mod CONTENTS is inc ALLOPS .

sort Contents .
subsort Contents < Soup .

*** clo--

op CLoContents : -> Contents .
eq CLoContents = Cd14 .

*** clm--

op CLmContents : -> Contents .
eq CLmContents = Adam17 Dap12 Erbb2 IfnaR1 IL1Rap IL2Ra IL6R Itgb3 Muc1 
Pag1 Plscr1 ProTgfa Lrp6  .

*** cli--

op CLiContents : -> Contents .
eq CLiContents =  Cltc Fyn Pld1 Pld2
[Cdc42 - GDP] 
Gnai1 Gnai3
[Hras - GDP] [Kras - GDP] [Mras - GDP] [Nras - GDP] 
[Rab5a - GDP] [Rab5b - GDP] [Rab5c - GDP] 
[Rac1 - GDP] [Rala - GDP] [Ralb - GDP] [Rap1a - GDP] [Rap2a - GDP] 
[Rap2b - GDP] 
[Rhoa - GDP] [Rhoq - GDP] [Rit1 - GDP] 
[Rras - GDP] [Rras2 - GDP] 
Src Lck Parva .

*** clc--

op CLcContents : -> Contents .
eq CLcContents = 
Abi1 Abl1 Akt1 Ampk Apc Aps Araf ArhGef4 ArhGef7 Arms Ask1 Atf2 Azi2
Bcl10 Bad Bmx Braf Btk Btrc
Casp1 Cbl Cblb Ciap1 Ciap2 Cin85 Crk CrkL Csk Csnk1a1 Csnk1e Ctnnb1 
Dbl Dok1 Dok2 Dvl1 
Eef2 [Eef2k - act] Eif3 Eif4a1 Eif4b Eif4e Eif4g1 Elmo2 EndA1 Eps8 Eps15 Erc1 Erk5 Erks Ets1
Fak1 Fak2 Fes Foxo3 Freud1 Frs2 Gab1 Gab2 Gab3 Git1 Grb2 Grb10
[Gsk3s - act] *** [Gsk3b - act]
Hck Hgs
Hpk1 Ikbb Ikke IqGap1 Irak1 Irak4 Irf3 Irf5 Irf7 Irs1 Irs2 Itch Itgam 
(Ikk1 : Ikk2 : Nemo) 
(Ikba : Rela) (Ikbb : Rela)
Jak1 Jak2 Jak3 Jnks Lkb1 
Malt1 Map4k5 Mapkapk2 Mef2c Mek1 Mek5 
Mekk1 Mekk2 Mekk3 Mkk3 Mkk4 Mkk7 Mlk3 Mnk1 [Mnk2 - act] Myd88 
(Mtor : Mlst8 : Raptor)
(Mtor : Mlst8 : Sin1 : Rictor)  
(Nfkb1 : Tnip2 : Tpl2)          
P38s Pak1 Pak2 Pak3 Pdpk1 Peli1 Peli2 Pi3k Pi4k2a Pip5k1b PKA Pkcd Pkce Pkci Pkcz Plce1 Plcg1 Pml Ppm1a Ptk6 Pxn 
Raf1 RalGds RapGef1 Rasa1 RasGrp3 Rictor Rin1 Ripk1 Ripk2 Rnf11 Rps6 Rsk1 Rsk2 Rsk3 
S6k1 Sh2b1 Sh2d3a Sh2d3c Shc1 Shp2 Shoc2 Sin1 Smad2 Smad3 Smad4 Smurf1 Smurf2
Socs1 Sos1 Sqstm1 Stam Stam2 Stat1 Stat3 Stat4 Stat5a Stat5b Stat6 Syk 
(Tak1 : Tab1 : Tab2)
*** Tab1
Tank Tax1bp1 Tbk1 Thoc5 Trif Ticam2 Tiprl Tirap Tnik Tnk2 Tnfaip3 Tns3 Tollip Tpl2
Tradd Traf2 Traf3 Traf5 Traf6 Tsc2 Tyk2 
Ube2l3 Uev1a Ubc13 Unc93b1
Vav1 Vav2 Vav3 Ywhab Ywhaz Zfyve16 Znf274 .

*** nuc--

op NUcContents : -> Contents .
eq NUcContents = 
*************** proteins
Atf1 Atm Atr Atrip Brca1 Cebpb Chek2 
Creb1
Ctdsp1 Cdkn1b Claspin
Elk1 Egr1 Ep300 
Fancd2 Fos Fosl1 Fosl2 Foxo1 Fbxw7 
Hif1a Hipk2 HistH3 Hmgb1 Hmgb2 Hmgb3
Irf1 Irf2 Jun Junb Lmo4
Mdc1 Mdm4 Med23 Msk1 Msk2 Myc 
(Mre11 : Rad50 : Nbs1)
*** [Nfkb1 - p50] 
Nfkbiz Pias1 Pias2 Pias2a Pias4 Pin1 Rap80 Rnf8
Sae1 Senp1 Smc1a Uba2 Ube2i
Tcf7l2 Tip60 Tp53 Tp53bp1 Ube2d1 Ube2d2
**************** genes
A2m-gene Adm-gene Aicda-gene Alox15-gene Arg1-gene 
Bax-gene Bcl2-gene Bcl3-gene Bclxl-gene 
C3-gene CcL2-gene CcL3-gene CcL4-gene CcL5-gene CcL7-gene CcL11-gene CcL26-gene
Cdk1-gene Cdk2-gene Cdkn1a-gene Cdkn2b-gene Cebpb-gene Cebpd-gene Cezanne-gene
Ch25h-gene Clic4-gene Csf2-gene Csf3-gene 
CxcL1-gene CxcL2-gene CxcL9-gene CxcL10-gene 
CyclinC-gene CyclinD1-gene CyclinD2-gene CyclinD3-gene 
[Deptor-gene - on]
Egr1-gene Egr2-gene Eselectin-gene 
FceR2-gene Fos-gene Fosb-gene Fosl1-gene 
Gzmb-gene Hif1a-gene 
Icam1-gene Ifi16-gene Ifit1-gene Ifit2-gene Ifit3-gene Ifna4-gene Ifnb1-gene Ifng-gene
Ikba-gene Ikbb-gene Ikke-gene IL1b-gene IL2Ra-gene IL4R-gene IL13Ra2-gene
IL6-gene IL8-gene IL18R1-gene IL18Rap-gene IL10-gene IL12a-gene IL12b-gene
Irf1-gene Jun-gene Junb-gene 
Mdm2-gene Myc-gene Nfil3-gene Nfkbiz-gene OpRm1-gene Pai1-gene RankL-gene 
Nos2a-gene
Smad6-gene Smad7-gene Socs1-gene Socs3-gene 
TLR2-gene ProTnf-gene Tnfaip3-gene Tbp-gene
Tp53aip1-gene 
TrailR2-gene 
Vegf-gene .

*** chr--

op CHRContents : -> Contents .
eq CHRContents = H2ax .

*** cvc--

op CVcContents : -> Contents .
eq CVcContents = Atp6V1 (Lamtor1 : Lamtor2 : Lamtor3) [Rheb - GTP] Tsc1 .

*** cvm--

op CVmContents : -> Contents .
eq CVmContents = Atp6V0 .

*** dna--

op DNACContents : -> Contents .
eq DNACContents = Max .

*** rna--

op RNACContents : -> Contents .
eq RNACContents = (capped-mRNA : Eif4e : Eif4ebp1) .  *** rule 856c
                             *** ~/evidence/Initial-State-Evidence/Eif4e.txt



endm
