Table A1.
The VPC cell network as a discrete dynamical system.
| Rule | References |
|---|---|
| APX-1*(t + 1) = APX-1*(t) | Chen and Greenwald, 2004 |
| CWN-1*(t + 1) = CWN-1*(t) | Gleason et al., 2006; Pénigault and Félix, 2011b |
| CWN-2*(t + 1) = CWN-2*(t) | Gleason et al., 2006 |
| DSL-1*(t + 1) = DSL-1*(t) | Chen and Greenwald, 2004 |
| EGL-20*(t + 1) = EGL-20*(t) | Gleason et al., 2006; Pénigault and Félix, 2011b |
| LAG-2*(t + 1) = LAG-2*(t) | Chen and Greenwald, 2004 |
| LIN-3*(t + 1) = LIN-3*(t) | Ferguson and Horvitz, 1985; Hill and Sternberg, 1992 |
| LIN-44*(t + 1) = LIN-44*(t) | Green et al., 2008; Gleason et al., 2006 |
| MOM-2*(t + 1) = MOM-2*(t) | Green et al., 2008; Gleason et al., 2006 |
| APH-1(t + 1) = APH-1(t) | Francis et al., 2002; Goutte et al., 2002 |
| APH-2(t + 1) = APH-1(t) | Goutte et al., 2000; Levitan et al., 2001; Goutte et al., 2002 |
| APR-1(t + 1) = NOT (MIG-5(t)) | Hoier et al., 2000; Gleason et al., 2002; Eisenmann, 2005 |
| APX-1(t + 1) = MC(t) | Chen and Greenwald, 2004 |
| ARK-1(t + 1) = CSL(t) AND SEM-5(t) | Yoo et al., 2004; Hopper et al., 2000 |
| BAR-1(t + 1) = NOT (GSK-3(t)) | Eisenmann et al., 1998; Gleason et al., 2002; Eisenmann, 2005 |
| CAM-1(t + 1) = EGL-20*(t) AND VANG-1(t) | Green et al., 2008 |
| CEH-13(t + 1) = CEH-13(t) | Bürglin and Ruvkun, 1993; Tihanyi et al., 2010 |
| CEH-20(t + 1) = CEH-20(t) | Yang et al., 2005 |
| CSL(t + 1) = {1 IF (LIN-12-3(t) AND SEL-8(t) AND LAG-1(t)) OR RAL-1(t) ELSE 0} | Doyle et al., 2000; Greenwald, 2005; Zand et al., 2011 |
| DPY-23(t + 1) = CSL(t) | Yoo et al., 2004 |
| DSL-1(t + 1) = MC(t) | Chen and Greenwald, 2004 |
| EFF-1(t + 1) = {0 IF REF-2(t) OR EGL-18(t) OR ELT-6(t) OR CSL(t) ELSE 1} | Alper and Kenyon, 2002; Shemer and Podbilewicz, 2002; Shemer et al., 2004; Podbilewicz, 2006; Podbilewicz et al., 2006; Alper and Podbilewicz, 2008; Rasmussen et al., 2008 |
| EGL-17(t + 1) = {1 IF LIN-39a(t) == 2, ELSE 0} | Burdine et al., 1997, 1998; Cui and Han, 2003 |
| EGL-18(t + 1) = {1 IF (LIN-39a(t) == 2) ELSE 0} | Koh et al., 2002, 2004; Alper and Podbilewicz, 2008 |
| ELT-6(t + 1) = {1 IF (LIN-39a(t) == 2) ELSE 0} | Koh et al., 2002, 2004; Alper and Podbilewicz, 2008 |
| GAP-1(t + 1) = GAP-1(t) | Hajnal et al., 1997 |
| GSK-3(t + 1) = KIN-19(t) AND APR-1(t) AND PRY-1(t) | Peters et al., 1999; Hoier et al., 2000; Korswagen et al., 2002; Eisenmann, 2005; Oosterveen et al., 2007 |
