Regulation of nuclear SMAD2/3 signaling Entity Mean Std Dev Mean of Up Perturbations Number of Up Perturbations Mean of Down Perturbations Number of Down Perturbations Number of Total Perturbations EP300 0.025 0.034 -9999.0 0.0 -9999.0 0.0 0.0 HSPA8 0.036 0.015 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/ER alpha 0.048 0.083 -9999.0 0.0 -0.157 1.0 1.0 AKT1 0.043 0.003 -9999.0 0.0 -9999.0 0.0 0.0 GSC 0.058 0.059 -9999.0 0.0 -9999.0 0.0 0.0 NKX2-5 0.025 0.044 -9999.0 0.0 -0.124 1.0 1.0 muscle cell differentiation -0.056 0.069 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4/SP1 0.121 0.056 -9999.0 0.0 -9999.0 0.0 0.0 SMAD4 0.035 0.043 -9999.0 0.0 -9999.0 0.0 0.0 CBFB 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 SAP18 0.038 0.011 -9999.0 0.0 -9999.0 0.0 0.0 Cbp/p300/MSG1 0.052 0.054 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/VDR 0.066 0.114 -9999.0 0.0 -9999.0 0.0 0.0 MYC 0.025 0.024 -9999.0 0.0 -9999.0 0.0 0.0 CDKN2B -0.047 0.181 -9999.0 0.0 -0.564 1.0 1.0 AP1 -0.005 0.14 -9999.0 0.0 -0.265 3.0 3.0 SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.0 0.064 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.022 0.026 -9999.0 0.0 -9999.0 0.0 0.0 SP3 0.03 0.033 -9999.0 0.0 -9999.0 0.0 0.0 CREB1 0.035 0.014 -9999.0 0.0 -9999.0 0.0 0.0 FOXH1 0.03 0.039 -9999.0 0.0 -0.093 1.0 1.0 SMAD3/SMAD4/GR 0.073 0.075 -9999.0 0.0 -9999.0 0.0 0.0 GATA3 0.041 0.011 -9999.0 0.0 -9999.0 0.0 0.0 SKI/SIN3/HDAC complex/NCoR1 -0.022 0.075 -9999.0 0.0 -0.246 1.0 1.0 MEF2C/TIF2 0.06 0.083 0.273 1.0 -9999.0 0.0 1.0 endothelial cell migration 0.146 0.431 1.2 2.0 -9999.0 0.0 2.0 MAX 0.044 0.021 -9999.0 0.0 -9999.0 0.0 0.0 RBBP7 0.032 0.017 -9999.0 0.0 -9999.0 0.0 0.0 RBBP4 0.041 0.001 -9999.0 0.0 -9999.0 0.0 0.0 RUNX2 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 RUNX3 0.014 0.096 -9999.0 0.0 -0.332 1.0 1.0 RUNX1 0.014 0.096 -9999.0 0.0 -0.332 1.0 1.0 CTBP1 0.041 0.0 -9999.0 0.0 -9999.0 0.0 0.0 NR3C1 0.041 0.018 -9999.0 0.0 -9999.0 0.0 0.0 VDR 0.011 0.096 -9999.0 0.0 -0.332 1.0 1.0 CDKN1A 0.022 0.024 -9999.0 0.0 -9999.0 0.0 0.0 KAT2B -0.003 0.006 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2/SMAD2/SMAD4/FOXH1 0.087 0.05 -9999.0 0.0 -9999.0 0.0 0.0 DCP1A 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 SKI 0.041 0.001 -9999.0 0.0 -9999.0 0.0 0.0 SERPINE1 -0.149 0.437 -9999.0 0.0 -1.216 2.0 2.0 SMAD3/SMAD4/ATF2 0.071 0.06 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/ATF3 0.067 0.059 -9999.0 0.0 -9999.0 0.0 0.0 SAP30 0.032 0.017 -9999.0 0.0 -9999.0 0.0 0.0 Cbp/p300/PIAS3 0.054 0.059 -9999.0 0.0 -9999.0 0.0 0.0 JUN -0.022 0.132 -9999.0 0.0 -0.267 3.0 3.0 SMAD3/SMAD4/IRF7 0.079 0.058 -9999.0 0.0 -9999.0 0.0 0.0 TFE3 0.008 0.058 -9999.0 0.0 -0.131 1.0 1.0 COL1A2 0.031 0.02 -9999.0 0.0 -9999.0 0.0 0.0 mesenchymal cell differentiation -0.067 0.059 -9999.0 0.0 -9999.0 0.0 0.0 DLX1 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 TCF3 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 FOS 0.019 0.042 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/Max 0.076 0.069 -9999.0 0.0 -9999.0 0.0 0.0 Cbp/p300/SNIP1 0.061 0.049 -9999.0 0.0 -9999.0 0.0 0.0 ZBTB17 0.034 0.019 -9999.0 0.0 -9999.0 0.0 0.0 LAMC1 -0.003 0.094 0.208 1.0 -0.26 1.0 2.0 TGIF2/HDAC complex/SMAD3/SMAD4 0.067 0.059 -9999.0 0.0 -9999.0 0.0 0.0 IRF7 0.039 0.011 -9999.0 0.0 -9999.0 0.0 0.0 ESR1 0.001 0.095 -9999.0 0.0 -0.335 1.0 1.0 HNF4A 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 MEF2C 0.017 0.058 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4 0.083 0.061 -9999.0 0.0 -9999.0 0.0 0.0 Cbp/p300/Src-1 0.039 0.084 -9999.0 0.0 -0.204 1.0 1.0 IGHV3OR16-13 0.012 0.014 -9999.0 0.0 -9999.0 0.0 0.0 TGIF2/HDAC complex 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 CREBBP 0.027 0.03 -9999.0 0.0 -9999.0 0.0 0.0 SKIL 