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 0.021 0.062 -9999.0 0.0 -0.411 1.0 1.0 HSPA8 -0.017 0.112 -9999.0 0.0 -0.414 4.0 4.0 SMAD3/SMAD4/ER alpha -0.061 0.159 0.216 1.0 -0.282 14.0 15.0 AKT1 0.018 0.009 -9999.0 0.0 -9999.0 0.0 0.0 GSC -0.427 0.609 -9999.0 0.0 -1.282 18.0 18.0 NKX2-5 -0.005 0.086 -9999.0 0.0 -0.307 4.0 4.0 muscle cell differentiation 0.048 0.166 0.367 8.0 -9999.0 0.0 8.0 SMAD2-3/SMAD4/SP1 -0.005 0.124 -9999.0 0.0 -0.277 5.0 5.0 SMAD4 -0.03 0.105 -9999.0 0.0 -0.299 5.0 5.0 CBFB 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 SAP18 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 Cbp/p300/MSG1 0.03 0.08 -9999.0 0.0 -0.227 3.0 3.0 SMAD3/SMAD4/VDR 0.034 0.095 -9999.0 0.0 -0.225 1.0 1.0 MYC 0.01 0.044 -9999.0 0.0 -0.305 1.0 1.0 CDKN2B -0.012 0.087 -9999.0 0.0 -9999.0 0.0 0.0 AP1 -0.055 0.171 -9999.0 0.0 -0.372 9.0 9.0 SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.011 0.064 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.033 0.106 -9999.0 0.0 -0.275 4.0 4.0 SP3 0.02 0.0 -9999.0 0.0 -9999.0 0.0 0.0 CREB1 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 FOXH1 -0.018 0.052 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/GR 0.002 0.101 -9999.0 0.0 -0.254 4.0 4.0 GATA3 -0.002 0.083 -9999.0 0.0 -0.288 4.0 4.0 SKI/SIN3/HDAC complex/NCoR1 0.034 0.032 -9999.0 0.0 -9999.0 0.0 0.0 MEF2C/TIF2 -0.037 0.132 -9999.0 0.0 -0.649 1.0 1.0 endothelial cell migration -0.016 0.175 1.197 1.0 -9999.0 0.0 1.0 MAX 0.017 0.008 -9999.0 0.0 -9999.0 0.0 0.0 RBBP7 -0.009 0.091 -9999.0 0.0 -0.328 4.0 4.0 RBBP4 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 RUNX2 0.006 0.06 -9999.0 0.0 -0.3 2.0 2.0 RUNX3 -0.089 0.182 -9999.0 0.0 -0.395 14.0 14.0 RUNX1 -0.004 0.09 -9999.0 0.0 -0.374 3.0 3.0 CTBP1 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 NR3C1 0.005 0.061 -9999.0 0.0 -0.303 2.0 2.0 VDR -0.016 0.106 -9999.0 0.0 -0.344 5.0 5.0 CDKN1A -0.072 0.366 -9999.0 0.0 -1.185 5.0 5.0 KAT2B 0.004 0.006 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2/SMAD2/SMAD4/FOXH1 -0.055 0.141 -9999.0 0.0 -0.256 12.0 12.0 DCP1A 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 SKI 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 SERPINE1 0.015 0.177 -9999.0 0.0 -1.213 1.0 1.0 SMAD3/SMAD4/ATF2 0.009 0.087 -9999.0 0.0 -0.24 2.0 2.0 SMAD3/SMAD4/ATF3 0.002 0.098 -9999.0 0.0 -0.236 4.0 4.0 SAP30 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 Cbp/p300/PIAS3 0.061 0.059 -9999.0 0.0 -0.228 1.0 1.0 JUN -0.058 0.168 -9999.0 0.0 -0.371 9.0 9.0 SMAD3/SMAD4/IRF7 0.009 0.096 -9999.0 0.0 -0.254 3.0 3.0 TFE3 0.019 0.018 -9999.0 0.0 -9999.0 0.0 0.0 COL1A2 -0.032 0.207 -9999.0 0.0 -0.683 4.0 4.0 mesenchymal cell differentiation -0.002 0.098 0.24 4.0 -9999.0 0.0 4.0 DLX1 -0.032 0.118 -9999.0 0.0 -0.313 8.0 8.0 TCF3 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 FOS -0.084 0.167 -9999.0 0.0 -0.36 14.0 14.0 SMAD3/SMAD4/Max 0.008 0.089 -9999.0 0.0 -0.243 2.0 2.0 Cbp/p300/SNIP1 0.031 0.063 -9999.0 0.0 -0.223 3.0 3.0 ZBTB17 0.017 0.006 -9999.0 0.0 -9999.0 0.0 0.0 LAMC1 0.008 0.096 -9999.0 0.0 -0.341 2.0 2.0 TGIF2/HDAC complex/SMAD3/SMAD4 -0.012 0.113 -9999.0 0.0 -0.262 6.0 6.0 IRF7 0.013 0.045 -9999.0 0.0 -0.292 1.0 1.0 ESR1 -0.096 0.188 -9999.0 0.0 -0.397 15.0 15.0 HNF4A 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 MEF2C -0.048 0.138 -9999.0 0.0 -0.688 1.0 1.0 SMAD2-3/SMAD4 -0.018 0.106 -9999.0 0.0 -0.253 4.0 4.0 Cbp/p300/Src-1 0.048 0.046 -9999.0 0.0 -0.227 1.0 1.0 IGHV3OR16-13 -0.015 0.03 -9999.0 0.0 -9999.0 0.0 0.0 TGIF2/HDAC complex -0.014 0.112 -9999.0 0.0 -0.41 4.0 4.0 CREBBP 0.025 0.012 -9999.0 0.0 -9999.0 0.0 0.0 SKIL -0.022 0.113 -9999.0 0.0 -0.337 6.0 6.0 HDAC1 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 HDAC2 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 SNIP1 -0.001 0.081 -9999.0 0.0 -0.412 2.0 2.0 GCN5L2 0.027 0.014 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3/SMAD4/TFE3 0.019 0.098 -9999.0 0.0 -0.276 2.0 2.0 MSG1/HSC70 -0.024 0.112 -9999.0 0.0 -0.284 8.0 8.0 SMAD2 -0.017 0.052 -9999.0 0.0 -9999.0 0.0 0.0 SMAD3 0.002 0.078 -9999.0 0.0 -0.298 2.0 2.0 SMAD3/E2F4-5/DP1/p107/SMAD4 0.001 0.094 -9999.0 0.0 -0.313 2.0 2.0 SMAD2/SMAD2/SMAD4 -0.009 0.055 -9999.0 0.0 -0.222 2.0 2.0 NCOR1 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 NCOA2 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 NCOA1 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 MYOD/E2A -0.005 0.088 -9999.0 0.0 -0.251 6.0 6.0 SMAD2-3/SMAD4/SP1/MIZ-1 0.008 0.118 -9999.0 0.0 -0.261 4.0 4.0 IFNB1 0.006 0.099 -9999.0 0.0 -0.497 1.0 1.0 SMAD3/SMAD4/MEF2C -0.035 0.145 -9999.0 0.0 -0.49 2.0 2.0 CITED1 -0.016 0.106 -9999.0 0.0 -0.344 5.0 5.0 SMAD2-3/SMAD4/ARC105 -0.004 0.096 -9999.0 0.0 -0.244 2.0 2.0 RBL1 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.02 0.072 -9999.0 0.0 -9999.0 0.0 0.0 RUNX1-3/PEBPB2 -0.041 0.132 -9999.0 0.0 -0.264 12.0 12.0 SMAD7 -0.049 