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R Graphics Output TNF signaling pathway all genes sink node genes ● ●● ●● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ●●● ● ●● ● ● ● ● ● ● ●● ●● ● ● ● ● ●● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ●● ● ● ●● ●●● ●●● ●●● ● ● ● ●●● ● ●●● ● maximum = 3 maximum = 2 2 1 s> 10 0 <log −1 −2 2 1 x a m s 0 10 log −1 −2 group 1 group 2 group 3 group 4 group 5 group 6 group 7 group 8 TNF_signaling_pathway genes with data CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway sink nodes CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway group 1 CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway group 2 CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway group 3 CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway group 4 CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway group 5 CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway group 6 CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway group 7 CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1 TNF_signaling_pathway group 8 CASP10 CCL2 CCL5 CCL20 CASP7 FADD CXCL1 CXCL1 CXCL1 CASP3 CASP8 CXCL5 CXCL10 CX3CL1 CSF1 CSF2 BIRC2 ITCH CFLAR FAS IL18R1 JAG1 MAP3K5 IL1B IL6 IL15 LIF LTA TAB1 MAP2K7 MAPK8 FOS BCL3 NFKBIA SOCS3 TNFAIP3 TRAF1 TRAF2 MAP3K7 TNF TNFRSF1A TRADD RIPK1 MAP2K3 MAPK14 CEBPB MAP3K8 NFKB1 RPS6KA4 CREB3 BAG4 MAP3K14 MAP2K1 MAPK1 FOS JUN JUNB MMP3 MMP9 MMP14 IKBKB NFKBIA CHUK EDN1 VEGFC IKBKG NFKB1 NOD2 RIPK1 RIPK3 MLKL PGAM5 ICAM1 SELE VCAM1 DNM1L PGAM5 PTGS2 PIK3CA AKT3 NFKB1 MAP3K14 CHUK NFKBIA TRAF1 LTA TNFRSF1B TRAF2 BIRC2 RIPK1 MAP2K3 MAPK14 TRAF3 DAB2IP MAPK8 JUN IRF1 IFNB1.
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