TPBG,VCAN,VIP,WARS
IL1B	cytokine		0.178	9.04	ADRB2,AVPR1A,BDKRB1,C1R,CCL11,CX3CR1,CXCL11,CXCL9,FST,GADD45A,GBP1,GCH1,GYS1,HIF1A,IDO1,IGF1,IGFBP4,IGFBP5,IGFBP6,IL23R,LOX,MMP11,MMP3,NPPA,OAS2,OSMR,PCSK1,PLA2G2A,PSMB9,SLC2A4,SLC6A4,TBX21,TGFB3,TIMP1,TLR3,TLR7,TNFAIP6,TNFSF11,VCAN
STAT3	transcription regulator	Inhibited	−2.600	8.85	AGT,BOC,BST2,CASP1,CCL11,COL3A1,CXCL9,FST,GADD45A,HIF1A,IFIH1,IGFBP5,IL23R,KLRC4-KLRK1/KLRK1,MMP3,NPPA,OAS2,OAS3,PCSK1,PLA2G2A,PSMB9,TBX21,TIMP1,TLR3,TNFSF11,VCAN,VIP,WARS
TGFB1	growth factor	Inhibited	−3.305	8.77	ACKR1,ADGRG2,B2M,CASP1,CCL11,CHST8,COL3A1,CPXM1,CTNND1,CX3CR1,CYP21A2,ECM1,FBLN2,FERMT1,GADD45A,GBP1,GDF6,GJB2,GREM1,HIF1A,IFIH1,IGF1,IGFBP4,IGFBP5,IGFBP6,IL23R,ITGA7,ITGAL,KDELR2,KLRC4-KLRK1/KLRK1,KLRD1,KRT10,LOX,LTBP1,MMP11,MMP3,MYO1C,NME1,NPPA,OSR2,PPP2R5A,RBPMS,RHOD,SCG5,SLC39A14,SLN,TBX21,TGFB3,TIMP1,TNC,TNFAIP6,TNFSF11,TUBB3,UCK2,USP25,VCAN,VIP,XPNPEP2
SB203580	chemical - kinase inhibitor		0.741	8.27	ADAMTS9,ADRB2,AGT,BDKRB1,BST2,CCL11,COL3A1,CX3CR1,CXCL11,CXCL9,GADD45A,GPI,HIF1A,IDO1,LMO2,MMP3,NPPA,TGFB3,TIMP1,TLR3,TNFAIP6,TNFSF11,ZFYVE26
IL6	cytokine		−1.288	7.97	AGT,BST2,CASP1,CCL11,COL3A1,COX4I1,CX3CR1,GADD45A,GREM1,HIF1A,IDO1,IGF1,IGFBP4,IGFBP5,IGFBP6,IL23R,KLRD1,LGALS1,MMP3,PLA2G2A,PSMB9,PTP4A3,SLC2A4,SLC39A14,SMOX,TIMP1,TLR3,TLR7,TNC,TNFSF11,VIP,WARS,XPNPEP2
estrogen	chemical drug		−0.763	7.96	AGT,COL14A1,COL15A1,COL3A1,GJB2,HIF1A,HMGCR,IDO1,IGF1,IGFBP4,IGFBP5,IGFBP6,LGALS1,MTA3,NGFR,NME1,SLC6A4,TBX21,TGFB3,TNFSF11
IFNL1	cytokine	Activated	3.293	7.76	BST2,CXCL11,CXCL9,DDX60,GBP1,IFI44L,IFIH1,OAS2,OAS3,PSMB9,TDRD7
tretinoin	chemical - endogenous mammalian		0.159	7.51	AGT,ALDH1A3,CASP1,COL3A1,CRABP2,CX3CR1,CYP21A2,DAPK2,DDX60,DIO2,FERMT1,FST,GBP4,GIMAP2,GREM1,IFI44L,IFIH1,IGF1,IGFBP4,IGFBP5,IGFBP6,IL23R,ITGAL,LGALS1,MMP11,MMP3,MYO1C,NPPA,NUMB,OAS2,OAS3,PRDX2,PRKCH,PSMB9,PTP4A3,RTKN2,RXRG,SLC2A4,SMOX,TGFB3,TIMP1,TLR3,TNC,TNFAIP6,TNFSF11,TRPC4,TUBB3,UBA7,VIP,YPEL1
rosiglitazone	chemical drug		0.836	7.48	AGT,APOL3,CCL11,COX4I1,CXCL11,CXCL9,DIO2,GBP1,GPR65,IGF1,IGFBP5,IGFBP6,ITGAL,KLF11,LOX,NPPA,OAS2,OAS3,SERPINF1,SLC2A4,TBX21,TGFB3,TIMP1,TNC
IL1RN	cytokine	Inhibited	−2.514	7.32	BDKRB1,BTN3A1,CXCL11,GBP1,IFI44L,IFIH1,IGF1,IGFBP4,IGFBP5,OAS2,OAS3,SLC6A4,TIMP1
STAT1	transcription regulator	Activated	2.169	7.31	AGT,ALDH1A3,B2M,BATF2,CASP1,CLIC5,CXCL11,CXCL9,GBP1,HIF1A,IDO1,IGF1,NPPA,OAS2,PSMB9,TBX21,TLR3,TP53BP2,WARS
IL1	group		−0.269	7.29	ADRB2,CASP1,CXCL11,CXCL9,FST,FZD5,HIF1A,HMGCR,IDO1,IGF1,LOX,MMP3,NGFR,PLA2G2A,TGFB3,TIMP1,TLR7,TNC,TNFAIP6,TNFSF11,VCAN