_____________________________________________________________________

TNF (Tumor Necrosis Factor) Rules

___________________

Author:
Beatriz Santos

October, 28 2017

Contents

1 Initial State: TNFDish
2 Comparison of breast cancer subtypes
 2.1 HER2 vs LUMA
 2.2 HER2 vs LUMB
 2.3 HER2 vs BASAL
 2.4 LUMA vs BASAL
 2.5 LUMB vs BASAL
 2.6 LUMA vs LUMB
3 Classification of rules by breast cancer subtypes
 3.1 In all subtypes
 3.2 In Her2, lumA, lumB
 3.3 In Her2, LumA, Basal
 3.4 In Her2, LumB, Basal
 3.5 In lumA, lumB, Basal
 3.6 In Her2, lumA
 3.7 In her2, lumB
 3.8 In her2, Basal
 3.9 In lumA, lumB
 3.10 In lumB, Basal
 3.11 In lumA, Basal
 3.12 Only in LumA
 3.13 Only in LumB
 3.14 Only in Her2
 3.15 Only in Basal
 3.16 Not in any subtype

1 Initial State: TNFDish

http://stella.csl.sri.com/~pl/Evidence/STM7/SDishes/TnfDish.maude




Figure 1: TNF Dish (initial state) simplified. Rules that do not appear in any subtype were erased. The remaining ones are classified into subtypes.

eq TnfDish = PD( 
{XOut | Tnf} 
{TnfR1C | TnfR1} 
{EgfRC | EgfR} 
{CLo | empty} 
{CLm | Muc1}{CLi | Cltc Pld1 Pld2} 
{CLc | [Gsk3s - act] Akt1 Ask1 Atf2 Azi2 Ciap1 Csnk1a1 Eif4e Eif4ebp1 Erks Ikba Ikbb Ikk1 Ikk2 Irak1 Itch Jnks Map4k5 Mapkapk2 Mek1 Mekk1 Mekk2 Mekk3 Mkk4 Mkk7 Mlk3 Mlst8 Mnk1 Mtor Nemo P38s Pin1 Pkci Pkcz Raptor Rela Rela Ripk1 Rnf11 Rsk2 S6k1 Stat1 Syk Syk Tab1Tab2 Tab3 Tak1 Tank Tax1bp1 Tbk1 Tnfaip3 Tpl2 Tradd Traf2 Tsc1 Ubc13} 
{NUc | Atf1 CcL2-gene CcL5-gene Cezanne-gene Creb1 CxcL1-gene CxcL2-gene CxcL10-gene Ep300 Egr1 Egr1-gene Eselectin-gene Fos-gene Cd54-gene Ikba-gene IL1b-gene IL6-gene IL8-gene Irf1-gene Jun Junb-gene Msk1 TLR2-gene ProTnf-gene Tnfaip3-gene }) .

2 Comparison of breast cancer subtypes

2.1 HER2 vs LUMA




Figure 2: Graph comparing Her2 vs LumA. Pink occurrences and rules are common to both Her2 and LumA. Blue occurrences and rules are only in LumA. Purple occurrences and rules are only in Her2.

2.2 HER2 vs LUMB




Figure 3: Graph comparing Her2 vs LumB. Pink occurrences and rules are common to both Her2 and LumB. Blue occurrences and rules are only in LumB. Purple occurrences and rules are only in Her2.

2.3 HER2 vs BASAL




Figure 4: Graph comparing Her2 vs Basal. Pink occurrences and rules are common to both Her2 and Basal. Blue occurrences and rules are only in Basal. Purple occurrences and rules are only in Her2.

2.4 LUMA vs BASAL




Figure 5: Graph comparing lumA vs Basal. Pink occurrences and rules are common to both lumA and Basal. Blue occurrences and rules are only in Basal. Purple occurrences and rules are only in lumA.

2.5 LUMB vs BASAL




Figure 6: Graph comparing LumB vs Basal. Pink occurrences and rules are common to both LumB and Basal. Blue occurrences and rules are only in Basal. Purple occurrences and rules are only in lumB.

2.6 LUMA vs LUMB




Figure 7: Graph comparing LumA vs lumB. Pink occurrences and rules are common to both LumA and lumB. Blue occurrences and rules are only in lumB. Purple occurrences and rules are only in lumA.

3 Classification of rules by breast cancer subtypes

3.1 In all subtypes

Rewrite Rule 107

rl[107.TnfR1.by.Tnf]: 
  {XOut   | xout   Tnf           } 
  {TnfR1C | tnfr1c TnfR1         } 
  => 
  {XOut   | xout                 } 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } . 
  ---------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/TnfR1.by.Tnf.107.txt

Rewrite Rule 114

rl[114.Ciap1.to.TnfR1]: 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf) Tradd Traf2       } 
  {CLc    | clc     Ciap1                           } 
  => 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf) Tradd Traf2 Ciap1 } 
  {CLc    | clc                                     } . 
  ----------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ciap1.to.TnfR1.114.txt

