TABLE IV.

Modifications to remove aggregate source nodes and apply the original paper’s cellular context.

Model Name	PMID	Modification
Signaling in Macrophage Activation	18433497	Constant nodes: BAG4 = GAS2 = DNA = IRF4 = IFNGR2 = BCL3 = ProCASP10 = TICAM1 = NOS2Agene = MAP3K7IP2 = IKBKE = TRADD = CFLAR = JAK1 = EP300 = PTPN2 = BID = FAS = TLR9 = TLR7 = DAXX = SOCS1 = TLR5 = ProCASP8 = IFNGR1 = TRAF6 = CD40 = DFFA = TNFRSF17 = TBK1 = ProCASP4 = TIRAP = APAF1 = Proteasome = PRKRA = IL1R1 = MAP3K7IP1 = TLR2 = PRKCZ = CHUK = TLR3 = FAF1 = TICAM2 = PTP = IKBKB = FADD = MYD88 = PARP = TOLLIP = IRAK2 = TNFRSF10B = TNFRSF1B = LMNA = HSPA1A = ProCASP1 = IRF9 = TRAF5 = NFKB2p100 = SPI1 = SOCS3 = MAP3K7 = TYK2 = TLR6 = TRAF3 = TRAF2cytoplasm = RIPK3 = ProCASP2 = TNFRSF10A = TNFRSF1A = IRAK4 = RPS6KA5 = Ub = IKBKG = PRKCD = IRAK1 = BIRC2 = IFNAR2 = CREBBP = IFNAR1 = JAK2 = ATF2 = RELB = RIPK1 = 1. We removed the merged node External_Activator implemented in the Cell Collective version.
T Cell Receptor Signaling	17722974	We removed the merged source nodes unknown_input, unknown_input2, and unknown_input3 implemented in the Cell Collective version and fixed their targets in the states indicated in the original paper: akap79 = calpr1 = cdc42 = gap = pten = ship1 = 0 and bcl10 = card11 = ccblr = cd45 = gadd45 = lckr = malt1 = rac1r = 1.
Yeast Apoptosis	23233838	Constants nodes: DRE2_TAH18 = AIF1_MT = EMC4 = NDI1 = MCD1_MT = STM1_CYT = CDC48 = MMI1 = FVY10 = POR1_2 = SRO7 = SOD2 = SNO1 = SVF1 = MDV1= FIS1 = 1. We removed the merged node HK.