| HOXCO(t + 1) = {1 IF CEH-20(t) AND UNC-62(t) AND (NOT(CEH-13(t) OR MAB5(t)) OR LIN-39(t) == 2), ELSE 0} | Yang et al., 2005; Tihanyi et al., 2010; Pénigault and Félix, 2011b |
| KIN-19(t + 1) = APR-1(t) | Peters et al., 1999; Eisenmann, 2005 |
| KSR-1(t + 1) = KSR-1(t) | Roy et al., 2002; Ohmachi et al., 2002 |
| KSR-2(t + 1) = KSR-2(t) | Roy et al., 2002; Ohmachi et al., 2002 |
| LAG-1(t + 1) = LAG-1(t) | Christensen et al., 1996; Doyle et al., 2000 |
| LAG-2(t + 1) = {1 IF MC(t) OR (LIN-39a(t) > 0), ELSE 0} | Chen and Greenwald, 2004; Takács-Vellai et al., 2007; Zhang and Greenwald, 2011 |
| LET-23(t + 1) = {3 IF LET-23ML(t) AND (LIN-3*(t) == 3), 2 IF LET-23ML(t) AND LIN-3*(t) == 2) AND NOT( ARK-1(t)), 1 IF (ARK-1(t) AND LET-23ML(t) AND LIN-3*(t) == 2) OR (LET-23ML(t) AND LIN-3*(t) == 1) ELSE 0} | Ferguson and Horvitz, 1985; Aroian and Sternberg, 1991; Kaech et al., 1998; Hopper et al., 2000; Schlessinger, 2000; Worby and Margolis, 2000; Sundaram, 2006 |
| LET-23ML(t + 1) = LIN-2(t) AND LIN-7(t) and LIN-10(t) | Simske et al., 1996; Kaech et al., 1998 |
| LET-60(t + 1) = SOS-1(t) | Han et al., 1990; Hajnal et al., 1997; Chang et al., 2000 |
| LIN-1(t + 1) = LIN-1(t) | Ferguson and Horvitz, 1985; Beitel et al., 1995; Jacobs et al., 1998; Tan et al., 1998; Tiensuu et al., 2005 |
| LIN-10(t + 1) = LIN-10(t) | Ferguson and Horvitz, 1985; Kaech et al., 1998 |
| LIN-11(t + 1) = CSL(t) | Ferguson and Horvitz, 1985; Gupta et al., 2003; Chen and Greenwald, 2004 |
| LIN-12(t + 1) = {1 IF (CSL(t) == 1 OR LIN-39a(t) ≥ 1) ELSE 0} | Greenwald et al., 1983; Christensen et al., 1996; Takács-Vellai et al., 2007 |
| LIN-12-1(t + 1) = {1 IF (LIN-12(t) == 1 AND LIN-14(t) == 0 AND (MC(t) == 0 OR VAV-1(t) == 0)) ELSE 0} | Shaye and Greenwald, 2002, 2005; Yoo and Greenwald, 2005; Li and Greenwald, 2010 |
| LIN-12-2(t + 1) = {1 IF (LIN-12-1(t) AND SUP-17(t) AND LS(t) ) ELSE 0} | Wen et al., 1997; Jarriault and Greenwald, 2005 |
| LIN-12-3(t + 1) = {1 IF (LIN-12-2(t) AND SEL-12(t)) ELSE 0} | Westlund et al., 1999; Goutte et al., 2000; Levitan et al., 2001; Francis et al., 2002; Greenwald, 2005 |
| LIN-14(t + 1) = NOT(lin-4(t)) | Li and Greenwald, 2010 |
| LIN-17(t + 1) = CWN-1*(t) OR CWN-2*(t) OR LIN-44*(t) | Ferguson and Horvitz, 1985; Sawa et al., 1996; Deshpande et al., 2005; Gleason et al., 2006; Green et al., 2008 |