Rewrite Rule 168

rl[168.Ikks.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Tradd Traf2   } 
  {CLc    | clc    (Ikk1 : Ikk2 : Nemo)                    } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Tradd Traf2 
                   (Ikk1 : Ikk2 : Nemo)                    } 
  {CLc    | clc                                            } . 
  --------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ikks.to.TnfR1.168.txt

Rewrite Rule 169c

rl[169c.Ikk1.Ikk2.Nemo.complex]: 
  {CLc | clc  Ikk1 Ikk2 Nemo       } 
  => 
  {CLc | clc  (Ikk1 : Ikk2 : Nemo) } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Ikk1.Ikk2.Nemo.complex.169c.txt

Rewrite Rules 555c, 555c-1

rl[555c.Tab1.Tab23.Tak1.complex]: 
  {CLc | clc  Tab1   tab23:Tab23S   Tak1  } 
  => 
  {CLc | clc (Tab1 : tab23:Tab23S : Tak1) } . 
  ------------------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Tab1.Tab23.Tak1.complex.555c.txt

Rewrite Rule 561, 561-1

rl[561.Tak1.TabS.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Muc1 [Ripk1 - ubiq]  } 
  {CLc    | clc    (Tak1 : Tab1 : tab23s:Tab23S)                    } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Muc1 [Ripk1 - ubiq] 
                   (Tak1 : Tab1 : tab23s:Tab23S)                    } 
  {CLc    | clc                                                   } . 
  ------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Tak1.TabS.to.TnfR1.561.txt

Rewrite Rule 944

rl[944.Pkci.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)              } 
  {CLc    | clc     Pkci                                  } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Pkci - act] } 
  {CLc    | clc                                           } . 
  ----------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Pkci.irt.Tnf.944.txt

Rewrite Rules 844, 844-1

rl[844.Tak1.Tabs.irt.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   (Tak1 : Tab1 : tab23s:Tab23S)                               } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Tak1.irt.Tnf.844.txt

Rewrite Rule 802

rl[802.Muc1.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Tradd Traf2       } 
  {CLm    | clm    Muc1                                        } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Tradd Traf2 Muc1  } 
  {CLm    | clm                                                } . 
  ---------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Muc1.to.TnfR1.802.txt

Rewrite Rule 821

rl[821.Mekk3.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)               } 
  {CLc    | clc    Mekk3                                   } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk3 - act] } 
  {CLc    | clc                                            } . 
  ------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Mekk3.irt.Tnf.821.txt

Rewrite Rules 891, 891-1

rl[891.Ikks.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) ciap12:Ciap12S 
                   [Mekk3 - act] Muc1 [Pkci - act] [Ripk1 - ubiq] Traf2 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   (Ikk1 : Ikk2 : Nemo)                                        } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) ciap12:Ciap12S 
                   [Mekk3 - act] Muc1 [Pkci - act] [Ripk1 - ubiq] Traf2 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq])               } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Ikks.irt.Tnf.891.txt

Rewrite Rule 894

rl[894.Tradd.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)        } 
  {CLc    | clc    Tradd                            } 
  => 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf) Tradd } 
  {CLc    | clc                                     } . 
  ----------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Tradd.to.TnfR1.894.txt

Rewrite Rule 895

rl[895.Traf2.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Tradd       } 
  {CLc    | clc    Traf2                                 } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Tradd Traf2 } 
  {CLc    | clc                                          } . 
  ----------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Traf2.to.TnfR1.895.txt

Rewrite Rule 981

rl[981.Ripk1.ubiq.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)  Ripk1         Tradd Traf2 } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] Tradd Traf2 } . 
  ------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ripk1.ubiq.irt.Tnf.981.txt

Rewrite Rule 896

rl[896.Ripk1.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {CLc    | clc    Ripk1                           } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Ripk1 } 
  {CLc    | clc                                    } . 
  ---------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ripk1.to.TnfR1.896.txt

3.2 In Her2, lumA, lumB

none

3.3 In Her2, LumA, Basal

none

3.4 In Her2, LumB, Basal

Rewrite Rule 784

rl[784.Tbk1.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {CLc    | clc     Tbk1                     } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {CLc    | clc    [Tbk1 - act]              } . 
  ---------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Tbk1.irt.Tnf.784.txt

Rewrite Rule 943

rl[943.Map4k5.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Traf2 - K63ubiq] } 
  {CLc    | clc    Map4k5                                      } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Traf2 - K63ubiq] 
                   [Map4k5 - act]                              } 
  {CLc    | clc                                                } . 
  ---------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Map4k5.irt.Tnf.943.txt

3.5 In lumA, lumB, Basal

Rewrite Rule 014c

rl[014c.ErkS.by.Mek1]: 
  {CLc | clc [Mek1 - act] [Erks - erksmods]               } 
  => 
  {CLc | clc [Mek1 - act] [Erks - erksmods act phos(TEY)] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/ErkS.by.Mek1.014c.txt