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 HDAC1 0.041 0.001 -9999.0 0.0 -9999.0 0.0 0.0 HDAC2 0.035 0.014 -9999.0 0.0 -9999.0 0.0 0.0 SNIP1 0.042 0.002 -9999.0 0.0 -9999.0 0.0 0.0 GCN5L2 -0.005 0.01 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/TFE3 0.051 0.072 -9999.0 0.0 -9999.0 0.0 0.0 MSG1/HSC70 0.053 0.022 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2 0.042 0.018 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3 0.019 0.081 -9999.0 0.0 -0.235 1.0 1.0 SMAD3/E2F4-5/DP1/p107/SMAD4 0.038 0.036 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2/SMAD2/SMAD4 0.007 0.064 0.157 1.0 -0.165 1.0 2.0 NCOR1 0.032 0.017 -9999.0 0.0 -9999.0 0.0 0.0 NCOA2 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 NCOA1 0.014 0.096 -9999.0 0.0 -0.332 1.0 1.0 MYOD/E2A 0.056 0.015 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4/SP1/MIZ-1 0.137 0.061 -9999.0 0.0 -9999.0 0.0 0.0 IFNB1 0.02 0.035 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/MEF2C 0.084 0.104 0.306 1.0 -9999.0 0.0 1.0 CITED1 0.035 0.014 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4/ARC105 0.1 0.068 -9999.0 0.0 -9999.0 0.0 0.0 RBL1 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.011 0.065 -9999.0 0.0 -9999.0 0.0 0.0 RUNX1-3/PEBPB2 0.036 0.1 -9999.0 0.0 -0.204 2.0 2.0 SMAD7 0.02 0.107 -9999.0 0.0 -9999.0 0.0 0.0 MYC/MIZ-1 0.037 0.034 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4 -0.042 0.157 -9999.0 0.0 -0.418 2.0 2.0 IL10 0.022 0.038 -9999.0 0.0 -9999.0 0.0 0.0 PIASy/HDAC complex 0.041 0.013 -9999.0 0.0 -9999.0 0.0 0.0 PIAS3 0.029 0.027 -9999.0 0.0 -9999.0 0.0 0.0 CDK2 0.028 0.029 -9999.0 0.0 -9999.0 0.0 0.0 IL5 0.022 0.038 -9999.0 0.0 -9999.0 0.0 0.0 CDK4 0.021 0.032 -9999.0 0.0 -9999.0 0.0 0.0 PIAS4 0.041 0.013 -9999.0 0.0 -9999.0 0.0 0.0 ATF3 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/SP1 0.085 0.06 -9999.0 0.0 -9999.0 0.0 0.0 FOXG1 0.026 0.019 -9999.0 0.0 -9999.0 0.0 0.0 FOXO3 -0.013 0.014 -9999.0 0.0 -9999.0 0.0 0.0 FOXO1 -0.015 0.014 -9999.0 0.0 -9999.0 0.0 0.0 FOXO4 -0.013 0.014 -9999.0 0.0 -9999.0 0.0 0.0 heart looping 0.017 0.058 -9999.0 0.0 -9999.0 0.0 0.0 CEBPB 0.039 0.011 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/DLX1 0.071 0.06 -9999.0 0.0 -9999.0 0.0 0.0 MYOD1 0.035 0.014 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/HNF4 0.067 0.059 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/GATA3 0.082 0.06 -9999.0 0.0 -9999.0 0.0 0.0 SnoN/SIN3/HDAC complex/NCoR1 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/RUNX1-3/PEBPB2 0.087 0.101 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/SP1-3 0.1 0.079 -9999.0 0.0 -9999.0 0.0 0.0 MED15 0.041 0.0 -9999.0 0.0 -9999.0 0.0 0.0 SP1 0.037 0.032 -9999.0 0.0 -9999.0 0.0 0.0 SIN3B 0.038 0.011 -9999.0 0.0 -9999.0 0.0 0.0 SIN3A 0.041 0.001 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.094 0.062 -9999.0 0.0 -9999.0 0.0 0.0 ITGB5 0.013 0.092 -9999.0 0.0 -0.274 1.0 1.0 TGIF/SIN3/HDAC complex/CtBP -0.024 0.098 -9999.0 0.0 -0.339 1.0 1.0 SMAD3/SMAD4/AR 0.029 0.11 -9999.0 0.0 -0.196 2.0 2.0 AR -0.018 0.129 -9999.0 0.0 -0.332 2.0 2.0 negative regulation of cell growth 0.048 0.043 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/MYOD 0.075 0.057 -9999.0 0.0 -9999.0 0.0 0.0 E2F5 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 E2F4 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.112 0.06 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4/FOXO1-3a-4 0.023 0.028 -9999.0 0.0 -9999.0 0.0 0.0 TFDP1 0.035 0.014 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/AP1 0.022 0.157 -9999.0 0.0 -0.268 3.0 3.0 SMAD3/SMAD4/RUNX2 0.067 0.059 -9999.0 0.0 -9999.0 0.0 0.0 TGIF2 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 TGIF1 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0 ATF2 0.038 0.01 -9999.0 0.0 -9999.0 0.0 0.0