| LIN-18(t + 1) = MOM-2*(t) OR CWN-2*(t) | Ferguson and Horvitz, 1985; Inoue et al., 2004; Deshpande et al., 2005; Green et al., 2008 |
| LIN-2(t + 1) = LIN-2(t) | Ferguson and Horvitz, 1985; Kaech et al., 1998 |
| LIN-25(t + 1) = {1 IF MPK-1(t) == 2, ELSE 0} | Ferguson and Horvitz, 1985; Tuck and Greenwald, 1995; Nilsson et al., 1998 |
| LIN-31(t + 1) = LIN-31(t) | Ferguson and Horvitz, 1985; Tan et al., 1998; Miller et al., 2000; Wagmaister et al., 2006a |
| LIN-39(t + 1) = {2 IF (PJW5(t) == 2) AND (POP-1b(t) == 1) AND (LIN-39a(t) ≥ 1) AND (MC(t) == 1), 1 IF ((POP-1b(t) == 1 OR PJW5(t) ≥ 1 OR (LIN39a(t) == 2 AND MC(t))) AND NOT ((PJW5(t) == 2) AND (POP-1b(t) == 1) AND (LIN-39a(t) ≥ 1) AND (MC(t) == 1)), ELSE 0} | Bürglin and Ruvkun, 1993; Clark et al., 1993; Tan et al., 1998; Maloof and Kenyon, 1998; Shemer and Podbilewicz, 2002; Wagmaister et al., 2006a,b |
| LIN-39a(t + 1) = {2 IF MPK-1(t) ≥ 1 AND LIN-39(t) == 2 AND HCO(t), 1 IF NOT (MPK-1(t) ≥ 1 AND LIN-39(t) == 2 AND HCO(t)) AND (LIN39(t) ≥ 1 AND HCO(t)), ELSE 0} | Sternberg and Horvitz, 1986; Eisenmann et al., 1998; Grandien and Sommer, 2001; Yang et al., 2005; Wagmaister et al., 2006b |
| lin-4(t + 1) = lin-4(t) | Ferguson and Horvitz, 1985; Lee et al., 1993; Li and Greenwald, 2010 |
| LIN-45(t + 1) = {3 IF LET-60(t) == 3, 2 IF LET-60(t) == 2, 1 IF LET-60(t) == 1, ELSE 0} | Han et al., 1993; Hsu et al., 2002 |
| LIN-7(t + 1) = LIN-7(t) | Ferguson and Horvitz, 1985; Kaech et al., 1998 |
| LIP-1(t + 1) = CSL(t) | Berset et al., 2001; Yoo et al., 2004 |
| LIT-1(t + 1) = LIT-1(t) | Kaletta et al., 1997; Siegfried and Kimble, 2002; Lo et al., 2004; Takeshita and Sawa, 2005; Green et al., 2008 |
| LS(t+1) = APX-1*(t) OR DSL-1*(t) OR LAG-2*(t) | Chen and Greenwald, 2004 |
| LST-1(t + 1) = CSL(t) | Yoo et al., 2004 |
| LST-2(t + 1) = CSL(t) | Yoo et al., 2004 |
| LST-3(t + 1) = CSL(t) | Yoo et al., 2004 |
| LST-4(t + 1) = CSL(t) | Yoo et al., 2004 |
| MAB-5(t + 1) = {1 IF EGL-20*(t) == 2, ELSE 0} | Bürglin and Ruvkun, 1993; Harris et al., 1996; Maloof and Kenyon, 1998; Alper and Kenyon, 2002; Korswagen et al., 2002; Yuan Jiang and Liu, 2009 |
| MC(t + 1) = LIN-25(t) AND SUR-2(t) | Nilsson et al., 1998 |
| MEK-2(t + 1) = {3 IF (KSR-1(t) OR KSR-2(t)) and (LIN-45(t) == 3), 2 IF (NOT (KSR-1(t) OR KSR-2(t)) AND (LIN-45(t) == 3)) OR (KSR-1(t) OR KSR-2(t)) AND (LIN-45(t) == 2), 1 IF (NOT (KSR-1(t) OR KSR-2(t)) AND (LIN-45(t) == 2)) OR (KSR-1(t) OR KSR-2(t)) AND (LIN-45(t) == 1), ELSE 0} | Wu et al., 1995; Lackner and Kim, 1998; Sundaram, 2006 |