Rewrite Rule 086

 
rl[086.Mekk1.irt.Tnf]: 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf)               } 
  {CLc    | clc     Mekk1                                   } 
  => 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf) [Mekk1 - act] } 
  {CLc    | clc                                             } . 
  ------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Mekk1.irt.Tnf.086.txt

Rewrite Rules 839, 839-1

rl[839.ErkS.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] 
                   [Syk - act] [Tpl2 - act] Tradd Traf2 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {CLc    | clc    [Mek1 - act]  [Erks - erksmods]                             } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] 
                   [Syk - act] [Tpl2 - act] Tradd Traf2 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {CLc    | clc    [Mek1 - act] [Erks - erksmods act phos(TEY)]                } . 
  -------------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/ErkS.irt.Tnf.839.txt

Rewrite Rule 840

rl[840.Mek1.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tpl2 - act]  } 
  {CLc    | clc    Mek1                                    } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tpl2 - act]  } 
  {CLc    | clc    [Mek1 - act]                            } . 
  ------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Mek1.irt.Tnf.840.txt

Rewrite Rule 841

rl[841.Syk.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)             } 
  {CLc    | clc    Syk                       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Syk - act] } 
  {CLc    | clc                              } . 
  ---------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Syk.irt.Tnf.841.txt

Rewrite Rule 843

rl[843.Tpl2.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] [Syk - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   Traf2                                                } 
  {CLc    | clc    Tpl2                                                 } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] [Syk - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   Traf2 [Tpl2 - act]                                   } 
  {CLc    | clc                                                         } . 
  ------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Tpl2.irt.Tnf.843.txt

Rewrite Rule 846

rl[846.Mkk4.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tpl2 - act] } 
  {CLc    | clc    Mkk4                                   } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tpl2 - act] } 
  {CLc    | clc    [Mkk4 - act]                           } . 
  ----------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Mkk4.irt.Tnf.846.txt

Rewrite Rule 942

rl[942.Mekk2.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)               } 
  {CLc    | clc    Mekk2                                   } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk2 - act] } 
  {CLc    | clc                                            } . 
  ------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Mekk2.irt.Tnf.942.txt

3.6 In Her2, lumA

none

3.7 In her2, lumB

none

3.8 In her2, Basal

Rewrite Rule 255

rl[255.Tank.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)               } 
  {CLc    | clc    Tank                                    } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tank - phos] } 
  {CLc    | clc                                            } . 
  ------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Tank.irt.Tnf.255.txt

Rewrite Rule 788

rl[788.CxcL10-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {NUc    | nuc    CxcL10-gene         } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {NUc    | nuc    [CxcL10-gene - on]  } . 
  ----------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/CxcL10-gene.irt.Tnf.788.txt

Rewrite Rule 818

rl[818.IL8-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tank - phos] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) } 
  {CLc    | clc    Irak1                                         } 
  {NUc    | nuc    IL8-gene                                      } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tank - phos] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) } 
  {CLc    | clc    Irak1                                         } 
  {NUc    | nuc    [IL8-gene - on]                               } . 
  ----------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/IL8-gene.irt.Tnf.818.txt

3.9 In lumA, lumB

Rewrite Rule 780

rl[780.Cezanne-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)          } 
  {NUc    | nuc    Cezanne-gene           } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)          } 
  {NUc    | nuc    [Cezanne-gene - on]    } . 
  ----------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Cezanne-gene.irt.Tnf.780.txt

3.10 In lumB, Basal

Rewrite Rule 072

rl[072.Mkk7.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {CLc    | clc     Mkk7                     } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {CLc    | clc    [Mkk7 - act]              } . 
  ---------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Mkk7.irt.Tnf.072.txt

Rewrite Rule 832, 832-1, 832-2, 832-3

rl[832.JnkS.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ask1 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Map4k5 - act] [Mekk1 - act] [Mlk3 - act] [Ripk1 - ubiq] 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Syk - act] Tradd [Traf2 - K63ubiq]                       } 
  {CLc    | clc    [mkk47s:Mkk47S - act] Jnks  Ubc13                         } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ask1 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Map4k5 - act] [Mekk1 - act] [Mlk3 - act] [Ripk1 - ubiq] 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Syk - act] Tradd [Traf2 - K63ubiq]                       } 
  {CLc    | clc    [mkk47s:Mkk47S - act] [Jnks - act] Ubc13                  } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/JnkS.irt.Tnf.832.txt

Rewrite Rule 812c

rl[812c.Jnks.by.Mkk4]: 
  {CLc | clc [Mkk4 - act]  Jnks } 
  => 
  {CLc | clc [Mkk4 - act] [Jnks - act] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Jnks.by.Mkk4.812c.txt

Rewrite Rule 526c

rl[526c.Jnks.by.Mkk7]: 
  {CLc | clc [Mkk7 - act]  Jnks        } 
  => 
  {CLc | clc [Mkk7 - act] [Jnks - act] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Jnks.by.Mkk7.526c.txt

Rewrite Rule 953

rl[953.Ask1.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Traf2               } 
  {CLc    | clc    Ask1                              } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Traf2  [Ask1 - act] } 
  {CLc    | clc                                      } . 
  ------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Ask1.irt.Tnf.953.txt