0.191 -9999.0 0.0 -0.493 5.0 5.0 MYC/MIZ-1 0.019 0.034 -9999.0 0.0 -0.201 1.0 1.0 SMAD3/SMAD4 0.091 0.131 0.287 11.0 -9999.0 0.0 11.0 IL10 0.001 0.105 -9999.0 0.0 -0.295 3.0 3.0 PIASy/HDAC complex 0.0 0.058 -9999.0 0.0 -0.41 1.0 1.0 PIAS3 0.021 0.006 -9999.0 0.0 -9999.0 0.0 0.0 CDK2 0.014 0.06 -9999.0 0.0 -0.287 2.0 2.0 IL5 0.006 0.094 -9999.0 0.0 -0.339 1.0 1.0 CDK4 0.027 0.014 -9999.0 0.0 -9999.0 0.0 0.0 PIAS4 0.0 0.058 -9999.0 0.0 -0.41 1.0 1.0 ATF3 0.006 0.06 -9999.0 0.0 -0.3 2.0 2.0 SMAD3/SMAD4/SP1 0.004 0.119 -9999.0 0.0 -0.271 4.0 4.0 FOXG1 -0.13 0.196 -9999.0 0.0 -0.383 20.0 20.0 FOXO3 0.024 0.012 -9999.0 0.0 -9999.0 0.0 0.0 FOXO1 0.024 0.011 -9999.0 0.0 -9999.0 0.0 0.0 FOXO4 0.024 0.011 -9999.0 0.0 -9999.0 0.0 0.0 heart looping -0.047 0.136 -9999.0 0.0 -0.679 1.0 1.0 CEBPB 0.012 0.043 -9999.0 0.0 -0.298 1.0 1.0 SMAD3/SMAD4/DLX1 -0.022 0.116 -9999.0 0.0 -0.276 4.0 4.0 MYOD1 -0.026 0.124 -9999.0 0.0 -0.374 6.0 6.0 SMAD3/SMAD4/HNF4 0.009 0.087 -9999.0 0.0 -0.24 2.0 2.0 SMAD3/SMAD4/GATA3 0.007 0.114 -9999.0 0.0 -0.325 2.0 2.0 SnoN/SIN3/HDAC complex/NCoR1 -0.022 0.112 -9999.0 0.0 -0.336 6.0 6.0 SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.036 0.146 -9999.0 0.0 -0.349 6.0 6.0 SMAD3/SMAD4/SP1-3 0.025 0.108 -9999.0 0.0 -0.258 2.0 2.0 MED15 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 SP1 0.007 0.044 -9999.0 0.0 -0.154 1.0 1.0 SIN3B 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 SIN3A 0.016 0.002 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.046 0.142 -9999.0 0.0 -0.291 6.0 6.0 ITGB5 0.014 0.088 -9999.0 0.0 -0.235 1.0 1.0 TGIF/SIN3/HDAC complex/CtBP 0.031 0.054 -9999.0 0.0 -0.3 1.0 1.0 SMAD3/SMAD4/AR -0.04 0.145 -9999.0 0.0 -0.314 9.0 9.0 AR -0.062 0.158 -9999.0 0.0 -0.37 11.0 11.0 negative regulation of cell growth 0.003 0.107 -9999.0 0.0 -0.321 3.0 3.0 SMAD3/SMAD4/MYOD -0.018 0.122 -9999.0 0.0 -0.264 8.0 8.0 E2F5 -0.024 0.119 -9999.0 0.0 -0.355 6.0 6.0 E2F4 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0 SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.019 0.109 -9999.0 0.0 -0.227 2.0 2.0 SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.077 -9999.0 0.0 -9999.0 0.0 0.0 TFDP1 0.012 0.043 -9999.0 0.0 -0.3 1.0 1.0 SMAD3/SMAD4/AP1 -0.046 0.179 -9999.0 0.0 -0.376 9.0 9.0 SMAD3/SMAD4/RUNX2 0.002 0.099 -9999.0 0.0 -0.241 4.0 4.0 TGIF2 -0.014 0.112 -9999.0 0.0 -0.411 4.0 4.0 TGIF1 -0.004 0.09 -9999.0 0.0 -0.374 3.0 3.0 ATF2 0.017 0.0 -9999.0 0.0 -9999.0 0.0 0.0