| MIG-1(t + 1) = {1 IF (LIN-44*(t) == 1 OR MOM-2*(t) == 1) ELSE 0} | Gleason et al., 2006 |
| MIG-5(t + 1) = LIN-17(t) OR MOM-5(t) | Walston et al., 2006 |
| mir61(t + 1) = CSL(t) | Yoo and Greenwald, 2005 |
| MOM-5(t + 1) = CWN-1*(t) OR (EGL-20*(t) > 0) | Park et al., 2005; Gleason et al., 2006 |
| MPK-1(t + 1) = {2 IF (MEK-2(t) == 3 OR (MEK-2(t) == 2 AND LIP-1(t) == 0)), 1 IF((MEK-2(t) == 2 AND LIP-1(t) == 1) OR (MEK-2 == 1 AND LIP-1(t) == 0)), ELSE 0} | Lackner and Kim, 1998; Berset et al., 2001 |
| PEN-2(t + 1) = PEN-2(t) | Francis et al., 2002 |
| PJW5(t + 1) = {2 IF (LIN-31(t) == 1 AND LIN-1(t) == 1 AND MPK-1(t) ≥ 1), 1 IF LIN-1(t) == 0 AND MPK1(t) ≥ 1, ELSE 0} | Wagmaister et al., 2006a |
| POP-1(t + 1) = WRM-1(t) AND LIT-1(t) | Lin et al., 1995; Lo et al., 2004 |
| POP-1b(t + 1) = POP-1(t) AND (SYS-1(t) OR BAR-1(t)) | Eisenmann, 2005; KiddIII et al., 2005; Phillips et al., 2007; Green et al., 2008 |
| PRY-1(t + 1) = APR-1(t) | Korswagen et al., 2002 |
| RAL-1(t + 1) = RGL-1(t) | Zand et al., 2011 |
| REF-2(t + 1) = {1 IF (LIN-39 ≥ 1), ELSE 0} | Alper and Kenyon, 2002; Alper and Podbilewicz, 2008 |
| RGL-1(t + 1) = {1 IF (LET-60(t) == 1), ELSE 0} | Zand et al., 2011 |
| SEL-12(t + 1) = APH-1(t) AND APH-2(t) AND PEN-2(t) | Westlund et al., 1999; Goutte et al., 2000; Levitan et al., 2001; Francis et al., 2002; Goutte et al., 2002; Greenwald, 2005 |
| SEL-8(t + 1) = SEL-8 | Doyle et al., 2000; Petcherski and Kimble, 2000; Greenwald, 2005 |
| SEM-5(t + 1) = LET-23(t) | Clark et al., 1992; Hopper et al., 2000; Worby and Margolis, 2000 |
| SOS-1(t + 1) = SEM-5(t) | Chang et al., 2000; Worby and Margolis, 2000 |
| SUP-17(t + 1) = SUP-17(t) | Jarriault and Greenwald, 2005 |
| SUR-2(t +1) = {1 IF (MPK-1(t) == 2) ELSE 0} | Singh and Han, 1995; Nilsson et al., 1998; Berset et al., 2001 |
| SYS-1(t +1) = NOT (GSK-3(t)) | Eisenmann, 2005; KiddIII et al., 2005; Phillips et al., 2007; Green et al., 2008 |
| UNC-62(t + 1) = UNC-62(t) | Yang et al., 2005; Wagmaister et al., 2006a; Pénigault and Félix, 2011b |
| VANG-1(t + 1) = VANG-1(t) | Green et al., 2008 |
| VAV-1(t + 1) = NOT( mir-61(t)) | Yoo and Greenwald, 2005 |
| WRM-1(t + 1) = (NOT GSK-3(t)) AND (LIN-17(t) OR LIN-18(t) OR CAM-1(t) | Lo et al., 2004; Takeshita and Sawa, 2005; Green et al., 2008 |