Rewrite Rule 163

rl[163.Mlk3.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)              } 
  {CLc    | clc    Mlk3                                   } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mlk3 - act] } 
  {CLc    | clc                                           } . 
  ----------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Mlk3.irt.Tnf.163.txt

Rewrite Rule 698

rl[698.Traf2.ubiq.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)  Traf2            } 
  {CLc    | clc    Ubc13                                       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Traf2 - K63ubiq] } 
  {CLc    | clc    Ubc13                                       } . 
  ---------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Traf2.ubiq.irt.Tnf.698.txt

3.11 In lumA, Basal

none

3.12 Only in LumA

none

3.13 Only in LumB

none

3.14 Only in Her2

Rewrite Rule 619c

rl[619c.Akt1.act]: 
  {CLc | clc [Akt1 - phos(S 473)phos(T 308)] } 
  => 
  {CLc | clc [Akt1 - act]                    } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Akt1.act.619c.txt

Rewrite Rule 730

rl[730.Akt1.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)                    } 
  {CLc    | clc    Akt1                             } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)                    } 
  {CLc    | clc    [Akt1 - phos(S 473)phos(T 308)]  } . 
  ----------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Akt1.irt.Tnf.730.txt

Rewrite Rule 1599c

rl[1599c.Akt1.by.Tbk1]: 
  {CLc | clc [Tbk1 - act] Akt1                            } 
  => 
  {CLc | clc [Tbk1 - act] [Akt1 - phos(S 473)phos(T 308)] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Akt1.by.Tbk1.1599c.txt

3.15 Only in Basal

Rewrite Rule 023

rl[023.Rsk2.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)              } 
  {CLc    | clc    Rsk2                       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Rsk2 - act] } 
  {CLc    | clc                               } . 
  ---------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Rsk2.irt.Tnf.023.txt

Rewrite Rule 121, 121-1

rl[121.Rela.S536.phos.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Traf2 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Mekk3 - act] 
                    Rela                                                     } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Traf2 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Mekk3 - act] 
                   [Rela - phos(S 536)]                                      } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Rela.S536.phos.irt.Tnf.121.txt

Rewrite Rule 248, 248-1

 
rl[248.Rela.to.Nuc.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Muc1 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Rela - phos(S 536)]                                      } 
  {NUc    | nuc                                                              } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Muc1 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {NUc    | nuc    [Rela - phos(S 536)]                                      } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Rela.to.Nuc.irt.Tnf.248.txt

Rewrite Rule 542, 542-1

rl[542.Ikba.phosed.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) ciap12:Ciap12S 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Mekk3 - act] Muc1 [Ripk1 - ubiq] [Rsk2 - act] [Syk - act] 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   Tradd  (Ikba : Rela)                                        } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) ciap12:Ciap12S 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Mekk3 - act] Muc1 [Ripk1 - ubiq] [Rsk2 - act] [Syk - act] 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   Tradd  ([Ikba - phos] : Rela)                               } . 
  ------------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ikba.phosed.irt.Tnf.542.txt

Rewrite Rule 636, 636-1

rl[636.Ikba.degraded.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) ciap12:Ciap12S 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Mekk3 - act] Muc1 [Ripk1 - ubiq] [Syk - act] 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   Tradd Traf2 [Tpl2 - act] 
                   ([Ikba - phos] : Rela)                                    } 
  {CLc    | clc                                                              } 
  {Sig    | sig                                                              } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) ciap12:Ciap12S 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Mekk3 - act] Muc1 [Ripk1 - ubiq] [Syk - act] 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   Tradd Traf2 [Tpl2 - act] Rela                             } 
  {CLc    | clc    [Ikba - degraded]                                         } 
  {Sig    | sig                                                              } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Ikba.degraded.irt.Tnf.636.txt

Rewrite Rule 704c

rl[704c.Ikba.Rela.complex]: 
  {CLc | clc   Ikba   Rela  } 
  => 
  {CLc | clc  (Ikba : Rela) } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Ikba.Rela.complex.704c.txt

Rewrite Rule 779

rl[779.CcL5-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] } 
  {NUc    | nuc    [Rela - act] CcL5-gene       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] } 
  {NUc    | nuc    [Rela - act] [CcL5-gene - on]} . 
  ------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/CcL5-gene.irt.Tnf.779.txt

Rewrite Rule 782

rl[782.CxcL1-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {NUc    | nuc    CxcL1-gene          } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {NUc    | nuc    [CxcL1-gene - on]   } . 
  ------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/CxcL1-gene.irt.Tnf.782.txt

Rewrite Rule 786

rl[786.CxcL2-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {NUc    | nuc    CxcL2-gene          } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {NUc    | nuc    [CxcL2-gene - on]   } . 
  ----------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/CxcL2-gene.irt.Tnf.786.txt

Rewrite Rule 807c

rl[807c.Ikbb.Rela.complex]: 
  {CLc | clc   Ikbb   Rela  } 
  => 
  {CLc | clc  (Ikbb : Rela) } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Ikbb.Rela.complex.807c.txt

Rewrite Rule 809

rl[809.Ikba.Rela.to.Ikk.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk3 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq])  } 
  {CLc    | clc    (Ikba : Rela)                                  } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk3 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   (Ikba : Rela)                                  } 
  {CLc    | clc                                                   } . 
  -------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ikba.Rela.to.Ikk.irt.Tnf.809.txt

Rewrite Rule 829

rl[829.Ikbb.degraded.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk2 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   (Ikbb : Rela)                                   } 
  {CLc | clc                                                       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk2 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq])   } 
  {CLc    | clc    [Ikbb - degraded] Rela                          } . 
  -------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ikbb.degraded.irt.Tnf.829.txt

Rewrite Rule 814

rl[814.Ikbb.to.Ikk.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk2 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq])  } 
 
  {CLc    | clc    (Ikbb :  Rela)                                        } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk2 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   (Ikbb : Rela)                                         } 
  {CLc    | clc                                                          } . 
  ------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ikbb.to.Ikk.irt.Tnf.814.txt

Rewrite Rule 884

rl[884.TLR2-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)                } 
  {CLc    | clc    [Tbk1 - act]                 } 
  {NUc    | nuc    [Rela - act] TLR2-gene       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)                 } 
  {CLc    | clc    [Tbk1 - act]                  } 
  {NUc    | nuc    [Rela - act] [TLR2-gene - on] } . 
  ---------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/TLR2-gene.irt.Tnf.884.txt

Rewrite Rules 888, 888-1

rl[888.Tnfaip3-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   Rnf11                                                       } 
  {NUc    | nuc    [Rela - act] Tnfaip3-gene                                   } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   Rnf11                                                       } 
  {NUc    | nuc    [Rela - act] [Tnfaip3-gene - on]                            } . 
  ------------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Tnfaip3-gene.irt.Tnf.888.txt

Rewrite Rule 1568

rl[1568.Rnf11.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {CLc    | clc    Rnf11                           } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Rnf11 } 
  {CLc    | clc                                    } . 
  ---------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Rnf11.to.TnfR1.1568.txt

Rewrite Rules 833, 833-1

rl[833.P38s.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk1 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Ripk1 - ubiq] [Syk - act] Tradd                          } 
  {CLc    | clc    P38s                                                      } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Mekk1 - act] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Ripk1 - ubiq] [Syk - act] Tradd                          } 
  {CLc    | clc    [P38s - act]                                              } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/P38s.irt.Tnf.833.txt

Rewrite Rule 774

rl[774.CcL2-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Ciap1 [Ripk1 - ubiq] } 
  {NUc    | nuc     CcL2-gene                         } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Ciap1 [Ripk1 - ubiq] } 
  {NUc    | nuc    [CcL2-gene - on]                   } . 
  ------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/CcL2-gene.irt.Tnf.774.txt

Rewrite Rule 1530c-3

rl[1530c.Msk1.by.Erks]: 
  {CLc | clc [Erks - erksmods act] } 
  {NUc | nuc  Msk1                 } 
  => 
  {CLc | clc [Erks - erksmods act] } 
  {NUc | nuc [Msk1 - act]          } . 
  ------------------------------------ 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Msk1.by.Erks.1530c.txt

Rewrite Rule 262c

rl[262c.Mnk1.by.P38]: 
  {AnyLoc | anyloc [P38s - act]  Mnk1                           } 
  => 
  {AnyLoc | anyloc [P38s - act] [Mnk1 - phos(T 250)phos(T 257)] } . 
  ----------------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Mnk1.by.P38.262c.txt

Rewrite Rule 1656c

rl[1656c.Mnk1.act]: 
  {AnyLoc | anyloc [Mnk1 - mnk1mods phos(T 250)phos(T 257)]      } 
  => 
  {AnyLoc | anyloc [Mnk1 - mnk1mods act phos(T 250)phos(T 257)]  } . 
  ------------------------------------------------------------------ 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Mnk1.act.1656c.txt

Rewrite Rule 302

rl[302.Msk1.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tpl2 - act] } 
  {NUc    | nuc    Msk1                                   } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tpl2 - act] } 
  {NUc    | nuc    [Msk1 - act]                           } . 
  ----------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Msk1.irt.Tnf.302.txt

Rewrite Rule 883

rl[883.Cd54-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] } 
  {NUc    | nuc     Cd54-gene                   } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] } 
  {NUc    | nuc    [Cd54-gene - on]             } . 
  ------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Cd54-gene.irt.Tnf.883.txt

Rewrite Rule 1638

rl[1638.Mnk1.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)   } 
  {CLc    | clc    Mnk1                        } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)   } 
  {CLc    | clc    [Mnk1 - act]                } . 
  ------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Mnk1.irt.Tnf.1638.txt

Rewrite Rule 258

rl[258.Rela.acetyl.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)                          } 
  {NUc    | nuc     Ep300 [Msk1 - act] 
                   [Rela - phos(S 276)phos(S 536)]                    } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)                          } 
  {NUc    | nuc     Ep300 [Msk1 - act] 
                   [Rela - phos(S 276)phos(S 536)acetyl(K 310)]       } . 
  ----------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Rela.acetyl.irt.Tnf.258.txt

Rewrite Rule 324

rl[324.Rela.S276.phos.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tpl2 - act]      } 
  {NUc    | nuc  [Msk1 - act] [Rela - phos(S 536)]             } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tpl2 - act]      } 
  {NUc    | nuc  [Msk1 - act] [Rela - phos(S 276)phos(S 536)]  } . 
  ---------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Rela.S276.phos.irt.Tnf.324.txt

Rewrite Rule 577

rl[577.Rela.act.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq])      } 
  {NUc    | nuc    [Msk1 - act] 
                   [Rela - phos(S 276)phos(S 536)acetyl(K 310)]       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq])      } 
  {NUc    | nuc    [Msk1 - act] [Rela - act]                          } . 
  --------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Rela.act.irt.Tnf.577.txt

Rewrite Rule 799

rl[799.IL1b-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)      } 
  {NUc    | nuc    IL1b-gene          } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)      } 
  {NUc    | nuc    [IL1b-gene - on]   } . 
  ---------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/IL1b-gene.irt.Tnf.799.txt

Rewrite Rule 855-3

rl[855.ProTnf-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)                          } 
  {CLc    | clc    [Erks - erksmods act] [Jnks - act]     } 
  {NUc    | nuc    Egr1 ProTnf-gene                       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)                          } 
  {CLc    | clc    [Erks - erksmods act] [Jnks - act]     } 
  {NUc    | nuc    Egr1 [ProTnf-gene - on]                } . 
  ----------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/ProTnf-gene.irt.Tnf.855.txt

Rewrite Rule 443c

rl[443c.P38s.by.Mkk4]: 
  {CLc | clc [Mkk4 - act]  P38s        } 
  => 
  {CLc | clc [Mkk4 - act] [P38s - act] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/P38s.by.Mkk4.443c.txt

3.16 Not in any subtype

Rewrite Rules 034, 034-1

rl[034.EgfR.Sphos.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {EgfRC  | egfrc  EgfR                                                        } 
  {CLc    | clc    [P38s - act]                                                } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {EgfRC  | egfrc  [EgfR - phos(S 1070)phos(S 1071)]                           } 
  {CLc    | clc    [P38s - act]                                                } . 
  -------------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/EgfR.Sphos.irt.Tnf.034.txt

Rewrite Rule 036-2, 036-3, 036-6, 036-7

rl[036.EgfR.Tphos.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {EgfRC  | egfrc  EgfR                                                        } 
  {CLi    | cli    Cltc                                                        } 
  {CLc    | clc    [Erks - erksmods]                                           } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {EgfRC  | egfrc  [EgfR - phos(T 693)]                                        } 
  {CLi    | cli    Cltc                                                        } 
  {CLc    | clc    [Erks - erksmods]                                           } . 
  -------------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/EgfR.Tphos.irt.Tnf.036.txt

Rewrite Rule 063c

rl[063c.Atf2.by.P38s]: 
  {CLc | clc [P38s - act]  Atf2                         } 
  => 
  {CLc | clc [P38s - act] [Atf2 - phos(T 69)phos(T 71)] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Atf2.by.P38s.063c.txt 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Atf2.by.P38a.txt 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Atf2.by.P38b.txt 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Atf2.by.P38g.txt

Rewrite Rule 122c

rl[122c.Gsk3s.by.Akt]: 
  {CLc | clc [Akt1 - act] [Gsk3s - act]        } 
  => 
  {CLc | clc [Akt1 - act] [Gsk3s - phos(SFAE)] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Gsk3s.by.Akt1.122c.txt

Rewrite Rule 213c

rl[213c.Mlk3.by.Akt1]: 
  {CLc | clc [Akt1 - act]  Mlk3         } 
  => 
  {CLc | clc [Akt1 - act] [Mlk3 - phos] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Mlk3.by.Akt1.213c.txt

Rewrite Rule 472c

rl[472c.Mlst8.Mtor.complex]: 
  {CLc | clc   Mtor   Mlst8  } 
  => 
  {CLc | clc  (Mtor : Mlst8) } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Mlst8.Mtor.complex.472c.txt

Rewrite Rule 489

rl[489.Irf1-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)    } 
  {NUc    | nuc    Irf1-gene        } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)    } 
  {NUc    | nuc    [Irf1-gene - on] } . 
  ------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Irf1-gene.irt.Tnf.489.txt

Rewrite Rule 511c

rl[511c.Atf2.by.Jnks]: 
  {CLc | clc [Mkk4 - act] [Jnks - act]  Atf2                                   } 
  => 
  {CLc | clc [Mkk4 - act] [Jnks - act] [Atf2 - phos(T 69)phos(T 71)phos(S 90)] } . 
  -------------------------------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Atf2.by.Jnks.511c.txt

Rewrite Rules 514c-3

rl[514c.Atf2.by.Erks]: 
  {CLc | clc [Mek1 - act] [Erks - erksmods act]  Atf2               } 
  => 
  {CLc | clc [Mek1 - act] [Erks - erksmods act] [Atf2 - phos(T 71)] } . 
  -------------------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Atf2.by.Erks.514c.txt

Rewrite Rule 793

rl[793.Egr1-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {NUc    | nuc    Egr1-gene                 } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {NUc    | nuc    [Egr1-gene - on]          } . 
  ---------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Egr1-gene.irt.Tnf.793.txt

Rewrite Rule 795

rl[795.Eselectin-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)              } 
  {CLc    | clc    [Tbk1 - act] [Gsk3s - act] } 
  {NUc    | nuc    Eselectin-gene             } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)              } 
  {CLc    | clc    [Tbk1 - act] [Gsk3s - act] } 
  {NUc    | nuc    [Eselectin-gene - on]      } . 
  ---------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Eselectin-gene.irt.Tnf.795.txt

Rewrite Rule 796

rl[796.Ikba-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Rnf11  } 
  {CLc    | clc    [Ikba - degraded]    } 
  {NUc    | nuc    Ikba-gene            } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Rnf11  } 
  {CLc    | clc    [Ikba - degraded]    } 
  {NUc    | nuc    [Ikba-gene - on]     } . 
  --------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ikba-gene.irt.Tnf.796.txt

Rewrite Rules 816, 816-1

 
rl[816.IL6-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Ripk1 - ubiq]  [Syk - act] [Tpl2 - act]                  } 
  {CLc    | clc    [Ikba - degraded]                                         } 
  {NUc    | nuc    [msk12s:Msk12S - act] IL6-gene                            } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                    [Ripk1 - ubiq]  [Syk - act] [Tpl2 - act]                 } 
  {CLc    | clc    [Ikba - degraded]                                         } 
  {NUc    | nuc    [msk12s:Msk12S - act] [IL6-gene - on]                     } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/IL6-gene.irt.Tnf.816.txt

Rewrite Rule 819c

rl[819c.Eif4ebp1.by.Akt1]: 
  {CLc | clc [Akt1 - act]  Eif4ebp1                         } 
  => 
  {CLc | clc [Akt1 - act] [Eif4ebp1 - phos(S 65)] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Eif4ebp1.by.Akt1.819c.txt

Rewrite Rule 825

rl[825.Junb-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {NUc    | nuc    Junb-gene                 } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {NUc    | nuc    [Junb-gene - on]          } . 
  ----------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Junb-gene.irt.Tnf.825.txt

Rewrite Rule 830

rl[830.Stat1.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {CLc    | clc     Stat1              } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Stat1 } 
  {CLc    | clc                        } . 
  ---------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Stat1.to.TnfR1.830.txt

Rewrite Rule 842

rl[842.Stat1.phos.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)  Stat1         } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Stat1 - phos] } . 
  ------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Stat1.phos.irt.Tnf.842.txt

Rewrite Rule 899

rl[899.Atf2.irt.Tnf]: 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf)                  } 
  {CLc    | clc     Atf2                           } 
  {NUc    | nuc                                    } 
  => 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf)                  } 
  {CLc    | clc                                    } 
  {NUc    | nuc     [Atf2 - phos] } . 
  --------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Atf2.irt.Tnf.899.txt

Rewrite Rule 903, 903-1

rl[903.Jun.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] Tradd 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {CLc    | clc    [Jnks - act]                                              } 
  {NUc    | nuc    Jun                                                       } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Ripk1 - ubiq] Tradd 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) } 
  {CLc    | clc    [Jnks - act]                                              } 
  {NUc    | nuc    [Jun - act]                                               } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Jun.irt.Tnf.903.txt

Rewrite Rules 916c, 916c-1

rl[916c.Mtorc1.complex]: 
  {CLi | cli  plds:PldS                        } 
  {CLc | clc  (Mtor : Mlst8)  Raptor           } 
  => 
  {CLi | cli  plds:PldS                        } 
  {CLc | clc  (Mtor : Mlst8 : Raptor)          } . 
  ---------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Mtorc1.complex.916c.txt

Rewrite Rules 957, 957-1

rl[957.Nfkb.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Ciap1 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Mekk3 - act] [Ripk1 - ubiq] 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Syk - act] [Tank - phos] [Tpl2 - act] 
                    Tradd traf25s:Traf25S                                    } 
  {CLc    | clc    Azi2 Csnk1a1 [Ikba - degraded] Pin1 Pkcz                  } 
  {NUc    | nuc    [Rela - act]                                              } 
  {Sig    | sig                                                              } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Ciap1 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Mekk3 - act] [Ripk1 - ubiq] 
                   ([Tak1 - K63ubiq act phos] : [Tab1 - phos] : tab23s:Tab23S) 
                   [Syk - act] [Tank - phos] [Tpl2 - act] 
                    Tradd traf25s:Traf25S                                    } 
  {CLc    | clc    Azi2 Csnk1a1 [Ikba - degraded] Pin1 Pkcz                  } 
  {NUc    | nuc    [Rela - act]                                              } 
  {Sig    | sig    NFKB-REPORTER-ON                                          } . 
  ------------------------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Nfkb.irt.Tnf.957.txt

Rewrite Rule 1050

rl[1050.Mapkapk2.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)      } 
  {CLc    | clc    Mapkapk2           } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)      } 
  {CLc    | clc    [Mapkapk2 - act]   } . 
  ------------------------------------------------------------ 
  *** ~/evidence/Tnf-Evidence/Mapkapk2.irt.Tnf.1050.txt

Rewrite Rule 1058c

rl[1058c.Rela.by.Tbk1]: 
  {CLc | clc [Tbk1 - act]  Rela         } 
  => 
  {CLc | clc [Tbk1 - act] [Rela - phos] } . 
  ------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Rela.by.Tbk1.1058c.txt

Rewrite Rule 1317

rl[1317.Fos-gene.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)             } 
  {NUc    | nuc    Fos-gene                  } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)             } 
  {NUc    | nuc    [Fos-gene - on]           } . 
  ----------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Fos-gene.irt.Tnf.1317.txt

Rewrite Rule 1564

rl[1564.Tax1bp1.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)         } 
  {CLc    | clc    Tax1bp1                           } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Tax1bp1 } 
  {CLc    | clc                                      } . 
  ---------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Tax1bp1.to.TnfR1.1564.txt

Rewrite Rule 1565

rl[1565.Tax1bp1.phos.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Tax1bp1 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq])           } 
  {CLc    | clc                                                            } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) [Tax1bp1 - phos] 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq])           } 
  {CLc    | clc                                                            } . 
  ----------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Tax1bp1.phos.irt.Tnf.1565.txt

Rewrite Rule 1566

rl[1566.Itch.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Tax1bp1 - phos] Tnfaip3                             } 
  {CLc    | clc     Itch                                                } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) 
                   ([Ikk1 - act] : [Ikk2 - act] : [Nemo - ubiq]) 
                   [Tax1bp1 - phos] Tnfaip3 Itch                        } 
  {CLc    | clc                                                         } . 
  ------------------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Itch.to.TnfR1.1566.txt

Rewrite Rule 1567

rl[1567.Tnfaip3.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)          } 
  {CLc    | clc    Tnfaip3                            } 
  => 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf) Tnfaip3 } 
  {CLc    | clc                                       } . 
  ------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Tnfaip3.to.TnfR1.1567.txt

Rewrite Rule 1569

rl[1569.Ubc13.to.TnfR1]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf)       } 
  {CLc    | clc    Ubc13                           } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) Ubc13 } 
  {CLc    | clc                                    } . 
  ---------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Ubc13.to.TnfR1.1569.txt

Rewrite Rule 1609c

rl[1609c.Ikk2.Tsc2.complex]: 
  {CLc | clc  Ikk2   Tsc1  } 
  => 
  {CLc | clc (Ikk2 : Tsc1) } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Ikk2.Tsc2.complex.1609c.txt

Rewrite Rule 1613

rl[1613.Eif4ebp1.phos.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {CLc    | clc    Eif4ebp1                  } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {CLc    | clc    Eif4ebp1                  } . 
  ---------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Eif4ebp1.phos.irt.Tnf.1613.txt 
) 
rl[1613.Eif4ebp1.phos.irt.Tnf]: 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {CLc    | clc    Eif4ebp1                  } 
  => 
  {TnfR1C | tnfr1c (TnfR1 : Tnf) } 
  {CLc    | clc    [Eif4ebp1 - phos(S 65)]   } . 
---------------------------------------------- 
*** ~/evidence/Tnf-Evidence/Eif4ebp1.phos.irt.Tnf.1613.txt

Rewrite Rule 1631c-3

rl[1631c.Eif4ebp1.by.Erks]: 
  {CLc | clc [Erks - erksmods act]  Eif4ebp1               } 
  => 
  {CLc | clc [Erks - erksmods act] [Eif4ebp1 - phos(S 65)] } . 
  ----------------------------------------------------------- 
  *** ~/Repositories/IOP++/PLA4/Package/Models/STM7/evidence/Common-Rule-Evidence/Eif4ebp1.by.Erks.1631c.txt

Rewrite Rule 1787

rl[1787.Creb1.irt.Tnf]: 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf)         } 
  {NUc    | nuc     Creb1                 } 
  => 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf)         } 
  {NUc    | nuc     [Creb1 - phos(S 133)] } . 
  --------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Creb1.irt.Tnf.1787.txt

Rewrite Rule 1005

rl[1005.Atf1.irt.Tnf]: 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf)       } 
  {NUc    | nuc     Atf1                } 
  => 
  {TnfR1C | tnfr1c  (TnfR1 : Tnf)       } 
  {NUc    | nuc     [Atf1 - phos(S 63)] } . 
  --------------------------------------------------------------- 
  *** ~/evidence/Tnf-Evidence/Atf1.irt.Tnf.1005.txt